Query 003054
Match_columns 852
No_of_seqs 519 out of 3544
Neff 9.1
Searched_HMMs 46136
Date Thu Mar 28 16:07:17 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/003054.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/003054hhsearch_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 1.7E-82 3.7E-87 665.2 45.8 705 4-749 104-846 (897)
2 KOG4440 NMDA selective glutama 100.0 6.4E-75 1.4E-79 610.6 30.0 676 6-750 116-859 (993)
3 KOG1053 Glutamate-gated NMDA-t 100.0 5.1E-69 1.1E-73 586.3 49.0 671 9-745 122-853 (1258)
4 KOG1052 Glutamate-gated kainat 100.0 3.6E-67 7.8E-72 624.0 56.1 599 106-749 4-625 (656)
5 cd06390 PBP1_iGluR_AMPA_GluR1 100.0 2E-37 4.3E-42 340.2 30.1 292 2-308 68-363 (364)
6 cd06387 PBP1_iGluR_AMPA_GluR3 100.0 3.3E-35 7.2E-40 321.7 29.9 293 2-308 75-371 (372)
7 cd06379 PBP1_iGluR_NMDA_NR1 N- 100.0 3.4E-35 7.4E-40 327.7 29.4 273 2-329 97-377 (377)
8 cd06393 PBP1_iGluR_Kainate_Glu 100.0 4.7E-35 1E-39 326.8 29.0 292 2-309 84-382 (384)
9 cd06389 PBP1_iGluR_AMPA_GluR2 100.0 7.3E-35 1.6E-39 322.2 29.9 295 2-309 69-369 (370)
10 cd06388 PBP1_iGluR_AMPA_GluR4 100.0 1.7E-34 3.6E-39 318.6 30.2 292 2-309 75-370 (371)
11 cd06380 PBP1_iGluR_AMPA N-term 100.0 2E-34 4.3E-39 322.4 30.8 299 2-308 74-381 (382)
12 cd06392 PBP1_iGluR_delta_1 N-t 100.0 2.5E-34 5.4E-39 315.7 27.5 294 2-309 74-399 (400)
13 cd06361 PBP1_GPC6A_like Ligand 100.0 9.5E-34 2.1E-38 316.4 30.1 271 2-308 115-397 (403)
14 cd06367 PBP1_iGluR_NMDA N-term 100.0 7E-34 1.5E-38 315.6 27.8 275 3-328 79-362 (362)
15 cd06365 PBP1_Pheromone_recepto 100.0 9.6E-34 2.1E-38 323.1 28.4 291 2-305 115-453 (469)
16 cd06391 PBP1_iGluR_delta_2 N-t 100.0 7.5E-33 1.6E-37 307.3 30.8 297 2-309 74-399 (400)
17 cd06376 PBP1_mGluR_groupIII Li 100.0 4.9E-33 1.1E-37 318.1 30.1 292 2-304 115-452 (463)
18 cd06374 PBP1_mGluR_groupI Liga 100.0 3.3E-33 7.1E-38 320.1 28.5 296 2-309 129-468 (472)
19 cd06386 PBP1_NPR_C_like Ligand 100.0 5E-33 1.1E-37 310.5 27.7 278 2-304 79-378 (387)
20 cd06362 PBP1_mGluR Ligand bind 100.0 6.9E-33 1.5E-37 316.8 29.4 296 2-308 115-450 (452)
21 cd06364 PBP1_CaSR Ligand-bindi 100.0 1.7E-32 3.6E-37 314.9 32.1 296 2-305 130-494 (510)
22 cd06375 PBP1_mGluR_groupII Lig 100.0 2.2E-32 4.9E-37 310.6 30.1 290 2-304 117-454 (458)
23 cd06385 PBP1_NPR_A Ligand-bind 100.0 6.3E-32 1.4E-36 304.4 29.7 280 2-306 86-392 (405)
24 cd06363 PBP1_Taste_receptor Li 100.0 1.3E-31 2.8E-36 301.9 27.9 270 2-305 119-396 (410)
25 cd06366 PBP1_GABAb_receptor Li 100.0 1.3E-31 2.9E-36 296.1 26.2 263 2-310 78-348 (350)
26 cd06384 PBP1_NPR_B Ligand-bind 100.0 3.8E-31 8.3E-36 297.1 28.6 283 2-306 85-393 (399)
27 cd06373 PBP1_NPR_like Ligand b 100.0 3.5E-31 7.7E-36 297.5 26.9 284 2-306 85-390 (396)
28 cd06371 PBP1_sensory_GC_DEF_li 100.0 1E-30 2.2E-35 291.1 27.6 278 2-307 78-376 (382)
29 cd06378 PBP1_iGluR_NMDA_NR2 N- 100.0 9.2E-31 2E-35 287.0 24.7 277 3-329 78-362 (362)
30 cd06352 PBP1_NPR_GC_like Ligan 100.0 4.9E-30 1.1E-34 287.9 27.9 287 2-308 80-385 (389)
31 cd06370 PBP1_Speract_GC_like L 100.0 5.1E-30 1.1E-34 288.3 26.3 271 4-295 81-384 (404)
32 cd06372 PBP1_GC_G_like Ligand- 100.0 8.8E-30 1.9E-34 285.7 28.1 283 2-306 80-387 (391)
33 PF01094 ANF_receptor: Recepto 100.0 4.8E-29 1E-33 275.5 24.9 279 2-293 63-348 (348)
34 cd06382 PBP1_iGluR_Kainate N-t 100.0 3.4E-29 7.4E-34 274.1 22.7 247 2-308 75-326 (327)
35 KOG1056 Glutamate-gated metabo 100.0 3.4E-28 7.3E-33 277.6 25.8 315 2-339 137-494 (878)
36 cd06394 PBP1_iGluR_Kainate_KA1 100.0 9.9E-29 2.1E-33 266.5 18.6 249 3-309 79-332 (333)
37 PRK15404 leucine ABC transport 100.0 8.4E-28 1.8E-32 266.4 22.6 256 2-295 104-363 (369)
38 cd06342 PBP1_ABC_LIVBP_like Ty 100.0 4.4E-27 9.5E-32 258.4 23.9 253 2-292 78-334 (334)
39 cd06368 PBP1_iGluR_non_NMDA_li 100.0 3.1E-27 6.8E-32 258.4 22.3 248 2-308 74-323 (324)
40 cd06338 PBP1_ABC_ligand_bindin 99.9 4.9E-27 1.1E-31 259.2 21.4 252 2-292 83-345 (345)
41 cd06381 PBP1_iGluR_delta_like 99.9 6.6E-26 1.4E-30 249.0 26.7 262 2-308 74-362 (363)
42 cd06345 PBP1_ABC_ligand_bindin 99.9 1.9E-26 4.1E-31 254.3 22.4 246 2-284 79-338 (344)
43 cd06346 PBP1_ABC_ligand_bindin 99.9 4.5E-26 9.7E-31 247.6 20.6 228 2-288 79-309 (312)
44 cd06340 PBP1_ABC_ligand_bindin 99.9 1.4E-25 3E-30 247.5 19.9 248 2-285 82-342 (347)
45 cd06348 PBP1_ABC_ligand_bindin 99.9 5.4E-25 1.2E-29 242.8 23.3 258 2-288 79-342 (344)
46 cd06360 PBP1_alkylbenzenes_lik 99.9 6.7E-25 1.4E-29 241.3 23.5 251 3-287 78-332 (336)
47 cd06355 PBP1_FmdD_like Peripla 99.9 9.6E-25 2.1E-29 240.7 24.4 257 2-295 79-340 (348)
48 cd06329 PBP1_SBP_like_3 Peripl 99.9 6.8E-25 1.5E-29 241.6 21.9 239 7-284 90-337 (342)
49 cd06344 PBP1_ABC_ligand_bindin 99.9 5.3E-25 1.1E-29 241.5 20.1 245 2-285 78-327 (332)
50 cd06327 PBP1_SBP_like_1 Peripl 99.9 1.1E-24 2.3E-29 239.4 21.1 248 2-286 78-331 (334)
51 TIGR03669 urea_ABC_arch urea A 99.9 3E-24 6.5E-29 237.6 24.3 262 2-303 80-349 (374)
52 cd06350 PBP1_GPCR_family_C_lik 99.9 1.3E-24 2.9E-29 240.1 21.6 231 2-305 103-340 (348)
53 cd06383 PBP1_iGluR_AMPA_Like N 99.9 1.4E-24 3E-29 239.1 19.6 266 2-284 79-352 (368)
54 cd06328 PBP1_SBP_like_2 Peripl 99.9 3.9E-24 8.4E-29 234.5 22.9 247 2-287 80-331 (333)
55 cd06359 PBP1_Nba_like Type I p 99.9 3.7E-24 8.1E-29 234.8 22.4 252 2-291 77-332 (333)
56 cd06336 PBP1_ABC_ligand_bindin 99.9 2.2E-24 4.8E-29 237.9 20.5 248 3-288 84-345 (347)
57 COG0683 LivK ABC-type branched 99.9 4.6E-24 1E-28 236.1 22.2 257 2-293 90-353 (366)
58 TIGR03407 urea_ABC_UrtA urea A 99.9 2.9E-23 6.4E-28 229.8 26.5 240 2-278 80-322 (359)
59 cd06331 PBP1_AmiC_like Type I 99.9 8.2E-24 1.8E-28 232.2 21.6 240 2-278 79-320 (333)
60 cd06343 PBP1_ABC_ligand_bindin 99.9 2.2E-23 4.8E-28 231.6 23.8 261 2-295 86-360 (362)
61 cd06349 PBP1_ABC_ligand_bindin 99.9 2.6E-23 5.7E-28 229.0 23.8 254 2-295 79-338 (340)
62 cd06347 PBP1_ABC_ligand_bindin 99.9 3.5E-23 7.7E-28 227.4 23.4 246 3-287 80-331 (334)
63 cd06332 PBP1_aromatic_compound 99.9 3.2E-23 6.9E-28 227.7 23.0 247 3-286 78-328 (333)
64 cd06330 PBP1_Arsenic_SBP_like 99.9 2.3E-23 5E-28 230.0 20.8 245 2-279 79-332 (346)
65 cd06357 PBP1_AmiC Periplasmic 99.9 1.6E-22 3.5E-27 224.0 25.7 256 2-292 79-337 (360)
66 cd06334 PBP1_ABC_ligand_bindin 99.9 5.8E-23 1.3E-27 226.2 20.9 251 2-278 78-343 (351)
67 cd06358 PBP1_NHase Type I peri 99.9 1.3E-22 2.9E-27 222.6 22.8 245 2-285 79-327 (333)
68 PF13458 Peripla_BP_6: Peripla 99.9 9.9E-23 2.2E-27 224.7 21.9 256 2-295 81-342 (343)
69 cd06377 PBP1_iGluR_NMDA_NR3 N- 99.9 9.2E-22 2E-26 212.4 27.7 272 2-328 94-382 (382)
70 cd06351 PBP1_iGluR_N_LIVBP_lik 99.9 1.7E-22 3.7E-27 221.3 21.7 243 2-304 75-322 (328)
71 cd06356 PBP1_Amide_Urea_BP_lik 99.9 2.6E-22 5.6E-27 220.2 22.4 242 2-283 79-328 (334)
72 cd06335 PBP1_ABC_ligand_bindin 99.9 2.9E-22 6.4E-27 221.0 22.4 243 2-276 79-329 (347)
73 cd06337 PBP1_ABC_ligand_bindin 99.9 1.6E-22 3.5E-27 223.8 19.2 238 2-278 81-340 (357)
74 PRK10797 glutamate and asparta 99.9 7.7E-21 1.7E-25 204.0 22.6 223 344-697 39-272 (302)
75 PRK09495 glnH glutamine ABC tr 99.9 9.6E-21 2.1E-25 198.4 22.9 221 344-698 24-245 (247)
76 TIGR03863 PQQ_ABC_bind ABC tra 99.9 2E-21 4.3E-26 212.1 17.2 231 2-286 71-310 (347)
77 cd06339 PBP1_YraM_LppC_lipopro 99.9 4.4E-21 9.6E-26 210.3 19.2 231 2-282 71-329 (336)
78 PF00497 SBP_bac_3: Bacterial 99.9 1.2E-20 2.6E-25 194.3 17.9 222 347-696 1-224 (225)
79 PRK11260 cystine transporter s 99.8 7.2E-20 1.6E-24 193.9 22.9 223 343-697 39-262 (266)
80 KOG1055 GABA-B ion channel rec 99.8 2.3E-21 5E-26 214.3 11.3 302 4-330 126-445 (865)
81 cd06326 PBP1_STKc_like Type I 99.8 7.5E-20 1.6E-24 201.2 21.6 244 3-282 81-329 (336)
82 PRK15007 putative ABC transpor 99.8 3E-19 6.5E-24 186.7 21.6 217 344-696 20-242 (243)
83 PF13433 Peripla_BP_5: Peripla 99.8 3.5E-19 7.7E-24 187.9 22.0 235 4-278 82-322 (363)
84 PRK11917 bifunctional adhesin/ 99.8 5.3E-19 1.1E-23 185.9 22.8 218 343-695 36-258 (259)
85 PRK15010 ABC transporter lysin 99.8 8.6E-19 1.9E-23 185.1 22.4 222 343-696 24-254 (260)
86 TIGR01096 3A0103s03R lysine-ar 99.8 1.4E-18 3.1E-23 182.4 22.0 218 345-695 24-250 (250)
87 cd06269 PBP1_glutamate_recepto 99.8 5.2E-19 1.1E-23 190.3 19.0 152 2-156 83-235 (298)
88 TIGR02995 ectoine_ehuB ectoine 99.8 8.7E-19 1.9E-23 186.5 20.1 225 342-695 30-260 (275)
89 PRK15437 histidine ABC transpo 99.8 3.7E-18 8E-23 180.1 21.2 222 343-696 24-254 (259)
90 cd06341 PBP1_ABC_ligand_bindin 99.8 8.2E-18 1.8E-22 185.3 20.6 230 8-274 84-319 (341)
91 PRK09959 hybrid sensory histid 99.8 1.8E-17 4E-22 212.4 25.5 217 344-696 301-520 (1197)
92 PRK10859 membrane-bound lytic 99.7 4.2E-17 9.1E-22 186.3 20.6 222 342-697 40-267 (482)
93 cd06333 PBP1_ABC-type_HAAT_lik 99.7 3.2E-17 7E-22 178.2 18.6 204 3-222 79-293 (312)
94 PF00060 Lig_chan: Ligand-gate 99.7 9.8E-19 2.1E-23 167.8 2.9 107 474-580 1-115 (148)
95 cd04509 PBP1_ABC_transporter_G 99.7 1E-16 2.2E-21 172.5 16.8 205 3-220 80-290 (299)
96 TIGR03870 ABC_MoxJ methanol ox 99.7 1.9E-16 4.2E-21 165.4 17.7 210 346-694 1-241 (246)
97 COG0834 HisJ ABC-type amino ac 99.7 1.1E-15 2.5E-20 162.8 20.8 226 343-696 32-264 (275)
98 cd06369 PBP1_GC_C_enterotoxin_ 99.7 1.9E-15 4.2E-20 159.1 21.0 261 3-308 94-368 (380)
99 cd06268 PBP1_ABC_transporter_L 99.7 1.3E-15 2.9E-20 163.7 18.3 205 3-222 79-287 (298)
100 TIGR02285 conserved hypothetic 99.7 9.3E-16 2E-20 162.6 16.2 230 344-697 17-262 (268)
101 TIGR03871 ABC_peri_MoxJ_2 quin 99.7 3.6E-15 7.7E-20 154.7 19.0 212 346-695 1-228 (232)
102 PRK09959 hybrid sensory histid 99.7 1.5E-15 3.2E-20 194.9 19.2 222 343-697 54-278 (1197)
103 cd00134 PBPb Bacterial peripla 99.6 1.6E-14 3.5E-19 146.9 21.6 214 347-695 1-218 (218)
104 smart00062 PBPb Bacterial peri 99.6 3.3E-14 7.2E-19 144.4 19.9 216 346-695 1-219 (219)
105 smart00079 PBPe Eukaryotic hom 99.3 1.5E-11 3.3E-16 115.6 11.4 122 569-696 1-133 (134)
106 COG4623 Predicted soluble lyti 99.3 3.5E-11 7.6E-16 123.7 13.8 224 343-700 21-251 (473)
107 cd01391 Periplasmic_Binding_Pr 99.0 8.5E-09 1.8E-13 108.2 14.7 186 6-220 74-261 (269)
108 TIGR01098 3A0109s03R phosphate 98.8 5.3E-08 1.1E-12 102.4 15.3 199 344-681 31-254 (254)
109 PRK00489 hisG ATP phosphoribos 98.7 7.1E-08 1.5E-12 102.7 11.9 163 411-696 52-219 (287)
110 PF10613 Lig_chan-Glu_bd: Liga 98.6 9.5E-09 2.1E-13 80.8 1.1 61 359-421 1-65 (65)
111 PF04348 LppC: LppC putative l 98.2 3.5E-05 7.6E-10 88.8 16.0 217 14-282 304-524 (536)
112 TIGR03431 PhnD phosphonate ABC 98.1 7.6E-05 1.6E-09 80.0 15.9 115 570-690 127-258 (288)
113 cd01537 PBP1_Repressors_Sugar_ 97.7 0.0004 8.8E-09 72.7 12.9 136 6-149 71-211 (264)
114 PRK11553 alkanesulfonate trans 97.4 0.0015 3.2E-08 71.0 13.4 68 570-643 121-193 (314)
115 cd06267 PBP1_LacI_sugar_bindin 97.4 0.0016 3.5E-08 68.2 12.8 136 7-149 71-210 (264)
116 cd01536 PBP1_ABC_sugar_binding 97.4 0.0027 5.8E-08 66.7 14.5 138 6-151 72-215 (267)
117 PF12974 Phosphonate-bd: ABC t 97.2 0.0034 7.4E-08 65.4 12.7 120 569-694 96-230 (243)
118 cd06282 PBP1_GntR_like_2 Ligan 97.0 0.0091 2E-07 62.8 13.8 132 6-147 71-207 (266)
119 TIGR01729 taurine_ABC_bnd taur 96.9 0.0034 7.4E-08 67.7 8.9 68 570-643 92-164 (300)
120 cd06300 PBP1_ABC_sugar_binding 96.9 0.014 3.1E-07 61.6 13.6 128 6-143 77-211 (272)
121 cd06273 PBP1_GntR_like_1 This 96.8 0.019 4E-07 60.5 13.6 134 7-147 71-209 (268)
122 TIGR03427 ABC_peri_uca ABC tra 96.7 0.0099 2.1E-07 64.4 10.7 68 570-643 98-170 (328)
123 PF13379 NMT1_2: NMT1-like fam 96.6 0.0078 1.7E-07 63.1 8.6 71 569-644 105-188 (252)
124 cd06325 PBP1_ABC_uncharacteriz 96.4 0.031 6.7E-07 59.3 12.1 125 10-140 77-208 (281)
125 cd06298 PBP1_CcpA_like Ligand- 96.3 0.047 1E-06 57.4 13.1 139 6-151 70-213 (268)
126 cd06320 PBP1_allose_binding Pe 96.3 0.085 1.8E-06 55.7 14.5 137 7-152 75-217 (275)
127 TIGR01481 ccpA catabolite cont 96.1 0.084 1.8E-06 57.6 14.0 132 7-145 131-265 (329)
128 cd06319 PBP1_ABC_sugar_binding 96.1 0.093 2E-06 55.5 13.8 141 5-152 71-220 (277)
129 cd06323 PBP1_ribose_binding Pe 95.9 0.14 2.9E-06 53.8 13.8 135 8-152 74-215 (268)
130 cd01545 PBP1_SalR Ligand-bindi 95.8 0.13 2.8E-06 54.1 13.3 132 6-144 72-207 (270)
131 TIGR01728 SsuA_fam ABC transpo 95.7 0.14 3E-06 54.5 13.0 69 569-643 92-165 (288)
132 cd06312 PBP1_ABC_sugar_binding 95.6 0.2 4.3E-06 52.9 14.0 129 7-141 75-208 (271)
133 cd06317 PBP1_ABC_sugar_binding 95.6 0.22 4.7E-06 52.5 14.1 140 7-151 74-221 (275)
134 PF09084 NMT1: NMT1/THI5 like; 95.5 0.071 1.5E-06 54.2 9.6 56 570-631 85-145 (216)
135 cd06295 PBP1_CelR Ligand bindi 95.5 0.16 3.5E-06 53.6 12.6 134 8-148 81-218 (275)
136 cd06271 PBP1_AglR_RafR_like Li 95.4 0.22 4.8E-06 52.2 13.1 134 8-148 76-213 (268)
137 cd06301 PBP1_rhizopine_binding 95.3 0.3 6.6E-06 51.4 14.1 140 6-152 73-219 (272)
138 cd06305 PBP1_methylthioribose_ 95.3 0.25 5.5E-06 52.0 13.4 139 7-152 73-218 (273)
139 TIGR02990 ectoine_eutA ectoine 95.3 0.3 6.4E-06 50.3 13.0 132 5-140 62-207 (239)
140 cd06288 PBP1_sucrose_transcrip 95.3 0.18 3.9E-06 52.9 12.1 133 11-150 75-211 (269)
141 cd06309 PBP1_YtfQ_like Peripla 95.2 0.42 9E-06 50.4 14.5 138 7-149 73-218 (273)
142 cd06310 PBP1_ABC_sugar_binding 94.9 0.67 1.4E-05 48.8 15.1 138 7-152 75-218 (273)
143 PF03466 LysR_substrate: LysR 94.9 0.74 1.6E-05 45.6 14.8 180 378-682 20-205 (209)
144 cd06284 PBP1_LacI_like_6 Ligan 94.8 0.34 7.3E-06 50.7 12.7 126 12-144 75-204 (267)
145 cd01575 PBP1_GntR Ligand-bindi 94.8 0.43 9.2E-06 50.0 13.3 134 8-148 72-209 (268)
146 cd01542 PBP1_TreR_like Ligand- 94.8 0.4 8.6E-06 50.0 13.0 133 6-150 70-207 (259)
147 cd06278 PBP1_LacI_like_2 Ligan 94.8 0.37 8E-06 50.4 12.8 126 7-141 70-200 (266)
148 COG3107 LppC Putative lipoprot 94.7 0.43 9.4E-06 53.0 12.9 174 13-192 341-538 (604)
149 cd06289 PBP1_MalI_like Ligand- 94.7 0.39 8.4E-06 50.3 12.7 134 6-146 71-208 (268)
150 cd06313 PBP1_ABC_sugar_binding 94.7 0.76 1.7E-05 48.5 14.9 135 10-152 76-217 (272)
151 cd06274 PBP1_FruR Ligand bindi 94.7 0.5 1.1E-05 49.5 13.4 134 9-149 73-211 (264)
152 cd06270 PBP1_GalS_like Ligand 94.6 0.52 1.1E-05 49.5 13.4 132 8-146 72-207 (268)
153 cd06299 PBP1_LacI_like_13 Liga 94.6 0.41 8.8E-06 50.1 12.5 135 8-149 72-208 (265)
154 cd06283 PBP1_RegR_EndR_KdgR_li 94.6 0.51 1.1E-05 49.3 13.2 135 8-149 72-211 (267)
155 cd01540 PBP1_arabinose_binding 94.6 0.79 1.7E-05 48.7 14.8 147 6-152 71-230 (289)
156 TIGR02122 TRAP_TAXI TRAP trans 94.5 0.16 3.5E-06 55.1 9.4 59 569-633 132-197 (320)
157 cd06294 PBP1_ycjW_transcriptio 94.5 0.45 9.8E-06 49.9 12.6 133 8-146 77-213 (270)
158 PRK10653 D-ribose transporter 94.5 0.76 1.6E-05 49.2 14.4 137 6-151 99-240 (295)
159 cd06292 PBP1_LacI_like_10 Liga 94.5 0.56 1.2E-05 49.3 13.2 134 10-149 79-214 (273)
160 PF13407 Peripla_BP_4: Peripla 94.4 0.38 8.2E-06 50.2 11.8 134 5-143 71-209 (257)
161 cd06285 PBP1_LacI_like_7 Ligan 94.4 0.47 1E-05 49.7 12.5 128 9-145 73-204 (265)
162 cd06291 PBP1_Qymf_like Ligand 94.3 0.54 1.2E-05 49.2 12.7 129 11-148 72-205 (265)
163 cd05466 PBP2_LTTR_substrate Th 94.3 2.7 5.9E-05 40.3 17.0 69 377-459 13-81 (197)
164 COG1609 PurR Transcriptional r 94.3 0.77 1.7E-05 50.2 14.1 130 6-144 129-265 (333)
165 cd06324 PBP1_ABC_sugar_binding 94.3 0.69 1.5E-05 49.8 13.6 143 7-152 75-239 (305)
166 PRK10703 DNA-binding transcrip 94.3 0.49 1.1E-05 51.8 12.7 135 9-149 133-272 (341)
167 PRK10014 DNA-binding transcrip 94.2 0.87 1.9E-05 49.8 14.5 130 7-143 137-270 (342)
168 PRK11480 tauA taurine transpor 94.1 0.35 7.5E-06 52.6 11.0 66 569-640 113-183 (320)
169 cd06275 PBP1_PurR Ligand-bindi 94.1 0.77 1.7E-05 48.1 13.4 132 11-149 76-211 (269)
170 cd06272 PBP1_hexuronate_repres 94.1 0.53 1.1E-05 49.2 12.1 133 9-149 69-205 (261)
171 cd06308 PBP1_sensor_kinase_lik 94.1 0.98 2.1E-05 47.4 14.2 135 9-152 76-217 (270)
172 PF13377 Peripla_BP_3: Peripla 94.0 0.19 4.2E-06 48.0 7.9 97 50-148 1-100 (160)
173 COG3221 PhnD ABC-type phosphat 94.0 1.5 3.2E-05 46.7 14.9 110 568-683 134-260 (299)
174 PF07885 Ion_trans_2: Ion chan 94.0 0.16 3.5E-06 42.3 6.3 56 507-562 21-78 (79)
175 cd06297 PBP1_LacI_like_12 Liga 93.9 0.87 1.9E-05 47.9 13.3 132 8-149 72-213 (269)
176 cd06296 PBP1_CatR_like Ligand- 93.9 0.72 1.6E-05 48.4 12.6 138 7-150 71-213 (270)
177 cd08442 PBP2_YofA_SoxR_like Th 93.9 4.5 9.6E-05 39.1 17.6 69 377-459 13-81 (193)
178 cd08438 PBP2_CidR The C-termin 93.9 4.7 0.0001 39.1 17.8 69 377-459 13-81 (197)
179 cd06281 PBP1_LacI_like_5 Ligan 93.8 0.74 1.6E-05 48.4 12.5 132 6-146 71-206 (269)
180 TIGR00363 lipoprotein, YaeC fa 93.8 1.3 2.9E-05 46.1 13.9 122 568-694 106-250 (258)
181 cd06290 PBP1_LacI_like_9 Ligan 93.6 0.86 1.9E-05 47.7 12.6 126 13-145 76-205 (265)
182 cd01574 PBP1_LacI Ligand-bindi 93.4 1.3 2.8E-05 46.3 13.5 129 11-149 76-207 (264)
183 cd06311 PBP1_ABC_sugar_binding 93.4 1.8 3.8E-05 45.6 14.6 137 8-152 79-220 (274)
184 cd06293 PBP1_LacI_like_11 Liga 93.4 1.3 2.9E-05 46.4 13.6 131 12-149 76-210 (269)
185 cd06307 PBP1_uncharacterized_s 93.4 1.5 3.3E-05 46.1 14.1 137 8-152 77-220 (275)
186 cd08426 PBP2_LTTR_like_5 The C 93.4 4.9 0.00011 39.1 17.0 69 377-459 13-81 (199)
187 cd08412 PBP2_PAO1_like The C-t 93.4 4.3 9.4E-05 39.4 16.6 70 376-459 12-81 (198)
188 cd08463 PBP2_DntR_like_4 The C 93.3 6.2 0.00013 39.0 17.8 70 377-459 13-82 (203)
189 PRK11303 DNA-binding transcrip 93.3 1.7 3.6E-05 47.3 14.5 131 10-149 137-271 (328)
190 PRK10423 transcriptional repre 93.2 1.1 2.4E-05 48.6 13.1 130 13-149 135-268 (327)
191 cd08468 PBP2_Pa0477 The C-term 93.2 6.1 0.00013 38.8 17.6 72 377-459 13-84 (202)
192 TIGR00787 dctP tripartite ATP- 93.2 0.34 7.4E-06 50.8 8.5 103 568-682 126-231 (257)
193 cd08433 PBP2_Nac The C-teminal 93.1 8.2 0.00018 37.5 18.2 69 377-459 13-81 (198)
194 cd08418 PBP2_TdcA The C-termin 93.1 6.1 0.00013 38.5 17.3 71 377-459 13-83 (201)
195 CHL00180 rbcR LysR transcripti 93.1 5.8 0.00012 42.6 18.2 71 378-459 109-179 (305)
196 cd08459 PBP2_DntR_NahR_LinR_li 92.9 4.7 0.0001 39.5 16.1 69 377-459 13-81 (201)
197 cd01544 PBP1_GalR Ligand-bindi 92.9 1.3 2.7E-05 46.7 12.5 131 9-147 69-210 (270)
198 cd01543 PBP1_XylR Ligand-bindi 92.9 1.3 2.9E-05 46.3 12.6 137 8-151 65-207 (265)
199 cd06277 PBP1_LacI_like_1 Ligan 92.8 1.3 2.7E-05 46.5 12.4 130 7-144 73-205 (268)
200 cd08440 PBP2_LTTR_like_4 TThe 92.8 9.5 0.00021 36.7 18.1 69 377-459 13-81 (197)
201 PRK11233 nitrogen assimilation 92.8 3.9 8.4E-05 44.0 16.3 69 377-459 105-173 (305)
202 cd08421 PBP2_LTTR_like_1 The C 92.7 7.4 0.00016 37.8 17.3 68 378-459 14-81 (198)
203 cd06306 PBP1_TorT-like TorT-li 92.7 1.6 3.4E-05 45.9 13.0 132 8-149 75-215 (268)
204 PF00532 Peripla_BP_1: Peripla 92.7 0.76 1.6E-05 48.8 10.5 137 6-149 72-214 (279)
205 cd06287 PBP1_LacI_like_8 Ligan 92.7 2 4.3E-05 45.3 13.7 133 10-149 75-211 (269)
206 cd06303 PBP1_LuxPQ_Quorum_Sens 92.6 3.8 8.2E-05 43.3 15.9 113 36-152 107-225 (280)
207 PRK12684 transcriptional regul 92.6 4.6 9.9E-05 43.6 16.7 115 571-695 184-304 (313)
208 cd08417 PBP2_Nitroaromatics_li 92.6 5.4 0.00012 38.9 16.1 69 377-459 13-81 (200)
209 cd06279 PBP1_LacI_like_3 Ligan 92.6 1.5 3.2E-05 46.5 12.7 130 8-145 73-224 (283)
210 cd01539 PBP1_GGBP Periplasmic 92.5 2.4 5.2E-05 45.5 14.2 144 8-152 76-241 (303)
211 cd06316 PBP1_ABC_sugar_binding 92.2 2.7 5.9E-05 44.8 14.2 139 8-151 75-219 (294)
212 PRK10727 DNA-binding transcrip 92.2 1.6 3.6E-05 47.7 12.8 110 38-148 156-269 (343)
213 PRK11242 DNA-binding transcrip 92.2 6.7 0.00014 41.8 17.2 69 377-459 104-172 (296)
214 cd01541 PBP1_AraR Ligand-bindi 92.0 2 4.3E-05 45.1 12.8 134 9-149 78-216 (273)
215 cd08415 PBP2_LysR_opines_like 91.9 9.1 0.0002 37.0 16.7 69 377-459 13-81 (196)
216 PRK09526 lacI lac repressor; R 91.9 2.6 5.6E-05 46.0 13.9 126 13-148 143-272 (342)
217 cd08419 PBP2_CbbR_RubisCO_like 91.7 13 0.00029 35.8 17.8 68 378-459 13-80 (197)
218 TIGR02417 fruct_sucro_rep D-fr 91.5 2.6 5.6E-05 45.8 13.3 129 10-148 136-269 (327)
219 PRK12679 cbl transcriptional r 91.5 11 0.00023 40.8 18.0 208 344-696 92-306 (316)
220 cd06322 PBP1_ABC_sugar_binding 91.4 4.5 9.7E-05 42.2 14.6 124 8-140 74-203 (267)
221 PRK09492 treR trehalose repres 91.4 2.5 5.3E-05 45.6 12.8 99 38-140 155-256 (315)
222 PRK09860 putative alcohol dehy 91.3 1.5 3.3E-05 48.8 11.2 90 45-134 18-109 (383)
223 PRK11151 DNA-binding transcrip 91.3 11 0.00024 40.4 17.7 69 377-459 104-172 (305)
224 cd06354 PBP1_BmpA_PnrA_like Pe 91.3 2.2 4.7E-05 44.8 12.0 128 6-139 72-206 (265)
225 cd08429 PBP2_NhaR The C-termin 91.3 12 0.00025 37.2 16.8 103 572-683 93-201 (204)
226 PRK09791 putative DNA-binding 91.2 6 0.00013 42.3 15.6 85 344-459 94-178 (302)
227 cd08462 PBP2_NodD The C-termin 91.1 7.4 0.00016 38.1 15.2 67 378-459 14-80 (200)
228 PRK11063 metQ DL-methionine tr 91.1 5.2 0.00011 42.2 14.4 120 569-694 120-263 (271)
229 cd06280 PBP1_LacI_like_4 Ligan 91.1 2.7 5.9E-05 43.8 12.5 128 11-148 74-204 (263)
230 cd06318 PBP1_ABC_sugar_binding 91.0 5.8 0.00012 41.8 15.1 136 8-149 74-222 (282)
231 PRK09701 D-allose transporter 91.0 5.7 0.00012 42.8 15.2 138 10-151 103-250 (311)
232 cd01538 PBP1_ABC_xylose_bindin 91.0 4.3 9.2E-05 43.2 14.0 128 8-142 74-216 (288)
233 cd08460 PBP2_DntR_like_1 The C 90.7 6.3 0.00014 38.6 14.2 69 376-459 12-80 (200)
234 cd06302 PBP1_LsrB_Quorum_Sensi 90.6 5.3 0.00012 42.7 14.4 127 8-141 75-210 (298)
235 PRK11041 DNA-binding transcrip 90.5 1.9 4.1E-05 46.3 10.9 111 38-149 132-246 (309)
236 cd08457 PBP2_OccR The C-termin 90.5 18 0.00038 35.1 17.3 69 377-459 13-81 (196)
237 cd06321 PBP1_ABC_sugar_binding 90.5 4.5 9.8E-05 42.3 13.6 133 9-152 77-215 (271)
238 cd08466 PBP2_LeuO The C-termin 90.4 14 0.0003 35.9 16.4 69 377-459 13-81 (200)
239 cd06286 PBP1_CcpB_like Ligand- 90.2 2.2 4.8E-05 44.4 10.8 108 38-146 94-205 (260)
240 COG2984 ABC-type uncharacteriz 90.2 6.5 0.00014 41.6 13.7 123 13-140 108-240 (322)
241 cd08461 PBP2_DntR_like_3 The C 90.2 14 0.00031 35.8 16.2 69 377-459 13-81 (198)
242 PRK15454 ethanol dehydrogenase 90.1 2.2 4.8E-05 47.7 11.1 91 45-135 36-128 (395)
243 PRK14987 gluconate operon tran 90.0 3.8 8.3E-05 44.5 12.9 133 9-149 137-272 (331)
244 cd08451 PBP2_BudR The C-termin 90.0 19 0.00041 34.8 18.4 69 378-459 15-83 (199)
245 PRK10339 DNA-binding transcrip 89.8 3.7 8E-05 44.6 12.6 131 8-146 130-264 (327)
246 TIGR02405 trehalos_R_Ecol treh 89.8 4.4 9.6E-05 43.6 13.1 118 11-140 133-253 (311)
247 PRK12681 cysB transcriptional 89.8 8 0.00017 42.0 15.1 104 570-683 183-293 (324)
248 COG1454 EutG Alcohol dehydroge 89.8 2.6 5.6E-05 46.3 10.9 94 45-138 16-111 (377)
249 PRK12683 transcriptional regul 89.7 13 0.00029 40.0 16.6 105 571-684 184-294 (309)
250 cd08413 PBP2_CysB_like The C-t 89.7 12 0.00026 36.5 15.3 70 377-459 13-82 (198)
251 PF12727 PBP_like: PBP superfa 89.7 4.8 0.0001 40.0 12.0 101 569-680 82-191 (193)
252 cd08420 PBP2_CysL_like C-termi 89.7 20 0.00043 34.5 18.1 69 377-459 13-81 (201)
253 PRK12680 transcriptional regul 89.6 15 0.00032 40.0 17.0 84 344-459 92-175 (327)
254 PRK15395 methyl-galactoside AB 89.6 7 0.00015 42.6 14.4 135 8-143 100-253 (330)
255 TIGR02424 TF_pcaQ pca operon t 89.5 14 0.00031 39.3 16.7 85 344-459 92-176 (300)
256 cd08411 PBP2_OxyR The C-termin 89.5 17 0.00037 35.3 16.2 68 378-459 15-82 (200)
257 PRK10837 putative DNA-binding 89.5 27 0.0006 36.8 18.8 104 571-682 178-287 (290)
258 cd08443 PBP2_CysB The C-termin 89.4 22 0.00047 34.7 16.9 71 376-459 12-82 (198)
259 COG3473 Maleate cis-trans isom 89.4 7.1 0.00015 38.4 12.1 135 3-140 56-205 (238)
260 cd06314 PBP1_tmGBP Periplasmic 89.4 9.8 0.00021 39.8 15.1 132 11-152 77-214 (271)
261 cd08189 Fe-ADH5 Iron-containin 89.3 4.2 9.1E-05 45.2 12.5 92 46-137 14-107 (374)
262 cd08434 PBP2_GltC_like The sub 89.2 21 0.00046 34.2 16.8 69 377-459 13-81 (195)
263 PRK10401 DNA-binding transcrip 89.0 3.2 7E-05 45.5 11.4 110 38-148 156-269 (346)
264 cd08449 PBP2_XapR The C-termin 89.0 22 0.00047 34.3 16.4 71 377-459 13-83 (197)
265 cd08192 Fe-ADH7 Iron-containin 88.9 3.2 6.9E-05 46.1 11.2 91 46-136 12-104 (370)
266 cd08425 PBP2_CynR The C-termin 88.9 20 0.00042 34.7 16.0 68 378-459 15-82 (197)
267 cd08467 PBP2_SyrM The C-termin 88.8 23 0.00051 34.5 16.6 69 377-459 13-81 (200)
268 TIGR01256 modA molybdenum ABC 88.7 8.1 0.00018 39.0 13.3 73 605-683 132-205 (216)
269 PF03480 SBP_bac_7: Bacterial 88.7 0.51 1.1E-05 50.4 4.6 103 568-682 126-231 (286)
270 cd08441 PBP2_MetR The C-termin 88.7 24 0.00052 34.2 16.6 68 378-459 14-81 (198)
271 PF13531 SBP_bac_11: Bacterial 88.7 2.5 5.4E-05 43.3 9.6 193 376-692 10-225 (230)
272 cd08435 PBP2_GbpR The C-termin 88.7 24 0.00052 34.1 18.1 70 378-459 14-83 (201)
273 cd08190 HOT Hydroxyacid-oxoaci 88.6 3.2 6.9E-05 46.8 11.0 89 46-134 11-101 (414)
274 PRK10624 L-1,2-propanediol oxi 88.3 3.8 8.2E-05 45.7 11.3 89 46-134 18-108 (382)
275 cd08193 HVD 5-hydroxyvalerate 88.1 3.8 8.3E-05 45.6 11.2 90 46-135 14-105 (376)
276 PRK12682 transcriptional regul 88.1 29 0.00063 37.2 17.9 70 377-459 106-175 (309)
277 cd06304 PBP1_BmpA_like Peripla 88.1 6.3 0.00014 41.1 12.4 126 8-139 73-202 (260)
278 PRK10936 TMAO reductase system 88.0 7.5 0.00016 42.6 13.4 122 10-140 124-254 (343)
279 cd08551 Fe-ADH iron-containing 87.9 3.9 8.5E-05 45.4 11.2 91 46-136 11-103 (370)
280 PRK10341 DNA-binding transcrip 87.6 17 0.00036 39.2 15.6 70 378-459 111-180 (312)
281 cd08469 PBP2_PnbR The C-termin 87.4 24 0.00051 35.1 15.9 69 377-459 13-81 (221)
282 cd08427 PBP2_LTTR_like_2 The C 87.3 29 0.00062 33.3 16.4 71 377-459 13-83 (195)
283 cd08430 PBP2_IlvY The C-termin 87.1 30 0.00064 33.4 17.1 70 377-459 13-82 (199)
284 TIGR02638 lactal_redase lactal 86.9 4.8 0.0001 44.8 11.1 89 46-134 17-107 (379)
285 PF00465 Fe-ADH: Iron-containi 86.8 2.8 6.2E-05 46.4 9.2 90 46-137 11-102 (366)
286 cd08445 PBP2_BenM_CatM_CatR Th 86.8 25 0.00054 34.3 15.4 69 377-459 14-82 (203)
287 cd08423 PBP2_LTTR_like_6 The C 86.7 31 0.00067 33.2 16.2 71 378-459 14-86 (200)
288 cd08194 Fe-ADH6 Iron-containin 86.5 5.4 0.00012 44.3 11.2 88 46-133 11-100 (375)
289 cd08456 PBP2_LysR The C-termin 86.1 33 0.00072 33.0 16.0 69 377-459 13-81 (196)
290 cd08458 PBP2_NocR The C-termin 86.1 34 0.00074 33.1 16.6 68 378-459 14-81 (196)
291 cd08437 PBP2_MleR The substrat 86.0 35 0.00075 33.0 16.4 70 378-459 14-83 (198)
292 cd08444 PBP2_Cbl The C-termina 85.8 36 0.00078 33.1 16.7 70 377-459 13-82 (198)
293 PF03808 Glyco_tran_WecB: Glyc 85.7 10 0.00022 37.0 11.4 105 41-155 32-138 (172)
294 KOG3857 Alcohol dehydrogenase, 85.7 4.6 0.0001 42.6 9.1 96 30-125 38-137 (465)
295 cd08453 PBP2_IlvR The C-termin 85.6 36 0.00079 32.9 16.8 71 378-459 14-84 (200)
296 cd08465 PBP2_ToxR The C-termin 85.4 24 0.00052 34.5 14.4 69 377-459 13-81 (200)
297 cd08188 Fe-ADH4 Iron-containin 85.2 7.2 0.00016 43.4 11.4 89 46-134 16-106 (377)
298 PRK11482 putative DNA-binding 85.0 38 0.00082 36.5 16.8 66 378-459 131-196 (317)
299 cd06533 Glyco_transf_WecG_TagA 85.0 6.2 0.00013 38.4 9.5 103 41-153 30-134 (171)
300 cd08185 Fe-ADH1 Iron-containin 84.8 6.6 0.00014 43.8 10.9 89 46-135 14-105 (380)
301 COG1910 Periplasmic molybdate- 84.5 16 0.00035 36.4 11.7 104 570-685 89-201 (223)
302 PRK11062 nhaR transcriptional 84.4 30 0.00066 36.8 15.5 72 377-459 106-177 (296)
303 cd08414 PBP2_LTTR_aromatics_li 84.4 40 0.00086 32.3 16.9 68 378-459 14-81 (197)
304 TIGR02955 TMAO_TorT TMAO reduc 84.2 18 0.00038 38.6 13.6 118 13-140 80-207 (295)
305 COG0725 ModA ABC-type molybdat 84.1 23 0.0005 37.0 13.7 115 570-694 124-252 (258)
306 cd08436 PBP2_LTTR_like_3 The C 83.7 42 0.0009 32.1 18.1 70 377-459 13-82 (194)
307 cd08176 LPO Lactadehyde:propan 83.5 7.9 0.00017 43.1 10.8 89 46-134 16-106 (377)
308 TIGR02637 RhaS rhamnose ABC tr 83.5 40 0.00086 35.9 16.1 124 10-141 77-210 (302)
309 PF13407 Peripla_BP_4: Peripla 83.5 2.3 5E-05 44.2 6.2 78 61-140 1-81 (257)
310 cd08181 PPD-like 1,3-propanedi 83.5 9.3 0.0002 42.1 11.2 86 47-133 15-103 (357)
311 cd08191 HHD 6-hydroxyhexanoate 83.4 9.4 0.0002 42.6 11.3 89 47-136 12-102 (386)
312 COG0715 TauA ABC-type nitrate/ 83.2 3.8 8.3E-05 44.6 8.1 70 569-644 127-202 (335)
313 PF14503 YhfZ_C: YhfZ C-termin 83.2 1.5 3.3E-05 44.3 4.4 105 580-695 114-224 (232)
314 TIGR03339 phn_lysR aminoethylp 83.1 63 0.0014 33.7 17.5 66 380-459 100-165 (279)
315 cd08464 PBP2_DntR_like_2 The C 82.8 47 0.001 32.0 16.7 69 377-459 13-81 (200)
316 PRK15421 DNA-binding transcrip 82.7 42 0.00091 36.2 15.9 67 379-459 104-170 (317)
317 PRK11013 DNA-binding transcrip 82.6 49 0.0011 35.5 16.3 102 571-682 184-291 (309)
318 cd08486 PBP2_CbnR The C-termin 82.5 25 0.00053 34.4 13.1 69 377-459 14-82 (198)
319 cd08416 PBP2_MdcR The C-termin 81.9 50 0.0011 31.7 16.6 71 377-459 13-83 (199)
320 cd08448 PBP2_LTTR_aromatics_li 81.8 50 0.0011 31.6 17.2 69 377-459 13-81 (197)
321 cd08182 HEPD Hydroxyethylphosp 81.7 11 0.00023 41.9 10.9 86 47-135 12-99 (367)
322 PRK09508 leuO leucine transcri 81.3 28 0.00061 37.4 13.9 69 377-459 125-193 (314)
323 COG1879 RbsB ABC-type sugar tr 81.2 35 0.00075 36.9 14.7 133 6-142 108-245 (322)
324 cd08187 BDH Butanol dehydrogen 80.5 11 0.00025 41.9 10.7 88 46-134 17-107 (382)
325 cd08186 Fe-ADH8 Iron-containin 80.3 12 0.00026 41.7 10.8 90 46-135 11-106 (383)
326 cd08170 GlyDH Glycerol dehydro 79.7 6.2 0.00013 43.4 8.1 85 47-134 12-98 (351)
327 PRK11074 putative DNA-binding 79.5 63 0.0014 34.4 15.8 85 344-459 91-175 (300)
328 PF04392 ABC_sub_bind: ABC tra 79.1 21 0.00045 38.1 11.8 104 15-125 82-194 (294)
329 cd07766 DHQ_Fe-ADH Dehydroquin 78.8 14 0.0003 40.3 10.5 92 47-140 12-105 (332)
330 TIGR02634 xylF D-xylose ABC tr 78.7 35 0.00077 36.4 13.5 128 7-141 72-209 (302)
331 PLN03192 Voltage-dependent pot 78.6 3 6.4E-05 51.7 5.7 55 509-563 249-305 (823)
332 PRK15408 autoinducer 2-binding 78.4 36 0.00077 37.2 13.5 128 7-141 98-234 (336)
333 PRK09861 cytoplasmic membrane 78.0 50 0.0011 34.8 13.9 121 567-694 119-264 (272)
334 cd08485 PBP2_ClcR The C-termin 77.1 74 0.0016 30.8 16.0 69 377-459 14-82 (198)
335 cd08171 GlyDH-like2 Glycerol d 76.9 14 0.0003 40.6 9.7 88 46-135 11-100 (345)
336 COG1638 DctP TRAP-type C4-dica 76.0 4.4 9.5E-05 44.0 5.4 101 569-684 158-264 (332)
337 PF12683 DUF3798: Protein of u 75.8 79 0.0017 32.8 13.8 168 45-227 18-222 (275)
338 PRK10355 xylF D-xylose transpo 75.8 35 0.00076 37.1 12.6 127 8-141 100-236 (330)
339 PRK10094 DNA-binding transcrip 75.7 1.2E+02 0.0026 32.5 16.7 69 379-459 108-176 (308)
340 PRK09986 DNA-binding transcrip 75.5 1.1E+02 0.0024 32.1 18.2 71 377-459 110-180 (294)
341 PRK09906 DNA-binding transcrip 74.6 97 0.0021 32.7 15.6 68 378-459 104-171 (296)
342 PRK03692 putative UDP-N-acetyl 74.2 26 0.00056 36.2 10.2 90 42-138 90-180 (243)
343 PF13685 Fe-ADH_2: Iron-contai 73.8 21 0.00045 37.0 9.5 99 48-152 9-109 (250)
344 PLN02245 ATP phosphoribosyl tr 73.4 28 0.00061 38.4 10.6 102 570-681 179-294 (403)
345 cd08183 Fe-ADH2 Iron-containin 73.4 23 0.0005 39.3 10.5 84 47-135 12-97 (374)
346 cd06353 PBP1_BmpA_Med_like Per 73.3 18 0.0004 37.7 9.2 85 60-152 1-89 (258)
347 TIGR00696 wecB_tagA_cpsF bacte 72.6 32 0.0007 33.6 10.0 88 42-137 33-122 (177)
348 cd06305 PBP1_methylthioribose_ 72.5 14 0.00031 38.5 8.3 77 61-140 2-81 (273)
349 PRK09423 gldA glycerol dehydro 72.3 14 0.00029 41.0 8.3 85 46-133 18-104 (366)
350 cd06276 PBP1_FucR_like Ligand- 72.2 41 0.00089 34.7 11.6 120 8-146 70-192 (247)
351 PRK15408 autoinducer 2-binding 70.8 16 0.00035 39.9 8.4 82 57-140 22-106 (336)
352 PRK11716 DNA-binding transcrip 70.7 1.1E+02 0.0025 31.4 14.8 69 378-459 81-149 (269)
353 KOG1419 Voltage-gated K+ chann 70.5 5.7 0.00012 44.6 4.6 89 475-563 234-324 (654)
354 cd06267 PBP1_LacI_sugar_bindin 70.4 14 0.00029 38.1 7.5 76 61-140 2-79 (264)
355 PRK11119 proX glycine betaine 70.0 30 0.00064 37.7 10.1 63 340-432 24-87 (331)
356 cd08446 PBP2_Chlorocatechol Th 69.4 1.1E+02 0.0023 29.3 16.9 69 377-459 14-82 (198)
357 cd08450 PBP2_HcaR The C-termin 68.7 1.1E+02 0.0024 29.2 16.4 69 377-459 13-81 (196)
358 cd01537 PBP1_Repressors_Sugar_ 68.7 14 0.0003 38.0 7.2 78 60-140 1-80 (264)
359 cd06301 PBP1_rhizopine_binding 67.9 16 0.00035 38.0 7.6 78 60-140 1-82 (272)
360 cd06315 PBP1_ABC_sugar_binding 67.4 86 0.0019 32.8 13.0 133 8-143 75-216 (280)
361 cd06312 PBP1_ABC_sugar_binding 67.4 17 0.00037 37.9 7.6 79 60-140 1-83 (271)
362 cd08178 AAD_C C-terminal alcoh 67.1 26 0.00057 39.2 9.3 80 55-134 18-99 (398)
363 PRK10677 modA molybdate transp 66.4 66 0.0014 33.5 11.6 70 379-459 41-116 (257)
364 PRK10537 voltage-gated potassi 65.8 13 0.00027 41.6 6.2 56 506-561 164-221 (393)
365 PRK00002 aroB 3-dehydroquinate 65.5 71 0.0015 35.2 12.1 104 33-140 9-119 (358)
366 PF04273 DUF442: Putative phos 65.5 90 0.002 27.8 10.5 84 53-136 23-107 (110)
367 cd08452 PBP2_AlsR The C-termin 65.4 1.3E+02 0.0029 28.9 16.2 68 378-459 14-81 (197)
368 PRK14498 putative molybdopteri 64.8 51 0.0011 39.6 11.6 66 57-125 185-262 (633)
369 cd08550 GlyDH-like Glycerol_de 64.4 24 0.00052 38.8 8.2 85 46-133 11-97 (349)
370 cd06306 PBP1_TorT-like TorT-li 64.1 21 0.00046 37.2 7.5 80 60-140 1-82 (268)
371 cd08175 G1PDH Glycerol-1-phosp 64.1 34 0.00073 37.6 9.3 86 46-133 11-100 (348)
372 cd06303 PBP1_LuxPQ_Quorum_Sens 63.7 19 0.00042 37.8 7.1 81 60-140 1-85 (280)
373 COG2358 Imp TRAP-type uncharac 63.6 16 0.00034 39.1 6.1 75 570-651 129-213 (321)
374 PRK13348 chromosome replicatio 63.4 2E+02 0.0044 30.3 15.8 101 571-681 180-285 (294)
375 cd08197 DOIS 2-deoxy-scyllo-in 63.2 65 0.0014 35.5 11.2 100 47-150 12-118 (355)
376 cd08481 PBP2_GcdR_like The C-t 62.6 1.4E+02 0.0031 28.3 12.9 98 571-677 86-190 (194)
377 cd08179 NADPH_BDH NADPH-depend 61.8 34 0.00074 38.0 8.8 79 56-134 21-102 (375)
378 PRK11139 DNA-binding transcrip 61.4 1.6E+02 0.0034 31.2 13.8 102 570-679 180-286 (297)
379 cd02071 MM_CoA_mut_B12_BD meth 61.4 57 0.0012 29.6 8.8 61 74-140 15-79 (122)
380 cd06167 LabA_like LabA_like pr 61.1 1.3E+02 0.0027 28.1 11.6 68 73-140 52-124 (149)
381 PRK03635 chromosome replicatio 60.9 2.2E+02 0.0049 30.0 15.1 65 380-459 106-170 (294)
382 cd08177 MAR Maleylacetate redu 60.8 34 0.00075 37.3 8.5 87 46-135 11-99 (337)
383 PF04392 ABC_sub_bind: ABC tra 60.8 73 0.0016 33.9 10.9 65 60-125 1-69 (294)
384 PF01634 HisG: ATP phosphoribo 60.5 13 0.00027 35.8 4.3 100 570-681 58-159 (163)
385 cd01391 Periplasmic_Binding_Pr 60.2 28 0.00061 35.4 7.5 78 60-140 1-83 (269)
386 cd06282 PBP1_GntR_like_2 Ligan 60.2 30 0.00065 35.7 7.8 77 61-140 2-80 (266)
387 cd06322 PBP1_ABC_sugar_binding 60.1 32 0.0007 35.6 8.0 77 61-140 2-81 (267)
388 PRK07377 hypothetical protein; 59.6 21 0.00046 34.4 5.6 62 344-429 74-135 (184)
389 PF12683 DUF3798: Protein of u 59.4 95 0.0021 32.2 10.5 101 40-140 113-224 (275)
390 cd08184 Fe-ADH3 Iron-containin 59.2 75 0.0016 34.9 10.7 86 46-135 11-103 (347)
391 cd06316 PBP1_ABC_sugar_binding 58.9 27 0.00058 37.0 7.3 79 60-140 1-82 (294)
392 cd06289 PBP1_MalI_like Ligand- 58.7 33 0.00072 35.4 7.8 77 61-140 2-80 (268)
393 PRK13583 hisG ATP phosphoribos 58.6 1.3E+02 0.0028 30.7 11.3 90 570-669 111-212 (228)
394 cd01538 PBP1_ABC_xylose_bindin 58.2 42 0.0009 35.5 8.6 77 61-140 2-81 (288)
395 TIGR03414 ABC_choline_bnd chol 57.7 2.2E+02 0.0047 30.3 13.8 40 380-430 24-63 (290)
396 cd06277 PBP1_LacI_like_1 Ligan 57.4 44 0.00096 34.6 8.5 75 61-140 2-81 (268)
397 cd01536 PBP1_ABC_sugar_binding 57.3 35 0.00076 35.1 7.7 78 60-140 1-81 (267)
398 PF07287 DUF1446: Protein of u 57.1 72 0.0016 35.0 9.9 114 5-144 62-189 (362)
399 PF13380 CoA_binding_2: CoA bi 56.5 15 0.00033 33.1 4.0 87 59-152 1-89 (116)
400 COG0040 HisG ATP phosphoribosy 56.4 85 0.0018 33.1 9.8 102 570-683 107-211 (290)
401 cd06302 PBP1_LsrB_Quorum_Sensi 56.1 39 0.00084 36.0 7.9 78 61-140 2-82 (298)
402 cd06318 PBP1_ABC_sugar_binding 56.0 35 0.00075 35.7 7.5 77 61-140 2-81 (282)
403 cd06299 PBP1_LacI_like_13 Liga 55.2 46 0.00099 34.4 8.2 76 61-140 2-79 (265)
404 PRK01741 cell division protein 55.1 34 0.00073 36.5 6.7 14 833-846 97-110 (332)
405 cd06310 PBP1_ABC_sugar_binding 55.0 38 0.00083 35.2 7.6 80 60-140 1-83 (273)
406 PF03401 TctC: Tripartite tric 54.8 1.3E+02 0.0029 31.6 11.5 128 560-693 81-241 (274)
407 cd01540 PBP1_arabinose_binding 54.5 34 0.00074 36.0 7.1 76 61-140 2-80 (289)
408 cd01545 PBP1_SalR Ligand-bindi 54.4 41 0.00089 34.8 7.7 78 61-140 2-81 (270)
409 cd08173 Gro1PDH Sn-glycerol-1- 53.3 93 0.002 34.0 10.4 82 48-133 14-98 (339)
410 cd06300 PBP1_ABC_sugar_binding 53.3 46 0.001 34.6 7.8 80 60-140 1-86 (272)
411 COG4521 TauA ABC-type taurine 53.1 85 0.0018 31.9 8.7 108 569-682 121-240 (334)
412 KOG1420 Ca2+-activated K+ chan 53.1 9.5 0.00021 42.7 2.4 53 503-555 281-335 (1103)
413 cd08549 G1PDH_related Glycerol 53.1 92 0.002 33.9 10.2 85 47-133 12-100 (332)
414 cd01324 cbb3_Oxidase_CcoQ Cyto 53.0 13 0.00028 27.6 2.4 28 476-503 12-39 (48)
415 PF14981 FAM165: FAM165 family 52.9 29 0.00062 25.0 3.9 33 715-747 3-35 (51)
416 PRK00843 egsA NAD(P)-dependent 52.6 1.1E+02 0.0024 33.6 10.8 84 46-133 21-107 (350)
417 PF06506 PrpR_N: Propionate ca 52.3 39 0.00085 32.9 6.5 107 17-140 38-144 (176)
418 cd08180 PDD 1,3-propanediol de 52.1 40 0.00086 36.7 7.2 79 54-133 18-98 (332)
419 COG1879 RbsB ABC-type sugar tr 52.0 51 0.0011 35.5 8.1 81 59-140 34-117 (322)
420 PF02608 Bmp: Basic membrane p 51.8 48 0.001 35.6 7.7 88 59-153 2-94 (306)
421 PRK09189 uroporphyrinogen-III 51.8 75 0.0016 32.6 8.9 89 43-137 101-191 (240)
422 COG1794 RacX Aspartate racemas 51.7 60 0.0013 32.7 7.5 86 44-140 103-189 (230)
423 PF02602 HEM4: Uroporphyrinoge 51.0 31 0.00067 35.1 5.9 93 39-138 97-190 (231)
424 TIGR02370 pyl_corrinoid methyl 50.9 97 0.0021 30.8 9.2 89 59-153 85-177 (197)
425 cd06295 PBP1_CelR Ligand bindi 50.5 62 0.0013 33.7 8.3 77 58-140 3-88 (275)
426 COG0134 TrpC Indole-3-glycerol 50.4 47 0.001 34.3 6.8 88 47-142 69-159 (254)
427 KOG3713 Voltage-gated K+ chann 50.2 19 0.00041 40.3 4.1 62 487-552 358-421 (477)
428 cd08169 DHQ-like Dehydroquinat 50.1 1.1E+02 0.0023 33.6 10.2 100 47-150 12-117 (344)
429 TIGR00249 sixA phosphohistidin 50.1 66 0.0014 30.5 7.5 98 38-136 23-120 (152)
430 PRK01686 hisG ATP phosphoribos 50.0 1.5E+02 0.0033 29.9 10.3 92 579-681 114-207 (215)
431 cd06317 PBP1_ABC_sugar_binding 49.9 56 0.0012 33.9 7.8 77 61-140 2-82 (275)
432 PRK10355 xylF D-xylose transpo 49.8 67 0.0015 34.9 8.6 80 58-140 25-107 (330)
433 PRK10936 TMAO reductase system 49.8 60 0.0013 35.5 8.2 81 58-140 46-129 (343)
434 PRK10014 DNA-binding transcrip 49.4 73 0.0016 34.5 8.9 79 59-140 65-145 (342)
435 cd06315 PBP1_ABC_sugar_binding 49.0 73 0.0016 33.4 8.6 79 59-140 1-82 (280)
436 PF07302 AroM: AroM protein; 49.0 1.1E+02 0.0025 30.9 9.1 74 59-136 126-201 (221)
437 cd06323 PBP1_ribose_binding Pe 48.8 60 0.0013 33.5 7.8 77 61-140 2-81 (268)
438 TIGR00288 conserved hypothetic 48.7 2.5E+02 0.0055 26.9 11.1 85 46-140 43-130 (160)
439 PRK13957 indole-3-glycerol-pho 48.6 1.5E+02 0.0033 30.6 10.2 88 47-142 64-154 (247)
440 TIGR02637 RhaS rhamnose ABC tr 48.5 58 0.0012 34.6 7.8 72 67-140 9-82 (302)
441 TIGR00070 hisG ATP phosphoribo 48.3 84 0.0018 30.8 7.9 73 570-654 101-173 (182)
442 cd01539 PBP1_GGBP Periplasmic 48.3 69 0.0015 34.1 8.3 78 60-140 1-83 (303)
443 cd06270 PBP1_GalS_like Ligand 48.2 70 0.0015 33.1 8.2 76 61-140 2-79 (268)
444 cd00886 MogA_MoaB MogA_MoaB fa 48.1 89 0.0019 29.6 8.1 63 60-124 2-70 (152)
445 TIGR02667 moaB_proteo molybden 48.0 1.1E+02 0.0024 29.4 8.7 65 58-124 4-72 (163)
446 PRK09701 D-allose transporter 47.7 71 0.0015 34.2 8.3 84 56-140 22-108 (311)
447 PRK11303 DNA-binding transcrip 47.2 85 0.0018 33.8 8.9 80 58-140 61-142 (328)
448 PF02310 B12-binding: B12 bind 47.2 1.5E+02 0.0032 26.4 9.2 59 74-138 16-78 (121)
449 PLN02428 lipoic acid synthase 47.0 4.2E+02 0.0092 29.0 14.9 108 40-150 129-257 (349)
450 cd06324 PBP1_ABC_sugar_binding 47.0 53 0.0012 35.0 7.2 77 61-140 2-83 (305)
451 cd08447 PBP2_LTTR_aromatics_li 46.8 2.6E+02 0.0056 26.5 16.5 69 377-459 13-81 (198)
452 cd06309 PBP1_YtfQ_like Peripla 46.4 51 0.0011 34.3 6.9 72 66-140 9-81 (273)
453 cd06278 PBP1_LacI_like_2 Ligan 46.4 64 0.0014 33.2 7.6 75 61-140 2-78 (266)
454 PRK11070 ssDNA exonuclease Rec 46.3 94 0.002 36.6 9.3 87 59-152 70-159 (575)
455 cd02067 B12-binding B12 bindin 46.2 1.9E+02 0.004 25.9 9.6 66 68-139 9-78 (119)
456 cd06320 PBP1_allose_binding Pe 46.1 62 0.0013 33.7 7.5 80 60-140 1-83 (275)
457 cd06273 PBP1_GntR_like_1 This 45.8 78 0.0017 32.6 8.1 76 61-140 2-79 (268)
458 TIGR02634 xylF D-xylose ABC tr 45.8 66 0.0014 34.3 7.7 72 66-140 8-80 (302)
459 cd06296 PBP1_CatR_like Ligand- 45.6 70 0.0015 33.1 7.7 76 61-140 2-79 (270)
460 cd08432 PBP2_GcdR_TrpI_HvrB_Am 45.5 2.7E+02 0.0058 26.2 12.6 64 378-458 14-77 (194)
461 cd06319 PBP1_ABC_sugar_binding 45.3 67 0.0015 33.4 7.6 77 61-140 2-81 (277)
462 PF02310 B12-binding: B12 bind 45.1 95 0.0021 27.7 7.6 71 45-123 16-87 (121)
463 PRK15138 aldehyde reductase; P 45.1 1.2E+02 0.0026 33.9 9.7 84 47-134 20-106 (387)
464 cd06281 PBP1_LacI_like_5 Ligan 44.9 76 0.0017 32.9 7.9 77 61-140 2-80 (269)
465 PF00218 IGPS: Indole-3-glycer 44.3 1.4E+02 0.0031 31.0 9.4 89 45-141 69-160 (254)
466 TIGR00640 acid_CoA_mut_C methy 44.3 2.2E+02 0.0048 26.2 9.7 60 75-140 19-82 (132)
467 cd01575 PBP1_GntR Ligand-bindi 44.1 73 0.0016 32.8 7.6 76 61-140 2-79 (268)
468 KOG0498 K+-channel ERG and rel 43.9 23 0.00049 42.4 3.8 71 510-580 294-371 (727)
469 PRK05569 flavodoxin; Provision 43.8 1.5E+02 0.0032 27.4 8.9 85 59-154 2-95 (141)
470 PRK10653 D-ribose transporter 43.8 88 0.0019 33.1 8.2 80 58-140 26-108 (295)
471 cd08422 PBP2_CrgA_like The C-t 43.7 1.7E+02 0.0036 27.7 9.7 66 377-459 14-79 (197)
472 PF01102 Glycophorin_A: Glycop 43.2 36 0.00077 30.9 4.1 27 721-747 67-93 (122)
473 cd08195 DHQS Dehydroquinate sy 43.1 2.3E+02 0.0049 31.0 11.4 92 48-140 13-112 (345)
474 PF01936 NYN: NYN domain; Int 42.7 1.2E+02 0.0026 28.0 8.1 94 45-140 21-120 (146)
475 PF06305 DUF1049: Protein of u 42.2 71 0.0015 25.3 5.5 27 721-747 24-50 (68)
476 cd08487 PBP2_BlaA The C-termin 42.0 3E+02 0.0065 25.9 13.1 99 572-678 85-186 (189)
477 TIGR00288 conserved hypothetic 41.9 1.5E+02 0.0032 28.4 8.3 79 48-135 70-149 (160)
478 cd00758 MoCF_BD MoCF_BD: molyb 41.6 1.1E+02 0.0024 28.1 7.5 49 73-124 19-67 (133)
479 cd02070 corrinoid_protein_B12- 41.4 2.1E+02 0.0046 28.5 10.0 88 59-152 83-174 (201)
480 cd06307 PBP1_uncharacterized_s 41.2 80 0.0017 32.8 7.4 80 60-140 1-84 (275)
481 cd06283 PBP1_RegR_EndR_KdgR_li 41.2 93 0.002 32.0 7.8 76 61-140 2-79 (267)
482 cd06321 PBP1_ABC_sugar_binding 40.9 93 0.002 32.2 7.8 77 61-140 2-83 (271)
483 TIGR00644 recJ single-stranded 40.8 1.8E+02 0.0038 34.2 10.6 109 25-140 26-136 (539)
484 PRK06703 flavodoxin; Provision 40.8 1.3E+02 0.0029 28.2 8.1 82 60-153 3-93 (151)
485 cd01574 PBP1_LacI Ligand-bindi 40.7 1.1E+02 0.0023 31.5 8.2 77 61-140 2-80 (264)
486 TIGR01501 MthylAspMutase methy 40.7 2.9E+02 0.0064 25.6 9.8 70 75-152 18-91 (134)
487 PRK02261 methylaspartate mutas 40.2 2.5E+02 0.0053 26.1 9.5 85 59-150 4-92 (137)
488 PRK11914 diacylglycerol kinase 39.9 1.3E+02 0.0028 32.3 8.8 78 55-137 5-86 (306)
489 PRK05452 anaerobic nitric oxid 39.7 2.3E+02 0.0049 32.7 11.1 90 57-154 250-349 (479)
490 TIGR00035 asp_race aspartate r 39.5 59 0.0013 33.3 5.7 43 45-90 104-146 (229)
491 cd01542 PBP1_TreR_like Ligand- 39.5 1E+02 0.0023 31.5 7.9 76 61-140 2-79 (259)
492 cd06285 PBP1_LacI_like_7 Ligan 39.4 1.2E+02 0.0025 31.3 8.3 76 61-140 2-79 (265)
493 COG0541 Ffh Signal recognition 39.3 2.2E+02 0.0048 31.9 10.1 120 30-154 97-224 (451)
494 TIGR00177 molyb_syn molybdenum 39.2 1.3E+02 0.0028 28.2 7.6 49 73-124 27-75 (144)
495 cd06275 PBP1_PurR Ligand-bindi 39.2 2.2E+02 0.0048 29.2 10.4 62 61-125 2-65 (269)
496 PRK13805 bifunctional acetalde 39.2 1.8E+02 0.0038 36.5 10.8 78 57-134 479-560 (862)
497 PF12273 RCR: Chitin synthesis 39.1 29 0.00064 31.9 3.1 24 723-746 3-26 (130)
498 cd06313 PBP1_ABC_sugar_binding 39.0 83 0.0018 32.8 7.1 71 67-140 10-81 (272)
499 PRK00278 trpC indole-3-glycero 38.8 2.7E+02 0.0059 29.1 10.6 88 45-140 71-161 (260)
500 PF05368 NmrA: NmrA-like famil 38.7 2.6E+02 0.0057 28.2 10.6 86 44-147 9-100 (233)
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=1.7e-82 Score=665.16 Aligned_cols=705 Identities=19% Similarity=0.319 Sum_probs=581.2
Q ss_pred hHHHHhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHHHHH
Q 003054 4 NFIIQLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTDALQ 83 (852)
Q Consensus 4 ~~v~~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~~l~ 83 (852)
+.+..+|...++|+|+++. -++..+++..++.|. ...++++++.+++|.+++++| |.+-|...++.+.+.+.
T Consensus 104 ~~ltsfc~aLh~~~vtpsf----p~~~~~~Fviq~RP~---l~~al~s~i~hy~W~~fv~ly-D~~rg~s~Lqai~~~a~ 175 (897)
T KOG1054|consen 104 NTLTSFCGALHVSFVTPSF----PTDGDNQFVIQMRPA---LKGALLSLIDHYKWEKFVYLY-DTDRGLSILQAIMEAAA 175 (897)
T ss_pred hhhhhhccceeeeeecccC----CcCCCceEEEEeCch---HHHHHHHHHHhcccceEEEEE-cccchHHHHHHHHHHHH
Confidence 4566789999999999765 234567899999998 778999999999999999999 88899999999999999
Q ss_pred hCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHcCCcccceEEEEcCccccccccCCch
Q 003054 84 AIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLEPS 163 (852)
Q Consensus 84 ~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~~~~~~~~~~~~ 163 (852)
+++..|.....-.+ .+...|..+++.+...+.+-+++.|..+....++.|+-+.|-..++|++|.++......+. ..
T Consensus 176 ~~nw~VtA~~v~~~-~d~~~yr~~f~~l~~r~e~rv~iDce~~~~~~il~q~i~~~k~~~~YHYvlaNl~f~d~dl--~~ 252 (897)
T KOG1054|consen 176 QNNWQVTAINVGNI-NDVKEYRMLFEMLDRRQENRVLIDCESERRNRILLQVIELGKHVKGYHYVLANLGFTDIDL--ER 252 (897)
T ss_pred hcCceEEEEEcCCc-ccHHHHHHHHHHHhccccceEEEEcccHHHHHHHHHHHHHhhhccceEEEEeeCCCchhhH--HH
Confidence 99999987765443 3455699999999988999899999999998999999999988899999998764433332 12
Q ss_pred hhcccceEEEEEecCCCChHHHHHHHHHHHhccccCCCCcccccchhhHhHhhHHHHHHHHHHHhcccCcCccccccCCC
Q 003054 164 VIDSMQGVIGVGPHVPKTKALENFRVRWKRNFLQENPSIVDVELNIFGLLAYDATRALAEAVEKAGITSFGFDKTNVSRN 243 (852)
Q Consensus 164 ~~~~~~gv~~~~~~~~~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~a~~aYDAv~~lA~Al~~a~~~~~~~~~~~~~~~ 243 (852)
......++.+++..+.++|..++|.++|++.-..++++..+.++.+.++.+|||+.++++|++.+..++.+..+. +.
T Consensus 253 f~~g~aNitgFqivn~~~~~~~k~~~~~~~l~~~~~~g~~~~~~k~tsAlthDailV~~eaf~~~~~q~~~~~rR---G~ 329 (897)
T KOG1054|consen 253 FQHGGANITGFQIVNKNNPMVKKFIQRWKELDEREYPGASNDPIKYTSALTHDAILVMAEAFRSLRRQRIDISRR---GN 329 (897)
T ss_pred HhcCCcceeEEEEecCCChHHHHHHHHHhhhcccccCCCCCCCcchhhhhhhhHHHHHHHHHHHHHHhhhchhcc---CC
Confidence 345567789999999999999999999999888888888777889999999999999999999987766443332 22
Q ss_pred CCCCc--cccccCChHHHHHHhhccceeeeeeeEEee-cCccccceEEEEEcc-CCcEEEEEEcCCCCcccccCCCcccc
Q 003054 244 ATDLE--AFGISQNGPKLLQALSSTRFKGLTGDYIFV-DGQLQSSAFEIINVN-NGARGVGFWTPEKGLTQKLSSNSTTK 319 (852)
Q Consensus 244 ~~~~~--~~~~~~~g~~l~~al~~~~f~GltG~v~f~-~G~~~~~~~~I~~~~-~g~~~vG~w~~~~g~~~~~~~~~~~~ 319 (852)
..||- +...|..|..+.+||++++++|+||.++|| .|.+.+...+|+.++ +|.+.+|+|+...|+....+
T Consensus 330 ~GD~~an~~~p~~qG~~I~ralk~v~~eGLTGniqFd~~G~R~Nyt~~i~elk~~~~rk~~~W~e~~~fv~~~t------ 403 (897)
T KOG1054|consen 330 AGDCLANPAVPWEQGIDIERALKQVQVEGLTGNIQFDKYGRRTNYTIDIVELKSNGSRKVGYWNEGEGFVPGST------ 403 (897)
T ss_pred CccccCCCCCchhcchhHHHHHHheeecccccceeecccCccccceEEEEEeccCCcceeeeecccCceeeccc------
Confidence 22332 345688999999999999999999999999 999999999999999 99999999999888764322
Q ss_pred CCccceEeCCCCCCCCCcccccCCCceEEEeeecccCcccceEEeeCCC--CCCCceEEEeeHHHHHHHHHHCCCccceE
Q 003054 320 SKLKPIIWPGDSTSDPKGWEVPTNEKKLRIGVPVKKGFSDFVNVTIDPK--TQEPTSVTGYCVDVFKAVIQELPYAVAYD 397 (852)
Q Consensus 320 ~~~~~i~Wpg~~~~~p~~~~~~~~~~~lrv~v~~~~~~~~~~~~~~d~~--~~~~~~~~G~~~dl~~~ia~~l~~~~~~~ 397 (852)
+ ...+.-.-..+.+...|.+....||. +..++.. .++. ++.|||+||+.+||++.++.+++.
T Consensus 404 -----~-------a~~~~d~~~~~n~tvvvttiL~spyv---m~kkn~~~~egn~-ryEGyCvdLa~~iAkhi~~~Y~l~ 467 (897)
T KOG1054|consen 404 -----V-------AQSRNDQASKENRTVVVTTILESPYV---MLKKNHEQLEGNE-RYEGYCVDLAAEIAKHIGIKYKLF 467 (897)
T ss_pred -----c-------ccccccccccccceEEEEEecCCchh---HHHhhHHHhcCCc-ccceeHHHHHHHHHHhcCceEEEE
Confidence 0 00011111123555666666555544 3333322 4667 899999999999999999866655
Q ss_pred EEecCCCCCC--CCCC-hhHHHHHHhcCcccEEEeeeeeecCcceeeeccccccccceEEEEEccCCCCCCceEeecccc
Q 003054 398 FVPYGQPDGS--SSGS-YNDLVYQVFLGEFDAVVGDITIVFNRSNYVDFTLPYTESGVSMIVPIKDSKKRNAWVFLQPLT 474 (852)
Q Consensus 398 ~~~~~~~~g~--~ngs-~~~li~~l~~g~~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv~~~~~~~~~~~~~l~PF~ 474 (852)
.+..+. .|. ..++ |+||++.|..|++|+++++++||.+|.+.+|||.|++..|+++++++|+...+..+.|+.|+.
T Consensus 468 iv~dgk-yGardaD~k~WnGMvGeLv~grAdiavApLTIt~~REeviDFSKPfMslGISIMIKKPqKsk~gVFSFldPLa 546 (897)
T KOG1054|consen 468 IVGDGK-YGARDADTKIWNGMVGELVYGRADIAVAPLTITLVREEVIDFSKPFMSLGISIMIKKPQKSKPGVFSFLDPLA 546 (897)
T ss_pred EecCCc-ccccCCCcccccchhHHHhcCccceEEeeeeeehhhhhhhccccchhhcCeEEEEeCcccCCCCeeeecchhH
Confidence 554322 232 4556 999999999999999999999999999999999999999999999999988999999999999
Q ss_pred hhHHHHHHHHHHHHHhhhhheecccCCCCC------CCc-------ccccchhHHHHHHHhhhcccc-ccccchhhHHHH
Q 003054 475 WDLWVTCFCFFIFIGFVVWVLEHRVNEDFR------GPA-------GQQVGTSFWFSFSTMVFSQRE-RVISNLARIVVI 540 (852)
Q Consensus 475 ~~lW~~i~~~~i~~~~v~~~l~~~~~~~~~------~~~-------~~~~~~~~~~~~~~l~~~~~~-~~~s~~~R~v~~ 540 (852)
.++|++++..++-+++++++..|.++-+|+ |+. ..++.+++||+++++++|+.. .|++.++|++-.
T Consensus 547 ~eIWm~ivfaYiGVSvvlFLVSrFSPYEwh~Ee~~rg~~t~~~~~NeFgifNsLWFsLgAFMQQG~DI~PRslSGRIvgg 626 (897)
T KOG1054|consen 547 YEIWMCIVFAYIGVSVVLFLVSRFSPYEWHTEEFERGRFTPSDPPNEFGIFNSLWFSLGAFMQQGCDISPRSLSGRIVGG 626 (897)
T ss_pred HHHHHHHHHHHhcceEEEEEEeccCchheeccccccCCCCCCCCCccchhhHHHHHHHHHHHhcCCCCCccccccceecc
Confidence 999999999999999999999998776643 221 247889999999999999965 789999999999
Q ss_pred HHHHHHHHHHHHhhhhccceeeecccCCCcCCHHHHHhcCC-eEEEEeCchHHHHHHhcCCCC----------cc-eeec
Q 003054 541 VWCFVVLILTQSYTASLTSLLTVQQLQPTITDVKMLIKRGD-NVGYQKGSFVLGILKQLGFDE----------RK-LVVY 608 (852)
Q Consensus 541 ~w~~~~lil~~~Yta~L~s~Lt~~~~~~~i~sl~dL~~~~~-~vg~~~~s~~~~~l~~~~~~~----------~~-~~~~ 608 (852)
+||||.|||.++|||+|+++||++++.+||.+.|||+++.+ .+|+..+....+++++...+- .. -+-+
T Consensus 627 vWWFFTlIIiSSYTANLAAFLTvErMvsPIESaEDLAkQteIaYGt~~~GSTkeFFr~Skiavy~kMW~yM~SaepsVFv 706 (897)
T KOG1054|consen 627 VWWFFTLIIISSYTANLAAFLTVERMVSPIESAEDLAKQTEIAYGTLDSGSTKEFFRRSKIAVYEKMWTYMKSAEPSVFV 706 (897)
T ss_pred chhhhhhhhhhhhhhHHHHHHhHHhhcCcchhHHHHhhcceeeeeecCCCchHHHHhhhhHHHHHHHHHHHhcCCcceee
Confidence 99999999999999999999999999999999999999987 788877776777765421110 00 0223
Q ss_pred CCHhHHHHHhhcccccCceeEEEechhHHHHHHhhc-CCceEeecccccccceEEEecCCCCchhhHHHHHHhccccChh
Q 003054 609 NSPEDCHELFQKGSVNGGIAAAFDEIPYMKLLIGQY-CSKYAMIEPKFKTAGFGFVFPLHSPLVHDVSKAILNVTEGDKM 687 (852)
Q Consensus 609 ~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~~-~~~~~~v~~~~~~~~~~~~~~k~spl~~~in~~il~l~e~G~~ 687 (852)
.+..|.++.+++.+ |-+|++.|...-+|.-.+. |+ -+.||..+.+.+||++.||||.|+..+|-++++|.|.|++
T Consensus 707 ~t~aeGv~rVRksK---GkyAfLLEsTmNey~eqRkPCD-TMKVGgNLds~GYGiATp~Gsslr~~vNLAvLkL~E~G~L 782 (897)
T KOG1054|consen 707 RTTAEGVARVRKSK---GKYAFLLESTMNEYIEQRKPCD-TMKVGGNLDSKGYGIATPKGSSLRNAVNLAVLKLNEQGLL 782 (897)
T ss_pred ehhhhHHHHHHhcC---CceEeehHhhhhhhhhccCCcc-ceecccccCCcceeecCCCCcccccchhhhhhhhcccchH
Confidence 35556677776655 6799999988777776544 97 5568999999999999999999999999999999999999
Q ss_pred HHHHHHHccCCCCCCCCC--CCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhcccc
Q 003054 688 KEIEDAWFKKHSSCPDAS--TVVSSRSLGLNSFWGLFLIAGVAAILALIIFMAVFIHQHWNVLK 749 (852)
Q Consensus 688 ~~i~~kw~~~~~~c~~~~--~~~~~~~L~l~~~~g~f~il~ig~~lsl~vf~~e~~~~~r~~~~ 749 (852)
+++++||+.+.+.|.... ...+...|+|.++.|+||||..|++||+++.++|++|+.|...+
T Consensus 783 dKLkNKWWYDkGeC~sg~~ds~~ktsaLsLSnVAGvFYIL~gGl~laMlvALiEF~yksr~Eak 846 (897)
T KOG1054|consen 783 DKLKNKWWYDKGECGSGGGDSKDKTSALSLSNVAGVFYILVGGLGLAMLVALIEFCYKSRAEAK 846 (897)
T ss_pred HHhhhhhcccccccCCCCCCCCcchhhcchhhccceeeeehhhHHHHHHHHHHHHHHHhhHHHH
Confidence 999999999999999876 33455789999999999999999999999999999999877755
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=6.4e-75 Score=610.61 Aligned_cols=676 Identities=21% Similarity=0.351 Sum_probs=560.2
Q ss_pred HHHhcCCCCccEEeeecCCCCCCC-CCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHHHHHh
Q 003054 6 IIQLGNKSQVPILSFSATSPSLTS-IRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTDALQA 84 (852)
Q Consensus 6 v~~i~~~~~vP~Is~~ats~~lt~-~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~~l~~ 84 (852)
++.-+..|++|+|.....+..+++ .-++.|.|+.|+.+.|+....+.+..|.|++|.++.+||.-|+.....++..+++
T Consensus 116 vSYT~gFY~iPV~G~~~Rda~fSdKnIh~sFlRtvpPyshqa~VwleMl~~~~y~~vi~l~s~d~~gra~~~r~qt~~e~ 195 (993)
T KOG4440|consen 116 VSYTAGFYRIPVLGLTTRDAIFSDKNIHLSFLRTVPPYSHQASVWLEMLRVYSYNHVILLVSDDHEGRAAQKRLQTLLEE 195 (993)
T ss_pred ceeeccceeeeeeeeeehhhhhccCceeeeEeecCCCccchhHHHHHHHHHhhcceEEEEEcccccchhHHhHHHHHHHH
Confidence 444567899999999999999988 5689999999999999999999999999999999999999999998888888887
Q ss_pred CCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHcCCcccceEEEEcCccccccccCCchh
Q 003054 85 IDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLEPSV 164 (852)
Q Consensus 85 ~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~~~~~~~~~~~~~ 164 (852)
...++.....+.++ ..+++..|...|..++||+++....++|..+++.|.+++|+++|||||.+......
T Consensus 196 ~~~~~e~v~~f~p~--~~~~t~~l~~~k~~~~rv~~~~as~dDA~~ifr~Ag~lnmTG~G~VWiV~E~a~~~-------- 265 (993)
T KOG4440|consen 196 RESKAEKVLQFDPG--TKNVTALLMEAKELEARVIILSASEDDAATIFRAAGMLNMTGSGYVWIVGERAISG-------- 265 (993)
T ss_pred HhhhhhhheecCcc--cchHHHHHhhhhhhhheeEEeecccchHHHHHHhhhhhcccCceEEEEEecccccc--------
Confidence 77776666666654 67899999999999999999999999999999999999999999999998764322
Q ss_pred hcccceEEEEEecCCCChHHHHHHHHHHHhccccCCCCcccccchhhHhHhhHHHHHHHHHHHhcccCcCccccccCCCC
Q 003054 165 IDSMQGVIGVGPHVPKTKALENFRVRWKRNFLQENPSIVDVELNIFGLLAYDATRALAEAVEKAGITSFGFDKTNVSRNA 244 (852)
Q Consensus 165 ~~~~~gv~~~~~~~~~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~a~~aYDAv~~lA~Al~~a~~~~~~~~~~~~~~~~ 244 (852)
.+..+|++|.+.....+ ..+..-|++.++|.|+++......-.+.+.
T Consensus 266 nn~PdG~LGlqL~~~~~----------------------------~~~hirDsv~vlasAv~e~~~~e~I~~~P~----- 312 (993)
T KOG4440|consen 266 NNLPDGILGLQLINGKN----------------------------ESAHIRDSVGVLASAVHELLEKENITDPPR----- 312 (993)
T ss_pred CCCCCceeeeEeecCcc----------------------------ccceehhhHHHHHHHHHHHHhhccCCCCCC-----
Confidence 23468999987653322 134567999999999999764432222221
Q ss_pred CCCccccccCChHHHHHHhhccc-eeeeeeeEEee-cCccccceEEEEEcc-C-CcEEEEEEcCCCCcccccCCCccccC
Q 003054 245 TDLEAFGISQNGPKLLQALSSTR-FKGLTGDYIFV-DGQLQSSAFEIINVN-N-GARGVGFWTPEKGLTQKLSSNSTTKS 320 (852)
Q Consensus 245 ~~~~~~~~~~~g~~l~~al~~~~-f~GltG~v~f~-~G~~~~~~~~I~~~~-~-g~~~vG~w~~~~g~~~~~~~~~~~~~ 320 (852)
..+++..+|..|..|.+.+...+ -+|.||+|.|+ +||+....|+|+|+- + ..+.+|.++. .... .
T Consensus 313 ~c~d~~~~w~~g~~l~~~l~s~~~~~g~TgrV~Fnd~gdRi~a~YdiiN~hq~rk~Vg~~~yd~---~r~~--------~ 381 (993)
T KOG4440|consen 313 GCVDNTNIWKTGPLLKRVLMSSKYADGVTGRVEFNDDGDRIFANYDIINLHQNRKLVGVGIYDG---TRVI--------P 381 (993)
T ss_pred cccCccchhcccHHHHHHHhhhcccCCcceeEEEcCCCceeeccceeEehhhhhhhhhhccccc---eeec--------c
Confidence 12345566889999999888755 58999999996 999999999999995 2 2444444442 2111 2
Q ss_pred CccceEeCCCCCCCCCcccccCCCceEEEeeecccCcccceEEe---------------eC--------------CCCC-
Q 003054 321 KLKPIIWPGDSTSDPKGWEVPTNEKKLRIGVPVKKGFSDFVNVT---------------ID--------------PKTQ- 370 (852)
Q Consensus 321 ~~~~i~Wpg~~~~~p~~~~~~~~~~~lrv~v~~~~~~~~~~~~~---------------~d--------------~~~~- 370 (852)
+.+.|+|||+.+.+|+|..+| ++|||.+.+.+|| +++. .| |.+.
T Consensus 382 nd~~IiWpGg~~~KP~gi~~p---thLrivTi~~~PF---VYv~p~~sd~~c~eef~~~~d~~~k~~c~gpn~s~p~s~~ 455 (993)
T KOG4440|consen 382 NDRKIIWPGGETEKPRGIQMP---THLRIVTIHQEPF---VYVKPTLSDGTCKEEFTVNGDPVKKVICTGPNDSSPGSPR 455 (993)
T ss_pred CCceeecCCCCcCCCcccccc---ceeEEEEeccCCe---EEEecCCCCcchhhhccccCCcccceeecCCCCCCCCCcc
Confidence 457899999999999999998 6899999888775 3332 11 1111
Q ss_pred ---CCceEEEeeHHHHHHHHHHCCCccceEEEecCCCCC--------CCC-CChhHHHHHHhcCcccEEEeeeeeecCcc
Q 003054 371 ---EPTSVTGYCVDVFKAVIQELPYAVAYDFVPYGQPDG--------SSS-GSYNDLVYQVFLGEFDAVVGDITIVFNRS 438 (852)
Q Consensus 371 ---~~~~~~G~~~dl~~~ia~~l~~~~~~~~~~~~~~~g--------~~n-gs~~~li~~l~~g~~D~~~g~~~it~~r~ 438 (852)
.- |+.|||||++-.+++.+||+++..+++.+..+. ..| ..|+|+++.|.+|++||++++++|++||.
T Consensus 456 ~t~~f-CC~G~cIDLLi~Ls~~~Nftyd~~l~~dg~fg~~~~vnnsseT~~kew~G~iGEL~~~~ADMivaplTINpERa 534 (993)
T KOG4440|consen 456 HTVPF-CCYGFCIDLLIKLSRTMNFTYDVHLVADGKFGTQERVNNSSETNKKEWNGMIGELLSGQADMIVAPLTINPERA 534 (993)
T ss_pred cCcch-hhhHHHHHHHHHHHHhhcceEEEEEeecccccceeeeecccccccceehhhhhhhhCCccceEeeceeeChhhh
Confidence 22 789999999999999999998888887553221 122 36999999999999999999999999999
Q ss_pred eeeeccccccccceEEEEEccCCCCCCceEeecccchhHHHHHHHHHHHHHhhhhheecccCCC-CCCC-------cccc
Q 003054 439 NYVDFTLPYTESGVSMIVPIKDSKKRNAWVFLQPLTWDLWVTCFCFFIFIGFVVWVLEHRVNED-FRGP-------AGQQ 510 (852)
Q Consensus 439 ~~vdft~p~~~~~~~~vv~~~~~~~~~~~~~l~PF~~~lW~~i~~~~i~~~~v~~~l~~~~~~~-~~~~-------~~~~ 510 (852)
++++||.|+...|+.++.+++ .+.+....||+||+..+|++++++.+++++++|++.|..+-+ |... ..-.
T Consensus 535 ~yieFskPfkYqGitILeKk~-~r~Stl~SFlQPfqstLW~lv~~SVhvVal~lYlLDrfSPFgRFk~~ds~~~ee~aln 613 (993)
T KOG4440|consen 535 QYIEFSKPFKYQGITILEKKE-IRRSTLDSFLQPFQSTLWLLVGLSVHVVALMLYLLDRFSPFGRFKVNDSEEEEEDALN 613 (993)
T ss_pred hheeccCcccccceEEEeeCC-CCCchHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccceeeccCccchhhhcc
Confidence 999999999999999999988 456689999999999999999999999999999999987643 3322 3358
Q ss_pred cchhHHHHHHHhhhcc-cc-ccccchhhHHHHHHHHHHHHHHHHhhhhccceeeecccCCCcCCHHHHHhcC----CeEE
Q 003054 511 VGTSFWFSFSTMVFSQ-RE-RVISNLARIVVIVWCFVVLILTQSYTASLTSLLTVQQLQPTITDVKMLIKRG----DNVG 584 (852)
Q Consensus 511 ~~~~~~~~~~~l~~~~-~~-~~~s~~~R~v~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~i~sl~dL~~~~----~~vg 584 (852)
++.++||+|+.|+.+| +| .|+|.++|++-++|+=|+||+.++|||+|++||...+.+..++.+.|-.-.+ ...+
T Consensus 614 lssAmWF~WGVLLNSGigEgtPRSfSARvLGmVWaGFaMIiVASYTANLAAFLVLdrPe~~ltGinDpRLRNps~nf~~a 693 (993)
T KOG4440|consen 614 LSSAMWFSWGVLLNSGIGEGTPRSFSARVLGMVWAGFAMIIVASYTANLAAFLVLDRPEERLTGINDPRLRNPSDNFIYA 693 (993)
T ss_pred hhhhHHHHhHhhhccccCCCCCcchhHHHHHHHHhhhheeeehhhhhhhhhheeecCccccccCCCCccccCcccceeEE
Confidence 9999999999999988 55 7899999999999999999999999999999999999999999999876433 3678
Q ss_pred EEeCchHHHHHHhcC-----CCCcceeecCCHhHHHHHhhcccccCceeEEEechhHHHHHHhhcCCceEeecccccccc
Q 003054 585 YQKGSFVLGILKQLG-----FDERKLVVYNSPEDCHELFQKGSVNGGIAAAFDEIPYMKLLIGQYCSKYAMIEPKFKTAG 659 (852)
Q Consensus 585 ~~~~s~~~~~l~~~~-----~~~~~~~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~ 659 (852)
.+++|.+..|+++.- +..-.-..|.+.+|.++++++|+ .+|++.+..-++|-.+++|. +...|+.|...+
T Consensus 694 TVk~SsVd~YFrRqVELS~MyR~ME~hNy~~A~eAiq~v~~gk----L~AFIWDS~rLEfEAs~~Ce-LvT~GeLFgRSg 768 (993)
T KOG4440|consen 694 TVKQSSVDIYFRRQVELSTMYRHMEKHNYESAAEAIQAVRDGK----LHAFIWDSARLEFEASQKCE-LVTTGELFGRSG 768 (993)
T ss_pred EecCccHHHHHHHHhHHHHHHHhhhhcchhhHHHHHHHHHcCc----eeEEEeecceeeehhhcccc-eEeccccccccc
Confidence 899999999987620 11111235667889999999999 99999999999999999996 888999999999
Q ss_pred eEEEecCCCCchhhHHHHHHhccccChhHHHHHHHccCC--CCCCCCCCCcccccccccchhHHHHHHHHHHHHHHHHHH
Q 003054 660 FGFVFPLHSPLVHDVSKAILNVTEGDKMKEIEDAWFKKH--SSCPDASTVVSSRSLGLNSFWGLFLIAGVAAILALIIFM 737 (852)
Q Consensus 660 ~~~~~~k~spl~~~in~~il~l~e~G~~~~i~~kw~~~~--~~c~~~~~~~~~~~L~l~~~~g~f~il~ig~~lsl~vf~ 737 (852)
||+.++|+||+.+.+.-+|+++.|+|+|+++.++|+... ..|.. ....+..|++.++.|+|++.+.|.++++++.+
T Consensus 769 yGIGlqK~SPWt~~vtlaIL~~hEsGfMEkLDk~Wi~~Ggpq~c~~--~~k~PatLgl~NMagvFiLV~~Gia~GifLif 846 (993)
T KOG4440|consen 769 YGIGLQKDSPWTQNVTLAILKSHESGFMEKLDKTWIRYGGPQECDS--RSKAPATLGLENMAGVFILVAGGIAAGIFLIF 846 (993)
T ss_pred cccccccCCCCcchhhHHHHHhhhcchHHHHHHHHHhcCCcchhhh--hccCcccccccccccEEEEEecchhheeeEEE
Confidence 999999999999999999999999999999999999653 33433 33478899999999999999999999999999
Q ss_pred HHHHHHhhccccC
Q 003054 738 AVFIHQHWNVLKN 750 (852)
Q Consensus 738 ~e~~~~~r~~~~~ 750 (852)
+|+.|+|++..++
T Consensus 847 iEv~Ykrh~~~k~ 859 (993)
T KOG4440|consen 847 IEVAYKRHKDAKR 859 (993)
T ss_pred Eeehhhhhhhhhh
Confidence 9999998877653
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=5.1e-69 Score=586.27 Aligned_cols=671 Identities=22% Similarity=0.380 Sum_probs=527.5
Q ss_pred hcCCCCccEEeeecCCCC-CCCC-CCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHHHHHh--
Q 003054 9 LGNKSQVPILSFSATSPS-LTSI-RSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTDALQA-- 84 (852)
Q Consensus 9 i~~~~~vP~Is~~ats~~-lt~~-~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~~l~~-- 84 (852)
+..+.+||+|+..+.+.- ++++ ..-.|+++.++-.+|+.++.++|++|+|.+++++...-+.-+.....++...++
T Consensus 122 iSs~t~iPIisi~gg~a~~~~~kd~gs~flQlg~Sieqqa~Vml~iL~~ydW~~Fs~vtt~~pg~~~f~~~ir~~~d~s~ 201 (1258)
T KOG1053|consen 122 ISSQTHIPIISIHGGAAMVLTPKDLGSTFLQLGPSIEQQAQVMLKILEEYDWYNFSLVTTQFPGNRTFVSLIRQTNDNSH 201 (1258)
T ss_pred HHHhcCCcEEEEecCccceecCCCCcceEEEeCCcHHHHHHHHHHHHHHcCcceeEEEEeecCchHHHHHHHHHhhhhcc
Confidence 567789999998886554 4542 335799999999999999999999999999999998887777777777777665
Q ss_pred CCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHcCCcccceEEEEcCccccccccCCchh
Q 003054 85 IDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLEPSV 164 (852)
Q Consensus 85 ~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~~~~~~~~~~~~~ 164 (852)
.|+++.......++. +++......+||+-++.||++.|+.+++..||..|.++|+++++|+||++...... +...
T Consensus 202 vgwe~i~v~~l~~s~-~d~~a~~q~qLkki~a~VillyC~~eea~~IF~~A~q~Gl~g~~y~Wi~pqlv~g~-~~~p--- 276 (1258)
T KOG1053|consen 202 VGWEMINVLTLDPST-DDLLAKLQAQLKKIQAPVILLYCSREEAERIFEEAEQAGLTGPGYVWIVPQLVEGL-EPRP--- 276 (1258)
T ss_pred ccceeeeeeecCCCC-CchHHHHHHHHHhcCCcEEEEEecHHHHHHHHHHHHhcCCcCCceEEEeehhccCC-CCCC---
Confidence 466665555555442 33344455567777799999999999999999999999999999999996544332 1111
Q ss_pred hcccceEEEEEecCCCChHHHHHHHHHHHhccccCCCCcccccchhhHhHhhHHHHHHHHHHHhcccCcCccccccCCCC
Q 003054 165 IDSMQGVIGVGPHVPKTKALENFRVRWKRNFLQENPSIVDVELNIFGLLAYDATRALAEAVEKAGITSFGFDKTNVSRNA 244 (852)
Q Consensus 165 ~~~~~gv~~~~~~~~~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~a~~aYDAv~~lA~Al~~a~~~~~~~~~~~~~~~~ 244 (852)
.+..-|.+.+..- .| -..+.+..-|++-++|.|...+......... ...+|
T Consensus 277 a~~P~GLisv~~~------------~w---------------~~~l~~rVrdgvaiva~aa~s~~~~~~~lp~--~~~~C 327 (1258)
T KOG1053|consen 277 AEFPLGLISVSYD------------TW---------------RYSLEARVRDGVAIVARAASSMLRIHGFLPE--PKMDC 327 (1258)
T ss_pred ccCccceeeeecc------------ch---------------hhhHHHHHhhhHHHHHHHHHHHHhhcccCCC--ccccc
Confidence 1223455544321 11 1234567789999999999887655433211 11222
Q ss_pred CCCccccccCChHHHHHHhhccceeeeeeeEEee-cCccccceEEEEEcc--CCcEEEEEEcCCCCcccccCCCccccCC
Q 003054 245 TDLEAFGISQNGPKLLQALSSTRFKGLTGDYIFV-DGQLQSSAFEIINVN--NGARGVGFWTPEKGLTQKLSSNSTTKSK 321 (852)
Q Consensus 245 ~~~~~~~~~~~g~~l~~al~~~~f~GltG~v~f~-~G~~~~~~~~I~~~~--~g~~~vG~w~~~~g~~~~~~~~~~~~~~ 321 (852)
..- .......++.+...|.|++|+| +++.|. +|-..++...++... .-|.+||.|.... ..
T Consensus 328 ~~~-~~~~~~~~~~l~r~l~NvT~~g--~~lsf~~~g~~v~p~lvvI~l~~~r~We~VG~We~~~-------------L~ 391 (1258)
T KOG1053|consen 328 REQ-EETRLTSGETLHRFLANVTWDG--RDLSFNEDGYLVHPNLVVIDLNRDRTWERVGSWENGT-------------LV 391 (1258)
T ss_pred ccc-cCccccchhhhhhhhheeeecc--cceeecCCceeeccceEEEecCCCcchheeceecCCe-------------EE
Confidence 111 1112456889999999999999 899997 888777777777665 3399999998643 24
Q ss_pred ccceEeCCCCCCCCCcccccCCCceEEEeeecccCcccceEEeeCCCCC---------------------------CCce
Q 003054 322 LKPIIWPGDSTSDPKGWEVPTNEKKLRIGVPVKKGFSDFVNVTIDPKTQ---------------------------EPTS 374 (852)
Q Consensus 322 ~~~i~Wpg~~~~~p~~~~~~~~~~~lrv~v~~~~~~~~~~~~~~d~~~~---------------------------~~~~ 374 (852)
++..+|| .....+.+. | ...||+|.+.+++||.--. +-||.++ + +|
T Consensus 392 M~y~vWP-r~~~~~q~~--~-d~~HL~VvTLeE~PFVive--~vDP~t~~C~~ntvpc~s~~~~t~ss~~~~~~tvK-kC 464 (1258)
T KOG1053|consen 392 MKYPVWP-RYHKFLQPV--P-DKLHLTVVTLEERPFVIVE--DVDPLTQTCVRNTVPCRSQLNSTFSSGDEANRTVK-KC 464 (1258)
T ss_pred Eeccccc-cccCccCCC--C-CcceeEEEEeccCCeEEEe--cCCCCcCcCCCCCCcchhhhhhccCCCccCCchHH-hh
Confidence 6788999 333333222 1 3559999999888754222 2334422 2 38
Q ss_pred EEEeeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCcccEEEeeeeeecCcceeeeccccccccceEE
Q 003054 375 VTGYCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGEFDAVVGDITIVFNRSNYVDFTLPYTESGVSM 454 (852)
Q Consensus 375 ~~G~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~~D~~~g~~~it~~r~~~vdft~p~~~~~~~~ 454 (852)
+.||||||++.|++.+||++++-.+-.+..+-+.||.|+|||+.|..+++||+++.++|+++|++.+|||.||.++|+++
T Consensus 465 CkGfCIDiLkKlA~~v~FtYDLYlVtnGKhGkk~ng~WnGmIGev~~~rA~MAVgSltINeeRSevVDFSvPFveTgIsV 544 (1258)
T KOG1053|consen 465 CKGFCIDILKKLARDVKFTYDLYLVTNGKHGKKINGVWNGMIGEVVYQRADMAVGSLTINEERSEVVDFSVPFVETGISV 544 (1258)
T ss_pred hhhhhHHHHHHHHhhcCcceEEEEecCCcccceecCcchhhHHHHHhhhhheeeeeeEechhhhccccccccccccceEE
Confidence 89999999999999999987776655443333589999999999999999999999999999999999999999999999
Q ss_pred EEEccCCCCCCceEeecccchhHHHHHHHHHHHH-HhhhhheecccCCCC---------CCCcccccchhHHHHHHHhhh
Q 003054 455 IVPIKDSKKRNAWVFLQPLTWDLWVTCFCFFIFI-GFVVWVLEHRVNEDF---------RGPAGQQVGTSFWFSFSTMVF 524 (852)
Q Consensus 455 vv~~~~~~~~~~~~~l~PF~~~lW~~i~~~~i~~-~~v~~~l~~~~~~~~---------~~~~~~~~~~~~~~~~~~l~~ 524 (852)
+|...+ ...+.-+||.||++.+|++++++++++ ++.++++|+.++-.+ .|.+..+++.++|..++.++.
T Consensus 545 mV~rsn-gtvspsAFLePfs~svWVmmFVm~livaai~vFlFEy~SPvgyn~~l~~gkkpggp~FtigkaiwllwaLvFn 623 (1258)
T KOG1053|consen 545 MVARSN-GTVSPSAFLEPFSPSVWVMMFVMCLIVAAITVFLFEYFSPVGYNRNLANGKKPGGPSFTIGKAIWLLWALVFN 623 (1258)
T ss_pred EEEecC-CccCchhhcCCcchHHHHHHHHHHHHHHHHHHHHHhhcCcccccccccCCCCCCCcceehhhHHHHHHHHHhC
Confidence 999884 456888999999999999999888755 667778998764332 234568999999999976665
Q ss_pred cc--ccccccchhhHHHHHHHHHHHHHHHHhhhhccceeeecccCCCcCCHHHHHhc-------CCeEEEEeCchHHHHH
Q 003054 525 SQ--RERVISNLARIVVIVWCFVVLILTQSYTASLTSLLTVQQLQPTITDVKMLIKR-------GDNVGYQKGSFVLGIL 595 (852)
Q Consensus 525 ~~--~~~~~s~~~R~v~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~i~sl~dL~~~-------~~~vg~~~~s~~~~~l 595 (852)
.. .++|+...+||++.+|.||++|+.++|||||+++|....+..++..+.|-.-+ +.+.|.+.++..++++
T Consensus 624 nsVpv~nPKgtTskiMv~VWAfFavifLAsYTANLAAfMIqE~~~d~vSGlsD~KfqrP~dq~PpFRFGTVpngSTE~ni 703 (1258)
T KOG1053|consen 624 NSVPVENPKGTTSKIMVLVWAFFAVIFLASYTANLAAFMIQEEYYDTVSGLSDPKFQRPHDQYPPFRFGTVPNGSTERNI 703 (1258)
T ss_pred CCcCCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhccccCcccccCccccCCCcccccCCCCchhhhH
Confidence 44 56889999999999999999999999999999999999999999999887632 3488988877777777
Q ss_pred HhcCCCC--cceeecC--CHhHHHHHhhcccccCceeEEEechhHHHHHHhhc--CCceEeec--ccccccceEEEecCC
Q 003054 596 KQLGFDE--RKLVVYN--SPEDCHELFQKGSVNGGIAAAFDEIPYMKLLIGQY--CSKYAMIE--PKFKTAGFGFVFPLH 667 (852)
Q Consensus 596 ~~~~~~~--~~~~~~~--~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~~--~~~~~~v~--~~~~~~~~~~~~~k~ 667 (852)
++. +++ ..++.|+ ..++.++.|++|+ .||||.|...++|...++ |+ +..+| ..|...+||+++|||
T Consensus 704 R~N-yp~MHeYM~kyNq~~v~dal~sLK~gK----LDAFIyDaAVLnY~agkDegCK-LvTIGsgKvFAttGYGIal~k~ 777 (1258)
T KOG1053|consen 704 RSN-YPEMHEYMVKYNQPGVEDALESLKNGK----LDAFIYDAAVLNYMAGKDEGCK-LVTIGSGKVFATTGYGIALPKN 777 (1258)
T ss_pred Hhc-cHHHHHHHHHhccCchHHHHHHHhccc----chhHHHHHHHHHHhhccCCCce-EEEecCCceeeecceeeecCCC
Confidence 652 332 3455555 5689999999999 999999999999999876 96 66676 899999999999999
Q ss_pred CCchhhHHHHHHhccccChhHHHHHHHccCCCCCCCCCCCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 003054 668 SPLVHDVSKAILNVTEGDKMKEIEDAWFKKHSSCPDASTVVSSRSLGLNSFWGLFLIAGVAAILALIIFMAVFIHQHW 745 (852)
Q Consensus 668 spl~~~in~~il~l~e~G~~~~i~~kw~~~~~~c~~~~~~~~~~~L~l~~~~g~f~il~ig~~lsl~vf~~e~~~~~r 745 (852)
||++..||.+|++....|+|+++++.|+ .+.|......+.+.+|++++|.|+||+|++|++||+++|++|.+++.+
T Consensus 778 Spwkr~IdlallQy~gdGeme~Le~~Wl--tgic~n~k~evmSsqLdIdnmaGvFymL~~amgLSllvfi~EHlvYw~ 853 (1258)
T KOG1053|consen 778 SPWKRQIDLALLQYLGDGEMEMLETLWL--TGICHNSKNEVMSSQLDIDNMAGVFYMLAVAMGLSLLVFIWEHLVYWK 853 (1258)
T ss_pred CcchhhHHHHHHHHhccchHHHHHHHHh--hcccccchhhhhhcccChhhhhhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999 678887777788999999999999999999999999999999776543
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=3.6e-67 Score=623.97 Aligned_cols=599 Identities=35% Similarity=0.610 Sum_probs=510.5
Q ss_pred HHHHHhhcCCceEEEEEeChhhHHHHHHHHHHcCCcccceEEEEcCccccccccCC-chhhcccceEEEEEecCCCChHH
Q 003054 106 KELYKLFTMQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLE-PSVIDSMQGVIGVGPHVPKTKAL 184 (852)
Q Consensus 106 ~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~~~~~~~~~~-~~~~~~~~gv~~~~~~~~~~~~~ 184 (852)
..+.+++....+++++++.+..+..++.+|.++||+..+|+|+.+.......+... ....+.++|+++.+.+.|.+...
T Consensus 4 ~~~~~~~~~~~~~~v~~~~~~~~~~~~~~a~~~~~~~~~~~~i~t~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~s~~~ 83 (656)
T KOG1052|consen 4 KLLLKLKAMRTRVFVLHMFPILALAIFSQAEELGMMQFGYVWILTNLLTDALDLDELYSLIDVMNGVLGLRGHIPRSELL 83 (656)
T ss_pred hHHHHhhccCceEEEEeCCHHHHHHHHHHHHHhCccccCeEEEEEecchhhhcccccccchhheeeEEeeccCCCccHHH
Confidence 35566777899999999998899999999999999999999999998776655443 33556788999999999999999
Q ss_pred HHHHHHHHHhccccCCCCcccccchhhHhHhhHHHHHHHHHHHhcc-cCcCccccccCCCCCCCccccccCChHHHHHHh
Q 003054 185 ENFRVRWKRNFLQENPSIVDVELNIFGLLAYDATRALAEAVEKAGI-TSFGFDKTNVSRNATDLEAFGISQNGPKLLQAL 263 (852)
Q Consensus 185 ~~F~~~~~~~~~~~~~~~~~~~~~~~a~~aYDAv~~lA~Al~~a~~-~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~al 263 (852)
++|..+|+.. .. ..+.+++++||+++++|.|++.+.. .... ..|...+.+.++..+.+.+
T Consensus 84 ~~~~~~~~~~-~~--------~~~~~~~~~~D~~~~~a~~~~~~~~~~~~~----------~~~~~~~~~~~~~~~~~~~ 144 (656)
T KOG1052|consen 84 QNFVTRWQTS-NV--------ELLVYALWAYDAIQALARAVESLLNIGNLS----------LSCGRNNSWLDALGVFNFG 144 (656)
T ss_pred HHHHHHHhhc-cc--------cccchhhHHHHHHHHHHHHHHHhhcCCCCc----------eecCCCCcccchhHHHHHH
Confidence 9999999877 32 5788899999999999999999874 1111 1222234466777788877
Q ss_pred hcccee---eeeeeEEee-cCccccceEEEEEcc-CCcEEEEEEcCCCCcccccCCCccccCCccceEeCCCCCCCCCcc
Q 003054 264 SSTRFK---GLTGDYIFV-DGQLQSSAFEIINVN-NGARGVGFWTPEKGLTQKLSSNSTTKSKLKPIIWPGDSTSDPKGW 338 (852)
Q Consensus 264 ~~~~f~---GltG~v~f~-~G~~~~~~~~I~~~~-~g~~~vG~w~~~~g~~~~~~~~~~~~~~~~~i~Wpg~~~~~p~~~ 338 (852)
...... |.+|.+.+. ++.+....++|+|+. .|.+.||.|++..| .++.|||.....|++|
T Consensus 145 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~n~~~~~~~~ig~W~~~~~---------------~~i~~~~~~~~~~~~~ 209 (656)
T KOG1052|consen 145 KKLLVVNLSGVTGQFQFFRGGLLEYFKYEILNLNGSGERRIGYWYPRGG---------------ENISWPGKDYFVPKGW 209 (656)
T ss_pred HhhhhhccccceeEEEecCCCccccceEEEEEecCcCceeEEEecCCCC---------------ceeeccCCcccCcCCc
Confidence 776433 566777777 778888999999998 88888999998765 4688999999999999
Q ss_pred cccCCCceEEEeeecccCcccceEEeeCCCCCCCceEEEeeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHH
Q 003054 339 EVPTNEKKLRIGVPVKKGFSDFVNVTIDPKTQEPTSVTGYCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQ 418 (852)
Q Consensus 339 ~~~~~~~~lrv~v~~~~~~~~~~~~~~d~~~~~~~~~~G~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~ 418 (852)
.+|.+++++||+|+..+||..++... ....++. .+.|+|+||++++++++||+++++.++.+.....++|+|+|++++
T Consensus 210 ~~~~~~~~l~v~~~~~~P~~~~~~~~-~~~~~~~-~~~G~~idll~~l~~~l~f~~~~~~~~~~~g~~~~~g~~~g~v~~ 287 (656)
T KOG1052|consen 210 FFPTNGKPLRVGVVTEPPFVDLVEDL-AILNGND-RIEGFEIDLLQALAKRLNFSYEIIFVPDGSGSRDPNGNWDGLVGQ 287 (656)
T ss_pred cccCCCceEEEEEeccCCceeeeecc-cccCCCC-ccceEEehHHHHHHHhCCCceEEEEcCCCCCCCCCCCChhHHHHH
Confidence 99999999999999988866555432 1334566 899999999999999999999998888776333466899999999
Q ss_pred HhcCcccEEEeeeeeecCcceeeeccccccccceEEEEEccCCCCCCceEeecccchhHHHHHHHHHHHHHhhhhheecc
Q 003054 419 VFLGEFDAVVGDITIVFNRSNYVDFTLPYTESGVSMIVPIKDSKKRNAWVFLQPLTWDLWVTCFCFFIFIGFVVWVLEHR 498 (852)
Q Consensus 419 l~~g~~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv~~~~~~~~~~~~~l~PF~~~lW~~i~~~~i~~~~v~~~l~~~ 498 (852)
|.+|++|++ ++++++++|+.++|||.||+..+.++++++++.... .|.|++||++++|++++++++++++++|+++|+
T Consensus 288 l~~~~advg-~~~tit~~R~~~vdfT~p~~~~~~~i~~~~~~~~~~-~~~fl~Pf~~~vW~~i~~~~l~~~~~~~~~~~~ 365 (656)
T KOG1052|consen 288 LVDGEADVG-ADITITPERSKYVDFTIPYLQFGIVIIVRKPDSRSK-LWNFLAPFSPEVWLLILASLLLVGLLLWILERL 365 (656)
T ss_pred HhcCccccc-cceEEeecccccEEeccceEeccEEEEEEecCCccc-ceEEecCCcHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 999999999 899999999999999999999999999999977666 999999999999999999999999999999999
Q ss_pred cCCCCCCCc-----ccccchhHHHHHHHhhhcc-ccccccchhhHHHHHHHHHHHHHHHHhhhhccceeeecccCCCcCC
Q 003054 499 VNEDFRGPA-----GQQVGTSFWFSFSTMVFSQ-RERVISNLARIVVIVWCFVVLILTQSYTASLTSLLTVQQLQPTITD 572 (852)
Q Consensus 499 ~~~~~~~~~-----~~~~~~~~~~~~~~l~~~~-~~~~~s~~~R~v~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~i~s 572 (852)
.+.++ .++ .....+++|+++++++.++ .+.|++.++|+++++||++++||+++|||+|+|+||++++.++|++
T Consensus 366 ~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~q~~~~~p~~~~~Rll~~~w~~~~lil~ssYTa~L~a~Lt~~~~~~~i~~ 444 (656)
T KOG1052|consen 366 SPYEL-PPRQIVTSLFSLLNCLWLTVGSLLQQGSDEIPRSLSTRLLLGAWWLFVLILISSYTANLTAFLTVPRLRSPIDS 444 (656)
T ss_pred ccccC-CccccceeEeecccchhhhhHHHhccCCCccccchhhhHHHHHHHHHHHHHHHHHHHHHHHHhcccccCCcccC
Confidence 99888 222 1233457899999999877 5688999999999999999999999999999999999999999999
Q ss_pred HHHHHh-cCCeEEEEeCchHHHHHHhc----CCCCc-ceeecCCHhHHHHHhhcccccCceeEEEechhHHHHHHhhc-C
Q 003054 573 VKMLIK-RGDNVGYQKGSFVLGILKQL----GFDER-KLVVYNSPEDCHELFQKGSVNGGIAAAFDEIPYMKLLIGQY-C 645 (852)
Q Consensus 573 l~dL~~-~~~~vg~~~~s~~~~~l~~~----~~~~~-~~~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~~-~ 645 (852)
++||++ ++..+|...+++...++++. .+... ..+.+.+++++.+++.+|.. +|+.++.++.++.+++.+++ |
T Consensus 445 ~~dL~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~v~~~~~-~~~~~~~~~~~~~~~~~~~~~c 523 (656)
T KOG1052|consen 445 LDDLADQSNIPYGTQRGSFTRIYLEESEDMWAFKVSQRSVPLASPEEGVERVRKGPS-GGYAFASDELYLAYLFLRDEIC 523 (656)
T ss_pred HHHHHHhcCCeEEEEecchHHHHHHHHHHHHhhhccCCCccCCCHHHHHHHHHcCCC-CceEEEeccHHHHHHHhhcCCC
Confidence 999995 77799999999999998764 23333 67788999999999999986 55666666666666666655 7
Q ss_pred CceEeecccccccceEEEecCCCCchhhHHHHHHhccccChhHHHHHHHccCC---CCCCCCCCCcccccccccchhHHH
Q 003054 646 SKYAMIEPKFKTAGFGFVFPLHSPLVHDVSKAILNVTEGDKMKEIEDAWFKKH---SSCPDASTVVSSRSLGLNSFWGLF 722 (852)
Q Consensus 646 ~~~~~v~~~~~~~~~~~~~~k~spl~~~in~~il~l~e~G~~~~i~~kw~~~~---~~c~~~~~~~~~~~L~l~~~~g~f 722 (852)
.++++++.+...+++ ++||||||++.++++|+++.|.|++++|+++|+... ..|.... +.+.|++++++|+|
T Consensus 524 -~~~~v~~~~~~~~~~-~~~~~Spl~~~is~~Il~l~e~g~l~~~~~kw~~~~~~~~~~~~~~---~~~~l~~~~~~g~F 598 (656)
T KOG1052|consen 524 -DLTEVGEPFLYKGYG-AFPKGSPLRSLISRAILKLQETGILQKLKRKWFSKKPCLPKCSQTE---KTKALDLESFWGLF 598 (656)
T ss_pred -ceEEeCCcccCCCcc-eecCCCccHHHHHHHHHhhccccHHHHHHHHhccCCCCCCCCCCcc---cccccchhhHHHHH
Confidence 599999999999999 999999999999999999999999999999999865 4454444 67889999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhcccc
Q 003054 723 LIAGVAAILALIIFMAVFIHQHWNVLK 749 (852)
Q Consensus 723 ~il~ig~~lsl~vf~~e~~~~~r~~~~ 749 (852)
+++++|+++|+++|++|++|++++...
T Consensus 599 ~i~~~g~~lal~vfi~E~~~~~~~~~~ 625 (656)
T KOG1052|consen 599 LILLVGYLLALLVFILELLYSRRRTLL 625 (656)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence 999999999999999999999888853
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=2e-37 Score=340.22 Aligned_cols=292 Identities=19% Similarity=0.280 Sum_probs=245.7
Q ss_pred hhhHHHHhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHHH
Q 003054 2 QTNFIIQLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTDA 81 (852)
Q Consensus 2 ~a~~v~~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~~ 81 (852)
.|+.|+.+|+..+||+|+++. |..+ ..+|+.++.|+ +++|+++++++|||++|++||+ ++||...++.|.++
T Consensus 68 ~a~~v~sic~~~~vP~i~~~~--~~~~--~~~~~i~~~P~---~~~Ai~diI~~~~W~~v~iIYd-~d~g~~~lq~l~~~ 139 (364)
T cd06390 68 TVNMLTSFCGALHVCFITPSF--PVDT--SNQFVLQLRPE---LQDALISVIEHYKWQKFVYIYD-ADRGLSVLQKVLDT 139 (364)
T ss_pred HHHHHHHhhcCCCCCceecCC--CCCC--CCceEEEeChh---HHHHHHHHHHHcCCcEEEEEEe-CCccHHHHHHHHHh
Confidence 578899999999999999755 4333 34679999998 8999999999999999999995 55999999999999
Q ss_pred HHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHcCCcccceEEEEcCccccccccCC
Q 003054 82 LQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLE 161 (852)
Q Consensus 82 l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~~~~~~~~~~ 161 (852)
+++.|++|.+...++ .+++|+..+|++++.+++|+||++|+++.+..+++++.+.+|+..+|+||+|+......+ .
T Consensus 140 ~~~~~~~I~~~~~~~--~~~~d~~~~L~~ik~~~~rvIVl~~~~~~~~~~L~~a~~~~~~~~gy~wI~t~l~~~~~~--~ 215 (364)
T cd06390 140 AAEKNWQVTAVNILT--TTEEGYRKLFQDLDKKKERLIVVDCESERLNAILNQIIKLEKNGIGYHYILANLGFMDID--L 215 (364)
T ss_pred hhccCceeeEEEeec--CChHHHHHHHHhccccCCeEEEEECCHHHHHHHHHHHHHhhccCCceEEEecCCCccccc--H
Confidence 999999999887766 346799999999999999999999999999999999999999999999999983222222 1
Q ss_pred chhhcccceEEEEEecCCCChHHHHHHHHHHHhccccCCCCcccccchhhHhHhhHHHHHHHHHHHhcccCcCccccccC
Q 003054 162 PSVIDSMQGVIGVGPHVPKTKALENFRVRWKRNFLQENPSIVDVELNIFGLLAYDATRALAEAVEKAGITSFGFDKTNVS 241 (852)
Q Consensus 162 ~~~~~~~~gv~~~~~~~~~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~a~~aYDAv~~lA~Al~~a~~~~~~~~~~~~~ 241 (852)
......++|++|++.+.|+++.+++|..+|++....++|+....+++.+++++|||||++|+|++++..........
T Consensus 216 ~~~~~~~~nitg~r~~~~~~~~~~~~~~~w~~~~~~~~~~~~~~~~~~~~~l~yDaV~~~A~A~~~l~~~~~~~~~~--- 292 (364)
T cd06390 216 TKFRESGANVTGFQLVNYTDTTVSRIMQQWKNFDARDLPRVDWKRPKYTSALTYDGVRVMAEAFQNLRKQRIDISRR--- 292 (364)
T ss_pred HHHhcCCcCceEEEEecCCCHHHHHHHHHHHhhccccCCCCCcCCcchHHHHHHHHHHHHHHHHHHHHHcCCCcccC---
Confidence 23456789999999999999999999999998887766665555789999999999999999999875433221111
Q ss_pred CCCCCCcc--ccccCChHHHHHHhhccceeeeeeeEEee-cCccccceEEEEEcc-CCcEEEEEEcCCCCc
Q 003054 242 RNATDLEA--FGISQNGPKLLQALSSTRFKGLTGDYIFV-DGQLQSSAFEIINVN-NGARGVGFWTPEKGL 308 (852)
Q Consensus 242 ~~~~~~~~--~~~~~~g~~l~~al~~~~f~GltG~v~f~-~G~~~~~~~~I~~~~-~g~~~vG~w~~~~g~ 308 (852)
++..+|.. ...|..|..|+++|++++|+|+||+++|+ +|++....|+|+|++ +|+++||+|++..|+
T Consensus 293 ~~~~~C~~~~~~~w~~G~~l~~~i~~~~f~GlTG~i~F~~~G~r~~~~~~I~~~~~~g~~~vG~W~~~~g~ 363 (364)
T cd06390 293 GNAGDCLANPAVPWGQGIDIQRALQQVRFEGLTGNVQFNEKGRRTNYTLHVIEMKHDGIRKIGYWNEDEKL 363 (364)
T ss_pred CCCCCCCCCCCCCCccHHHHHHHHHhhcccccccceeeCCCCCcccceEEEEEecCCcceEEEEECCCCCc
Confidence 11123332 23588999999999999999999999997 899999999999999 899999999998886
No 6
>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=3.3e-35 Score=321.67 Aligned_cols=293 Identities=17% Similarity=0.247 Sum_probs=243.1
Q ss_pred hhhHHHHhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHHH
Q 003054 2 QTNFIIQLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTDA 81 (852)
Q Consensus 2 ~a~~v~~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~~ 81 (852)
.+.++..+|+..+||+|.+.-. .+...+|.+++.|+ ..+|+++++++|||++|++|| |+++|...++.|.++
T Consensus 75 s~~~v~s~c~~~~iP~i~~~~~----~~~~~~~~l~l~P~---l~~Ai~diI~~~~Wr~~~~iY-d~d~gl~~Lq~L~~~ 146 (372)
T cd06387 75 SMNTLTSFCGALHTSFITPSFP----TDADVQFVIQMRPA---LKGAILSLLAHYKWEKFVYLY-DTERGFSILQAIMEA 146 (372)
T ss_pred HHHHHHHhhccccCCeeeeCCC----CCCCCceEEEEChh---HHHHHHHHHHhcCCCEEEEEe-cCchhHHHHHHHHHh
Confidence 3677899999999999987332 12345788999998 799999999999999999999 889999999999999
Q ss_pred HHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHcCCcccceEEEEcCccccccccCC
Q 003054 82 LQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLE 161 (852)
Q Consensus 82 l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~~~~~~~~~~ 161 (852)
++..+.+|......+.. ...++...|++|+.++.++||++|+++.+..+++||.++||+.++|+||+|+......+...
T Consensus 147 ~~~~~~~V~~~~v~~~~-~~~~~~~~l~el~~~~~r~iIld~s~~~~~~il~~a~e~gM~~~~y~~ilt~ld~~~~dl~~ 225 (372)
T cd06387 147 AVQNNWQVTARSVGNIK-DVQEFRRIIEEMDRRQEKRYLIDCEVERINTILEQVVILGKHSRGYHYMLANLGFTDISLER 225 (372)
T ss_pred hccCCceEEEEEeccCC-chHHHHHHHHHhccccceEEEEECCHHHHHHHHHHHHHcCccccceEEEEecCCcccccHHH
Confidence 99999998877654433 45689999999999999999999999999999999999999999999999984333332211
Q ss_pred chhhcccceEEEEEecCCCChHHHHHHHHHHHhccccCCCCcccccchhhHhHhhHHHHHHHHHHHhcccCcCccccccC
Q 003054 162 PSVIDSMQGVIGVGPHVPKTKALENFRVRWKRNFLQENPSIVDVELNIFGLLAYDATRALAEAVEKAGITSFGFDKTNVS 241 (852)
Q Consensus 162 ~~~~~~~~gv~~~~~~~~~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~a~~aYDAv~~lA~Al~~a~~~~~~~~~~~~~ 241 (852)
......+++|++.+.++++.+++|.++|++++..++|+....+++.+++++||||+++|+|++++........+..
T Consensus 226 --~~~g~~NItg~rl~~~~~~~~~~f~~~w~~~~~~~~~~~~~~~l~~~~al~yDaV~~~A~A~~~l~~~~~~~~~~~-- 301 (372)
T cd06387 226 --VMHGGANITGFQIVNNENPMVQQFLQRWVRLDEREFPEAKNSPLKYTSALTHDAILVIAEAFRYLRRQRVDVSRRG-- 301 (372)
T ss_pred --hccCCcceeEEEEecCCCchHHHHHHHHHhCCcccCCCCCCCCcchHHHHHHHHHHHHHHHHHHHHhcCCCcccCC--
Confidence 2223344999999999999999999999998877776665556788999999999999999998754433322221
Q ss_pred CCCCCCc--cccccCChHHHHHHhhccceeeeeeeEEee-cCccccceEEEEEcc-CCcEEEEEEcCCCCc
Q 003054 242 RNATDLE--AFGISQNGPKLLQALSSTRFKGLTGDYIFV-DGQLQSSAFEIINVN-NGARGVGFWTPEKGL 308 (852)
Q Consensus 242 ~~~~~~~--~~~~~~~g~~l~~al~~~~f~GltG~v~f~-~G~~~~~~~~I~~~~-~g~~~vG~w~~~~g~ 308 (852)
...+|. ....|..|..|+++|++++|+|+||+++|+ +|++.+..|+|+|+. +|+++||+|++..|+
T Consensus 302 -~~~~C~~~~~~~W~~G~~l~~~ik~v~~~GLTG~i~F~~~G~R~~~~ldIinl~~~g~~kIG~W~~~~g~ 371 (372)
T cd06387 302 -SAGDCLANPAVPWSQGIDIERALKMVQVQGMTGNIQFDTYGRRTNYTIDVYEMKPSGSRKAGYWNEYERF 371 (372)
T ss_pred -CCCCcCCCCCCCccchHHHHHHHHhcccCCCccceeeCCCCCcccceEEEEEecCCCceeEEEECCCCCc
Confidence 122332 234589999999999999999999999997 799999999999999 999999999999886
No 7
>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=3.4e-35 Score=327.67 Aligned_cols=273 Identities=20% Similarity=0.322 Sum_probs=229.9
Q ss_pred hhhHHHHhcCCCCccEEeeecCCCCCCCC-CCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHH
Q 003054 2 QTNFIIQLGNKSQVPILSFSATSPSLTSI-RSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTD 80 (852)
Q Consensus 2 ~a~~v~~i~~~~~vP~Is~~ats~~lt~~-~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~ 80 (852)
.+.+++.+++.++||+|+++++++.+++. .+||+||+.|++..|+++++++++++||++|++||++++||++..+.|++
T Consensus 97 ~~~~v~~~~~~~~iP~Is~~a~~~~ls~~~~~~~~~R~~psd~~~~~a~~~~l~~~~w~~vaii~~~~~~g~~~~~~~~~ 176 (377)
T cd06379 97 TPTSVSYTAGFYRIPVVGISTRDSIFSDKNIHLSFLRTVPPYSHQADVWLEMLRSFKWNKVILLVSDDHEGRAAQKRFET 176 (377)
T ss_pred cHHHHHHHhhCCCCcEEecccCCccccCccccccEEEecCCHHHHHHHHHHHHHHcCCeEEEEEEEcCcchhHHHHHHHH
Confidence 35677889999999999999999999864 58999999999999999999999999999999999999999999999999
Q ss_pred HHHhCCc----eeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHcCCcccceEEEEcCccccc
Q 003054 81 ALQAIDT----RVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNL 156 (852)
Q Consensus 81 ~l~~~g~----~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~~~~~ 156 (852)
.+++.|+ +|+..+.++. ++.|+..+|++|++.++|+|+++++.+++..+++||+++||++++|+||+++.+...
T Consensus 177 ~~~~~g~~~~~~v~~~~~~~~--~~~d~~~~l~~ik~~~~~vIvl~~~~~~~~~l~~qa~~~g~~~~~~~wi~t~~~~~~ 254 (377)
T cd06379 177 LLEEREIEFKIKVEKVVEFEP--GEKNVTSLLQEAKELTSRVILLSASEDDAAVIYRNAGMLNMTGEGYVWIVSEQAGAA 254 (377)
T ss_pred HHHhcCCccceeeeEEEecCC--chhhHHHHHHHHhhcCCeEEEEEcCHHHHHHHHHHHHHcCCCCCCEEEEEecccccc
Confidence 9999999 8888777764 478999999999999999999999999999999999999999999999999987432
Q ss_pred cccCCchhhcccceEEEEEecCCCChHHHHHHHHHHHhccccCCCCcccccchhhHhHhhHHHHHHHHHHHhcccCcCcc
Q 003054 157 LRTLEPSVIDSMQGVIGVGPHVPKTKALENFRVRWKRNFLQENPSIVDVELNIFGLLAYDATRALAEAVEKAGITSFGFD 236 (852)
Q Consensus 157 ~~~~~~~~~~~~~gv~~~~~~~~~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~a~~aYDAv~~lA~Al~~a~~~~~~~~ 236 (852)
.+...|++++++..+ ..+++++||||+++|+|++++......
T Consensus 255 --------~~~~~g~~g~~~~~~----------------------------~~~~~~~yDAV~~~A~Al~~~~~~~~~-- 296 (377)
T cd06379 255 --------RNAPDGVLGLQLING----------------------------KNESSHIRDAVAVLASAIQELFEKENI-- 296 (377)
T ss_pred --------ccCCCceEEEEECCC----------------------------CCHHHHHHHHHHHHHHHHHHHHcCCCC--
Confidence 134578999887532 124679999999999999998642110
Q ss_pred ccccCCCCCCCccc-cccCChHHHHHHhhccceeeeeeeEEee-cCccccceEEEEEcc-CCcEEEEEEcCCCCcccccC
Q 003054 237 KTNVSRNATDLEAF-GISQNGPKLLQALSSTRFKGLTGDYIFV-DGQLQSSAFEIINVN-NGARGVGFWTPEKGLTQKLS 313 (852)
Q Consensus 237 ~~~~~~~~~~~~~~-~~~~~g~~l~~al~~~~f~GltG~v~f~-~G~~~~~~~~I~~~~-~g~~~vG~w~~~~g~~~~~~ 313 (852)
.....+|.+. ..|.+|..|+++|++++|+|++|++.|| +|++....|+|+|++ .+++.||+|++. .+. +
T Consensus 297 ----~~~~~~c~~~~~~~~~g~~l~~~l~~v~f~G~tg~i~Fd~~Gd~~~~~~~I~~~~~~~~~~VG~w~~~-~l~--~- 368 (377)
T cd06379 297 ----TEPPRECVGNTVIWETGPLFKRALMSSKYPGETGRVEFNDDGDRKFANYDIMNIQNRKLVQVGLYNGD-ILR--L- 368 (377)
T ss_pred ----CCCCccccCCCCCCcchHHHHHHHHhCCcCCccCceEECCCCCccCccEEEEEecCCCceEeeEEcCc-EEE--e-
Confidence 0011223322 2478899999999999999999999998 999977899999999 889999999873 222 1
Q ss_pred CCccccCCccceEeCC
Q 003054 314 SNSTTKSKLKPIIWPG 329 (852)
Q Consensus 314 ~~~~~~~~~~~i~Wpg 329 (852)
+.+.|.|||
T Consensus 369 -------~~~~i~W~~ 377 (377)
T cd06379 369 -------NDRSIIWPG 377 (377)
T ss_pred -------cCceeeCCC
Confidence 236799986
No 8
>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=4.7e-35 Score=326.85 Aligned_cols=292 Identities=19% Similarity=0.284 Sum_probs=238.5
Q ss_pred hhhHHHHhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHHH
Q 003054 2 QTNFIIQLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTDA 81 (852)
Q Consensus 2 ~a~~v~~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~~ 81 (852)
.+.++++++++++||+|++++++|.+++. .+|++|+.|++..++.++++++++++|++|++||++++ |...++.|.+.
T Consensus 84 ~~~av~~i~~~~~iP~Is~~~t~~~lt~~-~~~~~~~~~~~~~~~~a~~~~~~~~~wk~vaily~~~~-g~~~l~~~~~~ 161 (384)
T cd06393 84 CTNAVQSICNALEVPHIQLRWKHHPLDNK-DTFYVNLYPDYASLSHAILDLVQYLKWRSATVVYDDST-GLIRLQELIMA 161 (384)
T ss_pred HHHHHHHHHhccCCCeEeccCCCcccCcc-ceeEEEeccCHHHHHHHHHHHHHHcCCcEEEEEEeCch-hHHHHHHHHHh
Confidence 57889999999999999999999999864 46788888999999999999999999999999996654 66666788888
Q ss_pred HHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHcCCcccceEEEEcCccccccccCC
Q 003054 82 LQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLE 161 (852)
Q Consensus 82 l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~~~~~~~~~~ 161 (852)
+++.|++|+.. .++. ++.||+++|++||+.++++||++++.+++..+++||+++||+.+.|+|+.++......+.
T Consensus 162 ~~~~g~~v~~~-~~~~--~~~d~~~~L~~ik~~~~~~iil~~~~~~~~~il~qa~~~gm~~~~~~~~~~~~~~~~~~~-- 236 (384)
T cd06393 162 PSRYNIRLKIR-QLPT--DSDDARPLLKEMKRGREFRIIFDCSHQMAAQILKQAMAMGMMTEYYHFIFTTLDLYALDL-- 236 (384)
T ss_pred hhccCceEEEE-ECCC--CchHHHHHHHHHhhcCceEEEEECCHHHHHHHHHHHHHhccccCceEEEEccCccccccc--
Confidence 99999998864 4553 478999999999999999999999999999999999999999999999987764332221
Q ss_pred chhhcccceEEEEEecCCCChHHHHHHHHHHHh-cccc-CCCCc--ccccchhhHhHhhHHHHHHHHHHHhcccCcCccc
Q 003054 162 PSVIDSMQGVIGVGPHVPKTKALENFRVRWKRN-FLQE-NPSIV--DVELNIFGLLAYDATRALAEAVEKAGITSFGFDK 237 (852)
Q Consensus 162 ~~~~~~~~gv~~~~~~~~~~~~~~~F~~~~~~~-~~~~-~~~~~--~~~~~~~a~~aYDAv~~lA~Al~~a~~~~~~~~~ 237 (852)
.........+.+++...++++.+++|+++|+++ ++.. .++.. +..++.+++++||||+++|+|+++++...
T Consensus 237 ~~~~~~~~~it~~~~~~~~~~~~~~f~~~~~~~~~~~~p~~~~~~~~~~~~~~aal~yDav~~~a~A~~~~~~~~----- 311 (384)
T cd06393 237 EPYRYSGVNLTGFRILNVDNPHVSSIVEKWSMERLQAAPKPETGLLDGVMMTDAALLYDAVHMVSVCYQRAPQMT----- 311 (384)
T ss_pred hhhhcCcceEEEEEecCCCcHHHHHHHHHHHhhhhccccccccccccccccchhHHhhhhHHHHHHHHhhhhhcC-----
Confidence 111112223577888888899999999999854 6542 11111 11236789999999999999999876321
Q ss_pred cccCCCCCCCccccccCChHHHHHHhhccceeeeeeeEEee--cCccccceEEEEEcc-CCcEEEEEEcCCCCcc
Q 003054 238 TNVSRNATDLEAFGISQNGPKLLQALSSTRFKGLTGDYIFV--DGQLQSSAFEIINVN-NGARGVGFWTPEKGLT 309 (852)
Q Consensus 238 ~~~~~~~~~~~~~~~~~~g~~l~~al~~~~f~GltG~v~f~--~G~~~~~~~~I~~~~-~g~~~vG~w~~~~g~~ 309 (852)
...++|+....|..|++|+++|++++|+|+||+++|+ +|+|.+..++|+|+. +|++.||+|++..|+.
T Consensus 312 ----~~~~~c~~~~~w~~G~~i~~~l~~~~~~GltG~i~Fd~~~g~r~~~~~~i~~~~~~g~~~vg~W~~~~g~~ 382 (384)
T cd06393 312 ----VNSLQCHRHKAWRFGGRFMNFIKEAQWEGLTGRIVFNKTSGLRTDFDLDIISLKEDGLEKVGVWNPNTGLN 382 (384)
T ss_pred ----CCCCCCCCCCCCcccHHHHHHHhheeecccccceEecCCCCeeeeeEEEEEEecCCcceeeEEEcCCCCcC
Confidence 1224566677899999999999999999999999996 578889999999999 8999999999999875
No 9
>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=7.3e-35 Score=322.20 Aligned_cols=295 Identities=19% Similarity=0.255 Sum_probs=237.1
Q ss_pred hhhHHHHhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHHH
Q 003054 2 QTNFIIQLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTDA 81 (852)
Q Consensus 2 ~a~~v~~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~~ 81 (852)
.+.+++++|++++||+|+++++ ++..++|.+++.|+ ...+++++++++||++|++||+ ++||...++.|.+.
T Consensus 69 ~~~~v~~i~~~~~IP~I~~~~~----~~~~~~f~~~~~p~---~~~ai~d~i~~~~wk~vailYd-sd~gl~~lq~l~~~ 140 (370)
T cd06389 69 SVNTITSFCGTLHVSFITPSFP----TDGTHPFVIQMRPD---LKGALLSLIEYYQWDKFAYLYD-SDRGLSTLQAVLDS 140 (370)
T ss_pred HHHHHHHhhccCCCCeeeecCC----CCCCCceEEEecch---hhhHHHHHHHhcCCcEEEEEec-CchHHHHHHHHHHh
Confidence 4778999999999999998665 23457888888888 6899999999999999999996 66999999999999
Q ss_pred HHhCCceeeeeee--cCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHcCCcccceEEEEcCcccccccc
Q 003054 82 LQAIDTRVPYRSV--ISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRT 159 (852)
Q Consensus 82 l~~~g~~v~~~~~--~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~~~~~~~~ 159 (852)
+++.|++|+.... +.....+.||+++|++|++.++|+||+.++++++..+++||+++||+.++|+||+++......+.
T Consensus 141 ~~~~g~~V~~~~~~~i~~~~~~~d~~~~L~~ik~~~~~~Iil~~~~~~~~~il~qa~~~gm~~~~y~~il~~~~~~~~~l 220 (370)
T cd06389 141 AAEKKWQVTAINVGNINNDRKDEAYRSLFQDLENKKERRVILDCERDKVNDIVDQVITIGKHVKGYHYIIANLGFTDGDL 220 (370)
T ss_pred hccCCceEEEEEeecCCCccchHHHHHHHHHhccccceEEEEECCHHHHHHHHHHHHHhCccccceEEEEccCCccccch
Confidence 9999988875442 22223467999999999999999999999999999999999999999999999987753322222
Q ss_pred CCchhhcccceEEEEEecCCCChHHHHHHHHHHHhccccCCCCcccccchhhHhHhhHHHHHHHHHHHhcccCcCccccc
Q 003054 160 LEPSVIDSMQGVIGVGPHVPKTKALENFRVRWKRNFLQENPSIVDVELNIFGLLAYDATRALAEAVEKAGITSFGFDKTN 239 (852)
Q Consensus 160 ~~~~~~~~~~gv~~~~~~~~~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~a~~aYDAv~~lA~Al~~a~~~~~~~~~~~ 239 (852)
.. ......++.+++...++.+.+++|.++|++....++++.....|+..++++||||+++|+|+++++.......+.
T Consensus 221 ~~--~~~~~~nitg~~~~~~~~~~v~~f~~~~~~~~~~~~~~~~~~~~~~~aAl~yDAV~v~a~A~~~l~~~~~~~~~~- 297 (370)
T cd06389 221 SK--IQFGGANVSGFQIVDYDDPLVSKFIQRWSTLEEKEYPGAHTKTIKYTSALTYDAVQVMTEAFRNLRKQRIEISRR- 297 (370)
T ss_pred hh--hccCCcceEEEEEecCCCchHHHHHHHHHhcCccccCCCCCcCcchHHHHHHHHHHHHHHHHHHHHHcCCCcccC-
Confidence 11 112234678888888889999999999997444444333333688999999999999999999986443222211
Q ss_pred cCCCCCCCc--cccccCChHHHHHHhhccceeeeeeeEEee-cCccccceEEEEEcc-CCcEEEEEEcCCCCcc
Q 003054 240 VSRNATDLE--AFGISQNGPKLLQALSSTRFKGLTGDYIFV-DGQLQSSAFEIINVN-NGARGVGFWTPEKGLT 309 (852)
Q Consensus 240 ~~~~~~~~~--~~~~~~~g~~l~~al~~~~f~GltG~v~f~-~G~~~~~~~~I~~~~-~g~~~vG~w~~~~g~~ 309 (852)
++..+|. ....|.+|..|+++|++++|+|+||+++|+ +|++....++|++++ +|++.||+|++..|+.
T Consensus 298 --~~~~~C~~~~~~~w~~G~~i~~~l~~~~~~GlTG~i~Fd~~G~r~~~~~~ii~l~~~g~~kvG~W~~~~~~~ 369 (370)
T cd06389 298 --GNAGDCLANPAVPWGQGVEIERALKQVQVEGLTGNIKFDQNGKRINYTINVMELKSNGPRKIGYWSEVDKMV 369 (370)
T ss_pred --CCCCCcCCCCCCCCCCcHHHHHHHHhcccCccccceEeCCCCccccceEEEEEecCCcceEEEEEcCCCCcc
Confidence 1122343 245688999999999999999999999997 999988899999999 9999999999988874
No 10
>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=1.7e-34 Score=318.59 Aligned_cols=292 Identities=20% Similarity=0.266 Sum_probs=232.0
Q ss_pred hhhHHHHhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHHH
Q 003054 2 QTNFIIQLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTDA 81 (852)
Q Consensus 2 ~a~~v~~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~~ 81 (852)
.+.+++++|++++||+|+++++ +.. +|.||+...+. +..+++++++++||++|++|| |+++|...++.|.++
T Consensus 75 ~~~~v~~i~~~~~IP~I~~~~~----~~~--~~~f~i~~~p~-~~~a~~~~i~~~~wk~vaiiY-d~~~~~~~lq~l~~~ 146 (371)
T cd06388 75 SVHTLTSFCSALHISLITPSFP----TEG--ESQFVLQLRPS-LRGALLSLLDHYEWNRFVFLY-DTDRGYSILQAIMEK 146 (371)
T ss_pred HHHHHHHHhhCCCCCeeecCcc----ccC--CCceEEEeChh-hhhHHHHHHHhcCceEEEEEe-cCCccHHHHHHHHHh
Confidence 5789999999999999998654 222 34555554444 567888899999999999999 444566779999999
Q ss_pred HHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHcCCcccceEEEEcCccccccccCC
Q 003054 82 LQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLE 161 (852)
Q Consensus 82 l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~~~~~~~~~~ 161 (852)
+++.|++|+.....+.+ +.||+++|++|+++++|+||+.|+++.+..|++||+++||+.++|+||+++......+.
T Consensus 147 ~~~~g~~v~~~~~~~~~--~~d~~~~L~~ik~~~~~~iil~~~~~~~~~il~qa~~~gm~~~~y~~il~~~~~~~~~l-- 222 (371)
T cd06388 147 AGQNGWQVSAICVENFN--DASYRRLLEDLDRRQEKKFVIDCEIERLQNILEQIVSVGKHVKGYHYIIANLGFKDISL-- 222 (371)
T ss_pred hHhcCCeeeeEEeccCC--cHHHHHHHHHhcccccEEEEEECCHHHHHHHHHHHHhcCccccceEEEEccCccccccH--
Confidence 99999999886655433 66999999999999999999999999999999999999999999999998753222221
Q ss_pred chhhcccceEEEEEecCCCChHHHHHHHHHHHhccccCCCCcccccchhhHhHhhHHHHHHHHHHHhcccCcCccccccC
Q 003054 162 PSVIDSMQGVIGVGPHVPKTKALENFRVRWKRNFLQENPSIVDVELNIFGLLAYDATRALAEAVEKAGITSFGFDKTNVS 241 (852)
Q Consensus 162 ~~~~~~~~gv~~~~~~~~~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~a~~aYDAv~~lA~Al~~a~~~~~~~~~~~~~ 241 (852)
.+......++.+++...++++.+++|+++|++++..++++... .|...++++||||+++|+|+++++.......+.
T Consensus 223 ~~~~~g~~nitg~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~-~~~~~aAl~YDaV~l~a~A~~~l~~~~~~~~~~--- 298 (371)
T cd06388 223 ERFMHGGANVTGFQLVDFNTPMVTKLMQRWKKLDQREYPGSES-PPKYTSALTYDGVLVMAEAFRNLRRQKIDISRR--- 298 (371)
T ss_pred HHHhccCCceEEEEeecCCChhHHHHHHHHHhcCccccCCCCC-CccchHHHHHHHHHHHHHHHHHHHhcCCCcccC---
Confidence 1111223447888888888899999999999888766544322 578899999999999999999985332211111
Q ss_pred CCCCCC--ccccccCChHHHHHHhhccceeeeeeeEEee-cCccccceEEEEEcc-CCcEEEEEEcCCCCcc
Q 003054 242 RNATDL--EAFGISQNGPKLLQALSSTRFKGLTGDYIFV-DGQLQSSAFEIINVN-NGARGVGFWTPEKGLT 309 (852)
Q Consensus 242 ~~~~~~--~~~~~~~~g~~l~~al~~~~f~GltG~v~f~-~G~~~~~~~~I~~~~-~g~~~vG~w~~~~g~~ 309 (852)
+...+| +....|..|..|+++|++++|+|+||++.|+ +|++....++|++++ +|+++||+|++..|+.
T Consensus 299 ~~~~~C~~~~~~~w~~G~~i~~~lk~~~~~GlTG~i~Fd~~G~r~~~~l~Ii~l~~~g~~kvG~W~~~~g~~ 370 (371)
T cd06388 299 GNAGDCLANPAAPWGQGIDMERTLKQVRIQGLTGNIQFDHYGRRVNYTMDVFELKSNGPRKIGYWNDMDKLV 370 (371)
T ss_pred CCCCCcCCCCCCCCcccHHHHHHHHhcCcCCCccceeECCCCCcccceEEEEEccCCCceEEEEEcCCCCcc
Confidence 111234 3345689999999999999999999999997 899988899999999 9999999999998874
No 11
>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=2e-34 Score=322.38 Aligned_cols=299 Identities=21% Similarity=0.305 Sum_probs=235.2
Q ss_pred hhhHHHHhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHHH
Q 003054 2 QTNFIIQLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTDA 81 (852)
Q Consensus 2 ~a~~v~~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~~ 81 (852)
.+.++++++++++||+|+++++++.++ .++||+||+.|+ +..+++++++++||++|++||++++ |...++.+.+.
T Consensus 74 ~~~~~~~~~~~~~iP~i~~~~~~~~l~-~~~~~~fr~~p~---~~~a~~~~~~~~~wk~vaii~~~~~-~~~~~~~~~~~ 148 (382)
T cd06380 74 SVNTLTSYSDALHVPFITPSFPTNDLD-DGNQFVLQMRPS---LIQALVDLIEHYGWRKVVYLYDSDR-GLLRLQQLLDY 148 (382)
T ss_pred HHHHHHHHHhcCCCCeEecCCCcccCC-CCCcEEEEeccc---hhHHHHHHHHhcCCeEEEEEECCCc-chHHHHHHHHH
Confidence 466889999999999999999999886 467999999886 3458899999999999999996664 66778888889
Q ss_pred HHhCC--ceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHcCCcccceEEEEcCcccccccc
Q 003054 82 LQAID--TRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRT 159 (852)
Q Consensus 82 l~~~g--~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~~~~~~~~ 159 (852)
+++.| ++|.... +....++.||.++|++||+.++|+||+.++.+++..+++||+++||+.++|+||+++......+.
T Consensus 149 ~~~~g~~i~v~~~~-~~~~~~~~d~~~~L~~ik~~~~~~iil~~~~~~~~~i~~qa~~~gm~~~~y~~i~~~~~~~~~~~ 227 (382)
T cd06380 149 LREKDNKWQVTARR-VDNVTDEEEFLRLLEDLDRRKEKRIVLDCESERLNKILEQIVDVGKNRKGYHYILANLGFDDIDL 227 (382)
T ss_pred HhccCCceEEEEEE-ecCCCcHHHHHHHHHHhhcccceEEEEECCHHHHHHHHHHHHHhhhcccceEEEEccCCcccccH
Confidence 99888 6665432 33222457999999999999999999999999999999999999999999999988754433322
Q ss_pred CCchhhcccceEEEEEecCCCChHHHHHHHHHHHhccccCCCCcccccchhhHhHhhHHHHHHHHHHHhcccCcCc-c--
Q 003054 160 LEPSVIDSMQGVIGVGPHVPKTKALENFRVRWKRNFLQENPSIVDVELNIFGLLAYDATRALAEAVEKAGITSFGF-D-- 236 (852)
Q Consensus 160 ~~~~~~~~~~gv~~~~~~~~~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~a~~aYDAv~~lA~Al~~a~~~~~~~-~-- 236 (852)
. .......++.+++...+..+..++|.++|+++++.+.+......++.+++++||||+++|+|+++++...... .
T Consensus 228 ~--~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~aa~aYDav~~~a~Al~~~~~~~~~~~~~~ 305 (382)
T cd06380 228 S--KFLFGGVNITGFQLVDNTNPTVQKFLQRWKKLDPREWPGAGTSPIKYTAALAHDAVLVMAEAFRSLRRQRGSGRHRI 305 (382)
T ss_pred H--HhccCceeeEEEeccCCCCHHHHHHHHHHHhcCccccCcCCcCCcchHHHHHHHHHHHHHHHHHHHHHhcccccccc
Confidence 1 1112234566777667778899999999999997654433333578899999999999999999997532110 0
Q ss_pred ccccCCCCCCC--ccccccCChHHHHHHhhccceeeeeeeEEee-cCccccceEEEEEcc-CCcEEEEEEcCCCCc
Q 003054 237 KTNVSRNATDL--EAFGISQNGPKLLQALSSTRFKGLTGDYIFV-DGQLQSSAFEIINVN-NGARGVGFWTPEKGL 308 (852)
Q Consensus 237 ~~~~~~~~~~~--~~~~~~~~g~~l~~al~~~~f~GltG~v~f~-~G~~~~~~~~I~~~~-~g~~~vG~w~~~~g~ 308 (852)
.......+..| +....|.+|++|+++|++++|+|++|++.|| +|++....++|++++ +|.+.||+|++..|+
T Consensus 306 ~~~~~~~~~~C~~~~~~~~~~g~~i~~~l~~~~~~G~tG~i~Fd~~G~~~~~~~~i~~~~~~~~~~vg~w~~~~g~ 381 (382)
T cd06380 306 DISRRGNGGDCLANPAVPWEHGIDIERALKKVQFEGLTGNVQFDEFGQRTNYTLDVVELKTRGLRKVGYWNEDDGL 381 (382)
T ss_pred ccccCCCCCcCCCCCCCCccchHHHHHHHHhcccCCcccceEECCCCCcccccEEEEEecCCCceEEEEECCCcCc
Confidence 00001111222 2455688999999999999999999999997 999988889999999 789999999998886
No 12
>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=2.5e-34 Score=315.68 Aligned_cols=294 Identities=20% Similarity=0.265 Sum_probs=223.4
Q ss_pred hhhHHHHhcCCCCccEEeeec-----------CCCCCCCCCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeCCc
Q 003054 2 QTNFIIQLGNKSQVPILSFSA-----------TSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDNQY 70 (852)
Q Consensus 2 ~a~~v~~i~~~~~vP~Is~~a-----------ts~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~~~ 70 (852)
.|+.++.+|+.++||+|++++ ++|.++..++|++.|. + ..+.+|+++++++|+|++|++|| |++|
T Consensus 74 ~a~~v~sic~~l~VP~is~~~~~~~~~~~~~~~~p~~~~~~~~~~lrp--~-~~~~~Ai~dlV~~~~W~~v~~iY-D~d~ 149 (400)
T cd06392 74 SANALQSLTDAMHIPHLFVQRNSGGSPRTACHLNPSPEGEEYTLAARP--P-VRLNDVMLKLVTELRWQKFIVFY-DSEY 149 (400)
T ss_pred HHHHHHHHhccCcCCcEeecccccccccccccCCCCcCcCceeEEecC--c-hHHHHHHHHHHHhCCCcEEEEEE-ECcc
Confidence 588999999999999999866 4455555555555554 4 46788999999999999999999 8999
Q ss_pred ccccHHHHHHHHHhCCceeeeeee-------cCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHcCCccc
Q 003054 71 GEEMIPSLTDALQAIDTRVPYRSV-------ISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEIGLMNK 143 (852)
Q Consensus 71 G~~~~~~l~~~l~~~g~~v~~~~~-------~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~G~~~~ 143 (852)
|...++.|.+++.+.+.+|.+... +++.. .+.....|.+++.+. ++||++|+++.+..+++||.++||+..
T Consensus 150 gl~~lq~L~~~~~~~~~~I~~~~v~~~~~~~~~~~l-~~~~~~~L~~~~~~~-r~iVv~~s~~~~~~il~qA~~lgM~~~ 227 (400)
T cd06392 150 DIRGLQSFLDQASRLGLDVSLQKVDRNISRVFTNLF-TTMKTEELNRYRDTL-RRAILLLSPRGAQTFINEAVETNLASK 227 (400)
T ss_pred cHHHHHHHHHHHhhcCceEEEEEcccCcchhhhhHH-HHHHHhhhhhccccc-eEEEEEcCcHHHHHHHHHHHHhCcccC
Confidence 999999999999999999987662 22111 222344555555556 999999999999999999999999999
Q ss_pred ceEEEEcCccccccccCCchhhcccc-eEEEEEecCCCChHHHHHH----HHHHHhccccCCCCcccccchhhHhHhhHH
Q 003054 144 GCVWIMTDGMTNLLRTLEPSVIDSMQ-GVIGVGPHVPKTKALENFR----VRWKRNFLQENPSIVDVELNIFGLLAYDAT 218 (852)
Q Consensus 144 ~~vwi~~~~~~~~~~~~~~~~~~~~~-gv~~~~~~~~~~~~~~~F~----~~~~~~~~~~~~~~~~~~~~~~a~~aYDAv 218 (852)
+|+||+|+......+... .....- ++.+++.+.|.++...+|. .+|++.......+ ....++.+++++||||
T Consensus 228 ~y~wI~t~~~~~~~dl~~--~~~g~~~niT~~r~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~-~~~~l~~~aalayDaV 304 (400)
T cd06392 228 DSHWVFVNEEISDTEILE--LVHSALGRMTVIRQIFPLSKDNNQRCIRNNHRISSLLCDPQEG-YLQMLQVSNLYLYDSV 304 (400)
T ss_pred CeEEEEecCCcccccHHH--HhcccccceeeEEEecCCcHHHHHHHHHHHHHHHhhhcccccc-cccccchhHHHHHHHH
Confidence 999999998776443221 222222 3445999988877555554 6776544331111 1114788999999999
Q ss_pred HHHHHHHHHhcccCcCccccccCCCCCCC--ccccccCChHHHHHHhhccceeeeeeeEEee-cCccccceEEEEEcc--
Q 003054 219 RALAEAVEKAGITSFGFDKTNVSRNATDL--EAFGISQNGPKLLQALSSTRFKGLTGDYIFV-DGQLQSSAFEIINVN-- 293 (852)
Q Consensus 219 ~~lA~Al~~a~~~~~~~~~~~~~~~~~~~--~~~~~~~~g~~l~~al~~~~f~GltG~v~f~-~G~~~~~~~~I~~~~-- 293 (852)
|++|+|+++...+.... .....+| +...+|..|..|+++|++++|+|+||+++|+ +|++.++.|+|+|++
T Consensus 305 ~~~A~Al~~ll~~~~~~-----~~~~l~C~~~~~~~w~~G~~ll~~ik~v~f~GLTG~I~F~~~G~r~~~~ldIi~l~~~ 379 (400)
T cd06392 305 LMLANAFHRKLEDRKWH-----SMASLNCIRKSTKPWNGGRSMLETIKKGHITGLTGVMEFKEDGANPHVQFEILGTSYS 379 (400)
T ss_pred HHHHHHHHHHhhccccC-----CCCCCccCCCCCCCCCChHHHHHHHHhCCCccCccceeECCCCCCcCCceEEEecccc
Confidence 99999999743211111 1112455 4567899999999999999999999999997 999999999999964
Q ss_pred ----CCcEEEEEEcCCCCcc
Q 003054 294 ----NGARGVGFWTPEKGLT 309 (852)
Q Consensus 294 ----~g~~~vG~w~~~~g~~ 309 (852)
.|.++||+|++.+|+.
T Consensus 380 ~~~g~g~~~iG~W~~~~gl~ 399 (400)
T cd06392 380 ETFGKDVRRLATWDSEKGLN 399 (400)
T ss_pred ccCCCCceEeEEecCCCCCC
Confidence 4499999999999874
No 13
>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=9.5e-34 Score=316.43 Aligned_cols=271 Identities=20% Similarity=0.259 Sum_probs=227.1
Q ss_pred hhhHHHHhcCCCCccEEeeecCCCCCCC-CCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHH
Q 003054 2 QTNFIIQLGNKSQVPILSFSATSPSLTS-IRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTD 80 (852)
Q Consensus 2 ~a~~v~~i~~~~~vP~Is~~ats~~lt~-~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~ 80 (852)
++.+++++++.++||+||++|++|.|++ .++|||||+.|+|..|+++++++++++||++|++|++|++||++..+.|++
T Consensus 115 ~s~ava~v~~~~~IP~IS~~ats~~Ls~~~~~~~ffRt~p~D~~qa~ai~~li~~~~w~~Vaii~~~d~yG~~~~~~f~~ 194 (403)
T cd06361 115 ISMAVSRMLNLQLIPQVSYASTAEILSDKIRFPSFLRTVPSDFYQTKAMAHLIKKSGWNWVGIIITDDDYGRSALETFII 194 (403)
T ss_pred HHHHHHHHhccCCcceEecCcCCcccCCcccCCCeeECCCchHhHHHHHHHHHHHcCCcEEEEEEecCchHHHHHHHHHH
Confidence 5678999999999999999999999997 578999999999999999999999999999999999999999999999999
Q ss_pred HHHhCCceeeeeeecCCCCCh-----HHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHcCCcccceEEEEcCcccc
Q 003054 81 ALQAIDTRVPYRSVISPLATD-----DQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTN 155 (852)
Q Consensus 81 ~l~~~g~~v~~~~~~~~~~~~-----~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~~~~ 155 (852)
++++.|+||+..+.++.+.++ .++..+++++++++|||||+.++.+++..++++|+++|+ +++||++++|..
T Consensus 195 ~~~~~GicIa~~e~~~~~~~~~~~~~~~~~~~~~~ik~~~a~vVvv~~~~~~~~~l~~~a~~~g~---~~~wigs~~w~~ 271 (403)
T cd06361 195 QAEANGVCIAFKEILPASLSDNTKLNRIIRTTEKIIEENKVNVIVVFARQFHVFLLFNKAIERNI---NKVWIASDNWST 271 (403)
T ss_pred HHHHCCeEEEEEEEecCccCcchhHHHHHHHHHHHHhcCCCeEEEEEeChHHHHHHHHHHHHhCC---CeEEEEECcccC
Confidence 999999999999988764322 566777777899999999999999999999999999998 588999999986
Q ss_pred ccccCCchhhcccceEEEEEecCCCChHHHHHHHHHHHhccccCCCCcccccchhhHhHhhHHHHHHHHHHHhcccCcCc
Q 003054 156 LLRTLEPSVIDSMQGVIGVGPHVPKTKALENFRVRWKRNFLQENPSIVDVELNIFGLLAYDATRALAEAVEKAGITSFGF 235 (852)
Q Consensus 156 ~~~~~~~~~~~~~~gv~~~~~~~~~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~a~~aYDAv~~lA~Al~~a~~~~~~~ 235 (852)
..............|++++.+..+.. +.|.+.|++.+ ..++||||+++|+||++++...
T Consensus 272 ~~~~~~~~~~~~~~g~ig~~~~~~~~---~~F~~~~~~~~---------------~~~v~~AVyaiA~Al~~~~~~~--- 330 (403)
T cd06361 272 AKKILTDPNVKKIGKVVGFTFKSGNI---SSFHQFLKNLL---------------IHSIQLAVFALAHAIRDLCQER--- 330 (403)
T ss_pred ccccccCCcccccceEEEEEecCCcc---chHHHHHHHhh---------------HHHHHHHHHHHHHHHHHhccCC---
Confidence 44433332335677899988866444 45555555544 2358999999999999976321
Q ss_pred cccccCCCCCCCccccccCChHHHHHHhhccceeeeeeeEEee-cCccccceEEEEEcc--CC---cEEEEEEcCCCCc
Q 003054 236 DKTNVSRNATDLEAFGISQNGPKLLQALSSTRFKGLTGDYIFV-DGQLQSSAFEIINVN--NG---ARGVGFWTPEKGL 308 (852)
Q Consensus 236 ~~~~~~~~~~~~~~~~~~~~g~~l~~al~~~~f~GltG~v~f~-~G~~~~~~~~I~~~~--~g---~~~vG~w~~~~g~ 308 (852)
.|... ...++++|+++|++++|+|++|++.|+ +||. ...|+|+||+ +| ++.||.|++.+..
T Consensus 331 ----------~c~~~-~~~~~~~l~~~L~~~~f~g~~~~v~Fd~~gd~-~~~y~I~~~~~~~~~~~~~~vg~~~~~~~~ 397 (403)
T cd06361 331 ----------QCQNP-NAFQPWELLGQLKNVTFEDGGNMYHFDANGDL-NLGYDVVLWKEDNGHMTVTIMAEYDPQNDV 397 (403)
T ss_pred ----------CCCCC-CCcCHHHHHHHHheeEEecCCceEEECCCCCC-CcceEEEEeEecCCcEEEEEEEEEeCCCCE
Confidence 12211 145789999999999999999999998 9997 6789999999 44 8999999987654
No 14
>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=7e-34 Score=315.61 Aligned_cols=275 Identities=20% Similarity=0.284 Sum_probs=229.5
Q ss_pred hhHHHHhcCCCCccEEeeecCCCCC-CC-CCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHH
Q 003054 3 TNFIIQLGNKSQVPILSFSATSPSL-TS-IRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTD 80 (852)
Q Consensus 3 a~~v~~i~~~~~vP~Is~~ats~~l-t~-~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~ 80 (852)
+.+++++++.++||+|+++++++.+ ++ ..+|||||+.|++..|+++++++++++||++|++||++++||++..+.+++
T Consensus 79 ~~~~~~v~~~~~iP~Is~~~~~~~~~s~~~~~~~~~R~~p~~~~~~~ai~~ll~~~~w~~vaii~~~~~~g~~~~~~l~~ 158 (362)
T cd06367 79 AQILDFTSAQTRIPVVGISGRESIFMSDKNIHSLFLQTGPSLEQQADVMLEILEEYDWHQFSVVTSRDPGYRDFLDRVET 158 (362)
T ss_pred hhhhhhhhhhhcCcEEEeeccccccccCCCcccceEeecCcHHHHHHHHHHHHHHcCCeEEEEEEEcCcccHHHHHHHHH
Confidence 6889999999999999999999998 76 678999999999999999999999999999999999999999999999999
Q ss_pred HHHhCCce--eeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHcCCcccceEEEEcCccccccc
Q 003054 81 ALQAIDTR--VPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLR 158 (852)
Q Consensus 81 ~l~~~g~~--v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~~~~~~~ 158 (852)
.+++.|++ ++....++... .+++...+.++++.++|+|+++++.+++..++++|+++||+.++|+||+++.+.....
T Consensus 159 ~l~~~g~~~~i~~~~~~~~~~-~~~~~~~l~~l~~~~~~vivl~~~~~~~~~il~~a~~~g~~~~~~~wI~~~~~~~~~~ 237 (362)
T cd06367 159 TLEESFVGWEFQLVLTLDLSD-DDGDARLLRQLKKLESRVILLYCSKEEAERIFEAAASLGLTGPGYVWIVGELALGSGL 237 (362)
T ss_pred HHHhcccceeeeeeEEeccCC-CcchHHHHHHHHhcCCcEEEEeCCHHHHHHHHHHHHHcCCCCCCcEEEECcccccccC
Confidence 99999998 77666666432 2289999999999999999999999999999999999999999999999999874211
Q ss_pred cCCchhhcccceEEEEEecCCCChHHHHHHHHHHHhccccCCCCcccccchhhHhHhhHHHHHHHHHHHhcccCcCcccc
Q 003054 159 TLEPSVIDSMQGVIGVGPHVPKTKALENFRVRWKRNFLQENPSIVDVELNIFGLLAYDATRALAEAVEKAGITSFGFDKT 238 (852)
Q Consensus 159 ~~~~~~~~~~~gv~~~~~~~~~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~a~~aYDAv~~lA~Al~~a~~~~~~~~~~ 238 (852)
...+...|++++++..+ ..+++++||||+++|+|++++.......
T Consensus 238 ----~~~~~~~G~~g~~~~~~----------------------------~~~~~~~~Dav~~~a~Al~~~~~~~~~~--- 282 (362)
T cd06367 238 ----APEGLPVGLLGVGLDTW----------------------------YSLEARVRDAVAIVARAAESLLRDKGAL--- 282 (362)
T ss_pred ----CccCCCCeeEEEEeccc----------------------------ccHHHHHHHHHHHHHHHHHHHHHhcCCC---
Confidence 12245679999987532 2357899999999999999876432110
Q ss_pred ccCCCCCCCccccc--cCChHHHHHHhhccceeeeeeeEEee-cCccccceEEEEEcc--CCcEEEEEEcCCCCcccccC
Q 003054 239 NVSRNATDLEAFGI--SQNGPKLLQALSSTRFKGLTGDYIFV-DGQLQSSAFEIINVN--NGARGVGFWTPEKGLTQKLS 313 (852)
Q Consensus 239 ~~~~~~~~~~~~~~--~~~g~~l~~al~~~~f~GltG~v~f~-~G~~~~~~~~I~~~~--~g~~~vG~w~~~~g~~~~~~ 313 (852)
.....+|..... +.+|..|.++|++++|+|++|++.|+ +|++....|+|+|++ .|+++||.|++ +.
T Consensus 283 --~~~~~~C~~~~~~~~~~g~~l~~~l~~~~f~G~tg~v~F~~~G~~~~~~~~I~~l~~~~~~~~VG~W~~---~~---- 353 (362)
T cd06367 283 --PEPPVNCYDTANKRESSGQYLARFLMNVTFDGETGDVSFNEDGYLSNPKLVIINLRRNRKWERVGSWEN---GK---- 353 (362)
T ss_pred --CCCCCCcCCCCCCCCCchHHHHHHHhcccccCCCCceeECCCcccccceEEEEEecCCCcceEEEEEcC---Cc----
Confidence 111123444322 68899999999999999999999998 999977899999998 57999999985 21
Q ss_pred CCccccCCccceEeC
Q 003054 314 SNSTTKSKLKPIIWP 328 (852)
Q Consensus 314 ~~~~~~~~~~~i~Wp 328 (852)
.+.+.|.||
T Consensus 354 ------~~~~~i~w~ 362 (362)
T cd06367 354 ------LVMRYIVWP 362 (362)
T ss_pred ------eecCcCCCC
Confidence 134668898
No 15
>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=9.6e-34 Score=323.06 Aligned_cols=291 Identities=18% Similarity=0.244 Sum_probs=233.0
Q ss_pred hhhHHHHhcCCCCccEEeeecCCCCCCC-CCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHH
Q 003054 2 QTNFIIQLGNKSQVPILSFSATSPSLTS-IRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTD 80 (852)
Q Consensus 2 ~a~~v~~i~~~~~vP~Is~~ats~~lt~-~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~ 80 (852)
++.+++++++.++||+|+++++++.|++ .++|||||+.|+|..|+.|+++++++|||++|++|+.|++||+..++.|.+
T Consensus 115 ~s~~va~i~~~~~IP~Is~~sts~~lsd~~~yp~ffRt~psd~~q~~ai~~li~~f~W~~Vaiv~~d~~yg~~~~~~~~~ 194 (469)
T cd06365 115 LSATIATLLGLYKFPQLTYGPFDPLLSDRVQFPSLYQMAPKDTSLPLGMVSLMLHFSWTWVGLVISDDDRGEQFLSDLRE 194 (469)
T ss_pred HHHHHHHHhhhhcccceeeccCCccccchhhCCcceEecCCchhHHHHHHHHHHhcCCeEEEEEEecChhHHHHHHHHHH
Confidence 5788999999999999999999999987 578999999999999999999999999999999999999999999999999
Q ss_pred HHHhCCceeeeeeecCCCCCh--HHHHHHHHHhhcCCceEEEEEeChhhHHHH-HHHHHHcCCcccceEEEEcCcccccc
Q 003054 81 ALQAIDTRVPYRSVISPLATD--DQIEKELYKLFTMQTRVFILHMLPSLGSRI-FEKANEIGLMNKGCVWIMTDGMTNLL 157 (852)
Q Consensus 81 ~l~~~g~~v~~~~~~~~~~~~--~d~~~~l~~l~~~~~~viv~~~~~~~~~~i-~~~a~~~G~~~~~~vwi~~~~~~~~~ 157 (852)
++++.|++|+..+.++....+ .++..+|.+|+++++||||++++..++..+ ++++++.| .+++||++++|....
T Consensus 195 ~~~~~gi~I~~~~~i~~~~~~~~~~~~~~l~~i~~~~arvIvl~~~~~~~~~l~~~~~~~~~---~~~~wi~s~~w~~~~ 271 (469)
T cd06365 195 EMQRNGICLAFVEKIPVNMQLYLTRAEKYYNQIMTSSAKVIIIYGDTDSLLEVSFRLWQYLL---IGKVWITTSQWDVTT 271 (469)
T ss_pred HHHHCCeEEEEEEEecCCchhhHHHHHHHHHHhhcCCCeEEEEEcCcHHHHHHHHHHHHhcc---CceEEEeeccccccc
Confidence 999999999999988765433 488999999999999999999998888655 55555554 468899999987543
Q ss_pred ccCCchhhcccceEEEEEecCCCChHHHHHHH---------------HHHHhccccCCCC-----------cc-------
Q 003054 158 RTLEPSVIDSMQGVIGVGPHVPKTKALENFRV---------------RWKRNFLQENPSI-----------VD------- 204 (852)
Q Consensus 158 ~~~~~~~~~~~~gv~~~~~~~~~~~~~~~F~~---------------~~~~~~~~~~~~~-----------~~------- 204 (852)
... ....+.++|++++.++.++.+.+++|.+ .|+..|+|..+.. ..
T Consensus 272 ~~~-~~~~~~~~G~lg~~~~~~~~~~f~~fl~~l~~~~~~~npw~~efwe~~f~c~~~~~~~~~~~~c~~~~~~~~~~~~ 350 (469)
T cd06365 272 SPK-DFTLNSFHGTLIFSHHHSEIPGFKDFLQTVNPSKYPEDIFLEKLWWIYFNCSLSKSSCKTLKNCLSNASLEWLPLH 350 (469)
T ss_pred ccc-ccccceeeEEEEEEeccCcCcchHHHhhccCcccCCCccHHHhhHhHhcCcccCcCCccccCCCCCCccccccccc
Confidence 222 2245679999999999888888777654 4777777652110 00
Q ss_pred ---cccchhhHhHhhHHHHHHHHHHHhcccCcCccccccCCCCCCCccccccCChHHHHHHhhccceeeeeee-EEee-c
Q 003054 205 ---VELNIFGLLAYDATRALAEAVEKAGITSFGFDKTNVSRNATDLEAFGISQNGPKLLQALSSTRFKGLTGD-YIFV-D 279 (852)
Q Consensus 205 ---~~~~~~a~~aYDAv~~lA~Al~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~al~~~~f~GltG~-v~f~-~ 279 (852)
......+.+.||||+++|+||+++........+ ..+|. .....+.+|++.|++++|.|.+|. |.|| |
T Consensus 351 ~~~~~~~~~~~~v~dAVya~AhALh~~l~c~~~~~~------~~~~~--~~~~~~~~l~~~l~~v~F~~~~g~~v~Fd~n 422 (469)
T cd06365 351 YFDMAMSEESYNVYNAVYAVAHALHEMLLQQVETQS------ENNGK--RLIFLPWQLHSFLKNIQFKNPAGDEVNLNQK 422 (469)
T ss_pred cccchhhhhHHHHHHHHHHHHHHHHHHHHhhccCCC------cCCCC--CCCccHHHHHHHHHhccccCCCCCEEEecCC
Confidence 002346788999999999999998754321100 01111 124568899999999999999985 9998 9
Q ss_pred CccccceEEEEEcc---CC---cEEEEEEcCC
Q 003054 280 GQLQSSAFEIINVN---NG---ARGVGFWTPE 305 (852)
Q Consensus 280 G~~~~~~~~I~~~~---~g---~~~vG~w~~~ 305 (852)
||. ...|+|+|++ ++ ++.||.|++.
T Consensus 423 Gd~-~~~YdI~n~q~~~~~~~~~~~VG~~~~~ 453 (469)
T cd06365 423 RKL-DTEYDILNYWNFPQGLGLKVKVGEFSPQ 453 (469)
T ss_pred CCc-CceeeEEEEEECCCCCEEEEEEEEEeCC
Confidence 997 6789999998 22 7999999863
No 16
>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=7.5e-33 Score=307.26 Aligned_cols=297 Identities=20% Similarity=0.267 Sum_probs=231.2
Q ss_pred hhhHHHHhcCCCCccEEee----ecCC-----CCCCC--CCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeCCc
Q 003054 2 QTNFIIQLGNKSQVPILSF----SATS-----PSLTS--IRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDNQY 70 (852)
Q Consensus 2 ~a~~v~~i~~~~~vP~Is~----~ats-----~~lt~--~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~~~ 70 (852)
.+..++.+|+.++||+|++ ++++ |.+++ .++|+++| |+ ..+++|+++++++|+|++|+++| |++|
T Consensus 74 ~~~~v~~~~~~~~vP~i~~~~~~~~t~~~~~~~~~~~~~~~y~~~~r--p~-~~~~~ai~~li~~f~W~~v~i~~-d~~~ 149 (400)
T cd06391 74 SAGSLQSLADAMHIPHLFIQRSTAGTPRSSCGLTRSNRNDDYTLSVR--PP-VYLNDVILRVVTEYAWQKFIIFY-DTDY 149 (400)
T ss_pred HHHHHHHHhccCcCCeEEeecccccCccccCCCCCCCCcccceEEec--Ch-HHHHHHHHHHHHHcCCcEEEEEE-eCCc
Confidence 4677889999999999985 4433 34443 45677777 44 68899999999999999998764 7889
Q ss_pred ccccHHHHHHHHHhCCceeeeeeecCCCCCh---HHHHH-HHHHhhc--CCceEEEEEeChhhHHHHHHHHHHcCCcccc
Q 003054 71 GEEMIPSLTDALQAIDTRVPYRSVISPLATD---DQIEK-ELYKLFT--MQTRVFILHMLPSLGSRIFEKANEIGLMNKG 144 (852)
Q Consensus 71 G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~---~d~~~-~l~~l~~--~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~ 144 (852)
|...++.+.+++++.|++|..... .....+ ..+.. .+.+|+. .+.++||++++++.+..++++|+++||++++
T Consensus 150 ~~~~l~~l~~~~~~~~i~I~~~~~-~~~~~~~~~~~~~~~~~~~l~~~~~~~rviVl~~~~~~~~~ll~~a~~~gm~~~~ 228 (400)
T cd06391 150 DIRGIQEFLDKVSQQGMDVALQKV-ENNINKMITGLFRTMRIEELNRYRDTLRRAILVMNPATAKSFITEVVETNLVAFD 228 (400)
T ss_pred cHHHHHHHHHHHHHcCCeEEEEec-CcchhhhhHHHHHHHHHHHHHhhcccccEEEEECCcHHHHHHHHHHHHcCCCCCC
Confidence 999999999999999999987542 211111 12332 4455654 5679999999999999999999999999999
Q ss_pred eEEEEcCccccccccCCchhhcccceEEEEEecCCCChHHHHHHHHHHHhccccC--CCCc-ccccchhhHhHhhHHHHH
Q 003054 145 CVWIMTDGMTNLLRTLEPSVIDSMQGVIGVGPHVPKTKALENFRVRWKRNFLQEN--PSIV-DVELNIFGLLAYDATRAL 221 (852)
Q Consensus 145 ~vwi~~~~~~~~~~~~~~~~~~~~~gv~~~~~~~~~~~~~~~F~~~~~~~~~~~~--~~~~-~~~~~~~a~~aYDAv~~l 221 (852)
|+||++++....++... ...+.+.|+.+++++.|.+....+|..+|.+++.... |+.. ...++.+++++|||||++
T Consensus 229 y~wi~t~~~~~~~dl~~-~~~~~~~~v~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~alayDaV~~~ 307 (400)
T cd06391 229 CHWIIINEEISDMDVQE-LVRRSIGRLTIIRQTFPLPQNISQRCFRGNHRISSSLCDPKDPFAQMMEISNLYIYDTVLLL 307 (400)
T ss_pred eEEEEeCccccccccch-HHhcccceEEEeccCCchHHHHHHHHHHHhhhccccccCccccccccccchhhHHHHHHHHH
Confidence 99999999888777533 2345677889999999988888999999998875322 2221 124678999999999999
Q ss_pred HHHHHHhcccCcCccccccCCCCCCC--ccccccCChHHHHHHhhccceeeeeeeEEee-cCccccceEEEEEc-----c
Q 003054 222 AEAVEKAGITSFGFDKTNVSRNATDL--EAFGISQNGPKLLQALSSTRFKGLTGDYIFV-DGQLQSSAFEIINV-----N 293 (852)
Q Consensus 222 A~Al~~a~~~~~~~~~~~~~~~~~~~--~~~~~~~~g~~l~~al~~~~f~GltG~v~f~-~G~~~~~~~~I~~~-----~ 293 (852)
|+|+++........+. ...+| +....|..|..|+++|++++|+|+||+++|+ +|++.++.|+|+|+ .
T Consensus 308 A~A~~~l~~~~~~~~~-----~~~~c~~~~~~~w~~G~~ll~~i~~~~f~GlTG~i~f~~~g~r~~~~~dIin~~~~~~~ 382 (400)
T cd06391 308 ANAFHKKLEDRKWHSM-----ASLSCIRKNSKPWQGGRSMLETIKKGGVSGLTGELEFNENGGNPNVHFEILGTNYGEDL 382 (400)
T ss_pred HHHHHHHHhhccccCC-----CCcccccCCCCCCCChHHHHHHHHhcCcccceeceEECCCCCccCCceEEEEeeccccC
Confidence 9999987522211111 11123 2345799999999999999999999999997 79999999999999 2
Q ss_pred -CCcEEEEEEcCCCCcc
Q 003054 294 -NGARGVGFWTPEKGLT 309 (852)
Q Consensus 294 -~g~~~vG~w~~~~g~~ 309 (852)
+|.++||+|++..|+.
T Consensus 383 ~~g~rkiG~Ws~~~gl~ 399 (400)
T cd06391 383 GRGVRKLGCWNPITGLN 399 (400)
T ss_pred CCcceEEEEEcCCcCCC
Confidence 6899999999998873
No 17
>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=4.9e-33 Score=318.07 Aligned_cols=292 Identities=21% Similarity=0.327 Sum_probs=234.5
Q ss_pred hhhHHHHhcCCCCccEEeeecCCCCCCC-CCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHH
Q 003054 2 QTNFIIQLGNKSQVPILSFSATSPSLTS-IRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTD 80 (852)
Q Consensus 2 ~a~~v~~i~~~~~vP~Is~~ats~~lt~-~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~ 80 (852)
++.+++++++.++||+|+++++++.|++ .++|||||+.|+|..|+++++++++++||++|++||.|++||.+..+.|.+
T Consensus 115 ~t~ava~i~~~~~iP~Is~~ats~~ls~~~~~~~ffR~~p~d~~~~~ai~~~i~~~~w~~Vaii~~~~~yg~~~~~~~~~ 194 (463)
T cd06376 115 VSIMVANILRLFQIPQISYASTAPELSDDRRYDFFSRVVPPDSFQAQAMVDIVKALGWNYVSTLASEGNYGESGVEAFTQ 194 (463)
T ss_pred HHHHHHHHhccccCcccccccCChhhcccccCCceEEccCCHHHHHHHHHHHHHHcCCeEEEEEEeCChHHHHHHHHHHH
Confidence 5788999999999999999999999987 568999999999999999999999999999999999999999999999999
Q ss_pred HHHhCC-ceeeeeeecCCCCChHHHHHHHHHhhc-CCceEEEEEeChhhHHHHHHHHHHcCCcccceEEEEcCccccccc
Q 003054 81 ALQAID-TRVPYRSVISPLATDDQIEKELYKLFT-MQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLR 158 (852)
Q Consensus 81 ~l~~~g-~~v~~~~~~~~~~~~~d~~~~l~~l~~-~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~~~~~~~ 158 (852)
.+++.| .+|.....++...++.|+..+|++|++ .++|+||+.++.+++..++++|+++|+.+ .|+||++++|.....
T Consensus 195 ~~~~~g~~~v~~~~~i~~~~~~~d~~~~l~~ik~~~~~~vIvl~~~~~~~~~ll~~a~~~~~~g-~~~wig~d~~~~~~~ 273 (463)
T cd06376 195 ISREAGGVCIAQSIKIPREPRPGEFDKIIKRLLETPNARAVIIFANEDDIRRVLEAAKRANQVG-HFLWVGSDSWGAKIS 273 (463)
T ss_pred HHHHcCCceEEEEEecCCCCCHHHHHHHHHHHhccCCCeEEEEecChHHHHHHHHHHHhcCCcC-ceEEEEecccccccc
Confidence 999975 677666666555668899999999986 79999999999999999999999999864 499999999875433
Q ss_pred cCCchhhcccceEEEEEecCCCChHHHHH---------------HHHHHHhccccCC--CCc--------c---------
Q 003054 159 TLEPSVIDSMQGVIGVGPHVPKTKALENF---------------RVRWKRNFLQENP--SIV--------D--------- 204 (852)
Q Consensus 159 ~~~~~~~~~~~gv~~~~~~~~~~~~~~~F---------------~~~~~~~~~~~~~--~~~--------~--------- 204 (852)
... ...+.+.|++++.+.....+.+++| .+.|+..|+|..+ ... .
T Consensus 274 ~~~-~~~~~~~G~~~~~~~~~~~~~F~~~~~~l~~~~~~~~~~~~~~w~~~f~c~~~~~~~~~~~~~~~C~~~~~~~~~~ 352 (463)
T cd06376 274 PIL-QQEDVAEGAITILPKRASIEGFDAYFTSRTLENNRRNVWFAEFWEENFNCKLTISGSKKEDTDRKCTGQERIGRDS 352 (463)
T ss_pred ccc-cCcceeeeEEEEEeccccchhHHHHHHhCCcccCCCCcHHHHHHHHhCCCcccCCCCccccccCcCcchhhccccC
Confidence 222 1234688999998877666665554 4468888877532 100 0
Q ss_pred -cccchhhHhHhhHHHHHHHHHHHhcccCcCccccccCCCCCCCccccccCChHHHHHHhhccceeeeee-eEEee-cCc
Q 003054 205 -VELNIFGLLAYDATRALAEAVEKAGITSFGFDKTNVSRNATDLEAFGISQNGPKLLQALSSTRFKGLTG-DYIFV-DGQ 281 (852)
Q Consensus 205 -~~~~~~a~~aYDAv~~lA~Al~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~al~~~~f~GltG-~v~f~-~G~ 281 (852)
......+++.||||+++|+|++++...... . .. ..|... .+.+|.+|+++|++++|+|++| +|.|| +|+
T Consensus 353 ~~~~~~~~~~v~dAVyaiA~ALh~l~~~~c~-~---~~---~~C~~~-~~~~~~~l~~~L~~v~F~g~tg~~v~Fd~~G~ 424 (463)
T cd06376 353 TYEQEGKVQFVIDAVYAMAHALHSMHKDLCP-G---YT---GVCPEM-EPADGKKLLKYIRAVNFNGSAGTPVMFNENGD 424 (463)
T ss_pred cccccchhHHHHHHHHHHHHHHHHHHHhhCC-C---CC---CCCccC-CCCCHHHHHHHHHhCCccCCCCCeEEeCCCCC
Confidence 011236889999999999999998533210 0 01 123222 2567899999999999999999 79998 999
Q ss_pred cccceEEEEEcc-C-----CcEEEEEEcC
Q 003054 282 LQSSAFEIINVN-N-----GARGVGFWTP 304 (852)
Q Consensus 282 ~~~~~~~I~~~~-~-----g~~~vG~w~~ 304 (852)
+ ...|+|+|++ . +++.||.|++
T Consensus 425 ~-~~~Ydi~n~q~~~~~~~~~~~VG~w~~ 452 (463)
T cd06376 425 A-PGRYDIFQYQITNTSSPGYRLIGQWTD 452 (463)
T ss_pred C-CCceEEEEEEecCCCceeEEEEEEECC
Confidence 8 4689999998 2 2899999985
No 18
>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=3.3e-33 Score=320.08 Aligned_cols=296 Identities=20% Similarity=0.281 Sum_probs=236.2
Q ss_pred hhhHHHHhcCCCCccEEeeecCCCCCCC-CCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHH
Q 003054 2 QTNFIIQLGNKSQVPILSFSATSPSLTS-IRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTD 80 (852)
Q Consensus 2 ~a~~v~~i~~~~~vP~Is~~ats~~lt~-~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~ 80 (852)
.+.+++++++.++||+|+++++++.+++ .++|||||+.|+|..|+.+++++++++||++|++||+|++||+...+.|.+
T Consensus 129 ~~~ava~~~~~~~iP~Is~~ats~~ls~~~~~p~~fRt~p~d~~~~~al~~l~~~~~W~~Vaii~~~~~yg~~~~~~~~~ 208 (472)
T cd06374 129 VAIQVQNLLQLFNIPQIAYSATSIDLSDKTLFKYFLRVVPSDTLQARAMLDIVKRYNWTYVSAVHTEGNYGESGMEAFKE 208 (472)
T ss_pred HHHHHHHHhhhhcccccccccCchhhcccccCCceEEcCCChHHHHHHHHHHHHHCCCcEEEEEEecchHHHHHHHHHHH
Confidence 5788999999999999999999999997 479999999999999999999999999999999999999999999999999
Q ss_pred HHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCce--EEEEEeChhhHHHHHHHHHHcCCcccceEEEEcCccccccc
Q 003054 81 ALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTR--VFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLR 158 (852)
Q Consensus 81 ~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~--viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~~~~~~~ 158 (852)
.+++.|++|+..+.++...++.|+..+|.+||++++| ||++.+...++..++++|+++||. ++++||++++|.....
T Consensus 209 ~~~~~gi~i~~~~~i~~~~~~~d~~~~l~~lk~~~~da~vvv~~~~~~~~~~~l~~a~~~g~~-~~~~wi~s~~~~~~~~ 287 (472)
T cd06374 209 LAAHEGLCIAHSDKIYSNAGEQSFDRLLRKLRSRLPKARVVVCFCEGMTVRGLLMAMRRLGVG-GEFQLIGSDGWADRDD 287 (472)
T ss_pred HHHHCCeeEEEEEEecCCCchHHHHHHHHHHHhcCCCcEEEEEEechHHHHHHHHHHHHhcCC-CceEEEEecccccchH
Confidence 9999999999888876555678999999999976555 566667777899999999999995 4589999999875322
Q ss_pred cCCchhhcccceEEEEEecCCCChHHHHH---------------HHHHHHhccccCCCCcc------------------c
Q 003054 159 TLEPSVIDSMQGVIGVGPHVPKTKALENF---------------RVRWKRNFLQENPSIVD------------------V 205 (852)
Q Consensus 159 ~~~~~~~~~~~gv~~~~~~~~~~~~~~~F---------------~~~~~~~~~~~~~~~~~------------------~ 205 (852)
... ...+.++|++++.+..+..+.+++| .+.|+..|.|..+.... .
T Consensus 288 ~~~-~~~~~~~G~l~~~~~~~~~~~F~~~l~~l~~~~~~~~~~~~~~w~~~f~c~~~~~~~~~~~~~~~c~~~~~~~~~~ 366 (472)
T cd06374 288 VVE-GYEEEAEGGITIKLQSPEVPSFDDYYLKLRPETNTRNPWFREFWQHRFQCRLPGHPQENPNYIKICTGNESLDEQY 366 (472)
T ss_pred hhh-cchhhhheeEEEEecCCCCccHHHHHHhCCcccCCCChHHHHHHHHhcCCCcCCccCcCCccCCCCCCcccccccc
Confidence 222 2456689999998887776666654 55688888765321100 0
Q ss_pred ccchhhHhHhhHHHHHHHHHHHhcccCcCccccccCCCCCCCccccccCChHHHHHHhhccceeeeee-eEEee-cCccc
Q 003054 206 ELNIFGLLAYDATRALAEAVEKAGITSFGFDKTNVSRNATDLEAFGISQNGPKLLQALSSTRFKGLTG-DYIFV-DGQLQ 283 (852)
Q Consensus 206 ~~~~~a~~aYDAv~~lA~Al~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~al~~~~f~GltG-~v~f~-~G~~~ 283 (852)
....+++++|||||++|+||+++...... .....|.... ..+|..|+++|++++|+|++| +|.|+ +|++.
T Consensus 367 ~~~~~~~~vyDAVyaiA~ALh~~~~~~~~-------~~~~~c~~~~-~~~~~~l~~~l~~v~F~g~tG~~v~Fd~~G~~~ 438 (472)
T cd06374 367 VQDSKMGFVINAIYAMAHGLHNMHQDLCP-------GHVGLCDAMK-PIDGRKLLEYLLKTSFSGVSGEEVYFDENGDSP 438 (472)
T ss_pred cccceeHHHHHHHHHHHHHHHHHHHhhCC-------CCCCCCcCCC-CCCHHHHHHHHHhCcccCCCCCeEEEcCCCCCC
Confidence 11245679999999999999998533211 0001233222 467899999999999999999 79998 99984
Q ss_pred cceEEEEEcc---CC---cEEEEEEcCCCCcc
Q 003054 284 SSAFEIINVN---NG---ARGVGFWTPEKGLT 309 (852)
Q Consensus 284 ~~~~~I~~~~---~g---~~~vG~w~~~~g~~ 309 (852)
..|+|+|++ +| ++.||.|++ .+|.
T Consensus 439 -~~ydI~n~~~~~~~~~~~~~VG~w~~-~~l~ 468 (472)
T cd06374 439 -GRYDIMNLQYTEDLRFDYINVGSWHE-GDLG 468 (472)
T ss_pred -CceEEEEEEECCCCCEEEEEEEEEeC-Cccc
Confidence 589999999 22 899999974 3543
No 19
>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=5e-33 Score=310.49 Aligned_cols=278 Identities=15% Similarity=0.190 Sum_probs=228.3
Q ss_pred hhhHHHHhcCCCCccEEeeecCCCCCCC--CCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeCCccccc---HH
Q 003054 2 QTNFIIQLGNKSQVPILSFSATSPSLTS--IRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDNQYGEEM---IP 76 (852)
Q Consensus 2 ~a~~v~~i~~~~~vP~Is~~ats~~lt~--~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~~~G~~~---~~ 76 (852)
++.+++++++.++||+|+++++++.+++ ..+||+||+.|++..++.++++++++++|++|++||++++||++. ++
T Consensus 79 ~~~~va~ia~~~~iP~Is~~a~~~~~s~~~~~yp~~~R~~p~~~~~~~a~~~ll~~~~W~~vaiiy~~~~~~~~~~~~~~ 158 (387)
T cd06386 79 AAAPVARLASHWNIPMISAGALAAGFSHKKSEYSHLTRVAPSYVKMGETFSALFERFHWRSALLVYEDDKQERNCYFTLE 158 (387)
T ss_pred HHHHHHHHHHhCCCcEEccccCchhhccCcccCCeeEEecCchHHHHHHHHHHHHhCCCeEEEEEEEcCCCCccceehHH
Confidence 5788999999999999999999999976 358889999999999999999999999999999999999999887 99
Q ss_pred HHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHcCCcccceEEEEcCccc-c
Q 003054 77 SLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMT-N 155 (852)
Q Consensus 77 ~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~~~-~ 155 (852)
.|.+++++.|++|+....++ .++.|+..+|.++++.+ |+||++++.+++..++++|+++||+..+|+||..+... .
T Consensus 159 ~l~~~~~~~gi~v~~~~~~~--~~~~d~~~~l~~ik~~~-rvii~~~~~~~~~~ll~~A~~~gm~~~~yv~i~~d~~~~~ 235 (387)
T cd06386 159 GVHHVFQEEGYHMSIYPFDE--TKDLDLDEIIRAIQASE-RVVIMCAGADTIRSIMLAAHRRGLTSGDYIFFNIELFNSS 235 (387)
T ss_pred HHHHHHHhcCceEEEEecCC--CCcccHHHHHHHHHhcC-cEEEEecCHHHHHHHHHHHHHcCCCCCCEEEEEEeccccc
Confidence 99999999999998776554 33678999999999888 99999999999999999999999999999999997653 1
Q ss_pred cc--------ccCC---chhhcccceEEEEEecCCCChHHHHHHHHHHHhccccCCCCcccccchhhHhHhhHHHHHHHH
Q 003054 156 LL--------RTLE---PSVIDSMQGVIGVGPHVPKTKALENFRVRWKRNFLQENPSIVDVELNIFGLLAYDATRALAEA 224 (852)
Q Consensus 156 ~~--------~~~~---~~~~~~~~gv~~~~~~~~~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~a~~aYDAv~~lA~A 224 (852)
.. +..+ ....+.++|+.+++++ .+.+++|.++|++++.......+...++.+++++|||++++|+|
T Consensus 236 ~~~~~~w~~~~~~~~~~~~a~~~~~~v~~~~~~---~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~aa~~yDav~l~A~A 312 (387)
T cd06386 236 SYGDGSWKRGDKHDFEAKQAYSSLNTVTLLRTV---KPEFEKFSMEVKSSVEKAGDLNDCDYVNMFVEGFHDAILLYALA 312 (387)
T ss_pred ccCCCCCccCCCcCHHHHHHHHhheEEeccCCC---ChHHHHHHHHHHHHHHhCCCCcccccchHHHHHHHHHHHHHHHH
Confidence 00 1112 1233456666665554 46788999999866543211111124678999999999999999
Q ss_pred HHHhcccCcCccccccCCCCCCCccccccCChHHHHHHhhccceeeeeeeEEee-cCccccceEEEEEcc---C-CcEEE
Q 003054 225 VEKAGITSFGFDKTNVSRNATDLEAFGISQNGPKLLQALSSTRFKGLTGDYIFV-DGQLQSSAFEIINVN---N-GARGV 299 (852)
Q Consensus 225 l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~al~~~~f~GltG~v~f~-~G~~~~~~~~I~~~~---~-g~~~v 299 (852)
++++.... +.+.+|.+|+++|++++|+|++|++.|| +|++ ...|.|+.++ + +++.|
T Consensus 313 l~~~~~~g------------------~~~~~g~~l~~~l~~~~f~G~tG~v~~d~~g~r-~~~~~v~~~~~~~~~~~~~~ 373 (387)
T cd06386 313 LHEVLKNG------------------YSKKDGTKITQRMWNRTFEGIAGQVSIDANGDR-YGDFSVIAMTDVEAGTYEVV 373 (387)
T ss_pred HHHHhhCC------------------CCCCCHHHHHHHHhCCceeeccccEEECCCCCc-cccEEEEEccCCCCccEEEE
Confidence 99985211 1256899999999999999999999998 9999 5699999997 3 39999
Q ss_pred EEEcC
Q 003054 300 GFWTP 304 (852)
Q Consensus 300 G~w~~ 304 (852)
|.|..
T Consensus 374 ~~~~~ 378 (387)
T cd06386 374 GNYFG 378 (387)
T ss_pred eEEcc
Confidence 99975
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=6.9e-33 Score=316.84 Aligned_cols=296 Identities=24% Similarity=0.325 Sum_probs=238.1
Q ss_pred hhhHHHHhcCCCCccEEeeecCCCCCCC-CCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHH
Q 003054 2 QTNFIIQLGNKSQVPILSFSATSPSLTS-IRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTD 80 (852)
Q Consensus 2 ~a~~v~~i~~~~~vP~Is~~ats~~lt~-~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~ 80 (852)
.+.+++++++.++||+|+++++++.+++ .++|||||+.|++..|+.+++++++++||++|++|+.|++||.+..+.|.+
T Consensus 115 ~~~av~~~~~~~~ip~Is~~sts~~ls~~~~~~~~fR~~p~d~~~~~a~~~~l~~~~w~~vaii~~~~~~G~~~~~~~~~ 194 (452)
T cd06362 115 VSIQVANLLRLFKIPQISYASTSPELSDKTRYDYFSRTVPPDSFQAQAMVDIVKAFNWTYVSTVASEGNYGEKGIEAFEK 194 (452)
T ss_pred hHHHHHHHhccccCcccccccCchhhccccccCCEEEecCChHHHHHHHHHHHHHCCCcEEEEEEeCCHHHHHHHHHHHH
Confidence 5788999999999999999999999987 578999999999999999999999999999999999999999999999999
Q ss_pred HHHhCCceeeeeeecCCCCChHHHHHHHHHhhc-CCceEEEEEeChhhHHHHHHHHHHcCCcccceEEEEcCcccccccc
Q 003054 81 ALQAIDTRVPYRSVISPLATDDQIEKELYKLFT-MQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRT 159 (852)
Q Consensus 81 ~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~-~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~~~~~~~~ 159 (852)
.+++.|++|+..+.++...++.|+.++|++|++ .++|+||+.+...++..+++||+++|++ ..++||++++|......
T Consensus 195 ~~~~~gi~i~~~~~~~~~~~~~d~~~~l~~l~~~~~a~viil~~~~~~~~~~~~~a~~~g~~-~~~~~i~~~~~~~~~~~ 273 (452)
T cd06362 195 LAAERGICIAGSEKIPSSATEEEFDNIIRKLLSKPNARVVVLFCREDDIRGLLAAAKRLNAE-GHFQWIASDGWGARNSV 273 (452)
T ss_pred HHHHCCeeEEEEEEcCCCCCHHHHHHHHHHHhhcCCCeEEEEEcChHHHHHHHHHHHHcCCc-CceEEEEeccccccchh
Confidence 999999999998888765567899999999987 5799999999999999999999999996 45899999998754322
Q ss_pred CCchhhcccceEEEEEecCCCChHHHH---------------HHHHHHHhccccCCCCcc----------------cccc
Q 003054 160 LEPSVIDSMQGVIGVGPHVPKTKALEN---------------FRVRWKRNFLQENPSIVD----------------VELN 208 (852)
Q Consensus 160 ~~~~~~~~~~gv~~~~~~~~~~~~~~~---------------F~~~~~~~~~~~~~~~~~----------------~~~~ 208 (852)
. ......++|++++.++....+.+++ |.+.|+..|.+..+.... ...+
T Consensus 274 ~-~~~~~~~~g~~~~~~~~~~i~~f~~~l~~l~~~~~~~~~~~~~~w~~~~~c~~~~~~~~~~~~~c~~~~~~~~~~~~~ 352 (452)
T cd06362 274 V-EGLEDVAEGAITIELQSAEVPGFDEYFLSLTPENNSRNPWFREFWEQKFNCKLTGNGSTKDNTCCTERILLLSNYEQE 352 (452)
T ss_pred h-cccccccceEEEEEecccccccHHHHhhhCCcCcCCCChHHHHHHHHhcCCCcCCCCccccCCCCccccccccccccc
Confidence 1 2234668999988877655444443 334466666653211110 1235
Q ss_pred hhhHhHhhHHHHHHHHHHHhcccCcCccccccCCCCCCCccccccCChHHHHHHhhccceeeeee-eEEee-cCccccce
Q 003054 209 IFGLLAYDATRALAEAVEKAGITSFGFDKTNVSRNATDLEAFGISQNGPKLLQALSSTRFKGLTG-DYIFV-DGQLQSSA 286 (852)
Q Consensus 209 ~~a~~aYDAv~~lA~Al~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~al~~~~f~GltG-~v~f~-~G~~~~~~ 286 (852)
.++++.||||+++|+||+++........ ...|... .+.+|.+|+++|++++|.|++| +|.|+ +|++ ...
T Consensus 353 ~~~~~vyDAV~a~A~AL~~~l~~~~~~~-------~~~c~~~-~~~~~~~l~~~l~~v~f~g~tg~~v~Fd~~G~~-~~~ 423 (452)
T cd06362 353 SKVQFVIDAVYAMAHALHNMHRDLCPGT-------TGLCDAM-KPIDGRKLLFYLRNVSFSGLAGGPVRFDANGDG-PGR 423 (452)
T ss_pred cchhHHHHHHHHHHHHHHHHHHhhCCCC-------CCCCcCc-cCCCHHHHHHHHHhCCcCCCCCceEEECCCCCC-CCc
Confidence 5889999999999999999853321100 0113222 2567999999999999999998 79998 9998 468
Q ss_pred EEEEEcc--C---CcEEEEEEcCCCCc
Q 003054 287 FEIINVN--N---GARGVGFWTPEKGL 308 (852)
Q Consensus 287 ~~I~~~~--~---g~~~vG~w~~~~g~ 308 (852)
|+|+|++ + +++.||+|++..|+
T Consensus 424 y~I~~~~~~~~~~~~~~VG~w~~~~~~ 450 (452)
T cd06362 424 YDIFNYQRTNGKYDYVKVGSWKGELSL 450 (452)
T ss_pred eEEEEEEEcCCceEEEEEEEEeccccc
Confidence 9999998 2 38999999887664
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=1.7e-32 Score=314.88 Aligned_cols=296 Identities=19% Similarity=0.276 Sum_probs=237.2
Q ss_pred hhhHHHHhcCCCCccEEeeecCCCCCCC-CCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHH
Q 003054 2 QTNFIIQLGNKSQVPILSFSATSPSLTS-IRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTD 80 (852)
Q Consensus 2 ~a~~v~~i~~~~~vP~Is~~ats~~lt~-~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~ 80 (852)
++.+++++++.++||+|+++++++.|++ ..+|||||+.|+|..|+++++++++++||++|++|+.|++||+...+.|++
T Consensus 130 ~s~ava~~~~~~~IP~IS~~sss~~ls~~~~yp~ffRt~psd~~q~~Ai~~l~~~f~wk~VaiI~~dd~yG~~~~~~~~~ 209 (510)
T cd06364 130 VSTAVANLLGLFYIPQVSYASSSRLLSNKNQFKSFLRTIPNDEHQATAMADIIEYFRWNWVGTIAADDDYGRPGIEKFRE 209 (510)
T ss_pred HHHHHHHHhccccccccccccCCcccCCccccCCeeEcCCChHHHHHHHHHHHHHcCCeEEEEEEecCcchHHHHHHHHH
Confidence 5788999999999999999999999987 578999999999999999999999999999999999999999999999999
Q ss_pred HHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHcCCcccceEEEEcCccccccccC
Q 003054 81 ALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTL 160 (852)
Q Consensus 81 ~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~~~~~~~~~ 160 (852)
.+++.|+||+..+.++...++.|+.++|.+|+++++||||+.+...++..++++|+++|+. +++||++++|.......
T Consensus 210 ~~~~~Gi~I~~~~~i~~~~~~~d~~~~l~klk~~~a~vVvl~~~~~~~~~ll~qa~~~g~~--~~iwI~s~~w~~~~~~~ 287 (510)
T cd06364 210 EAEERDICIDFSELISQYSDEEEIQRVVEVIQNSTAKVIVVFSSGPDLEPLIKEIVRRNIT--GKIWLASEAWASSSLIA 287 (510)
T ss_pred HHHHCCcEEEEEEEeCCCCCHHHHHHHHHHHHhcCCeEEEEEeCcHHHHHHHHHHHHhCCC--CcEEEEEchhhcccccc
Confidence 9999999999988776544678999999999999999999999999999999999999994 57999999987544333
Q ss_pred CchhhcccceEEEEEecCCCChHHHHH---------------HHHHHHhccccCCC--C---------------------
Q 003054 161 EPSVIDSMQGVIGVGPHVPKTKALENF---------------RVRWKRNFLQENPS--I--------------------- 202 (852)
Q Consensus 161 ~~~~~~~~~gv~~~~~~~~~~~~~~~F---------------~~~~~~~~~~~~~~--~--------------------- 202 (852)
.....+.+.|++++.+.....+.+++| .+.|++.|+|..+. .
T Consensus 288 ~~~~~~~~gg~lg~~~~~~~i~~f~~~l~~l~p~~~~~~~~~~~~we~~f~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 367 (510)
T cd06364 288 MPEYFDVMGGTIGFALKAGQIPGFREFLQKVHPKKSSHNGFAKEFWEETFNCYLEDSPKNALPVDTFLGHEESGDDSENG 367 (510)
T ss_pred cCCccceeeEEEEEEECCCcCccHHHHHHhCCcccCCCChHHHHHHHHhcCCCCCCCccccccccccccccccccccccc
Confidence 333456788999998776555544443 44578888865321 0
Q ss_pred ----c-c------c----------ccchhhHhHhhHHHHHHHHHHHhcccCcCccccccCCCCCCCccccccCChHHHHH
Q 003054 203 ----V-D------V----------ELNIFGLLAYDATRALAEAVEKAGITSFGFDKTNVSRNATDLEAFGISQNGPKLLQ 261 (852)
Q Consensus 203 ----~-~------~----------~~~~~a~~aYDAv~~lA~Al~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~ 261 (852)
. . . ....++.+.||||+++|+||+++......... ...+ .|.... ..++.+|++
T Consensus 368 ~~~~~~~C~~~~~~~~~~~~~~~~~~~~~~~~v~~AVyAvAhaLh~~~~c~~~~~~-~~~~---~c~~~~-~~~~~~l~~ 442 (510)
T cd06364 368 STAFRPLCTGDENIASVETPYLDYTHLRISYNVYLAVYSIAHALQDIYTCTPGKGL-FTNG---SCADIK-KVEAWQVLK 442 (510)
T ss_pred ccccCCCCCChhhhcccCCccccccchhhHHHHHHHHHHHHHHHHHHhcCCCCCCC-ccCC---CCCCCC-CCCHHHHHH
Confidence 0 0 0 01234678999999999999998743321110 0011 232221 356899999
Q ss_pred Hhhccceeeeee-eEEee-cCccccceEEEEEcc--C--C---cEEEEEEcCC
Q 003054 262 ALSSTRFKGLTG-DYIFV-DGQLQSSAFEIINVN--N--G---ARGVGFWTPE 305 (852)
Q Consensus 262 al~~~~f~GltG-~v~f~-~G~~~~~~~~I~~~~--~--g---~~~vG~w~~~ 305 (852)
.|++++|.|.+| +|.|| +||. ...|+|+||+ . | ++.||.|++.
T Consensus 443 ~L~~v~F~~~~g~~v~Fd~~Gd~-~~~YdI~n~q~~~~~~~~~~v~VG~~~~~ 494 (510)
T cd06364 443 HLRHLNFTDNMGEQVRFDEGGDL-VGNYSIINWHLSPEDGSVVFKEVGYYNVY 494 (510)
T ss_pred HHHhcEEecCCCCEEEEecCCCC-ccceeEEEeeecCCCCcEEEEEEEEEcCC
Confidence 999999999987 68998 9997 5789999999 2 3 7899999864
No 22
>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=2.2e-32 Score=310.57 Aligned_cols=290 Identities=20% Similarity=0.283 Sum_probs=236.6
Q ss_pred hhhHHHHhcCCCCccEEeeecCCCCCCC-CCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHH
Q 003054 2 QTNFIIQLGNKSQVPILSFSATSPSLTS-IRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTD 80 (852)
Q Consensus 2 ~a~~v~~i~~~~~vP~Is~~ats~~lt~-~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~ 80 (852)
.+.+++++++.++||+|+++++++.|++ .++|||||+.|+|..|++|++++++++||++|++||+|++||++.++.|.+
T Consensus 117 ~s~ava~~~~~~~IP~Is~~sts~~Ls~~~~~~~ffRt~psd~~qa~ai~~ll~~~~W~~Vaii~~~~~yG~~~~~~~~~ 196 (458)
T cd06375 117 VSIQVANLLRLFQIPQISYASTSAKLSDKSRYDYFARTVPPDFYQAKAMAEILRFFNWTYVSTVASEGDYGETGIEAFEQ 196 (458)
T ss_pred HHHHHHHHhhhccccceeeccCChhhcccccCCCeEEecCCcHHHHHHHHHHHHHCCCeEEEEEEeCchHHHHHHHHHHH
Confidence 5778999999999999999999999997 578999999999999999999999999999999999999999999999999
Q ss_pred HHHhCCceeeeeeecCCCCChHHHHHHHHHhhc-CCceEEEEEeChhhHHHHHHHHHHcCCcccceEEEEcCcccccccc
Q 003054 81 ALQAIDTRVPYRSVISPLATDDQIEKELYKLFT-MQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRT 159 (852)
Q Consensus 81 ~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~-~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~~~~~~~~ 159 (852)
++++.|++|+..+.++...++.|+..++++|++ .++||||+.++..++..++++|+++|+. ++||++++|......
T Consensus 197 ~~~~~gi~i~~~~~i~~~~~~~d~~~~l~~l~~~~~a~vVvl~~~~~~~~~ll~~a~~~g~~---~~wigs~~~~~~~~~ 273 (458)
T cd06375 197 EARLRNICIATSEKVGRSADRKSYDSVIRKLLQKPNARVVVLFTRSEDARELLAAAKRLNAS---FTWVASDGWGAQESI 273 (458)
T ss_pred HHHHCCeeEEEEEEecCCCCHHHHHHHHHHHhccCCCEEEEEecChHHHHHHHHHHHHcCCc---EEEEEeccccccchh
Confidence 999999999998888766667899999999875 6999999999999999999999999985 789999999743221
Q ss_pred CCchhhcccceEEEEEecCCCChHHHHHH---------------HHHHHhccccCCCCcc----------------cccc
Q 003054 160 LEPSVIDSMQGVIGVGPHVPKTKALENFR---------------VRWKRNFLQENPSIVD----------------VELN 208 (852)
Q Consensus 160 ~~~~~~~~~~gv~~~~~~~~~~~~~~~F~---------------~~~~~~~~~~~~~~~~----------------~~~~ 208 (852)
.. ...+.++|++++.+.....+.+++|. +.|+..|+|..+.... ....
T Consensus 274 ~~-~~~~~~~G~i~~~~~~~~i~~f~~yl~~l~p~~~~~n~w~~e~w~~~f~c~~~~~~~~~~~C~~~~~~~~~~~~~~~ 352 (458)
T cd06375 274 VK-GSEDVAEGAITIELASHPIPDFDRYFQSLTPETNTRNPWFKDFWEQKFQCSLQNRDCANTTTNDKERLLDKVNYEQE 352 (458)
T ss_pred hh-ccchhhceEEEEEeccccchhHHHHHHhCCcCcCCCCcHHHHHHHHHcCCCCCCCCccCCCCCchhcccccCccccc
Confidence 22 13456899999998877766666554 4588888775432110 0124
Q ss_pred hhhHhHhhHHHHHHHHHHHhcccCcCccccccCCCCCCCccccccCChHHHH-HHhhcccee-----eeee-eEEee-cC
Q 003054 209 IFGLLAYDATRALAEAVEKAGITSFGFDKTNVSRNATDLEAFGISQNGPKLL-QALSSTRFK-----GLTG-DYIFV-DG 280 (852)
Q Consensus 209 ~~a~~aYDAv~~lA~Al~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~-~al~~~~f~-----GltG-~v~f~-~G 280 (852)
..+.+.||||+++|+||+++........ . ..|... ...++.+|+ +.|++++|. |.+| +|.|| +|
T Consensus 353 ~~~~~v~~AVyA~AhaLh~~l~~~c~~~----~---~~c~~~-~~~~~~~l~~~~L~~v~F~~~~~~~~~g~~v~Fd~nG 424 (458)
T cd06375 353 SKIMFVVNAVYAMAHALHNMQRDLCPNT----T---KLCDAM-KPLDGKKLYKEYLLNVSFTAPFRPDLADSEVKFDSQG 424 (458)
T ss_pred chHHHHHHHHHHHHHHHHHHHHhcCCCC----C---CCCCCC-CCCCHHHHHHHHHHhccccccccCCCCCCeeEECCCC
Confidence 5688999999999999999874332110 0 123332 145788999 599999999 9988 68998 99
Q ss_pred ccccceEEEEEcc---CC----cEEEEEEcC
Q 003054 281 QLQSSAFEIINVN---NG----ARGVGFWTP 304 (852)
Q Consensus 281 ~~~~~~~~I~~~~---~g----~~~vG~w~~ 304 (852)
|. ...|+|+|++ +| ++.||.|+.
T Consensus 425 d~-~~~YdI~n~q~~~~~~~~~~~~VG~w~~ 454 (458)
T cd06375 425 DG-LGRYNIFNYQRTGNSYGYRYVGVGAWAN 454 (458)
T ss_pred CC-CcceEEEEEEEcCCCCcEEEEEEEEEec
Confidence 97 5789999999 33 679999964
No 23
>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=6.3e-32 Score=304.40 Aligned_cols=280 Identities=18% Similarity=0.205 Sum_probs=227.4
Q ss_pred hhhHHHHhcCCCCccEEeeecCCCCCCC-CCCCceEeccCCchhHHHHHHHHHHHcCCcEEEE-EEEeCC-cccc---cH
Q 003054 2 QTNFIIQLGNKSQVPILSFSATSPSLTS-IRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVP-IYVDNQ-YGEE---MI 75 (852)
Q Consensus 2 ~a~~v~~i~~~~~vP~Is~~ats~~lt~-~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vai-i~~d~~-~G~~---~~ 75 (852)
++.+++++++.++||+|+++++++.+++ ..+||+||+.|++..++.+++++++++||+++++ +|.++. +|++ ..
T Consensus 86 ~~~~va~~a~~~~iP~Is~~a~~~~l~~~~~~~~~~R~~p~~~~~~~a~~~~~~~~~w~~va~ii~~~~~~~~~~~~~~~ 165 (405)
T cd06385 86 TASPVARFTTHWDVPLVTAGAPALGFGVKDEYATITRTGPTHKKLGEFVLHIHQHFGWRSHAMLIYSDNKVDDRPCYFAM 165 (405)
T ss_pred hHHHHHHHHhccCCcEEccccChhhcCCcccCcceEEecCchHHHHHHHHHHHHhCCCeEEEEEEEecCcccccchHHHH
Confidence 5788999999999999999999999987 6799999999999999999999999999999984 565444 3344 46
Q ss_pred HHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHcCCcccceEEEEcCcccc
Q 003054 76 PSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTN 155 (852)
Q Consensus 76 ~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~~~~ 155 (852)
+.+.+.+++.|++|+..+..+ .++.|+..+|++|++.. |+||++++..++..++++|+++||+.++|+||+++.+..
T Consensus 166 ~~l~~~~~~~gi~v~~~~~~~--~~~~d~~~~l~~ik~~~-~iii~~~~~~~~~~i~~~a~~~g~~~~~y~~i~~~~~~~ 242 (405)
T cd06385 166 EGLYMELKKNNITVVDLVFEE--DDLINYTTLLQDIKQKG-RVIYVCCSPDIFRRLMLQFWREGLPSEDYVFFYIDLFGA 242 (405)
T ss_pred HHHHHHHHhCCeEEEEeeccC--CchhhHHHHHHHHhhcc-eEEEEeCCHHHHHHHHHHHHHcCCCCCcEEEEEeecchh
Confidence 889999999999999876433 23679999999999755 999999999999999999999999999999999866542
Q ss_pred cccc------------CCchhhcccceEEEEEecCCCChHHHHHHHHHHHh----ccccCCCCcccccchhhHhHhhHHH
Q 003054 156 LLRT------------LEPSVIDSMQGVIGVGPHVPKTKALENFRVRWKRN----FLQENPSIVDVELNIFGLLAYDATR 219 (852)
Q Consensus 156 ~~~~------------~~~~~~~~~~gv~~~~~~~~~~~~~~~F~~~~~~~----~~~~~~~~~~~~~~~~a~~aYDAv~ 219 (852)
.... .+....+.+++++....+.+.++.+++|.++|+++ |+... ....|+.+++++||||+
T Consensus 243 ~~~~~~~~~~w~~~~~~~~~~~~a~~~v~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~---~~~~~~~~aa~~YDav~ 319 (405)
T cd06385 243 SLQGPDPKRPWYRGDADDAAAREAFQSVKILTYKEPQNPEYKEFLSDLKTDAKEMFNFTV---EDSLMNIIAGGFYDGVM 319 (405)
T ss_pred hccCCCCCCCCCCCCcccHHHHHhhheeEEEeCCCCCChhHHHHHHHHHHHhhccCCCcc---chhhHHHHHHHHHHHHH
Confidence 2211 11223456789988887777888899999999986 43310 01137789999999999
Q ss_pred HHHHHHHHhcccCcCccccccCCCCCCCccccccCChHHHHHHhhccceeeeeeeEEee-cCccccceEEEEEcc---CC
Q 003054 220 ALAEAVEKAGITSFGFDKTNVSRNATDLEAFGISQNGPKLLQALSSTRFKGLTGDYIFV-DGQLQSSAFEIINVN---NG 295 (852)
Q Consensus 220 ~lA~Al~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~al~~~~f~GltG~v~f~-~G~~~~~~~~I~~~~---~g 295 (852)
++|+|++++.... +.+.+|++|+++|++++|+|++|++.|| +|++ ...|.|++++ +|
T Consensus 320 l~a~Al~~~~~~~------------------~~~~~g~~i~~~l~~~~f~G~tG~v~fd~~G~r-~~~~~~~~~~~~~~g 380 (405)
T cd06385 320 LYAHALNETMAKG------------------GTRPPGTAITQRMWNRTFYGVTGFVKIDDNGDR-ETDFALWDMTDTESG 380 (405)
T ss_pred HHHHHHHHHHhcC------------------CCCCCHHHHHHHhhCceEeeceeEEEEcCCCCE-eceeEEEEccCCCCC
Confidence 9999999974221 1135789999999999999999999998 8998 4788888664 44
Q ss_pred -cEEEEEEcCCC
Q 003054 296 -ARGVGFWTPEK 306 (852)
Q Consensus 296 -~~~vG~w~~~~ 306 (852)
++.||+|+..+
T Consensus 381 ~~~~v~~~~~~~ 392 (405)
T cd06385 381 DFQVVSVYNGTQ 392 (405)
T ss_pred cEEEEEEEcccC
Confidence 99999998643
No 24
>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=1.3e-31 Score=301.92 Aligned_cols=270 Identities=18% Similarity=0.254 Sum_probs=224.5
Q ss_pred hhhHHHHhcCCCCccEEeeecCCCCCCC-CCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHH
Q 003054 2 QTNFIIQLGNKSQVPILSFSATSPSLTS-IRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTD 80 (852)
Q Consensus 2 ~a~~v~~i~~~~~vP~Is~~ats~~lt~-~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~ 80 (852)
++.++++++++++||+|+++++++.+++ ..+||+||+.|++..++.++++++++++|++|++|+.|++||.+..+.+.+
T Consensus 119 ~~~av~~i~~~~~vp~is~~~~~~~lt~~~~~~~~fr~~~~~~~~~~al~~~l~~~~~k~vaii~~~~~~g~~~~~~~~~ 198 (410)
T cd06363 119 LALTVAPLFSFFLIPQISYGASSEVLSNKELYPSFLRTVPSDKDQIEAMVQLLQEFGWNWVAFLGSDDEYGRDGLQLFSE 198 (410)
T ss_pred HHHHHHHHhcccccccccccccCccccccccCCCeeEecCCcHHHHHHHHHHHHHCCCcEEEEEEeCChhHHHHHHHHHH
Confidence 5788999999999999999999999986 578999999999999999999999999999999999999999999999999
Q ss_pred HHHhCCceeeeeeecCCC-CChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHcCCcccceEEEEcCcccccccc
Q 003054 81 ALQAIDTRVPYRSVISPL-ATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRT 159 (852)
Q Consensus 81 ~l~~~g~~v~~~~~~~~~-~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~~~~~~~~ 159 (852)
.+++.|++|+..+.++.. .++.|+.++|.+|++++||+|++++..+++..+++||+++||.. .+||++++|......
T Consensus 199 ~l~~~gi~i~~~~~~~~~~~~~~d~~~~l~~i~~~~~dvIil~~~~~~~~~il~qa~~~g~~~--~~~i~~~~~~~~~~~ 276 (410)
T cd06363 199 LIANTGICIAYQGLIPLDTDPETDYQQILKQINQTKVNVIVVFASRQPAEAFFNSVIQQNLTG--KVWIASEAWSLNDEL 276 (410)
T ss_pred HHHHCCeEEEEEEEecCCCchHHHHHHHHHHHhcCCCeEEEEEcChHHHHHHHHHHHhcCCCC--CEEEEeCcccccccc
Confidence 999999999998887653 24789999999999999999999999999999999999999944 479998877633222
Q ss_pred CCchhhcccceEEEEEecCCCChHHHHHHHHHHHhccccCCCCcccccchhhHhHhhHHHHHHHHHHHhcccCcCccccc
Q 003054 160 LEPSVIDSMQGVIGVGPHVPKTKALENFRVRWKRNFLQENPSIVDVELNIFGLLAYDATRALAEAVEKAGITSFGFDKTN 239 (852)
Q Consensus 160 ~~~~~~~~~~gv~~~~~~~~~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~a~~aYDAv~~lA~Al~~a~~~~~~~~~~~ 239 (852)
......+...+++++....+..+..++|+++ +++.+||||+++|+|++++.....
T Consensus 277 ~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~-------------------~~~~~YDaV~~~a~Al~~a~~~~~------ 331 (410)
T cd06363 277 PSLPGIRNIGTVLGVAQQTVTIPGFSDFIYS-------------------FAFSVYAAVYAVAHALHNVLQCGS------ 331 (410)
T ss_pred cCCccceeeccEEEEEeCCCCCccHHHHHHH-------------------HHHHHHHHHHHHHHHHHHHhCCCC------
Confidence 1111223455678877777777887777766 356799999999999999853211
Q ss_pred cCCCCCCCccccccCChHHHHHHhhccceeeeeeeEEee-cCccccceEEEEEcc-C----CcEEEEEEcCC
Q 003054 240 VSRNATDLEAFGISQNGPKLLQALSSTRFKGLTGDYIFV-DGQLQSSAFEIINVN-N----GARGVGFWTPE 305 (852)
Q Consensus 240 ~~~~~~~~~~~~~~~~g~~l~~al~~~~f~GltG~v~f~-~G~~~~~~~~I~~~~-~----g~~~vG~w~~~ 305 (852)
..|.. ..+.++++|+++|++++|+|++|++.|+ +|++ ...+.|++++ + +.+.||+|++.
T Consensus 332 -----~~~~~-~~~~~~~~l~~~L~~~~~~g~~g~i~fd~~G~~-~~~~~i~~~~~~~~~~~~~~vG~~~~~ 396 (410)
T cd06363 332 -----GGCPK-RVPVYPWQLLEELKKVNFTLLGQTVRFDENGDP-NFGYDIVVWWWDNSSGTFEEVGSYSFY 396 (410)
T ss_pred -----CCCCC-CCCCCHHHHHHHHhccEEecCCcEEEeCCCCCC-ccceEEEEEEEcCCceeEEEEEEEECC
Confidence 11111 1256789999999999999999999998 8996 4578899996 3 29999999874
No 25
>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=1.3e-31 Score=296.12 Aligned_cols=263 Identities=44% Similarity=0.793 Sum_probs=230.4
Q ss_pred hhhHHHHhcCCCCccEEeeecCCCCCCC-CCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHH
Q 003054 2 QTNFIIQLGNKSQVPILSFSATSPSLTS-IRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTD 80 (852)
Q Consensus 2 ~a~~v~~i~~~~~vP~Is~~ats~~lt~-~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~ 80 (852)
.+.++++++++++||+|+++++++.+++ ..+||+||+.|++..++.+++++++++||++|++||.|++||++..+.+.+
T Consensus 78 ~~~a~~~~~~~~~ip~i~~~~~~~~l~~~~~~~~~~r~~p~~~~~~~a~~~~~~~~~~~~v~ii~~~~~~g~~~~~~~~~ 157 (350)
T cd06366 78 VAEFVAEVANEWNVPVLSFAATSPSLSSRLQYPYFFRTTPSDSSQNPAIAALLKKFGWRRVATIYEDDDYGSGGLPDLVD 157 (350)
T ss_pred HHHHHHHHhhcCCeeEEeccCCCccccccccCCceEEcccchHhHHHHHHHHHHHCCCcEEEEEEEcCcccchhHHHHHH
Confidence 4678899999999999999999999954 578999999999999999999999999999999999999999999999999
Q ss_pred HHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHcCCcccceEEEEcCcccccc---
Q 003054 81 ALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLL--- 157 (852)
Q Consensus 81 ~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~~~~~~--- 157 (852)
.+++.|++|+....++.+.+..|+..+|++|++.+||+|++++...++..+++||+++||..++|+||.++.+...+
T Consensus 158 ~~~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~dvvi~~~~~~~~~~~~~~a~~~g~~~~~~~~i~~~~~~~~~~~~ 237 (350)
T cd06366 158 ALQEAGIEISYRAAFPPSANDDDITDALKKLKEKDSRVIVVHFSPDLARRVFCEAYKLGMMGKGYVWILTDWLSSNWWSS 237 (350)
T ss_pred HHHHcCCEEEEEeccCCCCChhHHHHHHHHHhcCCCeEEEEECChHHHHHHHHHHHHcCCcCCCEEEEECcchhhhhccC
Confidence 99999999999988875434689999999999999999999999999999999999999988899999998766443
Q ss_pred -ccCCchhhcccceEEEEEecCCC-ChHHHHHHHHHHHhccccCCCCcccccchhhHhHhhHHHHHHHHHHHhcccCcCc
Q 003054 158 -RTLEPSVIDSMQGVIGVGPHVPK-TKALENFRVRWKRNFLQENPSIVDVELNIFGLLAYDATRALAEAVEKAGITSFGF 235 (852)
Q Consensus 158 -~~~~~~~~~~~~gv~~~~~~~~~-~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~a~~aYDAv~~lA~Al~~a~~~~~~~ 235 (852)
........+.++|++++.++.++ ++..++|+++|+++++.+.+. ..+|+.+++.+|||+++
T Consensus 238 ~~~~~~~~~~~~~gv~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~--~~~p~~~a~~~YDav~~--------------- 300 (350)
T cd06366 238 SDCTDEEMLEAMQGVIGVRSYVPNSSMTLQEFTSRWRKRFGNENPE--LTEPSIYALYAYDAVWA--------------- 300 (350)
T ss_pred CCCChHHHHHhhceEEEEeecccccCccHHHHHHHHHHHhcccCcC--cCCCCcccchhhhheee---------------
Confidence 22233345678999999998887 888999999999999863111 11478899999999998
Q ss_pred cccccCCCCCCCccccccCChHHHHHHhhccceeeeeeeEEee-cCccccceEEEEEcc-CCcEEEEEEcCCCCccc
Q 003054 236 DKTNVSRNATDLEAFGISQNGPKLLQALSSTRFKGLTGDYIFV-DGQLQSSAFEIINVN-NGARGVGFWTPEKGLTQ 310 (852)
Q Consensus 236 ~~~~~~~~~~~~~~~~~~~~g~~l~~al~~~~f~GltG~v~f~-~G~~~~~~~~I~~~~-~g~~~vG~w~~~~g~~~ 310 (852)
+.+|+|++|++.|+ +|++....|.++++. ++++.||+|++..|+..
T Consensus 301 -----------------------------~~~~~G~~G~v~fd~~~~~~~~~~~~~~~~~~~~~~vg~~~~~~~~~~ 348 (350)
T cd06366 301 -----------------------------STNFNGLSGPVQFDGGRRLASPAFEIINIIGKGYRKIGFWSSESGLSV 348 (350)
T ss_pred -----------------------------eceEEeeeeeEEEcCCCccCCcceEEEEecCCceEEEEEEeCCCCccc
Confidence 24799999999998 888878899999999 77999999999888764
No 26
>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=3.8e-31 Score=297.10 Aligned_cols=283 Identities=14% Similarity=0.175 Sum_probs=225.8
Q ss_pred hhhHHHHhcCCCCccEEeeecCCCCCCC--CCCCceEeccCCchhHHHHHHHHHHHcCCc-EEEEEEEeCCccc----cc
Q 003054 2 QTNFIIQLGNKSQVPILSFSATSPSLTS--IRSPYFFRGSLNDSSQAGAITAIIKAFGWR-EAVPIYVDNQYGE----EM 74 (852)
Q Consensus 2 ~a~~v~~i~~~~~vP~Is~~ats~~lt~--~~~py~fR~~p~d~~~~~aia~~l~~~gw~-~vaii~~d~~~G~----~~ 74 (852)
.+.++++++++++||+|+++++++.+++ ..+||+||+.|++..++.++..++++++|+ ++++||.++.++. ..
T Consensus 85 ~~~av~~i~~~~~iP~Is~~at~~~ls~~~~~y~~~fR~~p~~~~~~~~~~~i~~~~~w~~~vaiiy~~~~~~~~~~~~~ 164 (399)
T cd06384 85 PTASVARFATHWRLPLITAGAPAFGFSNKTDEYRTTVRTGPSTTKLGEFVNHLHEHFNWTSRAALLYLDLKTDDRPHYFI 164 (399)
T ss_pred HHHHHHHHHhhcCCcEEeeccchhhhccccccCCceEEecCcHHHHHHHHHHHHHhCCCcEEEEEEEecCCccCCcceEe
Confidence 5788999999999999999999999986 378999999999999999988888999999 6889996543321 24
Q ss_pred HHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHcCCcccceEEEEcCccc
Q 003054 75 IPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMT 154 (852)
Q Consensus 75 ~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~~~ 154 (852)
.+.+.+.+++.|++|+....+. .++.|+.++|+++|+ ++|+|+++++..++..+++||+++||+.++|+||+.+.+.
T Consensus 165 ~~~~~~~~~~~gi~v~~~~~~~--~~~~d~~~~l~~ik~-~~~vIi~~~~~~~~~~i~~qa~~~g~~~~~y~~i~~d~~~ 241 (399)
T cd06384 165 SEGVFLALQEENANVSAHPYHI--EKNSDIIEIIQFIKQ-NGRIVYICGPLETFLEIMLQAQREGLTPGDYVFFYLDVFG 241 (399)
T ss_pred hHHHHHHHHhcCceEEEEEEec--cchhhHHHHHHHHhh-cccEEEEeCCchHHHHHHHHHHHcCCCCCcEEEEEehhcc
Confidence 6778888999999999876555 347899999999997 9999999999999999999999999999999999877644
Q ss_pred cccc-------------cCCchhhcccceEEEEEecCCCChHHHHHHHHHHHhccccCCCC-cccccchhhHhHhhHHHH
Q 003054 155 NLLR-------------TLEPSVIDSMQGVIGVGPHVPKTKALENFRVRWKRNFLQENPSI-VDVELNIFGLLAYDATRA 220 (852)
Q Consensus 155 ~~~~-------------~~~~~~~~~~~gv~~~~~~~~~~~~~~~F~~~~~~~~~~~~~~~-~~~~~~~~a~~aYDAv~~ 220 (852)
..+. .......+.+++++++..+.+.++.+++|.++|++++...+... .+...+.+++++|||+++
T Consensus 242 ~~~~~~~~~~~~~~~~~~~~~~~~~a~~~v~~~~~~~~~~~~~~~F~~~~~~~~~~~~~~~~~p~~~~~~aa~~YDav~l 321 (399)
T cd06384 242 ESLRVKSPRESYKQMNHSSWTVLKEAFKSVFVITYREPENPEYKEFQRELHARAKEDFGVELEPSLMNFIAGCFYDGVML 321 (399)
T ss_pred cccccCCCCccccCCCCcccHHHHHHHhheEEeecCCCCCchHHHHHHHHHHHHhhhcCCCcCcchHhhhhhhhHHHHHH
Confidence 2111 00122345788999999888888889999999998643211100 000137789999999999
Q ss_pred HHHHHHHhcccCcCccccccCCCCCCCccccccCChHHHHHHhhccceeeeeeeEEee-cCccccceEEEE---EccCC-
Q 003054 221 LAEAVEKAGITSFGFDKTNVSRNATDLEAFGISQNGPKLLQALSSTRFKGLTGDYIFV-DGQLQSSAFEII---NVNNG- 295 (852)
Q Consensus 221 lA~Al~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~al~~~~f~GltG~v~f~-~G~~~~~~~~I~---~~~~g- 295 (852)
+|.|++++.... +.+.+|.+|+++|++++|+|++|++.|+ +|++ ...|.++ ++++|
T Consensus 322 ~a~Al~~~~~~~------------------~~~~~g~~i~~~l~~~~f~GvtG~v~fd~~G~r-~~~~~~~~~~~~~~g~ 382 (399)
T cd06384 322 YAMALNETLAEG------------------GSQKDGLNITRKMQDRRFWGVTGLVSIDKNNDR-DIDFDLWAMTDHETGK 382 (399)
T ss_pred HHHHHHHHHhcC------------------CCCCCcHhHHHHHhCceeecceeEEEECCCCCc-ccceEEEEeecCCCCe
Confidence 999999984221 1245789999999999999999999998 9998 4566663 55544
Q ss_pred cEEEEEEcCCC
Q 003054 296 ARGVGFWTPEK 306 (852)
Q Consensus 296 ~~~vG~w~~~~ 306 (852)
+..+|+|+..+
T Consensus 383 ~~~v~~~~~~~ 393 (399)
T cd06384 383 YEVVAHYNGIT 393 (399)
T ss_pred EEEEEEEcCCC
Confidence 99999998743
No 27
>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=99.98 E-value=3.5e-31 Score=297.53 Aligned_cols=284 Identities=17% Similarity=0.238 Sum_probs=228.9
Q ss_pred hhhHHHHhcCCCCccEEeeecCCCCCCC-CCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeCCcc----cccHH
Q 003054 2 QTNFIIQLGNKSQVPILSFSATSPSLTS-IRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDNQYG----EEMIP 76 (852)
Q Consensus 2 ~a~~v~~i~~~~~vP~Is~~ats~~lt~-~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~~~G----~~~~~ 76 (852)
++.++++++++++||+|+++++++.+++ ..+||+||+.|++..++.+++++++++||++|++||.+++++ ....+
T Consensus 85 ~~~av~~~~~~~~ip~Is~~as~~~lt~~~~~~~~fr~~p~~~~~~~a~~~~~~~~~w~~vaii~~~~~~~~~~~~~~~~ 164 (396)
T cd06373 85 AAAPVARFAAHWNVPVLTAGAPAAGFSDKSEYSTLTRTGPSYTKLGEFVLALHEHFNWSRAALLYHDDKNDDRPCYFTLE 164 (396)
T ss_pred hhHHHHHHHhcCCCceECccCCccccccchhcCceeeccccHHHHHHHHHHHHHHcCCeEEEEEEECCCCCcchHHHHHH
Confidence 5788999999999999999999999987 678999999999999999999999999999999999887774 55788
Q ss_pred HHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHcCCcccceEEEEcCccccc
Q 003054 77 SLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNL 156 (852)
Q Consensus 77 ~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~~~~~ 156 (852)
.+.+++++.|++|+.. .+..+....|+.++|+++++.. |+||++++..++..+++||+++||+.++||||..+.....
T Consensus 165 ~~~~~~~~~g~~v~~~-~~~~~~~~~d~~~~l~~ik~~~-~vii~~~~~~~~~~~~~qa~~~g~~~~~yv~i~~~~~~~~ 242 (396)
T cd06373 165 GVYTVLKEENITVSDF-PFDEDKELDDYKELLRDISKKG-RVVIMCASPDTVREIMLAAHRLGLTSGEYVFFNIDLFGSS 242 (396)
T ss_pred HHHHHHhhcCceeeEE-eecCCccccCHHHHHHHHHhcC-cEEEEecCHHHHHHHHHHHHHcCCCCCcEEEEEEccchhh
Confidence 9999999999998754 3443211478999999999865 9999999999999999999999999999999987644321
Q ss_pred c-----------ccCCchhhcccceEEEEEecCCCChHHHHHHHHHHHhccccCC-CCcccccchhhHhHhhHHHHHHHH
Q 003054 157 L-----------RTLEPSVIDSMQGVIGVGPHVPKTKALENFRVRWKRNFLQENP-SIVDVELNIFGLLAYDATRALAEA 224 (852)
Q Consensus 157 ~-----------~~~~~~~~~~~~gv~~~~~~~~~~~~~~~F~~~~~~~~~~~~~-~~~~~~~~~~a~~aYDAv~~lA~A 224 (852)
. ........+..+|++++..+.++++..++|.++|+++...++. ...+..|+.+++++|||++++++|
T Consensus 243 ~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~~a~~~YDav~~~a~A 322 (396)
T cd06373 243 LYGGGPWWWERGDEDDEKAKEAYQALMTITLREPDNPEYKEFSLEVKERAKKKFNTTSDDSLVNFFAGAFYDAVLLYALA 322 (396)
T ss_pred hccCCCCcCCCCCcccHHHHHHHHHheEEecCCCCChHHHHHHHHHHHHhhhcCCCCcchhHHHHHHHHHHHHHHHHHHH
Confidence 1 0011223345678888888888888999999999986332211 111225788999999999999999
Q ss_pred HHHhcccCcCccccccCCCCCCCccccccCChHHHHHHhhccceeeeeeeEEee-cCccccceEEEEEcc---CC-cEEE
Q 003054 225 VEKAGITSFGFDKTNVSRNATDLEAFGISQNGPKLLQALSSTRFKGLTGDYIFV-DGQLQSSAFEIINVN---NG-ARGV 299 (852)
Q Consensus 225 l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~al~~~~f~GltG~v~f~-~G~~~~~~~~I~~~~---~g-~~~v 299 (852)
|+++.... +...+|++|+++|++++|+|++|++.|| +|++ ...|.|+++. +| ++.+
T Consensus 323 l~~~~~~~------------------~~~~~~~~i~~~l~~~~f~G~tG~v~fd~~G~~-~~~~~v~~~~~~~~g~~~~~ 383 (396)
T cd06373 323 LNETLAEG------------------GDPRDGTNITRRMWNRTFEGITGNVSIDENGDR-ESDFSLWDMTDTETGTFEVV 383 (396)
T ss_pred HHHHHhcc------------------CCCCChHHHHHHhcCCceecccCceEeecCCcc-cceeeeeeccCCCCceEEEE
Confidence 99974221 1135789999999999999999999998 8998 5778887763 45 8899
Q ss_pred EEEcCCC
Q 003054 300 GFWTPEK 306 (852)
Q Consensus 300 G~w~~~~ 306 (852)
|.+++.+
T Consensus 384 ~~~~~~~ 390 (396)
T cd06373 384 ANYNGSN 390 (396)
T ss_pred eeccccc
Confidence 9998743
No 28
>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=99.98 E-value=1e-30 Score=291.09 Aligned_cols=278 Identities=19% Similarity=0.245 Sum_probs=219.8
Q ss_pred hhhHHHHhcCCCCccEEeeecCCCCCCC-CCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHH
Q 003054 2 QTNFIIQLGNKSQVPILSFSATSPSLTS-IRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTD 80 (852)
Q Consensus 2 ~a~~v~~i~~~~~vP~Is~~ats~~lt~-~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~ 80 (852)
.+.++++++++++||+|++++++|.+++ ..+|+|+|+.|++ +.++++++++++|++|++||++++||.+..+.+.+
T Consensus 78 ~~~a~a~va~~~~iP~Is~~a~~~~lt~~~~y~~f~r~~~~~---~~~~~~~~~~~~w~~vaii~~~~~~~~~~~~~l~~ 154 (382)
T cd06371 78 YCEAAALLAKEWDKALFSWGCVNYELDDVRSYPTFARTLPSP---SRVLFTVLRYFRWAHVAIVSSPQDIWVETAQKLAS 154 (382)
T ss_pred HHHHHHHHHHhcCceEEecccCchhhcCcccCCCceecCCCc---HHHHHHHHHHCCCeEEEEEEecccchHHHHHHHHH
Confidence 5789999999999999999999999997 6789999999886 56788999999999999999999999999999999
Q ss_pred HHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCC-ceEEEEEeCh-----hhHHHHHHHHHHcCCcccceEEEEcCccc
Q 003054 81 ALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQ-TRVFILHMLP-----SLGSRIFEKANEIGLMNKGCVWIMTDGMT 154 (852)
Q Consensus 81 ~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~-~~viv~~~~~-----~~~~~i~~~a~~~G~~~~~~vwi~~~~~~ 154 (852)
.+++.|++|+....++. ++.|+.++|++||+++ +||||++++. .++..+++||+++||+..+|+||++++..
T Consensus 155 ~l~~~gi~v~~~~~~~~--~~~d~~~~L~~lk~~~~~~viv~~~~~~~~~~~~~~~i~~qa~~~Gm~~~~y~~i~~d~~~ 232 (382)
T cd06371 155 ALRAHGLPVGLVTSMGP--DEKGAREALKKVRSADRVRVVIMCMHSVLIGGEEQRLLLETALEMGMTDGRYVFIPYDTLL 232 (382)
T ss_pred HHHHCCCcEEEEEEecC--CHHHHHHHHHHHhcCCCcEEEEEEeeccccCcHHHHHHHHHHHHcCCcCCcEEEEEecccc
Confidence 99999999998887774 4789999999999988 6999998876 67889999999999999999999998643
Q ss_pred ccc-------ccC--CchhhcccceEEEEEecCCCChHHHHHHHHHHHhccccCCC-CcccccchhhHhHhhHHHHHHHH
Q 003054 155 NLL-------RTL--EPSVIDSMQGVIGVGPHVPKTKALENFRVRWKRNFLQENPS-IVDVELNIFGLLAYDATRALAEA 224 (852)
Q Consensus 155 ~~~-------~~~--~~~~~~~~~gv~~~~~~~~~~~~~~~F~~~~~~~~~~~~~~-~~~~~~~~~a~~aYDAv~~lA~A 224 (852)
... ... +......+++++++..+.+..+..++|.++|+... .|. .....++.+++++|||++++|+|
T Consensus 233 ~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~f~~~~~~~~---~~~~~~~~~~~~~~~~~YDav~~~a~A 309 (382)
T cd06371 233 YSLPYRNVSYPALRNNSKLRRAYDAVLTITMDSGEQSFYEAFRAAQERGE---IPSDLEPEQVSPLFGTIYNSIYLLAHA 309 (382)
T ss_pred ccCCCCCccccCCCCCHHHHHHhHhhEEEEecCCCCcHHHHHHHHHhcCC---CCCCCCccccchhHHHHHHHHHHHHHH
Confidence 111 100 12222467888888776555555555555543211 110 01113456777999999999999
Q ss_pred HHHhcccCcCccccccCCCCCCCccccccCChHHHHHHhhccceeeeeeeEEee-cCccccceEEEEEcc-CCcEEEEE-
Q 003054 225 VEKAGITSFGFDKTNVSRNATDLEAFGISQNGPKLLQALSSTRFKGLTGDYIFV-DGQLQSSAFEIINVN-NGARGVGF- 301 (852)
Q Consensus 225 l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~al~~~~f~GltG~v~f~-~G~~~~~~~~I~~~~-~g~~~vG~- 301 (852)
+++++... ...+|.+|+++|++++|+|++|++.|| +|++ .+.|.|+++. +|+|-+-.
T Consensus 310 l~~a~~~g-------------------~~~d~~~l~~~l~~~~f~GvtG~v~fd~~g~~-~~~~~v~~~~~~~~~~~~~~ 369 (382)
T cd06371 310 VENARAAG-------------------GGVSGANLAQHTRNLEFQGFNQRLRTDSGGGG-QAPYVVLDTDGKGDQLYPTY 369 (382)
T ss_pred HHHHHHhC-------------------CCccHHHHHHHHhCccccccceEEEecCCCCc-ccceEEEecCCCCCeeeeeE
Confidence 99997321 135689999999999999999999998 8887 7999999999 77554433
Q ss_pred -EcCCCC
Q 003054 302 -WTPEKG 307 (852)
Q Consensus 302 -w~~~~g 307 (852)
+++++|
T Consensus 370 ~~~~~~~ 376 (382)
T cd06371 370 TLDPSTG 376 (382)
T ss_pred EeccccC
Confidence 344444
No 29
>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=99.97 E-value=9.2e-31 Score=286.96 Aligned_cols=277 Identities=17% Similarity=0.225 Sum_probs=213.9
Q ss_pred hhHHHHhcCCCCccEEeeecCCC-CCCC-CCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHH
Q 003054 3 TNFIIQLGNKSQVPILSFSATSP-SLTS-IRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTD 80 (852)
Q Consensus 3 a~~v~~i~~~~~vP~Is~~ats~-~lt~-~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~ 80 (852)
|+.++.++++++||+|+++++++ .+++ ..+|||+|+.|++..|++|+++++++|+|++|++||++++.+....+.+++
T Consensus 78 a~~~s~~~~~~~vP~is~~~~s~~~ls~~~~~p~flr~~Psd~~q~~Ai~~Ii~~f~W~~v~iV~~~~~g~~~~~~~l~~ 157 (362)
T cd06378 78 AQILDFISAQTFLPILGIHGGSSMIMAAKDSGSTFLQFGPSIEQQAAVMLKIMEEYDWHAFSVVTSRFPGYDDFVSAVRT 157 (362)
T ss_pred chhhhhhhhceeccEEEecccccccccCCCCCceEEEeCCCHHHHHHHHHHHHHHCCCeEEEEEEEcCCCHHHHHHHHHH
Confidence 46788899999999999987766 5555 678999999999999999999999999999999999998877777778877
Q ss_pred HHHhCCceeeeeeecCCCCC-hHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHcCCcccceEEEEcCcccccccc
Q 003054 81 ALQAIDTRVPYRSVISPLAT-DDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRT 159 (852)
Q Consensus 81 ~l~~~g~~v~~~~~~~~~~~-~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~~~~~~~~ 159 (852)
.+++.+.++.....++...+ +.++..++.+++..+++|||++|+.+++..++++|+++||++++|+||+++......+.
T Consensus 158 ~~~~~~~~~~i~~~~~~~~~~~~~~~~~l~~lk~~~arViVl~~s~~~a~~if~~A~~~gm~g~~yvWI~t~~~~~~~~~ 237 (362)
T cd06378 158 TVDNSFVGWELQSVLTLDMSDDDGDARTQRQLKKLESQVILLYCSKEEAEYIFRAARSAGLTGPGYVWIVPSLVLGNTDL 237 (362)
T ss_pred HHhhcccceeEEEEEeeccCCCcchHHHHHHHHhcCCCEEEEECCHHHHHHHHHHHHHcCCcCCCeEEEecccccCCCcc
Confidence 77766555443333332222 23478899999999999999999999999999999999999999999999987655321
Q ss_pred CCchhhcccceEEEEEecCCCChHHHHHHHHHHHhccccCCCCcccccchhhHhHhhHHHHHHHHHHHhcccCcCccccc
Q 003054 160 LEPSVIDSMQGVIGVGPHVPKTKALENFRVRWKRNFLQENPSIVDVELNIFGLLAYDATRALAEAVEKAGITSFGFDKTN 239 (852)
Q Consensus 160 ~~~~~~~~~~gv~~~~~~~~~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~a~~aYDAv~~lA~Al~~a~~~~~~~~~~~ 239 (852)
.. .+...|++++.. ++|++ .+.+..||||+++|+|++.+........
T Consensus 238 ~~---~~~~~G~i~v~~------------~~w~~---------------~~~a~~~DaV~vva~Al~~l~~~~~~~~--- 284 (362)
T cd06378 238 GP---SEFPVGLISVSY------------DGWRY---------------SLRARVRDGVAIIATGASAMLRQHGFIP--- 284 (362)
T ss_pred cc---ccCCcceEeecc------------ccccc---------------cHHHHHHHHHHHHHHHHHHHHhccCCCC---
Confidence 11 123467776552 22321 1355789999999999997643211111
Q ss_pred cCCCCCCCcc-cc-ccCChHHHHHHhhccceeeeeeeEEee-cCccccceEEEEEcc-C-CcEEEEEEcCCCCcccccCC
Q 003054 240 VSRNATDLEA-FG-ISQNGPKLLQALSSTRFKGLTGDYIFV-DGQLQSSAFEIINVN-N-GARGVGFWTPEKGLTQKLSS 314 (852)
Q Consensus 240 ~~~~~~~~~~-~~-~~~~g~~l~~al~~~~f~GltG~v~f~-~G~~~~~~~~I~~~~-~-g~~~vG~w~~~~g~~~~~~~ 314 (852)
....+|.. .. .|..|..|+++|++++|+|+ +++|+ +|++.++.|+|+|++ + |+++||+|++ .+|.
T Consensus 285 --~~~~~C~~~~~~~~~~G~~l~~~l~~v~~~G~--~i~F~~~G~r~~~~ldIinl~~~~g~~kVG~W~~-~~L~----- 354 (362)
T cd06378 285 --EAKGSCYGQAEKRDLPPNTLHRYMMNVTWEGR--DLSFTEDGYLVNPKLVVISLNKERVWEEVGKWEN-GSLR----- 354 (362)
T ss_pred --CCCCCcCCCCCCCCCchHHHHHHhhcceECCC--ceeECCCCeEccceEEEEEecCCCCceEEEEEcC-CeEE-----
Confidence 11123322 22 37889999999999999997 99997 999999999999999 4 8999999994 3443
Q ss_pred CccccCCccceEeCC
Q 003054 315 NSTTKSKLKPIIWPG 329 (852)
Q Consensus 315 ~~~~~~~~~~i~Wpg 329 (852)
++.+.|||
T Consensus 355 -------~~~~~wp~ 362 (362)
T cd06378 355 -------LKYPVWPR 362 (362)
T ss_pred -------EecCCCCC
Confidence 57789996
No 30
>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=99.97 E-value=4.9e-30 Score=287.95 Aligned_cols=287 Identities=17% Similarity=0.239 Sum_probs=241.9
Q ss_pred hhhHHHHhcCCCCccEEeeecCCCCCCC-CCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeCC-cccccHHHHH
Q 003054 2 QTNFIIQLGNKSQVPILSFSATSPSLTS-IRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDNQ-YGEEMIPSLT 79 (852)
Q Consensus 2 ~a~~v~~i~~~~~vP~Is~~ats~~lt~-~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~~-~G~~~~~~l~ 79 (852)
++.++++++++++||+|+++++++.+++ ..+||+||+.|++..++.+++++++++||+++++++.++. ||....+.+.
T Consensus 80 ~~~a~~~~~~~~~ip~Is~~~~~~~~~~~~~~~~~fr~~~~~~~~~~a~~~~l~~~~~~~v~ii~~~~~~~g~~~~~~~~ 159 (389)
T cd06352 80 ACAPVARLAAHWNIPMISWGCVALSLSDKSEYPTLTRTLPPARKLGEAVLALLRWFNWHVAVVVYSDDSENCFFTLEALE 159 (389)
T ss_pred HHHHHHHHHhcCCCCEecccccccccCccccCCceeecCCcHHHHHHHHHHHHHHcCceEEEEEEecCCccHHHHHHHHH
Confidence 5788999999999999999999999986 4789999999999999999999999999999999998888 9999999999
Q ss_pred HHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHcCCcccceEEEEcCccccccc-
Q 003054 80 DALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLR- 158 (852)
Q Consensus 80 ~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~~~~~~~- 158 (852)
+++++.|++|+....++...+..|+..+|+++++.+ |+|++++.++++..+++|++++|+...+|+||+++.+.....
T Consensus 160 ~~~~~~G~~v~~~~~~~~~~~~~d~~~~l~~i~~~~-~vii~~~~~~~~~~~l~q~~~~g~~~~~~~~i~~~~~~~~~~~ 238 (389)
T cd06352 160 AALREFNLTVSHVVFMEDNSGAEDLLEILQDIKRRS-RIIIMCGSSEDVRELLLAAHDLGLTSGDYVFILIDLFNYSLPY 238 (389)
T ss_pred HHHHhcCCeEEEEEEecCCccchhHHHHHHHhhhcc-eEEEEECCHHHHHHHHHHHHHcCCCCCcEEEEEEehhcccccc
Confidence 999999999999888875322578999999999887 999999999999999999999999888899999877664421
Q ss_pred ----------cCCchhhcccceEEEEEecCCCChHHHHHHHHHHHhccccCCC--CcccccchhhHhHhhHHHHHHHHHH
Q 003054 159 ----------TLEPSVIDSMQGVIGVGPHVPKTKALENFRVRWKRNFLQENPS--IVDVELNIFGLLAYDATRALAEAVE 226 (852)
Q Consensus 159 ----------~~~~~~~~~~~gv~~~~~~~~~~~~~~~F~~~~~~~~~~~~~~--~~~~~~~~~a~~aYDAv~~lA~Al~ 226 (852)
.......+.++|++++.++.+.++..++|+++|+++++..... .....|+.+++.+|||++++++|++
T Consensus 239 ~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~a~~~YDav~~~a~Al~ 318 (389)
T cd06352 239 QNSYPWERGDGDDEKAKEAYDAVLTITLRPPDNPEYEEFSEEVKEAAKRPPFNTDAEPEQVSPYAGYLYDAVLLYAHALN 318 (389)
T ss_pred CCCCCcccCCcccHHHHHHHHhheEEEecCCCCchHHHHHHHHHHHHhcccCccCCCccccchhhhhHHHHHHHHHHHHH
Confidence 1122234567899998888888889999999999999752100 0122568899999999999999999
Q ss_pred HhcccCcCccccccCCCCCCCccccccCChHHHHHHhhccceeeeeeeEEee-cCccccceEEEEEcc-C-C-cEEEEEE
Q 003054 227 KAGITSFGFDKTNVSRNATDLEAFGISQNGPKLLQALSSTRFKGLTGDYIFV-DGQLQSSAFEIINVN-N-G-ARGVGFW 302 (852)
Q Consensus 227 ~a~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~al~~~~f~GltG~v~f~-~G~~~~~~~~I~~~~-~-g-~~~vG~w 302 (852)
+++.... .+.++.++.++|++++|+|++|++.|+ +|++ ...|.|++++ + + +..++.+
T Consensus 319 ~~~~~~~------------------~~~~~~~v~~~l~~~~f~g~~G~v~fd~~G~~-~~~~~v~~~~~~~~~~~~~~~~ 379 (389)
T cd06352 319 ETLAEGG------------------DYNGGLIITRRMWNRTFSGITGPVTIDENGDR-EGDYSLLDLDSTGGQLEVVYLY 379 (389)
T ss_pred HHHHhCC------------------CCCchHHHHHHhcCcEEEeeeeeEEEcCCCCe-eeeEEEEEecCCCceEEEEEec
Confidence 9864321 035678999999999999999999998 9998 5789999999 4 3 8888888
Q ss_pred cCCCCc
Q 003054 303 TPEKGL 308 (852)
Q Consensus 303 ~~~~g~ 308 (852)
.+.++.
T Consensus 380 ~~~~~~ 385 (389)
T cd06352 380 DTSSGG 385 (389)
T ss_pred ccccee
Confidence 776653
No 31
>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=99.97 E-value=5.1e-30 Score=288.34 Aligned_cols=271 Identities=14% Similarity=0.235 Sum_probs=220.1
Q ss_pred hHHHHhcCCCCccEEeeecCCCCCCC-CCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHHHH
Q 003054 4 NFIIQLGNKSQVPILSFSATSPSLTS-IRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTDAL 82 (852)
Q Consensus 4 ~~v~~i~~~~~vP~Is~~ats~~lt~-~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~~l 82 (852)
.+++.++++++||+|+++++++.+++ ..+|+|||+.|++..++.+++++++++||++|++||.+++||++..+.|++.+
T Consensus 81 ~~~a~i~~~~~iP~Is~~a~~~~l~~~~~~~~f~r~~~~~~~~~~a~~~~~~~~~w~~vaii~~~~~~g~~~~~~~~~~~ 160 (404)
T cd06370 81 TTEARLAAAWNLPMISYKCDEEPVSDKSKYPTFARTVPPSIQVVKSVIALLKHFNWNKFSVVYENDSKYSSVFETLKEEA 160 (404)
T ss_pred HHHHHHHhhcCCcEEecccCCccccccccCCCeEEcCCCHHHHHHHHHHHHHHCCCcEEEEEEecCcccHHHHHHHHHHH
Confidence 45678999999999999999999987 57899999999999999999999999999999999999999999999999999
Q ss_pred HhCCceeeeeeecCCCC-----ChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHcCCc-ccceEEEEcCcccc-
Q 003054 83 QAIDTRVPYRSVISPLA-----TDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEIGLM-NKGCVWIMTDGMTN- 155 (852)
Q Consensus 83 ~~~g~~v~~~~~~~~~~-----~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~G~~-~~~~vwi~~~~~~~- 155 (852)
++.|++|+..+.++... ...++...|+++++. ++++|+++...++..+++||+++||+ ..+|+||+++....
T Consensus 161 ~~~g~~iv~~~~~~~~~~~~~~~~~~~~~~l~~~~~~-~~~~v~~~~~~~~~~~l~qa~~~g~~~~~~y~~i~~~~~~~~ 239 (404)
T cd06370 161 ELRNITISHVEYYADFYPPDPIMDNPFEDIIQRTKET-TRIYVFIGEANELRQFLMSMLDEGLLESGDYMVLGVDIEYYD 239 (404)
T ss_pred HHcCCEEEEEEEECCCCCchhhhHHHHHHHHHhccCC-CEEEEEEcCHHHHHHHHHHHHHcCCCCCCcEEEEEEchhhcc
Confidence 99999999998887541 247899999998865 67777778888999999999999998 67899998653110
Q ss_pred -----c---------cc---cCCchhhcccceEEEEEecCCCChHHHHHHHHHHHhcccc-CCC-----CcccccchhhH
Q 003054 156 -----L---------LR---TLEPSVIDSMQGVIGVGPHVPKTKALENFRVRWKRNFLQE-NPS-----IVDVELNIFGL 212 (852)
Q Consensus 156 -----~---------~~---~~~~~~~~~~~gv~~~~~~~~~~~~~~~F~~~~~~~~~~~-~~~-----~~~~~~~~~a~ 212 (852)
. .. .......+.++|++++.+..+ ++..++|.++|++++... ++. .....|+.+++
T Consensus 240 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~aa 318 (404)
T cd06370 240 RDSQDYYSLHRGFQSREYNRSDDEKALEAMKSVLIIVPTPV-SPDYDSFSIFVRKYNLEPPFNGDLGESELVLEIDIEAA 318 (404)
T ss_pred ccchhhhhhhhhhccccccccccHHHHHHhHheEEEecCCC-CchHHHHHHHHHHhccCCCCcccccccccccccceeee
Confidence 0 00 111234456889988876655 777899999999876431 110 01225788999
Q ss_pred hHhhHHHHHHHHHHHhcccCcCccccccCCCCCCCccccccCChHHHHHHhhccceeeeee-eEEee-cCccccceEEEE
Q 003054 213 LAYDATRALAEAVEKAGITSFGFDKTNVSRNATDLEAFGISQNGPKLLQALSSTRFKGLTG-DYIFV-DGQLQSSAFEII 290 (852)
Q Consensus 213 ~aYDAv~~lA~Al~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~al~~~~f~GltG-~v~f~-~G~~~~~~~~I~ 290 (852)
++|||++++|+|++++..... ...+|++|+++|++++|+|++| ++.|| +|++ ...|.|+
T Consensus 319 ~~yDAv~~~a~Al~~~~~~~~------------------~~~~g~~i~~~l~~~~f~GvtG~~v~fd~~G~~-~~~y~v~ 379 (404)
T cd06370 319 YLYDAVMLYAKALDETLLEGG------------------DIYNGTAIVSHILNRTYRSITGFDMYIDENGDA-EGNYSVL 379 (404)
T ss_pred hhHHHHHHHHHHHHHHHHhcC------------------CCCCHHHHHHHHhCcccccccCceEEEcCCCCc-ccceEEE
Confidence 999999999999999842210 1357899999999999999999 89998 9998 5889999
Q ss_pred EccCC
Q 003054 291 NVNNG 295 (852)
Q Consensus 291 ~~~~g 295 (852)
++++|
T Consensus 380 ~~~~~ 384 (404)
T cd06370 380 ALQPI 384 (404)
T ss_pred Eeccc
Confidence 99855
No 32
>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=99.97 E-value=8.8e-30 Score=285.69 Aligned_cols=283 Identities=15% Similarity=0.220 Sum_probs=220.2
Q ss_pred hhhHHHHhcCCCCccEEeeecCCCCCCC-CCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeC---Cccc--ccH
Q 003054 2 QTNFIIQLGNKSQVPILSFSATSPSLTS-IRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDN---QYGE--EMI 75 (852)
Q Consensus 2 ~a~~v~~i~~~~~vP~Is~~ats~~lt~-~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~---~~G~--~~~ 75 (852)
++.+++++++.++||+|+++++++.+++ ..+|+++|+.|++..++.+++++++++||++|++||.++ .||+ ...
T Consensus 80 ~~~av~~va~~~~iP~is~~s~s~~ls~~~~~~~~~r~~p~~~~~~~a~~~l~~~~~w~~vaii~~~~~~~~~~~~~~~~ 159 (391)
T cd06372 80 AAEVTGLLASQWNIPMFGFVGQTAKLDNRFLYDTYVKLVPPKQKIGEVLQKSLQHFGWKHIGLFGGSSRDSSWDEVDELW 159 (391)
T ss_pred HHHHHHHHHhccCccEEEeecCCccccccccCCceEEecCchhhHHHHHHHHHHHCCCeEEEEEEeccccchhhhHHHHH
Confidence 5778999999999999999999999986 568999999999999999999999999999999998543 3442 234
Q ss_pred HHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHcCCcccceEEEEcCc---
Q 003054 76 PSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDG--- 152 (852)
Q Consensus 76 ~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~--- 152 (852)
+.+.+.++ .+++++..+.++.+ +.|+...+.+.++.++|+||++++.+++..+++||+++||+.++|+||.+..
T Consensus 160 ~~~~~~~~-~~~~i~~~~~~~~~--~~d~~~~~l~~~~~~~~vii~~~~~~~~~~i~~~a~~~g~~~~~y~~i~~~~~~~ 236 (391)
T cd06372 160 KAVENQLK-FHFNITATVRYSSS--NPDLLQEKLRYISSVARVIILICSSEDAKAILQAAEKLGLMKGKFVFFLLQQFED 236 (391)
T ss_pred HHHHHHHh-hCEEEEEEEecCCC--ChHHHHHHHHhhhccceEEEEEcChHHHHHHHHHHHHcCCCCCCEEEEEehhhcC
Confidence 44555554 67888888877643 6788888877778999999999999999999999999999888899999532
Q ss_pred --ccccccc-CCchhhcccceEEEEEecCCC-ChHHHHHHHHHHHhcccc-CCC--CcccccchhhHhHhhHHHHHHHHH
Q 003054 153 --MTNLLRT-LEPSVIDSMQGVIGVGPHVPK-TKALENFRVRWKRNFLQE-NPS--IVDVELNIFGLLAYDATRALAEAV 225 (852)
Q Consensus 153 --~~~~~~~-~~~~~~~~~~gv~~~~~~~~~-~~~~~~F~~~~~~~~~~~-~~~--~~~~~~~~~a~~aYDAv~~lA~Al 225 (852)
|...... ......+..+|++++.+..+. .+..++|.++|+++++.. +.. ......+.+++++||||+++|+|+
T Consensus 237 ~~w~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~f~~~~~~~~~~~p~~~~~~~~~~~~~~a~~~yDav~~~A~Al 316 (391)
T cd06372 237 NFWKEVLTDDQVQHLPKVYESVFLIAPSSYGGYSGGYEFRKQVYQKLKRPPFQSSLSSEEQVSPYSAYLHDAVLLYALAV 316 (391)
T ss_pred ccccccCCCcchHHHHHHHhhEEEEecCCCCCCcchhHHHHHHHHHHhcCCccccccccccchHHHHHHHHHHHHHHHHH
Confidence 2211110 111133457888888776543 356778999988887642 100 011134788999999999999999
Q ss_pred HHhcccCcCccccccCCCCCCCccccccCChHHHHHHhh---ccceeeeeeeEEee-cCccccceEEEEEcc-CC----c
Q 003054 226 EKAGITSFGFDKTNVSRNATDLEAFGISQNGPKLLQALS---STRFKGLTGDYIFV-DGQLQSSAFEIINVN-NG----A 296 (852)
Q Consensus 226 ~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~al~---~~~f~GltG~v~f~-~G~~~~~~~~I~~~~-~g----~ 296 (852)
+++.... ..+.+|..|+++|+ +++|+|++|+|.|+ +|++ .+.|.|++++ +| .
T Consensus 317 ~~~~~~g------------------~~~~~g~~l~~~l~~~~~~~f~G~tG~v~fd~~G~r-~~~y~i~~~~~~~~~~~~ 377 (391)
T cd06372 317 KEMLKAG------------------KDFRNGRQLVSTLRGANQVELQGITGLVLLDEQGKR-QMDYSVYALQKSGNSSLF 377 (391)
T ss_pred HHHHhcC------------------CCCCCHHHHHHHHhhccCceEeccceeEEECCCCCc-ceeEEEEeccccCCccce
Confidence 9975321 11457899999999 68999999999998 8998 7899999998 22 8
Q ss_pred EEEEEEcCCC
Q 003054 297 RGVGFWTPEK 306 (852)
Q Consensus 297 ~~vG~w~~~~ 306 (852)
+.||.|+..+
T Consensus 378 ~~vg~~~~~~ 387 (391)
T cd06372 378 LPFLHYDSHQ 387 (391)
T ss_pred eeEEEecchh
Confidence 8999998743
No 33
>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=99.97 E-value=4.8e-29 Score=275.50 Aligned_cols=279 Identities=32% Similarity=0.470 Sum_probs=227.3
Q ss_pred hhhHHHHhcCCCCccEEeeecCCCCCCC--CCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHH
Q 003054 2 QTNFIIQLGNKSQVPILSFSATSPSLTS--IRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLT 79 (852)
Q Consensus 2 ~a~~v~~i~~~~~vP~Is~~ats~~lt~--~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~ 79 (852)
.+.+++.+++.++||+|+++++++.+++ ..+|+++|+.|++..+++++++++++++|++|++||+++++|.+..+.+.
T Consensus 63 ~~~~~~~~~~~~~ip~is~~~~~~~ls~~~~~~~~~~r~~p~~~~~~~a~~~~l~~~~w~~v~vv~~~~~~~~~~~~~~~ 142 (348)
T PF01094_consen 63 SAEAVASLASEWNIPQISPGSTSPSLSDRKTRYPTFFRTVPSDSSQARALVDLLKHFGWTRVSVVYSDDDYGNSLADSFQ 142 (348)
T ss_dssp HHHHHHHHHHHTT-EEEESSGGSGGGGSTTTTTTTEEESSB-HHHHHHHHHHHHHHTTSSEEEEEEESSHHHHHHHHHHH
T ss_pred ccchhheeecccccceeeccccccccccchhhccccccccccHHHHHHHHHHhhhcCCCceeeeeccccccccccchhhh
Confidence 4678999999999999999999999987 48999999999999999999999999999999999999999999999999
Q ss_pred HHHHhCCceeeee-eecCCCCChHHHHHHHHHhhc--CCceEEEEEeChhhHHHHHHHHHHcCCcccceEEEEcCccccc
Q 003054 80 DALQAIDTRVPYR-SVISPLATDDQIEKELYKLFT--MQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNL 156 (852)
Q Consensus 80 ~~l~~~g~~v~~~-~~~~~~~~~~d~~~~l~~l~~--~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~~~~~ 156 (852)
+.+++.++.+... ...... ..++...+.+++. .++++|++++...++..++++|.++||..++|+||+++.+...
T Consensus 143 ~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~l~~~~~~~rvvil~~~~~~~~~~l~~a~~~~~~~~~~~~i~~~~~~~~ 220 (348)
T PF01094_consen 143 DLLRERGGICVAFISVVISS--DSDAEELLKKLKEIKSGARVVILCSSPEDARQFLEAAYELGMTSGDYVWILTDLDNSS 220 (348)
T ss_dssp HHHHHHTTCEEEEEEEEETT--TSHHHHHHHHHHHHTTTTSEEEEESBHHHHHHHHHHHHHTTTSSTTSEEEEETTTTTT
T ss_pred hhhcccccceeccccccccc--ccchhhhhhhhhhccccceeeeeecccccccccccchhhhhccccceeEEeecccccc
Confidence 9999966544433 333322 3445555555555 9999999999999999999999999999999999999987755
Q ss_pred cccCCchhhcccceEEEEEecCCCChHHHHHHHHHHHhccccCCCCcccccchhhHhHhhHHHHHHHHHHHhcccCcCcc
Q 003054 157 LRTLEPSVIDSMQGVIGVGPHVPKTKALENFRVRWKRNFLQENPSIVDVELNIFGLLAYDATRALAEAVEKAGITSFGFD 236 (852)
Q Consensus 157 ~~~~~~~~~~~~~gv~~~~~~~~~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~a~~aYDAv~~lA~Al~~a~~~~~~~~ 236 (852)
.............|+++++...+..+.+++|.++|++.............++.+++++|||++++|+|++++........
T Consensus 221 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~yDAv~~~a~al~~~~~~~~~~~ 300 (348)
T PF01094_consen 221 FWQNNEDFREAFQGVLGFTPPPPSSPEFEDFMKKWKESNNQSSTSGSDQEPSPYAAYAYDAVYLLAHALNRALQDGGPVT 300 (348)
T ss_dssp HTSTHCHHHCCHTTEEEEEESTTTSHHHHHHHHHHHTTTHTTTTTTTTSSGCHHHHHHHHHHHHHHHHHHHHHHHHSTTT
T ss_pred cccccccccccccceeeeeeecccccchhhhhcccChhhccCcccccccccceeeeeehhhhHHHHHHHHHHHHhccCCC
Confidence 32223345677899999999999999999999999986432111122236789999999999999999999875432111
Q ss_pred ccccCCCCCCCccccccCChHHHHHHhhccceeeeeeeEEee--cCccccceEEEEEcc
Q 003054 237 KTNVSRNATDLEAFGISQNGPKLLQALSSTRFKGLTGDYIFV--DGQLQSSAFEIINVN 293 (852)
Q Consensus 237 ~~~~~~~~~~~~~~~~~~~g~~l~~al~~~~f~GltG~v~f~--~G~~~~~~~~I~~~~ 293 (852)
. ..+.+.+|..|.++|++++|+|++|++.|+ +|++....|.|+|++
T Consensus 301 ~-----------~~~~~~~g~~l~~~l~~~~f~G~tG~v~f~~~~G~~~~~~~~i~~~~ 348 (348)
T PF01094_consen 301 N-----------GRNPWQNGSQLLKYLRNVSFEGLTGRVSFDSNDGDRTNYDYDILNMQ 348 (348)
T ss_dssp S-----------SSGTSTTHHHHHHHHHTEEEEETTEEEEEETTTSBEESEEEEEEEE-
T ss_pred C-----------CccccccHHHHHHHHhheeeeCCCCCEEEeCCCCCcCCCEEEEEECC
Confidence 0 014578899999999999999999999996 688888999999975
No 34
>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=99.97 E-value=3.4e-29 Score=274.11 Aligned_cols=247 Identities=17% Similarity=0.254 Sum_probs=206.8
Q ss_pred hhhHHHHhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHHH
Q 003054 2 QTNFIIQLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTDA 81 (852)
Q Consensus 2 ~a~~v~~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~~ 81 (852)
.+.++++++++++||+|+++++++.++ .++|+||+.|++..++.+++++++++||++|+++|+|++++.. +.+.
T Consensus 75 ~~~av~~~~~~~~vP~Is~~~~~~~~~--~~~~~fr~~p~~~~~~~a~~~~~~~~~w~~vavl~~~~~~~~~----l~~~ 148 (327)
T cd06382 75 ASSIVQSICDAKEIPHIQTRWDPEPKS--NRQFTINLYPSNADLSRAYADIVKSFNWKSFTIIYESAEGLLR----LQEL 148 (327)
T ss_pred HHHHHHHHHhccCCCceeccCCcCccc--cccceEEeCCCHHHHHHHHHHHHHhcCCcEEEEEecChHHHHH----HHHH
Confidence 578899999999999999998888877 4689999999999999999999999999999999998886544 5555
Q ss_pred HHhCCc---eeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHcCCcccceEEEEcCccccccc
Q 003054 82 LQAIDT---RVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLR 158 (852)
Q Consensus 82 l~~~g~---~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~~~~~~~ 158 (852)
+++.|. .|.. ..++++ + |+.++|.+|++++||+|++++...++..+++||+++||+.+.|+|+.++......+
T Consensus 149 ~~~~~~~g~~v~~-~~~~~~--~-d~~~~l~~i~~~~~d~vv~~~~~~~~~~~~~qa~~~g~~~~~~~~i~~~~~~~~~~ 224 (327)
T cd06382 149 LQAFGISGITITV-RQLDDD--L-DYRPLLKEIKNSGDNRIIIDCSADILIELLKQAQQVGMMSEYYHYIITNLDLHTLD 224 (327)
T ss_pred HHhhccCCCeEEE-EEccCC--c-cHHHHHHHHHhcCceEEEEECCHHHHHHHHHHHHHhCccccceEEEEecCCccccc
Confidence 555554 4444 455543 4 99999999999999999999999999999999999999999999999776554433
Q ss_pred cCCchhhcccceEEEEEecCCCChHHHHHHHHHHHhccccCCCCcccccchhhHhHhhHHHHHHHHHHHhcccCcCcccc
Q 003054 159 TLEPSVIDSMQGVIGVGPHVPKTKALENFRVRWKRNFLQENPSIVDVELNIFGLLAYDATRALAEAVEKAGITSFGFDKT 238 (852)
Q Consensus 159 ~~~~~~~~~~~gv~~~~~~~~~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~a~~aYDAv~~lA~Al~~a~~~~~~~~~~ 238 (852)
... ......++.+++.+.++++.+++|+++|+++|+.+.+......|+.+++.+|||++++
T Consensus 225 l~~--~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~p~~~~a~~yDav~~~----------------- 285 (327)
T cd06382 225 LED--YRYSGVNITGFRLVDPDSPEVKEVIRSLELSWDEGCRILPSTGVTTESALMYDAVYLF----------------- 285 (327)
T ss_pred hhh--hccCceeEEEEEEecCCchhHHHHHHHHHhhcccccccCCCCCcchhhhhhhceEEEe-----------------
Confidence 211 2223457888888888899999999999999986433333335888999999999987
Q ss_pred ccCCCCCCCccccccCChHHHHHHhhccceeeeeeeEEee-cCccccceEEEEEcc-CCcEEEEEEcCCCCc
Q 003054 239 NVSRNATDLEAFGISQNGPKLLQALSSTRFKGLTGDYIFV-DGQLQSSAFEIINVN-NGARGVGFWTPEKGL 308 (852)
Q Consensus 239 ~~~~~~~~~~~~~~~~~g~~l~~al~~~~f~GltG~v~f~-~G~~~~~~~~I~~~~-~g~~~vG~w~~~~g~ 308 (852)
|+||+++|| +|+|.+..++|+|++ +|+++||+|++..|+
T Consensus 286 -------------------------------g~tG~v~f~~~g~r~~~~~~~~~~~~~~~~~vg~w~~~~~~ 326 (327)
T cd06382 286 -------------------------------GLTGRIEFDSSGQRSNFTLDVIELTESGLRKVGTWNSSEGL 326 (327)
T ss_pred -------------------------------ecccceeeCCCCCEeeeEEEEEeccccCceEEEEECCCCCc
Confidence 899999998 899999999999999 889999999998775
No 35
>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=99.96 E-value=3.4e-28 Score=277.58 Aligned_cols=315 Identities=22% Similarity=0.358 Sum_probs=260.8
Q ss_pred hhhHHHHhcCCCCccEEeeecCCCCCCC-CCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHH
Q 003054 2 QTNFIIQLGNKSQVPILSFSATSPSLTS-IRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTD 80 (852)
Q Consensus 2 ~a~~v~~i~~~~~vP~Is~~ats~~lt~-~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~ 80 (852)
.+.+++.+..-.+||+|+|+||++.|++ .+|+||.|+.|+|..|+.||++++++|+|++|..++++++||+.+.++|++
T Consensus 137 vsi~vanlLrlf~ipQisyaSts~~LSdk~ry~~F~RtVP~D~~Qa~Am~~il~~f~W~yVstv~s~~dYGE~Gieaf~~ 216 (878)
T KOG1056|consen 137 VSIAVANLLRLFLIPQISYASTSPDLSDKTRYDYFLRTVPSDVFQAQAMVDILKKFNWNYVSTVASEGDYGESGIEAFKE 216 (878)
T ss_pred HHHHHHHHHHhhcCceeccccCCcccccchhhhceeeecCChHHHHHHHHHHHHHhCeeEeeehhcCccchhhhHHHHHH
Confidence 4667888899999999999999999998 689999999999999999999999999999999999999999999999999
Q ss_pred HHHhCCceeeeeeecCCCCChHHHHHHHHHhhc-CCceEEEEEeChhhHHHHHHHHHHcCCcccceEEEEcCcccccccc
Q 003054 81 ALQAIDTRVPYRSVISPLATDDQIEKELYKLFT-MQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRT 159 (852)
Q Consensus 81 ~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~-~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~~~~~~~~ 159 (852)
..+++|++|...+.++..+.+..|...++++.. .+++++|+.+..++++.++++|+++++.+ .++||++++|....+.
T Consensus 217 ~a~~~~iCIa~s~ki~~~~~~~~~~~~l~kl~~~~~a~vvV~F~~~~~~r~~~~aa~~~n~~g-~~~wiaSd~W~~~~~~ 295 (878)
T KOG1056|consen 217 EAAERGICIAFSEKIYQLSIEQEFDCVLRKLLETPNARVVVVFCRGEDARRLLKAARRANLTG-EFLWIASDGWASQNSP 295 (878)
T ss_pred hHHhcCceEEehhhcccccchhHHHHHHHHHhhcCCCeEEEEecCcchHHHHHHHHHHhCCCc-ceEEEecchhhccCCh
Confidence 999999999999887766778889999999998 89999999999999999999999999854 4999999999975544
Q ss_pred CCchhhcccceEEEEEecCCCChHHHHH---------------HHHHHHhccccCCCCc----c-----------ccc--
Q 003054 160 LEPSVIDSMQGVIGVGPHVPKTKALENF---------------RVRWKRNFLQENPSIV----D-----------VEL-- 207 (852)
Q Consensus 160 ~~~~~~~~~~gv~~~~~~~~~~~~~~~F---------------~~~~~~~~~~~~~~~~----~-----------~~~-- 207 (852)
... ....++|++++....+..+.+++| .+.|+++|.|..+... . ...
T Consensus 296 ~~~-~e~~a~g~i~i~l~~~~v~~F~~y~~s~~p~nn~~n~w~~e~w~~~f~C~l~~~~~~~~~~~~~Ct~~e~~~~~~~ 374 (878)
T KOG1056|consen 296 TEA-PEREAEGAITIKLASPQVPGFDRYFQSLHPENNRRNPWFAEFWEDKFNCSLPNSAFKNENLIRLCTAVERITLDSA 374 (878)
T ss_pred hhh-hhhhhceeEEEEecCCcchhHHHHHHhcCccccccCcccchhhhhcccCCCCcccccchhhhhhcccchhhccccc
Confidence 332 334789999998877766665554 4568888888765331 0 011
Q ss_pred ---chhhHhHhhHHHHHHHHHHHhcccCcCccccccCCCCCCCccccccCChHHHHHHhhccceeeeeeeEEee-cCccc
Q 003054 208 ---NIFGLLAYDATRALAEAVEKAGITSFGFDKTNVSRNATDLEAFGISQNGPKLLQALSSTRFKGLTGDYIFV-DGQLQ 283 (852)
Q Consensus 208 ---~~~a~~aYDAv~~lA~Al~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~al~~~~f~GltG~v~f~-~G~~~ 283 (852)
..-....+|||+++|+||+.+...... +....|..+.. .+|..|.+.+.+++|.|..|.+.|| +||.
T Consensus 375 ~~q~~k~~~Vi~aVya~A~aLh~m~~~lc~-------~~~~~C~~m~~-~dg~~L~~~l~~vnF~~~~~~v~Fd~~gD~- 445 (878)
T KOG1056|consen 375 YEQDSKVQFVIDAVYAMAHALHNMHQDLCP-------GTSGLCSAMKA-IDGSLLLKYLLNVNFTGPAGSVRFDENGDG- 445 (878)
T ss_pred hhhhcccccHHHHHHHHHHHHHHHHHhhcC-------CccccCcCccc-cCHHHHHhhhheeEEecCCCceeecCCCCC-
Confidence 123457999999999999998644321 11133455443 7899999999999999999999998 9997
Q ss_pred cceEEEEEcc--C---CcEEEEEEcCCCCcccccCCCccccCCccceEeCCCCCCCCCccc
Q 003054 284 SSAFEIINVN--N---GARGVGFWTPEKGLTQKLSSNSTTKSKLKPIIWPGDSTSDPKGWE 339 (852)
Q Consensus 284 ~~~~~I~~~~--~---g~~~vG~w~~~~g~~~~~~~~~~~~~~~~~i~Wpg~~~~~p~~~~ 339 (852)
...|+|++++ + .+..+|+|++...+ +...+-|.++...+|+..|
T Consensus 446 ~~~y~I~~~~~~~~~~~y~~vg~w~~~~~l------------~i~~~~w~~~~~~v~~S~C 494 (878)
T KOG1056|consen 446 PGRYDILNYQLTNGSYTYKEVGYWSEGLSL------------NIEDLDWTTKPSGVPKSVC 494 (878)
T ss_pred ccceeEEEeeccCCCccceeeeeecccccc------------cceeeeeccCCCCCccccc
Confidence 7899999999 4 29999999975543 2456789999989998887
No 36
>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=99.96 E-value=9.9e-29 Score=266.54 Aligned_cols=249 Identities=18% Similarity=0.281 Sum_probs=195.5
Q ss_pred hhHHHHhcCCCCccEEeeecCC-CCCCCCCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHHH
Q 003054 3 TNFIIQLGNKSQVPILSFSATS-PSLTSIRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTDA 81 (852)
Q Consensus 3 a~~v~~i~~~~~vP~Is~~ats-~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~~ 81 (852)
+.+++++|++.+||+|+++... |.+...+++ ..++.|++..|++|+++++++|||++|++||+|+++ +..|.+.
T Consensus 79 ~~~v~~i~~~~~VP~Is~~~~~~~~~~~~~~~-~i~l~P~~~~~~~Ai~dli~~~~W~~v~~iYe~d~~----l~~L~~~ 153 (333)
T cd06394 79 SSIVSHICGEKEIPHFKVGPEETPKLQYLRFA-SVNLHPSNEDISVAVAGILNSFNYPTASLICAKAEC----LLRLEEL 153 (333)
T ss_pred HHHHHHHhhccCCceEEeccccCcccccccce-EEEecCCHHHHHHHHHHHHHhcCCCEEEEEEeCcHH----HHHHHHH
Confidence 4699999999999999986443 333333333 489999999999999999999999999999999886 5666667
Q ss_pred HHhCCceeeeeeecCCC--CChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHcCCcccceEEEEcCcccccccc
Q 003054 82 LQAIDTRVPYRSVISPL--ATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRT 159 (852)
Q Consensus 82 l~~~g~~v~~~~~~~~~--~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~~~~~~~~ 159 (852)
++..+. +...++.. .++.|++++|++|+.+++|+||++++++.+..+++||+++||+.++|+|++|+......+.
T Consensus 154 l~~~~~---~~~~i~~~~~~~~~d~~~~L~~ik~~~~~~iVv~~~~~~a~~il~qa~~lGm~~~~y~~i~T~l~~~~~~L 230 (333)
T cd06394 154 LRQFLI---SKETLSVRMLDDSRDPTPLLKEIRDDKTATIIIDANASMSHTILLKASELGMTSAFYKYILTTMDFPLLRL 230 (333)
T ss_pred HHhhcc---cCCceeeEEccCcccHHHHHHHHHhcCCCEEEEECChHHHHHHHHHHHHcCCCCCceEEEEecCCcccccH
Confidence 765433 12222221 2467899999999999999999999999999999999999999999999998876653332
Q ss_pred CCchhhcccceEEEEEecCCCChHHHHHHHHHHHhccccCCCCcccccchhhHhHhhHHHHHHHHHHHhcccCcCccccc
Q 003054 160 LEPSVIDSMQGVIGVGPHVPKTKALENFRVRWKRNFLQENPSIVDVELNIFGLLAYDATRALAEAVEKAGITSFGFDKTN 239 (852)
Q Consensus 160 ~~~~~~~~~~gv~~~~~~~~~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~a~~aYDAv~~lA~Al~~a~~~~~~~~~~~ 239 (852)
.. .......+.+++...++.+.+++|+++|+++|.+.........+...++.+||||+++
T Consensus 231 ~~--~~~~~~niTgF~l~d~~~~~v~~f~~~~~~~~~~~~~~~~~~~~~~~~al~~D~v~~~------------------ 290 (333)
T cd06394 231 DS--IVDDRSNILGFSMFNQSHAFYQEFIRSLNQSWRENCDHSPYTGPALSSALLFDAVYAV------------------ 290 (333)
T ss_pred HH--hhcCCcceEEEEeecCCcHHHHHHHHHHHHhhhhhcccccCCCcccceeeecceEEEE------------------
Confidence 22 1122455788889999999999999999988743211100012234677888887765
Q ss_pred cCCCCCCCccccccCChHHHHHHhhccceeeeeeeEEee-cCccccceEEEEEcc-CCcEEEEEEcCCCCcc
Q 003054 240 VSRNATDLEAFGISQNGPKLLQALSSTRFKGLTGDYIFV-DGQLQSSAFEIINVN-NGARGVGFWTPEKGLT 309 (852)
Q Consensus 240 ~~~~~~~~~~~~~~~~g~~l~~al~~~~f~GltG~v~f~-~G~~~~~~~~I~~~~-~g~~~vG~w~~~~g~~ 309 (852)
|+||+++|+ +|+|.+...+|+++. +|.++||+|++..|+.
T Consensus 291 ------------------------------glTg~i~f~~~g~R~~~~l~v~~l~~~g~~kig~W~~~~gl~ 332 (333)
T cd06394 291 ------------------------------GLTGRIEFNSKGQRSNYTLKILQKTRSGFRQIGQWHSNETLS 332 (333)
T ss_pred ------------------------------eeecceecCCCCcCcccEEEEEEecCCcceEEEEEeCCCCcC
Confidence 999999997 899999999999999 9999999999998875
No 37
>PRK15404 leucine ABC transporter subunit substrate-binding protein LivK; Provisional
Probab=99.96 E-value=8.4e-28 Score=266.43 Aligned_cols=256 Identities=20% Similarity=0.250 Sum_probs=220.0
Q ss_pred hhhHHHHhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHH-HHcCCcEEEEEEEeCCcccccHHHHHH
Q 003054 2 QTNFIIQLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAII-KAFGWREAVPIYVDNQYGEEMIPSLTD 80 (852)
Q Consensus 2 ~a~~v~~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l-~~~gw~~vaii~~d~~~G~~~~~~l~~ 80 (852)
++.++++++++.+||+|++.+++|.+++..+||+||+.+.+..++.++++++ ++++|++|++|+.|++||++..+.+++
T Consensus 104 ~~~a~~~~~~~~~ip~i~~~s~~~~l~~~~~~~~fr~~~~~~~~~~~~~~~~~~~~~~k~va~i~~d~~~g~~~~~~~~~ 183 (369)
T PRK15404 104 STQPASDIYEDEGILMITPAATAPELTARGYQLIFRTIGLDSDQGPTAAKYILEKVKPKRIAVLHDKQQYGEGLARSVKD 183 (369)
T ss_pred hHHHhHHHHHHCCCeEEecCCCCHHHhcCCCceEEeCCCCcHHHHHHHHHHHHHhcCCCEEEEEeCCCchhHHHHHHHHH
Confidence 4678899999999999999999999988778999999999999999999986 567999999999999999999999999
Q ss_pred HHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHcCCcccceEEEEcCccccccccC
Q 003054 81 ALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTL 160 (852)
Q Consensus 81 ~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~~~~~~~~~ 160 (852)
.+++.|++++....++.+ +.||.+++.++++.+||+|++.+...+...+++|++++|+..+ |++++++... . +
T Consensus 184 ~~~~~G~~v~~~~~~~~g--~~D~~~~v~~l~~~~~d~v~~~~~~~~~~~~~k~~~~~G~~~~---~i~~~~~~~~-~-~ 256 (369)
T PRK15404 184 GLKKAGANVVFFEGITAG--DKDFSALIAKLKKENVDFVYYGGYHPEMGQILRQAREAGLKTQ---FMGPEGVGNK-S-L 256 (369)
T ss_pred HHHHcCCEEEEEEeeCCC--CCchHHHHHHHHhcCCCEEEECCCchHHHHHHHHHHHCCCCCe---EEecCcCCCH-H-H
Confidence 999999999988888854 7889999999999999999988888899999999999999665 7766544321 1 1
Q ss_pred CchhhcccceEEEEEecCC-CChHHHHHHHHHHHhccccCCCCcccccchhhHhHhhHHHHHHHHHHHhcccCcCccccc
Q 003054 161 EPSVIDSMQGVIGVGPHVP-KTKALENFRVRWKRNFLQENPSIVDVELNIFGLLAYDATRALAEAVEKAGITSFGFDKTN 239 (852)
Q Consensus 161 ~~~~~~~~~gv~~~~~~~~-~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~a~~aYDAv~~lA~Al~~a~~~~~~~~~~~ 239 (852)
.....+..+|+++..++.. .+|..++|+++|+++++. +++.++..+||+++++++|+++++
T Consensus 257 ~~~~~~~~~Gv~~~~~~~~~~~~~~~~f~~~~~~~~~~--------~~~~~~~~~Y~~~~~l~~Al~~aG---------- 318 (369)
T PRK15404 257 SNIAGPASEGMLVTLPKRYDQDPANKAIVDAFKAKKQD--------PSGPFVWTTYAAVQSLAAGINRAG---------- 318 (369)
T ss_pred HHhhhhhhcCcEEEccCCCccChhHHHHHHHHHHhcCC--------CCccchHHHHHHHHHHHHHHHhhC----------
Confidence 1112356789887665433 468899999999998764 567788999999999999999998
Q ss_pred cCCCCCCCccccccCChHHHHHHhhccceeeeeeeEEee-cCccccceEEEEEcc-CC
Q 003054 240 VSRNATDLEAFGISQNGPKLLQALSSTRFKGLTGDYIFV-DGQLQSSAFEIINVN-NG 295 (852)
Q Consensus 240 ~~~~~~~~~~~~~~~~g~~l~~al~~~~f~GltG~v~f~-~G~~~~~~~~I~~~~-~g 295 (852)
..++++|+++|++.+|+|++|++.|+ +|+.....|.|++|+ +|
T Consensus 319 -------------~~~~~~l~~al~~~~~~~~~G~~~~~~~g~~~~~~~~i~~~~~~~ 363 (369)
T PRK15404 319 -------------SDDPAKVAKYLKANTFDTVIGPLSWDEKGDLKGFEFGVFEWHADG 363 (369)
T ss_pred -------------CCCHHHHHHHHHhCCCCcceEeeEECCCCCcccCCEEEEEEEcCC
Confidence 34578999999999999999999997 888877889999988 55
No 38
>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=99.95 E-value=4.4e-27 Score=258.43 Aligned_cols=253 Identities=24% Similarity=0.298 Sum_probs=219.9
Q ss_pred hhhHHHHhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHH-HHcCCcEEEEEEEeCCcccccHHHHHH
Q 003054 2 QTNFIIQLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAII-KAFGWREAVPIYVDNQYGEEMIPSLTD 80 (852)
Q Consensus 2 ~a~~v~~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l-~~~gw~~vaii~~d~~~G~~~~~~l~~ 80 (852)
.+.++++++++.+||+|+++++++.+++..+|++||+.|++..++.++++++ ++++|++|++++.|++||+...+.+++
T Consensus 78 ~~~~~~~~~~~~~ip~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~v~~~~~~g~~~~~~~~~ 157 (334)
T cd06342 78 VTIPASPIYADAGIVMISPAATNPKLTERGYKNVFRVVARDDQQGPAAAKYAVETLKAKKVAIIDDKTAYGQGLADEFKK 157 (334)
T ss_pred hHHHhHHHHHhCCCeEEecCCCCchhhcCCCceEEeccCCcHHHHHHHHHHHHHhcCCCEEEEEeCCcchhhHHHHHHHH
Confidence 4667889999999999999988788877678999999999999999999986 578999999999999999999999999
Q ss_pred HHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHcCCcccceEEEEcCccccccccC
Q 003054 81 ALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTL 160 (852)
Q Consensus 81 ~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~~~~~~~~~ 160 (852)
.+++.|++|+....++++ ..|+.+.+.++++.+||+|++.+..+++..+++++++.|+..+ |+.++++... . +
T Consensus 158 ~~~~~g~~v~~~~~~~~~--~~d~~~~l~~i~~~~~~~vi~~~~~~~~~~~~~~~~~~g~~~~---~~~~~~~~~~-~-~ 230 (334)
T cd06342 158 ALKAAGGKVVAREGTTDG--ATDFSAILTKIKAANPDAVFFGGYYPEAGPLVRQMRQLGLKAP---FMGGDGLCDP-E-F 230 (334)
T ss_pred HHHHcCCEEEEEecCCCC--CccHHHHHHHHHhcCCCEEEEcCcchhHHHHHHHHHHcCCCCc---EEecCccCCH-H-H
Confidence 999999999998888754 6889999999999999999999999999999999999999544 7776654321 1 1
Q ss_pred CchhhcccceEEEEEecCC--CChHHHHHHHHHHHhccccCCCCcccccchhhHhHhhHHHHHHHHHHHhcccCcCcccc
Q 003054 161 EPSVIDSMQGVIGVGPHVP--KTKALENFRVRWKRNFLQENPSIVDVELNIFGLLAYDATRALAEAVEKAGITSFGFDKT 238 (852)
Q Consensus 161 ~~~~~~~~~gv~~~~~~~~--~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~a~~aYDAv~~lA~Al~~a~~~~~~~~~~ 238 (852)
.....+..+|++...++.+ +++..++|.++|+++++. .|+.++..+||+++++++|+++++
T Consensus 231 ~~~~~~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~~~--------~~~~~~~~~yda~~~~~~al~~~~--------- 293 (334)
T cd06342 231 IKIAGDAAEGTYATFPGGPLEKMPAGKAFVARYKAKFGD--------PPGAYAPYAYDAANVLAEAIKKAG--------- 293 (334)
T ss_pred HHHhhHhhCCcEEEecCCCCCCChHHHHHHHHHHHHhCC--------CCchhHHHHHHHHHHHHHHHHHhC---------
Confidence 1112345789988877766 468899999999999986 578899999999999999999986
Q ss_pred ccCCCCCCCccccccCChHHHHHHhhccceeeeeeeEEee-cCccccceEEEEEc
Q 003054 239 NVSRNATDLEAFGISQNGPKLLQALSSTRFKGLTGDYIFV-DGQLQSSAFEIINV 292 (852)
Q Consensus 239 ~~~~~~~~~~~~~~~~~g~~l~~al~~~~f~GltG~v~f~-~G~~~~~~~~I~~~ 292 (852)
+.+++.++++|++.+|+|++|++.|+ +|++.+..+.|+||
T Consensus 294 --------------~~~~~~v~~~l~~~~~~g~~g~i~f~~~g~~~~~~~~~~~~ 334 (334)
T cd06342 294 --------------STDPAKVADALRKVDFDGVTGKISFDAKGDLKGAAVTVYQV 334 (334)
T ss_pred --------------CCCHHHHHHHHHhCCCCCcceeeEECCCCCcccCcEEEEeC
Confidence 34678999999999999999999997 99998999999986
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=99.95 E-value=3.1e-27 Score=258.39 Aligned_cols=248 Identities=24% Similarity=0.315 Sum_probs=203.5
Q ss_pred hhhHHHHhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHHH
Q 003054 2 QTNFIIQLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTDA 81 (852)
Q Consensus 2 ~a~~v~~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~~ 81 (852)
.+.++++++++++||+|+++++++.++ . ++.|+..|++..++.+++++++++||++|++||+|++++ ...+.+.+.
T Consensus 74 ~~~av~~i~~~~~ip~is~~~~~~~~~-~--~~~~~~~~~~~~~~~a~~~~~~~~~w~~vaii~~~~~~~-~~l~~~~~~ 149 (324)
T cd06368 74 SANTVQSICDALEIPHITTSWSPNPKP-R--QFTINLYPSMRDLSDALLDLIKYFGWRKFVYIYDSDEGL-LRLQELLDA 149 (324)
T ss_pred HHHHHHHHHhccCCCcEEecCCcCCCC-C--cceEEecCCHHHHHHHHHHHHHhcCCCEEEEEECCcHhH-HHHHHHHHh
Confidence 567899999999999999999999887 2 344455577779999999999999999999999776654 445667777
Q ss_pred HHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHcCCcccceEEEEcCccccccccCC
Q 003054 82 LQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLE 161 (852)
Q Consensus 82 l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~~~~~~~~~~ 161 (852)
+++.|++|+.....+ . .+|++++|.+|++.+||+||+.++.+++..+++||+++||+.++|+||+++......+.
T Consensus 150 ~~~~g~~v~~~~~~~-~--~~d~~~~l~~i~~~~~d~Vi~~~~~~~~~~i~~qa~~~g~~~~~~~~i~~~~~~~~~~~-- 224 (324)
T cd06368 150 LSPKGIQVTVRRLDD-D--TDMYRPLLKEIKREKERRIILDCSPERLKEFLEQAVEVGMMSEYYHYILTNLDFHTLDL-- 224 (324)
T ss_pred hccCCceEEEEEecC-C--chHHHHHHHHHhhccCceEEEECCHHHHHHHHHHHHHhccccCCcEEEEccCCccccch--
Confidence 888899998765433 2 33899999999999999999999999999999999999999999999987764432221
Q ss_pred chhhcccceEEEEEecCCCChHHHHHHHHHHHhccccCCCCcccccchhhHhHhhHHHHHHHHHHHhcccCcCccccccC
Q 003054 162 PSVIDSMQGVIGVGPHVPKTKALENFRVRWKRNFLQENPSIVDVELNIFGLLAYDATRALAEAVEKAGITSFGFDKTNVS 241 (852)
Q Consensus 162 ~~~~~~~~gv~~~~~~~~~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~a~~aYDAv~~lA~Al~~a~~~~~~~~~~~~~ 241 (852)
........++.++....++++..++|.++|+++|+...+......|+.+++.+|||++++
T Consensus 225 ~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~p~~~aa~~yDav~~~-------------------- 284 (324)
T cd06368 225 ELFRYGGVNITGFRLVDPDNPEVQKFIQRWERSDHRICPGSGLKPIKTESALTYDAVLLF-------------------- 284 (324)
T ss_pred hhhhcCCceEEEEEEecCCChHHHHHHHHHHhccccccCCCCCCCcchhhHhhhcEEEEe--------------------
Confidence 112223456777777788899999999999999986444333336889999999999986
Q ss_pred CCCCCCccccccCChHHHHHHhhccceeeeeeeEEee-cCccccceEEEEEcc-CCcEEEEEEcCCCCc
Q 003054 242 RNATDLEAFGISQNGPKLLQALSSTRFKGLTGDYIFV-DGQLQSSAFEIINVN-NGARGVGFWTPEKGL 308 (852)
Q Consensus 242 ~~~~~~~~~~~~~~g~~l~~al~~~~f~GltG~v~f~-~G~~~~~~~~I~~~~-~g~~~vG~w~~~~g~ 308 (852)
||+++|+ +|++.+..++|+++. +|++.+|+|++..|+
T Consensus 285 ------------------------------tg~~~f~~~g~~~~~~~~i~~~~~~~~~~~g~W~~~~~~ 323 (324)
T cd06368 285 ------------------------------TGRIQFDENGQRSNFTLDILELKEGGLRKVGTWNPEDGL 323 (324)
T ss_pred ------------------------------eeeeEeCCCCcCcceEEEEEEEcCCCceEEEEECCCCCC
Confidence 8999998 899999999999999 889999999997775
No 40
>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=99.95 E-value=4.9e-27 Score=259.24 Aligned_cols=252 Identities=19% Similarity=0.242 Sum_probs=212.6
Q ss_pred hhhHHHHhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHcC--CcEEEEEEEeCCcccccHHHHH
Q 003054 2 QTNFIIQLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAFG--WREAVPIYVDNQYGEEMIPSLT 79 (852)
Q Consensus 2 ~a~~v~~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~g--w~~vaii~~d~~~G~~~~~~l~ 79 (852)
.+.++++++++++||+|+++++++.++...+||+||+.|++..++.++++++++++ |+++++++.|++||+...+.+.
T Consensus 83 ~~~a~~~~~~~~~vp~i~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~v~~v~~~~~~g~~~~~~~~ 162 (345)
T cd06338 83 LTLAAAPVAEKYGVPMVAGSGASDSIFAQGFKYVFGTLPPASQYAKSLLEMLVALDPRPKKVAILYADDPFSQDVAEGAR 162 (345)
T ss_pred hHHHHHHHHHHhCCcEEecCCCCchHhhcCCceEEEecCchHHHHHHHHHHHHhcCCCCceEEEEecCCcccHHHHHHHH
Confidence 46778899999999999999998888866789999999999999999999998887 9999999999999999999999
Q ss_pred HHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHcCCcccceEEEE-cCccccccc
Q 003054 80 DALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIM-TDGMTNLLR 158 (852)
Q Consensus 80 ~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~-~~~~~~~~~ 158 (852)
+.+++.|++|+....++.+ .+||++++++|++.++|+|++++...++..+++++++.|+..+ ++. +.++...
T Consensus 163 ~~~~~~g~~v~~~~~~~~~--~~d~~~~v~~l~~~~~d~i~~~~~~~~~~~~~~~~~~~g~~~~---~~~~~~~~~~~-- 235 (345)
T cd06338 163 EKAEAAGLEVVYDETYPPG--TADLSPLISKAKAAGPDAVVVAGHFPDAVLLVRQMKELGYNPK---ALYMTVGPAFP-- 235 (345)
T ss_pred HHHHHcCCEEEEEeccCCC--ccchHHHHHHHHhcCCCEEEECCcchhHHHHHHHHHHcCCCCC---EEEEecCCCcH--
Confidence 9999999999988877744 6789999999999999999999999999999999999999765 332 2322211
Q ss_pred cCCchhhcccceEEEEEecCCC-------ChHHHHHHHHHHHhccccCCCCcccccchhhHhHhhHHHHHHHHHHHhccc
Q 003054 159 TLEPSVIDSMQGVIGVGPHVPK-------TKALENFRVRWKRNFLQENPSIVDVELNIFGLLAYDATRALAEAVEKAGIT 231 (852)
Q Consensus 159 ~~~~~~~~~~~gv~~~~~~~~~-------~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~a~~aYDAv~~lA~Al~~a~~~ 231 (852)
......+...+|+++...+.+. .|..+.|+++|+++|+. .|+.+++.+||+++++++|+++++
T Consensus 236 ~~~~~~g~~~~g~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~--------~p~~~~~~~y~a~~~~~~a~~~ag-- 305 (345)
T cd06338 236 AFVKALGADAEGVFGPTQWTPALDYKDDLFPSAAEFAAAYKEKYGK--------APDYHAAGAYAAGQVLQEAVERAG-- 305 (345)
T ss_pred HHHHHHhhhhCceeecceeccCcccccccCccHHHHHHHHHHHhCC--------CCCcccHHHHHHHHHHHHHHHHhC--
Confidence 0111123446888887776664 37799999999999987 577889999999999999999988
Q ss_pred CcCccccccCCCCCCCccccccCChHHHHHHhhccceeeeeeeEEee-cCccccceEEEEEc
Q 003054 232 SFGFDKTNVSRNATDLEAFGISQNGPKLLQALSSTRFKGLTGDYIFV-DGQLQSSAFEIINV 292 (852)
Q Consensus 232 ~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~al~~~~f~GltG~v~f~-~G~~~~~~~~I~~~ 292 (852)
..+++++.++|++++|+|++|++.|+ +|++.. .+.|++|
T Consensus 306 ---------------------~~~~~~v~~al~~~~~~~~~G~~~f~~~~~~~~-~~~~~~~ 345 (345)
T cd06338 306 ---------------------SLDPAAVRDALASNDFDTFYGPIKFDETGQNNH-PMTVVQW 345 (345)
T ss_pred ---------------------CCCHHHHHHHHHhCCCcccccCeeECCCCCcCC-CceeeeC
Confidence 34578999999999999999999998 888754 5556554
No 41
>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=99.95 E-value=6.6e-26 Score=248.99 Aligned_cols=262 Identities=17% Similarity=0.190 Sum_probs=196.0
Q ss_pred hhhHHHHhcCCCCccEEeeecCC---CC-----CCC-CCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeCCccc
Q 003054 2 QTNFIIQLGNKSQVPILSFSATS---PS-----LTS-IRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDNQYGE 72 (852)
Q Consensus 2 ~a~~v~~i~~~~~vP~Is~~ats---~~-----lt~-~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~~~G~ 72 (852)
.+.+++++++..+||+|++.+.. |. +.+ ...+|.|++.|++ .+..+++++++++||++|+++|++++ |.
T Consensus 74 ~~~av~~i~~~~~IP~Is~~~~~~~~~~~~~~~~~~~~~~~~~f~~rp~~-~~~~ai~~lv~~~~wkkvavly~~d~-g~ 151 (363)
T cd06381 74 SAIALQSLTDAMHIPHLFIQRGYGGSPRTACGLNPSPRGQQYTLALRPPV-RLNDVMLRLVTEWRWQKFVYFYDNDY-DI 151 (363)
T ss_pred HHHHHHHHhhCCCCCEEEeecCcCCCcccccccCCCcccceeEEEEeccH-HHHHHHHHHHHhCCCeEEEEEEECCc-hH
Confidence 57889999999999999976422 11 111 2345767777774 78899999999999999999998776 55
Q ss_pred ccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhh-------cCCceEEEEEeChhhHHHHHHHHHHcCCcccce
Q 003054 73 EMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLF-------TMQTRVFILHMLPSLGSRIFEKANEIGLMNKGC 145 (852)
Q Consensus 73 ~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~-------~~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~ 145 (852)
...+.+.+++++.|+.+.... ...+ ....+...++.++ ..+.++||++|+++.+..++++|+++||+..+|
T Consensus 152 ~~l~~~~~~~~~~g~~v~~~~-~~~~-~~~~~~~l~~~~~~~~l~~~~~~~~~vIl~~~~~~~~~~l~~a~~~gm~~~~~ 229 (363)
T cd06381 152 RGLQEFLDQLSRQGIDVLLQK-VDLN-ISKMATALFTTMRCEELNRYRDTLRRALLLLSPNGAYTFIDASVETNLAIKDS 229 (363)
T ss_pred HHHHHHHHHHHhcCceEEEEe-cccc-cchhhhhhhhHHHHHHHHhhcccceEEEEEcCcHHHHHHHHHHHHcCCCcCce
Confidence 556778888999998766432 2211 1122333333222 345568899999999999999999999999999
Q ss_pred EEEEcCccccccccCCchhhcccceEEEEEecCCCChHHH----HHHHHHHHhccccCCCCcccccchhhHhHhhHHHHH
Q 003054 146 VWIMTDGMTNLLRTLEPSVIDSMQGVIGVGPHVPKTKALE----NFRVRWKRNFLQENPSIVDVELNIFGLLAYDATRAL 221 (852)
Q Consensus 146 vwi~~~~~~~~~~~~~~~~~~~~~gv~~~~~~~~~~~~~~----~F~~~~~~~~~~~~~~~~~~~~~~~a~~aYDAv~~l 221 (852)
+||+++.|......+ ........|++|++..++..+..+ +|...|++.+... ++ ....+...++++||||+++
T Consensus 230 ~wi~~~~l~~~~~~l-~~~~~~~~nitgfrl~~~~~~~~~~~~~~~~~~~~~~~~~~-~~-~~~~~~~~~al~yDaV~~~ 306 (363)
T cd06381 230 HWFLINEEISDTEID-ELVRYAHGRMTVIRQTFSKEKTNQRCLRNNHRISSLLCDPK-DG-YLQMLEISNLYIYDSVLLL 306 (363)
T ss_pred EEEEeccccccchhh-HHHhhcCccEEEEEEecCCcCchHHHHHHHHHHHHhhcCCC-CC-CCCChhHHHHHHHHHHHHH
Confidence 999988887532222 235567899999999988776666 5555665443322 22 1125677899999999998
Q ss_pred HHHHHHhcccCcCccccccCCCCCCCccccccCChHHHHHHhhccceeeeeeeEEee-cCccccceEEEEEcc-CC----
Q 003054 222 AEAVEKAGITSFGFDKTNVSRNATDLEAFGISQNGPKLLQALSSTRFKGLTGDYIFV-DGQLQSSAFEIINVN-NG---- 295 (852)
Q Consensus 222 A~Al~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~al~~~~f~GltG~v~f~-~G~~~~~~~~I~~~~-~g---- 295 (852)
+++|++++|+|+||+++|+ +|++.+..++|+.+. +|
T Consensus 307 --------------------------------------~~~~~~~~~~GLTG~i~F~~~g~r~~~~l~i~~~~~~~~~~~ 348 (363)
T cd06381 307 --------------------------------------LETIKKGPITGLTGKLEFNEGGDNSNVQFEILGTGYSETLGK 348 (363)
T ss_pred --------------------------------------HHHHHhcCccCcceeEEeCCCCCccccEEEEEEeccCCcccc
Confidence 4567788999999999997 999999999999999 66
Q ss_pred -cEEEEEEcCCCCc
Q 003054 296 -ARGVGFWTPEKGL 308 (852)
Q Consensus 296 -~~~vG~w~~~~g~ 308 (852)
.+.+|+|++.+|+
T Consensus 349 ~~~~~~~w~~~~~~ 362 (363)
T cd06381 349 DGRWLATWNPSKGL 362 (363)
T ss_pred ceEEeeeccCCCCC
Confidence 8899999998876
No 42
>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=1.9e-26 Score=254.33 Aligned_cols=246 Identities=23% Similarity=0.268 Sum_probs=208.1
Q ss_pred hhhHHHHhcCCCCccEEeeecCCCCCCC----CCCCceEeccCCchhHHHHHHHHHHH-----cCCcEEEEEEEeCCccc
Q 003054 2 QTNFIIQLGNKSQVPILSFSATSPSLTS----IRSPYFFRGSLNDSSQAGAITAIIKA-----FGWREAVPIYVDNQYGE 72 (852)
Q Consensus 2 ~a~~v~~i~~~~~vP~Is~~ats~~lt~----~~~py~fR~~p~d~~~~~aia~~l~~-----~gw~~vaii~~d~~~G~ 72 (852)
++.++++++++++||+|+++++++.+++ ..+||+||+.|++..++.++++++.+ +||++|++++.|++||+
T Consensus 79 ~~~a~~~~~~~~~vp~i~~~~~~~~~t~~~~~~~~~~~fr~~~~~~~~~~~~~~~~~~~~~~~~~~~~va~l~~~~~~g~ 158 (344)
T cd06345 79 VVLALQDVAAENKVPFIVTGAASPEITTADDYETYKYVFRAGPTNSSYAQSVADALKETLVDKHGFKTAAIVAEDAAWGK 158 (344)
T ss_pred HHHHHHHHHHHcCCcEEeccCCCCcccccccccCCceEEecCCCcHHHHHHHHHHHHHhhcccCCCceEEEEecCchhhh
Confidence 4678899999999999999999998873 47899999999999999999998865 89999999999999999
Q ss_pred ccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHcCCcccceEEEEcCc
Q 003054 73 EMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDG 152 (852)
Q Consensus 73 ~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~ 152 (852)
...+.+++.+++.|++|+....++.+ +.|+.+++.+|++.++|+|++.+...++..+++++++.|+..+ +++...
T Consensus 159 ~~~~~~~~~~~~~G~~vv~~~~~~~~--~~d~~~~v~~l~~~~~d~v~~~~~~~~~~~~~~~~~~~g~~~~---~~~~~~ 233 (344)
T cd06345 159 GIDAGIKALLPEAGLEVVSVERFSPD--TTDFTPILQQIKAADPDVIIAGFSGNVGVLFTQQWAEQKVPIP---TIGISV 233 (344)
T ss_pred HHHHHHHHHHHHcCCeEEEEEecCCC--CCchHHHHHHHHhcCCCEEEEeecCchHHHHHHHHHHcCCCCc---eEEecC
Confidence 99999999999999999998888754 6789999999999999999999999999999999999998554 343332
Q ss_pred cccccccCCchhhcccceEEEEEecCC----CChHHHHHHHHHHHhccccCCCCcccccchhhHhHhhHHHHHHHHHHHh
Q 003054 153 MTNLLRTLEPSVIDSMQGVIGVGPHVP----KTKALENFRVRWKRNFLQENPSIVDVELNIFGLLAYDATRALAEAVEKA 228 (852)
Q Consensus 153 ~~~~~~~~~~~~~~~~~gv~~~~~~~~----~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~a~~aYDAv~~lA~Al~~a 228 (852)
+..... .........+|+++...+.+ .++..++|.++|+++|+. .|+.+++.+||+++++++|++++
T Consensus 234 ~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~y~~~~g~--------~p~~~~~~~yda~~~l~~A~~~a 304 (344)
T cd06345 234 EGNSPA-FWKATNGAGNYVITAESGAPGVEAITDKTVPFTEAYEAKFGG--------PPNYMGASTYDSIYILAEAIERA 304 (344)
T ss_pred CcCCHH-HHHhhchhcceEEeecccccCccCCCHHHHHHHHHHHHHhCC--------CCcccchHHHHHHHHHHHHHHHh
Confidence 221111 11112345677776655544 568899999999999987 78999999999999999999998
Q ss_pred cccCcCccccccCCCCCCCccccccCChHHHHHHhhccceeeeeeeEEee-cCcccc
Q 003054 229 GITSFGFDKTNVSRNATDLEAFGISQNGPKLLQALSSTRFKGLTGDYIFV-DGQLQS 284 (852)
Q Consensus 229 ~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~al~~~~f~GltG~v~f~-~G~~~~ 284 (852)
+ +.++++|+++|++.+|+|++|++.|+ +||+..
T Consensus 305 g-----------------------~~~~~~i~~al~~~~~~g~~G~i~f~~~g~~~~ 338 (344)
T cd06345 305 G-----------------------STDGDALVEALEKTDFVGTAGRIQFYGDDSAFA 338 (344)
T ss_pred c-----------------------CCCHHHHHHHHHhCCCcCCceeEEECCCCCcCc
Confidence 8 34578999999999999999999998 999743
No 43
>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=99.94 E-value=4.5e-26 Score=247.58 Aligned_cols=228 Identities=25% Similarity=0.362 Sum_probs=196.3
Q ss_pred hhhHH-HHhcCCCCccEEeeecCCCCCCC-CCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHH
Q 003054 2 QTNFI-IQLGNKSQVPILSFSATSPSLTS-IRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLT 79 (852)
Q Consensus 2 ~a~~v-~~i~~~~~vP~Is~~ats~~lt~-~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~ 79 (852)
.+.++ ++++++.++|+|+++++++.+++ ..++|+||+.|++..++.+++++++++||++|++||.|++||++..+.++
T Consensus 79 ~~~a~~~~~~~~~~vp~i~~~~~~~~l~~~~~~~~~fr~~~~~~~~~~~l~~~~~~~~~~~vail~~~~~~g~~~~~~~~ 158 (312)
T cd06346 79 VTIAALTSVAVPNGVVMISPSSTSPTLTTLDDNGLFFRTAPSDALQGQALAQLAAERGYKSVATTYINNDYGVGLADAFT 158 (312)
T ss_pred hhHhhhhhhhccCCcEEEecCCCCccceecCCCceEEEecCCcHHHHHHHHHHHHHcCCCeEEEEEccCchhhHHHHHHH
Confidence 45677 89999999999999999999987 45799999999999999999999999999999999999999999999999
Q ss_pred HHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHcCCcccceEEEEcCcccccccc
Q 003054 80 DALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRT 159 (852)
Q Consensus 80 ~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~~~~~~~~ 159 (852)
+.+++.|++|+....++++ +.||++++.+|++.+||+|++.+.+.++..+++|++++|+..+ |++++++.... .
T Consensus 159 ~~~~~~G~~vv~~~~~~~~--~~d~~~~v~~l~~~~pd~v~~~~~~~~~~~~~~~~~~~G~~~~---~~~~~~~~~~~-~ 232 (312)
T cd06346 159 KAFEALGGTVTNVVAHEEG--KSSYSSEVAAAAAGGPDALVVIGYPETGSGILRSAYEQGLFDK---FLLTDGMKSDS-F 232 (312)
T ss_pred HHHHHcCCEEEEEEeeCCC--CCCHHHHHHHHHhcCCCEEEEecccchHHHHHHHHHHcCCCCc---eEeeccccChH-H
Confidence 9999999999998888855 7899999999999999999999999999999999999999655 77766644321 1
Q ss_pred CCchhhcccceEEEEEecCCCChHHHHHHHHHHHhccccCCCCcccccchhhHhHhhHHHHHHHHHHHhcccCcCccccc
Q 003054 160 LEPSVIDSMQGVIGVGPHVPKTKALENFRVRWKRNFLQENPSIVDVELNIFGLLAYDATRALAEAVEKAGITSFGFDKTN 239 (852)
Q Consensus 160 ~~~~~~~~~~gv~~~~~~~~~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~a~~aYDAv~~lA~Al~~a~~~~~~~~~~~ 239 (852)
+.....+.++|+++..++.+. +..++|.++|+++|+. .|+.+++.+||+++++++|
T Consensus 233 ~~~~~~~~~~g~~~~~~~~~~-~~~~~f~~~~~~~~g~--------~p~~~~~~~Yd~~~~l~~A--------------- 288 (312)
T cd06346 233 LPADGGYILAGSYGTSPGAGG-PGLEAFTSAYKAAYGE--------SPSAFADQSYDAAALLALA--------------- 288 (312)
T ss_pred HHhhhHHHhCCcEEccCCCCc-hhHHHHHHHHHHHhCC--------CCCccchhhHHHHHHHHHH---------------
Confidence 111123457888887665544 8899999999999987 6889999999999999987
Q ss_pred cCCCCCCCccccccCChHHHHHHhhccceeeeeeeEEee-cCccccceEE
Q 003054 240 VSRNATDLEAFGISQNGPKLLQALSSTRFKGLTGDYIFV-DGQLQSSAFE 288 (852)
Q Consensus 240 ~~~~~~~~~~~~~~~~g~~l~~al~~~~f~GltG~v~f~-~G~~~~~~~~ 288 (852)
|+|++|++.|+ +|++.. .|.
T Consensus 289 ----------------------------~~g~~g~~~f~~~g~~~~-~~~ 309 (312)
T cd06346 289 ----------------------------YQGASGVVDFDENGDVAG-SYD 309 (312)
T ss_pred ----------------------------hCCCccceeeCCCCCccc-cee
Confidence 68999999997 888743 444
No 44
>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=99.93 E-value=1.4e-25 Score=247.53 Aligned_cols=248 Identities=18% Similarity=0.195 Sum_probs=208.1
Q ss_pred hhhHHHHhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHc------CCcEEEEEEEeCCcccccH
Q 003054 2 QTNFIIQLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAF------GWREAVPIYVDNQYGEEMI 75 (852)
Q Consensus 2 ~a~~v~~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~------gw~~vaii~~d~~~G~~~~ 75 (852)
.+.++++++++.+||+|+++++++.+++..+||+||+.|++..++.++++++.++ +|+++++++.|++||....
T Consensus 82 ~~~a~~~~~~~~~ip~i~~~~~~~~l~~~~~~~~fr~~p~~~~~~~~~~~~l~~~~~~~~~~~~~v~~l~~~~~~g~~~~ 161 (347)
T cd06340 82 VTLAASQVAERYGVPFVVDGAVSDSITERGFKYTFRITPHDGMFTRDMFDFLKDLNEKTGKPLKTVALVHEDTEFGTSVA 161 (347)
T ss_pred hHHHHHHHHHHhCCCEEeccccchHHhhcCCceEEecCCChHHHHHHHHHHHHHhhHhcCCCCceEEEEecCchHhHHHH
Confidence 4678889999999999999999998887778999999999999999999998765 5699999999999999999
Q ss_pred HHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHcCCcccceEEEEcCcccc
Q 003054 76 PSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTN 155 (852)
Q Consensus 76 ~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~~~~ 155 (852)
+.+++.+++.|++|+....++.+ +.||++++.+|++.++|+|++.++..++..+++|+++.|+..+ .++...++...
T Consensus 162 ~~~~~~~~~~G~~vv~~~~~~~~--~~d~~~~i~~l~~~~~d~v~~~~~~~~~~~~~~~~~~~G~~~~-~~~~~~~~~~~ 238 (347)
T cd06340 162 EAIKKFAKERGFEIVEDISYPAN--ARDLTSEVLKLKAANPDAILPASYTNDAILLVRTMKEQRVEPK-AVYSVGGGAED 238 (347)
T ss_pred HHHHHHHHHcCCEEEEeeccCCC--CcchHHHHHHHHhcCCCEEEEcccchhHHHHHHHHHHcCCCCc-EEEecCCCcCc
Confidence 99999999999999998888755 7799999999999999999999999999999999999999655 22222222221
Q ss_pred ccccCCchhhcccceEEEEEecCCC-ChHHHHHHHHHHHhccccCCCCcccccchhhHhHhhHHHHHHHHHHHhcccCcC
Q 003054 156 LLRTLEPSVIDSMQGVIGVGPHVPK-TKALENFRVRWKRNFLQENPSIVDVELNIFGLLAYDATRALAEAVEKAGITSFG 234 (852)
Q Consensus 156 ~~~~~~~~~~~~~~gv~~~~~~~~~-~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~a~~aYDAv~~lA~Al~~a~~~~~~ 234 (852)
. . +....++..+|+++..++.+. .+..++|.++|+++|+. .|+.+++.+||+++++++|+++++
T Consensus 239 ~-~-~~~~~g~~~~g~~~~~~~~~~~~~~~~~f~~~y~~~~~~--------~~~~~~~~~Y~a~~~l~~A~~~ag----- 303 (347)
T cd06340 239 P-S-FVKALGKDAEGILTRNEWSDPKDPMAKDLNKRFKARFGV--------DLSGNSARAYTAVLVIADALERAG----- 303 (347)
T ss_pred H-H-HHHHhhHhhheEEeccccCCCCChHHHHHHHHHHHHhCC--------CCChHHHHHHHHHHHHHHHHHHhc-----
Confidence 1 1 111233567899988877665 68899999999999987 688999999999999999999998
Q ss_pred ccccccCCCCCCCccccccCChHHHHH--Hhhcccee---eeeeeEEee-cCccccc
Q 003054 235 FDKTNVSRNATDLEAFGISQNGPKLLQ--ALSSTRFK---GLTGDYIFV-DGQLQSS 285 (852)
Q Consensus 235 ~~~~~~~~~~~~~~~~~~~~~g~~l~~--al~~~~f~---GltG~v~f~-~G~~~~~ 285 (852)
+.+++++++ +|++..++ ++.|++.|+ +|+..++
T Consensus 304 ------------------~~~~~~v~~~~~~~~~~~~~~~~~~g~~~f~~~g~~~~~ 342 (347)
T cd06340 304 ------------------SADPEKIRDLAALASTSGEDLIMPYGPIKFDAKGQNTNA 342 (347)
T ss_pred ------------------CCCHHHHHHHHHhccCCccccccCCCCeeECCCCCcccc
Confidence 345788884 88877765 578999998 9997654
No 45
>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=99.93 E-value=5.4e-25 Score=242.79 Aligned_cols=258 Identities=19% Similarity=0.298 Sum_probs=206.6
Q ss_pred hhhHHHHhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHH-HHHHHHHc-CCcEEEEEEEeCC-cccccHHHH
Q 003054 2 QTNFIIQLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGA-ITAIIKAF-GWREAVPIYVDNQ-YGEEMIPSL 78 (852)
Q Consensus 2 ~a~~v~~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~a-ia~~l~~~-gw~~vaii~~d~~-~G~~~~~~l 78 (852)
++.++.+++++.+||+|+++++++.+++ .+||+||+.+++..+... +..+++++ ||+++++||.+++ ||++..+.+
T Consensus 79 ~~~a~~~~~~~~~ip~i~~~~~~~~~~~-~~~~~fr~~~~~~~~~~~~~~~~~~~~~~~~~v~~l~~~~~~~g~~~~~~~ 157 (344)
T cd06348 79 QAFAADPIAERAGVPVVGPSNTAKGIPE-IGPYVFRVSAPEAVVAPAAIAAALKLNPGIKRVAVFYAQDDAFSVSETEIF 157 (344)
T ss_pred HHHhhhHHHHhCCCCEEeccCCCCCcCC-CCCeEEEccCcHHHHHHHHHHHHHHHhcCCeEEEEEEeCCchHHHHHHHHH
Confidence 3567789999999999999888877753 578999998877665554 44567777 9999999997555 999999999
Q ss_pred HHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHcCCcccceEEEEcCccccccc
Q 003054 79 TDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLR 158 (852)
Q Consensus 79 ~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~~~~~~~ 158 (852)
++.+++.|++|+....++.+ +.||.+++.+|++++||+|++.+.+.++..+++++++.|+..+ ++.++++... .
T Consensus 158 ~~~~~~~g~~v~~~~~~~~~--~~d~~~~v~~i~~~~~d~vi~~~~~~~~~~~~~~~~~~g~~~~---~~~~~~~~~~-~ 231 (344)
T cd06348 158 QKALRDQGLNLVTVQTFQTG--DTDFQAQITAVLNSKPDLIVISALAADGGNLVRQLRELGYNGL---IVGGNGFNTP-N 231 (344)
T ss_pred HHHHHHcCCEEEEEEeeCCC--CCCHHHHHHHHHhcCCCEEEECCcchhHHHHHHHHHHcCCCCc---eeccccccCH-H
Confidence 99999999999998888754 7899999999999999999999999999999999999999665 5655544321 1
Q ss_pred cCCchhhcccceEEEEEecCCC--ChHHHHHHHHHHHhccccCCCCcccccchhhHhHhhHHHHHHHHHHHhcccCcCcc
Q 003054 159 TLEPSVIDSMQGVIGVGPHVPK--TKALENFRVRWKRNFLQENPSIVDVELNIFGLLAYDATRALAEAVEKAGITSFGFD 236 (852)
Q Consensus 159 ~~~~~~~~~~~gv~~~~~~~~~--~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~a~~aYDAv~~lA~Al~~a~~~~~~~~ 236 (852)
+.....+..+|+++..++.+. .+..++|.++|+++|+. .|+.+++.+|||++++++|+++++.....
T Consensus 232 -~~~~~g~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~g~--------~p~~~~~~~yda~~~~~~A~~~a~~~~~~-- 300 (344)
T cd06348 232 -VFPVCQAACDGVLVAQAYSPENDTPVNRDFVEAYKKKYGK--------APPQFSAQAFDAVQVVAEALKRLNQKQKL-- 300 (344)
T ss_pred -HHHhhhHhhcCeEEEeeccCCCCCHHHHHHHHHHHHHHCC--------CccHHHHHHHHHHHHHHHHHHHhcCCCcc--
Confidence 111234567899888777653 57889999999999986 67888999999999999999999843110
Q ss_pred ccccCCCCCCCccccccCChHHHHHHhhccceeeeeeeEEee-cCccccceEE
Q 003054 237 KTNVSRNATDLEAFGISQNGPKLLQALSSTRFKGLTGDYIFV-DGQLQSSAFE 288 (852)
Q Consensus 237 ~~~~~~~~~~~~~~~~~~~g~~l~~al~~~~f~GltG~v~f~-~G~~~~~~~~ 288 (852)
.++ .....+++|+++|++.+|+|++|++.|+ +|++....|.
T Consensus 301 --------~~~---~~~~~~~~l~~~l~~~~~~g~~G~v~f~~~g~~~~~~~~ 342 (344)
T cd06348 301 --------AEL---PLPELRTALNAALLSGQYDTPLGEISFTPDGEVLQKAFY 342 (344)
T ss_pred --------ccc---hhhhHHHHHHHHHhccCCccceeeeEECCCCCcccCcee
Confidence 000 0112367899999999999999999998 8987666553
No 46
>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=99.93 E-value=6.7e-25 Score=241.31 Aligned_cols=251 Identities=16% Similarity=0.229 Sum_probs=212.3
Q ss_pred hhHHHHhcCCCCccEEeeecCCCCCCCC-CCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHHH
Q 003054 3 TNFIIQLGNKSQVPILSFSATSPSLTSI-RSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTDA 81 (852)
Q Consensus 3 a~~v~~i~~~~~vP~Is~~ats~~lt~~-~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~~ 81 (852)
+.++.+++++.++|+|+++++++.+++. .+||+||+.+++..++..+++++.+.+|++|++++.|+.||++..+.+++.
T Consensus 78 ~~~~~~~~~~~~ip~v~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~l~~~~~~~v~~l~~~~~~g~~~~~~~~~~ 157 (336)
T cd06360 78 ALAMVKVLREPGTPLINPNAGADDLTGRLCAPNFFRTSFSNAQWAAPMGKYAADDGYKKVVTVAWDYAFGYEVVEGFKEA 157 (336)
T ss_pred HHHHHHHHHhcCceEEecCCCCccccccCCCCcEEEEeCchHHHHHHHHHHHHHcCCCeEEEEeccchhhHHHHHHHHHH
Confidence 4567788999999999999989888863 479999999999999999999998889999999999999999999999999
Q ss_pred HHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHcCCcccceEEEEcCccccccccCC
Q 003054 82 LQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLE 161 (852)
Q Consensus 82 l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~~~~~~~~~~ 161 (852)
+++.|++++....++.+ +.||++++.++++.+||+|++.+...++..+++++++.|+..+ ..+++++.+.... ..
T Consensus 158 ~~~~G~~v~~~~~~~~~--~~d~~~~v~~~~~~~pd~v~~~~~~~~~~~~~~~~~~~g~~~~-~~~~~~~~~~~~~--~~ 232 (336)
T cd06360 158 FTEAGGKIVKELWVPFG--TSDFASYLAQIPDDVPDAVFVFFAGGDAIKFVKQYDAAGLKAK-IPLIGSGFLTDGT--TL 232 (336)
T ss_pred HHHcCCEEEEEEecCCC--CcchHHHHHHHHhcCCCEEEEecccccHHHHHHHHHHcCCccC-CeEEecccccCHH--HH
Confidence 99999999988777744 7899999999999999999999999999999999999999432 2356555443221 11
Q ss_pred chhhcccceEEEEEecCC--CChHHHHHHHHHHHhccccCCCCcccccchhhHhHhhHHHHHHHHHHHhcccCcCccccc
Q 003054 162 PSVIDSMQGVIGVGPHVP--KTKALENFRVRWKRNFLQENPSIVDVELNIFGLLAYDATRALAEAVEKAGITSFGFDKTN 239 (852)
Q Consensus 162 ~~~~~~~~gv~~~~~~~~--~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~a~~aYDAv~~lA~Al~~a~~~~~~~~~~~ 239 (852)
...++..+|++...++.+ +.+..++|.++|+++|+. +|+.++..+||+++++++|+++++..
T Consensus 233 ~~~g~~~~g~~~~~~~~~~~~~~~~~~f~~~y~~~~~~--------~~~~~~~~~yda~~~~~~A~~~a~~~-------- 296 (336)
T cd06360 233 GAAGEAAEGVITALHYADTLDNPANQAFVKAYRAAYPD--------TPSVYAVQGYDAGQALILALEAVGGD-------- 296 (336)
T ss_pred HhhHhhhcCceeccccCCCCCCHHHHHHHHHHHHHhCC--------CccHHHHHHHHHHHHHHHHHHHhCCC--------
Confidence 123456789888777765 468899999999999987 78899999999999999999999832
Q ss_pred cCCCCCCCccccccCChHHHHHHhhccceeeeeeeEEee-cCccccceE
Q 003054 240 VSRNATDLEAFGISQNGPKLLQALSSTRFKGLTGDYIFV-DGQLQSSAF 287 (852)
Q Consensus 240 ~~~~~~~~~~~~~~~~g~~l~~al~~~~f~GltG~v~f~-~G~~~~~~~ 287 (852)
..+++.+.++|++++|+|+.|+++|+ +|++..+.|
T Consensus 297 -------------~~~~~~v~~al~~~~~~~~~g~~~f~~~~~~~~~~~ 332 (336)
T cd06360 297 -------------LSDGQALIAAMAAAKIDSPRGPFTLDKAHNPIQDNY 332 (336)
T ss_pred -------------CCCHHHHHHHHhcCCccCCCcceEECCCCCcccceE
Confidence 13568899999999999999999997 888765544
No 47
>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=9.6e-25 Score=240.69 Aligned_cols=257 Identities=15% Similarity=0.099 Sum_probs=206.5
Q ss_pred hhhHHHHhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHH-cCCcEEEEEEEeCCcccccHHHHHH
Q 003054 2 QTNFIIQLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKA-FGWREAVPIYVDNQYGEEMIPSLTD 80 (852)
Q Consensus 2 ~a~~v~~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~-~gw~~vaii~~d~~~G~~~~~~l~~ 80 (852)
.+.++.+++++.++|+|++.+... ...+||+||+.+++..++..+++++.. .|+|+|++|+.|++||++..+.+++
T Consensus 79 ~~~a~~~~~~~~~~~~i~~~~~~~---~~~~~~~f~~~~~~~~~~~~~~~~~~~~~g~k~vaii~~d~~~g~~~~~~~~~ 155 (348)
T cd06355 79 SRKAVLPVFERHNGLLFYPVQYEG---LEQSPNVFYTGAAPNQQIIPAVDWLMSNKGGKRFYLVGSDYVYPRTANKILKA 155 (348)
T ss_pred hHHHHHHHHhccCCceecCCCccC---CCCCCCEEEeCCChHHhHHHHHHHHHhccCCCeEEEECCcchHHHHHHHHHHH
Confidence 467899999999999998754322 235799999999999999999998754 5799999999999999999999999
Q ss_pred HHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHcCCcccceEEEEcCccccccccC
Q 003054 81 ALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTL 160 (852)
Q Consensus 81 ~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~~~~~~~~~ 160 (852)
++++.|++|+....++.+ +.||++++.+|++.+||+|++...+.++..+++|+++.|+..+...++........+...
T Consensus 156 ~~~~~G~~vv~~~~~~~~--~~D~~~~v~~l~~~~pd~v~~~~~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~~~~~~ 233 (348)
T cd06355 156 QLESLGGEVVGEEYLPLG--HTDFQSIINKIKAAKPDVVVSTVNGDSNVAFFKQLKAAGITASKVPVLSFSVAEEELRGI 233 (348)
T ss_pred HHHHcCCeEEeeEEecCC--hhhHHHHHHHHHHhCCCEEEEeccCCchHHHHHHHHHcCCCccCCeeEEccccHHHHhhc
Confidence 999999999999888754 889999999999999999999999999999999999999965544455443222111111
Q ss_pred CchhhcccceEEEEEecCC--CChHHHHHHHHHHHhccccCCCCcccccchhhHhHhhHHHHHHHHHHHhcccCcCcccc
Q 003054 161 EPSVIDSMQGVIGVGPHVP--KTKALENFRVRWKRNFLQENPSIVDVELNIFGLLAYDATRALAEAVEKAGITSFGFDKT 238 (852)
Q Consensus 161 ~~~~~~~~~gv~~~~~~~~--~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~a~~aYDAv~~lA~Al~~a~~~~~~~~~~ 238 (852)
..+.++|+++...+.+ ++|..++|+++|+++|+... .++.+++.+||+++++++|++++|
T Consensus 234 ---g~~~~~g~~~~~~~~~~~~~~~~~~f~~~y~~~~g~~~------~~~~~a~~~Y~a~~~~~~Al~~ag--------- 295 (348)
T cd06355 234 ---GPENLAGHYAAWNYFQSVDTPENKKFVAAFKARYGQDR------VTNDPMEAAYIGVYLWKQAVEKAG--------- 295 (348)
T ss_pred ---ChHhhcCCEEeccchhhcCCHHHHHHHHHHHHHcCCCC------CCCcHHHHHHHHHHHHHHHHHHhC---------
Confidence 1235678877655544 56889999999999998621 346678899999999999999998
Q ss_pred ccCCCCCCCccccccCChHHHHHHhhccceeeeeeeEEeec-CccccceEEEEEcc-CC
Q 003054 239 NVSRNATDLEAFGISQNGPKLLQALSSTRFKGLTGDYIFVD-GQLQSSAFEIINVN-NG 295 (852)
Q Consensus 239 ~~~~~~~~~~~~~~~~~g~~l~~al~~~~f~GltG~v~f~~-G~~~~~~~~I~~~~-~g 295 (852)
+.++++|+++|++.+|+++.|.++|+. ++.....+.|.+++ +|
T Consensus 296 --------------~~~~~~i~~aL~~~~~~~~~g~~~f~~~~~~~~~~~~i~~~~~~g 340 (348)
T cd06355 296 --------------SFDVDKVRAALPGQSFDAPEGPVTVDPANHHLWKPVRIGRIQADG 340 (348)
T ss_pred --------------CCCHHHHHHHhccCcccCCCcceEeecCCCeeeeeeEEEEEcCCC
Confidence 346799999999999999999999973 33224455677776 55
No 48
>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=6.8e-25 Score=241.56 Aligned_cols=239 Identities=19% Similarity=0.170 Sum_probs=203.8
Q ss_pred HHhcCCCCccEEeeecCCCCCCC-CCCCceEeccCCchhHHHHHHHHHHHcC-CcEEEEEEEeCCcccccHHHHHHHHHh
Q 003054 7 IQLGNKSQVPILSFSATSPSLTS-IRSPYFFRGSLNDSSQAGAITAIIKAFG-WREAVPIYVDNQYGEEMIPSLTDALQA 84 (852)
Q Consensus 7 ~~i~~~~~vP~Is~~ats~~lt~-~~~py~fR~~p~d~~~~~aia~~l~~~g-w~~vaii~~d~~~G~~~~~~l~~~l~~ 84 (852)
+++++++++|+|+++++++.+++ ..+||+||+.|++..++.++++++.+.+ ||+|++++.|+.||++..+.+++++++
T Consensus 90 ~~~~~~~~ip~i~~~~~~~~~~~~~~~~~~fr~~~~~~~~~~~l~~~~~~~~~~k~v~i~~~~~~~g~~~~~~~~~~~~~ 169 (342)
T cd06329 90 NQRNPGKEVLYLNYASVAPALTGEKCSFWHFRTDANTDMKMEALASYIKKQPDGKKVYLINQDYSWGQDVAAAFKAMLAA 169 (342)
T ss_pred hhhhccCCeEEEecCCCCchhhhccCcceEEEecCChHHHHHHHHHHHHhcccCceEEEEeCChHHHHHHHHHHHHHHHh
Confidence 67888999999999998898886 4679999999999999999999997765 999999999999999999999999999
Q ss_pred --CCceeeeeeecCCCCCh-HHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHcCCcccceEEEEcCccccccccCC
Q 003054 85 --IDTRVPYRSVISPLATD-DQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLE 161 (852)
Q Consensus 85 --~g~~v~~~~~~~~~~~~-~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~~~~~~~~~~ 161 (852)
.|++|+....++.+ + +|+.+++.++++.+||+|++...+.++..++++++++|+..+ ++...+.... ..
T Consensus 170 ~~~G~~vv~~~~~~~~--~~~d~~~~i~~l~~~~~d~v~~~~~~~~~~~~~~~~~~~g~~~~---~~~~~~~~~~---~~ 241 (342)
T cd06329 170 KRPDIQIVGEDLHPLG--KVKDFSPYVAKIKASGADTVITGNWGNDLLLLVKQAADAGLKLP---FYTPYLDQPG---NP 241 (342)
T ss_pred hcCCcEEeceeccCCC--CCCchHHHHHHHHHcCCCEEEEcccCchHHHHHHHHHHcCCCce---EEeccccchh---HH
Confidence 99999988877754 6 789999999999999999999988899999999999999655 5544433221 11
Q ss_pred chhhcccceEEEEEecCC--CChHHHHHHHHHHHhccccCCCCcccccchhhHhHhhHHHHHHHHHHHhcccCcCccccc
Q 003054 162 PSVIDSMQGVIGVGPHVP--KTKALENFRVRWKRNFLQENPSIVDVELNIFGLLAYDATRALAEAVEKAGITSFGFDKTN 239 (852)
Q Consensus 162 ~~~~~~~~gv~~~~~~~~--~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~a~~aYDAv~~lA~Al~~a~~~~~~~~~~~ 239 (852)
....+..+|++...++.+ +++..++|.++|+++|+. .|+.+++.+||+++++++|+++++
T Consensus 242 ~~~g~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~~~--------~~~~~~~~~y~~~~~~~~a~~~ag---------- 303 (342)
T cd06329 242 AALGEAGLGLVVAVAYWHPNDTPANRAFVEAFKAKYGR--------VPDYYEGQAYNGIQMLADAIEKAG---------- 303 (342)
T ss_pred HhhcccccceEEeeeccCCCCCHHHHHHHHHHHHHhCC--------CCCchHHHHHHHHHHHHHHHHHhC----------
Confidence 223456788888777654 468899999999999986 688899999999999999999987
Q ss_pred cCCCCCCCccccccCChHHHHHHhhccceeeeeeeEEee--cCcccc
Q 003054 240 VSRNATDLEAFGISQNGPKLLQALSSTRFKGLTGDYIFV--DGQLQS 284 (852)
Q Consensus 240 ~~~~~~~~~~~~~~~~g~~l~~al~~~~f~GltG~v~f~--~G~~~~ 284 (852)
+.+++.+.++|++++|+|+.|++.|+ +++...
T Consensus 304 -------------~~~~~~v~~al~~~~~~~~~g~~~~~~~~~~~~~ 337 (342)
T cd06329 304 -------------STDPEAVAKALEGMEVDTPVGPVTMRASDHQAQQ 337 (342)
T ss_pred -------------CCCHHHHHHHHhCCccccCCCCeEEcccCcchhc
Confidence 34578999999999999999999997 444433
No 49
>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=99.93 E-value=5.3e-25 Score=241.47 Aligned_cols=245 Identities=20% Similarity=0.219 Sum_probs=204.2
Q ss_pred hhhHHHHhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHcC-CcEEEEEEEeCC-cccccHHHHH
Q 003054 2 QTNFIIQLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAFG-WREAVPIYVDNQ-YGEEMIPSLT 79 (852)
Q Consensus 2 ~a~~v~~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~g-w~~vaii~~d~~-~G~~~~~~l~ 79 (852)
.+.+++++++++++|+|+++++++.++ .++||+||+.+++..+++++++++++.+ |++|++||.|++ ||+...+.+.
T Consensus 78 ~~~a~~~~~~~~~ip~i~~~a~~~~lt-~~~~~~fr~~~~~~~~~~~~~~~~~~~~~~~~v~~i~~~~~~~g~~~~~~~~ 156 (332)
T cd06344 78 ATLAALDIYQKAKLVLISPTSTSVKLS-NPGPYFFRTVPSNAVAARALAKYLKKKNKIKKVAIFYNSTSPYSQSLKQEFT 156 (332)
T ss_pred HHHHHHHHHhhcCceEEccCcCchhhc-CCCCcEEEeCCCcHHHHHHHHHHHHhhcCCCeEEEEeCCCchHhHHHHHHHH
Confidence 456889999999999999998888888 4689999999999999999999998776 999999998876 9999999999
Q ss_pred HHHHh-CCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHcCCcccceEEEEcCccccccc
Q 003054 80 DALQA-IDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLR 158 (852)
Q Consensus 80 ~~l~~-~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~~~~~~~ 158 (852)
+.+++ .|++++....++ .++.|+..++.++++.+||+|++.++......+++++++.|...+ +++++++... +
T Consensus 157 ~~~~~~~g~~v~~~~~~~--~~~~~~~~~v~~i~~~~~d~v~~~~~~~~~~~~~~~~~~~~~~~~---i~~~~~~~~~-~ 230 (332)
T cd06344 157 SALLERGGGIVVTPCDLS--SPDFNANTAVSQAINNGATVLVLFPDTDTLDKALEVAKANKGRLT---LLGGDSLYTP-D 230 (332)
T ss_pred HHHHHhcCCeeeeeccCC--CCCCCHHHHHHHHHhcCCCEEEEeCChhHHHHHHHHHHhcCCCce---EEecccccCH-H
Confidence 99999 599987655444 346779999999999999999999999889999999999886333 5555554322 1
Q ss_pred cCCchhhcccceEEEEEecCCCChHHHHHHHHHHHhccccCCCCcccccchhhHhHhhHHHHHHHHHHHhcccCcCcccc
Q 003054 159 TLEPSVIDSMQGVIGVGPHVPKTKALENFRVRWKRNFLQENPSIVDVELNIFGLLAYDATRALAEAVEKAGITSFGFDKT 238 (852)
Q Consensus 159 ~~~~~~~~~~~gv~~~~~~~~~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~a~~aYDAv~~lA~Al~~a~~~~~~~~~~ 238 (852)
... ......+|+++..+|.++++..++|+++|+++|+. +|+.+++.+||+++++++|+++++.
T Consensus 231 ~~~-~~~~~~~G~~~~~~~~~~~~~~~~f~~~~~~~~~~--------~~~~~a~~~Yda~~~l~~A~~~ag~-------- 293 (332)
T cd06344 231 TLL-DGGKDLEGLVLAVPWHPLASPNSPFAKLAQQLWGG--------DVSWRTATAYDATKALIAALSQGPT-------- 293 (332)
T ss_pred HHH-hchhhhcCeEEEEecccccccchHHHHHHHHHhcC--------CchHHHHhHHHHHHHHHHHHHhCCC--------
Confidence 111 12346789999989888888889999999999987 6889999999999999999999873
Q ss_pred ccCCCCCCCccccccCChHHHH-HHhhccceeeeeeeEEee-cCccccc
Q 003054 239 NVSRNATDLEAFGISQNGPKLL-QALSSTRFKGLTGDYIFV-DGQLQSS 285 (852)
Q Consensus 239 ~~~~~~~~~~~~~~~~~g~~l~-~al~~~~f~GltG~v~f~-~G~~~~~ 285 (852)
.++..+. .++++..|+|+.|++.|+ +||+..+
T Consensus 294 ---------------~~~~~~~~~~~~~~~~~g~~g~i~f~~~g~~~~~ 327 (332)
T cd06344 294 ---------------REGVQQVELSLRNFSVQGATGKIKFLPSGDRNGQ 327 (332)
T ss_pred ---------------hhhhhhhhhhcccccccCCCceeEeCCCCcccCc
Confidence 2345555 677788899999999997 9998543
No 50
>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=1.1e-24 Score=239.37 Aligned_cols=248 Identities=16% Similarity=0.130 Sum_probs=207.9
Q ss_pred hhhHHHHhcCCCCccEEeeecCCCCCCCC-CCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHH
Q 003054 2 QTNFIIQLGNKSQVPILSFSATSPSLTSI-RSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTD 80 (852)
Q Consensus 2 ~a~~v~~i~~~~~vP~Is~~ats~~lt~~-~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~ 80 (852)
++.++++++++.+||+|+++++++.+++. .+||+||+.+++..++.++++++...++++|++++.|++||++..+.+++
T Consensus 78 ~~~a~~~~~~~~~vp~i~~~s~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~v~~i~~~~~~g~~~~~~~~~ 157 (334)
T cd06327 78 VALAVQEVAREKKKIYIVTGAGSDDLTGKDCSPYTFHWAYDTYMLANGTAPALVKAGGKKWFFLTADYAFGHSLERDARK 157 (334)
T ss_pred HHHHHHHHHHHhCceEEecCCCccccccCCCCCceEEccCChHHHHHHHHHHHHHhcCCeEEEEecchHHhHHHHHHHHH
Confidence 46678899999999999999999999864 57999999999999999999998777899999999999999999999999
Q ss_pred HHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHcCCcccceEEEEcCccccccccC
Q 003054 81 ALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTL 160 (852)
Q Consensus 81 ~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~~~~~~~~~ 160 (852)
++++.|++|+....++.+ .+||.+++.+|++.+||+|++.+...++..+++++++.|+..+ ..++....+....
T Consensus 158 ~~~~~G~~vv~~~~~~~~--~~d~~~~v~~l~~~~~d~v~~~~~~~~~~~~~~~~~~~g~~~~-~~~~~~~~~~~~~--- 231 (334)
T cd06327 158 VVKANGGKVVGSVRHPLG--TSDFSSYLLQAQASGADVLVLANAGADTVNAIKQAAEFGLTKG-QKLAGLLLFLTDV--- 231 (334)
T ss_pred HHHhcCCEEcCcccCCCC--CccHHHHHHHHHhCCCCEEEEeccchhHHHHHHHHHHhCCccC-CcEEEecccHHHH---
Confidence 999999999998888754 7889999999999999999999999999999999999998522 2233322222111
Q ss_pred CchhhcccceEEEEEecCCC--ChHHHHHHHHHHHhccccCCCCcccccchhhHhHhhHHHHHHHHHHHhcccCcCcccc
Q 003054 161 EPSVIDSMQGVIGVGPHVPK--TKALENFRVRWKRNFLQENPSIVDVELNIFGLLAYDATRALAEAVEKAGITSFGFDKT 238 (852)
Q Consensus 161 ~~~~~~~~~gv~~~~~~~~~--~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~a~~aYDAv~~lA~Al~~a~~~~~~~~~~ 238 (852)
.....+.++|+++..++.++ .+..++|+++|+++|+. .|+.+++.+||+++++++|++++|
T Consensus 232 ~~~~~~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~g~--------~p~~~~~~~Y~~~~~~~~A~~~ag--------- 294 (334)
T cd06327 232 HSLGLDAAQGLYLTTAWYWDLPNDETRAFVKRFQAKYGK--------MPSMVQAGAYSAVLHYLKAVEAAG--------- 294 (334)
T ss_pred HhhchhhhcCeEEeeeccccCCCHHHHHHHHHHHHHHCc--------CCCcHHHHHHHHHHHHHHHHHHHC---------
Confidence 11122457898888777543 68899999999999987 678899999999999999999998
Q ss_pred ccCCCCCCCccccccCChHHHHHHhhccc-eeeeeeeEEee--cCccccce
Q 003054 239 NVSRNATDLEAFGISQNGPKLLQALSSTR-FKGLTGDYIFV--DGQLQSSA 286 (852)
Q Consensus 239 ~~~~~~~~~~~~~~~~~g~~l~~al~~~~-f~GltG~v~f~--~G~~~~~~ 286 (852)
+.+++++.++|++++ ++++.|++.|+ +|+...+.
T Consensus 295 --------------~~~~~~v~~al~~~~~~~~~~g~~~~~~~~~~~~~~~ 331 (334)
T cd06327 295 --------------TDDADKVVAKMKETPIYDLFAGNGYIRACDHQMVHDM 331 (334)
T ss_pred --------------CCChHHHHHhccccceeccCCCCceeeccccchhccc
Confidence 345678999999975 68999999995 67764443
No 51
>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=99.93 E-value=3e-24 Score=237.56 Aligned_cols=262 Identities=13% Similarity=0.118 Sum_probs=206.3
Q ss_pred hhhHHHHhcCCCCccEEeeecCCCCCCC-CCCCceEeccCCchhHHHHHHHHHHH-cCCcEEEEEEEeCCcccccHHHHH
Q 003054 2 QTNFIIQLGNKSQVPILSFSATSPSLTS-IRSPYFFRGSLNDSSQAGAITAIIKA-FGWREAVPIYVDNQYGEEMIPSLT 79 (852)
Q Consensus 2 ~a~~v~~i~~~~~vP~Is~~ats~~lt~-~~~py~fR~~p~d~~~~~aia~~l~~-~gw~~vaii~~d~~~G~~~~~~l~ 79 (852)
.+.++++++++.++|+|.... ++. ...||+||+.+++..++.++++++.. .+ +++++++.|++||++..+.++
T Consensus 80 ~~~A~~~~~~~~~~~~i~~~~----~~~~~~~~~~Fr~~~~~~~~~~~~~~~~~~~~g-~~va~l~~d~~~g~~~~~~~~ 154 (374)
T TIGR03669 80 TREAIRPIIDRNEQLYFYTNQ----YEGGVCDEYTFAVGATARQQLGTVVPYMVEEYG-KKIYTIAADYNFGQLSADWVR 154 (374)
T ss_pred HHHHHHHHHHhcCceEEcCcc----cccccCCCCEEEcCCChHHHHHHHHHHHHHcCC-CeEEEEcCCcHHHHHHHHHHH
Confidence 467889999999999997432 222 34689999999999999999999854 56 789999999999999999999
Q ss_pred HHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHcCCcccceEEEEcCcccccccc
Q 003054 80 DALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRT 159 (852)
Q Consensus 80 ~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~~~~~~~~ 159 (852)
+.+++.|++|+....++.+ +.||.+++.+|++++||+|++.....+...+++|++++|+..+ ++...........
T Consensus 155 ~~~~~~G~~vv~~~~~~~g--~~Df~~~l~~i~~~~pD~V~~~~~g~~~~~~~kq~~~~G~~~~---~~~~~~~~~~~~~ 229 (374)
T TIGR03669 155 VIAKENGAEVVGEEFIPLS--VSQFSSTIQNIQKADPDFVMSMLVGANHASFYEQAASANLNLP---MGTSTAMAQGYEH 229 (374)
T ss_pred HHHHHcCCeEEeEEecCCC--cchHHHHHHHHHHcCCCEEEEcCcCCcHHHHHHHHHHcCCCCc---ccchhhhhhhhhh
Confidence 9999999999998888754 8899999999999999999999999999999999999999766 3322222211111
Q ss_pred CCchhhcccceEEEEEecCC--CChHHHHHHHHHHHhccccCCCCcccccchhhHhHhhHHHHHHHHHHHhcccCcCccc
Q 003054 160 LEPSVIDSMQGVIGVGPHVP--KTKALENFRVRWKRNFLQENPSIVDVELNIFGLLAYDATRALAEAVEKAGITSFGFDK 237 (852)
Q Consensus 160 ~~~~~~~~~~gv~~~~~~~~--~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~a~~aYDAv~~lA~Al~~a~~~~~~~~~ 237 (852)
... .....+|+++..+|.+ +++..++|+++|+++|+.. | .++.+++.+||+++++++|+++||
T Consensus 230 ~~~-~~~~~~g~~~~~~~~~~~~~~~~~~F~~~y~~~~g~~-p-----~~~~~a~~~Yda~~~l~~Ai~~AG-------- 294 (374)
T TIGR03669 230 KRF-EPPALKDVYAGVNYMEEIDTPENEAFVERFYAKFPDA-P-----YINQEAENNYFSVYMYKQAVEEAG-------- 294 (374)
T ss_pred hhc-CchhhCCcEEeeeccccCCCHHHHHHHHHHHHHcCCC-C-----CCChHHHHHHHHHHHHHHHHHHhC--------
Confidence 110 1234678877766665 4688999999999999752 1 246788999999999999999998
Q ss_pred cccCCCCCCCccccccCChHHHHHHhhc-cceeeeeeeEEee-cCccccceEEEEEcc-CC-cEEEEEEc
Q 003054 238 TNVSRNATDLEAFGISQNGPKLLQALSS-TRFKGLTGDYIFV-DGQLQSSAFEIINVN-NG-ARGVGFWT 303 (852)
Q Consensus 238 ~~~~~~~~~~~~~~~~~~g~~l~~al~~-~~f~GltG~v~f~-~G~~~~~~~~I~~~~-~g-~~~vG~w~ 303 (852)
+.++++|+++|++ .+|+|+.|++.|+ +++.....+.|.++. +| .+.+..|+
T Consensus 295 ---------------s~d~~av~~aL~~~~~~~~~~G~i~fd~~~~~~~~~~~v~~~~~~~~~~~~~~~~ 349 (374)
T TIGR03669 295 ---------------TTDQDAVRDVLESGVEMDAPEGKVCIDGATHHMSHTMRLARADADHNITFVKEQE 349 (374)
T ss_pred ---------------CCCHHHHHHHHHcCCeEECCCccEEEcCCCCeeeeeeEEEEEcCCCCEEEEEecC
Confidence 4567999999997 5799999999997 444334456677777 44 55555555
No 52
>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=99.93 E-value=1.3e-24 Score=240.12 Aligned_cols=231 Identities=29% Similarity=0.522 Sum_probs=195.2
Q ss_pred hhhHHHHhcCCCCccEEeeecCCCCCCC-CCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHH
Q 003054 2 QTNFIIQLGNKSQVPILSFSATSPSLTS-IRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTD 80 (852)
Q Consensus 2 ~a~~v~~i~~~~~vP~Is~~ats~~lt~-~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~ 80 (852)
.+.++++++++++||+|+++++++.+++ ..+||+||+.|++..++.+++++++++||++|++++.|++||.+..+.|++
T Consensus 103 ~~~a~~~~~~~~~vp~is~~~~~~~ls~~~~~~~~fr~~p~~~~~~~a~~~~~~~~~~~~v~~l~~~~~~g~~~~~~~~~ 182 (348)
T cd06350 103 VSMAVAELLGLFKIPQISYGATSPLLSDKLQFPSFFRTVPSDTSQALAIVALLKHFGWTWVGLVYSDDDYGRSGLSDLEE 182 (348)
T ss_pred HHHHHHHHHhcCcCceecccCCChhhccccccCCeeEecCCcHHHHHHHHHHHHHCCCeEEEEEEecchhHHHHHHHHHH
Confidence 4678899999999999999999999975 578999999999999999999999999999999999999999999999999
Q ss_pred HHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHcCCcccceEEEEcCccccccccC
Q 003054 81 ALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTL 160 (852)
Q Consensus 81 ~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~~~~~~~~~ 160 (852)
.+++.|++|+....++......|+..++++|+++++|+|+++++..++..++++|+++|+ .+. .|+++++|.......
T Consensus 183 ~~~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vvv~~~~~~~~~~~~~~a~~~g~-~~~-~~i~~~~~~~~~~~~ 260 (348)
T cd06350 183 ELEKNGICIAFVEAIPPSSTEEDIKRILKKLKSSTARVIVVFGDEDDALRLFCEAYKLGM-TGK-YWIISTDWDTSTCLL 260 (348)
T ss_pred HHHHCCCcEEEEEEccCCCcHHHHHHHHHHHHhCCCcEEEEEeCcHHHHHHHHHHHHhCC-CCe-EEEEEccccCccccc
Confidence 999999999999888754346899999999999999999999999999999999999999 444 455555555431111
Q ss_pred CchhhcccceEEEEEecCCCChHHHHHHHHHHHhccccCCCCcccccchhhHhHhhHHHHHHHHHHHhcccCcCcccccc
Q 003054 161 EPSVIDSMQGVIGVGPHVPKTKALENFRVRWKRNFLQENPSIVDVELNIFGLLAYDATRALAEAVEKAGITSFGFDKTNV 240 (852)
Q Consensus 161 ~~~~~~~~~gv~~~~~~~~~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~a~~aYDAv~~lA~Al~~a~~~~~~~~~~~~ 240 (852)
....+.++|++++.++.+.......|.+.|++ +++++|||+++
T Consensus 261 -~~~~~~~~g~~~~~~~~~~~~~~~~f~~~~~~----------------~~~~~YDav~~-------------------- 303 (348)
T cd06350 261 -LFTLDAFQGVLGFSGHAPRSGEIPGFKDFLRK----------------YAYNVYDAVYA-------------------- 303 (348)
T ss_pred -cCCcceeeeEEEEEEEeecCCcCCChHHHHHH----------------HHHHHHhheeE--------------------
Confidence 12346789999999988866556667766665 67899999997
Q ss_pred CCCCCCCccccccCChHHHHHHhhccceeeeeeeEEee-cCccccceEEEEEcc-C----CcEEEEEEcCC
Q 003054 241 SRNATDLEAFGISQNGPKLLQALSSTRFKGLTGDYIFV-DGQLQSSAFEIINVN-N----GARGVGFWTPE 305 (852)
Q Consensus 241 ~~~~~~~~~~~~~~~g~~l~~al~~~~f~GltG~v~f~-~G~~~~~~~~I~~~~-~----g~~~vG~w~~~ 305 (852)
.+.|+ +|++ ...+.|++++ . +++.||.|++.
T Consensus 304 ---------------------------------~v~f~~~gd~-~~~~~i~~~~~~~~~~~~~~vg~~~~~ 340 (348)
T cd06350 304 ---------------------------------EVKFDENGDR-LASYDIINWQIFPGGGGFVKVGFWDPQ 340 (348)
T ss_pred ---------------------------------EEEecCCCCc-ccceeEEEEEEcCCcEEEEEEEEEcCC
Confidence 67887 7998 5678888886 2 39999999873
No 53
>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=99.92 E-value=1.4e-24 Score=239.06 Aligned_cols=266 Identities=14% Similarity=0.147 Sum_probs=185.1
Q ss_pred hhhHHHHhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHH-
Q 003054 2 QTNFIIQLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTD- 80 (852)
Q Consensus 2 ~a~~v~~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~- 80 (852)
.|..|+.+++.++||+|+++.. ..++.++||++|+.|++..+++|+++++++|+|++|++||+|++.+......+..
T Consensus 79 ~a~~V~si~~~~~IP~Is~s~~--~~~~~~~p~~ir~~Ps~~~~~~Ai~dlI~~f~W~~v~iIYddd~gl~~~l~~~l~~ 156 (368)
T cd06383 79 DASEIKSVTGALGIPTFSASYG--QEGDLEQPYLIQLMPPADDIVEAIRDIVSYYNITNAAILYDDDFVMDHKYKSLLQN 156 (368)
T ss_pred hHHHHHHHHhccCCCEEEccCC--CcCcccCceEEEEeCChHHHHHHHHHHHHHCCCcEEEEEEEcCchhhHHHHHHHHh
Confidence 4678999999999999998553 3333578999999999999999999999999999999999666543323333322
Q ss_pred HHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCc-eEEEEEeChhhHHHHHHHHHHcCCcccceEEEEcCcccccccc
Q 003054 81 ALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQT-RVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRT 159 (852)
Q Consensus 81 ~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~-~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~~~~~~~~ 159 (852)
...+.+.++. +. ...++..+|++|+..+. +||+++..++.+..++++|.++||++++|+||+++......+.
T Consensus 157 ~~~~~~~~v~-----~~--~~~~~~~~Lk~lk~~~~~rIIi~~s~~~~~~~il~qA~~lgm~~~~y~wilt~ld~~~~dl 229 (368)
T cd06383 157 WPTRHVITII-----NS--IIDEVREQIKRLRNLDIKNIFILGSTEEIIRYVLDQALAEGFMGRKYAWFLGNPDLGIYDD 229 (368)
T ss_pred HHhcCCEEEE-----ec--cchhHHHHHHHHHhCCCeEEEEEeCCHHHHHHHHHHHHHcCCcCCceEEEEcCCCchhhhh
Confidence 3333344432 11 24568999999999998 5555555569999999999999999999999999986654332
Q ss_pred CCchhhcccceEEEEEecCCCChHHHHHHHHHHHhccccCCCCcccccchhhHhHhhHHHHHHHHHHHhcccCcCccccc
Q 003054 160 LEPSVIDSMQGVIGVGPHVPKTKALENFRVRWKRNFLQENPSIVDVELNIFGLLAYDATRALAEAVEKAGITSFGFDKTN 239 (852)
Q Consensus 160 ~~~~~~~~~~gv~~~~~~~~~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~a~~aYDAv~~lA~Al~~a~~~~~~~~~~~ 239 (852)
.. ......++.+++...+.....+.|.++|.+.. .+.....+...-++.+||||+++++|++......... .
T Consensus 230 ~~--~~~~~~Nitgfrl~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~aL~~Dav~~~~~a~~~l~~~~~~~---~ 301 (368)
T cd06383 230 LS--CQLRNASIFVTRPMMDYQSSVRGALLRTDEPT---LRPVFYFEWAFRLFLAYDAVLAVGEWPRRMRKKRVED---G 301 (368)
T ss_pred hh--hccccCcEEEeeccccchhhhccceeeccCCc---cCchhHHHHHHHHHHHHHHHHHhccccchhheeeccC---C
Confidence 21 22334678889886665555577777663211 0111111345678999999999999998753111111 0
Q ss_pred cCC-CCCCCccc---ccc-CChHHHHHHhhccceeeeeeeEEee-cCcccc
Q 003054 240 VSR-NATDLEAF---GIS-QNGPKLLQALSSTRFKGLTGDYIFV-DGQLQS 284 (852)
Q Consensus 240 ~~~-~~~~~~~~---~~~-~~g~~l~~al~~~~f~GltG~v~f~-~G~~~~ 284 (852)
+.+ ....|... -.| ..|..+.++|+.++|+|+||+|.|+ +|+|.+
T Consensus 302 ~~~~~~~~~~g~~~~~~w~~~g~~~~~~~k~~~~~gltG~i~f~~~g~R~~ 352 (368)
T cd06383 302 STGTSVLPGFGISPESPLMTLQSSPFNGSSEIKFEMLAGRVAIDEGSSVST 352 (368)
T ss_pred CcCccccCCCCCCcccchhhcccccccCccceeEeeecCeEEEecCceeee
Confidence 110 01122211 123 5666999999999999999999997 888743
No 54
>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=3.9e-24 Score=234.47 Aligned_cols=247 Identities=16% Similarity=0.169 Sum_probs=202.4
Q ss_pred hhhHHHHhcCCCCccEEeeecCCCCCCCC-CCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHH
Q 003054 2 QTNFIIQLGNKSQVPILSFSATSPSLTSI-RSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTD 80 (852)
Q Consensus 2 ~a~~v~~i~~~~~vP~Is~~ats~~lt~~-~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~ 80 (852)
++.++++++++.++|+|+++++++.++.. .++|+||+.+++..++.++++++... +++|++||.|++||++..+.+++
T Consensus 80 ~~~a~~~~~~~~~ip~i~~~~~~~~l~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~-~~~v~~i~~~~~~g~~~~~~~~~ 158 (333)
T cd06328 80 VALAVLPVAEENKKILIVEPAAADSITGKNWNRYTFRTGRNSSQDAIAAAAALGKP-GKKIATLAQDYAFGRDGVAAFKA 158 (333)
T ss_pred HHHHHHHHHHHhCCcEEecCCCCchhhccCCCCcEEEecCChHHHHHHHHHHHHhc-CCeEEEEecCccccHHHHHHHHH
Confidence 46788899999999999999999999864 46999999999999999999888665 79999999999999999999999
Q ss_pred HHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChh-hHHHHHHHHHHcCCcccceEEEEcCcccccccc
Q 003054 81 ALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPS-LGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRT 159 (852)
Q Consensus 81 ~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~-~~~~i~~~a~~~G~~~~~~vwi~~~~~~~~~~~ 159 (852)
++++.|++|+....++++ +.||.+++.+|++.+||+|++...+. +...+++++++.|+..+ ............
T Consensus 159 ~~~~~G~~vv~~~~~~~~--~~d~~~~v~~l~~~~pd~V~~~~~~~~~~~~~~~~~~~~g~~~~---~~~~~~~~~~~~- 232 (333)
T cd06328 159 ALEKLGAAIVTEEYAPTD--TTDFTPYAQRLLDALKKVLFVIWAGAGGPWPKLQQMGVLGYGIE---ITLAGDILANLT- 232 (333)
T ss_pred HHHhCCCEEeeeeeCCCC--CcchHHHHHHHHhcCCCEEEEEecCchhHHHHHHHhhhhcCCCe---EEecccccCccc-
Confidence 999999999999888854 78899999999999999998876655 67888999998887544 222222222111
Q ss_pred CCchhhcccceEEEEEecC-CCChHHHHHHHHHHHhccccCCCCcccccchhhHhHhhHHHHHHHHHHHhcccCcCcccc
Q 003054 160 LEPSVIDSMQGVIGVGPHV-PKTKALENFRVRWKRNFLQENPSIVDVELNIFGLLAYDATRALAEAVEKAGITSFGFDKT 238 (852)
Q Consensus 160 ~~~~~~~~~~gv~~~~~~~-~~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~a~~aYDAv~~lA~Al~~a~~~~~~~~~~ 238 (852)
........+|++...++. +.+|..+.|.++|+++|+. .|+.+++.+||++.++++|+++++
T Consensus 233 -~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~y~~~~g~--------~p~~~~~~~y~a~~~l~~Ai~~ag--------- 294 (333)
T cd06328 233 -MYKAGPGMSGASYYYHYFLPKNPVNDWLVEEHKARFGS--------PPDLFTAGGMSAAIAVVEALEETG--------- 294 (333)
T ss_pred -cccccccccceeeeecCCCCCCHHHHHHHHHHHHHhCC--------CcchhhHHHHHHHHHHHHHHHHhC---------
Confidence 111234467776665555 6788899999999999986 788999999999999999999998
Q ss_pred ccCCCCCCCccccccCChHHHHHHhhccceeeeeeeEEee--cCccccceE
Q 003054 239 NVSRNATDLEAFGISQNGPKLLQALSSTRFKGLTGDYIFV--DGQLQSSAF 287 (852)
Q Consensus 239 ~~~~~~~~~~~~~~~~~g~~l~~al~~~~f~GltG~v~f~--~G~~~~~~~ 287 (852)
..++++++++|++..|+++.|++.|+ +++...+.|
T Consensus 295 --------------~~~~~~v~~aL~~~~~~~~~g~~~f~~~~~~~~~~~~ 331 (333)
T cd06328 295 --------------DTDTEALIAAMEGMSFETPKGTMTFRKEDHQALQPMY 331 (333)
T ss_pred --------------CCCHHHHHHHHhCCeeecCCCceEECcccchhhhccc
Confidence 34578999999999999999999996 555544433
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=99.92 E-value=3.7e-24 Score=234.85 Aligned_cols=252 Identities=18% Similarity=0.237 Sum_probs=205.0
Q ss_pred hhhHHHHhcCCCCccEEeeecCCCCCCC-CCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHH
Q 003054 2 QTNFIIQLGNKSQVPILSFSATSPSLTS-IRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTD 80 (852)
Q Consensus 2 ~a~~v~~i~~~~~vP~Is~~ats~~lt~-~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~ 80 (852)
++.++++++++.+||+|+++++++.+.+ ..+||+||+.+++..++.+++++++..||++|++++.|++||++..+.+++
T Consensus 77 ~~~a~~~~~~~~~ip~i~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~g~~~vail~~~~~~g~~~~~~~~~ 156 (333)
T cd06359 77 VLLAVVPPVLESGTFYISTNAGPSQLAGKQCSPYFFSTSWQNDQVHEAMGKYAQDKGYKRVFLIAPNYQAGKDALAGFKR 156 (333)
T ss_pred HHHHHHHHHHHcCCeEEecCCCccccccccCCCcEEEeeCChHhhHHHHHHHHHHhCCCeEEEEecCchhhHHHHHHHHH
Confidence 4677889999999999999877777765 458999999999999999999999888999999999999999999999988
Q ss_pred HHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHcCCcccceEEEEcCccccccccC
Q 003054 81 ALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTL 160 (852)
Q Consensus 81 ~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~~~~~~~~~ 160 (852)
.++ .+++....++ .+.+||.+++.++++.+||+|++.....++..+++|++++|+..+ ..++.+...... +.
T Consensus 157 ~~~---~~v~~~~~~~--~~~~d~~~~i~~l~~~~pd~v~~~~~~~~~~~~~~~~~~~G~~~~-~~~~~~~~~~~~-~~- 228 (333)
T cd06359 157 TFK---GEVVGEVYTK--LGQLDFSAELAQIRAAKPDAVFVFLPGGMGVNFVKQYRQAGLKKD-IPLYSPGFSDEE-DT- 228 (333)
T ss_pred HhC---ceeeeeecCC--CCCcchHHHHHHHHhCCCCEEEEEccCccHHHHHHHHHHcCcccC-CeeeccCcccCH-HH-
Confidence 774 4666666555 347899999999999999999998888889999999999998432 235554443321 11
Q ss_pred CchhhcccceEEEEEecCC--CChHHHHHHHHHHHhccccCCCCcccccchhhHhHhhHHHHHHHHHHHhcccCcCcccc
Q 003054 161 EPSVIDSMQGVIGVGPHVP--KTKALENFRVRWKRNFLQENPSIVDVELNIFGLLAYDATRALAEAVEKAGITSFGFDKT 238 (852)
Q Consensus 161 ~~~~~~~~~gv~~~~~~~~--~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~a~~aYDAv~~lA~Al~~a~~~~~~~~~~ 238 (852)
....++.++|+++..++.+ +++..++|.++|+++|+. .|+.++..+||+++++++|+++++..
T Consensus 229 ~~~~g~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~~~--------~~~~~~~~~yda~~~~~~A~~~ag~~------- 293 (333)
T cd06359 229 LPAVGDAALGLYNTAQWAPDLDNPANKKFVADFEKKYGR--------LPTLYAAQAYDAAQLLDSAVRKVGGN------- 293 (333)
T ss_pred HHhcchhhcCeeeccccCCCCCCHHHHHHHHHHHHHhCC--------CCcHHHHHHHHHHHHHHHHHHHhcCC-------
Confidence 1123456789988887776 468899999999999986 68899999999999999999999732
Q ss_pred ccCCCCCCCccccccCChHHHHHHhhccceeeeeeeEEee-cCccccceEEEEE
Q 003054 239 NVSRNATDLEAFGISQNGPKLLQALSSTRFKGLTGDYIFV-DGQLQSSAFEIIN 291 (852)
Q Consensus 239 ~~~~~~~~~~~~~~~~~g~~l~~al~~~~f~GltG~v~f~-~G~~~~~~~~I~~ 291 (852)
..+++.+.++|++++|+|++|++.|+ +|+...+ +.|++
T Consensus 294 --------------~~~~~~v~~al~~~~~~~~~G~~~~~~~~~~~~~-~~~~~ 332 (333)
T cd06359 294 --------------LSDKDALRAALRAADFKSVRGAFRFGTNHFPIQD-FYLRE 332 (333)
T ss_pred --------------CCCHHHHHHHHhcCccccCccceEECCCCCccee-EEEEe
Confidence 12578999999999999999999997 7776433 44443
No 56
>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=99.92 E-value=2.2e-24 Score=237.93 Aligned_cols=248 Identities=20% Similarity=0.221 Sum_probs=204.6
Q ss_pred hhHHHHhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHHHH
Q 003054 3 TNFIIQLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTDAL 82 (852)
Q Consensus 3 a~~v~~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~~l 82 (852)
+.+ ++++++.++|+|+++++++.++...+||+||+.|++..++.+++.++++.+|++|++++.|++||++..+.+++.+
T Consensus 84 ~~~-~~~~~~~~ip~i~~~~~~~~~~~~~~~~~fr~~~~~~~~~~~~~~~~~~~~~~~v~il~~d~~~g~~~~~~~~~~l 162 (347)
T cd06336 84 TAA-QQITERNKVLLLTAYSSDLSIDTAGNPLTFRVPPIYNVYGVPFLAYAKKPGGKKVALLGPNDAYGQPWVAAYKAAW 162 (347)
T ss_pred hhh-hhhhhhcCceEEeccCCcccccccCCceEEEecCCchhHHHHHHHHHhhcCCceEEEEccCCchhHHHHHHHHHHH
Confidence 344 7899999999999999999998667899999999999999999999988999999999999999999999999999
Q ss_pred HhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChh-hHHHHHHHHHHcCCcccceEEEEcCccccccccCC
Q 003054 83 QAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPS-LGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLE 161 (852)
Q Consensus 83 ~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~-~~~~i~~~a~~~G~~~~~~vwi~~~~~~~~~~~~~ 161 (852)
++.|++|+....++.+ +.||++++.+|++.+||+|++.+... ++..++++++++|+..+ ++...+.... ....
T Consensus 163 ~~~G~~vv~~~~~~~~--~~D~s~~i~~i~~~~~d~v~~~~~~~~~~~~~~~~~~~~g~~~~---~~~~~~~~~~-~~~~ 236 (347)
T cd06336 163 EAAGGKVVSEEPYDPG--TTDFSPIVTKLLAEKPDVIFLGGPSPAPAALVIKQARELGFKGG---FLSCTGDKYD-ELLV 236 (347)
T ss_pred HHcCCEEeeecccCCC--CcchHHHHHHHHhcCCCEEEEcCCCchHHHHHHHHHHHcCCCcc---EEeccCCCch-HHHH
Confidence 9999999988888854 78999999999999999999999998 99999999999999765 3332222111 1011
Q ss_pred chhhcccceEEEEEecCC----CChHHHHHHHHHHHhccccCCCCcccccchhhHhHhhHHHHHHHHHHHhcccCcCccc
Q 003054 162 PSVIDSMQGVIGVGPHVP----KTKALENFRVRWKRNFLQENPSIVDVELNIFGLLAYDATRALAEAVEKAGITSFGFDK 237 (852)
Q Consensus 162 ~~~~~~~~gv~~~~~~~~----~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~a~~aYDAv~~lA~Al~~a~~~~~~~~~ 237 (852)
....+.++|++...++.+ .+|..++|+++|+++|+. .|+.++..+||+++++++|+++++..
T Consensus 237 ~~~~~~~~g~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~--------~p~~~~~~~y~~~~~~~~Al~~ag~~------ 302 (347)
T cd06336 237 ATGADFMEGVYFQFPDVDDPALAFPRAKAFVEEYKKRYGE--------PPNSEAAVSYDAVYILKAAMEAAGSV------ 302 (347)
T ss_pred HhcHHhhCceEEEeecccccccCCHHHHHHHHHHHHHHCC--------CCcHHHHHHHHHHHHHHHHHHhcCCC------
Confidence 112345789988877655 478899999999999987 68889999999999999999999833
Q ss_pred cccCCCCCCCccccccCChHHHHHHhhc--------cceeeeeeeEEee-cCccccceEE
Q 003054 238 TNVSRNATDLEAFGISQNGPKLLQALSS--------TRFKGLTGDYIFV-DGQLQSSAFE 288 (852)
Q Consensus 238 ~~~~~~~~~~~~~~~~~~g~~l~~al~~--------~~f~GltG~v~f~-~G~~~~~~~~ 288 (852)
++..+.+++.. ..|.++.|.+.|+ +||+..|.+.
T Consensus 303 -----------------~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~ 345 (347)
T cd06336 303 -----------------DDTAAVAALAAMLGVGKPAFGYARWWGKELFGVNGALVGPWPV 345 (347)
T ss_pred -----------------CcHHHHHHHhhccCCCcCccccccccccccccCCCccccCccc
Confidence 23444444432 5688999999998 9998765543
No 57
>COG0683 LivK ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]
Probab=99.92 E-value=4.6e-24 Score=236.12 Aligned_cols=257 Identities=25% Similarity=0.281 Sum_probs=207.3
Q ss_pred hhhHHHHhcCCCCccEEeeecCCCCCCCCCC-CceEeccCCchhHHHHHHHHHH-HcCCcEEEEEEEeCCcccccHHHHH
Q 003054 2 QTNFIIQLGNKSQVPILSFSATSPSLTSIRS-PYFFRGSLNDSSQAGAITAIIK-AFGWREAVPIYVDNQYGEEMIPSLT 79 (852)
Q Consensus 2 ~a~~v~~i~~~~~vP~Is~~ats~~lt~~~~-py~fR~~p~d~~~~~aia~~l~-~~gw~~vaii~~d~~~G~~~~~~l~ 79 (852)
.+.++.+++++.++|+|++++++|.++...+ +++||++|++.+|+.++++++. ..+.|+|++|+.|+.||++..+.++
T Consensus 90 ~~~a~~~v~~~~~i~~i~p~st~~~~~~~~~~~~vfr~~~~~~~q~~~~~~~l~~~~~~k~v~ii~~~~~yg~~~~~~~~ 169 (366)
T COG0683 90 VALAASPVAEEAGVPLISPSATAPQLTGRGLKPNVFRTGPTDNQQAAAAADYLVKKGGKKRVAIIGDDYAYGEGLADAFK 169 (366)
T ss_pred ccccchhhHhhcCceEEeecCCCCcccccccccceEEecCChHHHHHHHHHHHHHhcCCcEEEEEeCCCCcchhHHHHHH
Confidence 4678899999999999999999999887444 5699999999999999999974 5666699999999999999999999
Q ss_pred HHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHcCCcccceEEEEcCcccccccc
Q 003054 80 DALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRT 159 (852)
Q Consensus 80 ~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~~~~~~~~ 159 (852)
+.+++.|++++..+.+.+. +.||..++.++++.+||+|++.++.+++..+++|+++.|+... .+..++.... ..
T Consensus 170 ~~l~~~G~~~~~~~~~~~~--~~~~~~~v~~i~~~~~d~v~~~~~~~~~~~~~r~~~~~G~~~~---~~~~~~~~~~-~~ 243 (366)
T COG0683 170 AALKALGGEVVVEEVYAPG--DTDFSALVAKIKAAGPDAVLVGGYGPDAALFLRQAREQGLKAK---LIGGDGAGTA-EF 243 (366)
T ss_pred HHHHhCCCeEEEEEeeCCC--CCChHHHHHHHHhcCCCEEEECCCCccchHHHHHHHHcCCCCc---cccccccCch-hh
Confidence 9999999986666677654 5559999999999999999999999999999999999999766 3333333221 11
Q ss_pred CCchhhcccce-EEEEEe-cCC-CChHHHHHHHHHHHhccccCCCCcccccchhhHhHhhHHHHHHHHHHHhcccCcCcc
Q 003054 160 LEPSVIDSMQG-VIGVGP-HVP-KTKALENFRVRWKRNFLQENPSIVDVELNIFGLLAYDATRALAEAVEKAGITSFGFD 236 (852)
Q Consensus 160 ~~~~~~~~~~g-v~~~~~-~~~-~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~a~~aYDAv~~lA~Al~~a~~~~~~~~ 236 (852)
. .......++ .+.... +.+ ++|..+.|+++|+++++.+ ..++.++..+||+++++++|+++++.
T Consensus 244 ~-~~~~~~~~~~~~~~~~~~~~~~~p~~~~f~~~~~~~~g~~------~~~~~~~~~~y~a~~~~~~ai~~a~~------ 310 (366)
T COG0683 244 E-EIAGAGGAGAGLLATAYSTPDDSPANKKFVEAYKAKYGDP------AAPSYFAAAAYDAVKLLAKAIEKAGK------ 310 (366)
T ss_pred h-hhcccCccccEEEEecccccccCcchHHHHHHHHHHhCCC------CCcccchHHHHHHHHHHHHHHHHHhc------
Confidence 0 001122333 333333 333 4577888999999999931 16788999999999999999999983
Q ss_pred ccccCCCCCCCccccccCChHHHHHHhhccc-eeeeeeeEEee-cCccccceEEEEEcc
Q 003054 237 KTNVSRNATDLEAFGISQNGPKLLQALSSTR-FKGLTGDYIFV-DGQLQSSAFEIINVN 293 (852)
Q Consensus 237 ~~~~~~~~~~~~~~~~~~~g~~l~~al~~~~-f~GltG~v~f~-~G~~~~~~~~I~~~~ 293 (852)
..+++++.++|++.. +++.+|.+.|+ +|++....+.|++|+
T Consensus 311 ----------------~~d~~~v~~al~~~~~~~~~~G~v~~~~~~~~~~~~~~i~~~~ 353 (366)
T COG0683 311 ----------------SSDREAVAEALKGGKFFDTAGGPVTFDEKGDRGSKPVYVGQVQ 353 (366)
T ss_pred ----------------CCCHHHHHHHHhhCCCCccCCcceeECCCCCcCCCceEEEEEE
Confidence 123689999999887 78999999998 799888889888887
No 58
>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=99.92 E-value=2.9e-23 Score=229.81 Aligned_cols=240 Identities=13% Similarity=0.073 Sum_probs=193.3
Q ss_pred hhhHHHHhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHH-cCCcEEEEEEEeCCcccccHHHHHH
Q 003054 2 QTNFIIQLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKA-FGWREAVPIYVDNQYGEEMIPSLTD 80 (852)
Q Consensus 2 ~a~~v~~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~-~gw~~vaii~~d~~~G~~~~~~l~~ 80 (852)
++.++.+++++.++|+|++..... ...+||+||+.+++..++.++++++.+ .|.++|++++.|++||++..+.+++
T Consensus 80 ~~~a~~~~~~~~~~~~i~~~~~~~---~~~~~~~F~~~~~~~~~~~~~~~~~~~~~g~k~v~~l~~d~~~g~~~~~~~~~ 156 (359)
T TIGR03407 80 SRKAVLPVFEENNGLLFYPVQYEG---EECSPNIFYTGAAPNQQIIPAVDYLLSKKGAKRFFLLGSDYVFPRTANKIIKA 156 (359)
T ss_pred HHHHHHHHHhccCCceEeCCcccC---cccCCCEEEcCCChHHHHHHHHHHHHhccCCceEEEecCccHHHHHHHHHHHH
Confidence 456889999999999998643221 245799999999999999999998765 5999999999999999999999999
Q ss_pred HHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHcCCcccceEEEEcCccccccccC
Q 003054 81 ALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTL 160 (852)
Q Consensus 81 ~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~~~~~~~~~ 160 (852)
++++.|++|+....++.+ +.||++++.+|++.+||+|++.....++..+++|++++|+..+...++.+......+..+
T Consensus 157 ~~~~~G~~vv~~~~~~~~--~~D~s~~v~~l~~~~pDav~~~~~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~~~~~~ 234 (359)
T TIGR03407 157 YLKSLGGTVVGEDYTPLG--HTDFQTIINKIKAFKPDVVFNTLNGDSNVAFFKQLKNAGITAKDVPVVSFSVAEEEIRGI 234 (359)
T ss_pred HHHHcCCEEEeeEEecCC--hHhHHHHHHHHHHhCCCEEEEeccCCCHHHHHHHHHHcCCCccCCcEEEeecCHHHHhhc
Confidence 999999999998888754 889999999999999999998888888899999999999965433344432221111111
Q ss_pred CchhhcccceEEEEEecC--CCChHHHHHHHHHHHhccccCCCCcccccchhhHhHhhHHHHHHHHHHHhcccCcCcccc
Q 003054 161 EPSVIDSMQGVIGVGPHV--PKTKALENFRVRWKRNFLQENPSIVDVELNIFGLLAYDATRALAEAVEKAGITSFGFDKT 238 (852)
Q Consensus 161 ~~~~~~~~~gv~~~~~~~--~~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~a~~aYDAv~~lA~Al~~a~~~~~~~~~~ 238 (852)
..+.++|+++...+. .+.+..++|+++|+++|+... .++.+++.+||+++++++|+++++
T Consensus 235 ---g~~~~~G~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~------~~~~~~~~~y~a~~~~~~A~~~ag--------- 296 (359)
T TIGR03407 235 ---GPENLVGHLAAWNYFQSVDTPANKKFVKAFKAKYGDDR------VTNDPMEAAYLGVYLWKAAVEKAG--------- 296 (359)
T ss_pred ---ChHhhCCeEEeccchhcCCCHHHHHHHHHHHHHcCCCC------CCCcHHHHHHHHHHHHHHHHHHhC---------
Confidence 124568877654443 356889999999999997521 235567789999999999999998
Q ss_pred ccCCCCCCCccccccCChHHHHHHhhccceeeeeeeEEee
Q 003054 239 NVSRNATDLEAFGISQNGPKLLQALSSTRFKGLTGDYIFV 278 (852)
Q Consensus 239 ~~~~~~~~~~~~~~~~~g~~l~~al~~~~f~GltG~v~f~ 278 (852)
+.++++++++|++++|+++.|++.|+
T Consensus 297 --------------~~~~~~i~~al~~~~~~~~~G~i~f~ 322 (359)
T TIGR03407 297 --------------SFDVDAVRDAAIGIEFDAPEGKVKVD 322 (359)
T ss_pred --------------CCCHHHHHHHhcCCcccCCCccEEEe
Confidence 34679999999999999999999997
No 59
>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=8.2e-24 Score=232.20 Aligned_cols=240 Identities=14% Similarity=0.111 Sum_probs=198.9
Q ss_pred hhhHHHHhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHHH
Q 003054 2 QTNFIIQLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTDA 81 (852)
Q Consensus 2 ~a~~v~~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~~ 81 (852)
++.++.+++++.+||+|++++.+.. ...||+||+.|++..++.++++++...+|++|++|+.|+.||+...+.+++.
T Consensus 79 ~~~a~~~~~~~~~vp~i~~~~~~~~---~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~v~il~~d~~~g~~~~~~~~~~ 155 (333)
T cd06331 79 SRKAVLPVVERGRGLLFYPTQYEGG---ECSPNVFYTGATPNQQLLPLIPYLMEKYGKRFYLIGSDYVWPRESNRIARAL 155 (333)
T ss_pred HHHHHHHHHHhcCceEEeCCCCCCC---cCCCCeEEccCChHHhHHHHHHHHHHhcCCeEEEECCCchhHHHHHHHHHHH
Confidence 4578999999999999997653322 2468999999999999999999886666999999999999999999999999
Q ss_pred HHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHcCCcccceEEEEcCccccccccCC
Q 003054 82 LQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLE 161 (852)
Q Consensus 82 l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~~~~~~~~~~ 161 (852)
+++.|.+|+....++++ +.||++++.++++.+||+|++++..+++..+++|+++.|+......++ +..+... . ..
T Consensus 156 ~~~~G~~vv~~~~~~~~--~~d~~~~v~~~~~~~~d~v~~~~~~~~~~~~~~~~~~~g~~~~~~~~~-~~~~~~~-~-~~ 230 (333)
T cd06331 156 LEELGGEVVGEEYLPLG--TSDFGSVIEKIKAAGPDVVLSTLVGDSNVAFYRQFAAAGLDADRIPIL-SLTLDEN-E-LA 230 (333)
T ss_pred HHHcCCEEEEEEEecCC--cccHHHHHHHHHHcCCCEEEEecCCCChHHHHHHHHHcCCCcCCCeeE-Ecccchh-h-hh
Confidence 99999999998888855 789999999999999999999999999999999999999964333333 3332221 1 11
Q ss_pred chhhcccceEEEEEecCC--CChHHHHHHHHHHHhccccCCCCcccccchhhHhHhhHHHHHHHHHHHhcccCcCccccc
Q 003054 162 PSVIDSMQGVIGVGPHVP--KTKALENFRVRWKRNFLQENPSIVDVELNIFGLLAYDATRALAEAVEKAGITSFGFDKTN 239 (852)
Q Consensus 162 ~~~~~~~~gv~~~~~~~~--~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~a~~aYDAv~~lA~Al~~a~~~~~~~~~~~ 239 (852)
.......+|+++..+|.+ +.+..++|+++|+++++.+. .++.+++.+||+++++++|+++++
T Consensus 231 ~~~~~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~------~~~~~~~~~yda~~~~~~A~~~ag---------- 294 (333)
T cd06331 231 AIGAEAAEGHYSAASYFQSLDTPENKAFVARYRARYGDDA------VINSPAEAAYEAVYLWAAAVEKAG---------- 294 (333)
T ss_pred ccChhhhCCcEeechhhhhcCChhHHHHHHHHHHHcCCCc------CCCchhHHHHHHHHHHHHHHHHcC----------
Confidence 112345789888877765 46789999999999987521 378899999999999999999987
Q ss_pred cCCCCCCCccccccCChHHHHHHhhccceeeeeeeEEee
Q 003054 240 VSRNATDLEAFGISQNGPKLLQALSSTRFKGLTGDYIFV 278 (852)
Q Consensus 240 ~~~~~~~~~~~~~~~~g~~l~~al~~~~f~GltG~v~f~ 278 (852)
..++++|+++|++++|+|++|++.|+
T Consensus 295 -------------~~~~~~l~~al~~~~~~~~~G~i~f~ 320 (333)
T cd06331 295 -------------STDPEAVRAALEGVSFDAPQGPVRID 320 (333)
T ss_pred -------------CCCHHHHHHHhhcCcccCCCCceEec
Confidence 34579999999999999999999997
No 60
>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=99.91 E-value=2.2e-23 Score=231.64 Aligned_cols=261 Identities=15% Similarity=0.249 Sum_probs=210.1
Q ss_pred hhhHHHHhcCCCCccEEeeecCCCCCCCC-CCCceEeccCCchhHHHHHHHHH-HHcCCcEEEEEEEeCCcccccHHHHH
Q 003054 2 QTNFIIQLGNKSQVPILSFSATSPSLTSI-RSPYFFRGSLNDSSQAGAITAII-KAFGWREAVPIYVDNQYGEEMIPSLT 79 (852)
Q Consensus 2 ~a~~v~~i~~~~~vP~Is~~ats~~lt~~-~~py~fR~~p~d~~~~~aia~~l-~~~gw~~vaii~~d~~~G~~~~~~l~ 79 (852)
.+.++++++++.+||+|+++++++.+++. .+||+||+.|++..++.++++++ +++||++|++|+.|++||++..+.++
T Consensus 86 ~~~~~~~~~~~~~ip~i~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~g~~~v~ii~~~~~~g~~~~~~~~ 165 (362)
T cd06343 86 TNLAVQKYLNEKKVPQLFPASGASKWNDPKPFPWTFGWQPSYQDEARIYAKYLVEEKPNAKIAVLYQNDDFGKDYLKGLK 165 (362)
T ss_pred HHHHhHHHHHhcCCceEecccccHhhhCCCCCCceEecCCChHHHHHHHHHHHHHhCCCceEEEEEeccHHHHHHHHHHH
Confidence 35678899999999999998888888864 78999999999999999999975 67899999999999999999999999
Q ss_pred HHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHcCCcccceEEEEcCcccccccc
Q 003054 80 DALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRT 159 (852)
Q Consensus 80 ~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~~~~~~~~ 159 (852)
+.+++.|++++....++.+ ..||++++.++++.+||+|++.+...++..+++++++.|+..+ ++.++++......
T Consensus 166 ~~~~~~G~~vv~~~~~~~~--~~d~~~~v~~i~~~~~d~v~~~~~~~~~~~~~~~~~~~g~~~~---~~~~~~~~~~~~~ 240 (362)
T cd06343 166 DGLGDAGLEIVAETSYEVT--EPDFDSQVAKLKAAGADVVVLATTPKFAAQAIRKAAELGWKPT---FLLSSVSASVASV 240 (362)
T ss_pred HHHHHcCCeEEEEeeecCC--CccHHHHHHHHHhcCCCEEEEEcCcHHHHHHHHHHHHcCCCce---EEEEecccccHHH
Confidence 9999999999998888754 7889999999999999999999999999999999999999765 5555544322110
Q ss_pred CCchhhcccceEEEEEecC-------CCChHHHHHHHHHHHhccccCCCCcccccchhhHhHhhHHHHHHHHHHHhcccC
Q 003054 160 LEPSVIDSMQGVIGVGPHV-------PKTKALENFRVRWKRNFLQENPSIVDVELNIFGLLAYDATRALAEAVEKAGITS 232 (852)
Q Consensus 160 ~~~~~~~~~~gv~~~~~~~-------~~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~a~~aYDAv~~lA~Al~~a~~~~ 232 (852)
+.....+..+|+++...+. .+.+..++|.++|+++++... +++.+++.+||++.++++|+++++.
T Consensus 241 ~~~~~~~~~~g~~~~~~~~~~~~p~~~~~~~~~~f~~~~~~~~~~~~------~~~~~~~~~y~a~~~~~~a~~~ag~-- 312 (362)
T cd06343 241 LKPAGLEAAEGVIAAAYLKDPTDPAWADDPGVKEFIAFYKKYFPEGD------PPDTYAVYGYAAAETLVKVLKQAGD-- 312 (362)
T ss_pred HHHhhhHhhCceEEEEEecCCCccccccCHHHHHHHHHHHHhcCCCC------CCchhhhHHHHHHHHHHHHHHHhCC--
Confidence 1111234578887765542 246889999999999997621 4788999999999999999999872
Q ss_pred cCccccccCCCCCCCccccccCChHHHHHHhhccce---e-eeeeeEEee-cCccccceEEEEEccCC
Q 003054 233 FGFDKTNVSRNATDLEAFGISQNGPKLLQALSSTRF---K-GLTGDYIFV-DGQLQSSAFEIINVNNG 295 (852)
Q Consensus 233 ~~~~~~~~~~~~~~~~~~~~~~~g~~l~~al~~~~f---~-GltG~v~f~-~G~~~~~~~~I~~~~~g 295 (852)
..+++.|+++|+++++ . +..|++.|+ +++.....+.|.++++|
T Consensus 313 --------------------~~~~~~v~~aL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~g 360 (362)
T cd06343 313 --------------------DLTRENIMKQAESLKDVLPDLLPGIRINTSPDDHLPIEQMQLMRFEGG 360 (362)
T ss_pred --------------------CCCHHHHHHHHHhCCCCCccccCccceecCccccccceeEEEEEEecC
Confidence 2357899999999986 3 344688996 33333455667776633
No 61
>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=99.91 E-value=2.6e-23 Score=228.96 Aligned_cols=254 Identities=19% Similarity=0.272 Sum_probs=207.0
Q ss_pred hhhHHHHhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHH-HHcCCcEEEEEEEeCCcccccHHHHHH
Q 003054 2 QTNFIIQLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAII-KAFGWREAVPIYVDNQYGEEMIPSLTD 80 (852)
Q Consensus 2 ~a~~v~~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l-~~~gw~~vaii~~d~~~G~~~~~~l~~ 80 (852)
.+.++++++++.+||+|+++++++.+++ ..+|+||+.|++..++.++++++ +++||++|++++.|++||....+.+++
T Consensus 79 ~~~a~~~~~~~~~vp~i~~~~~~~~~~~-~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~v~ii~~~~~~g~~~~~~~~~ 157 (340)
T cd06349 79 VSMAASPIYQRAGLVQLSPTNSHPDFTK-GGDFIFRNSTSQAIEAPLLADYAVKDLGFKKVAILSVNTDWGRTSADIFVK 157 (340)
T ss_pred hHHHhHHHHHhCCCeEEecCCCCCcccc-CCCeEEEccCCcHHHHHHHHHHHHHHcCCcEEEEEecCChHhHHHHHHHHH
Confidence 4567899999999999999988888875 46999999999999999999996 778999999999999999999999999
Q ss_pred HHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHcCCcccceEEEEcCccccccccC
Q 003054 81 ALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTL 160 (852)
Q Consensus 81 ~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~~~~~~~~~ 160 (852)
++++.|++|+....++++ ..|+++++.++++++||+|++.+.+.++..+++++++.|+..+ ++....+... ...
T Consensus 158 ~~~~~g~~v~~~~~~~~~--~~d~~~~v~~l~~~~~d~v~~~~~~~~~~~~~~~~~~~g~~~~---~~~~~~~~~~-~~~ 231 (340)
T cd06349 158 AAEKLGGQVVAHEEYVPG--EKDFRPTITRLRDANPDAIILISYYNDGAPIARQARAVGLDIP---VVASSSVYSP-KFI 231 (340)
T ss_pred HHHHcCCEEEEEEEeCCC--CCcHHHHHHHHHhcCCCEEEEccccchHHHHHHHHHHcCCCCc---EEccCCcCCH-HHH
Confidence 999999999988888754 7789999999999999999999999999999999999999766 5554433211 111
Q ss_pred CchhhcccceEEEEEecCCC--ChHHHHHHHHHHHhccccCCCCcccccchhhHhHhhHHHHHHHHHHHhcccCcCcccc
Q 003054 161 EPSVIDSMQGVIGVGPHVPK--TKALENFRVRWKRNFLQENPSIVDVELNIFGLLAYDATRALAEAVEKAGITSFGFDKT 238 (852)
Q Consensus 161 ~~~~~~~~~gv~~~~~~~~~--~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~a~~aYDAv~~lA~Al~~a~~~~~~~~~~ 238 (852)
. ......+|+++..+|.++ .+..++|.++|+++|+. .|+.++..+||+++++++|+++++.+
T Consensus 232 ~-~~~~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~~~--------~p~~~~~~~y~~~~~~~~a~~~ag~~------- 295 (340)
T cd06349 232 E-LGGDAVEGVYTPTAFFPGDPRPEVQSFVSAYEAKYGA--------QPDAFAAQAYDAVGILAAAVRRAGTD------- 295 (340)
T ss_pred H-HhHHHhCCcEEecccCCCCCCHHHHHHHHHHHHHHCC--------CcchhhhhHHHHHHHHHHHHHHhCCC-------
Confidence 1 123457899888877764 57889999999999986 68889999999999999999999832
Q ss_pred ccCCCCCCCccccccCChHHHHHH-hhccceeeeeeeEEee-c-CccccceEEEEEccCC
Q 003054 239 NVSRNATDLEAFGISQNGPKLLQA-LSSTRFKGLTGDYIFV-D-GQLQSSAFEIINVNNG 295 (852)
Q Consensus 239 ~~~~~~~~~~~~~~~~~g~~l~~a-l~~~~f~GltG~v~f~-~-G~~~~~~~~I~~~~~g 295 (852)
+...+... +.+..+.|++|++.|+ + |+.. ..+.++.+++|
T Consensus 296 ----------------~~~~~~~~~~~~~~~~~~~g~i~~~~~~~~~~-~~~~~~~~~~g 338 (340)
T cd06349 296 ----------------RRAARDGFAKAEDVYSGVTGSTKFDPNTRRVI-KRFVPLVVRNG 338 (340)
T ss_pred ----------------CHHHHHHHHHhccCcccceEeEEECCCCCCcc-CceEEEEEeCC
Confidence 22333333 2455688999999997 4 5553 46777776544
No 62
>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=99.91 E-value=3.5e-23 Score=227.37 Aligned_cols=246 Identities=23% Similarity=0.305 Sum_probs=206.7
Q ss_pred hhHHHHhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHH-HHcCCcEEEEEEEeC-CcccccHHHHHH
Q 003054 3 TNFIIQLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAII-KAFGWREAVPIYVDN-QYGEEMIPSLTD 80 (852)
Q Consensus 3 a~~v~~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l-~~~gw~~vaii~~d~-~~G~~~~~~l~~ 80 (852)
+.++++++++++||+|+++++.+.+++. .+|+||+.+++..++.++++++ ++++|++|++|+.++ +|+....+.+++
T Consensus 80 ~~~v~~~~~~~~ip~i~~~~~~~~~~~~-~~~~fr~~~~~~~~~~~~~~~~~~~~~~~~v~ii~~~~~~~~~~~~~~~~~ 158 (334)
T cd06347 80 TLAAGPIAEDAKVPMITPSATNPKVTQG-KDYVFRVCFIDPFQGTVMAKFATENLKAKKAAVLYDNSSDYSKGLAKAFKE 158 (334)
T ss_pred HHHhHHHHHHCCCeEEcCCCCCCCcccC-CCeEEEeeCCcHHHHHHHHHHHHHhcCCcEEEEEEeCCCchhHHHHHHHHH
Confidence 5678899999999999999988887753 4699999999999999999986 678999999999875 899999999999
Q ss_pred HHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHcCCcccceEEEEcCccccccccC
Q 003054 81 ALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTL 160 (852)
Q Consensus 81 ~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~~~~~~~~~ 160 (852)
++++.|++++....++.+ ..|+.+.+.++++.++|+|++.+...+...+++++++.|+..+ |++++.|.....
T Consensus 159 ~~~~~g~~v~~~~~~~~~--~~d~~~~~~~~~~~~~d~i~~~~~~~~~~~~~~~~~~~g~~~~---i~~~~~~~~~~~-- 231 (334)
T cd06347 159 AFKKLGGEIVAEETFNAG--DTDFSAQLTKIKAKNPDVIFLPGYYTEVGLIAKQARELGIKVP---ILGGDGWDSPKL-- 231 (334)
T ss_pred HHHHcCCEEEEEEEecCC--CCcHHHHHHHHHhcCCCEEEEcCchhhHHHHHHHHHHcCCCCc---EEecccccCHHH--
Confidence 999999999988887754 6789999999999999999999999999999999999998544 777776653211
Q ss_pred CchhhcccceEEEEEecCCC--ChHHHHHHHHHHHhccccCCCCcccccchhhHhHhhHHHHHHHHHHHhcccCcCcccc
Q 003054 161 EPSVIDSMQGVIGVGPHVPK--TKALENFRVRWKRNFLQENPSIVDVELNIFGLLAYDATRALAEAVEKAGITSFGFDKT 238 (852)
Q Consensus 161 ~~~~~~~~~gv~~~~~~~~~--~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~a~~aYDAv~~lA~Al~~a~~~~~~~~~~ 238 (852)
........+|++...++.+. .+..+.|.++|+++++. .|+.++..+||+++++++|+++++.
T Consensus 232 ~~~~~~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~~~--------~~~~~~~~~yda~~~~~~Al~~ag~-------- 295 (334)
T cd06347 232 EEAGGAAAEGVYFTTHFSADDPTPKAKKFVKAYKAKYGK--------EPDAFAALGYDAYYLLADAIERAGS-------- 295 (334)
T ss_pred HHHHHHHhCCcEEecccCCCCCCHHHHHHHHHHHHHHCC--------CcchhHHHHHHHHHHHHHHHHHhCC--------
Confidence 11133567888887777664 58899999999999975 6888999999999999999999872
Q ss_pred ccCCCCCCCccccccCChHHHHHHhhcc-ceeeeeeeEEee-cCccccceE
Q 003054 239 NVSRNATDLEAFGISQNGPKLLQALSST-RFKGLTGDYIFV-DGQLQSSAF 287 (852)
Q Consensus 239 ~~~~~~~~~~~~~~~~~g~~l~~al~~~-~f~GltG~v~f~-~G~~~~~~~ 287 (852)
.+++.+.++|.+. +|+|++|++.|+ +|+.....+
T Consensus 296 ---------------~~~~~v~~~l~~~~~~~g~~G~v~f~~~g~~~~~~~ 331 (334)
T cd06347 296 ---------------TDPEAIRDALAKTKDFDGVTGKITIDENGNPVKSAV 331 (334)
T ss_pred ---------------CCHHHHHHHHHhCCCcccceeeeEECCCCCcCCCce
Confidence 3568999998865 699999999997 788754443
No 63
>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=3.2e-23 Score=227.66 Aligned_cols=247 Identities=17% Similarity=0.202 Sum_probs=204.1
Q ss_pred hhHHHHhcCCCCccEEeeecCCCCCCCC-CCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHHH
Q 003054 3 TNFIIQLGNKSQVPILSFSATSPSLTSI-RSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTDA 81 (852)
Q Consensus 3 a~~v~~i~~~~~vP~Is~~ats~~lt~~-~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~~ 81 (852)
+.++.+.+++.++|+|+++++++.+++. .+||+||+.|++..++..+++++...||+++++++.++.||++..+.+++.
T Consensus 78 ~~~~~~~~~~~~ip~v~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~l~~~g~~~v~il~~~~~~~~~~~~~~~~~ 157 (333)
T cd06332 78 ALAVVPSLTESGTFLISPNAGPSDLAGKLCSPNFFRTSWQNDQVHEAMGKYAADKGYKKVVIIAPDYAAGKDAVAGFKRT 157 (333)
T ss_pred HHHHHHHHhhcCCeEEecCCCCccccccCCCCcEEEeeCChHHhHHHHHHHHHHhCCceEEEEecCcchhHHHHHHHHHh
Confidence 4466788999999999999888888764 479999999999999999999999999999999999999999999999999
Q ss_pred HHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHcCCcccceEEEEcCccccccccCC
Q 003054 82 LQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLE 161 (852)
Q Consensus 82 l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~~~~~~~~~~ 161 (852)
++ .+++....++.+ ..|+.+++.++++.+||+|++...+..+..++++++++|+.. ...+++++.+.... ..
T Consensus 158 ~~---~~~~~~~~~~~~--~~d~~~~i~~l~~~~~d~i~~~~~~~~~~~~~~~~~~~g~~~-~~~~~~~~~~~~~~--~~ 229 (333)
T cd06332 158 FK---GEVVEEVYTPLG--QLDFSAELAQIRAAKPDAVFVFLPGGMAVNFVKQYDQAGLKK-KIPLYGPGFLTDQD--TL 229 (333)
T ss_pred hc---EEEeeEEecCCC--CcchHHHHHHHHhcCCCEEEEecccchHHHHHHHHHHcCccc-CCceeccCCCCCHH--HH
Confidence 98 466666666543 678999999999999999999988889999999999999933 22366655544321 11
Q ss_pred chhhcccceEEEEEecCCC--ChHHHHHHHHHHHhccccCCCCcccccchhhHhHhhHHHHHHHHHHHhcccCcCccccc
Q 003054 162 PSVIDSMQGVIGVGPHVPK--TKALENFRVRWKRNFLQENPSIVDVELNIFGLLAYDATRALAEAVEKAGITSFGFDKTN 239 (852)
Q Consensus 162 ~~~~~~~~gv~~~~~~~~~--~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~a~~aYDAv~~lA~Al~~a~~~~~~~~~~~ 239 (852)
......++|+++..++.++ ++..++|.++|+++|+. .|+.++..+||+++++++|+++++..
T Consensus 230 ~~~~~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~~~--------~~~~~~~~~yda~~~~~~a~~~ag~~-------- 293 (333)
T cd06332 230 PAQGDAAVGVLTALHWAPDLDNPANKRFVAAYKAAYGR--------VPSVYAAQGYDAAQLLDAALRAVGGD-------- 293 (333)
T ss_pred HhhchhhcCeeeeeccCCCCCCHHHHHHHHHHHHHhCC--------CCcHHHHHHHHHHHHHHHHHHHhcCC--------
Confidence 1234567899888887764 58899999999999986 68889999999999999999999732
Q ss_pred cCCCCCCCccccccCChHHHHHHhhccceeeeeeeEEee-cCccccce
Q 003054 240 VSRNATDLEAFGISQNGPKLLQALSSTRFKGLTGDYIFV-DGQLQSSA 286 (852)
Q Consensus 240 ~~~~~~~~~~~~~~~~g~~l~~al~~~~f~GltG~v~f~-~G~~~~~~ 286 (852)
..+++.|.++|++++|+|+.|++.|+ +|+...+.
T Consensus 294 -------------~~~~~~v~~al~~~~~~~~~g~i~f~~~~~~~~~~ 328 (333)
T cd06332 294 -------------LSDKDALRAALRAADFDSPRGPFKFNPNHNPIQDF 328 (333)
T ss_pred -------------CCCHHHHHHHHhcCceecCccceeECCCCCcccce
Confidence 23468899999999999999999997 88874443
No 64
>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=99.91 E-value=2.3e-23 Score=230.01 Aligned_cols=245 Identities=21% Similarity=0.202 Sum_probs=201.0
Q ss_pred hhhHHHHhcCCCCccEEeeecCCCCCCC-CCCCceEeccCCchhHHHHHHHHHHHc--CCcEEEEEEEeCCcccccHHHH
Q 003054 2 QTNFIIQLGNKSQVPILSFSATSPSLTS-IRSPYFFRGSLNDSSQAGAITAIIKAF--GWREAVPIYVDNQYGEEMIPSL 78 (852)
Q Consensus 2 ~a~~v~~i~~~~~vP~Is~~ats~~lt~-~~~py~fR~~p~d~~~~~aia~~l~~~--gw~~vaii~~d~~~G~~~~~~l 78 (852)
++.++++++++.+||+|++.++++.+++ ..+||+||+.|++..+..++++++++. +|++|++++.|++||.+..+.+
T Consensus 79 ~~~~~~~~~~~~~ip~i~~~s~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~v~~l~~~~~~g~~~~~~~ 158 (346)
T cd06330 79 VALAVAPVAEELKVFFIATDPGTPRLTEEPDNPYVFRTRNSTIMDAVAGALYAAKLDKKAKTWATINPDYAYGQDAWADF 158 (346)
T ss_pred HHHHHHHHHHHcCCeEEEcCCCCcccccCCCCCceEEecCChHHHHHHHHHHHHHhCcCccEEEEECCchHHHHHHHHHH
Confidence 4678899999999999999998888876 578999999999999999999999776 4999999999999999999999
Q ss_pred HHHHHhC--CceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHcCCcccceEEEEcCccccc
Q 003054 79 TDALQAI--DTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNL 156 (852)
Q Consensus 79 ~~~l~~~--g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~~~~~ 156 (852)
++.+++. |++++....++ ..++|+.+++.+|++.+||+|++.+.+.+...+++++++.|+.. +..|+.+.+....
T Consensus 159 ~~~~~~~g~~~~~v~~~~~~--~~~~d~~~~v~~i~~~~~d~ii~~~~~~~~~~~~~~~~~~g~~~-~~~~~~~~~~~~~ 235 (346)
T cd06330 159 KAALKRLRPDVEVVSEQWPK--LGAPDYGSEITALLAAKPDAIFSSLWGGDLVTFVRQANARGLFD-GTTVVLTLTGAPE 235 (346)
T ss_pred HHHHHHhCCCCeecccccCC--CCCcccHHHHHHHHhcCCCEEEEecccccHHHHHHHHHhcCccc-CceEEeeccchhh
Confidence 9999998 46666555444 34789999999999999999999999999999999999999854 4557766654432
Q ss_pred cccCCchhhcccceEEEEEe--cCC--CChHHHHHHHHHHHhccccCCCCcccccchhhHhHhhHHHHHHHHHHHhcccC
Q 003054 157 LRTLEPSVIDSMQGVIGVGP--HVP--KTKALENFRVRWKRNFLQENPSIVDVELNIFGLLAYDATRALAEAVEKAGITS 232 (852)
Q Consensus 157 ~~~~~~~~~~~~~gv~~~~~--~~~--~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~a~~aYDAv~~lA~Al~~a~~~~ 232 (852)
+. ....+..+|++.... +.. +++..++|+++|+++|+. .|+.++..+||+++++++|+++++...
T Consensus 236 ~~---~~~~~~~~g~~~~~~~~~~~~~~~~~~~~f~~~~~~~~g~--------~p~~~~~~~y~a~~~l~~a~~~a~~~~ 304 (346)
T cd06330 236 LA---PLGDEMPEGVIIGGRGPYFIPPDTPENKAFVDAYQEKYGD--------YPTYGAYGAYQAVMALAAAVEKAGATD 304 (346)
T ss_pred hh---hhhcccCCceEEeccccCCCCCCChHHHHHHHHHHHHHCC--------CCChHHHHHHHHHHHHHHHHHHhcCCC
Confidence 11 112345678765442 222 578899999999999985 678899999999999999999998432
Q ss_pred cCccccccCCCCCCCccccccCChHHHHHHhhccceeeeeeeEEeec
Q 003054 233 FGFDKTNVSRNATDLEAFGISQNGPKLLQALSSTRFKGLTGDYIFVD 279 (852)
Q Consensus 233 ~~~~~~~~~~~~~~~~~~~~~~~g~~l~~al~~~~f~GltG~v~f~~ 279 (852)
.. .+. +.++++|++++|+|+.|++.|+.
T Consensus 305 ~~------------------~~~-~~v~~al~~~~~~~~~G~~~f~~ 332 (346)
T cd06330 305 GG------------------APP-EQIAAALEGLSFETPGGPITMRA 332 (346)
T ss_pred CC------------------CcH-HHHHHHHcCCCccCCCCceeeec
Confidence 10 111 67999999999999999999974
No 65
>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=1.6e-22 Score=223.96 Aligned_cols=256 Identities=14% Similarity=0.118 Sum_probs=202.1
Q ss_pred hhhHHHHhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHHH
Q 003054 2 QTNFIIQLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTDA 81 (852)
Q Consensus 2 ~a~~v~~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~~ 81 (852)
++.++++++++.++|++++++... . ...|++|++.++...++.++++++.+.+-+++++|+.|++||++..+.+++.
T Consensus 79 ~~~a~~~~~~~~~~~~~~~~~~~~-~--~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~v~~i~~d~~~g~~~~~~~~~~ 155 (360)
T cd06357 79 SRKAVLPVVERHDALLWYPTLYEG-F--EYSPNVIYTGAAPNQNSVPLADYLLRHYGKRVFLVGSNYIYPYESNRIMRDL 155 (360)
T ss_pred HHHHHHHHHHhcCceEEeCCCccC-C--cccCCEEEeCCCcHHHHHHHHHHHHhcCCcEEEEECCCCcchHHHHHHHHHH
Confidence 357889999999999998765322 1 2347889988888888889999986655589999999999999999999999
Q ss_pred HHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHcCCcccceEEEEcCccccccccCC
Q 003054 82 LQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLE 161 (852)
Q Consensus 82 l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~~~~~~~~~~ 161 (852)
+++.|++|+....++.+.++.||++++.++++++||+|+++....++..+++|++++|+..+.. .+.+...... . ..
T Consensus 156 ~~~~G~~vv~~~~~~~~~~~~d~s~~v~~l~~~~pd~V~~~~~~~~~~~~~~~~~~~G~~~~~~-~~~~~~~~~~-~-~~ 232 (360)
T cd06357 156 LEQRGGEVLGERYLPLGASDEDFARIVEEIREAQPDFIFSTLVGQSSYAFYRAYAAAGFDPARM-PIASLTTSEA-E-VA 232 (360)
T ss_pred HHHcCCEEEEEEEecCCCchhhHHHHHHHHHHcCCCEEEEeCCCCChHHHHHHHHHcCCCccCc-eeEEeeccHH-H-Hh
Confidence 9999999988766665555889999999999999999999999999999999999999975522 2233222211 1 11
Q ss_pred chhhcccceEEEEEecCC--CChHHHHHHHHHHHhccccCCCCcccccchhhHhHhhHHHHHHHHHHHhcccCcCccccc
Q 003054 162 PSVIDSMQGVIGVGPHVP--KTKALENFRVRWKRNFLQENPSIVDVELNIFGLLAYDATRALAEAVEKAGITSFGFDKTN 239 (852)
Q Consensus 162 ~~~~~~~~gv~~~~~~~~--~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~a~~aYDAv~~lA~Al~~a~~~~~~~~~~~ 239 (852)
....+.++|+++..+|.+ ++|..++|.++|+++|+... .++.+++.+||+++++++|+++++
T Consensus 233 ~~~g~~~~g~~~~~~~~~~~~~p~~~~f~~~~~~~~g~~~------~~~~~~~~~yda~~~l~~Al~~ag---------- 296 (360)
T cd06357 233 AMGAEAAAGHITAAPYFSSIDTPANRAFVARYRARFGEDA------PVSACAEAAYFQVHLFARALQRAG---------- 296 (360)
T ss_pred hcchHhhCCcEEecccccccCChhHHHHHHHHHHHcCCCC------CCCcHHHHHHHHHHHHHHHHHHcC----------
Confidence 112356789988877654 56889999999999998621 367789999999999999999988
Q ss_pred cCCCCCCCccccccCChHHHHHHhhccceeeeeeeEEee-cCccccceEEEEEc
Q 003054 240 VSRNATDLEAFGISQNGPKLLQALSSTRFKGLTGDYIFV-DGQLQSSAFEIINV 292 (852)
Q Consensus 240 ~~~~~~~~~~~~~~~~g~~l~~al~~~~f~GltG~v~f~-~G~~~~~~~~I~~~ 292 (852)
+.+++.|+++|++.+|+|+.|.+.|+ .++.......+.++
T Consensus 297 -------------~~~~~~v~~aL~~~~~~~~~g~~~f~~~~~~~~~~~~~~~~ 337 (360)
T cd06357 297 -------------SDDPEDVLAALLGFSFDAPQGPVRIDPDNNHTYLWPRIARV 337 (360)
T ss_pred -------------CCCHHHHHHHhccCcccCCCcceEEeCCCCeeeeeeEEEEE
Confidence 34578999999999999999999997 44433344445565
No 66
>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=99.90 E-value=5.8e-23 Score=226.19 Aligned_cols=251 Identities=16% Similarity=0.103 Sum_probs=200.2
Q ss_pred hhhHHHHhcCCCCccEEeeecCCCCCCC-CCCCceEeccCCchhHHHHHHHHHHHcC-----CcEEEEEEEeCCcccccH
Q 003054 2 QTNFIIQLGNKSQVPILSFSATSPSLTS-IRSPYFFRGSLNDSSQAGAITAIIKAFG-----WREAVPIYVDNQYGEEMI 75 (852)
Q Consensus 2 ~a~~v~~i~~~~~vP~Is~~ats~~lt~-~~~py~fR~~p~d~~~~~aia~~l~~~g-----w~~vaii~~d~~~G~~~~ 75 (852)
++.++.+++++++||+|+++++++.+++ .++||+||+.|++..++.++++++.+.+ .++|++++.|++||++..
T Consensus 78 ~~~a~~~~~~~~~vp~i~~~~~~~~~~~~~~~~~~Fr~~~~~~~~~~~l~~~~~~~~~~~~~~~kvaiv~~~~~~g~~~~ 157 (351)
T cd06334 78 ITEALIPKIAADKIPLMSGSYGATLADDGAVFPYNFPVGPTYSDQARALVQYIAEQEGGKLKGKKIALVYHDSPFGKEPI 157 (351)
T ss_pred HHHHhhHHHhhcCCcEEecccchhhccCCCCCCeeeeCCCCHHHHHHHHHHHHHHhcccCCCCCeEEEEeCCCccchhhH
Confidence 4668899999999999999888777774 6789999999999999999999986654 799999999999999999
Q ss_pred HHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHcCCcccceEEEEcCcccc
Q 003054 76 PSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTN 155 (852)
Q Consensus 76 ~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~~~~ 155 (852)
+.+++.+++.|++|+....++.+ +.||++++.++++.+||+|++.+...++..+++|++++|+..+ ++.+.+...
T Consensus 158 ~~~~~~~~~~G~~vv~~~~~~~~--~~D~~~~v~~i~~~~pd~V~~~~~~~~~~~~~~~~~~~G~~~~---~~~~~~~~~ 232 (351)
T cd06334 158 EALKALAEKLGFEVVLEPVPPPG--PNDQKAQWLQIRRSGPDYVILWGWGVMNPVAIKEAKRVGLDDK---FIGNWWSGD 232 (351)
T ss_pred HHHHHHHHHcCCeeeeeccCCCC--cccHHHHHHHHHHcCCCEEEEecccchHHHHHHHHHHcCCCce---EEEeeccCc
Confidence 99999999999999998888754 7899999999999999999999999999999999999999544 554433221
Q ss_pred ccccCCchhhcccceEEEEEecCC--CChHHHHHHHHHHHhccccCCCCcccccchhhHhHhhHHHHHHHHHHHhcccCc
Q 003054 156 LLRTLEPSVIDSMQGVIGVGPHVP--KTKALENFRVRWKRNFLQENPSIVDVELNIFGLLAYDATRALAEAVEKAGITSF 233 (852)
Q Consensus 156 ~~~~~~~~~~~~~~gv~~~~~~~~--~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~a~~aYDAv~~lA~Al~~a~~~~~ 233 (852)
... ....++..+|+++..++.+ ++|..++|+++|+++|+.. +. ....++.+++.+||+++++++||++|+....
T Consensus 233 -~~~-~~~~g~~~~g~~~~~~~~~~~~~p~~~~f~~~~~~~~~~~-~~-~~~~~~~~~~~gy~a~~~l~~Al~~ag~~~~ 308 (351)
T cd06334 233 -EED-VKPAGDAAKGYKGVTPFAGGADDPVGKEIVKEVYDKGKGS-GN-DKEIGSVYYNRGVVNAMIMVEAIRRAQEKGG 308 (351)
T ss_pred -HHH-HHHhhhhhcCcEEeecccCCCCchHHHHHHHHHHHccCCC-CC-cccccccHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 111 1123456789888777655 5789999999999999751 10 0013468899999999999999999986542
Q ss_pred CccccccCCCCCCCccccccCCh-------HHHHHHhhccceeeeeeeEEee
Q 003054 234 GFDKTNVSRNATDLEAFGISQNG-------PKLLQALSSTRFKGLTGDYIFV 278 (852)
Q Consensus 234 ~~~~~~~~~~~~~~~~~~~~~~g-------~~l~~al~~~~f~GltG~v~f~ 278 (852)
.. ...+ +..++.+.+....|+.|++.|.
T Consensus 309 ~~-----------------~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~ 343 (351)
T cd06334 309 ET-----------------TIAGEEQLENLKLDAARLEELGAEGLGPPVSVS 343 (351)
T ss_pred CC-----------------CCcHHHHHHhhhhhhhhhhhcCcccccCCceec
Confidence 10 1111 2344556666788999999995
No 67
>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=1.3e-22 Score=222.57 Aligned_cols=245 Identities=17% Similarity=0.171 Sum_probs=198.0
Q ss_pred hhhHHHHhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHH-HHcCCcEEEEEEEeCCcccccHHHHHH
Q 003054 2 QTNFIIQLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAII-KAFGWREAVPIYVDNQYGEEMIPSLTD 80 (852)
Q Consensus 2 ~a~~v~~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l-~~~gw~~vaii~~d~~~G~~~~~~l~~ 80 (852)
++.++.++++ .+||+|++.+.+.. ...||+||+.+++..++.++++++ +..||++|++++.|++||++..+.+++
T Consensus 79 ~a~a~~~~~~-~~vp~i~~~~~~~~---~~~~~~f~~~~~~~~~~~~~~~~~~~~~g~~~v~i~~~~~~~g~~~~~~~~~ 154 (333)
T cd06358 79 VRNAVAPVVA-GRVPYVYTSLYEGG---ECNPGVFLTGETPEQQLAPAIPWLAEEKGARRWYLIGNDYVWPRGSLAAAKR 154 (333)
T ss_pred HHHHHHHHHh-cCceEEeCCCcCCC---CCCCCEEEcCCCcHHHHHHHHHHHHHhcCCCeEEEEeccchhhHHHHHHHHH
Confidence 3567889999 99999997654332 346999999999999998888876 667999999999999999999999999
Q ss_pred HHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHcCCcccceEEEEc-Ccccccccc
Q 003054 81 ALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMT-DGMTNLLRT 159 (852)
Q Consensus 81 ~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~-~~~~~~~~~ 159 (852)
.+++.|++|+....++++ ..||++++.++++.+||+|++.+...+...+++++++.|+..+ ++.. ..+....
T Consensus 155 ~~~~~G~~v~~~~~~~~~--~~d~~~~v~~l~~~~pd~v~~~~~~~~~~~~~~~~~~~G~~~~---~~~~~~~~~~~~-- 227 (333)
T cd06358 155 YIAELGGEVVGEEYVPLG--TTDFTSVLERIAASGADAVLSTLVGQDAVAFNRQFAAAGLRDR---ILRLSPLMDENM-- 227 (333)
T ss_pred HHHHcCCEEeeeeeecCC--hHHHHHHHHHHHHcCCCEEEEeCCCCchHHHHHHHHHcCCCcc---CceeecccCHHH--
Confidence 999999999998888854 8899999999999999999999999899999999999999776 3322 2222211
Q ss_pred CCchhhcccceEEEEEecCC--CChHHHHHHHHHHHhccccCCCCcccccchhhHhHhhHHHHHHHHHHHhcccCcCccc
Q 003054 160 LEPSVIDSMQGVIGVGPHVP--KTKALENFRVRWKRNFLQENPSIVDVELNIFGLLAYDATRALAEAVEKAGITSFGFDK 237 (852)
Q Consensus 160 ~~~~~~~~~~gv~~~~~~~~--~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~a~~aYDAv~~lA~Al~~a~~~~~~~~~ 237 (852)
........++|+++...+.+ ..+..++|.++|+++|+.+. ..++.+++.+||+++++++|+++++
T Consensus 228 ~~~~~~~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~g~~~-----~~~~~~~~~~yda~~~~~~A~~~ag-------- 294 (333)
T cd06358 228 LLASGAEAAEGLYSSSGYFASLQTPANAAFLARYRARFGDDA-----PPLNSLSESCYEAVHALAAAAERAG-------- 294 (333)
T ss_pred HHhcChHhhCCcEEeccchhhcCCHHHHHHHHHHHHHcCCCC-----CCCChHHHHHHHHHHHHHHHHHHhC--------
Confidence 11112245788887766554 56889999999999998631 1468889999999999999999987
Q ss_pred cccCCCCCCCccccccCChHHHHHHhhccceeeeeeeEEeecCccccc
Q 003054 238 TNVSRNATDLEAFGISQNGPKLLQALSSTRFKGLTGDYIFVDGQLQSS 285 (852)
Q Consensus 238 ~~~~~~~~~~~~~~~~~~g~~l~~al~~~~f~GltG~v~f~~G~~~~~ 285 (852)
..++++|+++|++.+|+|++|++.|+....+.+
T Consensus 295 ---------------~~~~~~v~~al~~~~~~~~~G~~~~~~~~~~~~ 327 (333)
T cd06358 295 ---------------SLDPEALIAALEDVSYDGPRGTVTMRGRHARQP 327 (333)
T ss_pred ---------------CCCHHHHHHHhccCeeeCCCcceEEcccccccc
Confidence 345789999999999999999999973333334
No 68
>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=9.9e-23 Score=224.70 Aligned_cols=256 Identities=28% Similarity=0.413 Sum_probs=211.6
Q ss_pred hhhHHHHhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHH-HHcCCcEEEEEEEeCCcccccHHHHHH
Q 003054 2 QTNFIIQLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAII-KAFGWREAVPIYVDNQYGEEMIPSLTD 80 (852)
Q Consensus 2 ~a~~v~~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l-~~~gw~~vaii~~d~~~G~~~~~~l~~ 80 (852)
++.++++++++.++|+|++++.++ ...+||+||+.|++..++.++++++ +++|.+++++|+.|++||+...+.+++
T Consensus 81 ~~~~~~~~~~~~~ip~i~~~~~~~---~~~~~~~f~~~~~~~~~~~~~~~~~~~~~g~~~v~iv~~~~~~g~~~~~~~~~ 157 (343)
T PF13458_consen 81 QAEAVAPIAEEAGIPYISPSASSP---SPDSPNVFRLSPSDSQQAAALAEYLAKKLGAKKVAIVYPDDPYGRSLAEAFRK 157 (343)
T ss_dssp HHHHHHHHHHHHT-EEEESSGGGG---TTTHTTEEESS--HHHHHHHHHHHHHHTTTTSEEEEEEESSHHHHHHHHHHHH
T ss_pred HHHHHHHHHHhcCcEEEEeeccCC---CCCCCcEEEEeccccHHHHHHHHHHHHHcCCcEEEEEecCchhhhHHHHHHHH
Confidence 467889999999999999765443 3567999999999999999999986 568999999999999999999999999
Q ss_pred HHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHcCCcccceEEEEcCccccccccC
Q 003054 81 ALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTL 160 (852)
Q Consensus 81 ~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~~~~~~~~~ 160 (852)
.+++.|++++....++.+ ..|+.+++.++++.+||+|++.+.+.+...+++++++.|+..+.+....+..+...+...
T Consensus 158 ~~~~~G~~vv~~~~~~~~--~~d~~~~~~~l~~~~~d~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~ 235 (343)
T PF13458_consen 158 ALEAAGGKVVGEIRYPPG--DTDFSALVQQLKSAGPDVVVLAGDPADAAAFLRQLRQLGLKPPRIPLFGTSLDDASLQQL 235 (343)
T ss_dssp HHHHTTCEEEEEEEE-TT--SSHHHHHHHHHHHTTTSEEEEESTHHHHHHHHHHHHHTTGCSCTEEEEEGGGSSHHHHHH
T ss_pred HHhhcCceeccceecccc--cccchHHHHHHhhcCCCEEEEeccchhHHHHHHHHHhhccccccceeeccccCcHHHHHh
Confidence 999999999888888855 689999999999999999999999999999999999999865544444444333222211
Q ss_pred CchhhcccceEEEEEecCC--CChHHHHHHHHHHHhccccCCCCcccccchhhHhHhhHHHHHHHHHHHhcccCcCcccc
Q 003054 161 EPSVIDSMQGVIGVGPHVP--KTKALENFRVRWKRNFLQENPSIVDVELNIFGLLAYDATRALAEAVEKAGITSFGFDKT 238 (852)
Q Consensus 161 ~~~~~~~~~gv~~~~~~~~--~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~a~~aYDAv~~lA~Al~~a~~~~~~~~~~ 238 (852)
....++|+++..++.+ +.|..++|.++|+++|+.+. .|+.++..+||++.++++|+++++
T Consensus 236 ---~~~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~------~~~~~~~~~yda~~~~~~al~~~g--------- 297 (343)
T PF13458_consen 236 ---GGDALEGVYIVSPWFPDPDSPAVKQFQERYRAAYGEEP------PPSLYAAQGYDAARLLAQALERAG--------- 297 (343)
T ss_dssp ---HGGGGTTEEEEESGGGTGGSHHHHHHHHHHHHHHSSTG------GTCHHHHHHHHHHHHHHHHHHHHT---------
T ss_pred ---hhhhccCceeecccCCCCCCHHHHHHHHHHHHHcCCCC------CCchhHHHHHHHHHHHHHHHHHhC---------
Confidence 2346889999888776 46889999999999998721 389999999999999999999987
Q ss_pred ccCCCCCCCccccccCChHHHHHHhhccceeeeeeeEEee--cCccccceEEEEEcc-CC
Q 003054 239 NVSRNATDLEAFGISQNGPKLLQALSSTRFKGLTGDYIFV--DGQLQSSAFEIINVN-NG 295 (852)
Q Consensus 239 ~~~~~~~~~~~~~~~~~g~~l~~al~~~~f~GltG~v~f~--~G~~~~~~~~I~~~~-~g 295 (852)
..+++.++++|++++|+|+.|++.|+ +|+. ...+.|++++ +|
T Consensus 298 --------------~~~~~~v~~al~~~~~~g~~g~~~~~~~~~~~-~~~~~i~~v~~~G 342 (343)
T PF13458_consen 298 --------------SLDREAVREALESLKYDGLFGPISFDPPDHQA-NKPVYIVQVKSDG 342 (343)
T ss_dssp --------------SHHHHHHHHHHHTSEEEETTEEEEEETTTSBE-EEEEEEEEEETTT
T ss_pred --------------CCCHHHHHHHHHhCCCcccccceEEeCCCCcc-ccCeEEEEEecCC
Confidence 34579999999999999999999996 5554 6778888887 65
No 69
>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=99.90 E-value=9.2e-22 Score=212.43 Aligned_cols=272 Identities=17% Similarity=0.212 Sum_probs=185.0
Q ss_pred hhhHHHHhcCCCCccEEeeecCCCCCCCCCCCceE--eccCCchhHHHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHH
Q 003054 2 QTNFIIQLGNKSQVPILSFSATSPSLTSIRSPYFF--RGSLNDSSQAGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLT 79 (852)
Q Consensus 2 ~a~~v~~i~~~~~vP~Is~~ats~~lt~~~~py~f--R~~p~d~~~~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~ 79 (852)
.+..+..+|+.++||+|+++..++...+ ..++.| ++.|+...++.|+.++|++|+|++|++||+.++ |....+.+.
T Consensus 94 ~~~~v~sic~~l~IP~I~~~~~~~~~~~-~~~~~l~L~l~P~~~~l~~a~~~ll~~~~W~~f~~iy~~~~-gl~~lq~l~ 171 (382)
T cd06377 94 ELVQLDFVSAALEIPVVSIVRREFPRGS-QNPFHLQMSWASPLSTLLDVLLSVLQRNGWEDVSLVLCRER-DPTGLLLLW 171 (382)
T ss_pred HHHHHHHHhcCCCCCEEEecCCcccccC-CCceeEEEEecCCHHHHHHHHHHHHHHCCCcEEEEEEecCc-CHHHHHHHH
Confidence 3567788999999999998665533311 234445 669999999999999999999999999997766 333333333
Q ss_pred HHHHhCCc-eeeeeeecCCC-CChHHH-HHHHHHhhcCC-ceEEEEEeChhhHHHHHHHHHHcCCcccceEEEEcCcccc
Q 003054 80 DALQAIDT-RVPYRSVISPL-ATDDQI-EKELYKLFTMQ-TRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTN 155 (852)
Q Consensus 80 ~~l~~~g~-~v~~~~~~~~~-~~~~d~-~~~l~~l~~~~-~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~~~~ 155 (852)
+.....+. .+......+.. .+..++ ...|++++..+ .++|++.|+.+.+..+++++.+ +|+||+++...
T Consensus 172 ~~~~~~~~~~~i~v~~~~~~~~d~~~~~~~~L~~i~~~~~~~~ill~cs~e~~~~il~~~~~------~y~wIv~~~~~- 244 (382)
T cd06377 172 TNHARFHLGSVLNLSRNDPSTADLLDFLRAQLELLKDPPGPAVVLFGCDVARARRVLELTPP------GPHWILGDPLP- 244 (382)
T ss_pred HHhcccccCceEEEEeccCccCChhHHHHHHHHHhhcccCceEEEEECCHHHHHHHHHhhcc------ceEEEEcCCcC-
Confidence 32222221 12222222211 134556 99999999999 9999999999999999988754 49999987221
Q ss_pred ccccCCchhhcccceEEEEEecCCCChHHHHHHHHHHHhccccCCCCcccccchhhHhHhhHHHHHHHHHHHhcccCcCc
Q 003054 156 LLRTLEPSVIDSMQGVIGVGPHVPKTKALENFRVRWKRNFLQENPSIVDVELNIFGLLAYDATRALAEAVEKAGITSFGF 235 (852)
Q Consensus 156 ~~~~~~~~~~~~~~gv~~~~~~~~~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~a~~aYDAv~~lA~Al~~a~~~~~~~ 235 (852)
++... ....--|+++ |. +. .....+++.||||+++|+|++.+.......
T Consensus 245 -le~~~--~~g~nigLl~-----------------~~-~~----------~~~~l~ali~DAV~lvA~a~~~l~~~~~~~ 293 (382)
T cd06377 245 -PEALR--TEGLPPGLLA-----------------HG-ET----------TQPPLEAYVQDALELVARAVGSATLVQPEL 293 (382)
T ss_pred -hhhcc--CCCCCceEEE-----------------Ee-ec----------ccccHHHHHHHHHHHHHHHHHHhhhccccc
Confidence 11111 1111223331 11 01 111238899999999999999864211111
Q ss_pred cccccCCCCCCCccc--c-ccCChHHHHHHhhccceeeeeeeEEeecCcc--ccceEEEEEcc---CC---cEEEEEEcC
Q 003054 236 DKTNVSRNATDLEAF--G-ISQNGPKLLQALSSTRFKGLTGDYIFVDGQL--QSSAFEIINVN---NG---ARGVGFWTP 304 (852)
Q Consensus 236 ~~~~~~~~~~~~~~~--~-~~~~g~~l~~al~~~~f~GltG~v~f~~G~~--~~~~~~I~~~~---~g---~~~vG~w~~ 304 (852)
. ......+|... + .|.+|..|.++|++++|+|+||+|.|+.|.+ .+..++|++++ +| |++||+|++
T Consensus 294 ~---l~~~~~~C~~~~~~~~W~~G~~l~~~Lknv~~eGlTG~I~F~~g~R~~~~~~l~I~~L~~~~~G~~~W~kVG~W~~ 370 (382)
T cd06377 294 A---LIPATVNCMDLPTKGNESSGQYLARFLANTSFDGRTGPVWVTGSSQVHSSRHFKVWSLRRDPVGQPTWTTVGSWQG 370 (382)
T ss_pred c---cCCCCCCcccCCCCCCCCchHHHHHHHHhCcccccceeEEEccCeeecccceEEEEEeccccCCCccceEEEEecC
Confidence 1 11111344333 4 7999999999999999999999999987887 78899999998 56 599999998
Q ss_pred CCCcccccCCCccccCCccceEeC
Q 003054 305 EKGLTQKLSSNSTTKSKLKPIIWP 328 (852)
Q Consensus 305 ~~g~~~~~~~~~~~~~~~~~i~Wp 328 (852)
...+ .++.++||
T Consensus 371 ~~~~------------~~~~~~wp 382 (382)
T cd06377 371 GRKI------------VMDQGLWP 382 (382)
T ss_pred CCce------------ecccCCCC
Confidence 6332 35778897
No 70
>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=99.90 E-value=1.7e-22 Score=221.27 Aligned_cols=243 Identities=22% Similarity=0.294 Sum_probs=191.5
Q ss_pred hhhHHHHhcCCCCccEEeeecCCCCCCC-CCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHH
Q 003054 2 QTNFIIQLGNKSQVPILSFSATSPSLTS-IRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTD 80 (852)
Q Consensus 2 ~a~~v~~i~~~~~vP~Is~~ats~~lt~-~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~ 80 (852)
.+.+++++++.++||+|+++++++.+++ ..+||+||+.|++..+++++++++++++|++|++||++++++... +.+.+
T Consensus 75 ~~~~v~~~~~~~~iP~is~~~~~~~~~~~~~~~~~~~~~p~~~~~~~a~~~~l~~~~w~~v~iiy~~~~~~~~l-~~~~~ 153 (328)
T cd06351 75 SASAVQSICDALEIPHISISGGSEGLSDKEESSTTLQLYPSLEDLADALLDLLEYYNWTKFAIIYDSDEGLSRL-QELLD 153 (328)
T ss_pred HHHHHHHHhccCCCCeEEeecCcccccccccccceEEecCCHHHHHHHHHHHHHHcCCcEEEEEEeCchHHHHH-HHHHH
Confidence 4678899999999999999998888875 578999999999999999999999999999999999888854433 33333
Q ss_pred HHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCc-eEEEEEeChhhHHHHHHHHHHcCCcccceEEEEcCcccccccc
Q 003054 81 ALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQT-RVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRT 159 (852)
Q Consensus 81 ~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~-~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~~~~~~~~ 159 (852)
.....+..+... .+..+ .+|+...|.++++.++ ++|++++..+++..+++||+++||+.++|+||.++......+.
T Consensus 154 ~~~~~~~~v~~~-~~~~~--~~~~~~~l~~l~~~~~~~vil~~~~~~~~~~~l~~a~~~gm~~~~~~~i~~~~~~~~~d~ 230 (328)
T cd06351 154 ESGIKGIQVTVR-RLDLD--DDNYRQLLKELKRSESRRIILDCSSEEEAKEILEQAVELGMMGYGYHWILTNLDLSDIDL 230 (328)
T ss_pred hhcccCceEEEE-EecCC--chhHHHHHHHHhhcccceEEEECCcHHHHHHHHHHHHHhccccCCcEEEEecCCccccch
Confidence 333334444433 44433 3489999999999999 6666655559999999999999999999999999987654432
Q ss_pred CCchhhcccceEEEEEecCCCChHHHHHHHHHHHhccccCCCCcccccchhhHhHhhHHHHHHHHHHHhcccCcCccccc
Q 003054 160 LEPSVIDSMQGVIGVGPHVPKTKALENFRVRWKRNFLQENPSIVDVELNIFGLLAYDATRALAEAVEKAGITSFGFDKTN 239 (852)
Q Consensus 160 ~~~~~~~~~~gv~~~~~~~~~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~a~~aYDAv~~lA~Al~~a~~~~~~~~~~~ 239 (852)
. .......|+++++...++.+...+|..+|.... +......+...++..||+++++
T Consensus 231 ~--~~~~~~~~i~g~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~d~~~~~------------------ 286 (328)
T cd06351 231 E--PFQYGPANITGFRLVDPDSPDVSQFLQRWLEES----PGVNLRAPIYDAALLYDAVLLL------------------ 286 (328)
T ss_pred h--hhccCCcceEEEEEeCCCchHHHHHHHhhhhcc----CCCCcCccchhhHhhhcEEEEE------------------
Confidence 1 234567899999999999999999999993322 2222234566677777776543
Q ss_pred cCCCCCCCccccccCChHHHHHHhhccceeeeeeeEEee-cCccccceEEEEEcc--CCcEEEEEEcC
Q 003054 240 VSRNATDLEAFGISQNGPKLLQALSSTRFKGLTGDYIFV-DGQLQSSAFEIINVN--NGARGVGFWTP 304 (852)
Q Consensus 240 ~~~~~~~~~~~~~~~~g~~l~~al~~~~f~GltG~v~f~-~G~~~~~~~~I~~~~--~g~~~vG~w~~ 304 (852)
+|++.|+ +|++.+..++|+++. .+++.||.|++
T Consensus 287 --------------------------------tg~i~f~~~g~r~~~~l~i~~l~~~~~~~~vg~W~~ 322 (328)
T cd06351 287 --------------------------------TGTVSFDEDGVRSNFTLDIIELNRSRGWRKVGTWNG 322 (328)
T ss_pred --------------------------------EeeEEECCCCcccceEEEEEEecCCCCceEEEEecC
Confidence 8999998 899999999999997 77999999994
No 71
>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=99.90 E-value=2.6e-22 Score=220.15 Aligned_cols=242 Identities=14% Similarity=0.116 Sum_probs=194.5
Q ss_pred hhhHHHHhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHHH
Q 003054 2 QTNFIIQLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTDA 81 (852)
Q Consensus 2 ~a~~v~~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~~ 81 (852)
.+.++.+++++.++|+|+..+... ....||+||+.+++..++.++++++.+.+-+++++|+.|++||++..+.+++.
T Consensus 79 ~~~a~~~~~~~~~vp~i~~~~~~~---~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~~vail~~d~~~g~~~~~~~~~~ 155 (334)
T cd06356 79 SREAIRPIMDRTKQLYFYTTQYEG---GVCDRNTFCTGATPAQQFSTLVPYMMEKYGKKVYTIAADYNFGQISAEWVRKI 155 (334)
T ss_pred HHHHHHHHHHhcCceEEeCCCccC---CcccCCEEEeCCCcHHHHHHHHHHHHHccCCeEEEECCCchhhHHHHHHHHHH
Confidence 457889999999999998643322 23468999999999999999999986654489999999999999999999999
Q ss_pred HHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHcCC-cccceEEEEcCccccc--cc
Q 003054 82 LQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEIGL-MNKGCVWIMTDGMTNL--LR 158 (852)
Q Consensus 82 l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~G~-~~~~~vwi~~~~~~~~--~~ 158 (852)
+++.|++++....++++ ..||++++.+|++.+||+|++.....+...+++++++.|+ ..+ ++........ ..
T Consensus 156 ~~~~G~~vv~~~~~~~~--~~d~~~~v~~l~~~~pd~v~~~~~~~~~~~~~~~~~~~G~~~~~---~~~~~~~~~~~~~~ 230 (334)
T cd06356 156 VEENGGEVVGEEFIPLD--VSDFGSTIQKIQAAKPDFVMSILVGANHLSFYRQWAAAGLGNIP---MASSTLGAQGYEHK 230 (334)
T ss_pred HHHcCCEEEeeeecCCC--chhHHHHHHHHHhcCCCEEEEeccCCcHHHHHHHHHHcCCccCc---eeeeecccchhHHh
Confidence 99999999998888854 7899999999999999999999999999999999999999 333 2222111111 11
Q ss_pred cCCchhhcccceEEEEEecCCC--ChHHHHHHHHHHHhccccCCCCcccccchhhHhHhhHHHHHHHHHHHhcccCcCcc
Q 003054 159 TLEPSVIDSMQGVIGVGPHVPK--TKALENFRVRWKRNFLQENPSIVDVELNIFGLLAYDATRALAEAVEKAGITSFGFD 236 (852)
Q Consensus 159 ~~~~~~~~~~~gv~~~~~~~~~--~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~a~~aYDAv~~lA~Al~~a~~~~~~~~ 236 (852)
.+ ....++|+++...|.++ .|..++|.++|+++|+.. | .++.+++.+||+++++++|+++++
T Consensus 231 ~~---~~~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~-p-----~~~~~~~~~y~a~~~~~~A~~~ag------- 294 (334)
T cd06356 231 RL---KPPALKDMYATANYIEELDTPANKAFVERFRAKFPDA-P-----YINEEAENNYEAIYLYKEAVEKAG------- 294 (334)
T ss_pred cc---CchhcCCeEEecchhhhcCCHHHHHHHHHHHHHcCCC-C-----CCCchhHHHHHHHHHHHHHHHHHC-------
Confidence 11 12457888887766553 678999999999999761 0 136789999999999999999998
Q ss_pred ccccCCCCCCCccccccCChHHHHHHhhc-cceeeeeeeEEee--cCccc
Q 003054 237 KTNVSRNATDLEAFGISQNGPKLLQALSS-TRFKGLTGDYIFV--DGQLQ 283 (852)
Q Consensus 237 ~~~~~~~~~~~~~~~~~~~g~~l~~al~~-~~f~GltG~v~f~--~G~~~ 283 (852)
+.++++|+++|++ ..|+|+.|++.|+ +++..
T Consensus 295 ----------------~~~~~~v~~aL~~~~~~~~~~g~~~~~~~~h~~~ 328 (334)
T cd06356 295 ----------------TTDRDAVIEALESGLVCDGPEGKVCIDGKTHHTS 328 (334)
T ss_pred ----------------CCCHHHHHHHHHhCCceeCCCceEEEecCCCcee
Confidence 3457899999997 5799999999997 44443
No 72
>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=99.89 E-value=2.9e-22 Score=221.01 Aligned_cols=243 Identities=19% Similarity=0.258 Sum_probs=194.4
Q ss_pred hhhHHHHhcCCCCccEEeeecCCCCCCC--CCCCceEeccCCchhHHHHHHHHH-HHcCCcEEEEEEEeCCcccccHHHH
Q 003054 2 QTNFIIQLGNKSQVPILSFSATSPSLTS--IRSPYFFRGSLNDSSQAGAITAII-KAFGWREAVPIYVDNQYGEEMIPSL 78 (852)
Q Consensus 2 ~a~~v~~i~~~~~vP~Is~~ats~~lt~--~~~py~fR~~p~d~~~~~aia~~l-~~~gw~~vaii~~d~~~G~~~~~~l 78 (852)
.+.++.+++++.+||+|++.++.+.+++ ..++|+||+.+++..++.++++++ ++.+|++|+++|.|++||+...+.+
T Consensus 79 ~~~a~~~~~~~~~vp~i~~~~~~~~l~~~~~~~~~~Fr~~~~~~~~~~~~a~~~~~~~~~~~v~ii~~~~~~g~~~~~~~ 158 (347)
T cd06335 79 VALANLEFIQQNKIPLIGPWAAGTPITRNGAPPNYIFRVSADDSIQAPFLVDEAVKRGGFKKVALLLDNTGWGRSNRKDL 158 (347)
T ss_pred HHHhhhHHHHhcCCcEEecCCCCcccccCCCCCCCEEEeccChHHHHHHHHHHHHHhcCCCeEEEEeccCchhhhHHHHH
Confidence 4567889999999999999888887765 356899999999999999999987 5567999999999999999999999
Q ss_pred HHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHcCCcccceEEEEcCccccccc
Q 003054 79 TDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLR 158 (852)
Q Consensus 79 ~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~~~~~~~ 158 (852)
++.+++.|++|+....++++ ..|+++++.+|++.+||+|++.+...++..+++++++.|+..+ ++....... ..
T Consensus 159 ~~~~~~~G~~v~~~~~~~~~--~~d~s~~i~~i~~~~~d~v~~~~~~~~~~~~~~~~~~~g~~~~---~~~~~~~~~-~~ 232 (347)
T cd06335 159 TAALAARGLKPVAVEWFNWG--DKDMTAQLLRAKAAGADAIIIVGNGPEGAQIANGMAKLGWKVP---IISHWGLSG-GN 232 (347)
T ss_pred HHHHHHcCCeeEEEeeecCC--CccHHHHHHHHHhCCCCEEEEEecChHHHHHHHHHHHcCCCCc---EecccCCcC-ch
Confidence 99999999999988888755 7789999999999999999999999999999999999999654 333222211 11
Q ss_pred cCCchhhcccceEEEEEecC---CCChHHHHHHHHHHHhccccCCCCcccccchhhHhHhhHHHHHHHHHHHhcccCcCc
Q 003054 159 TLEPSVIDSMQGVIGVGPHV---PKTKALENFRVRWKRNFLQENPSIVDVELNIFGLLAYDATRALAEAVEKAGITSFGF 235 (852)
Q Consensus 159 ~~~~~~~~~~~gv~~~~~~~---~~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~a~~aYDAv~~lA~Al~~a~~~~~~~ 235 (852)
... ...+..+|++....+. ++++..++|+++|+++|+..... ...++.+++.+||+++++++|+++++.
T Consensus 233 ~~~-~~g~~~~g~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~--~~~~~~~~~~aYd~~~~l~~A~~~ag~----- 304 (347)
T cd06335 233 FIE-GAGPAANDALMIQTFIFEPPSNPKAKAFLAAYHKKYPEKKPA--DIPAPVGAAHAYDAVHLLAAAIKQAGS----- 304 (347)
T ss_pred hhh-ccchhhcCcEEEEeeccccCCCHHHHHHHHHHHHHhCCCccc--ccCcchhHHHHHHHHHHHHHHHHHhcC-----
Confidence 111 1334568887765543 25688999999999999862100 112566778999999999999999983
Q ss_pred cccccCCCCCCCccccccCChHHHHHHhhcc--ceeeeeeeEE
Q 003054 236 DKTNVSRNATDLEAFGISQNGPKLLQALSST--RFKGLTGDYI 276 (852)
Q Consensus 236 ~~~~~~~~~~~~~~~~~~~~g~~l~~al~~~--~f~GltG~v~ 276 (852)
..++.++++|+++ .+.|+.|.+.
T Consensus 305 ------------------~~~~~v~~al~~~~~~~~G~~~~~~ 329 (347)
T cd06335 305 ------------------TDGRAIKRALENLKKPVEGLVKTYD 329 (347)
T ss_pred ------------------CCHHHHHHHHHhccCCceeeecccC
Confidence 2347899999876 4788888664
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=1.6e-22 Score=223.78 Aligned_cols=238 Identities=11% Similarity=0.087 Sum_probs=190.6
Q ss_pred hhhHHHHhcCCCCccEEeeecCCCCC-------CCCCCCceEeccCCchhHHHHHHHHHHHcC-CcEEEEEEEeCCcccc
Q 003054 2 QTNFIIQLGNKSQVPILSFSATSPSL-------TSIRSPYFFRGSLNDSSQAGAITAIIKAFG-WREAVPIYVDNQYGEE 73 (852)
Q Consensus 2 ~a~~v~~i~~~~~vP~Is~~ats~~l-------t~~~~py~fR~~p~d~~~~~aia~~l~~~g-w~~vaii~~d~~~G~~ 73 (852)
.+.++++++++.+||+|++.+..+.+ ...++||+||..+++..++.+++.+++..+ +++|++++.|++||+.
T Consensus 81 ~~~a~~~~~~~~~ip~i~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~k~v~ii~~~~~~g~~ 160 (357)
T cd06337 81 TTNPVSDQCEANGVPCISTMAPWQAWFFGRGGNPATGFKWTYHFFWGAEDVVATYVGMWKQLETNKKVGILYPNDPDGNA 160 (357)
T ss_pred hhhHHHHHHHHhCCCeEEeccchhhhhccCCCCcccCCceeEEecCCHHHHHHHHHHHHHhCCCCceEEEEeecCchhHH
Confidence 35678899999999999976543221 123478999999999889999999888877 9999999999999998
Q ss_pred cHHHHH---HHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHcCCcccceEEEEc
Q 003054 74 MIPSLT---DALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMT 150 (852)
Q Consensus 74 ~~~~l~---~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~ 150 (852)
..+.+. +++++.|++|+....++++ +.||++++.+|++++||+|++.+.++++..+++|++++|+..+ ++..
T Consensus 161 ~~~~~~~~~~~~~~~G~~vv~~~~~~~~--~~D~~~~v~~ik~a~pD~v~~~~~~~~~~~~~~~~~~~G~~~~---~~~~ 235 (357)
T cd06337 161 FADPVIGLPAALADAGYKLVDPGRFEPG--TDDFSSQINAFKREGVDIVTGFAIPPDFATFWRQAAQAGFKPK---IVTI 235 (357)
T ss_pred HHHhhhcccHHHHhCCcEEecccccCCC--CCcHHHHHHHHHhcCCCEEEeCCCccHHHHHHHHHHHCCCCCC---eEEE
Confidence 877665 5777899999999888855 7889999999999999999999999999999999999999766 4432
Q ss_pred -Cccc--cccccCCchhhcccceEEEEEecCCC--------ChHHHHHHHHHHHhccccCCCCcccccchhhHhHhhHHH
Q 003054 151 -DGMT--NLLRTLEPSVIDSMQGVIGVGPHVPK--------TKALENFRVRWKRNFLQENPSIVDVELNIFGLLAYDATR 219 (852)
Q Consensus 151 -~~~~--~~~~~~~~~~~~~~~gv~~~~~~~~~--------~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~a~~aYDAv~ 219 (852)
.+.. ..... ..+..+|++....|.+. ++..++|+++|+++|+. .|...+.++||+++
T Consensus 236 ~~~~~~~~~~~~----~g~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~~~~g~--------~~~~~~~~~~~~~~ 303 (357)
T cd06337 236 AKALLFPEDVEA----LGDRGDGMSTEVWWSPSHPFRSSLTGQSAAELADAYEAATGR--------QWTQPLGYAHALFE 303 (357)
T ss_pred eccccCHHHHHH----hhhhhcCccccceeccCCCcccccCCccHHHHHHHHHHHhCC--------CccCcchHHHHHHH
Confidence 2221 12221 22345777765554443 24589999999999987 56666788999999
Q ss_pred HHHHHHHHhcccCcCccccccCCCCCCCccccccCChHHHHHHhhccceeeeeeeEEee
Q 003054 220 ALAEAVEKAGITSFGFDKTNVSRNATDLEAFGISQNGPKLLQALSSTRFKGLTGDYIFV 278 (852)
Q Consensus 220 ~lA~Al~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~al~~~~f~GltG~v~f~ 278 (852)
+|++|+++|+.. .++++|+++|++++++++.|++.|+
T Consensus 304 ~l~~Ai~~Ags~----------------------~d~~~v~~aL~~~~~~~~~G~~~f~ 340 (357)
T cd06337 304 VGVKALVRADDP----------------------DDPAAVADAIATLKLDTVVGPVDFG 340 (357)
T ss_pred HHHHHHHHcCCC----------------------CCHHHHHHHHHcCCcccceeeeecC
Confidence 999999999831 3578999999999999999999997
No 74
>PRK10797 glutamate and aspartate transporter subunit; Provisional
Probab=99.87 E-value=7.7e-21 Score=204.04 Aligned_cols=223 Identities=16% Similarity=0.238 Sum_probs=187.7
Q ss_pred CceEEEeeecccCcccceEEeeCCCCCCCceEEEeeHHHHHHHHH----HCCC-ccceEEEecCCCCCCCCCChhHHHHH
Q 003054 344 EKKLRIGVPVKKGFSDFVNVTIDPKTQEPTSVTGYCVDVFKAVIQ----ELPY-AVAYDFVPYGQPDGSSSGSYNDLVYQ 418 (852)
Q Consensus 344 ~~~lrv~v~~~~~~~~~~~~~~d~~~~~~~~~~G~~~dl~~~ia~----~l~~-~~~~~~~~~~~~~g~~ngs~~~li~~ 418 (852)
.+.|+||+. +.|+||.+.+ +++ .+.||++|++++|++ ++|. .+++++++.. |..++..
T Consensus 39 ~g~L~Vg~~--~~~pP~~f~~-----~~g-~~~G~didl~~~ia~~l~~~lg~~~~~~~~v~~~---------~~~~i~~ 101 (302)
T PRK10797 39 NGVIVVGHR--ESSVPFSYYD-----NQQ-KVVGYSQDYSNAIVEAVKKKLNKPDLQVKLIPIT---------SQNRIPL 101 (302)
T ss_pred CCeEEEEEc--CCCCCcceEC-----CCC-CEeeecHHHHHHHHHHHHHhhCCCCceEEEEEcC---------hHhHHHH
Confidence 567999988 7788998865 456 899999997777655 6764 3678888753 7789999
Q ss_pred HhcCcccEEEeeeeeecCcceeeeccccccccceEEEEEccCCCCCCceEeecccchhHHHHHHHHHHHHHhhhhheecc
Q 003054 419 VFLGEFDAVVGDITIVFNRSNYVDFTLPYTESGVSMIVPIKDSKKRNAWVFLQPLTWDLWVTCFCFFIFIGFVVWVLEHR 498 (852)
Q Consensus 419 l~~g~~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv~~~~~~~~~~~~~l~PF~~~lW~~i~~~~i~~~~v~~~l~~~ 498 (852)
|..|++|++++++++|++|.+.++||.||..++..+++++.. .
T Consensus 102 L~~G~~Di~~~~~~~t~eR~~~~~fS~Py~~~~~~lv~r~~~--~----------------------------------- 144 (302)
T PRK10797 102 LQNGTFDFECGSTTNNLERQKQAAFSDTIFVVGTRLLTKKGG--D----------------------------------- 144 (302)
T ss_pred HHCCCccEEecCCccCcchhhcceecccEeeccEEEEEECCC--C-----------------------------------
Confidence 999999999989999999999999999999999999998652 1
Q ss_pred cCCCCCCCcccccchhHHHHHHHhhhccccccccchhhHHHHHHHHHHHHHHHHhhhhccceeeecccCCCcCCHHHHHh
Q 003054 499 VNEDFRGPAGQQVGTSFWFSFSTMVFSQRERVISNLARIVVIVWCFVVLILTQSYTASLTSLLTVQQLQPTITDVKMLIK 578 (852)
Q Consensus 499 ~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~s~~~R~v~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~i~sl~dL~~ 578 (852)
|++++||.
T Consensus 145 -----------------------------------------------------------------------i~sl~dL~- 152 (302)
T PRK10797 145 -----------------------------------------------------------------------IKDFADLK- 152 (302)
T ss_pred -----------------------------------------------------------------------CCChHHcC-
Confidence 78999996
Q ss_pred cCCeEEEEeCchHHHHHHhcC---CCCcceeecCCHhHHHHHhhcccccCceeEEEechhHHHHHHhhc--CCceEeecc
Q 003054 579 RGDNVGYQKGSFVLGILKQLG---FDERKLVVYNSPEDCHELFQKGSVNGGIAAAFDEIPYMKLLIGQY--CSKYAMIEP 653 (852)
Q Consensus 579 ~~~~vg~~~~s~~~~~l~~~~---~~~~~~~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~~--~~~~~~v~~ 653 (852)
|++||+..|+....++++.. .+..+++.+.+.++.+++|..|+ ++|++.+...+.+.+.+. -+.++++++
T Consensus 153 -Gk~V~v~~gs~~~~~l~~~~~~~~~~~~i~~~~~~~~~l~~L~~Gr----vDa~i~d~~~~~~~~~~~~~~~~l~i~~~ 227 (302)
T PRK10797 153 -GKAVVVTSGTTSEVLLNKLNEEQKMNMRIISAKDHGDSFRTLESGR----AVAFMMDDALLAGERAKAKKPDNWEIVGK 227 (302)
T ss_pred -CCEEEEeCCCcHHHHHHHHhhhcCCceEEEEeCCHHHHHHHHHcCC----ceEEEccHHHHHHHHHcCCCCcceEECCc
Confidence 89999999999988886532 22357888999999999999999 999999987776544332 335777888
Q ss_pred cccccceEEEecCCCC-chhhHHHHHHhccccChhHHHHHHHccC
Q 003054 654 KFKTAGFGFVFPLHSP-LVHDVSKAILNVTEGDKMKEIEDAWFKK 697 (852)
Q Consensus 654 ~~~~~~~~~~~~k~sp-l~~~in~~il~l~e~G~~~~i~~kw~~~ 697 (852)
.+...+++++++|+++ ++..+|++|.+++++|.+++|.++|+..
T Consensus 228 ~~~~~~~~~a~~k~~~~L~~~in~~L~~l~~~G~l~~i~~kw~~~ 272 (302)
T PRK10797 228 PQSQEAYGCMLRKDDPQFKKLMDDTIAQAQTSGEAEKWFDKWFKN 272 (302)
T ss_pred cCCcCceeEEEeCCCHHHHHHHHHHHHHHHhCchHHHHHHHHcCC
Confidence 7778889999999877 9999999999999999999999999974
No 75
>PRK09495 glnH glutamine ABC transporter periplasmic protein; Reviewed
Probab=99.87 E-value=9.6e-21 Score=198.44 Aligned_cols=221 Identities=22% Similarity=0.381 Sum_probs=188.1
Q ss_pred CceEEEeeecccCcccceEEeeCCCCCCCceEEEeeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCc
Q 003054 344 EKKLRIGVPVKKGFSDFVNVTIDPKTQEPTSVTGYCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGE 423 (852)
Q Consensus 344 ~~~lrv~v~~~~~~~~~~~~~~d~~~~~~~~~~G~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~ 423 (852)
.+.|+||+. ++|+||.+. +++ .+.|+++|+++++++++|. ++++++. +|.+++.+|.+|+
T Consensus 24 ~~~l~v~~~--~~~~P~~~~------~~g-~~~G~~vdl~~~ia~~lg~--~~~~~~~---------~~~~~~~~l~~G~ 83 (247)
T PRK09495 24 DKKLVVATD--TAFVPFEFK------QGD-KYVGFDIDLWAAIAKELKL--DYTLKPM---------DFSGIIPALQTKN 83 (247)
T ss_pred CCeEEEEeC--CCCCCeeec------CCC-ceEEEeHHHHHHHHHHhCC--ceEEEeC---------CHHHHHHHHhCCC
Confidence 578999976 568888764 246 8999999999999999996 4555543 4999999999999
Q ss_pred ccEEEeeeeeecCcceeeeccccccccceEEEEEccCCCCCCceEeecccchhHHHHHHHHHHHHHhhhhheecccCCCC
Q 003054 424 FDAVVGDITIVFNRSNYVDFTLPYTESGVSMIVPIKDSKKRNAWVFLQPLTWDLWVTCFCFFIFIGFVVWVLEHRVNEDF 503 (852)
Q Consensus 424 ~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv~~~~~~~~~~~~~l~PF~~~lW~~i~~~~i~~~~v~~~l~~~~~~~~ 503 (852)
+|+++++++.+++|.+.++||.||+.+++.+++++...
T Consensus 84 vDi~~~~~~~t~~R~~~~~fs~p~~~~~~~~~~~~~~~------------------------------------------ 121 (247)
T PRK09495 84 VDLALAGITITDERKKAIDFSDGYYKSGLLVMVKANNN------------------------------------------ 121 (247)
T ss_pred cCEEEecCccCHHHHhhccccchheecceEEEEECCCC------------------------------------------
Confidence 99998888999999999999999999999999985531
Q ss_pred CCCcccccchhHHHHHHHhhhccccccccchhhHHHHHHHHHHHHHHHHhhhhccceeeecccCCCcCCHHHHHhcCCeE
Q 003054 504 RGPAGQQVGTSFWFSFSTMVFSQRERVISNLARIVVIVWCFVVLILTQSYTASLTSLLTVQQLQPTITDVKMLIKRGDNV 583 (852)
Q Consensus 504 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~s~~~R~v~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~i~sl~dL~~~~~~v 583 (852)
++++++||. |++|
T Consensus 122 -----------------------------------------------------------------~~~~~~dL~--g~~I 134 (247)
T PRK09495 122 -----------------------------------------------------------------DIKSVKDLD--GKVV 134 (247)
T ss_pred -----------------------------------------------------------------CCCChHHhC--CCEE
Confidence 278999996 8899
Q ss_pred EEEeCchHHHHHHhcCCCCcceeecCCHhHHHHHhhcccccCceeEEEechhHHHHHHhhc-CCceEeecccccccceEE
Q 003054 584 GYQKGSFVLGILKQLGFDERKLVVYNSPEDCHELFQKGSVNGGIAAAFDEIPYMKLLIGQY-CSKYAMIEPKFKTAGFGF 662 (852)
Q Consensus 584 g~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~~-~~~~~~v~~~~~~~~~~~ 662 (852)
|+..|+....++++. .+..+++.+++.++.+++|.+|+ +|+++.+...+.+++++. ...+..++.......+++
T Consensus 135 ~v~~g~~~~~~l~~~-~~~~~i~~~~~~~~~~~~L~~gr----vDa~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 209 (247)
T PRK09495 135 AVKSGTGSVDYAKAN-IKTKDLRQFPNIDNAYLELGTGR----ADAVLHDTPNILYFIKTAGNGQFKAVGDSLEAQQYGI 209 (247)
T ss_pred EEecCchHHHHHHhc-CCCCceEEcCCHHHHHHHHHcCc----eeEEEeChHHHHHHHHhCCCCceEEecCcccccceEE
Confidence 999999888888764 45567888999999999999999 999999988888887764 335666666666778999
Q ss_pred EecCCCCchhhHHHHHHhccccChhHHHHHHHccCC
Q 003054 663 VFPLHSPLVHDVSKAILNVTEGDKMKEIEDAWFKKH 698 (852)
Q Consensus 663 ~~~k~spl~~~in~~il~l~e~G~~~~i~~kw~~~~ 698 (852)
+++|++.+++.+|++|..+.++|.+++|.+||+...
T Consensus 210 a~~~~~~l~~~~n~al~~~~~~g~~~~i~~k~~~~~ 245 (247)
T PRK09495 210 AFPKGSELREKVNGALKTLKENGTYAEIYKKWFGTE 245 (247)
T ss_pred EEcCcHHHHHHHHHHHHHHHHCCcHHHHHHHHcCCC
Confidence 999999999999999999999999999999999643
No 76
>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=99.87 E-value=2e-21 Score=212.06 Aligned_cols=231 Identities=15% Similarity=0.118 Sum_probs=178.1
Q ss_pred hhhHHHHhcCCCCccEEeeecCCCCCCC-CCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHH
Q 003054 2 QTNFIIQLGNKSQVPILSFSATSPSLTS-IRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTD 80 (852)
Q Consensus 2 ~a~~v~~i~~~~~vP~Is~~ats~~lt~-~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~ 80 (852)
.+.++.++++++++|+|+++++++.++. .++||+||+.+++..+++++++++.+.|.|+|++|+.|++||.+..+.+++
T Consensus 71 ~~~Av~~~a~~~~vp~i~~~a~~~~lt~~~c~~~~Fr~~~~~~~~~~ala~~~~~~g~kkvaii~~~~~~g~~~~~~~~~ 150 (347)
T TIGR03863 71 ALLALADAAKAKGALLFNAGAPDDALRGADCRANLLHTLPSRAMLADALAQYLAAKRWRRILLIQGPLPADALYADAFRR 150 (347)
T ss_pred HHHHHHHHHHhCCcEEEeCCCCChHHhCCCCCCCEEEecCChHhHHHHHHHHHHHcCCCEEEEEeCCCcccHHHHHHHHH
Confidence 5788999999999999999999999986 568999999999999999999998777999999999999999999999999
Q ss_pred HHHhCCceeeeeeecCCCCC--hHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHcCCcccceEEEEcCccccccc
Q 003054 81 ALQAIDTRVPYRSVISPLAT--DDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLR 158 (852)
Q Consensus 81 ~l~~~g~~v~~~~~~~~~~~--~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~~~~~~~ 158 (852)
.+++.|++|+..+.++.+.+ ..|+.......+.++||+|++.....+....+... .+...+ .+
T Consensus 151 ~~~~~G~~vv~~~~~~~~~~~~~~d~s~~~~~~~~s~pDvv~~~~~~~~~~~~~~~~--~~~~~~---~~---------- 215 (347)
T TIGR03863 151 SAKRFGAKIVAERPFTFSGDPRRTDQSEVPLFTQGADYDVVVVADEAGEFARYLPYA--TWLPRP---VA---------- 215 (347)
T ss_pred HHHHCCCEEEEeEEeccCCchhhhhcccCceeecCCCCCEEEEecchhhHhhhcccc--cccccc---cc----------
Confidence 99999999999988875422 23555323334458999999987665432211111 000000 01
Q ss_pred cCCchhhcccceEEEEEec-CCCChHHHHHHHHHHHhccccCCCCcccccchhhHhHhhHHHHHHHHHHHhcccCcCccc
Q 003054 159 TLEPSVIDSMQGVIGVGPH-VPKTKALENFRVRWKRNFLQENPSIVDVELNIFGLLAYDATRALAEAVEKAGITSFGFDK 237 (852)
Q Consensus 159 ~~~~~~~~~~~gv~~~~~~-~~~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~a~~aYDAv~~lA~Al~~a~~~~~~~~~ 237 (852)
...|+.....+ ..+.+..++|+++|+++|+. .|+.+++.+||+++++++|+++||
T Consensus 216 --------g~~G~~~~~~~~~~~~~~~~~f~~~f~~~~g~--------~p~~~~a~aY~av~~~a~Ai~~AG-------- 271 (347)
T TIGR03863 216 --------GSAGLVPTAWHRAWERWGATQLQSRFEKLAGR--------PMTELDYAAWLAVRAVGEAVTRTR-------- 271 (347)
T ss_pred --------cccCccccccCCcccchhHHHHHHHHHHHhCC--------CCChHHHHHHHHHHHHHHHHHHhc--------
Confidence 12233322211 22347789999999999987 688889999999999999999999
Q ss_pred cccCCCCCCCccccccCChHHHHHHhhccce--eeeee-eEEee--cCccccce
Q 003054 238 TNVSRNATDLEAFGISQNGPKLLQALSSTRF--KGLTG-DYIFV--DGQLQSSA 286 (852)
Q Consensus 238 ~~~~~~~~~~~~~~~~~~g~~l~~al~~~~f--~GltG-~v~f~--~G~~~~~~ 286 (852)
+.++++|+++|+++++ +++.| ++.|. ||+...+.
T Consensus 272 ---------------s~d~~aV~~aL~~~~~~~~~~~g~~~~~R~~Dhq~~~~~ 310 (347)
T TIGR03863 272 ---------------SADPATLRDYLLSDEFELAGFKGRPLSFRPWDGQLRQPV 310 (347)
T ss_pred ---------------CCCHHHHHHHHcCCCceecccCCCcceeeCCCcccccce
Confidence 5678999999999876 57887 69995 88875543
No 77
>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=4.4e-21 Score=210.29 Aligned_cols=231 Identities=17% Similarity=0.179 Sum_probs=185.2
Q ss_pred hhhHHHHhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHHH
Q 003054 2 QTNFIIQLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTDA 81 (852)
Q Consensus 2 ~a~~v~~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~~ 81 (852)
++.++++++++.+||+|+++++++ ++. .||+||+.+++..++.++++++.+.|+++|++|+.+++||++..+.|.++
T Consensus 71 ~~~a~~~~~~~~~ip~i~~~~~~~-~~~--~~~~f~~~~~~~~~~~~~~~~~~~~g~k~vaii~~~~~~g~~~~~~f~~~ 147 (336)
T cd06339 71 NVAALAAAAAELGVPVLALNNDES-VAA--GPNLFYFGLSPEDEARRAAEYARSQGKRRPLVLAPDGAYGQRVADAFRQA 147 (336)
T ss_pred HHHHHHhhhccCCCCEEEccCCcc-ccC--CCCEEEecCChHHHHHHHHHHHHhcCccceEEEecCChHHHHHHHHHHHH
Confidence 355677999999999999775544 332 58999999999999999999998889999999999999999999999999
Q ss_pred HHhCCceeeeeeecCCCCChHHHHHHHHHhhcC---------------------CceEEEEEeChh-hHHHHHHHHHHcC
Q 003054 82 LQAIDTRVPYRSVISPLATDDQIEKELYKLFTM---------------------QTRVFILHMLPS-LGSRIFEKANEIG 139 (852)
Q Consensus 82 l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~---------------------~~~viv~~~~~~-~~~~i~~~a~~~G 139 (852)
+++.|++|+....++. +..||++++.+|++. +||+|++.+.++ ++..+.++++..+
T Consensus 148 ~~~~G~~vv~~~~~~~--~~~d~~~~i~~i~~~~~~~~~~~~~~~~~~~~~~~~~~d~v~~~~~~~~~~~~~~~~~~~~~ 225 (336)
T cd06339 148 WQQLGGTVVAIESYDP--SPTDLSDAIRRLLGVDDSEQRIAQLKSLESEPRRRQDIDAIDAVALPDGEARLIKPQLLFYY 225 (336)
T ss_pred HHHcCCceeeeEecCC--CHHHHHHHHHHHhccccchhhhhhhhhcccCccccCCCCcEEEEecChhhhhhhcchhhhhc
Confidence 9999999999988885 488999999999998 999999999887 7778888887776
Q ss_pred C---cccceEEEEcCccccccccCCchhhcccceEEEEEecCCCChHHHHHHHHHHHhccccCCCCccccc-chhhHhHh
Q 003054 140 L---MNKGCVWIMTDGMTNLLRTLEPSVIDSMQGVIGVGPHVPKTKALENFRVRWKRNFLQENPSIVDVEL-NIFGLLAY 215 (852)
Q Consensus 140 ~---~~~~~vwi~~~~~~~~~~~~~~~~~~~~~gv~~~~~~~~~~~~~~~F~~~~~~~~~~~~~~~~~~~~-~~~a~~aY 215 (852)
. ..+ +++++++.... ... ...+..+|++...+... ...+|+++|+++|+. .| +.+++.+|
T Consensus 226 ~~~~~~~---~~g~~~~~~~~-~~~-~~g~~~~g~~~~~~~~~---~~~~f~~~y~~~~~~--------~p~~~~~a~~Y 289 (336)
T cd06339 226 GVPGDVP---LYGTSRWYSGT-PAP-LRDPDLNGAWFADPPWL---LDANFELRYRAAYGW--------PPLSRLAALGY 289 (336)
T ss_pred cCcCCCC---EEEeccccCCC-CCc-ccCcccCCcEEeCCCcc---cCcchhhhHHHHhcC--------CCCchHHHHHH
Confidence 4 444 77777766431 111 23356788876554221 223899999999987 67 89999999
Q ss_pred hHHHHHHHHHHHhcccCcCccccccCCCCCCCccccccCChHHHHHHhhc-cceeeeeeeEEee-cCcc
Q 003054 216 DATRALAEAVEKAGITSFGFDKTNVSRNATDLEAFGISQNGPKLLQALSS-TRFKGLTGDYIFV-DGQL 282 (852)
Q Consensus 216 DAv~~lA~Al~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~al~~-~~f~GltG~v~f~-~G~~ 282 (852)
||+.+++.++++++.+ . +|.+ ..|+|++|++.|+ +|+.
T Consensus 290 Da~~l~~~~~~~~~~~-----------------------~------al~~~~~~~g~~G~~~f~~~g~~ 329 (336)
T cd06339 290 DAYALAAALAQLGQGD-----------------------A------ALTPGAGFSGVTGVLRLDPDGVI 329 (336)
T ss_pred hHHHHHHHHHHccccc-----------------------c------ccCCCCccccCcceEEECCCCeE
Confidence 9999999888876521 1 3333 4699999999997 7875
No 78
>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=99.85 E-value=1.2e-20 Score=194.31 Aligned_cols=222 Identities=23% Similarity=0.372 Sum_probs=182.8
Q ss_pred EEEeeecccCcccceEEeeCCCCCCCceEEEeeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCcccE
Q 003054 347 LRIGVPVKKGFSDFVNVTIDPKTQEPTSVTGYCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGEFDA 426 (852)
Q Consensus 347 lrv~v~~~~~~~~~~~~~~d~~~~~~~~~~G~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~~D~ 426 (852)
||||+. ..++||.+.+ .++ ...|+++|+++++++++|+++++ ++. +|.+++.+|.+|++|+
T Consensus 1 l~V~~~--~~~~P~~~~~-----~~~-~~~G~~~dl~~~i~~~~g~~~~~--~~~---------~~~~~~~~l~~g~~D~ 61 (225)
T PF00497_consen 1 LRVGVD--EDYPPFSYID-----EDG-EPSGIDVDLLRAIAKRLGIKIEF--VPM---------PWSRLLEMLENGKADI 61 (225)
T ss_dssp EEEEEE--SEBTTTBEEE-----TTS-EEESHHHHHHHHHHHHHTCEEEE--EEE---------EGGGHHHHHHTTSSSE
T ss_pred CEEEEc--CCCCCeEEEC-----CCC-CEEEEhHHHHHHHHhhcccccce--eec---------cccccccccccccccc
Confidence 688886 5778888887 577 99999999999999999985444 442 3899999999999999
Q ss_pred EEeeeeeecCcceeeeccccccccceEEEEEccCCCCCCceEeecccchhHHHHHHHHHHHHHhhhhheecccCCCCCCC
Q 003054 427 VVGDITIVFNRSNYVDFTLPYTESGVSMIVPIKDSKKRNAWVFLQPLTWDLWVTCFCFFIFIGFVVWVLEHRVNEDFRGP 506 (852)
Q Consensus 427 ~~g~~~it~~r~~~vdft~p~~~~~~~~vv~~~~~~~~~~~~~l~PF~~~lW~~i~~~~i~~~~v~~~l~~~~~~~~~~~ 506 (852)
++++++.+++|.+.++||.||+....++++++.+...
T Consensus 62 ~~~~~~~~~~r~~~~~~s~p~~~~~~~~~~~~~~~~~------------------------------------------- 98 (225)
T PF00497_consen 62 IIGGLSITPERAKKFDFSDPYYSSPYVLVVRKGDAPP------------------------------------------- 98 (225)
T ss_dssp EESSEB-BHHHHTTEEEESESEEEEEEEEEETTSTCS-------------------------------------------
T ss_pred ccccccccccccccccccccccchhheeeeccccccc-------------------------------------------
Confidence 9989999999999999999999999999999752111
Q ss_pred cccccchhHHHHHHHhhhccccccccchhhHHHHHHHHHHHHHHHHhhhhccceeeecccCCCcCCHHHHHhcCCeEEEE
Q 003054 507 AGQQVGTSFWFSFSTMVFSQRERVISNLARIVVIVWCFVVLILTQSYTASLTSLLTVQQLQPTITDVKMLIKRGDNVGYQ 586 (852)
Q Consensus 507 ~~~~~~~~~~~~~~~l~~~~~~~~~s~~~R~v~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~i~sl~dL~~~~~~vg~~ 586 (852)
...+++++||. |++||+.
T Consensus 99 ------------------------------------------------------------~~~~~~~~dl~--~~~i~~~ 116 (225)
T PF00497_consen 99 ------------------------------------------------------------IKTIKSLDDLK--GKRIGVV 116 (225)
T ss_dssp ------------------------------------------------------------TSSHSSGGGGT--TSEEEEE
T ss_pred ------------------------------------------------------------cccccchhhhc--Ccccccc
Confidence 11277788994 7899999
Q ss_pred eCchHHHHHHhcCCCCcceeecCCHhHHHHHhhcccccCceeEEEechhHHHHHHhhcCCc-eEeecccccccceEEEec
Q 003054 587 KGSFVLGILKQLGFDERKLVVYNSPEDCHELFQKGSVNGGIAAAFDEIPYMKLLIGQYCSK-YAMIEPKFKTAGFGFVFP 665 (852)
Q Consensus 587 ~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~~~~~-~~~v~~~~~~~~~~~~~~ 665 (852)
.|+....++++......+++.+.+.++++++|.+|+ +++++.+...+.+++++.... ...........++++++.
T Consensus 117 ~g~~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~g~----~d~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 192 (225)
T PF00497_consen 117 RGSSYADYLKQQYPSNINIVEVDSPEEALEALLSGR----IDAFIVDESTAEYLLKRHPLENIVVIPPPISPSPVYFAVR 192 (225)
T ss_dssp TTSHHHHHHHHHTHHTSEEEEESSHHHHHHHHHTTS----SSEEEEEHHHHHHHHHHTTTCEEEEEEEEEEEEEEEEEEE
T ss_pred cchhHHHHhhhhccchhhhcccccHHHHHHHHhcCC----eeeeeccchhhhhhhhhcccccccccccccccceeEEeec
Confidence 999988888774222557788999999999999999 999999999999999887432 222245556667777776
Q ss_pred CC-CCchhhHHHHHHhccccChhHHHHHHHcc
Q 003054 666 LH-SPLVHDVSKAILNVTEGDKMKEIEDAWFK 696 (852)
Q Consensus 666 k~-spl~~~in~~il~l~e~G~~~~i~~kw~~ 696 (852)
++ +.|++.||++|.+|.++|.+++|.+||++
T Consensus 193 ~~~~~l~~~~n~~i~~l~~~G~~~~i~~ky~g 224 (225)
T PF00497_consen 193 KKNPELLEIFNKAIRELKQSGEIQKILKKYLG 224 (225)
T ss_dssp TTTHHHHHHHHHHHHHHHHTTHHHHHHHHHHS
T ss_pred ccccHHHHHHHHHHHHHHhCcHHHHHHHHHcC
Confidence 65 55999999999999999999999999996
No 79
>PRK11260 cystine transporter subunit; Provisional
Probab=99.85 E-value=7.2e-20 Score=193.95 Aligned_cols=223 Identities=21% Similarity=0.323 Sum_probs=190.2
Q ss_pred CCceEEEeeecccCcccceEEeeCCCCCCCceEEEeeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcC
Q 003054 343 NEKKLRIGVPVKKGFSDFVNVTIDPKTQEPTSVTGYCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLG 422 (852)
Q Consensus 343 ~~~~lrv~v~~~~~~~~~~~~~~d~~~~~~~~~~G~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g 422 (852)
..+.++||+. ..++||.+.+ .++ .+.|+.+|++++|++++|. ++++++. .|.+++.+|.+|
T Consensus 39 ~~~~l~v~~~--~~~~P~~~~~-----~~g-~~~G~~~dl~~~i~~~lg~--~~e~~~~---------~~~~~~~~l~~G 99 (266)
T PRK11260 39 ERGTLLVGLE--GTYPPFSFQG-----EDG-KLTGFEVEFAEALAKHLGV--KASLKPT---------KWDGMLASLDSK 99 (266)
T ss_pred cCCeEEEEeC--CCcCCceEEC-----CCC-CEEEehHHHHHHHHHHHCC--eEEEEeC---------CHHHHHHHHhcC
Confidence 4678999986 5688887654 456 8999999999999999996 4555553 489999999999
Q ss_pred cccEEEeeeeeecCcceeeeccccccccceEEEEEccCCCCCCceEeecccchhHHHHHHHHHHHHHhhhhheecccCCC
Q 003054 423 EFDAVVGDITIVFNRSNYVDFTLPYTESGVSMIVPIKDSKKRNAWVFLQPLTWDLWVTCFCFFIFIGFVVWVLEHRVNED 502 (852)
Q Consensus 423 ~~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv~~~~~~~~~~~~~l~PF~~~lW~~i~~~~i~~~~v~~~l~~~~~~~ 502 (852)
++|+++++++.+++|...+.||.||..+++.+++++....
T Consensus 100 ~~D~~~~~~~~~~~r~~~~~fs~p~~~~~~~~~~~~~~~~---------------------------------------- 139 (266)
T PRK11260 100 RIDVVINQVTISDERKKKYDFSTPYTVSGIQALVKKGNEG---------------------------------------- 139 (266)
T ss_pred CCCEEEeccccCHHHHhccccCCceeecceEEEEEcCCcC----------------------------------------
Confidence 9999988889999999999999999999999999865322
Q ss_pred CCCCcccccchhHHHHHHHhhhccccccccchhhHHHHHHHHHHHHHHHHhhhhccceeeecccCCCcCCHHHHHhcCCe
Q 003054 503 FRGPAGQQVGTSFWFSFSTMVFSQRERVISNLARIVVIVWCFVVLILTQSYTASLTSLLTVQQLQPTITDVKMLIKRGDN 582 (852)
Q Consensus 503 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~s~~~R~v~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~i~sl~dL~~~~~~ 582 (852)
.+++++||. |++
T Consensus 140 ------------------------------------------------------------------~~~~~~dL~--g~~ 151 (266)
T PRK11260 140 ------------------------------------------------------------------TIKTAADLK--GKK 151 (266)
T ss_pred ------------------------------------------------------------------CCCCHHHcC--CCE
Confidence 278899995 889
Q ss_pred EEEEeCchHHHHHHhcCCCCcceeecCCHhHHHHHhhcccccCceeEEEechhHHHHHHhhcCCceEeecccccccceEE
Q 003054 583 VGYQKGSFVLGILKQLGFDERKLVVYNSPEDCHELFQKGSVNGGIAAAFDEIPYMKLLIGQYCSKYAMIEPKFKTAGFGF 662 (852)
Q Consensus 583 vg~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~ 662 (852)
||+..|+....++++. ++..++..+++..+.+++|.+|+ +++++.+...+.+++++....+.+....+...++++
T Consensus 152 Igv~~G~~~~~~l~~~-~~~~~i~~~~~~~~~l~~L~~Gr----vD~~i~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 226 (266)
T PRK11260 152 VGVGLGTNYEQWLRQN-VQGVDVRTYDDDPTKYQDLRVGR----IDAILVDRLAALDLVKKTNDTLAVAGEAFSRQESGV 226 (266)
T ss_pred EEEecCCcHHHHHHHh-CCCCceEecCCHHHHHHHHHcCC----CCEEEechHHHHHHHHhCCCcceecCCccccCceEE
Confidence 9999999988888764 66667888999999999999999 999999988888888776544555556677788999
Q ss_pred EecCCCC-chhhHHHHHHhccccChhHHHHHHHccC
Q 003054 663 VFPLHSP-LVHDVSKAILNVTEGDKMKEIEDAWFKK 697 (852)
Q Consensus 663 ~~~k~sp-l~~~in~~il~l~e~G~~~~i~~kw~~~ 697 (852)
+++++++ ++..+|++|.++.++|.++++.+||+..
T Consensus 227 ~v~~~~~~l~~~ln~~l~~~~~~g~~~~i~~k~~~~ 262 (266)
T PRK11260 227 ALRKGNPDLLKAVNQAIAEMQKDGTLKALSEKWFGA 262 (266)
T ss_pred EEeCCCHHHHHHHHHHHHHHHhCCcHHHHHHHhcCC
Confidence 9999877 9999999999999999999999999964
No 80
>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=99.85 E-value=2.3e-21 Score=214.29 Aligned_cols=302 Identities=19% Similarity=0.308 Sum_probs=228.2
Q ss_pred hHHHHhcCCCCccEEeeecCCCCCCC-CCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHHHH
Q 003054 4 NFIIQLGNKSQVPILSFSATSPSLTS-IRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTDAL 82 (852)
Q Consensus 4 ~~v~~i~~~~~vP~Is~~ats~~lt~-~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~~l 82 (852)
..++.-+..++..++||++++|.|++ ..+|+|||+.|++......+..++++++|++|+.++++.+--....+.+...+
T Consensus 126 ~~iaea~~~w~l~~lsy~~ssp~ls~r~rfp~~frt~PS~~~~np~rl~l~~~~~w~rvgt~~q~e~~f~~~~~dl~~~~ 205 (865)
T KOG1055|consen 126 TLIAEAAKMWNLIVLSYGASSPALSNRKRFPTFFRTHPSANAHNPTRIKLLKKFGWKRVATLQQTEEVFSSTLNDLEARL 205 (865)
T ss_pred hHHHhhccccceeeecccCCCccccchhhcchhhhcCCccccCCcceeeechhcCcceeeeeeeehhhhcchHHHHHHhh
Confidence 35566677788889999999999998 78999999999999999999999999999999999999888888899999999
Q ss_pred HhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHcCCcccceEEEEcCccccccc----
Q 003054 83 QAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLR---- 158 (852)
Q Consensus 83 ~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~~~~~~~---- 158 (852)
.+.|++++.+..+. .|....+++++....|+|+-.-+...|+++++++++.+|.+..|+|+...+..+.+.
T Consensus 206 ~~~~ieiv~~qsf~-----~dp~~~vk~l~~~D~RiI~g~f~~~~Arkv~C~~Y~~~myg~ky~w~~~g~y~d~w~ev~~ 280 (865)
T KOG1055|consen 206 KEAGIEIVFRQSFS-----SDPADSVKNLKRQDARIIVGLFYETEARKVFCEAYKERLYGRKYVWFLIGWYADNWWEITH 280 (865)
T ss_pred hccccEEEEeeccc-----cCHHHHHhhccccchhheeccchHhhhhHHHHhhchhhcccceeEEEEEEeeccchhhccC
Confidence 99999999887764 345667899999999999999999999999999999999999999998776554332
Q ss_pred ----cCCchhhcccceEEEEEe--cCCCC------hHHHHHHHHHHHhccccCCCCcccccchhhHhHhhHHHHHHHHHH
Q 003054 159 ----TLEPSVIDSMQGVIGVGP--HVPKT------KALENFRVRWKRNFLQENPSIVDVELNIFGLLAYDATRALAEAVE 226 (852)
Q Consensus 159 ----~~~~~~~~~~~gv~~~~~--~~~~~------~~~~~F~~~~~~~~~~~~~~~~~~~~~~~a~~aYDAv~~lA~Al~ 226 (852)
..-.+...+++|.+++.. ..+.. -....|...+.++.+... .....+..+.++|||+|++|.|++
T Consensus 281 ~~~~ctveem~~A~eg~~s~e~~pl~~~~~~tisg~T~~~~l~~~~~~r~~~~---~~~~~~~~~~~ayd~Iwa~ala~n 357 (865)
T KOG1055|consen 281 PSENCTVEEMTEAAEGHITTEFVMLSPANITTISGMTAQEFLEELTKYRKRHP---EETGGFQEAPLAYDAIWALALALN 357 (865)
T ss_pred chhhhhHHHHHHHHhhheeeeeeccccccceeeccchhHHHHHHHHhhhcccc---ccccCcccCchHHHHHHHHHHHHH
Confidence 111235667788877643 33321 123455555554443211 112567788999999999999999
Q ss_pred HhcccCcCccccccCCCCCCCccccccCChHHHHHHhhccceeeeeeeEEeecCccccceEEEEEccCC-cEEEEEEcCC
Q 003054 227 KAGITSFGFDKTNVSRNATDLEAFGISQNGPKLLQALSSTRFKGLTGDYIFVDGQLQSSAFEIINVNNG-ARGVGFWTPE 305 (852)
Q Consensus 227 ~a~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~al~~~~f~GltG~v~f~~G~~~~~~~~I~~~~~g-~~~vG~w~~~ 305 (852)
++...... ... ...+. +.....-.+.|.+|+.+++|+|++|.|.|.+|++ ...-+|-|+++| ++.+|+++..
T Consensus 358 ~t~e~l~~-~~~----~l~~f-~y~~k~i~d~i~eamn~tsF~GvsG~V~F~~geR-~a~t~ieQ~qdg~y~k~g~Yds~ 430 (865)
T KOG1055|consen 358 KTMEGLGR-SHV----RLEDF-NYNNKTIADQIYEAMNSTSFEGVSGHVVFSNGER-MALTLIEQFQDGKYKKIGYYDST 430 (865)
T ss_pred HHHhcCCc-cce----ecccc-chhhhHHHHHHHHHhhcccccccccceEecchhh-HHHHHHHHHhCCceEeecccccc
Confidence 98644310 000 00111 1111234678999999999999999999988998 455567788866 9999999876
Q ss_pred CCcccccCCCccccCCccceEeCCC
Q 003054 306 KGLTQKLSSNSTTKSKLKPIIWPGD 330 (852)
Q Consensus 306 ~g~~~~~~~~~~~~~~~~~i~Wpg~ 330 (852)
.+ .++ -.++..|-|+
T Consensus 431 ~D---~ls-------~~n~~~w~~g 445 (865)
T KOG1055|consen 431 KD---DLS-------WINTEKWIGG 445 (865)
T ss_pred cc---hhh-------ccccceEecc
Confidence 55 221 2345578877
No 81
>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=99.84 E-value=7.5e-20 Score=201.18 Aligned_cols=244 Identities=16% Similarity=0.148 Sum_probs=194.3
Q ss_pred hhHHHHhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHHHH
Q 003054 3 TNFIIQLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTDAL 82 (852)
Q Consensus 3 a~~v~~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~~l 82 (852)
+.++.+++++.++|+|+++++++.++....||+||+.+++..++..+++++.+.||++|++++.|+.||....+.+++++
T Consensus 81 ~~~~~~~~~~~~iP~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~g~~~v~~l~~~~~~~~~~~~~~~~~~ 160 (336)
T cd06326 81 TAAALPLLEEAGVPLVGPFTGASSLRDPPDRNVFNVRASYADEIAAIVRHLVTLGLKRIAVFYQDDAFGKDGLAGVEKAL 160 (336)
T ss_pred HHHHHHHHHHcCCeEEEecCCcHHhcCCCCCceEEeCCChHHHHHHHHHHHHHhCCceEEEEEecCcchHHHHHHHHHHH
Confidence 45677889999999999887777666545789999999999999999999999999999999999999999999999999
Q ss_pred HhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHcCCcccceEEEEcCccccccccCCc
Q 003054 83 QAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLEP 162 (852)
Q Consensus 83 ~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~~~~~~~~~~~ 162 (852)
++.|++++....++.+ ..|+.+++.++++.+||+|++......+..++++++++|+..+ ++......... ...
T Consensus 161 ~~~G~~~~~~~~~~~~--~~d~~~~~~~l~~~~~dav~~~~~~~~a~~~i~~~~~~G~~~~---~~~~~~~~~~~--~~~ 233 (336)
T cd06326 161 AARGLKPVATASYERN--TADVAAAVAQLAAARPQAVIMVGAYKAAAAFIRALRKAGGGAQ---FYNLSFVGADA--LAR 233 (336)
T ss_pred HHcCCCeEEEEeecCC--cccHHHHHHHHHhcCCCEEEEEcCcHHHHHHHHHHHhcCCCCc---EEEEeccCHHH--HHH
Confidence 9999998877777643 6789999999999999999999988899999999999999654 23332222110 111
Q ss_pred hhhcccceEEEEE--ec--CCCChHHHHHHHHHHHhccccCCCCcccccchhhHhHhhHHHHHHHHHHHhcccCcCcccc
Q 003054 163 SVIDSMQGVIGVG--PH--VPKTKALENFRVRWKRNFLQENPSIVDVELNIFGLLAYDATRALAEAVEKAGITSFGFDKT 238 (852)
Q Consensus 163 ~~~~~~~gv~~~~--~~--~~~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~a~~aYDAv~~lA~Al~~a~~~~~~~~~~ 238 (852)
..+...+|++... ++ ....|..++|+++|+++++.. +|+.+++.+||+++++++|+++++.
T Consensus 234 ~~g~~~~g~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~-------~~~~~~~~~y~~~~~~~~a~~~~g~-------- 298 (336)
T cd06326 234 LLGEYARGVIVTQVVPNPWSRTLPIVREYQAAMKAYGPGA-------PPSYVSLEGYIAAKVLVEALRRAGP-------- 298 (336)
T ss_pred HhhhhhcceEEEEEecCccccCCHHHHHHHHHHHhhCCCC-------CCCeeeehhHHHHHHHHHHHHHcCC--------
Confidence 2334567876543 22 224688999999999988742 5778889999999999999999872
Q ss_pred ccCCCCCCCccccccCChHHHHHHhhccce-eeeeeeEEeecCcc
Q 003054 239 NVSRNATDLEAFGISQNGPKLLQALSSTRF-KGLTGDYIFVDGQL 282 (852)
Q Consensus 239 ~~~~~~~~~~~~~~~~~g~~l~~al~~~~f-~GltG~v~f~~G~~ 282 (852)
..++++|+++|++++. ++..|.+.|..+|+
T Consensus 299 --------------~~~~~~v~~al~~~~~~~~~g~~~~~~~~~h 329 (336)
T cd06326 299 --------------DPTRESLLAALEAMGKFDLGGFRLDFSPGNH 329 (336)
T ss_pred --------------CCCHHHHHHHHHhcCCCCCCCeEEecCcccc
Confidence 2357899999999875 55555889964444
No 82
>PRK15007 putative ABC transporter arginine-biding protein; Provisional
Probab=99.83 E-value=3e-19 Score=186.71 Aligned_cols=217 Identities=21% Similarity=0.360 Sum_probs=179.5
Q ss_pred CceEEEeeecccCcccceEEeeCCCCCCCceEEEeeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCc
Q 003054 344 EKKLRIGVPVKKGFSDFVNVTIDPKTQEPTSVTGYCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGE 423 (852)
Q Consensus 344 ~~~lrv~v~~~~~~~~~~~~~~d~~~~~~~~~~G~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~ 423 (852)
.+.|+||+. +.++||.+.+ .++ ++.|+++|+++++++++|.. ++++.. +|..++.++.+|+
T Consensus 20 ~~~l~v~~~--~~~~P~~~~~-----~~g-~~~G~~~dl~~~i~~~lg~~--~~~~~~---------~~~~~~~~l~~g~ 80 (243)
T PRK15007 20 AETIRFATE--ASYPPFESID-----ANN-QIVGFDVDLAQALCKEIDAT--CTFSNQ---------AFDSLIPSLKFRR 80 (243)
T ss_pred CCcEEEEeC--CCCCCceeeC-----CCC-CEEeeeHHHHHHHHHHhCCc--EEEEeC---------CHHHHhHHHhCCC
Confidence 568999997 6788888765 457 89999999999999999975 445442 5999999999999
Q ss_pred ccEEEeeeeeecCcceeeeccccccccceEEEEEccCCCCCCceEeecccchhHHHHHHHHHHHHHhhhhheecccCCCC
Q 003054 424 FDAVVGDITIVFNRSNYVDFTLPYTESGVSMIVPIKDSKKRNAWVFLQPLTWDLWVTCFCFFIFIGFVVWVLEHRVNEDF 503 (852)
Q Consensus 424 ~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv~~~~~~~~~~~~~l~PF~~~lW~~i~~~~i~~~~v~~~l~~~~~~~~ 503 (852)
+|+++++++.+++|...++||.||+..+..++.+...
T Consensus 81 ~D~~~~~~~~~~~r~~~~~fs~p~~~~~~~~v~~~~~------------------------------------------- 117 (243)
T PRK15007 81 VEAVMAGMDITPEREKQVLFTTPYYDNSALFVGQQGK------------------------------------------- 117 (243)
T ss_pred cCEEEEcCccCHHHhcccceecCccccceEEEEeCCC-------------------------------------------
Confidence 9998888889999999999999999988777766431
Q ss_pred CCCcccccchhHHHHHHHhhhccccccccchhhHHHHHHHHHHHHHHHHhhhhccceeeecccCCCcCCHHHHHhcCCeE
Q 003054 504 RGPAGQQVGTSFWFSFSTMVFSQRERVISNLARIVVIVWCFVVLILTQSYTASLTSLLTVQQLQPTITDVKMLIKRGDNV 583 (852)
Q Consensus 504 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~s~~~R~v~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~i~sl~dL~~~~~~v 583 (852)
+++++||. |++|
T Consensus 118 ------------------------------------------------------------------~~~~~dL~--g~~I 129 (243)
T PRK15007 118 ------------------------------------------------------------------YTSVDQLK--GKKV 129 (243)
T ss_pred ------------------------------------------------------------------CCCHHHhC--CCeE
Confidence 67899995 8899
Q ss_pred EEEeCchHHHHHHhcCCCCcceeecCCHhHHHHHhhcccccCceeEEEechhHHHHHHhhcCCceEeeccc-----cccc
Q 003054 584 GYQKGSFVLGILKQLGFDERKLVVYNSPEDCHELFQKGSVNGGIAAAFDEIPYMKLLIGQYCSKYAMIEPK-----FKTA 658 (852)
Q Consensus 584 g~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~~~~~~~~v~~~-----~~~~ 658 (852)
|+..|+....++++. .+..+++.+++.++.+++|.+|+ +++++.+...+.+++++... +..++.. +...
T Consensus 130 gv~~g~~~~~~l~~~-~~~~~~~~~~~~~~~~~~L~~gr----vDa~i~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~ 203 (243)
T PRK15007 130 GVQNGTTHQKFIMDK-HPEITTVPYDSYQNAKLDLQNGR----IDAVFGDTAVVTEWLKDNPK-LAAVGDKVTDKDYFGT 203 (243)
T ss_pred EEecCcHHHHHHHHh-CCCCeEEEcCCHHHHHHHHHcCC----CCEEEeCHHHHHHHHhcCCC-ceeecCcccccccCCc
Confidence 999999988888764 55667788899999999999999 99999998888887776543 3333322 2234
Q ss_pred ceEEEecCCCC-chhhHHHHHHhccccChhHHHHHHHcc
Q 003054 659 GFGFVFPLHSP-LVHDVSKAILNVTEGDKMKEIEDAWFK 696 (852)
Q Consensus 659 ~~~~~~~k~sp-l~~~in~~il~l~e~G~~~~i~~kw~~ 696 (852)
+++++++++.+ |+..||++|..+.++|.++++.++|++
T Consensus 204 ~~~~~~~~~~~~l~~~ln~~l~~l~~~g~~~~i~~~w~~ 242 (243)
T PRK15007 204 GLGIAVRQGNTELQQKLNTALEKVKKDGTYETIYNKWFQ 242 (243)
T ss_pred ceEEEEeCCCHHHHHHHHHHHHHHHhCCcHHHHHHHhcC
Confidence 57899988764 999999999999999999999999985
No 83
>PF13433 Peripla_BP_5: Periplasmic binding protein domain; PDB: 1QNL_A 1QO0_A 1PEA_A.
Probab=99.83 E-value=3.5e-19 Score=187.95 Aligned_cols=235 Identities=15% Similarity=0.156 Sum_probs=173.9
Q ss_pred hHHHHhcCCCCccEEeeecCCCCCCC--CCCCceEeccCCchhHHHHHHHHH-HHcCCcEEEEEEEeCCcccccHHHHHH
Q 003054 4 NFIIQLGNKSQVPILSFSATSPSLTS--IRSPYFFRGSLNDSSQAGAITAII-KAFGWREAVPIYVDNQYGEEMIPSLTD 80 (852)
Q Consensus 4 ~~v~~i~~~~~vP~Is~~ats~~lt~--~~~py~fR~~p~d~~~~~aia~~l-~~~gw~~vaii~~d~~~G~~~~~~l~~ 80 (852)
++|.|+.++.+-.+.- |..-+ ...|++|-+.....+|...+++++ +++|.+|+.+|.+|+.|++.....+++
T Consensus 82 KaVlPvvE~~~~LL~Y-----p~~YEG~E~S~nviYtGa~PNQ~~~pl~~~~~~~~G~~r~~lvGSdYv~pre~Nri~r~ 156 (363)
T PF13433_consen 82 KAVLPVVERHNALLFY-----PTQYEGFECSPNVIYTGAAPNQQLLPLIDYLLENFGAKRFYLVGSDYVYPRESNRIIRD 156 (363)
T ss_dssp HHHHHHHHHCT-EEEE------S--------TTEEE-S--GGGTHHHHHHHHHHHS--SEEEEEEESSHHHHHHHHHHHH
T ss_pred HHHHHHHHhcCceEEe-----ccccccccCCCceEEcCCCchhhHHHHHHHHHhccCCceEEEecCCccchHHHHHHHHH
Confidence 5677888888877764 23333 467999999999999999999985 889999999999999999999999999
Q ss_pred HHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHcCCcccceEEEEcCcccc-cccc
Q 003054 81 ALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTN-LLRT 159 (852)
Q Consensus 81 ~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~~~~-~~~~ 159 (852)
.+++.|++|+.+..+|.+ .+||...+.+|++.+||+|+-...++....|+++.+++|+..+ ..-|.+..... .+..
T Consensus 157 ~l~~~GgevvgE~Y~plg--~td~~~ii~~I~~~~Pd~V~stlvG~s~~aF~r~~~~aG~~~~-~~Pi~S~~~~E~E~~~ 233 (363)
T PF13433_consen 157 LLEARGGEVVGERYLPLG--ATDFDPIIAEIKAAKPDFVFSTLVGDSNVAFYRAYAAAGLDPE-RIPIASLSTSEAELAA 233 (363)
T ss_dssp HHHHTT-EEEEEEEE-S---HHHHHHHHHHHHHHT-SEEEEE--TTCHHHHHHHHHHHH-SSS----EEESS--HHHHTT
T ss_pred HHHHcCCEEEEEEEecCC--chhHHHHHHHHHhhCCCEEEEeCcCCcHHHHHHHHHHcCCCcc-cCeEEEEecCHHHHhh
Confidence 999999999999999965 8999999999999999999999999999999999999999754 34455444432 2222
Q ss_pred CCchhhcccceEEEEEecCC--CChHHHHHHHHHHHhccccCCCCcccccchhhHhHhhHHHHHHHHHHHhcccCcCccc
Q 003054 160 LEPSVIDSMQGVIGVGPHVP--KTKALENFRVRWKRNFLQENPSIVDVELNIFGLLAYDATRALAEAVEKAGITSFGFDK 237 (852)
Q Consensus 160 ~~~~~~~~~~gv~~~~~~~~--~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~a~~aYDAv~~lA~Al~~a~~~~~~~~~ 237 (852)
++ .+...|.++..+|.. ++|..++|+++|+++|+.+. .++.....+|.+|+++|+|+++||
T Consensus 234 ~g---~~~~~Gh~~~~~YFqsidtp~N~~Fv~~~~~~~g~~~------v~s~~~eaaY~~v~l~a~Av~~ag-------- 296 (363)
T PF13433_consen 234 MG---AEAAAGHYTSAPYFQSIDTPENQAFVARFRARYGDDR------VTSDPMEAAYFQVHLWAQAVEKAG-------- 296 (363)
T ss_dssp S----HHHHTT-EEEES--TT-SSHHHHHHHHHHHTTS-TT----------HHHHHHHHHHHHHHHHHHHHT--------
T ss_pred cC---hhhcCCcEEeehhhhhCCcHHHHHHHHHHHHHhCCCC------CCCcHHHHHHHHHHHHHHHHHHhC--------
Confidence 32 357899999999887 57999999999999998742 467778889999999999999999
Q ss_pred cccCCCCCCCccccccCChHHHHHHhhccceeeeeeeEEee
Q 003054 238 TNVSRNATDLEAFGISQNGPKLLQALSSTRFKGLTGDYIFV 278 (852)
Q Consensus 238 ~~~~~~~~~~~~~~~~~~g~~l~~al~~~~f~GltG~v~f~ 278 (852)
+.+.++++++|.+.+|+++.|.+.+|
T Consensus 297 ---------------s~d~~~vr~al~g~~~~aP~G~v~id 322 (363)
T PF13433_consen 297 ---------------SDDPEAVREALAGQSFDAPQGRVRID 322 (363)
T ss_dssp ---------------S--HHHHHHHHTT--EEETTEEEEE-
T ss_pred ---------------CCCHHHHHHHhcCCeecCCCcceEEc
Confidence 55679999999999999999999998
No 84
>PRK11917 bifunctional adhesin/ABC transporter aspartate/glutamate-binding protein; Reviewed
Probab=99.83 E-value=5.3e-19 Score=185.94 Aligned_cols=218 Identities=14% Similarity=0.222 Sum_probs=179.3
Q ss_pred CCceEEEeeecccCcccceEEeeCCCCCCCceEEEeeHHHHHHHHHHC-CCccceEEEecCCCCCCCCCChhHHHHHHhc
Q 003054 343 NEKKLRIGVPVKKGFSDFVNVTIDPKTQEPTSVTGYCVDVFKAVIQEL-PYAVAYDFVPYGQPDGSSSGSYNDLVYQVFL 421 (852)
Q Consensus 343 ~~~~lrv~v~~~~~~~~~~~~~~d~~~~~~~~~~G~~~dl~~~ia~~l-~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~ 421 (852)
..+.|+||+. ++++||.+.+. +++ ++.||++|+++++++++ |..+++++++.. |...+.+|.+
T Consensus 36 ~~g~l~vg~~--~~~pP~~~~~~----~~g-~~~G~~vdl~~~ia~~llg~~~~~~~~~~~---------~~~~~~~l~~ 99 (259)
T PRK11917 36 SKGQLIVGVK--NDVPHYALLDQ----ATG-EIKGFEIDVAKLLAKSILGDDKKIKLVAVN---------AKTRGPLLDN 99 (259)
T ss_pred hCCEEEEEEC--CCCCCceeeeC----CCC-ceeEeeHHHHHHHHHHhcCCCccEEEEEcC---------hhhHHHHHHC
Confidence 4789999998 67889987541 256 89999999999999994 866667776643 6667789999
Q ss_pred CcccEEEeeeeeecCcceeeeccccccccceEEEEEccCCCCCCceEeecccchhHHHHHHHHHHHHHhhhhheecccCC
Q 003054 422 GEFDAVVGDITIVFNRSNYVDFTLPYTESGVSMIVPIKDSKKRNAWVFLQPLTWDLWVTCFCFFIFIGFVVWVLEHRVNE 501 (852)
Q Consensus 422 g~~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv~~~~~~~~~~~~~l~PF~~~lW~~i~~~~i~~~~v~~~l~~~~~~ 501 (852)
|++|++++++++|++|.+.++||.||+.++..+++++.. .
T Consensus 100 g~~D~~~~~~~~t~eR~~~~~fs~py~~~~~~lvv~~~~--~-------------------------------------- 139 (259)
T PRK11917 100 GSVDAVIATFTITPERKRIYNFSEPYYQDAIGLLVLKEK--N-------------------------------------- 139 (259)
T ss_pred CCccEEEecccCChhhhheeeeccCceeeceEEEEECCC--C--------------------------------------
Confidence 999999999999999999999999999999999999653 1
Q ss_pred CCCCCcccccchhHHHHHHHhhhccccccccchhhHHHHHHHHHHHHHHHHhhhhccceeeecccCCCcCCHHHHHhcCC
Q 003054 502 DFRGPAGQQVGTSFWFSFSTMVFSQRERVISNLARIVVIVWCFVVLILTQSYTASLTSLLTVQQLQPTITDVKMLIKRGD 581 (852)
Q Consensus 502 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~s~~~R~v~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~i~sl~dL~~~~~ 581 (852)
+++++||. |+
T Consensus 140 --------------------------------------------------------------------~~s~~dL~--g~ 149 (259)
T PRK11917 140 --------------------------------------------------------------------YKSLADMK--GA 149 (259)
T ss_pred --------------------------------------------------------------------CCCHHHhC--CC
Confidence 78999996 99
Q ss_pred eEEEEeCchHHHHHHhc---CCCCcceeecCCHhHHHHHhhcccccCceeEEEechhHHHHHHhhcCCceEeeccccccc
Q 003054 582 NVGYQKGSFVLGILKQL---GFDERKLVVYNSPEDCHELFQKGSVNGGIAAAFDEIPYMKLLIGQYCSKYAMIEPKFKTA 658 (852)
Q Consensus 582 ~vg~~~~s~~~~~l~~~---~~~~~~~~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~~~~~~~~v~~~~~~~ 658 (852)
+||+..|+.....+.+. .....+++.+++..+.+++|..|+ +||++.+...+..+..+. ..++++.+...
T Consensus 150 ~V~v~~gs~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~l~~Gr----vDa~~~d~~~~~~~~~~~---~~~~~~~~~~~ 222 (259)
T PRK11917 150 NIGVAQAATTKKAIGEAAKKIGIDVKFSEFPDYPSIKAALDAKR----VDAFSVDKSILLGYVDDK---SEILPDSFEPQ 222 (259)
T ss_pred eEEEecCCcHHHHHHHhhHhcCCceeEEecCCHHHHHHHHHcCC----CcEEEecHHHHHHhhhcC---CeecCCcCCCC
Confidence 99999999877665442 112235667889999999999999 999999987766655432 34566777788
Q ss_pred ceEEEecCCCC-chhhHHHHHHhccccChhHHHHHHHc
Q 003054 659 GFGFVFPLHSP-LVHDVSKAILNVTEGDKMKEIEDAWF 695 (852)
Q Consensus 659 ~~~~~~~k~sp-l~~~in~~il~l~e~G~~~~i~~kw~ 695 (852)
+++++++|+.+ ++..+|++|.++.. .+++|.+||-
T Consensus 223 ~~~~a~~k~~~~l~~~ln~~l~~~~~--~~~~i~~kw~ 258 (259)
T PRK11917 223 SYGIVTKKDDPAFAKYVDDFVKEHKN--EIDALAKKWG 258 (259)
T ss_pred ceEEEEeCCCHHHHHHHHHHHHHHHH--HHHHHHHHhC
Confidence 89999999987 99999999999864 7999999994
No 85
>PRK15010 ABC transporter lysine/arginine/ornithine binding periplasmic protein; Provisional
Probab=99.82 E-value=8.6e-19 Score=185.06 Aligned_cols=222 Identities=15% Similarity=0.250 Sum_probs=177.4
Q ss_pred CCceEEEeeecccCcccceEEeeCCCCCCCceEEEeeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcC
Q 003054 343 NEKKLRIGVPVKKGFSDFVNVTIDPKTQEPTSVTGYCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLG 422 (852)
Q Consensus 343 ~~~~lrv~v~~~~~~~~~~~~~~d~~~~~~~~~~G~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g 422 (852)
..++|+||+. +.|+||.+.+ +++ ++.|+++||++++++++|. ++++++. .|..++.++..|
T Consensus 24 ~~~~l~v~~~--~~~pPf~~~~-----~~g-~~~G~~vdl~~~ia~~lg~--~~~~~~~---------~~~~~~~~l~~g 84 (260)
T PRK15010 24 LPETVRIGTD--TTYAPFSSKD-----AKG-DFVGFDIDLGNEMCKRMQV--KCTWVAS---------DFDALIPSLKAK 84 (260)
T ss_pred cCCeEEEEec--CCcCCceeEC-----CCC-CEEeeeHHHHHHHHHHhCC--ceEEEeC---------CHHHHHHHHHCC
Confidence 3678999987 5688898865 457 8999999999999999996 4555542 499999999999
Q ss_pred cccEEEeeeeeecCcceeeeccccccccceEEEEEccCCCCCCceEeecccchhHHHHHHHHHHHHHhhhhheecccCCC
Q 003054 423 EFDAVVGDITIVFNRSNYVDFTLPYTESGVSMIVPIKDSKKRNAWVFLQPLTWDLWVTCFCFFIFIGFVVWVLEHRVNED 502 (852)
Q Consensus 423 ~~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv~~~~~~~~~~~~~l~PF~~~lW~~i~~~~i~~~~v~~~l~~~~~~~ 502 (852)
++|++++++..+++|.+.++||.||+.++.++++++....
T Consensus 85 ~~Di~~~~~~~t~eR~~~~~fs~p~~~~~~~~~~~~~~~~---------------------------------------- 124 (260)
T PRK15010 85 KIDAIISSLSITDKRQQEIAFSDKLYAADSRLIAAKGSPI---------------------------------------- 124 (260)
T ss_pred CCCEEEecCcCCHHHHhhcccccceEeccEEEEEECCCCC----------------------------------------
Confidence 9999988899999999999999999999999999876321
Q ss_pred CCCCcccccchhHHHHHHHhhhccccccccchhhHHHHHHHHHHHHHHHHhhhhccceeeecccCCCcCCHHHHHhcCCe
Q 003054 503 FRGPAGQQVGTSFWFSFSTMVFSQRERVISNLARIVVIVWCFVVLILTQSYTASLTSLLTVQQLQPTITDVKMLIKRGDN 582 (852)
Q Consensus 503 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~s~~~R~v~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~i~sl~dL~~~~~~ 582 (852)
..+++||. |++
T Consensus 125 -------------------------------------------------------------------~~~~~dl~--g~~ 135 (260)
T PRK15010 125 -------------------------------------------------------------------QPTLDSLK--GKH 135 (260)
T ss_pred -------------------------------------------------------------------CCChhHcC--CCE
Confidence 23688995 889
Q ss_pred EEEEeCchHHHHHHhc-CCCCcceeecCCHhHHHHHhhcccccCceeEEEechhHHHH-HHhhc-CCceEeecccc----
Q 003054 583 VGYQKGSFVLGILKQL-GFDERKLVVYNSPEDCHELFQKGSVNGGIAAAFDEIPYMKL-LIGQY-CSKYAMIEPKF---- 655 (852)
Q Consensus 583 vg~~~~s~~~~~l~~~-~~~~~~~~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~-~~~~~-~~~~~~v~~~~---- 655 (852)
||+..|+....++.+. .....+++.+++.++++++|.+|+ +|+++.+...+.+ +..+. ...+...+..+
T Consensus 136 Igv~~gs~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~gr----iDa~i~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 211 (260)
T PRK15010 136 VGVLQGSTQEAYANETWRSKGVDVVAYANQDLVYSDLAAGR----LDAALQDEVAASEGFLKQPAGKDFAFAGPSVKDKK 211 (260)
T ss_pred EEEecCchHHHHHHHhcccCCceEEecCCHHHHHHHHHcCC----ccEEEeCcHHHHHHHHhCCCCCceEEecCcccccc
Confidence 9999999887777542 112235677889999999999999 9999998776654 33332 33454443322
Q ss_pred -cccceEEEecCCCC-chhhHHHHHHhccccChhHHHHHHHcc
Q 003054 656 -KTAGFGFVFPLHSP-LVHDVSKAILNVTEGDKMKEIEDAWFK 696 (852)
Q Consensus 656 -~~~~~~~~~~k~sp-l~~~in~~il~l~e~G~~~~i~~kw~~ 696 (852)
....++++++++.+ |+..+|++|.++.++|.+++|.+||++
T Consensus 212 ~~~~~~~~a~~~~~~~L~~~ln~~l~~l~~~G~~~~i~~ky~~ 254 (260)
T PRK15010 212 YFGDGTGVGLRKDDAELTAAFNKALGELRQDGTYDKMAKKYFD 254 (260)
T ss_pred ccCCceEEEEeCCCHHHHHHHHHHHHHHHhCCcHHHHHHHhcC
Confidence 22346789998865 999999999999999999999999996
No 86
>TIGR01096 3A0103s03R lysine-arginine-ornithine-binding periplasmic protein.
Probab=99.81 E-value=1.4e-18 Score=182.39 Aligned_cols=218 Identities=22% Similarity=0.398 Sum_probs=183.1
Q ss_pred ceEEEeeecccCcccceEEeeCCCCCCCceEEEeeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCcc
Q 003054 345 KKLRIGVPVKKGFSDFVNVTIDPKTQEPTSVTGYCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGEF 424 (852)
Q Consensus 345 ~~lrv~v~~~~~~~~~~~~~~d~~~~~~~~~~G~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~~ 424 (852)
+.|+||+. ..|+||.+.+ +++ ++.|+++|+++++++++|. ++++++. +|.+++.+|.+|++
T Consensus 24 ~~l~v~~~--~~~~P~~~~~-----~~g-~~~G~~~dl~~~i~~~lg~--~~~~~~~---------~~~~~~~~l~~G~~ 84 (250)
T TIGR01096 24 GSVRIGTE--TGYPPFESKD-----ANG-KLVGFDVDLAKALCKRMKA--KCKFVEQ---------NFDGLIPSLKAKKV 84 (250)
T ss_pred CeEEEEEC--CCCCCceEEC-----CCC-CEEeehHHHHHHHHHHhCC--eEEEEeC---------CHHHHHHHHhCCCc
Confidence 68999985 6788888765 466 8999999999999999996 5566553 48999999999999
Q ss_pred cEEEeeeeeecCcceeeeccccccccceEEEEEccCCCCCCceEeecccchhHHHHHHHHHHHHHhhhhheecccCCCCC
Q 003054 425 DAVVGDITIVFNRSNYVDFTLPYTESGVSMIVPIKDSKKRNAWVFLQPLTWDLWVTCFCFFIFIGFVVWVLEHRVNEDFR 504 (852)
Q Consensus 425 D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv~~~~~~~~~~~~~l~PF~~~lW~~i~~~~i~~~~v~~~l~~~~~~~~~ 504 (852)
|+++++++.+++|.+.+.||.|++.++..++++.....
T Consensus 85 D~~~~~~~~~~~r~~~~~~s~p~~~~~~~~~~~~~~~~------------------------------------------ 122 (250)
T TIGR01096 85 DAIMATMSITPKRQKQIDFSDPYYATGQGFVVKKGSDL------------------------------------------ 122 (250)
T ss_pred CEEEecCccCHHHhhccccccchhcCCeEEEEECCCCc------------------------------------------
Confidence 99988888999999999999999999999999866321
Q ss_pred CCcccccchhHHHHHHHhhhccccccccchhhHHHHHHHHHHHHHHHHhhhhccceeeecccCCCcCCHHHHHhcCCeEE
Q 003054 505 GPAGQQVGTSFWFSFSTMVFSQRERVISNLARIVVIVWCFVVLILTQSYTASLTSLLTVQQLQPTITDVKMLIKRGDNVG 584 (852)
Q Consensus 505 ~~~~~~~~~~~~~~~~~l~~~~~~~~~s~~~R~v~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~i~sl~dL~~~~~~vg 584 (852)
+.+++||. |++||
T Consensus 123 -----------------------------------------------------------------~~~~~dl~--g~~i~ 135 (250)
T TIGR01096 123 -----------------------------------------------------------------AKTLEDLD--GKTVG 135 (250)
T ss_pred -----------------------------------------------------------------CCChHHcC--CCEEE
Confidence 46788996 88999
Q ss_pred EEeCchHHHHHHhcCCC-CcceeecCCHhHHHHHhhcccccCceeEEEechhHHHHHHhhcC--CceEeecccccc----
Q 003054 585 YQKGSFVLGILKQLGFD-ERKLVVYNSPEDCHELFQKGSVNGGIAAAFDEIPYMKLLIGQYC--SKYAMIEPKFKT---- 657 (852)
Q Consensus 585 ~~~~s~~~~~l~~~~~~-~~~~~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~~~--~~~~~v~~~~~~---- 657 (852)
+..|+....++.+. ++ ..+++.+.+.++++++|.+|+ +|+++.+...+.+++++.. +.+.+++..+..
T Consensus 136 ~~~g~~~~~~l~~~-~~~~~~~~~~~s~~~~~~~L~~g~----vD~~v~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~ 210 (250)
T TIGR01096 136 VQSGTTHEQYLKDY-FKPGVDIVEYDSYDNANMDLKAGR----IDAVFTDASVLAEGFLKPPNGKDFKFVGPSVTDEKYF 210 (250)
T ss_pred EecCchHHHHHHHh-ccCCcEEEEcCCHHHHHHHHHcCC----CCEEEeCHHHHHHHHHhCCCCCceEEecccccccccc
Confidence 99999988888764 33 456778899999999999999 9999999999988887653 236666544332
Q ss_pred -cceEEEecCCCC-chhhHHHHHHhccccChhHHHHHHHc
Q 003054 658 -AGFGFVFPLHSP-LVHDVSKAILNVTEGDKMKEIEDAWF 695 (852)
Q Consensus 658 -~~~~~~~~k~sp-l~~~in~~il~l~e~G~~~~i~~kw~ 695 (852)
..++++++++++ |+..||++|.+|.++|.++.|.+||+
T Consensus 211 ~~~~~~~~~~~~~~l~~~ln~~l~~l~~~g~~~~i~~kw~ 250 (250)
T TIGR01096 211 GDGYGIGLRKGDTELKAAFNKALAAIRADGTYQKISKKWF 250 (250)
T ss_pred CCceEEEEeCCCHHHHHHHHHHHHHHHHCCcHHHHHHhhC
Confidence 247899999876 99999999999999999999999996
No 87
>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=99.81 E-value=5.2e-19 Score=190.35 Aligned_cols=152 Identities=31% Similarity=0.485 Sum_probs=141.6
Q ss_pred hhhHHHHhcCCCCccEEeeecCCCCCCC-CCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHH
Q 003054 2 QTNFIIQLGNKSQVPILSFSATSPSLTS-IRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTD 80 (852)
Q Consensus 2 ~a~~v~~i~~~~~vP~Is~~ats~~lt~-~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~ 80 (852)
.+.+++++++.++||+|+++++++.+++ ..+||+||+.|++..++.+++++++++||++|+++|+|+++|....+.+.+
T Consensus 83 ~~~~v~~~~~~~~iP~is~~~~~~~~~~~~~~~~~~~~~p~~~~~~~a~~~~l~~~~w~~v~~v~~~~~~~~~~~~~~~~ 162 (298)
T cd06269 83 SAEAVASLLGALHIPQISYSATSPLLSDKEQFPSFLRTVPSDSSQAQAIVDLLKHFGWTWVGLVYSDDDYGRRLLELLEE 162 (298)
T ss_pred HHHHHHHHhccCCCcEEecccCchhhcChhhCCCeEecCCCcHHHHHHHHHHHHHCCCeEEEEEEecchhhHHHHHHHHH
Confidence 4677899999999999999999999986 578999999999999999999999999999999999999999999999999
Q ss_pred HHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHcCCcccceEEEEcCccccc
Q 003054 81 ALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNL 156 (852)
Q Consensus 81 ~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~~~~~ 156 (852)
.+++.|+++.....++.. +.++...+++++..+++||++++.++++..++++|+++||+ .+++||+++.+...
T Consensus 163 ~~~~~~~~v~~~~~~~~~--~~~~~~~l~~l~~~~~~viv~~~~~~~~~~~l~~a~~~g~~-~~~~~i~~~~~~~~ 235 (298)
T cd06269 163 ELEKNGICVAFVESIPDG--SEDIRRLLKELKSSTARVIVVFSSEEDALRLLEEAVELGMM-TGYHWIITDLWLTS 235 (298)
T ss_pred HHHHCCeeEEEEEEcCCC--HHHHHHHHHHHHhcCCcEEEEEechHHHHHHHHHHHHcCCC-CCeEEEEEChhhcc
Confidence 999999999998887744 58999999999999999999999999999999999999999 88999999988653
No 88
>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=99.81 E-value=8.7e-19 Score=186.50 Aligned_cols=225 Identities=18% Similarity=0.210 Sum_probs=180.9
Q ss_pred CCCceEEEeeecccCcccceEEeeCCCCCCCceEEEeeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhc
Q 003054 342 TNEKKLRIGVPVKKGFSDFVNVTIDPKTQEPTSVTGYCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFL 421 (852)
Q Consensus 342 ~~~~~lrv~v~~~~~~~~~~~~~~d~~~~~~~~~~G~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~ 421 (852)
...+.|+||+. +++||.+.+ .++ ...|+++||++++++++|... +++.. .+|++++..+.+
T Consensus 30 ~~~~~l~v~~~---~~pP~~~~~-----~~g-~~~G~~~dl~~~i~~~lg~~~-~~~~~---------~~w~~~~~~l~~ 90 (275)
T TIGR02995 30 KEQGFARIAIA---NEPPFTYVG-----ADG-KVSGAAPDVARAIFKRLGIAD-VNASI---------TEYGALIPGLQA 90 (275)
T ss_pred HhCCcEEEEcc---CCCCceeEC-----CCC-ceecchHHHHHHHHHHhCCCc-eeecc---------CCHHHHHHHHHC
Confidence 34678999986 467787765 456 889999999999999999641 22222 259999999999
Q ss_pred CcccEEEeeeeeecCcceeeeccccccccceEEEEEccCCCCCCceEeecccchhHHHHHHHHHHHHHhhhhheecccCC
Q 003054 422 GEFDAVVGDITIVFNRSNYVDFTLPYTESGVSMIVPIKDSKKRNAWVFLQPLTWDLWVTCFCFFIFIGFVVWVLEHRVNE 501 (852)
Q Consensus 422 g~~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv~~~~~~~~~~~~~l~PF~~~lW~~i~~~~i~~~~v~~~l~~~~~~ 501 (852)
|++|+++++++++++|...++||.||+.+.+++++++....
T Consensus 91 G~~Di~~~~~~~t~eR~~~~~fs~py~~~~~~~~~~~~~~~--------------------------------------- 131 (275)
T TIGR02995 91 GRFDAIAAGLFIKPERCKQVAFTQPILCDAEALLVKKGNPK--------------------------------------- 131 (275)
T ss_pred CCcCEEeecccCCHHHHhccccccceeecceeEEEECCCCC---------------------------------------
Confidence 99999888889999999999999999999999999876322
Q ss_pred CCCCCcccccchhHHHHHHHhhhccccccccchhhHHHHHHHHHHHHHHHHhhhhccceeeecccCCCcCCHHHHHh-cC
Q 003054 502 DFRGPAGQQVGTSFWFSFSTMVFSQRERVISNLARIVVIVWCFVVLILTQSYTASLTSLLTVQQLQPTITDVKMLIK-RG 580 (852)
Q Consensus 502 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~s~~~R~v~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~i~sl~dL~~-~~ 580 (852)
.+++++||.. .|
T Consensus 132 -------------------------------------------------------------------~i~~~~dl~~~~g 144 (275)
T TIGR02995 132 -------------------------------------------------------------------GLKSYKDIAKNPD 144 (275)
T ss_pred -------------------------------------------------------------------CCCCHHHhccCCC
Confidence 1778899854 36
Q ss_pred CeEEEEeCchHHHHHHhcCCCCcceeecCCHhHHHHHhhcccccCceeEEEechhHHHHHHhhcC-CceEeeccc---cc
Q 003054 581 DNVGYQKGSFVLGILKQLGFDERKLVVYNSPEDCHELFQKGSVNGGIAAAFDEIPYMKLLIGQYC-SKYAMIEPK---FK 656 (852)
Q Consensus 581 ~~vg~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~~~-~~~~~v~~~---~~ 656 (852)
++||+..|+....++++.+++..+++.+++.++.+++|.+|+ +++++.+...+.+++++.- ..+..+.+. ..
T Consensus 145 ~~Igv~~g~~~~~~l~~~~~~~~~i~~~~~~~~~i~~L~~gr----vDa~i~d~~~~~~~~~~~~~~~~~~~~~~~~~~~ 220 (275)
T TIGR02995 145 AKIAAPGGGTEEKLAREAGVKREQIIVVPDGQSGLKMVQDGR----ADAYSLTVLTINDLASKAGDPNVEVLAPFKDAPV 220 (275)
T ss_pred ceEEEeCCcHHHHHHHHcCCChhhEEEeCCHHHHHHHHHcCC----CCEEecChHHHHHHHHhCCCCCceeecCccCCcc
Confidence 799999999999999886666667888999999999999999 9999999988888877542 133333221 11
Q ss_pred ccceEEEecCCCC-chhhHHHHHHhccccChhHHHHHHHc
Q 003054 657 TAGFGFVFPLHSP-LVHDVSKAILNVTEGDKMKEIEDAWF 695 (852)
Q Consensus 657 ~~~~~~~~~k~sp-l~~~in~~il~l~e~G~~~~i~~kw~ 695 (852)
...++|+++++.+ |++.||++|.++.++|.+++|.+||-
T Consensus 221 ~~~~~~~~~~~~~~l~~~~n~~l~~~~~sG~~~~i~~ky~ 260 (275)
T TIGR02995 221 RYYGGAAFRPEDKELRDAFNVELAKLKESGEFAKIIAPYG 260 (275)
T ss_pred ccceeEEECCCCHHHHHHHHHHHHHHHhChHHHHHHHHhC
Confidence 1233788888765 99999999999999999999999994
No 89
>PRK15437 histidine ABC transporter substrate-binding protein HisJ; Provisional
Probab=99.80 E-value=3.7e-18 Score=180.13 Aligned_cols=222 Identities=18% Similarity=0.280 Sum_probs=175.5
Q ss_pred CCceEEEeeecccCcccceEEeeCCCCCCCceEEEeeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcC
Q 003054 343 NEKKLRIGVPVKKGFSDFVNVTIDPKTQEPTSVTGYCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLG 422 (852)
Q Consensus 343 ~~~~lrv~v~~~~~~~~~~~~~~d~~~~~~~~~~G~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g 422 (852)
..+.|+|++. +.|+||.+.+ .++ ++.|+++|+++++++++|.+ +++++. .|..++.++.+|
T Consensus 24 ~~~~l~v~~~--~~~~P~~~~~-----~~g-~~~G~~vdi~~~ia~~lg~~--i~~~~~---------pw~~~~~~l~~g 84 (259)
T PRK15437 24 IPQNIRIGTD--PTYAPFESKN-----SQG-ELVGFDIDLAKELCKRINTQ--CTFVEN---------PLDALIPSLKAK 84 (259)
T ss_pred cCCeEEEEeC--CCCCCcceeC-----CCC-CEEeeeHHHHHHHHHHcCCc--eEEEeC---------CHHHHHHHHHCC
Confidence 3578999886 5678888765 467 89999999999999999975 444442 499999999999
Q ss_pred cccEEEeeeeeecCcceeeeccccccccceEEEEEccCCCCCCceEeecccchhHHHHHHHHHHHHHhhhhheecccCCC
Q 003054 423 EFDAVVGDITIVFNRSNYVDFTLPYTESGVSMIVPIKDSKKRNAWVFLQPLTWDLWVTCFCFFIFIGFVVWVLEHRVNED 502 (852)
Q Consensus 423 ~~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv~~~~~~~~~~~~~l~PF~~~lW~~i~~~~i~~~~v~~~l~~~~~~~ 502 (852)
++|+++++++.+++|...++||.||..++.++++++....
T Consensus 85 ~~D~~~~~~~~t~eR~~~~~fs~p~~~~~~~~~~~~~~~~---------------------------------------- 124 (259)
T PRK15437 85 KIDAIMSSLSITEKRQQEIAFTDKLYAADSRLVVAKNSDI---------------------------------------- 124 (259)
T ss_pred CCCEEEecCCCCHHHhhhccccchhhcCceEEEEECCCCC----------------------------------------
Confidence 9999998899999999999999999999999999875321
Q ss_pred CCCCcccccchhHHHHHHHhhhccccccccchhhHHHHHHHHHHHHHHHHhhhhccceeeecccCCCcCCHHHHHhcCCe
Q 003054 503 FRGPAGQQVGTSFWFSFSTMVFSQRERVISNLARIVVIVWCFVVLILTQSYTASLTSLLTVQQLQPTITDVKMLIKRGDN 582 (852)
Q Consensus 503 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~s~~~R~v~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~i~sl~dL~~~~~~ 582 (852)
..+++||. |++
T Consensus 125 -------------------------------------------------------------------~~~~~dl~--g~~ 135 (259)
T PRK15437 125 -------------------------------------------------------------------QPTVESLK--GKR 135 (259)
T ss_pred -------------------------------------------------------------------CCChHHhC--CCE
Confidence 34789995 889
Q ss_pred EEEEeCchHHHHHHhcCC-CCcceeecCCHhHHHHHhhcccccCceeEEEechhHHHH-HHhhc-CCceEeecc-----c
Q 003054 583 VGYQKGSFVLGILKQLGF-DERKLVVYNSPEDCHELFQKGSVNGGIAAAFDEIPYMKL-LIGQY-CSKYAMIEP-----K 654 (852)
Q Consensus 583 vg~~~~s~~~~~l~~~~~-~~~~~~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~-~~~~~-~~~~~~v~~-----~ 654 (852)
||+..|+..+.++++... ...+++.+.+.++.+++|.+|+ +|+++.+...+.+ +..+. -+.+.+.+. .
T Consensus 136 Igv~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~L~~gr----vD~~v~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~ 211 (259)
T PRK15437 136 VGVLQGTTQETFGNEHWAPKGIEIVSYQGQDNIYSDLTAGR----IDAAFQDEVAASEGFLKQPVGKDYKFGGPSVKDEK 211 (259)
T ss_pred EEEecCcHHHHHHHhhccccCceEEecCCHHHHHHHHHcCC----ccEEEechHHHHHHHHhCCCCCceEEecCcccccc
Confidence 999999988888765322 2346788889999999999999 9999988766543 33322 222333222 2
Q ss_pred ccccceEEEecCCCC-chhhHHHHHHhccccChhHHHHHHHcc
Q 003054 655 FKTAGFGFVFPLHSP-LVHDVSKAILNVTEGDKMKEIEDAWFK 696 (852)
Q Consensus 655 ~~~~~~~~~~~k~sp-l~~~in~~il~l~e~G~~~~i~~kw~~ 696 (852)
+....++++++++.+ |++.+|++|.++..+|.+++|.+||++
T Consensus 212 ~~~~~~~ia~~~~~~~l~~~~n~~l~~~~~~G~~~~i~~k~~~ 254 (259)
T PRK15437 212 LFGVGTGMGLRKEDNELREALNKAFAEMRADGTYEKLAKKYFD 254 (259)
T ss_pred ccCcceEEEEeCCCHHHHHHHHHHHHHHHHCCcHHHHHHHhcC
Confidence 223446788887655 999999999999999999999999996
No 90
>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=99.78 E-value=8.2e-18 Score=185.33 Aligned_cols=230 Identities=17% Similarity=0.102 Sum_probs=182.6
Q ss_pred HhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeCC-cccccHHHHHHHHHhCC
Q 003054 8 QLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDNQ-YGEEMIPSLTDALQAID 86 (852)
Q Consensus 8 ~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~~-~G~~~~~~l~~~l~~~g 86 (852)
+++++.++|+|+++++++.++. .|++|++.+++..++.++++++.+.|.+++++++.++. ||+...+.+++++++.|
T Consensus 84 ~~~~~~~ip~v~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~l~~~g~~~~~~i~~~~~~~g~~~~~~~~~~~~~~G 161 (341)
T cd06341 84 PYLAGAGIPVIGGAGTSAWELT--SPNSFPFSGGTPASLTTWGDFAKDQGGTRAVALVTALSAAVSAAAALLARSLAAAG 161 (341)
T ss_pred HHHhhcCCceecCCCCCchhhc--CCCeEEecCCCcchhHHHHHHHHHcCCcEEEEEEeCCcHHHHHHHHHHHHHHHHcC
Confidence 8889999999998887777664 57899999999999999999998889999999986665 99999999999999999
Q ss_pred ceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHcCCcccceEEEEcC-ccccccccCCchhh
Q 003054 87 TRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTD-GMTNLLRTLEPSVI 165 (852)
Q Consensus 87 ~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~-~~~~~~~~~~~~~~ 165 (852)
++++....++.+ ..|+.+++.++++.+||+|++.....++..++++++++|+..+ .+... ...... .....
T Consensus 162 ~~v~~~~~~~~~--~~d~~~~~~~i~~~~pdaV~~~~~~~~a~~~~~~~~~~G~~~~---~~~~~~~~~~~~---~~~~g 233 (341)
T cd06341 162 VSVAGIVVITAT--APDPTPQAQQAAAAGADAIITVLDAAVCASVLKAVRAAGLTPK---VVLSGTCYDPAL---LAAPG 233 (341)
T ss_pred CccccccccCCC--CCCHHHHHHHHHhcCCCEEEEecChHHHHHHHHHHHHcCCCCC---EEEecCCCCHHH---HHhcC
Confidence 999887776643 6789999999999999999999999899999999999999776 22222 222111 11234
Q ss_pred cccceEEEEEecCC---CChHHHHHHHHHHHhccccCCCCcccccchhhHhHhhHHHHHHHHHHHhcccCcCccccccCC
Q 003054 166 DSMQGVIGVGPHVP---KTKALENFRVRWKRNFLQENPSIVDVELNIFGLLAYDATRALAEAVEKAGITSFGFDKTNVSR 242 (852)
Q Consensus 166 ~~~~gv~~~~~~~~---~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~a~~aYDAv~~lA~Al~~a~~~~~~~~~~~~~~ 242 (852)
+..+|++....+.| +.|..+.|++.+++.... + ..+|+.+++.+||+++++++|+++++..
T Consensus 234 ~~~~g~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~-~----~~~~~~~~~~~yda~~~~~~a~~~ag~~----------- 297 (341)
T cd06341 234 PALAGVYIAVFYRPFESGTPAVALYLAAMARYAPQ-L----DPPEQGFALIGYIAADLFLRGLSGAGGC----------- 297 (341)
T ss_pred cccCceEEEeeeccccCCCHHHHHHHHHHHHhCCC-C----CCCcchHHHHHHHHHHHHHHHHHhcCCC-----------
Confidence 56899988887765 468888888765543322 1 1168899999999999999999999832
Q ss_pred CCCCCccccccCChHH-HHHHhhccceeeeeee
Q 003054 243 NATDLEAFGISQNGPK-LLQALSSTRFKGLTGD 274 (852)
Q Consensus 243 ~~~~~~~~~~~~~g~~-l~~al~~~~f~GltG~ 274 (852)
.++++ ++++|++++.....|-
T Consensus 298 -----------~~~~~~v~~al~~~~~~~~~g~ 319 (341)
T cd06341 298 -----------PTRASQFLRALRAVTDYDAGGL 319 (341)
T ss_pred -----------CChHHHHHHHhhcCCCCCCCCc
Confidence 23577 9999999875444443
No 91
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=99.77 E-value=1.8e-17 Score=212.39 Aligned_cols=217 Identities=16% Similarity=0.252 Sum_probs=181.2
Q ss_pred CceEEEeeecccCcccceEEeeCCCCCCCceEEEeeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCc
Q 003054 344 EKKLRIGVPVKKGFSDFVNVTIDPKTQEPTSVTGYCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGE 423 (852)
Q Consensus 344 ~~~lrv~v~~~~~~~~~~~~~~d~~~~~~~~~~G~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~ 423 (852)
.+.++||+. +.|+||.+.+ .++ ++.||++|++++|++++|. ++++++.. +|..++.+|.+|+
T Consensus 301 ~~~l~v~~~--~~~pP~~~~d-----~~g-~~~G~~~Dll~~i~~~~g~--~~~~v~~~--------~~~~~~~~l~~g~ 362 (1197)
T PRK09959 301 HPDLKVLEN--PYSPPYSMTD-----ENG-SVRGVMGDILNIITLQTGL--NFSPITVS--------HNIHAGTQLNPGG 362 (1197)
T ss_pred CCceEEEcC--CCCCCeeEEC-----CCC-cEeeehHHHHHHHHHHHCC--eEEEEecC--------CHHHHHHHHHCCC
Confidence 567888876 8899999986 467 8999999999999999995 67777765 6888999999999
Q ss_pred ccEEEeeeeeecCcceeeeccccccccceEEEEEccCCCCCCceEeecccchhHHHHHHHHHHHHHhhhhheecccCCCC
Q 003054 424 FDAVVGDITIVFNRSNYVDFTLPYTESGVSMIVPIKDSKKRNAWVFLQPLTWDLWVTCFCFFIFIGFVVWVLEHRVNEDF 503 (852)
Q Consensus 424 ~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv~~~~~~~~~~~~~l~PF~~~lW~~i~~~~i~~~~v~~~l~~~~~~~~ 503 (852)
+|++.+ ++.+++|.+.++||.||..+++++++++.. ..
T Consensus 363 ~D~i~~-~~~t~~r~~~~~fs~py~~~~~~~v~~~~~-~~---------------------------------------- 400 (1197)
T PRK09959 363 WDIIPG-AIYSEDRENNVLFAEAFITTPYVFVMQKAP-DS---------------------------------------- 400 (1197)
T ss_pred ceEeec-ccCCccccccceeccccccCCEEEEEecCC-CC----------------------------------------
Confidence 998654 668999999999999999999999987542 11
Q ss_pred CCCcccccchhHHHHHHHhhhccccccccchhhHHHHHHHHHHHHHHHHhhhhccceeeecccCCCcCCHHHHHhcCCeE
Q 003054 504 RGPAGQQVGTSFWFSFSTMVFSQRERVISNLARIVVIVWCFVVLILTQSYTASLTSLLTVQQLQPTITDVKMLIKRGDNV 583 (852)
Q Consensus 504 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~s~~~R~v~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~i~sl~dL~~~~~~v 583 (852)
+.++ . .|++|
T Consensus 401 ------------------------------------------------------------------~~~~---~-~g~~v 410 (1197)
T PRK09959 401 ------------------------------------------------------------------EQTL---K-KGMKV 410 (1197)
T ss_pred ------------------------------------------------------------------cccc---c-cCCEE
Confidence 2222 2 58899
Q ss_pred EEEeCchHHHHHHhcCCCCcceeecCCHhHHHHHhhcccccCceeEEEechhHHHHHHhhcC-Cc-eEeecccccccceE
Q 003054 584 GYQKGSFVLGILKQLGFDERKLVVYNSPEDCHELFQKGSVNGGIAAAFDEIPYMKLLIGQYC-SK-YAMIEPKFKTAGFG 661 (852)
Q Consensus 584 g~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~~~-~~-~~~v~~~~~~~~~~ 661 (852)
|+..|+....++++. ++..+++.+++.++++++|.+|+ ++|++.+...+.|+++++. .. +....+.+....++
T Consensus 411 av~~g~~~~~~~~~~-~p~~~~~~~~~~~~~l~av~~G~----~Da~i~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~ 485 (1197)
T PRK09959 411 AIPYYYELHSQLKEM-YPEVEWIKVDNASAAFHKVKEGE----LDALVATQLNSRYMIDHYYPNELYHFLIPGVPNASLS 485 (1197)
T ss_pred EEeCCcchHHHHHHH-CCCcEEEEcCCHHHHHHHHHcCC----CCEEehhhHHHHHHHHhcccccceeeecCCCCchheE
Confidence 999999888888764 67778999999999999999999 9999999999999988752 22 33344445567789
Q ss_pred EEecCCCC-chhhHHHHHHhccccChhHHHHHHHcc
Q 003054 662 FVFPLHSP-LVHDVSKAILNVTEGDKMKEIEDAWFK 696 (852)
Q Consensus 662 ~~~~k~sp-l~~~in~~il~l~e~G~~~~i~~kw~~ 696 (852)
|+++|+.| |+..+|++|..+.++ .++.+.+||+.
T Consensus 486 ~av~k~~~~L~~~lnk~l~~i~~~-~~~~i~~kW~~ 520 (1197)
T PRK09959 486 FAFPRGEPELKDIINKALNAIPPS-EVLRLTEKWIK 520 (1197)
T ss_pred EeeCCCCHHHHHHHHHHHHhCCHH-HHHHHHhhccc
Confidence 99999977 999999999999998 78899999995
No 92
>PRK10859 membrane-bound lytic transglycosylase F; Provisional
Probab=99.75 E-value=4.2e-17 Score=186.34 Aligned_cols=222 Identities=15% Similarity=0.163 Sum_probs=176.4
Q ss_pred CCCceEEEeeecccCcccceEEeeCCCCCCCceEEEeeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhc
Q 003054 342 TNEKKLRIGVPVKKGFSDFVNVTIDPKTQEPTSVTGYCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFL 421 (852)
Q Consensus 342 ~~~~~lrv~v~~~~~~~~~~~~~~d~~~~~~~~~~G~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~ 421 (852)
.+.+.||||+.. + |+.+.. +++ ...||++|+++++++++|.+ ++++... +|++++.+|.+
T Consensus 40 ~~~g~LrVg~~~-~---P~~~~~-----~~~-~~~G~~~DLl~~ia~~LGv~--~e~v~~~--------~~~~ll~aL~~ 99 (482)
T PRK10859 40 QERGELRVGTIN-S---PLTYYI-----GND-GPTGFEYELAKRFADYLGVK--LEIKVRD--------NISQLFDALDK 99 (482)
T ss_pred HhCCEEEEEEec-C---CCeeEe-----cCC-CcccHHHHHHHHHHHHhCCc--EEEEecC--------CHHHHHHHHhC
Confidence 346789999984 2 333333 233 44899999999999999974 5554433 69999999999
Q ss_pred CcccEEEeeeeeecCcceeeeccccccccceEEEEEccCCCCCCceEeecccchhHHHHHHHHHHHHHhhhhheecccCC
Q 003054 422 GEFDAVVGDITIVFNRSNYVDFTLPYTESGVSMIVPIKDSKKRNAWVFLQPLTWDLWVTCFCFFIFIGFVVWVLEHRVNE 501 (852)
Q Consensus 422 g~~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv~~~~~~~~~~~~~l~PF~~~lW~~i~~~~i~~~~v~~~l~~~~~~ 501 (852)
|++|++++++++|++|.+.++||.||...+.++++++.. .
T Consensus 100 G~iDi~~~~lt~T~eR~~~~~FS~Py~~~~~~lv~r~~~-~--------------------------------------- 139 (482)
T PRK10859 100 GKADLAAAGLTYTPERLKQFRFGPPYYSVSQQLVYRKGQ-P--------------------------------------- 139 (482)
T ss_pred CCCCEEeccCcCChhhhccCcccCCceeeeEEEEEeCCC-C---------------------------------------
Confidence 999998888999999999999999999999999998653 2
Q ss_pred CCCCCcccccchhHHHHHHHhhhccccccccchhhHHHHHHHHHHHHHHHHhhhhccceeeecccCCCcCCHHHHHhcCC
Q 003054 502 DFRGPAGQQVGTSFWFSFSTMVFSQRERVISNLARIVVIVWCFVVLILTQSYTASLTSLLTVQQLQPTITDVKMLIKRGD 581 (852)
Q Consensus 502 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~s~~~R~v~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~i~sl~dL~~~~~ 581 (852)
.+++++||. |+
T Consensus 140 -------------------------------------------------------------------~i~~l~dL~--Gk 150 (482)
T PRK10859 140 -------------------------------------------------------------------RPRSLGDLK--GG 150 (482)
T ss_pred -------------------------------------------------------------------CCCCHHHhC--CC
Confidence 278999996 89
Q ss_pred eEEEEeCchHHHHHHhcC--CCCcce--eecCCHhHHHHHhhcccccCceeEEEechhHHHHHHhhcCCceEeecccccc
Q 003054 582 NVGYQKGSFVLGILKQLG--FDERKL--VVYNSPEDCHELFQKGSVNGGIAAAFDEIPYMKLLIGQYCSKYAMIEPKFKT 657 (852)
Q Consensus 582 ~vg~~~~s~~~~~l~~~~--~~~~~~--~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~~~~~~~~v~~~~~~ 657 (852)
+||+..|+.....|++.. ++...+ ..+.+.++++++|.+|+ +|+++.+...+.+....+. .+.+.......
T Consensus 151 ~I~V~~gS~~~~~L~~l~~~~p~i~~~~~~~~s~~e~l~aL~~G~----iDa~v~d~~~~~~~~~~~p-~l~v~~~l~~~ 225 (482)
T PRK10859 151 TLTVAAGSSHVETLQELKKKYPELSWEESDDKDSEELLEQVAEGK----IDYTIADSVEISLNQRYHP-ELAVAFDLTDE 225 (482)
T ss_pred eEEEECCCcHHHHHHHHHHhCCCceEEecCCCCHHHHHHHHHCCC----CCEEEECcHHHHHHHHhCC-CceeeeecCCC
Confidence 999999999888876532 233333 34578999999999999 9999999877665544333 35554444456
Q ss_pred cceEEEecCC-CC-chhhHHHHHHhccccChhHHHHHHHccC
Q 003054 658 AGFGFVFPLH-SP-LVHDVSKAILNVTEGDKMKEIEDAWFKK 697 (852)
Q Consensus 658 ~~~~~~~~k~-sp-l~~~in~~il~l~e~G~~~~i~~kw~~~ 697 (852)
.+++++++|+ .+ |+..+|++|.++.++|.++++.+||++.
T Consensus 226 ~~~~~av~k~~~~~L~~~ln~~L~~i~~~G~l~~L~~kyfg~ 267 (482)
T PRK10859 226 QPVAWALPPSGDDSLYAALLDFFNQIKEDGTLARLEEKYFGH 267 (482)
T ss_pred ceeEEEEeCCCCHHHHHHHHHHHHHhhcCCHHHHHHHHHhhh
Confidence 7789999994 45 9999999999999999999999999975
No 93
>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=3.2e-17 Score=178.20 Aligned_cols=204 Identities=19% Similarity=0.225 Sum_probs=166.0
Q ss_pred hhHHHHhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHHHH
Q 003054 3 TNFIIQLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTDAL 82 (852)
Q Consensus 3 a~~v~~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~~l 82 (852)
+.++.+++++.++|+|+++++++.++ ...+|+||+.+++..++..+++++.+.||++|++++.++.+|+...+.+++++
T Consensus 79 ~~~~~~~~~~~~vP~v~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~l~~~g~~~vail~~~~~~~~~~~~~~~~~~ 157 (312)
T cd06333 79 TMAVAPVAEEAKTPMISLAPAAAIVE-PKRKWVFKTPQNDRLMAEAILADMKKRGVKTVAFIGFSDAYGESGLKELKALA 157 (312)
T ss_pred HHHHHHHHHhcCCCEEEccCCccccC-CCCCcEEEcCCCcHHHHHHHHHHHHHcCCCEEEEEecCcHHHHHHHHHHHHHH
Confidence 34677889999999999887665444 45689999999999999999999999999999999999999999999999999
Q ss_pred HhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHcCCcccceEEEEcCccccccccCCc
Q 003054 83 QAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLEP 162 (852)
Q Consensus 83 ~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~~~~~~~~~~~ 162 (852)
++.|++++....++.+ +.|+..++.++++.+||+|++......+..+++++++.|+..+ ++++++.... + +..
T Consensus 158 ~~~G~~v~~~~~~~~~--~~d~~~~~~~l~~~~pdaIi~~~~~~~~~~~~~~l~~~g~~~p---~~~~~~~~~~-~-~~~ 230 (312)
T cd06333 158 PKYGIEVVADERYGRT--DTSVTAQLLKIRAARPDAVLIWGSGTPAALPAKNLRERGYKGP---IYQTHGVASP-D-FLR 230 (312)
T ss_pred HHcCCEEEEEEeeCCC--CcCHHHHHHHHHhCCCCEEEEecCCcHHHHHHHHHHHcCCCCC---EEeecCcCcH-H-HHH
Confidence 9999999877777643 5689999999998999999999888888889999999999776 5545444321 1 111
Q ss_pred hhhcccceEEEEEec------CC----CChHHHHHHHHHHHhccccCCCCcccc-cchhhHhHhhHHHHHH
Q 003054 163 SVIDSMQGVIGVGPH------VP----KTKALENFRVRWKRNFLQENPSIVDVE-LNIFGLLAYDATRALA 222 (852)
Q Consensus 163 ~~~~~~~gv~~~~~~------~~----~~~~~~~F~~~~~~~~~~~~~~~~~~~-~~~~a~~aYDAv~~lA 222 (852)
..++..+|++.+..+ .| .++..++|.++|+++|+. + |+.+++.+|||+++++
T Consensus 231 ~~g~~~~g~~~~~~~~~~~~~~p~~~~~~~~~~~f~~~~~~~~g~--------~~~~~~~~~~Yda~~~~~ 293 (312)
T cd06333 231 LAGKAAEGAILPAGPVLVADQLPDSDPQKKVALDFVKAYEAKYGA--------GSVSTFGGHAYDALLLLA 293 (312)
T ss_pred HhhHhhcCcEeecccceeeeeCCCCCcchHHHHHHHHHHHHHhCC--------CCCCchhHHHHHHHHHHH
Confidence 233557888765422 22 246799999999999987 5 8889999999999999
No 94
>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=99.73 E-value=9.8e-19 Score=167.76 Aligned_cols=107 Identities=31% Similarity=0.623 Sum_probs=82.5
Q ss_pred chhHHHHHHHHHHHHHhhhhheecccCCCCCC-------CcccccchhHHHHHHHhhhcc-ccccccchhhHHHHHHHHH
Q 003054 474 TWDLWVTCFCFFIFIGFVVWVLEHRVNEDFRG-------PAGQQVGTSFWFSFSTMVFSQ-RERVISNLARIVVIVWCFV 545 (852)
Q Consensus 474 ~~~lW~~i~~~~i~~~~v~~~l~~~~~~~~~~-------~~~~~~~~~~~~~~~~l~~~~-~~~~~s~~~R~v~~~w~~~ 545 (852)
++++|++++++++++++++|++++..+.+++. +...++.+++|+.+++++.++ ...|++.+.|++.++|+++
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 57899999999999999999999987777665 234578899999999999765 5678999999999999999
Q ss_pred HHHHHHHhhhhccceeeecccCCCcCCHHHHHhcC
Q 003054 546 VLILTQSYTASLTSLLTVQQLQPTITDVKMLIKRG 580 (852)
Q Consensus 546 ~lil~~~Yta~L~s~Lt~~~~~~~i~sl~dL~~~~ 580 (852)
+++++++|+|+|+|+||.++++++|+|++||.+++
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 99999999999999999999999999999999777
No 95
>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=99.72 E-value=1e-16 Score=172.46 Aligned_cols=205 Identities=23% Similarity=0.317 Sum_probs=169.1
Q ss_pred hhHHHHhcCCCCccEEeeecCCCCCCC-CCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHHH
Q 003054 3 TNFIIQLGNKSQVPILSFSATSPSLTS-IRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTDA 81 (852)
Q Consensus 3 a~~v~~i~~~~~vP~Is~~ats~~lt~-~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~~ 81 (852)
+.+++++++..+||+|++.++++.+++ ..+|++||+.|++..++..++++++++||++|++++.++.+|....+.+++.
T Consensus 80 ~~~~~~~~~~~~iP~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~v~iv~~~~~~~~~~~~~~~~~ 159 (299)
T cd04509 80 ALAVAPVAEALKIPLISPGATAPGLTDKKGYPYLFRTGPSDEQQAEALADYIKEYNWKKVAILYDDDSYGRGLLEAFKAA 159 (299)
T ss_pred HHHHHHHHhhCCceEEeccCCCcccccccCCCCEEEecCCcHHHHHHHHHHHHHcCCcEEEEEecCchHHHHHHHHHHHH
Confidence 456788899999999999988877764 4689999999999999999999999999999999999999999999999999
Q ss_pred HHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHcCCcccceEEEEcCccccccccCC
Q 003054 82 LQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLE 161 (852)
Q Consensus 82 l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~~~~~~~~~~ 161 (852)
+++.|+++.....++.+ .+++...+.++++.++|+|++++....+..++++++++|+. +++.|++.+.+......
T Consensus 160 ~~~~g~~i~~~~~~~~~--~~~~~~~~~~l~~~~~~~v~~~~~~~~~~~~~~~~~~~g~~-~~~~~i~~~~~~~~~~~-- 234 (299)
T cd04509 160 FKKKGGTVVGEEYYPLG--TTDFTSLLQKLKAAKPDVIVLCGSGEDAATILKQAAEAGLT-GGYPILGITLGLSDVLL-- 234 (299)
T ss_pred HHHcCCEEEEEecCCCC--CccHHHHHHHHHhcCCCEEEEcccchHHHHHHHHHHHcCCC-CCCcEEecccccCHHHH--
Confidence 99999999877666543 46799999999988899999999889999999999999997 77889998876643321
Q ss_pred chhhcccceEEEEEecCCCC--hHHHHHH---HHHHHhccccCCCCcccccchhhHhHhhHHHH
Q 003054 162 PSVIDSMQGVIGVGPHVPKT--KALENFR---VRWKRNFLQENPSIVDVELNIFGLLAYDATRA 220 (852)
Q Consensus 162 ~~~~~~~~gv~~~~~~~~~~--~~~~~F~---~~~~~~~~~~~~~~~~~~~~~~a~~aYDAv~~ 220 (852)
....+.++|+++..++.+.. +..+.|. ..+++.++. +++.+++++|||+++
T Consensus 235 ~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--------~~~~~~~~~yda~~~ 290 (299)
T cd04509 235 EAGGEAAEGVLTGTPYFPGDPPPESFFFVRAAAREKKKYED--------QPDYFAALAYDAVLL 290 (299)
T ss_pred HHhHHhhcCcEEeeccCCCCCChHHHHHHhHHHHHHHHhCC--------CCChhhhhhcceeee
Confidence 12345678999888776643 3444443 445555544 788999999999998
No 96
>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=99.71 E-value=1.9e-16 Score=165.43 Aligned_cols=210 Identities=15% Similarity=0.104 Sum_probs=155.8
Q ss_pred eEEEeeecccCcccceEEeeCCCCCCCceEEEeeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHH---HHHhcC
Q 003054 346 KLRIGVPVKKGFSDFVNVTIDPKTQEPTSVTGYCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLV---YQVFLG 422 (852)
Q Consensus 346 ~lrv~v~~~~~~~~~~~~~~d~~~~~~~~~~G~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li---~~l~~g 422 (852)
+|+||+. +.|+||.+.+ . .||++||+++|++++|++ +++++. +|++++ ..|.+|
T Consensus 1 ~l~vg~~--~~~pPf~~~~---------~-~Gfdvdl~~~ia~~lg~~--~~~~~~---------~~~~~~~~~~~L~~g 57 (246)
T TIGR03870 1 TLRVCAA--TKEAPYSTKD---------G-SGFENKIAAALAAAMGRK--VVFVWL---------AKPAIYLVRDGLDKK 57 (246)
T ss_pred CeEEEeC--CCCCCCccCC---------C-CcchHHHHHHHHHHhCCC--eEEEEe---------ccchhhHHHHHHhcC
Confidence 4788887 8899998742 1 499999999999999974 555543 366655 699999
Q ss_pred cccEEEeeeeeecCcceeeeccccccccceEEEEEccCCCCCCceEeecccchhHHHHHHHHHHHHHhhhhheecccCCC
Q 003054 423 EFDAVVGDITIVFNRSNYVDFTLPYTESGVSMIVPIKDSKKRNAWVFLQPLTWDLWVTCFCFFIFIGFVVWVLEHRVNED 502 (852)
Q Consensus 423 ~~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv~~~~~~~~~~~~~l~PF~~~lW~~i~~~~i~~~~v~~~l~~~~~~~ 502 (852)
++|+++ +++++++| ++||.||+.++.++++++.....
T Consensus 58 ~~Dii~-~~~~t~~r---~~fS~PY~~~~~~~v~~k~~~~~--------------------------------------- 94 (246)
T TIGR03870 58 LCDVVL-GLDTGDPR---VLTTKPYYRSSYVFLTRKDRNLD--------------------------------------- 94 (246)
T ss_pred CccEEE-eCCCChHH---HhcccCcEEeeeEEEEeCCCCCC---------------------------------------
Confidence 999988 48888777 68999999999999999764221
Q ss_pred CCCCcccccchhHHHHHHHhhhccccccccchhhHHHHHHHHHHHHHHHHhhhhccceeeecccCCCcCCHHHHHhcCC-
Q 003054 503 FRGPAGQQVGTSFWFSFSTMVFSQRERVISNLARIVVIVWCFVVLILTQSYTASLTSLLTVQQLQPTITDVKMLIKRGD- 581 (852)
Q Consensus 503 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~s~~~R~v~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~i~sl~dL~~~~~- 581 (852)
+++++|+.-.|+
T Consensus 95 -------------------------------------------------------------------~~~~~d~~L~g~~ 107 (246)
T TIGR03870 95 -------------------------------------------------------------------IKSWNDPRLKKVS 107 (246)
T ss_pred -------------------------------------------------------------------CCCccchhhccCc
Confidence 677765222387
Q ss_pred eEEEEeCchHHHHHHhcCCC------CcceeecC---------CHhHHHHHhhcccccCceeEEEechhHHHHHHhhcCC
Q 003054 582 NVGYQKGSFVLGILKQLGFD------ERKLVVYN---------SPEDCHELFQKGSVNGGIAAAFDEIPYMKLLIGQYCS 646 (852)
Q Consensus 582 ~vg~~~~s~~~~~l~~~~~~------~~~~~~~~---------~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~~~~ 646 (852)
+||++.|+..+.++++.... ...+..+. +.++.+++|..|+ ++|++.+...+.+++.+.-.
T Consensus 108 ~vgv~~gs~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~aL~~Gr----vDa~i~~~~~~~~~~~~~~~ 183 (246)
T TIGR03870 108 KIGVIFGSPAETMLKQIGRYEDNFAYLYSLVNFKSPRNQYTQIDPRKLVSEVATGK----ADLAVAFAPEVARYVKASPE 183 (246)
T ss_pred eEEEecCChHHHHHHhcCccccccccccccccccCcccccccCCHHHHHHHHHcCC----CCEEEeeHHhHHHHHHhCCC
Confidence 99999999999998864211 11122222 3578899999999 99999987777777665322
Q ss_pred ceE--eecccc-------c--ccceEEEecCCCC-chhhHHHHHHhccccChhHHHHHHH
Q 003054 647 KYA--MIEPKF-------K--TAGFGFVFPLHSP-LVHDVSKAILNVTEGDKMKEIEDAW 694 (852)
Q Consensus 647 ~~~--~v~~~~-------~--~~~~~~~~~k~sp-l~~~in~~il~l~e~G~~~~i~~kw 694 (852)
.+. .+++.. . ...++++++|+.+ |++.||++|.+|. |.+++|..+|
T Consensus 184 ~~~~~~~~~~~~~~~~~~~~~~~~~~iav~k~~~~L~~~in~aL~~l~--~~~~~i~~~y 241 (246)
T TIGR03870 184 PLRMTVIPDDATRSDGAKIPMQYDQSMGVRKDDTALLAEIDAALAKAK--PRIDAILKEE 241 (246)
T ss_pred CceEEeccccccccCCCCcceeeEEEEEEccCCHHHHHHHHHHHHHhH--HHHHHHHHHc
Confidence 232 233221 0 1135899999987 9999999999998 4899999988
No 97
>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=1.1e-15 Score=162.76 Aligned_cols=226 Identities=23% Similarity=0.351 Sum_probs=181.4
Q ss_pred CCceEEEeeecccCcccceEEeeCCCCCCCceEEEeeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcC
Q 003054 343 NEKKLRIGVPVKKGFSDFVNVTIDPKTQEPTSVTGYCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLG 422 (852)
Q Consensus 343 ~~~~lrv~v~~~~~~~~~~~~~~d~~~~~~~~~~G~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g 422 (852)
..+.++|++.. ...+||.+.+. ..+ ++.||++|+.+++++.++.....++++. .|++++..|..|
T Consensus 32 ~~~~~~v~~~~-~~~~p~~~~~~----~~~-~~~G~dvdl~~~ia~~l~~~~~~~~~~~---------~~~~~~~~l~~g 96 (275)
T COG0834 32 ARGKLRVGTEA-TYAPPFEFLDA----KGG-KLVGFDVDLAKAIAKRLGGDKKVEFVPV---------AWDGLIPALKAG 96 (275)
T ss_pred hcCeEEEEecC-CCCCCcccccC----CCC-eEEeeeHHHHHHHHHHhCCcceeEEecc---------chhhhhHHHhcC
Confidence 46778888873 23347777652 116 8999999999999999986432444442 599999999999
Q ss_pred cccEEEeeeeeecCcceeeeccccccccceEEEEEccCCCCCCceEeecccchhHHHHHHHHHHHHHhhhhheecccCCC
Q 003054 423 EFDAVVGDITIVFNRSNYVDFTLPYTESGVSMIVPIKDSKKRNAWVFLQPLTWDLWVTCFCFFIFIGFVVWVLEHRVNED 502 (852)
Q Consensus 423 ~~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv~~~~~~~~~~~~~l~PF~~~lW~~i~~~~i~~~~v~~~l~~~~~~~ 502 (852)
++|+++..+++|++|.+.++||.||+.++..+++++.....
T Consensus 97 ~~D~~~~~~~~t~er~~~~~fs~py~~~~~~~~~~~~~~~~--------------------------------------- 137 (275)
T COG0834 97 KVDIIIAGMTITPERKKKVDFSDPYYYSGQVLLVKKDSDIG--------------------------------------- 137 (275)
T ss_pred CcCEEEeccccCHHHhccccccccccccCeEEEEECCCCcC---------------------------------------
Confidence 99999999999999999999999999999999999775321
Q ss_pred CCCCcccccchhHHHHHHHhhhccccccccchhhHHHHHHHHHHHHHHHHhhhhccceeeecccCCCcCCHHHHHhcCCe
Q 003054 503 FRGPAGQQVGTSFWFSFSTMVFSQRERVISNLARIVVIVWCFVVLILTQSYTASLTSLLTVQQLQPTITDVKMLIKRGDN 582 (852)
Q Consensus 503 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~s~~~R~v~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~i~sl~dL~~~~~~ 582 (852)
+++++||. |++
T Consensus 138 -------------------------------------------------------------------~~~~~DL~--gk~ 148 (275)
T COG0834 138 -------------------------------------------------------------------IKSLEDLK--GKK 148 (275)
T ss_pred -------------------------------------------------------------------cCCHHHhC--CCE
Confidence 67899997 899
Q ss_pred EEEEeCch--HHHHHHhcCCCCcceeecCCHhHHHHHhhcccccCceeEEEechhHHHHH--HhhcCCceEeecccccc-
Q 003054 583 VGYQKGSF--VLGILKQLGFDERKLVVYNSPEDCHELFQKGSVNGGIAAAFDEIPYMKLL--IGQYCSKYAMIEPKFKT- 657 (852)
Q Consensus 583 vg~~~~s~--~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~--~~~~~~~~~~v~~~~~~- 657 (852)
+|++.|+. ........ .+...++.+++..+.+++|..|+ ++|++.+...+.++ ..+.-............
T Consensus 149 v~v~~gt~~~~~~~~~~~-~~~~~~~~~~~~~~~~~al~~Gr----~Da~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~ 223 (275)
T COG0834 149 VGVQLGTTDEAEEKAKKP-GPNAKIVAYDSNAEALLALKNGR----ADAVVSDSAVLAGLKLLKKNPGLYVLLVFPGLSV 223 (275)
T ss_pred EEEEcCcchhHHHHHhhc-cCCceEEeeCCHHHHHHHHHcCC----ccEEEcchHhhhhhhhhhcCCCCceeeeccCCCc
Confidence 99999998 44444432 34567889999999999999999 99999999988884 33333222233333333
Q ss_pred cceEEEecCC--CCchhhHHHHHHhccccChhHHHHHHHcc
Q 003054 658 AGFGFVFPLH--SPLVHDVSKAILNVTEGDKMKEIEDAWFK 696 (852)
Q Consensus 658 ~~~~~~~~k~--spl~~~in~~il~l~e~G~~~~i~~kw~~ 696 (852)
.+++++++|+ ..+++.+|++|.++.++|.++++.++|+.
T Consensus 224 ~~~~~~~~~~~~~~l~~~in~~l~~l~~~G~~~~i~~kw~~ 264 (275)
T COG0834 224 EYLGIALRKGDDPELLEAVNKALKELKADGTLQKISDKWFG 264 (275)
T ss_pred ceeEEEeccCCcHHHHHHHHHHHHHHHhCccHHHHHHHhcC
Confidence 7899999999 47999999999999999999999999996
No 98
>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=99.69 E-value=1.9e-15 Score=159.10 Aligned_cols=261 Identities=13% Similarity=0.112 Sum_probs=190.6
Q ss_pred hhHHHHhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHH------HHcCCcEEEEEEEeCCcccc---
Q 003054 3 TNFIIQLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAII------KAFGWREAVPIYVDNQYGEE--- 73 (852)
Q Consensus 3 a~~v~~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l------~~~gw~~vaii~~d~~~G~~--- 73 (852)
+-.|+++...+++|+||.+|-.-+. ...+.+-|+.|+....+..+.++. ++++|+++. ||.+++--++
T Consensus 94 t~~~~~~~~~~~~P~ISaGsfglsc--d~k~~LTR~~pparK~~~~~~~f~~~~~~~~~~~W~~ay-vyk~~~~~edCf~ 170 (380)
T cd06369 94 TFQMVDDEFNLSLPIISAGSFGLSC--DYKENLTRLLPPARKISDFFVDFWKEKNFPKKPKWETAY-VYKKQENTEDCFW 170 (380)
T ss_pred hhhhhhhhhcCCCceEeccccccCC--CchhhhhhcCchHHHHHHHHHHHHhcccccCCCCCceeE-EEcCCCCccceee
Confidence 4567788889999999987733222 234588999999999999999998 488998766 8866642222
Q ss_pred cHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHcCCcccceEEEEcCcc
Q 003054 74 MIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGM 153 (852)
Q Consensus 74 ~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~~ 153 (852)
-++++....+..+..+....... +.+++...|++.+ ...||||+++.+.+.+.++.+ |+...+|++|..|..
T Consensus 171 ~i~al~a~~~~f~~~~~~~~~l~---~~~~~~~il~~~~-~~sRIiImCG~p~~ir~lm~~----~~~~gDYVf~~IDlF 242 (380)
T cd06369 171 YINALEAGVAYFSSALKFKELLR---TEEELQKLLTDKN-RKSNVIIMCGTPEDIVNLKGD----RAVAEDIVIILIDLF 242 (380)
T ss_pred EhHhhhhhhhhhhhcccceeeec---CchhHHHHHHHhc-cCccEEEEeCCHHHHHHHHhc----CccCCCEEEEEEecc
Confidence 24555555555555555444432 3478888888877 678999999999999999886 555579999998876
Q ss_pred ccccccCCchhhcccceEEEEEecCCCChHHHHHHHHHHHhccccCCCCcccccc-hhhHhHhhHHHHHHHHHHHhcccC
Q 003054 154 TNLLRTLEPSVIDSMQGVIGVGPHVPKTKALENFRVRWKRNFLQENPSIVDVELN-IFGLLAYDATRALAEAVEKAGITS 232 (852)
Q Consensus 154 ~~~~~~~~~~~~~~~~gv~~~~~~~~~~~~~~~F~~~~~~~~~~~~~~~~~~~~~-~~a~~aYDAv~~lA~Al~~a~~~~ 232 (852)
....- .+....++++.|+.+++..|+++..++ ...+.. +.. .+++.-||||.++|+||++.....
T Consensus 243 ~~sy~-~d~~a~~amqsVLvIT~~~p~~~~~~~-----~~~fn~--------~l~~~~aa~fyDaVLLYa~AL~EtL~~G 308 (380)
T cd06369 243 NDVYY-ENTTSPPYMRNVLVLTLPPRNSTNNSS-----FTTDNS--------LLKDDYVAAYHDGVLLFGHVLKKFLESQ 308 (380)
T ss_pred cchhc-cCcchHHHHhceEEEecCCCCCccccc-----CCCCCc--------chHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 54331 122345678999999988886654433 111211 223 899999999999999999876322
Q ss_pred cCccccccCCCCCCCccccccCChHHHHHHhhccceeeeeeeEEee-cCccccceEEEEEcc---CCcEEEEEEcCCCCc
Q 003054 233 FGFDKTNVSRNATDLEAFGISQNGPKLLQALSSTRFKGLTGDYIFV-DGQLQSSAFEIINVN---NGARGVGFWTPEKGL 308 (852)
Q Consensus 233 ~~~~~~~~~~~~~~~~~~~~~~~g~~l~~al~~~~f~GltG~v~f~-~G~~~~~~~~I~~~~---~g~~~vG~w~~~~g~ 308 (852)
. ...+.++.+.++|.+|.|++|.+.+| |||+ ...|.++-+. ++++.||.++...+.
T Consensus 309 ~-------------------~~~~~~I~~~m~NrTF~GitG~V~IDeNGDR-d~dfsLl~ms~~tg~y~vV~~y~t~~n~ 368 (380)
T cd06369 309 E-------------------GVQTFSFINEFRNISFEGAGGPYTLDEYGDR-DVNFTLLYTSTDTSKYKVLFEFDTSTNK 368 (380)
T ss_pred C-------------------CCCcHHHHHHHhCcceecCCCceEeCCCCCc-cCceEEEEeeCCCCCeEEEEEEECCCCe
Confidence 1 12337899999999999999999998 9999 7889998876 449999999875443
No 99
>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=99.67 E-value=1.3e-15 Score=163.68 Aligned_cols=205 Identities=25% Similarity=0.347 Sum_probs=170.9
Q ss_pred hhHHHHhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHcC-CcEEEEEEEeCCcccccHHHHHHH
Q 003054 3 TNFIIQLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAFG-WREAVPIYVDNQYGEEMIPSLTDA 81 (852)
Q Consensus 3 a~~v~~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~g-w~~vaii~~d~~~G~~~~~~l~~~ 81 (852)
+.++.+++++.+||+|++.++++.+++..+|++|++.+++..+++++++++...+ |++|++++.++++|....+.+.++
T Consensus 79 ~~~~~~~~~~~~ip~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~v~~~~~~~~~~~~~~~~~ 158 (298)
T cd06268 79 ALAAAPVAEEAGVPLISPGATSPALTGKGNPYVFRTAPSDAQQAAALADYLAEKGKVKKVAIIYDDYAYGRGLAAAFREA 158 (298)
T ss_pred HHhhHHHHHhCCCcEEccCCCCcccccCCCceEEEcccCcHHHHHHHHHHHHHhcCCCEEEEEEcCCchhHHHHHHHHHH
Confidence 3467889999999999998888777644579999999999999999999998877 999999999999999999999999
Q ss_pred HHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHcCCcccceEEEEcCccccccccCC
Q 003054 82 LQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLE 161 (852)
Q Consensus 82 l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~~~~~~~~~~ 161 (852)
+++.|++++....++.+ ..++...+.++++.++|+|++.+.+..+..+++++++.|+..+ |+..+.+......
T Consensus 159 ~~~~g~~i~~~~~~~~~--~~~~~~~~~~l~~~~~~~vi~~~~~~~~~~~~~~~~~~g~~~~---~~~~~~~~~~~~~-- 231 (298)
T cd06268 159 LKKLGGEVVAEETYPPG--ATDFSPLIAKLKAAGPDAVFLAGYGGDAALFLKQAREAGLKVP---IVGGDGAAAPALL-- 231 (298)
T ss_pred HHHcCCEEEEEeccCCC--CccHHHHHHHHHhcCCCEEEEccccchHHHHHHHHHHcCCCCc---EEecCccCCHHHH--
Confidence 99999999887766643 5679999999999999999999988999999999999998444 7777766543211
Q ss_pred chhhcccceEEEEEecCCC--ChHHHHHH-HHHHHhccccCCCCcccccchhhHhHhhHHHHHH
Q 003054 162 PSVIDSMQGVIGVGPHVPK--TKALENFR-VRWKRNFLQENPSIVDVELNIFGLLAYDATRALA 222 (852)
Q Consensus 162 ~~~~~~~~gv~~~~~~~~~--~~~~~~F~-~~~~~~~~~~~~~~~~~~~~~~a~~aYDAv~~lA 222 (852)
....+..+|+++..++.+. .+....|. +.|+++++. +|+.++..+||++++++
T Consensus 232 ~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--------~~~~~~~~~y~~~~~~~ 287 (298)
T cd06268 232 ELAGDAAEGVLGTTPYAPDDDDPAAAAFFQKAFKAKYGR--------PPDSYAAAAYDAVRLLA 287 (298)
T ss_pred HhhhHhhCCcEEeccCCCCCCChhhhHHHHHHHHHHhCC--------CcccchHHHHHHHHHHc
Confidence 1233567899888887664 34555665 888888876 78999999999999998
No 100
>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=99.67 E-value=9.3e-16 Score=162.63 Aligned_cols=230 Identities=13% Similarity=0.194 Sum_probs=164.1
Q ss_pred CceEEEeeecccCcccceEEeeCCCCCCCceEEEeeHHHHHHHHHHC-CCccceEEEecCCCCCCCCCChhHHHHHHhcC
Q 003054 344 EKKLRIGVPVKKGFSDFVNVTIDPKTQEPTSVTGYCVDVFKAVIQEL-PYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLG 422 (852)
Q Consensus 344 ~~~lrv~v~~~~~~~~~~~~~~d~~~~~~~~~~G~~~dl~~~ia~~l-~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g 422 (852)
.++|++++. +|+||.+.+ +++ ...|+..++++++++++ ++.++ +... .|.+++.++ .|
T Consensus 17 ~~~l~~~~~---~~pPf~~~~-----~~~-~~~G~~~~i~~~i~~~~~~~~~~--~~~~---------pw~r~l~~l-~~ 75 (268)
T TIGR02285 17 KEAITWIVN---DFPPFFIFS-----GPS-KGRGVFDVILQEIRRALPQYEHR--FVRV---------SFARSLKEL-QG 75 (268)
T ss_pred cceeEEEec---ccCCeeEeC-----CCC-CCCChHHHHHHHHHHHcCCCcee--EEEC---------CHHHHHHHH-hc
Confidence 568888765 577887764 345 67899999999999998 76444 4432 499999999 78
Q ss_pred cccEEEeeeeeecCcceeeeccccccc-cceEEEEEccCCCCCCceEeecccchhHHHHHHHHHHHHHhhhhheecccCC
Q 003054 423 EFDAVVGDITIVFNRSNYVDFTLPYTE-SGVSMIVPIKDSKKRNAWVFLQPLTWDLWVTCFCFFIFIGFVVWVLEHRVNE 501 (852)
Q Consensus 423 ~~D~~~g~~~it~~r~~~vdft~p~~~-~~~~~vv~~~~~~~~~~~~~l~PF~~~lW~~i~~~~i~~~~v~~~l~~~~~~ 501 (852)
+.|.++.++++|++|.+.++||.||.. ...++++++.....
T Consensus 76 ~~d~~~~~~~~t~eR~~~~~Fs~P~~~~~~~~~~~~~~~~~~-------------------------------------- 117 (268)
T TIGR02285 76 KGGVCTVNLLRTPEREKFLIFSDPTLRALPVGLVLRKELTAG-------------------------------------- 117 (268)
T ss_pred CCCeEEeeccCCcchhhceeecCCccccCCceEEEccchhhh--------------------------------------
Confidence 888777779999999999999999975 57888888653211
Q ss_pred CCCCCcccccchhHHHHHHHhhhccccccccchhhHHHHHHHHHHHHHHHHhhhhccceeeecccCCCcCCHHHHH-hcC
Q 003054 502 DFRGPAGQQVGTSFWFSFSTMVFSQRERVISNLARIVVIVWCFVVLILTQSYTASLTSLLTVQQLQPTITDVKMLI-KRG 580 (852)
Q Consensus 502 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~s~~~R~v~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~i~sl~dL~-~~~ 580 (852)
+ ..+.+...++.+|. .+|
T Consensus 118 -~------------------------------------------------------------~~~~d~~~~~~~l~~l~g 136 (268)
T TIGR02285 118 -V------------------------------------------------------------RDEQDGDVDLKKLLASKK 136 (268)
T ss_pred -c------------------------------------------------------------cccCCCCccHHHHhcCCC
Confidence 0 00000001233332 136
Q ss_pred CeEEEEeCchH----HHHHHhcCCCC-cceeecCCHhHHHHHhhcccccCceeEEEechhHHHHHHhhc---CCceEeec
Q 003054 581 DNVGYQKGSFV----LGILKQLGFDE-RKLVVYNSPEDCHELFQKGSVNGGIAAAFDEIPYMKLLIGQY---CSKYAMIE 652 (852)
Q Consensus 581 ~~vg~~~~s~~----~~~l~~~~~~~-~~~~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~~---~~~~~~v~ 652 (852)
+++|++.|+.. ..++++.+... .++..+++.++.+++|..|+ +|+++.+...+.+++++. ...+....
T Consensus 137 ~~vgv~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~Gr----vD~~v~d~~~~~~~~~~~~~~~~~~~~~~ 212 (268)
T TIGR02285 137 KRLGVIASRSYGQQIDDILSDSGYQHNTRIIGNAAMGNLFKMLEKGR----VNYTLAYPPEKTYYEELNNGALPPLKFLP 212 (268)
T ss_pred eEEEEecceeccHHHHHHHHhCCcccceeeeccchHHHHHHHHHcCC----ccEEEeCcHHHHHHHHhccCCcCCeeEee
Confidence 79999887654 44455433322 23556677888999999999 999999999899888743 22344332
Q ss_pred ccc--cccceEEEecCCC---CchhhHHHHHHhccccChhHHHHHHHccC
Q 003054 653 PKF--KTAGFGFVFPLHS---PLVHDVSKAILNVTEGDKMKEIEDAWFKK 697 (852)
Q Consensus 653 ~~~--~~~~~~~~~~k~s---pl~~~in~~il~l~e~G~~~~i~~kw~~~ 697 (852)
... ....++++++|+. .++..||++|.+|.++|.+++|.+||++.
T Consensus 213 ~~~~~~~~~~~i~~~k~~~~~~l~~~in~~L~~l~~dG~~~~i~~k~~~~ 262 (268)
T TIGR02285 213 VAGMPAHISVWVACPKTEWGRKVIADIDQALSELNVDPKYYKYFDRWLSP 262 (268)
T ss_pred cCCCccceEEEEEeCCCHHHHHHHHHHHHHHHHHhhCHHHHHHHHHhCCH
Confidence 211 2235788999974 49999999999999999999999999964
No 101
>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=99.66 E-value=3.6e-15 Score=154.71 Aligned_cols=212 Identities=15% Similarity=0.116 Sum_probs=159.3
Q ss_pred eEEEeeecccCcccceEEeeCCCCCCCceEEEeeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCccc
Q 003054 346 KLRIGVPVKKGFSDFVNVTIDPKTQEPTSVTGYCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGEFD 425 (852)
Q Consensus 346 ~lrv~v~~~~~~~~~~~~~~d~~~~~~~~~~G~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~~D 425 (852)
.||||+. +.|+||.+. ...|+++||++++++++|.++++++.+. .+..++..+.+|++|
T Consensus 1 ~l~v~~~--~~~~P~~~~----------~~~G~~~el~~~i~~~~g~~i~~~~~~~---------~~~~~~~~l~~g~~D 59 (232)
T TIGR03871 1 ALRVCAD--PNNLPFSNE----------KGEGFENKIAQLLADDLGLPLEYTWFPQ---------RRGFVRNTLNAGRCD 59 (232)
T ss_pred CeEEEeC--CCCCCccCC----------CCCchHHHHHHHHHHHcCCceEEEecCc---------chhhHHHHHhcCCcc
Confidence 3788877 778888741 2369999999999999998666654332 244467789999999
Q ss_pred EEEeeeeeecCcceeeeccccccccceEEEEEccCCCCCCceEeecccchhHHHHHHHHHHHHHhhhhheecccCCCCCC
Q 003054 426 AVVGDITIVFNRSNYVDFTLPYTESGVSMIVPIKDSKKRNAWVFLQPLTWDLWVTCFCFFIFIGFVVWVLEHRVNEDFRG 505 (852)
Q Consensus 426 ~~~g~~~it~~r~~~vdft~p~~~~~~~~vv~~~~~~~~~~~~~l~PF~~~lW~~i~~~~i~~~~v~~~l~~~~~~~~~~ 505 (852)
++++ +++|.+.++||.||...+++++++.....
T Consensus 60 i~~~----~~~r~~~~~fs~py~~~~~~lv~~~~~~~------------------------------------------- 92 (232)
T TIGR03871 60 VVIG----VPAGYEMVLTTRPYYRSTYVFVTRKDSLL------------------------------------------- 92 (232)
T ss_pred EEEe----ccCccccccccCCcEeeeEEEEEeCCCcc-------------------------------------------
Confidence 9865 47788899999999999999999976322
Q ss_pred CcccccchhHHHHHHHhhhccccccccchhhHHHHHHHHHHHHHHHHhhhhccceeeecccCCCcCCHHHHHhcCCeEEE
Q 003054 506 PAGQQVGTSFWFSFSTMVFSQRERVISNLARIVVIVWCFVVLILTQSYTASLTSLLTVQQLQPTITDVKMLIKRGDNVGY 585 (852)
Q Consensus 506 ~~~~~~~~~~~~~~~~l~~~~~~~~~s~~~R~v~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~i~sl~dL~~~~~~vg~ 585 (852)
.+++++|+...|++||+
T Consensus 93 ---------------------------------------------------------------~~~~~~d~~l~g~~V~v 109 (232)
T TIGR03871 93 ---------------------------------------------------------------DVKSLDDPRLKKLRIGV 109 (232)
T ss_pred ---------------------------------------------------------------cccchhhhhhcCCeEEE
Confidence 27889883224889999
Q ss_pred EeCchHHHHHHhcCCCCcceee---------cCCHhHHHHHhhcccccCceeEEEechhHHHHHHhhcCCceEeeccc--
Q 003054 586 QKGSFVLGILKQLGFDERKLVV---------YNSPEDCHELFQKGSVNGGIAAAFDEIPYMKLLIGQYCSKYAMIEPK-- 654 (852)
Q Consensus 586 ~~~s~~~~~l~~~~~~~~~~~~---------~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~~~~~~~~v~~~-- 654 (852)
..|+....++++.+... +++. ..+.++.+++|..|+ ++|++.+...+.+++++.-..+.+....
T Consensus 110 ~~g~~~~~~l~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~l~~G~----~Da~i~~~~~~~~~~~~~~~~~~~~~~~~~ 184 (232)
T TIGR03871 110 FAGTPPAHWLARHGLVE-NVVGYSLFGDYRPESPPGRMVEDLAAGE----IDVAIVWGPIAGYFAKQAGPPLVVVPLLPE 184 (232)
T ss_pred EcCChHHHHHHhcCccc-ccccccccccccccCCHHHHHHHHHcCC----cCEEEeccHHHHHHHHhCCCCceeeccccC
Confidence 99999999887654322 2221 337789999999999 9999999888888777542234433221
Q ss_pred ----ccccceEEEecCCCC-chhhHHHHHHhccccChhHHHHHHHc
Q 003054 655 ----FKTAGFGFVFPLHSP-LVHDVSKAILNVTEGDKMKEIEDAWF 695 (852)
Q Consensus 655 ----~~~~~~~~~~~k~sp-l~~~in~~il~l~e~G~~~~i~~kw~ 695 (852)
....+++++++++.+ ++..||++|.++. |.+++|.+||.
T Consensus 185 ~~~~~~~~~~~~~~~~~~~~l~~~~n~~l~~~~--~~~~~i~~kyg 228 (232)
T TIGR03871 185 DGGIPFDYRIAMGVRKGDKAWKDELNAVLDRRQ--AEIDAILREYG 228 (232)
T ss_pred CCCCCccceEEEEEecCCHHHHHHHHHHHHHHH--HHHHHHHHHcC
Confidence 123457888898866 9999999999985 47899999995
No 102
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=99.65 E-value=1.5e-15 Score=194.87 Aligned_cols=222 Identities=14% Similarity=0.138 Sum_probs=184.9
Q ss_pred CCceEEEeeecccCcccceEEeeCCCCCCCceEEEeeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcC
Q 003054 343 NEKKLRIGVPVKKGFSDFVNVTIDPKTQEPTSVTGYCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLG 422 (852)
Q Consensus 343 ~~~~lrv~v~~~~~~~~~~~~~~d~~~~~~~~~~G~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g 422 (852)
+.++++||+. ++++|+.+... .++ ++.||.+|+++.|++++|. ++++++.. +|++++.+|.+|
T Consensus 54 ~~~~l~vgv~--~~~~p~~~~~~----~~g-~~~G~~~D~l~~ia~~lG~--~~e~v~~~--------~~~~~l~~l~~g 116 (1197)
T PRK09959 54 SKKNLVIAVH--KSQTATLLHTD----SQQ-RVRGINADYLNLLKRALNI--KLTLREYA--------DHQKAMDALEEG 116 (1197)
T ss_pred hCCeEEEEec--CCCCCCceeec----CCC-ccceecHHHHHHHHHhcCC--ceEEEeCC--------CHHHHHHHHHcC
Confidence 4678999998 55555444321 367 8999999999999999995 77787764 799999999999
Q ss_pred cccEEEeeeeeecCcceeeeccccccccceEEEEEccCCCCCCceEeecccchhHHHHHHHHHHHHHhhhhheecccCCC
Q 003054 423 EFDAVVGDITIVFNRSNYVDFTLPYTESGVSMIVPIKDSKKRNAWVFLQPLTWDLWVTCFCFFIFIGFVVWVLEHRVNED 502 (852)
Q Consensus 423 ~~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv~~~~~~~~~~~~~l~PF~~~lW~~i~~~~i~~~~v~~~l~~~~~~~ 502 (852)
++|++.+.++.+++|.+.++||.||+.+..++++++...
T Consensus 117 ~iDl~~~~~~~~~~r~~~~~fs~py~~~~~~~v~~~~~~----------------------------------------- 155 (1197)
T PRK09959 117 EVDIVLSHLVASPPLNDDIAATKPLIITFPALVTTLHDS----------------------------------------- 155 (1197)
T ss_pred CCcEecCccccccccccchhcCCCccCCCceEEEeCCCC-----------------------------------------
Confidence 999998888999999999999999999999999997631
Q ss_pred CCCCcccccchhHHHHHHHhhhccccccccchhhHHHHHHHHHHHHHHHHhhhhccceeeecccCCCcCCHHHHHhcCCe
Q 003054 503 FRGPAGQQVGTSFWFSFSTMVFSQRERVISNLARIVVIVWCFVVLILTQSYTASLTSLLTVQQLQPTITDVKMLIKRGDN 582 (852)
Q Consensus 503 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~s~~~R~v~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~i~sl~dL~~~~~~ 582 (852)
+++++|+. +++
T Consensus 156 -------------------------------------------------------------------~~~~~~l~--~~~ 166 (1197)
T PRK09959 156 -------------------------------------------------------------------MRPLTSSK--PVN 166 (1197)
T ss_pred -------------------------------------------------------------------CCCccccc--CeE
Confidence 56777885 789
Q ss_pred EEEEeCchHHHHHHhcCCCCcceeecCCHhHHHHHhhcccccCceeEEEechhHHHHHHhhcC-CceEeecc-cccccce
Q 003054 583 VGYQKGSFVLGILKQLGFDERKLVVYNSPEDCHELFQKGSVNGGIAAAFDEIPYMKLLIGQYC-SKYAMIEP-KFKTAGF 660 (852)
Q Consensus 583 vg~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~~~-~~~~~v~~-~~~~~~~ 660 (852)
++++.|+....++++. ++..+++.|++.++++++|..|+ +||++.+...+.++++++. ..+.+++. .......
T Consensus 167 i~~~~g~~~~~~~~~~-~p~~~i~~~~s~~~al~av~~G~----~Da~i~~~~~~~~~i~~~~~~~l~~~~~~~~~~~~~ 241 (1197)
T PRK09959 167 IARVANYPPDEVIHQS-FPKATIISFTNLYQALASVSAGQ----NDYFIGSNIITSSMISRYFTHSLNVVKYYNSPRQYN 241 (1197)
T ss_pred EEEeCCCCCHHHHHHh-CCCCEEEeCCCHHHHHHHHHcCC----CCEEEccHHHHHHHHhcccccceEEEeeccCCCCce
Confidence 9999999998888875 78889999999999999999999 9999999999999998752 23444432 2223456
Q ss_pred EEEecCCCC-chhhHHHHHHhccccChhHHHHHHHccC
Q 003054 661 GFVFPLHSP-LVHDVSKAILNVTEGDKMKEIEDAWFKK 697 (852)
Q Consensus 661 ~~~~~k~sp-l~~~in~~il~l~e~G~~~~i~~kw~~~ 697 (852)
.++++|+.| |...+|++|..+.++|.. .+.+||+..
T Consensus 242 ~~~~~~~~~~L~~~lnkal~~i~~~~~~-~i~~kW~~~ 278 (1197)
T PRK09959 242 FFLTRKESVILNEVLNRFVDALTNEVRY-EVSQNWLDT 278 (1197)
T ss_pred eEEEcCCcHHHHHHHHHHHHhCCHHHHH-HHHHhccCC
Confidence 688899988 889999999999999887 899999963
No 103
>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=99.64 E-value=1.6e-14 Score=146.86 Aligned_cols=214 Identities=27% Similarity=0.446 Sum_probs=176.5
Q ss_pred EEEeeecccCcccceEEeeCCCCCCCceEEEeeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCcccE
Q 003054 347 LRIGVPVKKGFSDFVNVTIDPKTQEPTSVTGYCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGEFDA 426 (852)
Q Consensus 347 lrv~v~~~~~~~~~~~~~~d~~~~~~~~~~G~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~~D~ 426 (852)
|+||+. +.++||.+.+ +++ ...|++.++++.+++++|. ++++++. .+.+++.+|.+|++|+
T Consensus 1 l~i~~~--~~~~p~~~~~-----~~g-~~~G~~~~~~~~~~~~~g~--~~~~~~~---------~~~~~~~~l~~g~~D~ 61 (218)
T cd00134 1 LTVGTA--GTYPPFSFRD-----ANG-ELTGFDVDLAKAIAKELGV--KVKFVEV---------DWDGLITALKSGKVDL 61 (218)
T ss_pred CEEecC--CCCCCeeEEC-----CCC-CEEeeeHHHHHHHHHHhCC--eEEEEeC---------CHHHHHHHHhcCCcCE
Confidence 577777 7788888765 567 8999999999999999995 5555553 3889999999999999
Q ss_pred EEeeeeeecCcceeeeccccccccceEEEEEccCCCCCCceEeecccchhHHHHHHHHHHHHHhhhhheecccCCCCCCC
Q 003054 427 VVGDITIVFNRSNYVDFTLPYTESGVSMIVPIKDSKKRNAWVFLQPLTWDLWVTCFCFFIFIGFVVWVLEHRVNEDFRGP 506 (852)
Q Consensus 427 ~~g~~~it~~r~~~vdft~p~~~~~~~~vv~~~~~~~~~~~~~l~PF~~~lW~~i~~~~i~~~~v~~~l~~~~~~~~~~~ 506 (852)
+++....+.+|...+.|+.|+.....++++++...
T Consensus 62 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--------------------------------------------- 96 (218)
T cd00134 62 IAAGMTITPERAKQVDFSDPYYKSGQVILVKKGSP--------------------------------------------- 96 (218)
T ss_pred EeecCcCCHHHHhhccCcccceeccEEEEEECCCC---------------------------------------------
Confidence 98877778889888999999999999999997632
Q ss_pred cccccchhHHHHHHHhhhccccccccchhhHHHHHHHHHHHHHHHHhhhhccceeeecccCCCcCCHHHHHhcCCeEEEE
Q 003054 507 AGQQVGTSFWFSFSTMVFSQRERVISNLARIVVIVWCFVVLILTQSYTASLTSLLTVQQLQPTITDVKMLIKRGDNVGYQ 586 (852)
Q Consensus 507 ~~~~~~~~~~~~~~~l~~~~~~~~~s~~~R~v~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~i~sl~dL~~~~~~vg~~ 586 (852)
+.+++||. |+++++.
T Consensus 97 ---------------------------------------------------------------~~~~~dl~--g~~i~~~ 111 (218)
T cd00134 97 ---------------------------------------------------------------IKSVKDLK--GKKVAVQ 111 (218)
T ss_pred ---------------------------------------------------------------CCChHHhC--CCEEEEE
Confidence 56899996 8899999
Q ss_pred eCchHHHHHHhcCCCCcceeecCCHhHHHHHhhcccccCceeEEEechhHHHHHHhhc-CCceEeecc--cccccceEEE
Q 003054 587 KGSFVLGILKQLGFDERKLVVYNSPEDCHELFQKGSVNGGIAAAFDEIPYMKLLIGQY-CSKYAMIEP--KFKTAGFGFV 663 (852)
Q Consensus 587 ~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~~-~~~~~~v~~--~~~~~~~~~~ 663 (852)
.|+....++.+. .....+..+.+.++.+++|.+|+ +++++.+.....+...+. + .+.++.. ......++++
T Consensus 112 ~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~l~~g~----~d~~~~~~~~~~~~~~~~~~-~l~~~~~~~~~~~~~~~~~ 185 (218)
T cd00134 112 KGSTAEKYLKKA-LPEAKVVSYDDNAEALAALENGR----ADAVIVDEIALAALLKKHPP-ELKIVGPSIDLEPLGFGVA 185 (218)
T ss_pred cCchHHHHHHHh-CCcccEEEeCCHHHHHHHHHcCC----ccEEEeccHHHHHHHHhcCC-CcEEeccccCCCccceEEE
Confidence 888888887765 23456778889999999999999 999999988888877765 4 3665554 3445556777
Q ss_pred ecCCC-CchhhHHHHHHhccccChhHHHHHHHc
Q 003054 664 FPLHS-PLVHDVSKAILNVTEGDKMKEIEDAWF 695 (852)
Q Consensus 664 ~~k~s-pl~~~in~~il~l~e~G~~~~i~~kw~ 695 (852)
..+++ .+...++++|..++++|.++.+.+||+
T Consensus 186 ~~~~~~~l~~~~~~~l~~~~~~g~~~~i~~~~~ 218 (218)
T cd00134 186 VGKDNKELLDAVNKALKELRADGELKKISKKWF 218 (218)
T ss_pred EcCCCHHHHHHHHHHHHHHHhCccHHHHHHhhC
Confidence 77766 499999999999999999999999996
No 104
>smart00062 PBPb Bacterial periplasmic substrate-binding proteins. bacterial proteins, eukaryotic ones are in PBPe
Probab=99.61 E-value=3.3e-14 Score=144.39 Aligned_cols=216 Identities=28% Similarity=0.499 Sum_probs=179.0
Q ss_pred eEEEeeecccCcccceEEeeCCCCCCCceEEEeeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCccc
Q 003054 346 KLRIGVPVKKGFSDFVNVTIDPKTQEPTSVTGYCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGEFD 425 (852)
Q Consensus 346 ~lrv~v~~~~~~~~~~~~~~d~~~~~~~~~~G~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~~D 425 (852)
+|+||+. +.++||...+ .++ ...|+.+|+++.+.+++|. ++++.+. .|..++.++.+|++|
T Consensus 1 ~l~v~~~--~~~~p~~~~~-----~~g-~~~G~~~~~~~~~~~~~g~--~~~~~~~---------~~~~~~~~l~~g~~D 61 (219)
T smart00062 1 TLRVGTN--GDYPPFSFAD-----EDG-ELTGFDVDLAKAIAKELGL--KVEFVEV---------SFDNLLTALKSGKID 61 (219)
T ss_pred CEEEEec--CCCCCcEEEC-----CCC-CcccchHHHHHHHHHHhCC--eEEEEec---------cHHHHHHHHHCCccc
Confidence 4789997 6788887765 566 8899999999999999995 5555553 389999999999999
Q ss_pred EEEeeeeeecCcceeeeccccccccceEEEEEccCCCCCCceEeecccchhHHHHHHHHHHHHHhhhhheecccCCCCCC
Q 003054 426 AVVGDITIVFNRSNYVDFTLPYTESGVSMIVPIKDSKKRNAWVFLQPLTWDLWVTCFCFFIFIGFVVWVLEHRVNEDFRG 505 (852)
Q Consensus 426 ~~~g~~~it~~r~~~vdft~p~~~~~~~~vv~~~~~~~~~~~~~l~PF~~~lW~~i~~~~i~~~~v~~~l~~~~~~~~~~ 505 (852)
++++....+.+|...+.|+.|+...+.++++++..
T Consensus 62 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--------------------------------------------- 96 (219)
T smart00062 62 VVAAGMTITPERAKQVDFSDPYYKSGQVILVRKDS--------------------------------------------- 96 (219)
T ss_pred EEeccccCCHHHHhheeeccceeeceeEEEEecCC---------------------------------------------
Confidence 99987766788888899999999999999988652
Q ss_pred CcccccchhHHHHHHHhhhccccccccchhhHHHHHHHHHHHHHHHHhhhhccceeeecccCCCcCCHHHHHhcCCeEEE
Q 003054 506 PAGQQVGTSFWFSFSTMVFSQRERVISNLARIVVIVWCFVVLILTQSYTASLTSLLTVQQLQPTITDVKMLIKRGDNVGY 585 (852)
Q Consensus 506 ~~~~~~~~~~~~~~~~l~~~~~~~~~s~~~R~v~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~i~sl~dL~~~~~~vg~ 585 (852)
++++++||. |+++++
T Consensus 97 ---------------------------------------------------------------~~~~~~dL~--g~~i~~ 111 (219)
T smart00062 97 ---------------------------------------------------------------PIKSLEDLK--GKKVAV 111 (219)
T ss_pred ---------------------------------------------------------------CCCChHHhC--CCEEEE
Confidence 278999995 889999
Q ss_pred EeCchHHHHHHhcCCCCcceeecCCHhHHHHHhhcccccCceeEEEechhHHHHHHhhcC-CceEeecccccc-cceEEE
Q 003054 586 QKGSFVLGILKQLGFDERKLVVYNSPEDCHELFQKGSVNGGIAAAFDEIPYMKLLIGQYC-SKYAMIEPKFKT-AGFGFV 663 (852)
Q Consensus 586 ~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~~~-~~~~~v~~~~~~-~~~~~~ 663 (852)
..|+....++... .+..++..+.+..+.+++|.+|+ +++++...+...+...+.- ..+.++...... ..++++
T Consensus 112 ~~g~~~~~~~~~~-~~~~~~~~~~~~~~~~~~l~~g~----~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 186 (219)
T smart00062 112 VAGTTGEELLKKL-YPEAKIVSYDSQAEALAALKAGR----ADAAVADAPALAALVKQHGLPELKIVGDPLDTPEGYAFA 186 (219)
T ss_pred ecCccHHHHHHHh-CCCceEEEcCCHHHHHHHhhcCc----ccEEEeccHHHHHHHHhcCCCceeeccCCCCCCcceEEE
Confidence 9998888888765 34456778888999999999999 9999999888887776651 246666555444 788999
Q ss_pred ecCCCC-chhhHHHHHHhccccChhHHHHHHHc
Q 003054 664 FPLHSP-LVHDVSKAILNVTEGDKMKEIEDAWF 695 (852)
Q Consensus 664 ~~k~sp-l~~~in~~il~l~e~G~~~~i~~kw~ 695 (852)
++++++ +.+.++++|..+.++|.++++.++|+
T Consensus 187 ~~~~~~~~~~~~~~~l~~~~~~~~~~~i~~~~~ 219 (219)
T smart00062 187 VRKGDPELLDKINKALKELKADGTLKKIYEKWF 219 (219)
T ss_pred EECCCHHHHHHHHHHHHHHHhCchHHHHHhccC
Confidence 999986 89999999999999999999999985
No 105
>smart00079 PBPe Eukaryotic homologues of bacterial periplasmic substrate binding proteins. Prokaryotic homologues are represented by a separate alignment: PBPb
Probab=99.30 E-value=1.5e-11 Score=115.58 Aligned_cols=122 Identities=30% Similarity=0.485 Sum_probs=106.2
Q ss_pred CcCCHHHHHhc-CCeEEEEeCchHHHHHHhcCCCC----------cceeecCCHhHHHHHhhcccccCceeEEEechhHH
Q 003054 569 TITDVKMLIKR-GDNVGYQKGSFVLGILKQLGFDE----------RKLVVYNSPEDCHELFQKGSVNGGIAAAFDEIPYM 637 (852)
Q Consensus 569 ~i~sl~dL~~~-~~~vg~~~~s~~~~~l~~~~~~~----------~~~~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~ 637 (852)
||++++||..+ +++||++.|++.+.++++..... .+++.+++..+++.+|..|+ +|++.+.+.+
T Consensus 1 ~i~~~~dl~~~~~~~vgv~~gs~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~-----da~v~d~~~~ 75 (134)
T smart00079 1 PITSVEDLAKQTKIEYGTIRGSSTLAFFKRSGNPEYSRMWNYMSASPSVFVKSYAEGVQRVRVSN-----YAFLMESTYL 75 (134)
T ss_pred CCCChHHHhhCCCccceEecCchHHHHHHhCCChHHHHHHHHHHhCCCCCCCCHHHHHHHHHcCC-----CEEEeehHhH
Confidence 48899999843 26999999999999998753321 25678899999999999887 6899999999
Q ss_pred HHHHhhcCCceEeecccccccceEEEecCCCCchhhHHHHHHhccccChhHHHHHHHcc
Q 003054 638 KLLIGQYCSKYAMIEPKFKTAGFGFVFPLHSPLVHDVSKAILNVTEGDKMKEIEDAWFK 696 (852)
Q Consensus 638 ~~~~~~~~~~~~~v~~~~~~~~~~~~~~k~spl~~~in~~il~l~e~G~~~~i~~kw~~ 696 (852)
.++.++.|+ +.+++..+...+++++++|+++|++.||++|.++.++|.++++.++|+.
T Consensus 76 ~~~~~~~~~-~~~~~~~~~~~~~~ia~~k~~~l~~~vn~~l~~l~~~G~~~~l~~kw~~ 133 (134)
T smart00079 76 DYELSQNCD-LMTVGENFGRKGYGIAFPKGSPLRDDLSRAILKLSESGELQKLENKWWK 133 (134)
T ss_pred HHHHhCCCC-eEEcCcccCCCceEEEecCCCHHHHHHHHHHHHHHhcCcHHHHHHhhcc
Confidence 998887885 8888888888899999999999999999999999999999999999985
No 106
>COG4623 Predicted soluble lytic transglycosylase fused to an ABC-type amino acid-binding protein [Cell envelope biogenesis, outer membrane]
Probab=99.29 E-value=3.5e-11 Score=123.71 Aligned_cols=224 Identities=16% Similarity=0.138 Sum_probs=177.0
Q ss_pred CCceEEEeeecccCcccceEEeeCCCCCCCceEEEeeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcC
Q 003054 343 NEKKLRIGVPVKKGFSDFVNVTIDPKTQEPTSVTGYCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLG 422 (852)
Q Consensus 343 ~~~~lrv~v~~~~~~~~~~~~~~d~~~~~~~~~~G~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g 422 (852)
..+.|||+|.++|- ..|. +++ .-.|+++++.+++++.|| |+++.++.. +.+.|+.+|.+|
T Consensus 21 ~rGvLrV~tinsp~-sy~~--------~~~-~p~G~eYelak~Fa~yLg--V~Lki~~~~--------n~dqLf~aL~ng 80 (473)
T COG4623 21 ARGVLRVSTINSPL-SYFE--------DKG-GPTGLEYELAKAFADYLG--VKLKIIPAD--------NIDQLFDALDNG 80 (473)
T ss_pred hcCeEEEEeecCcc-ceec--------cCC-CccchhHHHHHHHHHHhC--CeEEEEecC--------CHHHHHHHHhCC
Confidence 36789999986543 2222 355 667999999999999999 567777765 678999999999
Q ss_pred cccEEEeeeeeecCcceeeeccccccccceEEEEEccCCCCCCceEeecccchhHHHHHHHHHHHHHhhhhheecccCCC
Q 003054 423 EFDAVVGDITIVFNRSNYVDFTLPYTESGVSMIVPIKDSKKRNAWVFLQPLTWDLWVTCFCFFIFIGFVVWVLEHRVNED 502 (852)
Q Consensus 423 ~~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv~~~~~~~~~~~~~l~PF~~~lW~~i~~~~i~~~~v~~~l~~~~~~~ 502 (852)
++|++..++...++|.+.+.....|+...+.+|.++...+
T Consensus 81 ~~DL~Aagl~~~~~~l~~~~~gP~y~svs~qlVyRkG~~R---------------------------------------- 120 (473)
T COG4623 81 NADLAAAGLLYNSERLKNFQPGPTYYSVSQQLVYRKGQYR---------------------------------------- 120 (473)
T ss_pred CcceecccccCChhHhcccCCCCceecccHHHHhhcCCCC----------------------------------------
Confidence 9999999999999998888888888888888888877433
Q ss_pred CCCCcccccchhHHHHHHHhhhccccccccchhhHHHHHHHHHHHHHHHHhhhhccceeeecccCCCcCCHHHHHhcCCe
Q 003054 503 FRGPAGQQVGTSFWFSFSTMVFSQRERVISNLARIVVIVWCFVVLILTQSYTASLTSLLTVQQLQPTITDVKMLIKRGDN 582 (852)
Q Consensus 503 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~s~~~R~v~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~i~sl~dL~~~~~~ 582 (852)
.+++++|. |..
T Consensus 121 -------------------------------------------------------------------p~~l~~L~--g~~ 131 (473)
T COG4623 121 -------------------------------------------------------------------PRSLGQLK--GRQ 131 (473)
T ss_pred -------------------------------------------------------------------CCCHHHcc--Cce
Confidence 67899997 778
Q ss_pred EEEEeCchHHHHHHh---cCCCCcceee--cCCHhHHHHHhhcccccCceeEEEechhHHHHHHhhcCCceEeecccccc
Q 003054 583 VGYQKGSFVLGILKQ---LGFDERKLVV--YNSPEDCHELFQKGSVNGGIAAAFDEIPYMKLLIGQYCSKYAMIEPKFKT 657 (852)
Q Consensus 583 vg~~~~s~~~~~l~~---~~~~~~~~~~--~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~~~~~~~~v~~~~~~ 657 (852)
+.+..|+.....++. ..+|....+. -...++.++++..|+ ++-.+.+...+..+..-+.+ +.+.-+.-..
T Consensus 132 i~v~~gs~~~~~l~~lk~~kyP~l~~k~d~~~~~~dLle~v~~Gk----ldytiads~~is~~q~i~P~-laVafd~tde 206 (473)
T COG4623 132 ITVAKGSAHVEDLKLLKETKYPELIWKVDDKLGVEDLLEMVAEGK----LDYTIADSVEISLFQRVHPE-LAVAFDLTDE 206 (473)
T ss_pred eeccCCcHHHHHHHHHHHhhcchhhhhhcccccHHHHHHHHhcCC----cceeeeccHHHHHHHHhCcc-ceeeeecccc
Confidence 889999987766543 3354432222 226789999999999 99999998888777666653 4444444445
Q ss_pred cceEEEecCC--CCchhhHHHHHHhccccChhHHHHHHHccCCCC
Q 003054 658 AGFGFVFPLH--SPLVHDVSKAILNVTEGDKMKEIEDAWFKKHSS 700 (852)
Q Consensus 658 ~~~~~~~~k~--spl~~~in~~il~l~e~G~~~~i~~kw~~~~~~ 700 (852)
.+.++++|.+ +-|...++.++..+.|.|.++.+++||++..+.
T Consensus 207 ~~v~Wy~~~~dd~tL~a~ll~F~~~~~e~g~larleeky~gH~~~ 251 (473)
T COG4623 207 QPVAWYLPRDDDSTLSAALLDFLNEAKEDGLLARLEEKYLGHGDD 251 (473)
T ss_pred cCceeeccCCchHHHHHHHHHHHHHhhcchHHHHHHHHHhccccc
Confidence 7899999996 559999999999999999999999999975433
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=98.96 E-value=8.5e-09 Score=108.24 Aligned_cols=186 Identities=23% Similarity=0.320 Sum_probs=140.9
Q ss_pred HHHhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeC-CcccccHHHHHHHHHh
Q 003054 6 IIQLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDN-QYGEEMIPSLTDALQA 84 (852)
Q Consensus 6 v~~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~-~~G~~~~~~l~~~l~~ 84 (852)
+...+.+.++|+|++.+..+... .+++++++.+++..+++.+++++.+.+|+++++++.+. .++....+.+++++++
T Consensus 74 ~~~~~~~~~ip~v~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~i~~i~~~~~~~~~~~~~~~~~~~~~ 151 (269)
T cd01391 74 VVELAAAAGIPVVSLDATAPDLT--GYPYVFRVGPDNEQAGEAAAEYLAEKGWKRVALIYGDDGAYGRERLEGFKAALKK 151 (269)
T ss_pred HHHHHHHcCCcEEEecCCCCccC--CCceEEEEcCCcHHHHHHHHHHHHHhCCceEEEEecCCcchhhHHHHHHHHHHHh
Confidence 56778889999999988766555 57899999999999999999999999999999999777 6788889999999999
Q ss_pred CCceeeeeeecCCCCChHHHHHHHHHhhcC-CceEEEEEeChhhHHHHHHHHHHcCCcccceEEEEcCccccccccCCch
Q 003054 85 IDTRVPYRSVISPLATDDQIEKELYKLFTM-QTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLEPS 163 (852)
Q Consensus 85 ~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~-~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~~~~~~~~~~~~ 163 (852)
.|.++......+.. .+.++......+++. ++++|++++. ..+..+++++++.|+.+.++.|++.+.+..... .
T Consensus 152 ~~~~~~~~~~~~~~-~~~~~~~~~~~l~~~~~~~~i~~~~~-~~a~~~~~~~~~~g~~~~~~~ii~~~~~~~~~~----~ 225 (269)
T cd01391 152 AGIEVVAIEYGDLD-TEKGFQALLQLLKAAPKPDAIFACND-EMAAGALKAAREAGLTPGDISIIGFDGSPAALL----A 225 (269)
T ss_pred cCcEEEeccccCCC-ccccHHHHHHHHhcCCCCCEEEEcCc-hHHHHHHHHHHHcCCCCCCCEEEeccccccccc----c
Confidence 99877655444322 225677777778776 7899999877 889999999999999755677777766554322 1
Q ss_pred hhcccceEEEEEecCCCChHHHHHHHHHHHhccccCCCCcccccchhhHhHhhHHHH
Q 003054 164 VIDSMQGVIGVGPHVPKTKALENFRVRWKRNFLQENPSIVDVELNIFGLLAYDATRA 220 (852)
Q Consensus 164 ~~~~~~gv~~~~~~~~~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~a~~aYDAv~~ 220 (852)
......++.++....+..+. . .++.+...+|||+.+
T Consensus 226 ~~~~~~~~~ti~~~~~~~~~-------------~--------~~~~~~~~~~~a~~~ 261 (269)
T cd01391 226 AGEAGPGLTTVAQPFPGDDP-------------D--------QPDYPAALGYDAVLL 261 (269)
T ss_pred cccccceEEecccCCCCCCC-------------C--------CCCccccceeeeeee
Confidence 12234455555555444332 1 567777888988876
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=98.84 E-value=5.3e-08 Score=102.39 Aligned_cols=199 Identities=18% Similarity=0.159 Sum_probs=140.4
Q ss_pred CceEEEeeecccCcccceEEeeCCCCCCCceEEEeeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCc
Q 003054 344 EKKLRIGVPVKKGFSDFVNVTIDPKTQEPTSVTGYCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGE 423 (852)
Q Consensus 344 ~~~lrv~v~~~~~~~~~~~~~~d~~~~~~~~~~G~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~ 423 (852)
.++|+||+. +.+.|+ .+.+...++.+.+++++|.+ ++++... +|++++..+.+|+
T Consensus 31 ~~~l~vg~~--~~~~~~-------------~~~~~~~~l~~~l~~~~g~~--v~~~~~~--------~~~~~~~~l~~g~ 85 (254)
T TIGR01098 31 PKELNFGIL--PGENAS-------------NLTRRWEPLADYLEKKLGIK--VQLFVAT--------DYSAVIEAMRFGR 85 (254)
T ss_pred CCceEEEEC--CCCCHH-------------HHHHHHHHHHHHHHHHhCCc--EEEEeCC--------CHHHHHHHHHcCC
Confidence 457999997 555443 23345679999999999964 5554433 6999999999999
Q ss_pred ccEEEeeeeeec---Ccceeeecccccccc------ceEEEEEccCCCCCCceEeecccchhHHHHHHHHHHHHHhhhhh
Q 003054 424 FDAVVGDITIVF---NRSNYVDFTLPYTES------GVSMIVPIKDSKKRNAWVFLQPLTWDLWVTCFCFFIFIGFVVWV 494 (852)
Q Consensus 424 ~D~~~g~~~it~---~r~~~vdft~p~~~~------~~~~vv~~~~~~~~~~~~~l~PF~~~lW~~i~~~~i~~~~v~~~ 494 (852)
+|+++.+..... +|....+|+.||... ...+++++..
T Consensus 86 ~Di~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lvv~~d~---------------------------------- 131 (254)
T TIGR01098 86 VDIAWFGPSSYVLAHYRANAEVFALTAVSTDGSPGYYSVIIVKADS---------------------------------- 131 (254)
T ss_pred ccEEEECcHHHHHHHHhcCCceEEeeccccCCCCceEEEEEEECCC----------------------------------
Confidence 999986544332 456667788776543 2466666432
Q ss_pred eecccCCCCCCCcccccchhHHHHHHHhhhccccccccchhhHHHHHHHHHHHHHHHHhhhhccceeeecccCCCcCCHH
Q 003054 495 LEHRVNEDFRGPAGQQVGTSFWFSFSTMVFSQRERVISNLARIVVIVWCFVVLILTQSYTASLTSLLTVQQLQPTITDVK 574 (852)
Q Consensus 495 l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~s~~~R~v~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~i~sl~ 574 (852)
+|++++
T Consensus 132 --------------------------------------------------------------------------~i~~~~ 137 (254)
T TIGR01098 132 --------------------------------------------------------------------------PIKSLK 137 (254)
T ss_pred --------------------------------------------------------------------------CCCChH
Confidence 288999
Q ss_pred HHHhcCCeEEEEe-CchH-----HHHHHh-cCCCC----cceeecCCHhHHHHHhhcccccCceeEEEechhHHHHHHhh
Q 003054 575 MLIKRGDNVGYQK-GSFV-----LGILKQ-LGFDE----RKLVVYNSPEDCHELFQKGSVNGGIAAAFDEIPYMKLLIGQ 643 (852)
Q Consensus 575 dL~~~~~~vg~~~-~s~~-----~~~l~~-~~~~~----~~~~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~ 643 (852)
||. |++|++.. ++.. ..++.+ .+.+. .++....+..+.+++|..|+ +||.+.+.+.+..+..+
T Consensus 138 dL~--gk~I~~~~~~s~~~~~~~~~~l~~~~~~~~~~~~~~i~~~~~~~~~~~al~~G~----~Da~~~~~~~~~~~~~~ 211 (254)
T TIGR01098 138 DLK--GKTFAFGDPASTSGYLVPRYQLKKEGGLDADGFFSEVVFSGSHDASALAVANGK----VDAATNNSSAIGRLKKR 211 (254)
T ss_pred Hhc--CCEEEeeCCCCccchHhHHHHHHHhcCCChHHhhhheeecCchHHHHHHHHcCC----CCeEEecHHHHHHHHHh
Confidence 996 89999864 3321 234443 33221 34555566788999999999 99999998888777665
Q ss_pred cC---CceEeecccccccceEEEecCC-CC-chhhHHHHHHhc
Q 003054 644 YC---SKYAMIEPKFKTAGFGFVFPLH-SP-LVHDVSKAILNV 681 (852)
Q Consensus 644 ~~---~~~~~v~~~~~~~~~~~~~~k~-sp-l~~~in~~il~l 681 (852)
.. ..++++.......+++++++|+ .+ +.+.||++|+.+
T Consensus 212 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~~l~~~ 254 (254)
T TIGR01098 212 GPSDMKKVRVIWKSPLIPNDPIAVRKDLPPELKEKIRDAFLTL 254 (254)
T ss_pred CccchhheEEEEecCCCCCCCEEEECCCCHHHHHHHHHHHhhC
Confidence 42 2577777666666789999999 54 999999999864
No 109
>PRK00489 hisG ATP phosphoribosyltransferase; Reviewed
Probab=98.73 E-value=7.1e-08 Score=102.73 Aligned_cols=163 Identities=13% Similarity=0.137 Sum_probs=131.0
Q ss_pred ChhHHHHHHhcCcccEEEeeeeeecCcceeeecccc--ccccceEEEEEccCCCCCCceEeecccchhHHHHHHHHHHHH
Q 003054 411 SYNDLVYQVFLGEFDAVVGDITIVFNRSNYVDFTLP--YTESGVSMIVPIKDSKKRNAWVFLQPLTWDLWVTCFCFFIFI 488 (852)
Q Consensus 411 s~~~li~~l~~g~~D~~~g~~~it~~r~~~vdft~p--~~~~~~~~vv~~~~~~~~~~~~~l~PF~~~lW~~i~~~~i~~ 488 (852)
++.+++..|.+|++|+++++..++.+|.+.++|+.| |....+++++|...
T Consensus 52 ~~~~i~~~L~sG~vDlgi~g~~~~~er~~~v~~~~~l~~~~~~lvvvvp~~~---------------------------- 103 (287)
T PRK00489 52 RPDDIPGYVADGVVDLGITGEDLLEESGADVEELLDLGFGKCRLVLAVPEDS---------------------------- 103 (287)
T ss_pred CcHHHHHHHHcCCCCEEEcchHHHHHCCCCceEeeeccCCceEEEEEEECCC----------------------------
Confidence 578999999999999999999999999888999887 67777888888552
Q ss_pred HhhhhheecccCCCCCCCcccccchhHHHHHHHhhhccccccccchhhHHHHHHHHHHHHHHHHhhhhccceeeecccCC
Q 003054 489 GFVVWVLEHRVNEDFRGPAGQQVGTSFWFSFSTMVFSQRERVISNLARIVVIVWCFVVLILTQSYTASLTSLLTVQQLQP 568 (852)
Q Consensus 489 ~~v~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~s~~~R~v~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~ 568 (852)
T Consensus 104 -------------------------------------------------------------------------------- 103 (287)
T PRK00489 104 -------------------------------------------------------------------------------- 103 (287)
T ss_pred --------------------------------------------------------------------------------
Confidence
Q ss_pred CcCCHHHHHhcCCeEEEEeCchHHHHHHhcCCCCcceeecCCHhHHHHHhhcccccCceeEEEechhHHHHHHhhcCCce
Q 003054 569 TITDVKMLIKRGDNVGYQKGSFVLGILKQLGFDERKLVVYNSPEDCHELFQKGSVNGGIAAAFDEIPYMKLLIGQYCSKY 648 (852)
Q Consensus 569 ~i~sl~dL~~~~~~vg~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~~~~~~ 648 (852)
+|++++||. |+++++..+.....++.+.+.+ .+++.+.+..+. ++..|. ++|+++.......+.+. .+
T Consensus 104 ~i~sl~DL~--Gk~ia~~~~~~~~~~l~~~gi~-~~iv~~~gs~ea--a~~~G~----aDaivd~~~~~~~l~~~---~L 171 (287)
T PRK00489 104 DWQGVEDLA--GKRIATSYPNLTRRYLAEKGID-AEVVELSGAVEV--APRLGL----ADAIVDVVSTGTTLRAN---GL 171 (287)
T ss_pred CCCChHHhC--CCEEEEcCcHHHHHHHHHcCCc-eEEEECCCchhh--hhcCCc----ccEEEeeHHHHHHHHHC---CC
Confidence 278999996 8899998888899999887663 355666644443 566688 99999887777666553 36
Q ss_pred EeecccccccceEEEecC--CCC-chhhHHHHHHhccccChhHHHHHHHcc
Q 003054 649 AMIEPKFKTAGFGFVFPL--HSP-LVHDVSKAILNVTEGDKMKEIEDAWFK 696 (852)
Q Consensus 649 ~~v~~~~~~~~~~~~~~k--~sp-l~~~in~~il~l~e~G~~~~i~~kw~~ 696 (852)
.++ +.+.....+++.+| .+| ....+|+.+.++ .|.+..+.+||+.
T Consensus 172 ~~v-~~~~~~~~~li~~k~~~~~~~~~~i~~~l~~l--~g~l~a~~~k~~~ 219 (287)
T PRK00489 172 KIV-EVILRSEAVLIARKGWLDPEKQEKIDQLLTRL--QGVLRARESKYLM 219 (287)
T ss_pred EEE-EeeeeeeEEEEEcccccChhHHHHHHHHHHHH--HHHHHhhceEEEE
Confidence 666 45566678999999 566 778899999999 5999999999996
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=98.62 E-value=9.5e-09 Score=80.77 Aligned_cols=61 Identities=30% Similarity=0.560 Sum_probs=43.2
Q ss_pred cceEEeeC--CCCCCCceEEEeeHHHHHHHHHHCCCccceEEEecCCCCCC--CCCChhHHHHHHhc
Q 003054 359 DFVNVTID--PKTQEPTSVTGYCVDVFKAVIQELPYAVAYDFVPYGQPDGS--SSGSYNDLVYQVFL 421 (852)
Q Consensus 359 ~~~~~~~d--~~~~~~~~~~G~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~--~ngs~~~li~~l~~ 421 (852)
||++..++ +.+++. ++.|||+||++++++.|||++++..++.+ ..|. +||+|+|++++|.+
T Consensus 1 Pfvm~~~~~~~~~g~~-~~eGyciDll~~la~~l~F~y~i~~~~Dg-~yG~~~~~g~W~GmiGeli~ 65 (65)
T PF10613_consen 1 PFVMLKEDGENLTGND-RYEGYCIDLLEELAEELNFTYEIYLVPDG-KYGSKNPNGSWNGMIGELIR 65 (65)
T ss_dssp TTBEE-TTSSGSBGGG-GEESHHHHHHHHHHHHHT-EEEEEE-TTS---EEBETTSEBEHHHHHHHT
T ss_pred CeEEEecCCcccCCCc-cEEEEHHHHHHHHHHHcCCeEEEEECCCC-CCcCcCCCCcCcCHHHHhcC
Confidence 56666555 445677 99999999999999999996655554332 2332 68999999999874
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=98.16 E-value=3.5e-05 Score=88.85 Aligned_cols=217 Identities=19% Similarity=0.247 Sum_probs=120.4
Q ss_pred CccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHHHHHhCCceeeeee
Q 003054 14 QVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTDALQAIDTRVPYRS 93 (852)
Q Consensus 14 ~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~~l~~~g~~v~~~~ 93 (852)
.||++.....+..-+ -+.+|...-+...+++.+|+.+..-|+++..||+.+++||+...++|.+.+++.|++++...
T Consensus 304 ~vp~LaLN~~~~~~~---~~~l~~f~LspEdEA~q~A~~a~~~g~~~alvl~p~~~~g~R~~~aF~~~W~~~gg~~~~~~ 380 (536)
T PF04348_consen 304 PVPVLALNQPDNSQA---PPNLYQFGLSPEDEARQAAQKAFQDGYRRALVLAPQNAWGQRMAEAFNQQWQALGGQVAEVS 380 (536)
T ss_dssp T-EEEES---TT-------TTEEE----HHHHHHHHHHHHHHTT--S-EEEEESSHHHHHHHHHHHHHHHHHHSS--EEE
T ss_pred CCceeeccCCCcccC---ccceEEEeCCcHHHHHHHHHHHHhcCCCCEEEEcCCChHHHHHHHHHHHHHHHcCCCceeeE
Confidence 789999887665422 24455556677889999999999999999999999999999999999999999999887666
Q ss_pred ecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHcCCcccceEEEEcCccccccccCCchhhcccceEEE
Q 003054 94 VISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLEPSVIDSMQGVIG 173 (852)
Q Consensus 94 ~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~~~~~~~~~~~~~~~~~~gv~~ 173 (852)
.+. ...|+...+..-.+.+.|.||+.+.+.+++.|--...-. . ..+--.+.++..... ..++.....++|+..
T Consensus 381 ~~~---~~~~~~~~i~~r~r~d~D~ifl~a~~~~ar~ikP~l~~~-~-a~~lPvyatS~~~~g--~~~~~~~~dL~gv~f 453 (536)
T PF04348_consen 381 YYG---SPADLQAAIQPRRRQDIDAIFLVANPEQARLIKPQLDFH-F-AGDLPVYATSRSYSG--SPNPSQDRDLNGVRF 453 (536)
T ss_dssp EES---STTHHHHHHHHS--TT--EEEE---HHHHHHHHHHHTT--T--TT-EEEE-GGG--H--HT-HHHHHHTTT-EE
T ss_pred ecC---CHHHHHHHHhhcCCCCCCEEEEeCCHHHHHHHhhhcccc-c-CCCCCEEEeccccCC--CCCcchhhhhcCCEE
Confidence 664 246888888866667899999999999988877665432 1 111114444443221 112233456899877
Q ss_pred EE-ecC--CCChHHHHHHHHHHHhccccCCCCcccccchhhHhHhhHHHHHHHHHHHhcccCcCccccccCCCCCCCccc
Q 003054 174 VG-PHV--PKTKALENFRVRWKRNFLQENPSIVDVELNIFGLLAYDATRALAEAVEKAGITSFGFDKTNVSRNATDLEAF 250 (852)
Q Consensus 174 ~~-~~~--~~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~a~~aYDAv~~lA~Al~~a~~~~~~~~~~~~~~~~~~~~~~ 250 (852)
+. ||. +..+..+.+...|.+... ...-.-+.+|||..++.+= ..
T Consensus 454 ~d~Pwll~~~~~~~~~~~~~~~~~~~---------~~~RL~AlG~DA~~L~~~l-~~----------------------- 500 (536)
T PF04348_consen 454 SDMPWLLDPNSPLRQQLAALWPNASN---------SLQRLYALGIDAYRLAPRL-PQ----------------------- 500 (536)
T ss_dssp EE-GGGG---SHHHHHHH-HHTTT-H---------HHHHHHHHHHHHHHHHHTH-HH-----------------------
T ss_pred eccccccCCCchHHHHHHhhccCCcc---------HHHHHHHHHHHHHHHHHHH-HH-----------------------
Confidence 65 333 233444444444422111 1233456788877654321 11
Q ss_pred cccCChHHHHHHhhccceeeeeeeEEee-cCcc
Q 003054 251 GISQNGPKLLQALSSTRFKGLTGDYIFV-DGQL 282 (852)
Q Consensus 251 ~~~~~g~~l~~al~~~~f~GltG~v~f~-~G~~ 282 (852)
+....+..+.|+||.+.++ +|..
T Consensus 501 ---------l~~~~~~~~~G~TG~L~~~~~g~i 524 (536)
T PF04348_consen 501 ---------LRQFPGYRLDGLTGQLSLDEDGRI 524 (536)
T ss_dssp ---------HHHSTT--EEETTEEEEE-TT-BE
T ss_pred ---------HhhCCCCcccCCceeEEECCCCeE
Confidence 2223345789999999998 7764
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=98.09 E-value=7.6e-05 Score=80.01 Aligned_cols=115 Identities=22% Similarity=0.173 Sum_probs=75.3
Q ss_pred cCCHHHHHhcCCeEEEE-eCchHHH-----HH-HhcCCCCc---ceeecC-CHhHHHHHhhcccccCceeEEEechhHHH
Q 003054 570 ITDVKMLIKRGDNVGYQ-KGSFVLG-----IL-KQLGFDER---KLVVYN-SPEDCHELFQKGSVNGGIAAAFDEIPYMK 638 (852)
Q Consensus 570 i~sl~dL~~~~~~vg~~-~~s~~~~-----~l-~~~~~~~~---~~~~~~-~~~~~~~~l~~g~~~~g~~a~~~~~~~~~ 638 (852)
|++++||. |++|++. .++.... .+ +..+.... +.+.+. +..+.+++|..|+ ++|++.+...+.
T Consensus 127 i~sl~DL~--Gk~v~~~~~~s~~~~~~~~~~l~~~~g~~~~~~~~~v~~~~~~~~~~~al~~G~----vDa~~~~~~~~~ 200 (288)
T TIGR03431 127 IKSLEDLK--GKTFGFVDPNSTSGFLVPSYYLFKKNGIKPKEYFKKVTFSGSHEAAILAVANGT----VDAATTNDENLD 200 (288)
T ss_pred CCcHHHhC--CCEEEeeCCCcchhhHHHHHHHHHhcCCChHHhHHhheecCchHHHHHHHHcCC----CCeEeccHHHHH
Confidence 88999995 8999985 3443221 22 33333221 223444 6788999999999 999998887777
Q ss_pred HHHhhc-C---CceEeecccccccceEEEecCCC-C-chhhHHHHHHhccccChhHHH
Q 003054 639 LLIGQY-C---SKYAMIEPKFKTAGFGFVFPLHS-P-LVHDVSKAILNVTEGDKMKEI 690 (852)
Q Consensus 639 ~~~~~~-~---~~~~~v~~~~~~~~~~~~~~k~s-p-l~~~in~~il~l~e~G~~~~i 690 (852)
.+..+. . ..+.++...-.....+++++++- + +.+.++++|..+.+++..+++
T Consensus 201 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~l~~~~~~~~~~~~ 258 (288)
T TIGR03431 201 RMIRKGQPDAMEDLRIIWKSPLIPNGPIVYRKDLPADLKAKIRKAFLNYHKTDKACFE 258 (288)
T ss_pred HHHHcCCCCchhheEEEEEcCCCCCCcEEEeCCCCHHHHHHHHHHHHhcCCCcHHHHH
Confidence 666532 1 12443332112234578889984 3 999999999999999665543
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=97.69 E-value=0.0004 Score=72.72 Aligned_cols=136 Identities=12% Similarity=0.100 Sum_probs=99.8
Q ss_pred HHHhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeCC--cccccHHHHHHHHH
Q 003054 6 IIQLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDNQ--YGEEMIPSLTDALQ 83 (852)
Q Consensus 6 v~~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~~--~G~~~~~~l~~~l~ 83 (852)
..+.+.+.++|+|.+.+..+. .++++++..++...+..+++++...|-++|+++..+.. ++....+.+++.++
T Consensus 71 ~~~~l~~~~ip~v~~~~~~~~-----~~~~~~v~~d~~~~~~~~~~~l~~~g~~~i~~i~~~~~~~~~~~~~~~~~~~~~ 145 (264)
T cd01537 71 IVKLARKAGIPVVLVDRDIPD-----GDRVPSVGSDNEQAGYLAGEHLAEKGHRRIALLAGPLGSSTARERVAGFKDALK 145 (264)
T ss_pred HHHHhhhcCCCEEEeccCCCC-----CcccceEecCcHHHHHHHHHHHHHhcCCcEEEEECCCCCCcHHHHHHHHHHHHH
Confidence 356778899999998776543 35677888899999999999998889999999986544 66777899999999
Q ss_pred hCC-ceeeeeeecCCCCChHHHHHHHHHhhcCC--ceEEEEEeChhhHHHHHHHHHHcCCcccceEEEE
Q 003054 84 AID-TRVPYRSVISPLATDDQIEKELYKLFTMQ--TRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIM 149 (852)
Q Consensus 84 ~~g-~~v~~~~~~~~~~~~~d~~~~l~~l~~~~--~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~ 149 (852)
+.| .++....... .+..+....+.++.+.+ +++|++... ..+..++++++++|+..++.+-+.
T Consensus 146 ~~~~~~~~~~~~~~--~~~~~~~~~~~~~l~~~~~~~~i~~~~~-~~a~~~~~~~~~~g~~i~~~i~i~ 211 (264)
T cd01537 146 EAGPIEIVLVQEGD--WDAEKGYQAAEELLTAHPDPTAIFAAND-DMALGALRALREAGLRVPDDISVI 211 (264)
T ss_pred HcCCcChhhhccCC--CCHHHHHHHHHHHHhcCCCCCEEEEcCc-HHHHHHHHHHHHhCCCCCCCeEEE
Confidence 887 4443332222 34666777888887776 566665543 567778999999998655444444
No 114
>PRK11553 alkanesulfonate transporter substrate-binding subunit; Provisional
Probab=97.45 E-value=0.0015 Score=70.98 Aligned_cols=68 Identities=31% Similarity=0.428 Sum_probs=48.7
Q ss_pred cCCHHHHHhcCCeEEEEeCchHHHHH----HhcCCCCcce-eecCCHhHHHHHhhcccccCceeEEEechhHHHHHHhh
Q 003054 570 ITDVKMLIKRGDNVGYQKGSFVLGIL----KQLGFDERKL-VVYNSPEDCHELFQKGSVNGGIAAAFDEIPYMKLLIGQ 643 (852)
Q Consensus 570 i~sl~dL~~~~~~vg~~~~s~~~~~l----~~~~~~~~~~-~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~ 643 (852)
|++++||. |++|++..|+..+.++ ++.+++...+ ..+.+..+..++|..|+ ++|++...++......+
T Consensus 121 i~s~~dL~--Gk~I~~~~gs~~~~~l~~~l~~~g~~~~dv~~v~~~~~~~~~al~~G~----vDa~~~~ep~~~~~~~~ 193 (314)
T PRK11553 121 IKTVADLK--GHKVAFQKGSSSHNLLLRALRKAGLKFTDIQPTYLTPADARAAFQQGN----VDAWAIWDPYYSAALLQ 193 (314)
T ss_pred CCCHHHhC--CCEEeecCCCcHHHHHHHHHHHcCCCHHHeEEEecChHHHHHHHHcCC----CCEEEEcCcHHHHHHhc
Confidence 78999997 8899998887666554 4445543333 23446667889999999 99998877766655544
No 115
>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=97.41 E-value=0.0016 Score=68.18 Aligned_cols=136 Identities=10% Similarity=0.041 Sum_probs=95.4
Q ss_pred HHhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeC--CcccccHHHHHHHHHh
Q 003054 7 IQLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDN--QYGEEMIPSLTDALQA 84 (852)
Q Consensus 7 ~~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~--~~G~~~~~~l~~~l~~ 84 (852)
.+.+.+.++|+|...+..+. +.+..+..++...++.+++++...|.+++++++.+. .++....+.+.+.+++
T Consensus 71 ~~~~~~~~ipvv~~~~~~~~------~~~~~v~~d~~~~g~~~~~~l~~~g~~~i~~i~~~~~~~~~~~r~~g~~~~~~~ 144 (264)
T cd06267 71 LEELAALGIPVVLVDRPLDG------LGVDSVGIDNRAGAYLAVEHLIELGHRRIAFIGGPPDLSTARERLEGYREALEE 144 (264)
T ss_pred HHHHHHcCCCEEEecccccC------CCCCEEeeccHHHHHHHHHHHHHCCCceEEEecCCCccchHHHHHHHHHHHHHH
Confidence 45678899999998765432 455566778888888888998777999999998554 3677788899999999
Q ss_pred CCceeeeeeecCCCCChHHHHHHHHHhhcCC--ceEEEEEeChhhHHHHHHHHHHcCCcccceEEEE
Q 003054 85 IDTRVPYRSVISPLATDDQIEKELYKLFTMQ--TRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIM 149 (852)
Q Consensus 85 ~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~--~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~ 149 (852)
.|.++..........+..+....+.++.+.. +|+|+.. +...+..+.+++++.|+..++.+.|.
T Consensus 145 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~i~~~-~~~~a~~~~~al~~~g~~~~~~i~i~ 210 (264)
T cd06267 145 AGIPLDEELIVEGDFSEESGYEAARELLASGERPTAIFAA-NDLMAIGALRALRELGLRVPEDVSVV 210 (264)
T ss_pred cCCCCCcceEEecccchhhHHHHHHHHHhcCCCCcEEEEc-CcHHHHHHHHHHHHhCCCCCCceEEE
Confidence 8854432222222223456677777777666 5666644 45567888999999998644444433
No 116
>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=97.41 E-value=0.0027 Score=66.74 Aligned_cols=138 Identities=9% Similarity=0.069 Sum_probs=94.3
Q ss_pred HHHhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHc--CCcEEEEEEEeC--CcccccHHHHHHH
Q 003054 6 IIQLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAF--GWREAVPIYVDN--QYGEEMIPSLTDA 81 (852)
Q Consensus 6 v~~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~--gw~~vaii~~d~--~~G~~~~~~l~~~ 81 (852)
+.+.+.+.++|+|......+. .+.+..+.+++...+..+++++.+. |-+++++++.+. .++....+.|+++
T Consensus 72 ~~~~l~~~~ip~V~~~~~~~~-----~~~~~~v~~d~~~~~~~~~~~l~~~~~g~~~i~~i~~~~~~~~~~~r~~gf~~~ 146 (267)
T cd01536 72 ALKKANAAGIPVVTVDSDIDG-----GNRLAYVGTDNYEAGRLAGEYLAKLLGGKGKVAIIEGPPGSSNAQERVKGFRDA 146 (267)
T ss_pred HHHHHHHCCCcEEEecCCCCc-----cceeEEEecCHHHHHHHHHHHHHHHhCCCceEEEEEcccccchHHHHHHHHHHH
Confidence 345566789999998664432 2345566777778888889988666 889999998554 4788888999999
Q ss_pred HHhCC-ceeeeeeecCCCCChHHHHHHHHHhhcCCceE-EEEEeChhhHHHHHHHHHHcCCcccceEEEEcC
Q 003054 82 LQAID-TRVPYRSVISPLATDDQIEKELYKLFTMQTRV-FILHMLPSLGSRIFEKANEIGLMNKGCVWIMTD 151 (852)
Q Consensus 82 l~~~g-~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~v-iv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~ 151 (852)
+++.| .++...... +.+..+....+.++.+..+++ .+++++...+..+++++++.|+. .+...++.+
T Consensus 147 ~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~i~~~~d~~a~~~~~~l~~~g~~-~~i~ivg~d 215 (267)
T cd01536 147 LKEYPDIEIVAVQDG--NWDREKALQAMEDLLQANPDIDAIFAANDSMALGAVAALKAAGRK-GDVKIVGVD 215 (267)
T ss_pred HHhCCCcEEEEEecC--CCcHHHHHHHHHHHHHhCCCccEEEEecCCchHHHHHHHHhcCCC-CCceEEecC
Confidence 99984 665433222 233456677888877655543 23334456778899999999985 444444443
No 117
>PF12974 Phosphonate-bd: ABC transporter, phosphonate, periplasmic substrate-binding protein ; PDB: 3N5L_B 3QUJ_C 3P7I_A 3QK6_A 3S4U_A.
Probab=97.24 E-value=0.0034 Score=65.37 Aligned_cols=120 Identities=23% Similarity=0.209 Sum_probs=75.1
Q ss_pred CcCCHHHHHhcCCeEEEEeCch------HHHHH-HhcCCCCc---ceeecCCHhHHHHHhhcccccCceeEEEechhHHH
Q 003054 569 TITDVKMLIKRGDNVGYQKGSF------VLGIL-KQLGFDER---KLVVYNSPEDCHELFQKGSVNGGIAAAFDEIPYMK 638 (852)
Q Consensus 569 ~i~sl~dL~~~~~~vg~~~~s~------~~~~l-~~~~~~~~---~~~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~ 638 (852)
+|++++||. |++|++...+. ....| ++.+++.. +.+...+.++.+++|.+|+ ++|.+......+
T Consensus 96 ~i~~l~dL~--Gk~v~~~~~~s~sg~l~~~~~L~~~~Gl~~~~~~~~~~~~~~~~~~~~l~~G~----~Da~~~~~~~~~ 169 (243)
T PF12974_consen 96 PITSLADLK--GKRVAFPDPSSTSGYLIPRYELLREAGLDPGDDFKQVFVGSHDAVLEALLNGK----ADAAAIPSDAFE 169 (243)
T ss_dssp S--SHHHHG--GSEEEEE-TT-TTTTHHHHHHTCCCCT--HHHHSSEEEEE-HHHHHHHHHTTS----SSEEEEEHHHHH
T ss_pred CCCChhhcC--CCEEEEecCCccHHHHHHHHHHHHHcCCChhHceeEEEeCCHHHHHHHHHcCC----ccEEEEechhHH
Confidence 489999996 99999965442 12234 45555531 3345568888999999999 888888776666
Q ss_pred HHHhhc---CCceEeecccccccceEEEecCCCC--chhhHHHHHHhccccChhHHHHHHH
Q 003054 639 LLIGQY---CSKYAMIEPKFKTAGFGFVFPLHSP--LVHDVSKAILNVTEGDKMKEIEDAW 694 (852)
Q Consensus 639 ~~~~~~---~~~~~~v~~~~~~~~~~~~~~k~sp--l~~~in~~il~l~e~G~~~~i~~kw 694 (852)
.+.... .+.++++...-......++..++-| .++.|-++++.+..+-.-..+.+.+
T Consensus 170 ~~~~~~~~~~~~~rvl~~s~~~p~~~~~~~~~~~~~~~~~l~~al~~~~~~~~~~~~l~~~ 230 (243)
T PF12974_consen 170 RLEAEGPDIPSQLRVLWTSPPYPNWPLVASPDLPPELRQRLRDALLSLSKDPEGKAILDAF 230 (243)
T ss_dssp HHHHH-HHHHTTEEEEEEEEEEE--EEEEETTS-HHHHHHHHHHHHHTTSSHHHHHHHHHT
T ss_pred HHHHccCcccccEEEEEEeCCCCCcEEEEeCCCCHHHHHHHHHHHHcCCCChhhHHHHHhc
Confidence 665542 3456666554333455677777755 8999999999998864444555444
No 118
>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=0.0091 Score=62.76 Aligned_cols=132 Identities=13% Similarity=0.119 Sum_probs=88.2
Q ss_pred HHHhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEE---eCCcccccHHHHHHHH
Q 003054 6 IIQLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYV---DNQYGEEMIPSLTDAL 82 (852)
Q Consensus 6 v~~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~---d~~~G~~~~~~l~~~l 82 (852)
+.+.+.+.++|+|......+ ...+++ ..++...+..+++++.+.|.++++++.. +.+++....+.+.+++
T Consensus 71 ~~~~~~~~~ipvV~~~~~~~----~~~~~v---~~d~~~~g~~~~~~l~~~g~~~i~~i~~~~~~~~~~~~r~~gf~~~l 143 (266)
T cd06282 71 ALDLLDAERVPYVLAYNDPQ----PGRPSV---SVDNRAAARDVAQALAALGHRRIAMLAGRLAASDRARQRYAGYRAAM 143 (266)
T ss_pred HHHHHhhCCCCEEEEeccCC----CCCCEE---eeCcHHHHHHHHHHHHHcCcccEEEeccccccCchHHHHHHHHHHHH
Confidence 44667788999988765332 223443 4567788888999987789999999973 2346777789999999
Q ss_pred HhCCceeeeeeecCCCCChHHHHHHHHHh-hcC-CceEEEEEeChhhHHHHHHHHHHcCCcccceEE
Q 003054 83 QAIDTRVPYRSVISPLATDDQIEKELYKL-FTM-QTRVFILHMLPSLGSRIFEKANEIGLMNKGCVW 147 (852)
Q Consensus 83 ~~~g~~v~~~~~~~~~~~~~d~~~~l~~l-~~~-~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vw 147 (852)
++.|+++....... .+..+....+.++ ++. .+++|+. ++...+..+++++++.|+..++-+-
T Consensus 144 ~~~~~~~~~~~~~~--~~~~~~~~~~~~~l~~~~~~~ai~~-~~d~~a~g~~~al~~~g~~~p~di~ 207 (266)
T cd06282 144 RAAGLAPLPPVEIP--FNTAALPSALLALLTAHPAPTAIFC-SNDLLALAVIRALRRLGLRVPDDLS 207 (266)
T ss_pred HHcCCCCCccccCC--CcHHHHHHHHHHHhcCCCCCCEEEE-CCcHHHHHHHHHHHHcCCCCCCceE
Confidence 99988654332222 2233334445544 332 4677666 5566778899999999986554443
No 119
>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=96.88 E-value=0.0034 Score=67.66 Aligned_cols=68 Identities=26% Similarity=0.258 Sum_probs=48.5
Q ss_pred cCCHHHHHhcCCeEEEEeCchHHH----HHHhcCCCCcceeec-CCHhHHHHHhhcccccCceeEEEechhHHHHHHhh
Q 003054 570 ITDVKMLIKRGDNVGYQKGSFVLG----ILKQLGFDERKLVVY-NSPEDCHELFQKGSVNGGIAAAFDEIPYMKLLIGQ 643 (852)
Q Consensus 570 i~sl~dL~~~~~~vg~~~~s~~~~----~l~~~~~~~~~~~~~-~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~ 643 (852)
|++++||. |++||+..++..+. +|++.+.+...+..+ -.+.+...+|.+|+ ++|++...++......+
T Consensus 92 I~s~~DLk--GK~Igv~~~s~~~~~l~~~L~~~Gl~~~dv~~v~~~~~~~~~al~~G~----vDa~~~~~p~~~~~~~~ 164 (300)
T TIGR01729 92 IEKPEDLK--GKNVAVPFVSTTHYSLLAALKHWKTDPREVNILNLKPPQIVAAWQRGD----IDAAYVWPPALSELLKS 164 (300)
T ss_pred CCChhHcC--CCEEEeCCCCcHHHHHHHHHHHcCCChhheEEEecCcHHHHHHHHcCC----cCEEEEecHHHHHHHhc
Confidence 89999997 99999987765443 455555554333222 24567899999999 99998888776655543
No 120
>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=96.87 E-value=0.014 Score=61.58 Aligned_cols=128 Identities=9% Similarity=0.058 Sum_probs=89.7
Q ss_pred HHHhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHc--CCcEEEEEEEe--CCcccccHHHHHHH
Q 003054 6 IIQLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAF--GWREAVPIYVD--NQYGEEMIPSLTDA 81 (852)
Q Consensus 6 v~~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~--gw~~vaii~~d--~~~G~~~~~~l~~~ 81 (852)
+...+.+.++|+|...... +. +.++++.+++...+..+++++.+. |-++++++..+ ...+....+.++++
T Consensus 77 ~l~~~~~~~iPvv~~~~~~---~~---~~~~~v~~d~~~~g~~~~~~l~~~~~g~~~i~~i~~~~~~~~~~~R~~g~~~a 150 (272)
T cd06300 77 VIEEACEAGIPVVSFDGTV---TT---PCAYNVNEDQAEFGKQGAEWLVKELGGKGNVLVVRGLAGHPVDEDRYAGAKEV 150 (272)
T ss_pred HHHHHHHCCCeEEEEecCC---CC---CceeEecCCHHHHHHHHHHHHHHHcCCCceEEEEECCCCCcchHHHHHHHHHH
Confidence 3455667899999986532 11 456778888888999999988665 88999999733 34556677889999
Q ss_pred HHhCC-ceeeeeeecCCCCChHHHHHHHHHhhcCCc--eEEEEEeChhhHHHHHHHHHHcCCccc
Q 003054 82 LQAID-TRVPYRSVISPLATDDQIEKELYKLFTMQT--RVFILHMLPSLGSRIFEKANEIGLMNK 143 (852)
Q Consensus 82 l~~~g-~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~--~viv~~~~~~~~~~i~~~a~~~G~~~~ 143 (852)
+++.| +++..... .+.+.++....+.++.+..+ ++|++.... +..+++.+++.|+..+
T Consensus 151 ~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~l~~~~~~~~i~~~~d~--A~g~~~al~~~g~~~p 211 (272)
T cd06300 151 LKEYPGIKIVGEVY--GDWDQAVAQKAVADFLASNPDVDGIWTQGGD--AVGAVQAFEQAGRDIP 211 (272)
T ss_pred HHHCCCcEEEeecC--CCCCHHHHHHHHHHHHHhCCCcCEEEecCCC--cHHHHHHHHHcCCCCc
Confidence 99887 77653322 22334556677777776655 555544333 8899999999998544
No 121
>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=96.79 E-value=0.019 Score=60.50 Aligned_cols=134 Identities=16% Similarity=0.125 Sum_probs=88.6
Q ss_pred HHhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEe---CCcccccHHHHHHHHH
Q 003054 7 IQLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVD---NQYGEEMIPSLTDALQ 83 (852)
Q Consensus 7 ~~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d---~~~G~~~~~~l~~~l~ 83 (852)
...+.+.++|+|......+. ...+| ...++...+..+++++...|.++|++|... +.++......|.++++
T Consensus 71 ~~~l~~~~iPvv~~~~~~~~---~~~~~---v~~d~~~~~~~~~~~l~~~g~~~i~~i~~~~~~~~~~~~r~~gf~~~l~ 144 (268)
T cd06273 71 LDLLARRGVPYVATWNYSPD---SPYPC---VGFDNREAGRLAARHLIALGHRRIAMIFGPTQGNDRARARRAGVRAALA 144 (268)
T ss_pred HHHHHhCCCCEEEEcCCCCC---CCCCE---EEeChHHHHHHHHHHHHHCCCCeEEEEeccccCCccHHHHHHHHHHHHH
Confidence 34566789999987653221 22343 346777888889998877799999999732 2356677899999999
Q ss_pred hCCceeeeeeecCCCCChHHHHHHHHHhhc--CCceEEEEEeChhhHHHHHHHHHHcCCcccceEE
Q 003054 84 AIDTRVPYRSVISPLATDDQIEKELYKLFT--MQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVW 147 (852)
Q Consensus 84 ~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~--~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vw 147 (852)
+.|+++.....+..+.+.++-...+.++.+ ..+++|+. ++...+..+++++++.|+..++-+-
T Consensus 145 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~-~~~~~a~~~~~~l~~~g~~~p~~i~ 209 (268)
T cd06273 145 EAGLELPELWQVEAPYSIADGRAALRQLLEQPPRPTAVIC-GNDVLALGALYEARRLGLSVPEDLS 209 (268)
T ss_pred HcCCCCCHHHeeeCCCcHHHHHHHHHHHHcCCCCCCEEEE-cChHHHHHHHHHHHHcCCCCCCceE
Confidence 998765432222211223334455666554 34777775 5666788899999999986554443
No 122
>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=96.70 E-value=0.0099 Score=64.45 Aligned_cols=68 Identities=22% Similarity=0.232 Sum_probs=49.7
Q ss_pred cCCHHHHHhcCCeEEEEeCchHHHH----HHhcCCCCcceeecC-CHhHHHHHhhcccccCceeEEEechhHHHHHHhh
Q 003054 570 ITDVKMLIKRGDNVGYQKGSFVLGI----LKQLGFDERKLVVYN-SPEDCHELFQKGSVNGGIAAAFDEIPYMKLLIGQ 643 (852)
Q Consensus 570 i~sl~dL~~~~~~vg~~~~s~~~~~----l~~~~~~~~~~~~~~-~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~ 643 (852)
|++++||. |++||+..|+..+-+ |++.+.....+...+ ++.+...++.+|+ +||+....++......+
T Consensus 98 i~svaDLK--GKkIav~~gs~~~~ll~~aL~~aGL~~~DV~~v~~~~~d~~aAl~~G~----VDAa~~~eP~~s~~~~~ 170 (328)
T TIGR03427 98 GKSLADLK--GQKVNLVELSVSHYLLARALESVGLSEKDVKVVNTSDADIVAAFITKD----VTAVVTWNPQLSEIKAQ 170 (328)
T ss_pred CCCHHHcC--CCEEeccCCChHHHHHHHHHHHcCCCHHHeEEEeCChHHHHHHHhcCC----CcEEEEcCchHHHHHhC
Confidence 89999997 999999999876544 445566543333222 4577899999999 99999888876655543
No 123
>PF13379 NMT1_2: NMT1-like family; PDB: 2G29_A 3UN6_A 2I4C_A 2I49_A 2I4B_A 2I48_A 3QSL_A.
Probab=96.57 E-value=0.0078 Score=63.05 Aligned_cols=71 Identities=25% Similarity=0.263 Sum_probs=49.2
Q ss_pred CcCCHHHHHh-----cCCeEEE-EeCchHH----HHHHhcCCCC---cceeecCCHhHHHHHhhcccccCceeEEEechh
Q 003054 569 TITDVKMLIK-----RGDNVGY-QKGSFVL----GILKQLGFDE---RKLVVYNSPEDCHELFQKGSVNGGIAAAFDEIP 635 (852)
Q Consensus 569 ~i~sl~dL~~-----~~~~vg~-~~~s~~~----~~l~~~~~~~---~~~~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~ 635 (852)
.+++++||.+ .|++|++ ..|+... .+|++.+.+. .+++..+. .+..+++..|+ +++++...+
T Consensus 105 ~~~~~~dl~~~~~~~kGk~i~~~~~gs~~~~~l~~~l~~~Gl~~~~dv~~~~~~~-~~~~~al~~g~----iDa~~~~eP 179 (252)
T PF13379_consen 105 DIKSLADLIKKRKAQKGKKIAVPFPGSTHDMLLRYLLKKAGLDPKDDVTLVNVPP-PEMVAALRAGE----IDAAVLWEP 179 (252)
T ss_dssp TTCCGHHHHHTCCSCSTEEEEESSTTSHHHHHHHHHHHHTT--TTTSSEEEE--G-HHHHHHHHTTS-----SEEEEETT
T ss_pred CccCHHHHHhhhcccCCcEEEEcCCCCHHHHHHHHHHHhCCCCcccceEEEecCH-HHHHHHHhCCC----cCEEEecCC
Confidence 3899999943 4889999 5556443 3455666655 45555555 89999999999 999999888
Q ss_pred HHHHHHhhc
Q 003054 636 YMKLLIGQY 644 (852)
Q Consensus 636 ~~~~~~~~~ 644 (852)
+......+.
T Consensus 180 ~~~~~~~~g 188 (252)
T PF13379_consen 180 FASQAEAKG 188 (252)
T ss_dssp HHHHHHHTT
T ss_pred HHHHHHhcc
Confidence 887777655
No 124
>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=96.39 E-value=0.031 Score=59.32 Aligned_cols=125 Identities=11% Similarity=0.139 Sum_probs=86.9
Q ss_pred cCCCCccEEeeecCCCCCC----CCCCCceEeccCCchhHHHHHHHHHHHc--CCcEEEEEEEeC-CcccccHHHHHHHH
Q 003054 10 GNKSQVPILSFSATSPSLT----SIRSPYFFRGSLNDSSQAGAITAIIKAF--GWREAVPIYVDN-QYGEEMIPSLTDAL 82 (852)
Q Consensus 10 ~~~~~vP~Is~~ats~~lt----~~~~py~fR~~p~d~~~~~aia~~l~~~--gw~~vaii~~d~-~~G~~~~~~l~~~l 82 (852)
..+.++|+|.++..++... ....+..+.+..++...+..+++++.+. |.+++++++.+. .++....+.+++++
T Consensus 77 ~~~~~iPvV~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~g~~~i~~l~~~~~~~~~~r~~g~~~~~ 156 (281)
T cd06325 77 NATKDIPIVFTAVTDPVGAGLVKSLEKPGGNVTGVSDLVPVETQLELLKKLLPDAKTVGVLYNPSEANSVVQVKELKKAA 156 (281)
T ss_pred HcCCCCCEEEEecCCccccccccccccCCCceeCeecccchHHHHHHHHHHCCCCcEEEEEeCCCCccHHHHHHHHHHHH
Confidence 5578999999875543211 1112222334456677778888888765 999999998544 37777789999999
Q ss_pred HhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHcCC
Q 003054 83 QAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEIGL 140 (852)
Q Consensus 83 ~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~G~ 140 (852)
++.|+++.... . ....++...++++.+ ++|+|++.. ...+..+++++++.|+
T Consensus 157 ~~~g~~~~~~~-~---~~~~~~~~~~~~~~~-~~dai~~~~-d~~a~~~~~~~~~~~~ 208 (281)
T cd06325 157 AKLGIEVVEAT-V---SSSNDVQQAAQSLAG-KVDAIYVPT-DNTVASAMEAVVKVAN 208 (281)
T ss_pred HhCCCEEEEEe-c---CCHHHHHHHHHHhcc-cCCEEEEcC-chhHHhHHHHHHHHHH
Confidence 99999876542 1 235677788888875 478877654 4567788888888876
No 125
>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=96.34 E-value=0.047 Score=57.36 Aligned_cols=139 Identities=14% Similarity=0.061 Sum_probs=89.3
Q ss_pred HHHhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEe---CCcccccHHHHHHHH
Q 003054 6 IIQLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVD---NQYGEEMIPSLTDAL 82 (852)
Q Consensus 6 v~~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d---~~~G~~~~~~l~~~l 82 (852)
+...+.+.++|+|......+ ....+| +.+++...++.+++++...|-++++++..+ ..++....+.|++++
T Consensus 70 ~~~~l~~~~ipvV~~~~~~~---~~~~~~---v~~d~~~~~~~~~~~l~~~g~~~i~~l~~~~~~~~~~~~r~~gf~~~~ 143 (268)
T cd06298 70 HREEFKRSPTPVVLAGSVDE---DNELPS---VNIDYKKAAFEATELLIKNGHKKIAFISGPLEDSINGDERLAGYKEAL 143 (268)
T ss_pred HHHHHhcCCCCEEEEccccC---CCCCCE---EEECcHHHHHHHHHHHHHcCCceEEEEeCCcccccchhHHHHHHHHHH
Confidence 34445667999998865322 112233 456777778888898877899999999843 336778889999999
Q ss_pred HhCCceeeeeeecCCCCChHHHHHHHHHhhcCC-ceEEEEEeChhhHHHHHHHHHHcCCcccceE-EEEcC
Q 003054 83 QAIDTRVPYRSVISPLATDDQIEKELYKLFTMQ-TRVFILHMLPSLGSRIFEKANEIGLMNKGCV-WIMTD 151 (852)
Q Consensus 83 ~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~-~~viv~~~~~~~~~~i~~~a~~~G~~~~~~v-wi~~~ 151 (852)
++.|+++.....+..+.+.......+.++.+.. +++|++ ++...+..+++.+++.|+..++-+ +++.+
T Consensus 144 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~ai~~-~~d~~a~~~~~~l~~~g~~vp~di~vvg~d 213 (268)
T cd06298 144 SEANIEFDESLIFEGDYTYESGYELAEELLEDGKPTAAFV-TDDELAIGILNAAQDAGLKVPEDFEIIGFN 213 (268)
T ss_pred HHcCCCCCHHHeEeCCCChhHHHHHHHHHhcCCCCCEEEE-cCcHHHHHHHHHHHHcCCCCccceEEEeec
Confidence 999876532211111111222334555665544 788776 455567889999999998755443 44433
No 126
>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=96.25 E-value=0.085 Score=55.75 Aligned_cols=137 Identities=9% Similarity=0.055 Sum_probs=85.9
Q ss_pred HHhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHc--CCcEEEEEEEeC--CcccccHHHHHHHH
Q 003054 7 IQLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAF--GWREAVPIYVDN--QYGEEMIPSLTDAL 82 (852)
Q Consensus 7 ~~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~--gw~~vaii~~d~--~~G~~~~~~l~~~l 82 (852)
...+.+.++|+|...... .....+| +..++...++.+++++... |.++++++.... .......+.+.+++
T Consensus 75 ~~~~~~~~iPvV~~~~~~---~~~~~~~---V~~d~~~~g~~~~~~l~~~~~g~~~i~~l~~~~~~~~~~~r~~g~~~~~ 148 (275)
T cd06320 75 VERAKKKGIPVVNVNDKL---IPNATAF---VGTDNKANGVRGAEWIIDKLAEGGKVAIIEGKAGAFAAEQRTEGFTEAI 148 (275)
T ss_pred HHHHHHCCCeEEEECCCC---CCccceE---EecCcHHHHHHHHHHHHHHhCCCceEEEEeCCCCCccHHHHHHHHHHHH
Confidence 455667899999875532 1111222 4667777788888988655 889999997432 23355568899999
Q ss_pred HhC-CceeeeeeecCCCCChHHHHHHHHHhhcCCceEEE-EEeChhhHHHHHHHHHHcCCcccceEEEEcCc
Q 003054 83 QAI-DTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFI-LHMLPSLGSRIFEKANEIGLMNKGCVWIMTDG 152 (852)
Q Consensus 83 ~~~-g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv-~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~ 152 (852)
++. |+++..... .+.+..+....+.++.+..+++-. ++.+...+..+++.+++.|+. .+...++.++
T Consensus 149 ~~~~~~~~~~~~~--~~~~~~~~~~~~~~~l~~~~~~~ai~~~~d~~a~~~~~al~~~g~~-~di~vig~d~ 217 (275)
T cd06320 149 KKASGIEVVASQP--ADWDREKAYDVATTILQRNPDLKAIYCNNDTMALGVVEAVKNAGKQ-GKVLVVGTDG 217 (275)
T ss_pred hhCCCcEEEEecC--CCccHHHHHHHHHHHHHhCCCccEEEECCchhHHHHHHHHHhcCCC-CCeEEEecCC
Confidence 998 888754322 122334455567676655544333 334555677888999999984 3333444433
No 127
>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=96.12 E-value=0.084 Score=57.55 Aligned_cols=132 Identities=13% Similarity=0.066 Sum_probs=85.9
Q ss_pred HHhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeC--C-cccccHHHHHHHHH
Q 003054 7 IQLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDN--Q-YGEEMIPSLTDALQ 83 (852)
Q Consensus 7 ~~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~--~-~G~~~~~~l~~~l~ 83 (852)
...+.+.++|+|......+ ....++ ...++..-+..+++++...|.++++++..+. . .+....+.|.++++
T Consensus 131 ~~~l~~~~iPvV~~~~~~~---~~~~~~---V~~D~~~~~~~a~~~L~~~G~~~I~~i~g~~~~~~~~~~R~~Gf~~~l~ 204 (329)
T TIGR01481 131 REEFSRSPVPVVLAGTVDK---ENELPS---VNIDYKQATKEAVGELIAKGHKSIAFVGGPLSDSINGEDRLEGYKEALN 204 (329)
T ss_pred HHHHHhcCCCEEEEecCCC---CCCCCE---EEECcHHHHHHHHHHHHHCCCCeEEEEecCcccccchHHHHHHHHHHHH
Confidence 3445667899988754321 122232 4556666677888888888999999996322 2 34667889999999
Q ss_pred hCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHcCCcccce
Q 003054 84 AIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEIGLMNKGC 145 (852)
Q Consensus 84 ~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~ 145 (852)
+.|+++........+.+..+-...+.++.+..|++|++ .+...+..+++++++.|+..|+-
T Consensus 205 ~~g~~~~~~~~~~~~~~~~~~~~~~~~ll~~~p~ai~~-~~d~~A~g~~~al~~~g~~vP~d 265 (329)
T TIGR01481 205 KAGIQFGEDLVCEGKYSYDAGYKAFAELKGSLPTAVFV-ASDEMAAGILNAAMDAGIKVPED 265 (329)
T ss_pred HcCCCCCcceEEecCCChHHHHHHHHHHhCCCCCEEEE-cCcHHHHHHHHHHHHcCCCCCCc
Confidence 99986543222211112223344566666667888776 45567889999999999865543
No 128
>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=96.09 E-value=0.093 Score=55.46 Aligned_cols=141 Identities=9% Similarity=0.056 Sum_probs=84.6
Q ss_pred HHHHhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHc------CCcEEEEEEEe--CCcccccHH
Q 003054 5 FIIQLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAF------GWREAVPIYVD--NQYGEEMIP 76 (852)
Q Consensus 5 ~v~~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~------gw~~vaii~~d--~~~G~~~~~ 76 (852)
.+.+.+.+.++|+|...... . ...++..+.+++..-+..+++++.+. |-++++++..+ ...+....+
T Consensus 71 ~~l~~~~~~~ipvV~~~~~~---~--~~~~~~~v~~d~~~~g~~~~~~l~~~~~~~~~g~~~i~~i~~~~~~~~~~~r~~ 145 (277)
T cd06319 71 TLLKLAAQAKIPVVIADIGA---E--GGDYVSYIKSDNYEGAYDLGKFLAAAMKAQGWADGKVGMVAIPQKRKNGQKRTK 145 (277)
T ss_pred HHHHHHHHCCCCEEEEecCC---C--CCceEEEEeeccHHHHHHHHHHHHHHHHhhCCCCCcEEEEeccCCCccHHHHHH
Confidence 34566777899999875421 1 11233445556666666777766443 67899999743 345677788
Q ss_pred HHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEE-EEEeChhhHHHHHHHHHHcCCcccceEEEEcCc
Q 003054 77 SLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVF-ILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDG 152 (852)
Q Consensus 77 ~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vi-v~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~ 152 (852)
.+++++++.|.++.... ...+.+..+-...+.++.+..++.- +++.+...+..+++++++.|+. ++...++-++
T Consensus 146 gf~~~l~~~~~~~~~~~-~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~~d~~a~g~~~al~~~g~~-~di~vvg~d~ 220 (277)
T cd06319 146 GFKEAMKEAGCDLAGIR-QQKDFSYQETFDYTNDLLTANPDIRAIWLQGSDRYQGALDAIATAGKT-GKVLLICFDA 220 (277)
T ss_pred HHHHHHHhcCCceEeec-cCCCCCHHHHHHHHHHHHHhCCCCCEEEECCCccchHHHHHHHHcCCC-CCEEEEEcCC
Confidence 99999999998754221 1112222333455666655555432 3334555567899999999985 3333444433
No 129
>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=95.86 E-value=0.14 Score=53.80 Aligned_cols=135 Identities=7% Similarity=0.072 Sum_probs=83.0
Q ss_pred HhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHc--CCcEEEEEEE--eCCcccccHHHHHHHHH
Q 003054 8 QLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAF--GWREAVPIYV--DNQYGEEMIPSLTDALQ 83 (852)
Q Consensus 8 ~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~--gw~~vaii~~--d~~~G~~~~~~l~~~l~ 83 (852)
..+.+.++|+|......+ ..+.+-.+..++...+..+++++... |-+++++++. +..++....+.+.++++
T Consensus 74 ~~l~~~~ipvv~~~~~~~-----~~~~~~~v~~d~~~~~~~~~~~l~~~~~g~~~i~~l~~~~~~~~~~~r~~g~~~~l~ 148 (268)
T cd06323 74 KAANEAGIPVFTIDREAN-----GGEVVSQIASDNVAGGKMAAEYLVKLLGGKGKVVELQGIPGASAARERGKGFHEVVD 148 (268)
T ss_pred HHHHHCCCcEEEEccCCC-----CCceEEEEccCcHHHHHHHHHHHHHHhCCCceEEEEeCCCCCccHHHHHHHHHHHHH
Confidence 445677999999865322 11223334555556678888888665 7899999985 33456777889999999
Q ss_pred hC-CceeeeeeecCCCCChHHHHHHHHHhhcCC--ceEEEEEeChhhHHHHHHHHHHcCCcccceEEEEcCc
Q 003054 84 AI-DTRVPYRSVISPLATDDQIEKELYKLFTMQ--TRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDG 152 (852)
Q Consensus 84 ~~-g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~--~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~ 152 (852)
+. |+++....... .+..+....+.++.+.. +++| ++.+...+..+++++++.|. ++..+++.+.
T Consensus 149 ~~~~~~~~~~~~~~--~~~~~~~~~~~~~l~~~~~~~ai-~~~~d~~a~~~~~~l~~~g~--~di~iig~d~ 215 (268)
T cd06323 149 KYPGLKVVASQPAD--FDRAKGLNVMENILQAHPDIKGV-FAQNDEMALGAIEALKAAGK--DDVKVVGFDG 215 (268)
T ss_pred hCCCcEEEecccCC--CCHHHHHHHHHHHHHHCCCcCEE-EEcCCchHHHHHHHHHHcCC--CCcEEEEeCC
Confidence 84 77765322212 22233334555555444 4553 34455566678999999998 4444554433
No 130
>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=95.80 E-value=0.13 Score=54.11 Aligned_cols=132 Identities=17% Similarity=0.160 Sum_probs=82.8
Q ss_pred HHHhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeCCcc--cccHHHHHHHHH
Q 003054 6 IIQLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDNQYG--EEMIPSLTDALQ 83 (852)
Q Consensus 6 v~~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~~~G--~~~~~~l~~~l~ 83 (852)
+.+.+...++|+|......+. ...++ ...+....++.+++++...|.++++++..+..+. ....+.|.++++
T Consensus 72 ~~~~~~~~~ipvv~i~~~~~~---~~~~~---V~~d~~~~g~~a~~~l~~~g~~~i~~i~~~~~~~~~~~R~~Gf~~~~~ 145 (270)
T cd01545 72 LLDLLDEAGVPYVRIAPGTPD---PDSPC---VRIDDRAAAREMTRHLIDLGHRRIAFIAGPPDHRASAERLEGYRDALA 145 (270)
T ss_pred HHHHHHhcCCCEEEEecCCCC---CCCCe---EEeccHHHHHHHHHHHHHCCCceEEEEeCCCCchhHHHHHHHHHHHHH
Confidence 345566788999988664332 22233 2346666668888888778999999998555443 344678999999
Q ss_pred hCCceeeeeeecCCCCChHHHHHHHHHhhc--CCceEEEEEeChhhHHHHHHHHHHcCCcccc
Q 003054 84 AIDTRVPYRSVISPLATDDQIEKELYKLFT--MQTRVFILHMLPSLGSRIFEKANEIGLMNKG 144 (852)
Q Consensus 84 ~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~--~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~ 144 (852)
+.|.++........+.+..+-...+.++.+ .++++|++ ++...+..+++.+++.|...++
T Consensus 146 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~i~~-~~d~~a~~~~~~~~~~g~~~p~ 207 (270)
T cd01545 146 EAGLPLDPELVAQGDFTFESGLEAAEALLALPDRPTAIFA-SNDDMAAGVLAVAHRRGLRVPD 207 (270)
T ss_pred HcCCCCChhhEEeCCCChhhHHHHHHHHHhCCCCCCEEEE-cCcHHHHHHHHHHHHcCCCCCC
Confidence 888765211111111111222244555543 35677774 5567788999999999986554
No 131
>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=95.68 E-value=0.14 Score=54.53 Aligned_cols=69 Identities=23% Similarity=0.319 Sum_probs=48.2
Q ss_pred CcCCHHHHHhcCCeEEEEeCchHHH----HHHhcCCCCccee-ecCCHhHHHHHhhcccccCceeEEEechhHHHHHHhh
Q 003054 569 TITDVKMLIKRGDNVGYQKGSFVLG----ILKQLGFDERKLV-VYNSPEDCHELFQKGSVNGGIAAAFDEIPYMKLLIGQ 643 (852)
Q Consensus 569 ~i~sl~dL~~~~~~vg~~~~s~~~~----~l~~~~~~~~~~~-~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~ 643 (852)
+|++++||. |++|++..++.... +|++.+.+...+. .+.+..+..+++.+|+ +++++...++...+..+
T Consensus 92 ~i~s~~dL~--Gk~i~~~~~~~~~~~~~~~l~~~G~~~~~v~~~~~~~~~~~~al~~g~----vda~~~~~p~~~~~~~~ 165 (288)
T TIGR01728 92 PIRTVADLK--GKRIAVPKGGSGHDLLLRALLKAGLSGDDVTILYLGPSDARAAFAAGQ----VDAWAIWEPWGSALVEE 165 (288)
T ss_pred CCCCHHHcC--CCEEEecCCccHHHHHHHHHHHcCCCccceeEEecCcHHHHHHHHCCC----CCEEEeccchHhHHhhc
Confidence 388999997 88999977764433 3444555543332 3345678899999999 89998877776665544
No 132
>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=95.64 E-value=0.2 Score=52.87 Aligned_cols=129 Identities=12% Similarity=0.132 Sum_probs=85.2
Q ss_pred HHhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHH-cCCcEEEEEEEe--CCcccccHHHHHHHHH
Q 003054 7 IQLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKA-FGWREAVPIYVD--NQYGEEMIPSLTDALQ 83 (852)
Q Consensus 7 ~~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~-~gw~~vaii~~d--~~~G~~~~~~l~~~l~ 83 (852)
...+.+.++|+|......+..+ ..+.+..+..++...+..+++++.+ .|-++++++..+ +..+....+.+.++++
T Consensus 75 l~~~~~~~ipvV~~~~~~~~~~--~~~~~~~V~~d~~~~g~~~~~~l~~~~g~~~i~~i~g~~~~~~~~~r~~g~~~~~~ 152 (271)
T cd06312 75 IKRAVAAGIPVISFNAGDPKYK--ELGALAYVGQDEYAAGEAAGERLAELKGGKNVLCVIHEPGNVTLEDRCAGFADGLG 152 (271)
T ss_pred HHHHHHCCCeEEEeCCCCCccc--cccceEEeccChHHHHHHHHHHHHHhcCCCeEEEEecCCCCccHHHHHHHHHHHHH
Confidence 3445677999999865332221 1245566778888999999999877 899999999743 3345667888999999
Q ss_pred hCCceeeeeeecCCCCChHHHHHHHHHhhcC--CceEEEEEeChhhHHHHHHHHHHcCCc
Q 003054 84 AIDTRVPYRSVISPLATDDQIEKELYKLFTM--QTRVFILHMLPSLGSRIFEKANEIGLM 141 (852)
Q Consensus 84 ~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~--~~~viv~~~~~~~~~~i~~~a~~~G~~ 141 (852)
+.|+.+... ....+..+....+.++.+. ++++|++ .+...+..+++.+++.|+.
T Consensus 153 ~~~~~~~~~---~~~~~~~~~~~~~~~~l~~~~~~~aI~~-~~d~~a~g~~~al~~~g~~ 208 (271)
T cd06312 153 GAGITEEVI---ETGADPTEVASRIAAYLRANPDVDAVLT-LGAPSAAPAAKALKQAGLK 208 (271)
T ss_pred hcCceeeEe---ecCCCHHHHHHHHHHHHHhCCCccEEEE-eCCccchHHHHHHHhcCCC
Confidence 888754321 1112233444555555433 3565544 3455677888889999985
No 133
>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=95.59 E-value=0.22 Score=52.48 Aligned_cols=140 Identities=14% Similarity=0.087 Sum_probs=81.2
Q ss_pred HHhcCCCCccEEeeecCCCCCCCCCCCceEecc-CCchhHHHHHHHHHHHc--CCcEEEEEEEeCCc--ccccHHHHHHH
Q 003054 7 IQLGNKSQVPILSFSATSPSLTSIRSPYFFRGS-LNDSSQAGAITAIIKAF--GWREAVPIYVDNQY--GEEMIPSLTDA 81 (852)
Q Consensus 7 ~~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~-p~d~~~~~aia~~l~~~--gw~~vaii~~d~~~--G~~~~~~l~~~ 81 (852)
...+.+.++|+|...... .....++++... +++...++.+++.+.+. |-++|+++..+.++ +....+.++++
T Consensus 74 l~~~~~~~iPvV~~~~~~---~~~~~~~v~~~v~~d~~~~g~~~~~~l~~~~~g~~~i~~l~~~~~~~~~~~r~~g~~~~ 150 (275)
T cd06317 74 LRKAKQAGIPVVITNSNI---SEKGFEFIKSFTGPDDISQGERSAEAMCKALGGKGQIVVIAGQPGNGTAIERQKGFEDE 150 (275)
T ss_pred HHHHHHCCCcEEEeCCCC---CCCccchhhhhccccHHHHHHHHHHHHHHHcCCCceEEEEecCCCCchHHHHHHHHHHH
Confidence 345677899999876532 222345554333 34445666777776444 77899999854443 34456889999
Q ss_pred HHhCCceeeeeeecCCCCChHHHHHHHHHhhc---CCceEEEEEeChhhHHHHHHHHHHcCCcccceEEEEcC
Q 003054 82 LQAIDTRVPYRSVISPLATDDQIEKELYKLFT---MQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTD 151 (852)
Q Consensus 82 l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~---~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~ 151 (852)
+++.|..+..........+..+....+.++.+ ..+++|++ .+...+..+++++++.|+. .+...++.+
T Consensus 151 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~ai~~-~~d~~a~g~~~~l~~~g~~-~dv~v~g~d 221 (275)
T cd06317 151 LAEVCPGVEVLDTQPADWDREKAQVAMEALITKFGDDIDGVYA-GDDNMARGALNAAKEAGLA-GGIVIVGAN 221 (275)
T ss_pred HHhhCCCCEEEeccCCCCCHHHHHHHHHHHHHhCCCCccEEEE-CCCcHHHHHHHHHHhcCCc-CCcEEEEeC
Confidence 99986433222222111112233333444332 34677775 4455678899999999985 333344433
No 134
>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=95.52 E-value=0.071 Score=54.17 Aligned_cols=56 Identities=27% Similarity=0.442 Sum_probs=39.9
Q ss_pred cCCHHHHHhcCCeEEEEeCchHH----HHHHhcCCCCcceeecC-CHhHHHHHhhcccccCceeEEE
Q 003054 570 ITDVKMLIKRGDNVGYQKGSFVL----GILKQLGFDERKLVVYN-SPEDCHELFQKGSVNGGIAAAF 631 (852)
Q Consensus 570 i~sl~dL~~~~~~vg~~~~s~~~----~~l~~~~~~~~~~~~~~-~~~~~~~~l~~g~~~~g~~a~~ 631 (852)
|++++||. |++||+..++... .+|++.+++...+.... +..+...+|.+|+ ++|++
T Consensus 85 i~~~~DLk--GK~i~v~~~s~~~~~~~~~l~~~g~~~~~v~~v~~~~~~~~~al~~g~----vDa~~ 145 (216)
T PF09084_consen 85 IKSPADLK--GKKIGVSRGSSSEYFLRALLKKNGIDPDDVKIVNLGPPELAQALLSGQ----VDAAI 145 (216)
T ss_dssp -SSGGGGT--TSEEEESTTSHHHHHHHHHHHHTTT-GGGSEEEES-HHHHHHHHHTTS----SSEEE
T ss_pred CCCHHHhC--CCEEEEecCcchhHHHHHHHHHhccccccceeeeeehhhhhhhhhcCC----CCEEE
Confidence 89999997 9999998876443 44566777666555433 3566777999999 89888
No 135
>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=95.50 E-value=0.16 Score=53.63 Aligned_cols=134 Identities=13% Similarity=0.054 Sum_probs=84.0
Q ss_pred HhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeC--CcccccHHHHHHHHHhC
Q 003054 8 QLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDN--QYGEEMIPSLTDALQAI 85 (852)
Q Consensus 8 ~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~--~~G~~~~~~l~~~l~~~ 85 (852)
..+...++|+|.++...+. ...+ .+.+++...+..+++++...|.++++++..+. ..+....+.|.+++++.
T Consensus 81 ~~~~~~~ipvV~~~~~~~~---~~~~---~V~~d~~~~g~~~a~~l~~~g~~~i~~i~~~~~~~~~~~r~~gf~~~~~~~ 154 (275)
T cd06295 81 ERLAETGLPFVVWGRPLPG---QPYC---YVGSDNVGGGRLATEHLLARGRRRIAFLGGPQDMPEGEERLEGYREALAEA 154 (275)
T ss_pred HHHHhCCCCEEEECCccCC---CCCC---EEEECcHHHHHHHHHHHHHCCCCeEEEEcCCCCcchhHHHHHHHHHHHHHc
Confidence 4456789999988653322 2223 35667777888888988888999999998433 23455678899999988
Q ss_pred CceeeeeeecCCCCChHHHHHHHHHhhcC--CceEEEEEeChhhHHHHHHHHHHcCCcccceEEE
Q 003054 86 DTRVPYRSVISPLATDDQIEKELYKLFTM--QTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWI 148 (852)
Q Consensus 86 g~~v~~~~~~~~~~~~~d~~~~l~~l~~~--~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi 148 (852)
|..+.....+..+.+...-...+.++.+. .+++|+.. ....+..+++.+++.|...++-+.|
T Consensus 155 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~-~~~~a~g~~~~l~~~g~~ip~~i~i 218 (275)
T cd06295 155 GLPLDPRLVAPGDFTEESGRAAMRALLERGPDFDAVFAA-SDLMALGALRALREAGRRVPEDVAV 218 (275)
T ss_pred CCCCChhhEEeccCCHHHHHHHHHHHHhCCCCCCEEEEC-CcHHHHHHHHHHHHhCCCCccceEE
Confidence 85543221222122223334455555444 35776665 3456778889999999864444433
No 136
>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=95.36 E-value=0.22 Score=52.17 Aligned_cols=134 Identities=13% Similarity=0.135 Sum_probs=84.1
Q ss_pred HhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeC--CcccccHHHHHHHHHhC
Q 003054 8 QLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDN--QYGEEMIPSLTDALQAI 85 (852)
Q Consensus 8 ~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~--~~G~~~~~~l~~~l~~~ 85 (852)
..+.+.++|+|.+....+ +...+|+ ..++...+..+++++...|-++++++.... ..+....+.|.+++++.
T Consensus 76 ~~~~~~~ipvV~~~~~~~---~~~~~~V---~~d~~~~~~~a~~~l~~~g~~~i~~i~~~~~~~~~~~R~~gf~~~~~~~ 149 (268)
T cd06271 76 ALLLERGFPFVTHGRTEL---GDPHPWV---DFDNEAAAYQAVRRLIALGHRRIALLNPPEDLTFAQHRRAGYRRALAEA 149 (268)
T ss_pred HHHHhcCCCEEEECCcCC---CCCCCeE---eeCcHHHHHHHHHHHHHcCCCcEEEecCccccchHHHHHHHHHHHHHHh
Confidence 344567899988754322 1234443 456667778888888778999999997432 23455678899999998
Q ss_pred CceeeeeeecCCCCChHHHHHHHHHhhcC--CceEEEEEeChhhHHHHHHHHHHcCCcccceEEE
Q 003054 86 DTRVPYRSVISPLATDDQIEKELYKLFTM--QTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWI 148 (852)
Q Consensus 86 g~~v~~~~~~~~~~~~~d~~~~l~~l~~~--~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi 148 (852)
|..+.....+....+...-...+.++.+. .+++|++. +...+..+++.+++.|+..++-+-+
T Consensus 150 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~-~d~~a~g~~~al~~~g~~vp~~i~i 213 (268)
T cd06271 150 GLPLDPALIVSGDMTEEGGYAAAAELLALPDRPTAIVCS-SELMALGVLAALAEAGLRPGRDVSV 213 (268)
T ss_pred CCCCCCceEEeCCCChHHHHHHHHHHHhCCCCCCEEEEc-CcHHHHHHHHHHHHhCCCCCcceeE
Confidence 87642222222112222333445555433 36777765 4566778999999999876644433
No 137
>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=95.33 E-value=0.3 Score=51.37 Aligned_cols=140 Identities=7% Similarity=0.014 Sum_probs=84.6
Q ss_pred HHHhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHc--CCcEEEEEEEeC--CcccccHHHHHHH
Q 003054 6 IIQLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAF--GWREAVPIYVDN--QYGEEMIPSLTDA 81 (852)
Q Consensus 6 v~~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~--gw~~vaii~~d~--~~G~~~~~~l~~~ 81 (852)
+...+.+.++|+|......+.. .+.+..+..++...+..+++++.+. |-+++++|.... .......+.|.++
T Consensus 73 ~~~~l~~~~iPvv~~~~~~~~~----~~~~~~V~~d~~~~g~~~~~~l~~~~~~~~~i~~i~~~~~~~~~~~R~~gf~~~ 148 (272)
T cd06301 73 IVKAANAAGIPLVYVNRRPENA----PKGVAYVGSDEVVAGRLQAEYVADKLGGKGNVAILMGPLGQSAQIDRTKGVEEV 148 (272)
T ss_pred HHHHHHHCCCeEEEecCCCCCC----CCeeEEEecChHHHHHHHHHHHHHHhCCCccEEEEECCCCCccHHHHHHHHHHH
Confidence 3345577899999875432211 1234456677778888888887554 557999997432 3345567889999
Q ss_pred HHhCC-ceeeeeeecCCCCChHHHHHHHHHhhcC--CceEEEEEeChhhHHHHHHHHHHcCCcccceEEEEcCc
Q 003054 82 LQAID-TRVPYRSVISPLATDDQIEKELYKLFTM--QTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDG 152 (852)
Q Consensus 82 l~~~g-~~v~~~~~~~~~~~~~d~~~~l~~l~~~--~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~ 152 (852)
+++.| .++... .....+...-...+.++.+. .+++| ++.+...+..+++.+++.|..+++...++.+.
T Consensus 149 l~~~~~~~~~~~--~~~~~~~~~~~~~~~~~l~~~~~~~ai-~~~~d~~a~~~~~~l~~~g~~~~di~ivg~d~ 219 (272)
T cd06301 149 LAKYPDIKVVEE--QTANWSRAEAMDLMENWLSSGGKIDAV-VANNDEMALGAIMALKAAGKSDKDVPVAGIDG 219 (272)
T ss_pred HHHCCCcEEEec--CCCCccHHHHHHHHHHHHHhCCCCCEE-EECCCchHHHHHHHHHHcCCCCCCcEEEeeCC
Confidence 99888 444322 11111222223455554433 45664 44555667789999999998743555555444
No 138
>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=95.31 E-value=0.25 Score=51.96 Aligned_cols=139 Identities=12% Similarity=0.014 Sum_probs=83.8
Q ss_pred HHhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHH--cCCcEEEEEEEe-CCcccccHHHHHHHHH
Q 003054 7 IQLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKA--FGWREAVPIYVD-NQYGEEMIPSLTDALQ 83 (852)
Q Consensus 7 ~~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~--~gw~~vaii~~d-~~~G~~~~~~l~~~l~ 83 (852)
...+.+.++|+|......+. +.+..+..++...++.+++++.+ .|.++++++... ..........+.++++
T Consensus 73 i~~~~~~~ipvV~~~~~~~~------~~~~~V~~d~~~~g~~~~~~l~~~~~g~~~i~~i~~~~~~~~~~R~~g~~~~~~ 146 (273)
T cd06305 73 VKRALDAGIPVVAFDVDSDN------PKVNNTTQDDYSLARLSLDQLVKDLGGKGNVGYVNVAGFPPLDRRYDVWQAVLK 146 (273)
T ss_pred HHHHHHcCCCEEEecCCCCC------CccceeeechHHHHHHHHHHHHHHhCCCCCEEEEEccCCchHHHHHHHHHHHHH
Confidence 34566789999988653221 22334566777888888888755 589999999743 2233445567888888
Q ss_pred hCC-ceeeeeeecCCCCChHHHHHHHHHhhcCCceE---EEEEeChhhHHHHHHHHHHcCCcccceEEEEcCc
Q 003054 84 AID-TRVPYRSVISPLATDDQIEKELYKLFTMQTRV---FILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDG 152 (852)
Q Consensus 84 ~~g-~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~v---iv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~ 152 (852)
+.+ .++..........+..+....+.++.+..+++ .+++.+...+..+++.+++.|+.. +...++.+.
T Consensus 147 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~ai~~~~d~~a~g~~~~l~~~g~~~-di~iig~d~ 218 (273)
T cd06305 147 AYPGIKEVAELGDVSNNTAQDAAAQVEAVLKKYPKGGIDAIWAAWDEFAKGAKQALDEAGRTD-EIKIYGVDI 218 (273)
T ss_pred HCCCcEEecccccccccchhHHHHHHHHHHHHCCCcccCeEEEcChhhhHHHHHHHHHcCCCC-CceEEEecC
Confidence 877 65543221111112233445566665445543 233345557788899999999853 333444443
No 139
>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=95.27 E-value=0.3 Score=50.26 Aligned_cols=132 Identities=12% Similarity=0.110 Sum_probs=95.4
Q ss_pred HHHHhcCCCCccEEeeecCCCCCCCCCCCceE------eccCCchhHHHHHHHHHHHcCCcEEEEEEEeCCcccccHHHH
Q 003054 5 FIIQLGNKSQVPILSFSATSPSLTSIRSPYFF------RGSLNDSSQAGAITAIIKAFGWREAVPIYVDNQYGEEMIPSL 78 (852)
Q Consensus 5 ~v~~i~~~~~vP~Is~~ats~~lt~~~~py~f------R~~p~d~~~~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l 78 (852)
+++.+....++=.|.|++|+.++-. +...+. +....-..-+.|+.+.++++|.+|++++. +|-.+..+.+
T Consensus 62 aa~~ll~~a~~dvi~~~cTsgs~~~-G~~~~~~~i~~~~~g~p~tt~~~A~~~AL~alg~~RIalvT---PY~~~v~~~~ 137 (239)
T TIGR02990 62 AAALILPDEELDVVAYSCTSASVVI-GDDEVTRAINAAKPGTPVVTPSSAAVDGLAALGVRRISLLT---PYTPETSRPM 137 (239)
T ss_pred HHHHhcCCCCCCEEEEccchhheec-CHHHHHHHHHhcCCCCCeeCHHHHHHHHHHHcCCCEEEEEC---CCcHHHHHHH
Confidence 4455556577888999999887621 111111 12234556778899999999999999997 4777899999
Q ss_pred HHHHHhCCceeeeeeecCCC-------CChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHH-HcCC
Q 003054 79 TDALQAIDTRVPYRSVISPL-------ATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKAN-EIGL 140 (852)
Q Consensus 79 ~~~l~~~g~~v~~~~~~~~~-------~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~-~~G~ 140 (852)
++.+++.|++|+....+... .+.+++...+.++...++|+|++.|..-....++.++. ++|.
T Consensus 138 ~~~l~~~G~eV~~~~~~~~~~~~~ia~i~p~~i~~~~~~~~~~~aDAifisCTnLrt~~vi~~lE~~lGk 207 (239)
T TIGR02990 138 AQYFAVRGFEIVNFTCLGLTDDREMARISPDCIVEAALAAFDPDADALFLSCTALRAATCAQRIEQAIGK 207 (239)
T ss_pred HHHHHhCCcEEeeeeccCCCCCceeeecCHHHHHHHHHHhcCCCCCEEEEeCCCchhHHHHHHHHHHHCC
Confidence 99999999999877554431 23455666677776789999999998888888888874 4454
No 140
>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=95.26 E-value=0.18 Score=52.90 Aligned_cols=133 Identities=12% Similarity=0.014 Sum_probs=84.2
Q ss_pred CCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeCC--cccccHHHHHHHHHhCCce
Q 003054 11 NKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDNQ--YGEEMIPSLTDALQAIDTR 88 (852)
Q Consensus 11 ~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~~--~G~~~~~~l~~~l~~~g~~ 88 (852)
...++|+|......+. ... ..+.+++...++.+++++...|-++++++..+.. ......+.|.+++++.|++
T Consensus 75 ~~~~ipvv~~~~~~~~---~~~---~~v~~d~~~~~~~a~~~l~~~g~~~i~~l~~~~~~~~~~~R~~gf~~~~~~~~~~ 148 (269)
T cd06288 75 ELLSVPTVLLNCYDAD---GAL---PSVVPDEEQGGYDATRHLLAAGHRRIAFINGEPWMLAAKDRLKGYRQALAEAGIP 148 (269)
T ss_pred HhcCCCEEEEecccCC---CCC---CeEEEccHHHHHHHHHHHHHcCCceEEEEeCCccchhHHHHHHHHHHHHHHcCCC
Confidence 4468898887543221 122 2356677788889999887779999999984432 3455678899999998865
Q ss_pred eeeeeecCCCCChHHHHHHHHHhhcC--CceEEEEEeChhhHHHHHHHHHHcCCcccceEEEEc
Q 003054 89 VPYRSVISPLATDDQIEKELYKLFTM--QTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMT 150 (852)
Q Consensus 89 v~~~~~~~~~~~~~d~~~~l~~l~~~--~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~ 150 (852)
+.....+....+..+....+.++.+. ++++|+. .+...+..+++++++.|+..++-+.+++
T Consensus 149 ~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~-~~d~~a~~~~~~l~~~g~~vp~di~v~g 211 (269)
T cd06288 149 FDPDLVVHGDWSADDGYEAAAALLDLDDRPTAIFC-GNDRMAMGAYQALLERGLRIPQDVSVVG 211 (269)
T ss_pred CCHHHeEeCCCChHHHHHHHHHHHhCCCCCCEEEE-eCcHHHHHHHHHHHHcCCCCcccceEEe
Confidence 42211111111223344455665544 4677754 5666778899999999987655555443
No 141
>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=95.15 E-value=0.42 Score=50.40 Aligned_cols=138 Identities=7% Similarity=0.003 Sum_probs=86.7
Q ss_pred HHhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHc--CCcEEEEEEEeCC--cccccHHHHHHHH
Q 003054 7 IQLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAF--GWREAVPIYVDNQ--YGEEMIPSLTDAL 82 (852)
Q Consensus 7 ~~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~--gw~~vaii~~d~~--~G~~~~~~l~~~l 82 (852)
...+.+.++|+|......+.. ...+++.++.+++...+..+++++... |-++++++..+.. ......+.|++++
T Consensus 73 i~~~~~~~iPvV~~~~~~~~~--~~~~~~~~v~~d~~~~g~~~~~~l~~~~~g~~~i~~i~~~~~~~~~~~R~~Gf~~~l 150 (273)
T cd06309 73 LKEAKAAGIPVILVDRGVDVK--DDSLYVTFIGSDFVEEGRRAADWLAKATGGKGNIVELQGTVGSSVAIDRKKGFAEVI 150 (273)
T ss_pred HHHHHHCCCCEEEEecCcCCc--cCcceeeEecCChHHHHHHHHHHHHHHcCCCceEEEEeCCCCCchHHHHHHHHHHHH
Confidence 345667899999987532211 123567778888888999999988665 8899999974332 2345578899999
Q ss_pred HhC-CceeeeeeecCCCCChHHHHHHHHHhhcC---CceEEEEEeChhhHHHHHHHHHHcCCcccceEEEE
Q 003054 83 QAI-DTRVPYRSVISPLATDDQIEKELYKLFTM---QTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIM 149 (852)
Q Consensus 83 ~~~-g~~v~~~~~~~~~~~~~d~~~~l~~l~~~---~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~ 149 (852)
++. +.++.... ....+..+-...+.++.+. .+++|+ +.+...+..+++.+++.|+..++-+-|+
T Consensus 151 ~~~~~~~~~~~~--~~~~~~~~~~~~~~~~l~~~~~~~~aI~-~~~d~~a~g~~~a~~~~g~~ip~di~ii 218 (273)
T cd06309 151 KKYPNMKIVASQ--TGDFTRAKGKEVMEALLKAHGDDIDAVY-AHNDEMALGAIQAIKAAGKKPGKDIKIV 218 (273)
T ss_pred HHCCCCEEeecc--CCcccHHHHHHHHHHHHHhCCCCccEEE-ECCcHHHHHHHHHHHHcCCCCCCCeEEE
Confidence 987 45543211 1111223333445555433 356554 3455566778999999998755444443
No 142
>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=94.89 E-value=0.67 Score=48.75 Aligned_cols=138 Identities=7% Similarity=-0.019 Sum_probs=81.8
Q ss_pred HHhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHc--CCcEEEEEEEeCCc--ccccHHHHHHHH
Q 003054 7 IQLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAF--GWREAVPIYVDNQY--GEEMIPSLTDAL 82 (852)
Q Consensus 7 ~~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~--gw~~vaii~~d~~~--G~~~~~~l~~~l 82 (852)
...+...++|+|......+ + ..+ +--+..++..-+..+++++.+. |.++++++....++ .....+.+++++
T Consensus 75 l~~~~~~~ipvV~~~~~~~---~-~~~-~~~v~~d~~~~~~~~~~~l~~~~~g~~~i~~i~~~~~~~~~~~r~~gf~~a~ 149 (273)
T cd06310 75 LKEAKDAGIPVVLIDSGLN---S-DIA-VSFVATDNVAAGKLAAEALAELLGKKGKVAVISFVPGSSTTDQREEGFLEGL 149 (273)
T ss_pred HHHHHHCCCCEEEecCCCC---C-Ccc-eEEEeeChHHHHHHHHHHHHHHcCCCceEEEEeCCCCCccHHHHHHHHHHHH
Confidence 3445568999998754221 1 111 1223445556667888887665 89999999743333 344568899999
Q ss_pred HhC-CceeeeeeecCCCCChHHHHHHHHHhhcCCceE-EEEEeChhhHHHHHHHHHHcCCcccceEEEEcCc
Q 003054 83 QAI-DTRVPYRSVISPLATDDQIEKELYKLFTMQTRV-FILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDG 152 (852)
Q Consensus 83 ~~~-g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~v-iv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~ 152 (852)
++. |+++... .....+..+-...+.++.+..+++ .+++++...+..+++.+++.|+. ++..+++.++
T Consensus 150 ~~~~~~~~~~~--~~~~~~~~~~~~~~~~~l~~~~~~~~i~~~~d~~a~g~~~~l~~~g~~-~di~vig~d~ 218 (273)
T cd06310 150 KEYPGIEIVAT--QYSDSDYAKALDITEDLLTANPDLKGIFGANEGSAVGAARAVRQAGKA-GKVKVVGFDA 218 (273)
T ss_pred HhCCCcEEEec--ccCCcCHHHHHHHHHHHHHhCCCceEEEecCchhHHHHHHHHHhcCCC-CCeEEEEeCC
Confidence 988 8776432 111112223334555655444332 24445566788899999999985 4444554443
No 143
>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=94.89 E-value=0.74 Score=45.63 Aligned_cols=180 Identities=15% Similarity=0.131 Sum_probs=113.3
Q ss_pred eeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCcccEEEeeeeeecCcceeeeccccccccceEEEEE
Q 003054 378 YCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGEFDAVVGDITIVFNRSNYVDFTLPYTESGVSMIVP 457 (852)
Q Consensus 378 ~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv~ 457 (852)
+-.+++..+.++.+- +.+++.. ++..+++++|.+|++|++++.... ....+. ..|+....++++++
T Consensus 20 ~l~~~l~~~~~~~P~-i~i~~~~---------~~~~~~~~~l~~g~~Dl~i~~~~~---~~~~~~-~~~l~~~~~~~~~~ 85 (209)
T PF03466_consen 20 LLPPLLAEFRERHPN-IRIEIRE---------GDSDELIEALRSGELDLAITFGPP---PPPGLE-SEPLGEEPLVLVVS 85 (209)
T ss_dssp THHHHHHHHHHHSTT-EEEEEEE---------ESHHHHHHHHHTTSSSEEEESSSS---SSTTEE-EEEEEEEEEEEEEE
T ss_pred HHHHHHHHHHHHCCC-cEEEEEe---------ccchhhhHHHhcccccEEEEEeec---cccccc-cccccceeeeeeee
Confidence 446889999998873 5555544 246899999999999999764443 222333 46777888999998
Q ss_pred ccCCCCCCceEeecccchhHHHHHHHHHHHHHhhhhheecccCCCCCCCcccccchhHHHHHHHhhhccccccccchhhH
Q 003054 458 IKDSKKRNAWVFLQPLTWDLWVTCFCFFIFIGFVVWVLEHRVNEDFRGPAGQQVGTSFWFSFSTMVFSQRERVISNLARI 537 (852)
Q Consensus 458 ~~~~~~~~~~~~l~PF~~~lW~~i~~~~i~~~~v~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~s~~~R~ 537 (852)
......
T Consensus 86 ~~~pl~-------------------------------------------------------------------------- 91 (209)
T PF03466_consen 86 PDHPLA-------------------------------------------------------------------------- 91 (209)
T ss_dssp TTSGGG--------------------------------------------------------------------------
T ss_pred cccccc--------------------------------------------------------------------------
Confidence 653110
Q ss_pred HHHHHHHHHHHHHHHhhhhccceeeecccCCCcCCHHHHHhcCCeEEEEe-CchHHHH----HHhcCCCCcceeecCCHh
Q 003054 538 VVIVWCFVVLILTQSYTASLTSLLTVQQLQPTITDVKMLIKRGDNVGYQK-GSFVLGI----LKQLGFDERKLVVYNSPE 612 (852)
Q Consensus 538 v~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~i~sl~dL~~~~~~vg~~~-~s~~~~~----l~~~~~~~~~~~~~~~~~ 612 (852)
+ ..++ +++||. +.++.... +...... +++.++........++.+
T Consensus 92 ---------------------------~-~~~i-~~~dL~--~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 140 (209)
T PF03466_consen 92 ---------------------------Q-KKPI-TLEDLA--DYPLILLSPGSPYRDQLDRWLREHGFSPNIVIEVDSFE 140 (209)
T ss_dssp ---------------------------T-TSSS-SGGGGT--TSEEEEESTTTSHHHHHHHHHHHTTEEEEEEEEESSHH
T ss_pred ---------------------------c-cccc-hhhhhh--hccccccccccccccccccccccccccccccccccchh
Confidence 0 1124 789997 56555533 4433333 344555555556788999
Q ss_pred HHHHHhhcccccCceeEEEechhHHHHHHhhcCCceEeecc-cccccceEEEecCCCCchhhHHHHHHhcc
Q 003054 613 DCHELFQKGSVNGGIAAAFDEIPYMKLLIGQYCSKYAMIEP-KFKTAGFGFVFPLHSPLVHDVSKAILNVT 682 (852)
Q Consensus 613 ~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~~~~~~~~v~~-~~~~~~~~~~~~k~spl~~~in~~il~l~ 682 (852)
...+++..|. ..+++-+.....+....... ...+.+ .+. ..++++.+++.+....+...+..+.
T Consensus 141 ~~~~~v~~g~----gi~~~p~~~~~~~~~~~~l~-~~~~~~~~~~-~~~~l~~~~~~~~~~~~~~~~~~l~ 205 (209)
T PF03466_consen 141 SILSLVASGD----GIAILPDSLAQDELESGELV-FLPLPDPPLP-RPIYLVWRKDRPLSPAIQWFIDLLR 205 (209)
T ss_dssp HHHHHHHTTS----EBEEEEHHHHHHHHHCTTEE-EEEESSSTEE-EEEEEEEETTGTTHHHHHHHHHHHH
T ss_pred hhcccccccc----ceeecCcccccccccCCCEE-EEECCCCCCc-eEEEEEEECCCCCCHHHHHHHHHHH
Confidence 9999999998 56666554333333222221 123344 444 7888999998776666666655544
No 144
>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=94.85 E-value=0.34 Score=50.74 Aligned_cols=126 Identities=11% Similarity=0.062 Sum_probs=80.7
Q ss_pred CCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEe--CCcccccHHHHHHHHHhCCcee
Q 003054 12 KSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVD--NQYGEEMIPSLTDALQAIDTRV 89 (852)
Q Consensus 12 ~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d--~~~G~~~~~~l~~~l~~~g~~v 89 (852)
..++|+|..+... .. +.+..+..++...++.+++++...|.++++++..+ +..+....+.|.+++++.|+++
T Consensus 75 ~~~ipvv~~~~~~---~~---~~~~~v~~d~~~~g~~~~~~l~~~g~~~i~~l~~~~~~~~~~~r~~gf~~~~~~~~~~~ 148 (267)
T cd06284 75 AKLPPIVQACEYI---PG---LAVPSVSIDNVAAARLAVDHLISLGHRRIALITGPRDNPLARDRLEGYRQALAEAGLPA 148 (267)
T ss_pred hcCCCEEEEeccc---CC---CCcceEEecccHHHHHHHHHHHHcCCceEEEEcCCccchhHHHHHHHHHHHHHHcCCCC
Confidence 3489999864321 11 22333566777888889998877899999999753 3456777899999999998654
Q ss_pred eeeeecCCCCChHHHHHHHHHhhcC--CceEEEEEeChhhHHHHHHHHHHcCCcccc
Q 003054 90 PYRSVISPLATDDQIEKELYKLFTM--QTRVFILHMLPSLGSRIFEKANEIGLMNKG 144 (852)
Q Consensus 90 ~~~~~~~~~~~~~d~~~~l~~l~~~--~~~viv~~~~~~~~~~i~~~a~~~G~~~~~ 144 (852)
........+.+.++-...+.++.+. .+++|+.. +...+..+++++++.|...++
T Consensus 149 ~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~-~~~~a~g~~~al~~~g~~~p~ 204 (267)
T cd06284 149 DEELIQEGDFSLESGYAAARRLLALPDRPTAIFCF-SDEMAIGAISALKELGLRVPE 204 (267)
T ss_pred CcceEEeCCCChHHHHHHHHHHHhCCCCCcEEEEc-CcHHHHHHHHHHHHcCCCCcc
Confidence 3221111111223334455555433 46776664 555577899999999986443
No 145
>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=94.80 E-value=0.43 Score=49.99 Aligned_cols=134 Identities=13% Similarity=0.114 Sum_probs=83.9
Q ss_pred HhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeC--CcccccHHHHHHHHHhC
Q 003054 8 QLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDN--QYGEEMIPSLTDALQAI 85 (852)
Q Consensus 8 ~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~--~~G~~~~~~l~~~l~~~ 85 (852)
..+.+.++|+|......+ + +.......+....+..+++++...|-++++++..+. .......+.|.+++++.
T Consensus 72 ~~~~~~~ipvv~~~~~~~---~---~~~~~v~~d~~~~~~~~~~~l~~~g~~~i~~i~~~~~~~~~~~r~~gf~~~l~~~ 145 (268)
T cd01575 72 QLLRAAGIPVVEIMDLPP---D---PIDMAVGFSHAEAGRAMARHLLARGYRRIGFLGARMDDTRAQQRLEGFRAALRAA 145 (268)
T ss_pred HHHHhcCCCEEEEecCCC---C---CCCCeEEeCcHHHHHHHHHHHHHCCCCcEEEecCCCCcccHHHHHHHHHHHHHHc
Confidence 445567899998743211 1 122234556777888888898888999999998543 34556678899999998
Q ss_pred CceeeeeeecCCCCChHHHHHHHHHhhcC--CceEEEEEeChhhHHHHHHHHHHcCCcccceEEE
Q 003054 86 DTRVPYRSVISPLATDDQIEKELYKLFTM--QTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWI 148 (852)
Q Consensus 86 g~~v~~~~~~~~~~~~~d~~~~l~~l~~~--~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi 148 (852)
|.............+...-...+.++.+. .+++|+. .+...+..+++.+++.|...++-+-+
T Consensus 146 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~-~~d~~a~~~~~~l~~~g~~~p~di~v 209 (268)
T cd01575 146 GLDPPLVVTTPEPSSFALGRELLAELLARWPDLDAVFC-SNDDLALGALFECQRRGISVPEDIAI 209 (268)
T ss_pred CCCCCceeEeccCCCHHHHHHHHHHHHhCCCCCCEEEE-CCcHHHHHHHHHHHHhCCCCCcceEE
Confidence 86432222221111223334455555433 4677664 45556778999999999865544433
No 146
>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=94.78 E-value=0.4 Score=49.99 Aligned_cols=133 Identities=11% Similarity=0.057 Sum_probs=85.4
Q ss_pred HHHhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEe-C--CcccccHHHHHHHH
Q 003054 6 IIQLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVD-N--QYGEEMIPSLTDAL 82 (852)
Q Consensus 6 v~~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d-~--~~G~~~~~~l~~~l 82 (852)
+...+.+.++|+|......+ ..+ .+..+....+..+++++.+.|-++++++... + ..+....+.|++++
T Consensus 70 ~~~~~~~~~ipvv~~~~~~~-----~~~---~v~~d~~~~~~~~~~~l~~~g~~~i~~v~~~~~~~~~~~~r~~gf~~~~ 141 (259)
T cd01542 70 HREAIKKLNVPVVVVGQDYP-----GIS---SVVYDDYGAGYELGEYLAQQGHKNIAYLGVSESDIAVGILRKQGYLDAL 141 (259)
T ss_pred HHHHHhcCCCCEEEEeccCC-----CCC---EEEECcHHHHHHHHHHHHHcCCCcEEEEcCCcccchhHHHHHHHHHHHH
Confidence 44556677899999854221 122 3556777788889999877899999998632 2 23456678899999
Q ss_pred HhCCc-eeeeeeecCCCCChHHHHHHHHHhhcCC-ceEEEEEeChhhHHHHHHHHHHcCCcccceEEEEc
Q 003054 83 QAIDT-RVPYRSVISPLATDDQIEKELYKLFTMQ-TRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMT 150 (852)
Q Consensus 83 ~~~g~-~v~~~~~~~~~~~~~d~~~~l~~l~~~~-~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~ 150 (852)
++.|. .+... .-. .+...-...+.++.+.. +++|++.. ...+..+++.+++.|+..++-+.+.+
T Consensus 142 ~~~~~~~~~~~-~~~--~~~~~~~~~~~~~l~~~~~~~i~~~~-d~~a~g~~~~l~~~g~~vp~di~v~g 207 (259)
T cd01542 142 KEHGICPPNIV-ETD--FSYESAYEAAQELLEPQPPDAIVCAT-DTIALGAMKYLQELGRRIPEDISVAG 207 (259)
T ss_pred HHcCCChHHee-ecc--CchhhHHHHHHHHhcCCCCCEEEEcC-cHHHHHHHHHHHHcCCCCCCceEEEe
Confidence 99887 21111 111 11223334555555444 67766654 55678899999999997666555553
No 147
>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=94.78 E-value=0.37 Score=50.38 Aligned_cols=126 Identities=13% Similarity=0.078 Sum_probs=80.9
Q ss_pred HHhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeC--CcccccHHHHHHHHHh
Q 003054 7 IQLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDN--QYGEEMIPSLTDALQA 84 (852)
Q Consensus 7 ~~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~--~~G~~~~~~l~~~l~~ 84 (852)
...+.+.++|+|......+ + +.+..+..++...+..+++++.+.|-++++++..+. .+.....+.|.+++++
T Consensus 70 ~~~~~~~~ipvV~~~~~~~---~---~~~~~v~~d~~~~g~~~~~~l~~~g~~~i~~i~~~~~~~~~~~R~~gf~~~~~~ 143 (266)
T cd06278 70 AEECRRNGIPVVLINRYVD---G---PGVDAVCSDNYEAGRLAAELLLAKGCRRIAFIGGPADTSTSRERERGFRDALAA 143 (266)
T ss_pred HHHHhhcCCCEEEECCccC---C---CCCCEEEEChHHHHHHHHHHHHHCCCceEEEEcCCCcccchHHHHHHHHHHHHH
Confidence 4456678999999855322 1 223446778888888999998888999999998443 3455667889999999
Q ss_pred CCceeeeeeecCCCCChHHHHHHHHHhhcC--CceEEEEEeChhhHHHHHHHHHHc-CCc
Q 003054 85 IDTRVPYRSVISPLATDDQIEKELYKLFTM--QTRVFILHMLPSLGSRIFEKANEI-GLM 141 (852)
Q Consensus 85 ~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~--~~~viv~~~~~~~~~~i~~~a~~~-G~~ 141 (852)
.|.++.... .. ..+..+....+.++.+. .+++|+.. +...+..+++.+++. |..
T Consensus 144 ~~~~~~~~~-~~-~~~~~~~~~~~~~~l~~~~~~~~i~~~-~~~~a~~~~~~l~~~~~~~ 200 (266)
T cd06278 144 AGVPVVVEE-AG-DYSYEGGYEAARRLLASRPRPDAIFCA-NDLLAIGVMDAARQEGGLR 200 (266)
T ss_pred cCCChhhhc-cC-CCCHHHHHHHHHHHHhcCCCCCEEEEc-CcHHHHHHHHHHHHhcCCC
Confidence 988753221 11 11223334455555544 45666554 444567788888875 443
No 148
>COG3107 LppC Putative lipoprotein [General function prediction only]
Probab=94.73 E-value=0.43 Score=53.00 Aligned_cols=174 Identities=12% Similarity=0.117 Sum_probs=99.8
Q ss_pred CCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHHHHHhCCceeeee
Q 003054 13 SQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTDALQAIDTRVPYR 92 (852)
Q Consensus 13 ~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~~l~~~g~~v~~~ 92 (852)
..+|++....++..= ..+-.+-..-+...+++..|+.+-.-|.+...++...+++|+...++|.+.+++.|+..+..
T Consensus 341 ~~i~vLALN~~~n~r---~~~~~cyfaLSPEDEa~~AA~~l~~qG~R~plvlvPr~~lG~Rv~~AF~~~Wq~~gg~~v~~ 417 (604)
T COG3107 341 QPIPVLALNQPENSR---NPAQLCYFALSPEDEARDAANHLWDQGKRNPLVLVPRNDLGDRVANAFNQEWQKLGGGTVLQ 417 (604)
T ss_pred CCCceeeecCCcccc---CcccceeeecChhHHHHHHHHHHHHccccCceEEecchHHHHHHHHHHHHHHHHhcCCchhH
Confidence 567777765543322 12333333455566888899999888999999999999999999999999999988743333
Q ss_pred eecCC----------------CCChHHHHHHH----HHhhcCC-ceEEEEEeChhhHHHHHHHHHHcCCcccceEEEEcC
Q 003054 93 SVISP----------------LATDDQIEKEL----YKLFTMQ-TRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTD 151 (852)
Q Consensus 93 ~~~~~----------------~~~~~d~~~~l----~~l~~~~-~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~ 151 (852)
..|-. .....|....+ ..+.+.. .|+|++...++++..|--.....+.... -..++++
T Consensus 418 ~~fg~~~~l~~~i~~~a~ir~~~~p~~~~~~~g~~~~p~~~~d~iDaVyivAtp~el~~IKP~ia~~~~~~~-~p~yaSS 496 (604)
T COG3107 418 QKFGSTSELRQGINDGAGIRLTGLPADLTTTNGLQTPPLDDQDTIDAVYIVATPSELALIKPMIAMANGSDS-PPLYASS 496 (604)
T ss_pred hhcCcHHHHHhhcccccceeecCCccchhcccCCCCCCcccccccceEEEEecchhHhHHhhHHHhhcCCCC-cceeeec
Confidence 22210 00011111000 1223334 7899998888887666444443333111 1133333
Q ss_pred ccccccccCCchhhcccceEEEE-EecC--CCChHHHHHHHHHH
Q 003054 152 GMTNLLRTLEPSVIDSMQGVIGV-GPHV--PKTKALENFRVRWK 192 (852)
Q Consensus 152 ~~~~~~~~~~~~~~~~~~gv~~~-~~~~--~~~~~~~~F~~~~~ 192 (852)
.... ..-+++....++|+... .|+. +..|..+....+|.
T Consensus 497 r~~~--gT~~P~~~~~m~GiqysdiP~l~~~~~p~~qq~a~~~p 538 (604)
T COG3107 497 RSSQ--GTNGPDFRLEMEGIQYSDIPWLAQPNPPLMQQAAAAWP 538 (604)
T ss_pred cccc--cCCCccHHHhccCccccCCchhcCCCchHHHHHHHhcC
Confidence 3221 11223455678887433 2332 34566666666653
No 149
>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=94.71 E-value=0.39 Score=50.28 Aligned_cols=134 Identities=11% Similarity=0.100 Sum_probs=82.1
Q ss_pred HHHhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeC--CcccccHHHHHHHHH
Q 003054 6 IIQLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDN--QYGEEMIPSLTDALQ 83 (852)
Q Consensus 6 v~~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~--~~G~~~~~~l~~~l~ 83 (852)
+...+...++|+|......+. ...+| +..++...++.+++++...|-++|+++..+. .......+.|.++++
T Consensus 71 ~~~~~~~~~ipvV~~~~~~~~---~~~~~---v~~d~~~~~~~~~~~l~~~g~~~i~~l~~~~~~~~~~~r~~gf~~~l~ 144 (268)
T cd06289 71 LLKRLAESGIPVVLVAREVAG---APFDY---VGPDNAAGARLATEHLISLGHRRIAFIGGLEDSSTRRERLAGYRAALA 144 (268)
T ss_pred HHHHHHhcCCCEEEEeccCCC---CCCCE---EeecchHHHHHHHHHHHHCCCCCEEEecCCccccchHHHHHHHHHHHH
Confidence 344566789999987543221 12232 4556667788888888777999999987432 345667899999999
Q ss_pred hCCceeeeeeecCCCCChHHHHHHHHHhhcC--CceEEEEEeChhhHHHHHHHHHHcCCcccceE
Q 003054 84 AIDTRVPYRSVISPLATDDQIEKELYKLFTM--QTRVFILHMLPSLGSRIFEKANEIGLMNKGCV 146 (852)
Q Consensus 84 ~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~--~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~v 146 (852)
+.|.++.....+..+.+.......+.++... .+++|+. .+...+..+++.+++.|+..++-+
T Consensus 145 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~i~~-~~~~~a~~~~~al~~~g~~~p~di 208 (268)
T cd06289 145 EAGLPFDSELVVEGPPSRQGGAEAVAQLLDLPPRPTAIVC-FNDLVAFGAMSGLRRAGLTPGRDI 208 (268)
T ss_pred HcCCCCCchhEEecCcchhhHHHHHHHHHcCCCCCCEEEE-cCcHHHHHHHHHHHHcCCCCCcce
Confidence 8885432211111111122233445554433 4576554 345557778999999998655433
No 150
>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=94.67 E-value=0.76 Score=48.48 Aligned_cols=135 Identities=7% Similarity=-0.024 Sum_probs=83.9
Q ss_pred cCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHc--CCcEEEEEEEeCC--cccccHHHHHHHHHhC
Q 003054 10 GNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAF--GWREAVPIYVDNQ--YGEEMIPSLTDALQAI 85 (852)
Q Consensus 10 ~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~--gw~~vaii~~d~~--~G~~~~~~l~~~l~~~ 85 (852)
+.+.+||+|...+..+. ...+.+..+.+++..-++.+++++.+. |.++++++..+.. ......+.|.+++++.
T Consensus 76 ~~~~~iPvV~~~~~~~~---~~~~~~~~v~~d~~~~g~~~~~~l~~~~~g~~~i~~l~g~~~~~~~~~R~~gf~~~~~~~ 152 (272)
T cd06313 76 AIARGIPVIDMGTLIAP---LQINVHSFLAPDNYFMGASVAQALCNAMGGKGKIAMLQGALGHTGAQGRAQGFNDVIKKY 152 (272)
T ss_pred HHHCCCcEEEeCCCCCC---CCCceEEEECCCcHHHHHHHHHHHHHHcCCCceEEEEECCCCCcchhHHHHHHHHHHHhC
Confidence 45579999998653321 112223446677788888999988666 8899999974432 3445688899999987
Q ss_pred C-ceeeeeeecCCCCChHHHHHHHHHhhcCC--ceEEEEEeChhhHHHHHHHHHHcCCcccceEEEEcCc
Q 003054 86 D-TRVPYRSVISPLATDDQIEKELYKLFTMQ--TRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDG 152 (852)
Q Consensus 86 g-~~v~~~~~~~~~~~~~d~~~~l~~l~~~~--~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~ 152 (852)
+ .++... .....+...-...+.++.+.+ +++|+. .+...+..+++.+++.|+ .+...++-+.
T Consensus 153 ~~~~~~~~--~~~~~~~~~~~~~~~~~l~~~~~~~ai~~-~nd~~a~g~~~al~~~g~--~di~vvgfd~ 217 (272)
T cd06313 153 PDIEVVDE--QPANWDVSKAARIWETWLTKYPQLDGAFC-HNDSMALAAYQIMKAAGR--TKIVIGGVDG 217 (272)
T ss_pred CCCEEEec--cCCCCCHHHHHHHHHHHHHhCCCCCEEEE-CCCcHHHHHHHHHHHcCC--CceEEEeecC
Confidence 5 555432 111122233345555554443 565444 556677888999999998 4444444433
No 151
>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=94.66 E-value=0.5 Score=49.48 Aligned_cols=134 Identities=13% Similarity=0.055 Sum_probs=82.3
Q ss_pred hcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeC--CcccccHHHHHHHHHhCC
Q 003054 9 LGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDN--QYGEEMIPSLTDALQAID 86 (852)
Q Consensus 9 i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~--~~G~~~~~~l~~~l~~~g 86 (852)
.+.+.++|+|......+ +...++ +..++..-+..+++++.+.|-++++++..+. .......+.+++++++.|
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 34567899998755332 122333 3445556667888888778999999997433 234556788999999988
Q ss_pred ceeeeeeecCCCCChHHHHHHHHHhhcC---CceEEEEEeChhhHHHHHHHHHHcCCcccceEEEE
Q 003054 87 TRVPYRSVISPLATDDQIEKELYKLFTM---QTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIM 149 (852)
Q Consensus 87 ~~v~~~~~~~~~~~~~d~~~~l~~l~~~---~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~ 149 (852)
..+.....+..+.+...-...+.++.+. .+++|++. +...+..+++++++.|+..++-+-|+
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 6532222111111222223344454332 46777754 56677889999999998755544443
No 152
>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=94.60 E-value=0.52 Score=49.46 Aligned_cols=132 Identities=12% Similarity=0.038 Sum_probs=83.5
Q ss_pred HhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeCC--cccccHHHHHHHHHhC
Q 003054 8 QLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDNQ--YGEEMIPSLTDALQAI 85 (852)
Q Consensus 8 ~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~~--~G~~~~~~l~~~l~~~ 85 (852)
..+.+.++|+|......+. ...++ +..++...++.+++++...|-+++++|..+.. ......+.|.+++++.
T Consensus 72 ~~~~~~~ipvV~~~~~~~~---~~~~~---v~~d~~~~~~~~~~~l~~~g~~~i~~i~~~~~~~~~~~R~~gf~~~~~~~ 145 (268)
T cd06270 72 IELAAQVPPLVLINRHIPG---LADRC---IWLDNEQGGYLATEHLIELGHRKIACITGPLTKEDARLRLQGYRDALAEA 145 (268)
T ss_pred HHHhhCCCCEEEEeccCCC---CCCCe---EEECcHHHHHHHHHHHHHCCCceEEEEeCCcccccHHHHHHHHHHHHHHc
Confidence 3445678999888653321 12233 45677788888899887779999999974322 2345577889999998
Q ss_pred CceeeeeeecCCCCChHHHHHHHHHhhcCC--ceEEEEEeChhhHHHHHHHHHHcCCcccceE
Q 003054 86 DTRVPYRSVISPLATDDQIEKELYKLFTMQ--TRVFILHMLPSLGSRIFEKANEIGLMNKGCV 146 (852)
Q Consensus 86 g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~--~~viv~~~~~~~~~~i~~~a~~~G~~~~~~v 146 (852)
|.++.....+..+.+..+....+.++.+.. +++|+. ++...+..+++.+++.|+..++-+
T Consensus 146 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~-~~d~~a~g~~~~l~~~g~~ip~di 207 (268)
T cd06270 146 GIALDESLIIEGDFTEEGGYAAMQELLARGAPFTAVFC-ANDEMAAGAISALREHGISVPQDV 207 (268)
T ss_pred CCCCCcceEEECCCCHHHHHHHHHHHHhCCCCCCEEEE-cCcHHHHHHHHHHHHcCCCCCCce
Confidence 876522211111222344455566665444 566554 445567889999999998655433
No 153
>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=94.59 E-value=0.41 Score=50.12 Aligned_cols=135 Identities=12% Similarity=0.098 Sum_probs=81.5
Q ss_pred HhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeC--CcccccHHHHHHHHHhC
Q 003054 8 QLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDN--QYGEEMIPSLTDALQAI 85 (852)
Q Consensus 8 ~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~--~~G~~~~~~l~~~l~~~ 85 (852)
.-+.+.++|+|......+. ...+|+ ..++..-+..+++++...|-++|+++.... .......+.|.+++++.
T Consensus 72 ~~l~~~~ipvV~~~~~~~~---~~~~~v---~~d~~~~~~~~~~~l~~~g~~~I~~i~~~~~~~~~~~R~~gf~~~~~~~ 145 (265)
T cd06299 72 EDLLKRGIPVVFVDREITG---SPIPFV---TSDPQPGMTEAVSLLVALGHKKIGYISGPQDTSTGRERLEAFRQACASL 145 (265)
T ss_pred HHHHhCCCCEEEEecccCC---CCCCEE---EECcHHHHHHHHHHHHHcCCCcEEEEeCCCCcccHHHHHHHHHHHHHHC
Confidence 4445679999987654322 233443 334444555666777777999999996432 33445567899999998
Q ss_pred CceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHcCCcccceEEEE
Q 003054 86 DTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIM 149 (852)
Q Consensus 86 g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~ 149 (852)
|.++.............+-...+.++.+.+|++|+. ++...+..+++.+++.|+..++-+.|.
T Consensus 146 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~av~~-~~d~~a~gv~~al~~~g~~vp~dv~v~ 208 (265)
T cd06299 146 GLEVNEDLVVLGGYSQESGYAGATKLLDQGATAIIA-GDSMMTIGAIRAIHDAGLVIGEDISLI 208 (265)
T ss_pred CCCCChHhEEecCcchHHHHHHHHHHHcCCCCEEEE-cCcHHHHHHHHHHHHhCCCCCcceeEE
Confidence 864322111111111223334555655455887655 556678889999999998755434333
No 154
>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=94.56 E-value=0.51 Score=49.32 Aligned_cols=135 Identities=13% Similarity=0.107 Sum_probs=83.9
Q ss_pred HhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeCC-c--ccccHHHHHHHHHh
Q 003054 8 QLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDNQ-Y--GEEMIPSLTDALQA 84 (852)
Q Consensus 8 ~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~~-~--G~~~~~~l~~~l~~ 84 (852)
..+.+.++|+|......+ ....++ +..++..-++.+++++...|-++++++..... + .....+.+.+++++
T Consensus 72 ~~~~~~~ipvV~~~~~~~---~~~~~~---v~~d~~~~g~~~~~~l~~~g~~~i~~l~~~~~~~~~~~~r~~g~~~~~~~ 145 (267)
T cd06283 72 QRLAKNGKPVVLVDRKIP---ELGVDT---VTLDNYEAAKEAVDHLIEKGYERILFVTEPLDEISPRMERYEGFKEALAE 145 (267)
T ss_pred HHHhcCCCCEEEEcCCCC---CCCCCE---EEeccHHHHHHHHHHHHHcCCCcEEEEecCccccccHHHHHHHHHHHHHH
Confidence 445677999999865322 122233 44566777888888888889999999974332 2 13566888999998
Q ss_pred CCceeeeeeecCCCCChHHHHHHHHHhhcCC--ceEEEEEeChhhHHHHHHHHHHcCCcccceEEEE
Q 003054 85 IDTRVPYRSVISPLATDDQIEKELYKLFTMQ--TRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIM 149 (852)
Q Consensus 85 ~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~--~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~ 149 (852)
.|..+..........+..+....+.++.+.. +++|++. +...+..+++.+++.|+..++-+-|+
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 8854322211111122334456666765443 5666654 45567788999999998655444333
No 155
>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=94.55 E-value=0.79 Score=48.71 Aligned_cols=147 Identities=9% Similarity=0.056 Sum_probs=83.0
Q ss_pred HHHhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHH----HcCC--cEEEEEE-E--eCCcccccHH
Q 003054 6 IIQLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIK----AFGW--REAVPIY-V--DNQYGEEMIP 76 (852)
Q Consensus 6 v~~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~----~~gw--~~vaii~-~--d~~~G~~~~~ 76 (852)
+...+.+.++|+|......+.......+.+-....+....+..+++++. ..|+ +++++|. . +........+
T Consensus 71 ~~~~~~~~~iPvV~~~~~~~~~~~~~~~~~~~V~~d~~~~g~~~~~~l~~~~~~~g~~~~~i~~i~~~~~~~~~~~~R~~ 150 (289)
T cd01540 71 IVAKAKAYNMKVVAVDDRLVDADGKPMEDVPHVGMSATKIGEQVGEAIADEMKKRGWDPKEVGALRITYDELDTAKPRTD 150 (289)
T ss_pred HHHHHHhCCCeEEEecCCCcccCCCccccceEecCCHHHHHHHHHHHHHHHHHhhcCCCcceEEEEecCCCCcchhhHHH
Confidence 3455677899999975533211100011222344566666666666543 3577 7888875 2 2235567788
Q ss_pred HHHHHHHhCCceeeeeeecCCCCC-hHHHHHHHHHhhcCC--ceE-EEEEeChhhHHHHHHHHHHcCCcccceEEEEcCc
Q 003054 77 SLTDALQAIDTRVPYRSVISPLAT-DDQIEKELYKLFTMQ--TRV-FILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDG 152 (852)
Q Consensus 77 ~l~~~l~~~g~~v~~~~~~~~~~~-~~d~~~~l~~l~~~~--~~v-iv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~ 152 (852)
.+++++++.|+............. .+.-...+.++.... ++. .+++++...+..+++.+++.|...++...++-++
T Consensus 151 G~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~i~~~~d~~a~g~~~al~~~g~~~~di~vig~d~ 230 (289)
T cd01540 151 GALEALKAPGFPEANIFQAPQKTTDTEGAFDAAASTLTKNPNVKNWIIYGLNDETVLGAVRATEQSGIAAADVIGVGING 230 (289)
T ss_pred HHHHHHhcCCCCcceEecccccCcchhhHHHHHHHHHHhCCCcCeeEEEeCCcHHHHHHHHHHHHcCCCCcceEEEecCC
Confidence 999999988875322111111111 111223455554443 454 4666667778899999999998743444454443
No 156
>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=94.50 E-value=0.16 Score=55.09 Aligned_cols=59 Identities=29% Similarity=0.336 Sum_probs=41.3
Q ss_pred CcCCHHHHHhcCCeEEEEe-CchH----HHHHHhcCCCCcc--eeecCCHhHHHHHhhcccccCceeEEEec
Q 003054 569 TITDVKMLIKRGDNVGYQK-GSFV----LGILKQLGFDERK--LVVYNSPEDCHELFQKGSVNGGIAAAFDE 633 (852)
Q Consensus 569 ~i~sl~dL~~~~~~vg~~~-~s~~----~~~l~~~~~~~~~--~~~~~~~~~~~~~l~~g~~~~g~~a~~~~ 633 (852)
++++++||. ++++++.. ++.. ..++++.+..... .+.+.+..+..++|..|+ +++++..
T Consensus 132 ~i~sl~dL~--gk~v~~~~~~s~~~~~~~~~l~~~G~~~~~~~~v~~~~~~~~~~al~~G~----vDa~~~~ 197 (320)
T TIGR02122 132 GIKTVADLK--GKRVAVGAPGSGTELNARAVLKAAGLTYDDVKKVEYLGYAEAADALKDGK----IDAAFYT 197 (320)
T ss_pred CCCcHHHcC--CCEEecCCCCcchHHHHHHHHHHcCCCHHHccchhcCCHHHHHHHHHCCC----ccEEEEe
Confidence 378999997 77887753 3322 3345555554333 356777888999999999 9999877
No 157
>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=94.48 E-value=0.45 Score=49.89 Aligned_cols=133 Identities=14% Similarity=0.121 Sum_probs=81.8
Q ss_pred HhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeCCc--ccccHHHHHHHHHhC
Q 003054 8 QLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDNQY--GEEMIPSLTDALQAI 85 (852)
Q Consensus 8 ~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~~~--G~~~~~~l~~~l~~~ 85 (852)
..+.+.++|+|......+. ....+| +..++...++.+++.+.+.|-++++++..+..+ .....+.|.+++++.
T Consensus 77 ~~~~~~~ipvV~~~~~~~~--~~~~~~---v~~d~~~~g~~~~~~l~~~g~~~i~~i~~~~~~~~~~~r~~gf~~~~~~~ 151 (270)
T cd06294 77 DYLKEEKFPFVVIGKPEDD--KENITY---VDNDNIQAGYDATEYLIKLGHKKIAFVGGDLDLEVTQDRLQGYKQALEDH 151 (270)
T ss_pred HHHHhcCCCEEEECCCCCC--CCCCCe---EEECcHHHHHHHHHHHHHcCCccEEEecCCcccHHHHHHHHHHHHHHHHc
Confidence 4456778999987643211 012222 345666777788888877799999999743332 344578899999998
Q ss_pred CceeeeeeecCCCCChHHHHHHHHHhhcC--CceEEEEEeChhhHHHHHHHHHHcCCcccceE
Q 003054 86 DTRVPYRSVISPLATDDQIEKELYKLFTM--QTRVFILHMLPSLGSRIFEKANEIGLMNKGCV 146 (852)
Q Consensus 86 g~~v~~~~~~~~~~~~~d~~~~l~~l~~~--~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~v 146 (852)
|..+........+.+..+....+.++.+. ++++|+. .+...+..+++.+++.|+..++-+
T Consensus 152 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~-~~d~~a~g~~~al~~~g~~iP~dv 213 (270)
T cd06294 152 GIPDRNEVIISLDFSEEGGYKALKKLLEQHPRPTAIVA-TDDLLALGVLKVLNELGLKVPEDL 213 (270)
T ss_pred CCCCCcceEEecCCchHHHHHHHHHHHhCCCCCCEEEE-CChHHHHHHHHHHHHcCCCCCcce
Confidence 86432111111112223344455555443 3676665 456678889999999998655444
No 158
>PRK10653 D-ribose transporter subunit RbsB; Provisional
Probab=94.46 E-value=0.76 Score=49.16 Aligned_cols=137 Identities=10% Similarity=0.095 Sum_probs=80.3
Q ss_pred HHHhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHH-cCCc-EEEEEEEeC--CcccccHHHHHHH
Q 003054 6 IIQLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKA-FGWR-EAVPIYVDN--QYGEEMIPSLTDA 81 (852)
Q Consensus 6 v~~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~-~gw~-~vaii~~d~--~~G~~~~~~l~~~ 81 (852)
....+.+.++|+|...... . ..+.+..+.+++..-+..+++++.+ .|.+ +++++..+. .......+.|.++
T Consensus 99 ~l~~~~~~~ipvV~~~~~~---~--~~~~~~~V~~D~~~~g~~~~~~l~~~~~~~~~i~~~~~~~~~~~~~~R~~gf~~a 173 (295)
T PRK10653 99 AVKMANQANIPVITLDRGA---T--KGEVVSHIASDNVAGGKMAGDFIAKKLGEGAKVIQLEGIAGTSAARERGEGFKQA 173 (295)
T ss_pred HHHHHHHCCCCEEEEccCC---C--CCceeeEEccChHHHHHHHHHHHHHHhCCCceEEEEEccCCCccHHHHHHHHHHH
Confidence 3456667899999986432 1 1123444555555556888888754 4543 566655322 2345667889999
Q ss_pred HHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEE-EEEeChhhHHHHHHHHHHcCCcccceEEEEcC
Q 003054 82 LQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVF-ILHMLPSLGSRIFEKANEIGLMNKGCVWIMTD 151 (852)
Q Consensus 82 l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vi-v~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~ 151 (852)
+++.|+++... .....+..+....+.++.+..++.- +++.+...+..+++++++.|+ .+...++-+
T Consensus 174 l~~~g~~~~~~--~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~~d~~A~g~l~al~~~G~--~dv~vig~d 240 (295)
T PRK10653 174 VAAHKFNVLAS--QPADFDRTKGLNVMQNLLTAHPDVQAVFAQNDEMALGALRALQTAGK--SDVMVVGFD 240 (295)
T ss_pred HhhCCCEEEEe--cCCCCCHHHHHHHHHHHHHhCCCcCEEEECCChhHHHHHHHHHHcCC--CceEEEEeC
Confidence 99999876432 1112223344455666665554432 333445566678999999998 233444443
No 159
>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=94.45 E-value=0.56 Score=49.35 Aligned_cols=134 Identities=13% Similarity=0.099 Sum_probs=83.2
Q ss_pred cCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeC--CcccccHHHHHHHHHhCCc
Q 003054 10 GNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDN--QYGEEMIPSLTDALQAIDT 87 (852)
Q Consensus 10 ~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~--~~G~~~~~~l~~~l~~~g~ 87 (852)
+.+.++|+|......+. ....++ +..++...+..+++.+...|-++++++.... .......+.|.+++++.|+
T Consensus 79 ~~~~~ipvV~i~~~~~~--~~~~~~---V~~d~~~~~~~~~~~l~~~g~~~i~~i~~~~~~~~~~~R~~gf~~~~~~~~~ 153 (273)
T cd06292 79 LAERGLPVVLVNGRAPP--PLKVPH---VSTDDALAMRLAVRHLVALGHRRIGFASGPGRTVPRRRKIAGFRAALEEAGL 153 (273)
T ss_pred HHhCCCCEEEEcCCCCC--CCCCCE---EEECcHHHHHHHHHHHHHCCCceEEEEeCCcccccHHHHHHHHHHHHHHcCC
Confidence 45678999988654322 012333 4567778888888988778999999987432 3345567889999999886
Q ss_pred eeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHcCCcccceEEEE
Q 003054 88 RVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIM 149 (852)
Q Consensus 88 ~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~ 149 (852)
+......+..+.+...-...+.++.+.++++|++. +...+..+++.+++.|+..++-+-|+
T Consensus 154 ~~~~~~i~~~~~~~~~~~~~~~~~l~~~~~ai~~~-~d~~a~g~~~~l~~~g~~ip~di~ii 214 (273)
T cd06292 154 EPPEALVARGMFSVEGGQAAAVELLGSGPTAIVAA-SDLMALGAIRAARRRGLRVPEDVSVV 214 (273)
T ss_pred CCChhheEeCCCCHHHHHHHHHHHhcCCCCEEEEc-CcHHHHHHHHHHHHcCCCCCcceEEE
Confidence 43211111111112222334445544458876654 56677788899999998655544443
No 160
>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=94.43 E-value=0.38 Score=50.20 Aligned_cols=134 Identities=9% Similarity=0.079 Sum_probs=86.3
Q ss_pred HHHHhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHH-HcCC-cEEEEEEEeCC--cccccHHHHHH
Q 003054 5 FIIQLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIK-AFGW-REAVPIYVDNQ--YGEEMIPSLTD 80 (852)
Q Consensus 5 ~v~~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~-~~gw-~~vaii~~d~~--~G~~~~~~l~~ 80 (852)
....-+...+||+|+..+. .....+......++....+..+++++. ..+- .+|+++....+ ......+.+.+
T Consensus 71 ~~l~~~~~~gIpvv~~d~~----~~~~~~~~~~v~~d~~~~G~~~a~~l~~~~~~~~~v~~~~~~~~~~~~~~r~~g~~~ 146 (257)
T PF13407_consen 71 PFLEKAKAAGIPVVTVDSD----EAPDSPRAAYVGTDNYEAGKLAAEYLAEKLGAKGKVLILSGSPGNPNTQERLEGFRD 146 (257)
T ss_dssp HHHHHHHHTTSEEEEESST----HHTTSTSSEEEEE-HHHHHHHHHHHHHHHHTTTEEEEEEESSTTSHHHHHHHHHHHH
T ss_pred HHHHHHhhcCceEEEEecc----ccccccceeeeeccHHHHHHHHHHHHHHHhccCceEEeccCCCCchHHHHHHHHHHH
Confidence 3445577789999997664 112234556677788889999999874 3432 68887763333 33456788999
Q ss_pred HHHh-CCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHcCCccc
Q 003054 81 ALQA-IDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEIGLMNK 143 (852)
Q Consensus 81 ~l~~-~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~G~~~~ 143 (852)
++++ .++++..... ..+.+.++-...+.++.+.++-..|++++...+..+++.+++.|+..+
T Consensus 147 ~l~~~~~~~~~~~~~-~~~~~~~~a~~~~~~~l~~~~~~~i~~~~~~~~~g~~~al~~~g~~~~ 209 (257)
T PF13407_consen 147 ALKEYPGVEIVDEYE-YTDWDPEDARQAIENLLQANPVDAIIACNDGMALGAAQALQQAGRAGK 209 (257)
T ss_dssp HHHHCTTEEEEEEEE-ECTTSHHHHHHHHHHHHHHTTEEEEEESSHHHHHHHHHHHHHTTCTTT
T ss_pred HHhhcceeeeeeeee-ccCCCHHHHHHHHHHhhhcCCceEEEeCCChHHHHHHHHHHHcCCccc
Confidence 9998 4666665322 223445566666666665554223455677778889999999998443
No 161
>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=94.39 E-value=0.47 Score=49.69 Aligned_cols=128 Identities=14% Similarity=0.087 Sum_probs=81.3
Q ss_pred hcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeC--CcccccHHHHHHHHHhCC
Q 003054 9 LGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDN--QYGEEMIPSLTDALQAID 86 (852)
Q Consensus 9 i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~--~~G~~~~~~l~~~l~~~g 86 (852)
.+...++|+|......+ ..+| +..++..-+..+++++...|-++++++..+. ..+....+.|.+++++.|
T Consensus 73 ~~~~~~iPvv~~~~~~~-----~~~~---V~~d~~~ag~~a~~~L~~~g~~~i~~i~~~~~~~~~~~R~~Gf~~~~~~~~ 144 (265)
T cd06285 73 ELTRRGVPFVLVLRHAG-----TSPA---VTGDDVLGGRLATRHLLDLGHRRIAVLAGPDYASTARDRLAGFRAALAEAG 144 (265)
T ss_pred HHHHcCCCEEEEccCCC-----CCCE---EEeCcHHHHHHHHHHHHHCCCccEEEEeCCcccccHHHHHHHHHHHHHHcC
Confidence 34567899988765321 2233 3556667777888888888999999998433 345566788999999998
Q ss_pred ceeeeeeecCCCCChHHHHHHHHHhhcC--CceEEEEEeChhhHHHHHHHHHHcCCcccce
Q 003054 87 TRVPYRSVISPLATDDQIEKELYKLFTM--QTRVFILHMLPSLGSRIFEKANEIGLMNKGC 145 (852)
Q Consensus 87 ~~v~~~~~~~~~~~~~d~~~~l~~l~~~--~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~ 145 (852)
+++.....+....+...-...+.++.+. .+++|+. ++...+..+++.+++.|+..++-
T Consensus 145 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~-~~d~~a~g~~~~l~~~g~~~p~d 204 (265)
T cd06285 145 IEVPPERIVYSGFDIEGGEAAAEKLLRSDSPPTAIFA-VNDFAAIGVMGAARDRGLRVPDD 204 (265)
T ss_pred CCCChhhEEeCCCCHHHHHHHHHHHHcCCCCCCEEEE-cCcHHHHHHHHHHHHcCCCCCcc
Confidence 7653221111111222233455555433 4566554 46667788999999999865433
No 162
>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=94.30 E-value=0.54 Score=49.21 Aligned_cols=129 Identities=15% Similarity=0.088 Sum_probs=80.1
Q ss_pred CCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeC---CcccccHHHHHHHHHhCCc
Q 003054 11 NKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDN---QYGEEMIPSLTDALQAIDT 87 (852)
Q Consensus 11 ~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~---~~G~~~~~~l~~~l~~~g~ 87 (852)
.+.++|+|......+ ...+| +..++...++.+++++...|.++++++.... .......+.|.+++++.|+
T Consensus 72 ~~~gipvv~~~~~~~----~~~~~---V~~d~~~~g~~~~~~l~~~g~~~i~~i~~~~~~~~~~~~r~~gf~~~l~~~~~ 144 (265)
T cd06291 72 ENIDLPIVSFDRYLS----ENIPI---VSSDNYEGGRLAAEELIERGCKHIAHIGGPNNTVSPTNLRYEGFLDVLKENGL 144 (265)
T ss_pred hcCCCCEEEEeCCCC----CCCCe---EeechHHHHHHHHHHHHHcCCcEEEEEccCcccccchHHHHHHHHHHHHHcCC
Confidence 467899998876432 22333 4556667778888888778999999997332 3455667889999999887
Q ss_pred eeeeeeecCCCCChHHHHHHHHHhhcCC--ceEEEEEeChhhHHHHHHHHHHcCCcccceEEE
Q 003054 88 RVPYRSVISPLATDDQIEKELYKLFTMQ--TRVFILHMLPSLGSRIFEKANEIGLMNKGCVWI 148 (852)
Q Consensus 88 ~v~~~~~~~~~~~~~d~~~~l~~l~~~~--~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi 148 (852)
++.... ...+.+..+-...+.++.+.. +++|+.. +...+..+++.+++.|...++-+-+
T Consensus 145 ~~~~~~-~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~-~d~~a~~~~~al~~~g~~vp~di~v 205 (265)
T cd06291 145 EVRIIE-IQENFDDAEKKEEIKELLEEYPDIDGIFAS-NDLTAILVLKEAQQRGIRVPEDLQI 205 (265)
T ss_pred CCChhe-eeccccchHHHHHHHHHHhCCCCCCEEEEC-ChHHHHHHHHHHHHcCCCCCcceEE
Confidence 643221 111111222234455554433 4665543 4456788999999999865543333
No 163
>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=94.30 E-value=2.7 Score=40.35 Aligned_cols=69 Identities=19% Similarity=0.294 Sum_probs=46.0
Q ss_pred EeeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCcccEEEeeeeeecCcceeeeccccccccceEEEE
Q 003054 377 GYCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGEFDAVVGDITIVFNRSNYVDFTLPYTESGVSMIV 456 (852)
Q Consensus 377 G~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv 456 (852)
.+..++++.+.++.+ .+++++... ...+++..|.+|++|++++.... ....++ ..++....+++++
T Consensus 13 ~~l~~~i~~~~~~~p-~i~i~~~~~---------~~~~~~~~l~~g~~D~~i~~~~~---~~~~~~-~~~l~~~~~~~~~ 78 (197)
T cd05466 13 YLLPPLLAAFRQRYP-GVELSLVEG---------GSSELLEALLEGELDLAIVALPV---DDPGLE-SEPLFEEPLVLVV 78 (197)
T ss_pred HHhHHHHHHHHHHCC-CCEEEEEEC---------ChHHHHHHHHcCCceEEEEcCCC---CCCcce-EeeeeccceEEEe
Confidence 345677788877776 256666543 35689999999999999864433 223333 3566677888888
Q ss_pred Ecc
Q 003054 457 PIK 459 (852)
Q Consensus 457 ~~~ 459 (852)
+..
T Consensus 79 ~~~ 81 (197)
T cd05466 79 PPD 81 (197)
T ss_pred cCC
Confidence 755
No 164
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=94.29 E-value=0.77 Score=50.17 Aligned_cols=130 Identities=12% Similarity=0.144 Sum_probs=91.5
Q ss_pred HHHhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEe--CCcccccHHHHHHHHH
Q 003054 6 IIQLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVD--NQYGEEMIPSLTDALQ 83 (852)
Q Consensus 6 v~~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d--~~~G~~~~~~l~~~l~ 83 (852)
......+.++|+|......+ +...++ ...++..-++.+++++-+.|-+++++|... ...+..-.+.+.++++
T Consensus 129 ~~~~l~~~~~P~V~i~~~~~---~~~~~~---V~~Dn~~~~~~a~~~L~~~G~~~i~~i~~~~~~~~~~~R~~Gf~~al~ 202 (333)
T COG1609 129 LLELLAAAGIPVVVIDRSPP---GLGVPS---VGIDNFAGAYLATEHLIELGHRRIAFIGGPLDSSASRERLEGYRAALR 202 (333)
T ss_pred HHHHHHhcCCCEEEEeCCCc---cCCCCE---EEEChHHHHHHHHHHHHHCCCceEEEEeCCCccccHhHHHHHHHHHHH
Confidence 34556677999998766544 222333 456778888899999999999999999954 4566788899999999
Q ss_pred hCCcee--eeeeecCCCCChHHHHHHHHHhhcCC---ceEEEEEeChhhHHHHHHHHHHcCCcccc
Q 003054 84 AIDTRV--PYRSVISPLATDDQIEKELYKLFTMQ---TRVFILHMLPSLGSRIFEKANEIGLMNKG 144 (852)
Q Consensus 84 ~~g~~v--~~~~~~~~~~~~~d~~~~l~~l~~~~---~~viv~~~~~~~~~~i~~~a~~~G~~~~~ 144 (852)
+.|+.. .....-. .+..+-...+.++.... |++||+ ++...|..+++.+++.|...|+
T Consensus 203 ~~~~~~~~~~i~~~~--~~~~~g~~~~~~ll~~~~~~ptAif~-~nD~~Alg~l~~~~~~g~~vP~ 265 (333)
T COG1609 203 EAGLPINPEWIVEGD--FSEESGYEAAERLLARGEPRPTAIFC-ANDLMALGALRALRELGLRVPE 265 (333)
T ss_pred HCCCCCCcceEEecC--CChHHHHHHHHHHHhcCCCCCcEEEE-cCcHHHHHHHHHHHHcCCCCCC
Confidence 999875 2222211 22344455555555433 677654 5667899999999999997664
No 165
>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=94.27 E-value=0.69 Score=49.80 Aligned_cols=143 Identities=12% Similarity=0.049 Sum_probs=86.2
Q ss_pred HHhcCCCCccEEeeecCCCCCCC--------CCCCceEeccCCchhHHHHHHHHHHHcCCcE--------EEEEEEe--C
Q 003054 7 IQLGNKSQVPILSFSATSPSLTS--------IRSPYFFRGSLNDSSQAGAITAIIKAFGWRE--------AVPIYVD--N 68 (852)
Q Consensus 7 ~~i~~~~~vP~Is~~ats~~lt~--------~~~py~fR~~p~d~~~~~aia~~l~~~gw~~--------vaii~~d--~ 68 (852)
...+.+.++|+|......+.... ...+|+-...+++...++.+++.+.+.|-++ ++++..+ +
T Consensus 75 ~~~~~~~giPvV~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~d~~~~g~~~~~~l~~~g~~~~~~~g~~~i~~i~~~~~~ 154 (305)
T cd06324 75 LRLAEGAGVKLFLVNSGLTEAQARELGPPREKFPDWLGQLLPNDEEAGYLMAEALISQARSVQAPGGRIDLLAISGDPTT 154 (305)
T ss_pred HHHHHhCCCeEEEEecCCCcchhhcccccccccCceeeeeccCcHHHHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCC
Confidence 34566789999998764332110 0112345567788888888899887767664 6666532 2
Q ss_pred CcccccHHHHHHHHHhCC-ceeeeeeecCCCCChHHHHHHHHHhhcC--CceEEEEEeChhhHHHHHHHHHHcCCcccc-
Q 003054 69 QYGEEMIPSLTDALQAID-TRVPYRSVISPLATDDQIEKELYKLFTM--QTRVFILHMLPSLGSRIFEKANEIGLMNKG- 144 (852)
Q Consensus 69 ~~G~~~~~~l~~~l~~~g-~~v~~~~~~~~~~~~~d~~~~l~~l~~~--~~~viv~~~~~~~~~~i~~~a~~~G~~~~~- 144 (852)
.......+.|++++++.| .++.. .+........-...+.++.+. .+|+|+ +.+...+..+++.+++.|+..++
T Consensus 155 ~~~~~R~~Gf~~~~~~~g~~~~~~--~~~~~~~~~~~~~~~~~~l~~~~~~~ai~-~~~d~~A~g~~~al~~~g~~vp~d 231 (305)
T cd06324 155 PAAILREAGLRRALAEHPDVRLRQ--VVYAGWSEDEAYEQAENLLKRYPDVRLIW-AANDQMAFGALRAAKEAGRKPGRD 231 (305)
T ss_pred hHHHHHHHHHHHHHHHCCCceEee--eecCCCCHHHHHHHHHHHHHHCCCccEEE-ECCchHHHHHHHHHHHcCCCcCCC
Confidence 334556788999999987 44322 122122233334455555433 467665 45666788899999999986544
Q ss_pred eEEEEcCc
Q 003054 145 CVWIMTDG 152 (852)
Q Consensus 145 ~vwi~~~~ 152 (852)
..+++-++
T Consensus 232 i~vig~D~ 239 (305)
T cd06324 232 VLFGGVNW 239 (305)
T ss_pred EEEEecCC
Confidence 33444333
No 166
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=94.27 E-value=0.49 Score=51.79 Aligned_cols=135 Identities=10% Similarity=0.063 Sum_probs=83.2
Q ss_pred hcCC-CCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEE--eCCcccccHHHHHHHHHhC
Q 003054 9 LGNK-SQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYV--DNQYGEEMIPSLTDALQAI 85 (852)
Q Consensus 9 i~~~-~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~--d~~~G~~~~~~l~~~l~~~ 85 (852)
.+.. .++|+|......+. ...+.+ ..+++...+..+++.+...|-+++++|.. ++..+....+.|.+++++.
T Consensus 133 ~l~~~~~iPvV~~d~~~~~---~~~~~~--v~~d~~~~g~~a~~~L~~~G~~~i~~i~~~~~~~~~~~R~~Gf~~~l~~~ 207 (341)
T PRK10703 133 MLEEYRHIPMVVMDWGEAK---ADFTDA--IIDNAFEGGYLAGRYLIERGHRDIGVIPGPLERNTGAGRLAGFMKAMEEA 207 (341)
T ss_pred HHHhcCCCCEEEEecccCC---cCCCCe--EEECcHHHHHHHHHHHHHCCCCcEEEEeCCccccchHHHHHHHHHHHHHc
Confidence 3344 68999987643221 111222 34444556778888887779999999963 3334556678999999999
Q ss_pred CceeeeeeecCCCCChHHHHHHHHHhhcC--CceEEEEEeChhhHHHHHHHHHHcCCcccceEEEE
Q 003054 86 DTRVPYRSVISPLATDDQIEKELYKLFTM--QTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIM 149 (852)
Q Consensus 86 g~~v~~~~~~~~~~~~~d~~~~l~~l~~~--~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~ 149 (852)
|+++........+....+....+.++.+. .+++|+. ++...+..+++.+++.|...++-+.|+
T Consensus 208 gi~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~-~nd~~a~g~~~al~~~g~~ip~dv~vv 272 (341)
T PRK10703 208 NIKVPEEWIVQGDFEPESGYEAMQQILSQKHRPTAVFC-GGDIMAMGAICAADEMGLRVPQDISVI 272 (341)
T ss_pred CCCCChHHeEeCCCCHHHHHHHHHHHHhCCCCCCEEEE-CCcHHHHHHHHHHHHcCCCCCCceEEE
Confidence 98764321111111223344455565443 4677665 456667789999999998655544443
No 167
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=94.18 E-value=0.87 Score=49.82 Aligned_cols=130 Identities=9% Similarity=0.029 Sum_probs=81.3
Q ss_pred HHhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeCC--cccccHHHHHHHHHh
Q 003054 7 IQLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDNQ--YGEEMIPSLTDALQA 84 (852)
Q Consensus 7 ~~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~~--~G~~~~~~l~~~l~~ 84 (852)
...+.+.++|+|...... .....++ +..++...+..++++|.+.|.+++++|..+.. ....-.+.|.+++++
T Consensus 137 ~~~l~~~~iPvV~~~~~~---~~~~~~~---V~~D~~~~~~~a~~~L~~~G~~~I~~i~g~~~~~~~~~R~~Gf~~al~~ 210 (342)
T PRK10014 137 REMAEEKGIPVVFASRAS---YLDDVDT---VRPDNMQAAQLLTEHLIRNGHQRIAWLGGQSSSLTRAERVGGYCATLLK 210 (342)
T ss_pred HHHHhhcCCCEEEEecCC---CCCCCCE---EEeCCHHHHHHHHHHHHHCCCCEEEEEcCCcccccHHHHHHHHHHHHHH
Confidence 345567789998875421 1122233 45567777788889988889999999974332 234456789999999
Q ss_pred CCceeeeeeecCCCCChHHHHHHHHHhhcC--CceEEEEEeChhhHHHHHHHHHHcCCccc
Q 003054 85 IDTRVPYRSVISPLATDDQIEKELYKLFTM--QTRVFILHMLPSLGSRIFEKANEIGLMNK 143 (852)
Q Consensus 85 ~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~--~~~viv~~~~~~~~~~i~~~a~~~G~~~~ 143 (852)
.|+.+.....+........-...+.++.+. .+++|+ +.+...+..+++.+.+.|+..+
T Consensus 211 ~g~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~-~~nd~~A~g~~~~l~~~g~~vp 270 (342)
T PRK10014 211 FGLPFHSEWVLECTSSQKQAAEAITALLRHNPTISAVV-CYNETIAMGAWFGLLRAGRQSG 270 (342)
T ss_pred cCCCCCcceEecCCCChHHHHHHHHHHHcCCCCCCEEE-ECCcHHHHHHHHHHHHcCCCCC
Confidence 997653322221111122233445555433 456665 4566677889999999998655
No 168
>PRK11480 tauA taurine transporter substrate binding subunit; Provisional
Probab=94.15 E-value=0.35 Score=52.60 Aligned_cols=66 Identities=26% Similarity=0.340 Sum_probs=47.6
Q ss_pred CcCCHHHHHhcCCeEEEEeCchHH----HHHHhcCCCCcceeecC-CHhHHHHHhhcccccCceeEEEechhHHHHH
Q 003054 569 TITDVKMLIKRGDNVGYQKGSFVL----GILKQLGFDERKLVVYN-SPEDCHELFQKGSVNGGIAAAFDEIPYMKLL 640 (852)
Q Consensus 569 ~i~sl~dL~~~~~~vg~~~~s~~~----~~l~~~~~~~~~~~~~~-~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~ 640 (852)
.|++++||. |++||+..++... .+|++.+.+...+.... .+.+..+++.+|+ ++|++...++....
T Consensus 113 ~I~s~~DLk--GK~Iav~~~s~~~~~l~~~L~~~Gl~~~dv~~v~~~~~~~~~Al~~G~----VDAa~~~~p~~~~~ 183 (320)
T PRK11480 113 TISKPEDLI--GKRIAVPFISTTHYSLLAALKHWGIKPGQVEIVNLQPPAIIAAWQRGD----IDGAYVWAPAVNAL 183 (320)
T ss_pred CCCChHHcC--CCEEecCCCCchHHHHHHHHHHcCCCHhheEEEECCcHHHHHHHHcCC----cCEEEEcchHHHHH
Confidence 389999997 9999997766433 34666777655544333 4577889999999 99988776665433
No 169
>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=94.14 E-value=0.77 Score=48.13 Aligned_cols=132 Identities=11% Similarity=0.007 Sum_probs=81.1
Q ss_pred CCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEe--CCcccccHHHHHHHHHhCCce
Q 003054 11 NKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVD--NQYGEEMIPSLTDALQAIDTR 88 (852)
Q Consensus 11 ~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d--~~~G~~~~~~l~~~l~~~g~~ 88 (852)
+..++|+|......+ +...++ +..++...++.+++++...|-++++++... +.......+.|.+++++.|++
T Consensus 76 ~~~~ipvV~i~~~~~---~~~~~~---V~~d~~~~~~~~~~~l~~~G~~~i~~i~~~~~~~~~~~r~~gf~~~~~~~~~~ 149 (269)
T cd06275 76 RYRHIPMVVMDWGPE---DDFADK---IQDNSEEGGYLATRHLIELGHRRIGCITGPLEKAPAQQRLAGFRRAMAEAGLP 149 (269)
T ss_pred hcCCCCEEEEecccC---CCCCCe---EeeCcHHHHHHHHHHHHHCCCceEEEEeCCCCCccHHHHHHHHHHHHHHcCCC
Confidence 456899998765322 122233 345666667778888878899999999742 233455678899999998877
Q ss_pred eeeeeecCCCCChHHHHHHHHHhhcC--CceEEEEEeChhhHHHHHHHHHHcCCcccceEEEE
Q 003054 89 VPYRSVISPLATDDQIEKELYKLFTM--QTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIM 149 (852)
Q Consensus 89 v~~~~~~~~~~~~~d~~~~l~~l~~~--~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~ 149 (852)
+..........+.......+.++.+. .+++|++ .+...+..+++.+++.|...|+-+-++
T Consensus 150 ~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~-~~d~~a~g~~~~l~~~g~~vp~di~vv 211 (269)
T cd06275 150 VNPGWIVEGDFECEGGYEAMQRLLAQPKRPTAVFC-GNDLMAMGALCAAQEAGLRVPQDLSII 211 (269)
T ss_pred CCHHHhccCCCChHHHHHHHHHHHcCCCCCcEEEE-CChHHHHHHHHHHHHcCCCCCcceEEE
Confidence 53221111111222334456665544 3566554 455667788899999998655444443
No 170
>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=94.13 E-value=0.53 Score=49.19 Aligned_cols=133 Identities=9% Similarity=0.074 Sum_probs=82.7
Q ss_pred hcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeCC--cccccHHHHHHHHHhCC
Q 003054 9 LGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDNQ--YGEEMIPSLTDALQAID 86 (852)
Q Consensus 9 i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~~--~G~~~~~~l~~~l~~~g 86 (852)
.+...++|+|......+ ...++ +..++...+..+++++...|-++++++..... ........|++++++.|
T Consensus 69 ~~~~~~ipvV~~~~~~~----~~~~~---V~~d~~~~~~~~~~~l~~~g~~~i~~i~~~~~~~~~~~R~~gf~~~~~~~~ 141 (261)
T cd06272 69 YKIKLAIPVVSYGVDYD----LKYPI---VNVDNEKAMELAVLYLAEKGHKKIAYIGDLSLDRRQRKRFKGFLETCDENG 141 (261)
T ss_pred HHHHcCCCEEEEcccCC----CCCCE---EEEChHHHHHHHHHHHHHcCchhEEEeecccccccHHHHHHHHHHHHHHcC
Confidence 34567899988755322 12233 45677777888889887789999999974433 33445678999999998
Q ss_pred ceeeeeeecCCCCChHHHHHHHHHhhcCC--ceEEEEEeChhhHHHHHHHHHHcCCcccceEEEE
Q 003054 87 TRVPYRSVISPLATDDQIEKELYKLFTMQ--TRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIM 149 (852)
Q Consensus 87 ~~v~~~~~~~~~~~~~d~~~~l~~l~~~~--~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~ 149 (852)
+.+..........+...-...+.++.+.. +++|+ +++...+..+++.+++.|+..++-+-++
T Consensus 142 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~-~~~d~~a~~~~~~l~~~g~~vp~dv~vv 205 (261)
T cd06272 142 ISISDSHIDVDGLSAEGGDNAAKKLLKESDLPTAII-CGSYDIALGVLSALNKQGISIPEDIEII 205 (261)
T ss_pred CCCCHHHeeeCCCCHHHHHHHHHHHHcCCCCCCEEE-ECCcHHHHHHHHHHHHhCCCCCCceEEE
Confidence 64432211111112233334555555443 56644 4556677889999999998655444333
No 171
>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=94.13 E-value=0.98 Score=47.44 Aligned_cols=135 Identities=13% Similarity=0.111 Sum_probs=84.3
Q ss_pred hcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHc--CCcEEEEEEEeCCc--ccccHHHHHHHHHh
Q 003054 9 LGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAF--GWREAVPIYVDNQY--GEEMIPSLTDALQA 84 (852)
Q Consensus 9 i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~--gw~~vaii~~d~~~--G~~~~~~l~~~l~~ 84 (852)
.+.+.++|+|.+.... .+. .+...+..++...+..+++++.+. |-++++++..+... .....+.+.+++++
T Consensus 76 ~~~~~~ipvV~~~~~~---~~~--~~~~~V~~d~~~~g~~~~~~l~~~~~g~~~i~~l~~~~~~~~~~~R~~g~~~~l~~ 150 (270)
T cd06308 76 EAYRAGIPVILLDRKI---LSD--KYTAYIGADNYEIGRQAGEYIANLLPGKGNILEIWGLEGSSPAIERHDGFKEALSK 150 (270)
T ss_pred HHHHCCCCEEEeCCCC---CCc--cceEEeecCcHHHHHHHHHHHHHHcCCCceEEEEECCCCCchHHHHHHHHHHHHHH
Confidence 3456899999886422 111 233345667777888888887664 89999999743332 34457889999999
Q ss_pred C-CceeeeeeecCCCCChHHHHHHHHHhhc--CCceEEEEEeChhhHHHHHHHHHHcCCcccceEEEEcCc
Q 003054 85 I-DTRVPYRSVISPLATDDQIEKELYKLFT--MQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDG 152 (852)
Q Consensus 85 ~-g~~v~~~~~~~~~~~~~d~~~~l~~l~~--~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~ 152 (852)
. |+++.... ..+...++-...+.++.+ .++++|+ +.+...+..+++.+++.|+. .+...++-|.
T Consensus 151 ~~~~~~~~~~--~~~~~~~~~~~~~~~~l~~~~~~~aI~-~~~d~~a~g~~~al~~~g~~-~dv~vvg~d~ 217 (270)
T cd06308 151 YPKIKIVAQQ--DGDWLKEKAEEKMEELLQANPDIDLVY-AHNDPMALGAYLAAKRAGRE-KEIKFIGIDG 217 (270)
T ss_pred CCCCEEEEec--CCCccHHHHHHHHHHHHHhCCCCcEEE-eCCcHHHHHHHHHHHHcCCC-CCcEEEEecC
Confidence 8 88765321 111122222334445433 3467654 44666778899999999987 5455555544
No 172
>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=94.03 E-value=0.19 Score=48.05 Aligned_cols=97 Identities=12% Similarity=0.096 Sum_probs=66.1
Q ss_pred HHHHHHcCCcEEEEEEE--eCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHH-HHhhcCCceEEEEEeChh
Q 003054 50 TAIIKAFGWREAVPIYV--DNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKEL-YKLFTMQTRVFILHMLPS 126 (852)
Q Consensus 50 a~~l~~~gw~~vaii~~--d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l-~~l~~~~~~viv~~~~~~ 126 (852)
++++.+.|.+++++|.. ++.+.....+.|.+++++.|++.......... ...+..... ..+++..||+||+ ++..
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 46778889999999993 33455777888999999999986655444322 233333222 2344447887766 7788
Q ss_pred hHHHHHHHHHHcCCcccceEEE
Q 003054 127 LGSRIFEKANEIGLMNKGCVWI 148 (852)
Q Consensus 127 ~~~~i~~~a~~~G~~~~~~vwi 148 (852)
.+..+++.+++.|+..+.-+-|
T Consensus 79 ~a~~~~~~l~~~g~~vP~di~v 100 (160)
T PF13377_consen 79 LALGVLRALRELGIRVPQDISV 100 (160)
T ss_dssp HHHHHHHHHHHTTSCTTTTSEE
T ss_pred HHHHHHHHHHHcCCcccccccE
Confidence 8999999999999965533333
No 173
>COG3221 PhnD ABC-type phosphate/phosphonate transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=94.02 E-value=1.5 Score=46.74 Aligned_cols=110 Identities=15% Similarity=0.133 Sum_probs=74.7
Q ss_pred CCcCCHHHHHhcCCeEEEEeCchHH------HHHHhcC-CCCc---ceeecCC-HhHHHHHhhcccccCceeEEEechhH
Q 003054 568 PTITDVKMLIKRGDNVGYQKGSFVL------GILKQLG-FDER---KLVVYNS-PEDCHELFQKGSVNGGIAAAFDEIPY 636 (852)
Q Consensus 568 ~~i~sl~dL~~~~~~vg~~~~s~~~------~~l~~~~-~~~~---~~~~~~~-~~~~~~~l~~g~~~~g~~a~~~~~~~ 636 (852)
++|++++||. |+++++..-+..- .+|.+.+ .+.. .-+.+.. -+..+.+|.+|+ +|+.......
T Consensus 134 s~i~sl~dlk--gk~~af~d~~StSG~l~P~~~L~~~g~~d~~~~f~~v~~~G~H~~a~~aV~nG~----vDva~~~~~~ 207 (299)
T COG3221 134 SPIKSLEDLK--GKRFAFGDPDSTSGYLFPLYYLAKEGGIDPDKFFGEVIFSGGHDAAVLAVANGQ----VDVAAVNSSA 207 (299)
T ss_pred CCcchHHHhc--CCeEeccCCCcchhhHhHHHHHHHhcCCChhhhhceeeccChHHHHHHHHHcCC----ceEEeccHHH
Confidence 3599999997 9999995443222 3344443 2211 1233333 678899999999 8888877666
Q ss_pred HHHHHhhc-C---CceEeecccccccceEEEecCCCC--chhhHHHHHHhccc
Q 003054 637 MKLLIGQY-C---SKYAMIEPKFKTAGFGFVFPLHSP--LVHDVSKAILNVTE 683 (852)
Q Consensus 637 ~~~~~~~~-~---~~~~~v~~~~~~~~~~~~~~k~sp--l~~~in~~il~l~e 683 (852)
...+.... - +++.++...-......++++++-| +++.+..+++.+.+
T Consensus 208 ~~~~~~~~~~~~~~~l~vi~~S~~iP~~pi~vr~~L~~~~k~kl~~af~~l~~ 260 (299)
T COG3221 208 RGLLKKAAPEGVAEKLRVIWKSPLIPNDPIAVRSDLPADLKEKLRDAFLDLAK 260 (299)
T ss_pred HhhhhhcccccchhhceEEEecCCCCCCCEEEeCCCCHHHHHHHHHHHHhcCc
Confidence 66555544 2 367777665455566778888755 99999999999986
No 174
>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=93.98 E-value=0.16 Score=42.30 Aligned_cols=56 Identities=21% Similarity=0.293 Sum_probs=47.5
Q ss_pred cccccchhHHHHHHHhhhcc-c-cccccchhhHHHHHHHHHHHHHHHHhhhhccceee
Q 003054 507 AGQQVGTSFWFSFSTMVFSQ-R-ERVISNLARIVVIVWCFVVLILTQSYTASLTSLLT 562 (852)
Q Consensus 507 ~~~~~~~~~~~~~~~l~~~~-~-~~~~s~~~R~v~~~w~~~~lil~~~Yta~L~s~Lt 562 (852)
...++.+++|+++.++...| + ..|.+..+|++.+++.++++.+.....+.+++.++
T Consensus 21 ~~~~~~da~yfs~~t~tTvGyGDi~p~t~~gr~~~~~~~~~G~~~~~~~~~~~~~~l~ 78 (79)
T PF07885_consen 21 EKWSFIDALYFSFVTITTVGYGDIVPQTPAGRIFTIIYMLIGIFLFALFLSVLASVLT 78 (79)
T ss_dssp STTSHHHHHHHHHHHHTT---SSSSTSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred ccCCHHHHHHHHHHHHhcccCCCccCCccchHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 35678999999999999877 4 46788889999999999999999999999988764
No 175
>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=93.89 E-value=0.87 Score=47.90 Aligned_cols=132 Identities=13% Similarity=0.058 Sum_probs=82.8
Q ss_pred HhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeC--C------cccccHHHHH
Q 003054 8 QLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDN--Q------YGEEMIPSLT 79 (852)
Q Consensus 8 ~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~--~------~G~~~~~~l~ 79 (852)
..+.+.++|+|...... ...++ +..++..-+..+++.|.+. .++++++..+. . .+....+.|+
T Consensus 72 ~~l~~~~iPvv~~~~~~-----~~~~~---v~~d~~~~g~~a~~~L~~~-~~~i~~i~~~~~~~~~~~~~~~~~R~~gf~ 142 (269)
T cd06297 72 ERRLPTERPVVLVDAEN-----PRFDS---FYLDNRLGGRLAGAYLADF-PGRIGAITVEEEPDRAFRRTVFAERRAGFQ 142 (269)
T ss_pred HHHhhcCCCEEEEccCC-----CCCCE---EEECcHHHHHHHHHHHHHh-CCceEEEeCccccccccccccHHHHHHHHH
Confidence 44566789999876522 12233 3467777777888887666 79999986332 2 3455688999
Q ss_pred HHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcC--CceEEEEEeChhhHHHHHHHHHHcCCcccceEEEE
Q 003054 80 DALQAIDTRVPYRSVISPLATDDQIEKELYKLFTM--QTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIM 149 (852)
Q Consensus 80 ~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~--~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~ 149 (852)
+++++.|+++.....+..+.+..+....+.++.+. ++++|++. +...+..+++.+++.|...|+-+-|+
T Consensus 143 ~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~-~d~~a~g~~~~l~~~g~~vP~di~vv 213 (269)
T cd06297 143 QALKDAGRPFSPDLLAITDHSEEGGRLAMRHLLEKASPPLAVFAS-ADQQALGALQEAVELGLTVGEDVRVV 213 (269)
T ss_pred HHHHHcCCCCChhhEEeCCCChhhHHHHHHHHHcCCCCCcEEEEc-CcHHHHHHHHHHHHcCCCCCCceEEE
Confidence 99999988754322221111223334556665543 35666654 55578889999999998665544443
No 176
>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=93.87 E-value=0.72 Score=48.36 Aligned_cols=138 Identities=12% Similarity=0.035 Sum_probs=84.5
Q ss_pred HHhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEe--CCcccccHHHHHHHHHh
Q 003054 7 IQLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVD--NQYGEEMIPSLTDALQA 84 (852)
Q Consensus 7 ~~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d--~~~G~~~~~~l~~~l~~ 84 (852)
...+...++|+|........ ....++ ..+++...++.+++.+...|.++++++..+ +.......+.|.+++++
T Consensus 71 ~~~~~~~~ipvV~i~~~~~~--~~~~~~---v~~d~~~~~~~a~~~l~~~g~~~i~~i~~~~~~~~~~~r~~gf~~~~~~ 145 (270)
T cd06296 71 RAALRRTGIPFVVVDPAGDP--DADVPS---VGATNWAGGLAATEHLLELGHRRIGFITGPPDLLCSRARLDGYRAALAE 145 (270)
T ss_pred HHHHhcCCCCEEEEecccCC--CCCCCE---EEeCcHHHHHHHHHHHHHcCCCcEEEEcCCCcchhHHHHHHHHHHHHHH
Confidence 34456678999988654211 112233 466777788888888877799999999743 23445667889999998
Q ss_pred CCceeeeeeecCCCCChHHHHHHHHHhhcC--CceEEEEEeChhhHHHHHHHHHHcCCcccceE-EEEc
Q 003054 85 IDTRVPYRSVISPLATDDQIEKELYKLFTM--QTRVFILHMLPSLGSRIFEKANEIGLMNKGCV-WIMT 150 (852)
Q Consensus 85 ~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~--~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~v-wi~~ 150 (852)
.|+.+..........+.+.....+.++.+. .+++|+. .+...+..+++.+++.|...++-+ +++-
T Consensus 146 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~-~~d~~a~~~~~~l~~~g~~~p~~i~v~~~ 213 (270)
T cd06296 146 AGIPVDPALVREGDFSTESGFRAAAELLALPERPTAIFA-GNDLMALGVYEAARERGLRIPEDLSVVGF 213 (270)
T ss_pred cCCCCChHHheeCCCCHHHHHHHHHHHHhCCCCCcEEEE-cCcHHHHHHHHHHHHhCCCCCCceEEEEE
Confidence 887653221111111223333445555433 4566554 455667889999999998654443 4433
No 177
>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=93.86 E-value=4.5 Score=39.14 Aligned_cols=69 Identities=14% Similarity=0.161 Sum_probs=46.2
Q ss_pred EeeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCcccEEEeeeeeecCcceeeeccccccccceEEEE
Q 003054 377 GYCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGEFDAVVGDITIVFNRSNYVDFTLPYTESGVSMIV 456 (852)
Q Consensus 377 G~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv 456 (852)
.+-.+++..+.++.+- +++++.. ++..+++..+.+|++|+++... +.....+. ..+.....+++++
T Consensus 13 ~~l~~~l~~~~~~~P~-i~l~i~~---------~~~~~~~~~l~~g~~Dl~i~~~---~~~~~~~~-~~~l~~~~~~~v~ 78 (193)
T cd08442 13 VRLPPLLAAYHARYPK-VDLSLST---------GTTGALIQAVLEGRLDGAFVAG---PVEHPRLE-QEPVFQEELVLVS 78 (193)
T ss_pred hhhHHHHHHHHHHCCC-ceEEEEe---------CCcHHHHHHHHCCCccEEEEeC---CCCCCCcE-EEEeecCcEEEEe
Confidence 4457889999888873 4555544 2467899999999999987532 22222232 3566677788887
Q ss_pred Ecc
Q 003054 457 PIK 459 (852)
Q Consensus 457 ~~~ 459 (852)
+..
T Consensus 79 ~~~ 81 (193)
T cd08442 79 PKG 81 (193)
T ss_pred cCC
Confidence 754
No 178
>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=93.85 E-value=4.7 Score=39.09 Aligned_cols=69 Identities=16% Similarity=0.244 Sum_probs=47.0
Q ss_pred EeeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCcccEEEeeeeeecCcceeeeccccccccceEEEE
Q 003054 377 GYCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGEFDAVVGDITIVFNRSNYVDFTLPYTESGVSMIV 456 (852)
Q Consensus 377 G~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv 456 (852)
.+..++++.+.++.+ .+++++.. ++..+++..|.+|++|+++..... ....+. ..++....+++++
T Consensus 13 ~~l~~~l~~~~~~~p-~v~i~i~~---------~~~~~~~~~L~~~~~Dl~i~~~~~---~~~~~~-~~~l~~~~~~~v~ 78 (197)
T cd08438 13 LLFAPLLAAFRQRYP-NIELELVE---------YGGKKVEQAVLNGELDVGITVLPV---DEEEFD-SQPLCNEPLVAVL 78 (197)
T ss_pred hhcHHHHHHHHHHCc-CeEEEEEE---------cCcHHHHHHHHcCCCCEEEEeccc---ccCCce-eEEeccccEEEEe
Confidence 455688999998876 35565544 246789999999999999864322 122232 3567778888888
Q ss_pred Ecc
Q 003054 457 PIK 459 (852)
Q Consensus 457 ~~~ 459 (852)
+..
T Consensus 79 ~~~ 81 (197)
T cd08438 79 PRG 81 (197)
T ss_pred cCC
Confidence 754
No 179
>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=93.79 E-value=0.74 Score=48.35 Aligned_cols=132 Identities=11% Similarity=0.032 Sum_probs=79.8
Q ss_pred HHHhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeC--CcccccHHHHHHHHH
Q 003054 6 IIQLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDN--QYGEEMIPSLTDALQ 83 (852)
Q Consensus 6 v~~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~--~~G~~~~~~l~~~l~ 83 (852)
+...+.+.++|+|......+ . ..++ +..++..-+..+++++...|-++++++.... ..+....+.|.++++
T Consensus 71 ~~~~~~~~~ipvV~i~~~~~--~--~~~~---V~~d~~~~g~~a~~~l~~~G~~~i~~l~~~~~~~~~~~R~~Gf~~~~~ 143 (269)
T cd06281 71 LVDALASLDLPIVLLDRDMG--G--GADA---VLFDHAAGMRQAVEYLISLGHRRIALVGGGSNTRPGRERLEGYKAAFA 143 (269)
T ss_pred HHHHHHhCCCCEEEEecccC--C--CCCE---EEECcHHHHHHHHHHHHHCCCcEEEEecCccccccHHHHHHHHHHHHH
Confidence 34455667899998865433 1 1232 3445555556777887777999999997432 233455688999999
Q ss_pred hCCceeeeeeecCCCCChHHHHHHHHHhhc--CCceEEEEEeChhhHHHHHHHHHHcCCcccceE
Q 003054 84 AIDTRVPYRSVISPLATDDQIEKELYKLFT--MQTRVFILHMLPSLGSRIFEKANEIGLMNKGCV 146 (852)
Q Consensus 84 ~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~--~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~v 146 (852)
+.|+++.....+..+. ...-...+.++.+ ..+++|+. .+...+..+++.+++.|+..++-+
T Consensus 144 ~~~~~~~~~~~~~~~~-~~~~~~~~~~~l~~~~~~~ai~~-~~d~~a~g~~~~l~~~g~~ip~dv 206 (269)
T cd06281 144 AAGLPPDPALVRLSTP-AASGFDATRALLALPDRPTAIIA-GGTQVLVGVLRALREAGLRIPRDL 206 (269)
T ss_pred HcCCCCCHHHeecCcH-HHHHHHHHHHHHcCCCCCcEEEE-cCcHHHHHHHHHHHHcCCCCCcce
Confidence 9987652211111111 1222334444432 34788764 455667789999999998655443
No 180
>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=93.77 E-value=1.3 Score=46.15 Aligned_cols=122 Identities=15% Similarity=0.111 Sum_probs=68.4
Q ss_pred CCcCCHHHHHhcCCeEEEEeCchHHH----HHHhcCCC------------------CcceeecC-CHhHHHHHhhccccc
Q 003054 568 PTITDVKMLIKRGDNVGYQKGSFVLG----ILKQLGFD------------------ERKLVVYN-SPEDCHELFQKGSVN 624 (852)
Q Consensus 568 ~~i~sl~dL~~~~~~vg~~~~s~~~~----~l~~~~~~------------------~~~~~~~~-~~~~~~~~l~~g~~~ 624 (852)
..+++++||. .|++|++..+..... .|++.++- +..+.... ...+...++.+|+
T Consensus 106 ~~~~sl~dlk-~G~~IAip~d~~n~~raL~~L~~aGLi~l~~~~~~~~t~~DI~~n~~~v~~vel~~~~~~~al~~g~-- 182 (258)
T TIGR00363 106 KKIKNVNELQ-DGAKVAVPNDPTNLGRALLLLQKQGLIKLKDGNGLLPTVLDIVENPKKLNITELETSQLPRALDDPK-- 182 (258)
T ss_pred cCCCCHHHcC-CCCEEEEeCCcchHHHHHHHHHHcCCceecCCCCCcCChhhhhcCCCCCEEEEcCHHHHHHHhhccc--
Confidence 3599999994 488999987654333 36665552 22232222 3456778999998
Q ss_pred CceeEEEechhHHHHHHhhcCCceEeecccccccceEEEecCCCCchhhHHHHHHhccccChhHHHHHHH
Q 003054 625 GGIAAAFDEIPYMKLLIGQYCSKYAMIEPKFKTAGFGFVFPLHSPLVHDVSKAILNVTEGDKMKEIEDAW 694 (852)
Q Consensus 625 ~g~~a~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~k~spl~~~in~~il~l~e~G~~~~i~~kw 694 (852)
++|++...+++.-.-...-+.-......-...-..++++...-=.+.+.+.+..++...+-+.|.++|
T Consensus 183 --vDaa~v~~~~~~~agl~~~~~~i~~e~~~~~~~n~l~~r~~~~~~~~~~~lv~~~~s~~v~~~i~~~~ 250 (258)
T TIGR00363 183 --VDLAVINTTYAGQVGLNPQDDGVFVEDKDSPYVNIIVSREDNKDAENVKDFIQSYQSEEVYQAAQKHF 250 (258)
T ss_pred --ccEEEEChHHHHHcCCCcCcCceeecCCCCCeeEEEEEcCCccCCHHHHHHHHHHcCHHHHHHHHHHc
Confidence 99998887765543111111111122111122245556655334456666666666665555665554
No 181
>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=93.61 E-value=0.86 Score=47.66 Aligned_cols=126 Identities=10% Similarity=0.049 Sum_probs=79.5
Q ss_pred CCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEe--CCcccccHHHHHHHHHhCCceee
Q 003054 13 SQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVD--NQYGEEMIPSLTDALQAIDTRVP 90 (852)
Q Consensus 13 ~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d--~~~G~~~~~~l~~~l~~~g~~v~ 90 (852)
.++|+|......+ +...+| +..++..-+..+++++...|-++++++..+ +.......+.|.+++++.|..+.
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 4799998865322 122333 445777777888888877799999999743 33445667889999998887653
Q ss_pred eeeecCCCCChHHHHHHHHHhhcC--CceEEEEEeChhhHHHHHHHHHHcCCcccce
Q 003054 91 YRSVISPLATDDQIEKELYKLFTM--QTRVFILHMLPSLGSRIFEKANEIGLMNKGC 145 (852)
Q Consensus 91 ~~~~~~~~~~~~d~~~~l~~l~~~--~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~ 145 (852)
....+..+.+...-...+.++.+. .+++|++ ++...+..+++.+++.|+..++-
T Consensus 150 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~aii~-~~~~~a~~~~~~l~~~g~~ip~d 205 (265)
T cd06290 150 PDLIVQGDFEEESGLEAVEELLQRGPDFTAIFA-ANDQTAYGARLALYRRGLRVPED 205 (265)
T ss_pred HHHEEecCCCHHHHHHHHHHHHcCCCCCCEEEE-cCcHHHHHHHHHHHHcCCCCCcc
Confidence 221111111122233445555543 3576664 56667888999999999865543
No 182
>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=93.42 E-value=1.3 Score=46.27 Aligned_cols=129 Identities=13% Similarity=0.138 Sum_probs=81.8
Q ss_pred CCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeCCc--ccccHHHHHHHHHhCCce
Q 003054 11 NKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDNQY--GEEMIPSLTDALQAIDTR 88 (852)
Q Consensus 11 ~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~~~--G~~~~~~l~~~l~~~g~~ 88 (852)
.+.++|+|......+ ...+| +..++..-++.+++++...|-++|+++..+..+ .....+.|.+++++.|++
T Consensus 76 ~~~~ipvv~~~~~~~----~~~~~---v~~d~~~~g~~~~~~l~~~g~~~i~~i~~~~~~~~~~~r~~gf~~~l~~~~~~ 148 (264)
T cd01574 76 APADVPVVFVDGSPS----PRVST---VSVDQEGGARLATEHLLELGHRTIAHVAGPEEWLSARARLAGWRAALEAAGIA 148 (264)
T ss_pred HhcCCCEEEEeccCC----CCCCE---EEeCcHHHHHHHHHHHHHCCCCEEEEEecCCccchHHHHHHHHHHHHHHCCCC
Confidence 467899999865321 12233 466777788888898888899999999744332 234567889999988876
Q ss_pred eeeeeecCCCCChHHHHHHHHHhhcCC-ceEEEEEeChhhHHHHHHHHHHcCCcccceEEEE
Q 003054 89 VPYRSVISPLATDDQIEKELYKLFTMQ-TRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIM 149 (852)
Q Consensus 89 v~~~~~~~~~~~~~d~~~~l~~l~~~~-~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~ 149 (852)
+... +..+.+.+.-...+.++.+.. +++|+. ++...+..+++.+++.|...++-+-|+
T Consensus 149 ~~~~--~~~~~~~~~~~~~~~~~l~~~~~~ai~~-~~d~~a~g~~~~~~~~g~~ip~~i~ii 207 (264)
T cd01574 149 PPPV--LEGDWSAESGYRAGRELLREGDPTAVFA-ANDQMALGVLRALHELGLRVPDDVSVV 207 (264)
T ss_pred ccee--eecCCCHHHHHHHHHHHHhCCCCcEEEE-cCcHHHHHHHHHHHHcCCCCccceEEe
Confidence 6432 211112233334455554433 677555 456678889999999997544433333
No 183
>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=93.38 E-value=1.8 Score=45.62 Aligned_cols=137 Identities=10% Similarity=0.017 Sum_probs=80.9
Q ss_pred HhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHc--CCcEEEEEEEeC-CcccccHHHHHHHHHh
Q 003054 8 QLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAF--GWREAVPIYVDN-QYGEEMIPSLTDALQA 84 (852)
Q Consensus 8 ~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~--gw~~vaii~~d~-~~G~~~~~~l~~~l~~ 84 (852)
..+.+.+||+|......+ +.. .....+.+++...+..+++++.+. |.++|+++..+. .......+.|.+.+++
T Consensus 79 ~~~~~~gIpvV~~d~~~~---~~~-~~~~~V~~d~~~~g~~aa~~l~~~~~g~~~i~~~~g~~~~~~~~R~~gf~~~l~~ 154 (274)
T cd06311 79 AKAKKAGIFVVVVDRGLS---SPG-AQDLYVAGDNYGMGRVAGEYIATKLGGNGNIVVLRGIPTPIDNERVDAFDAAIAK 154 (274)
T ss_pred HHHHHCCCeEEEEcCCCC---CCc-ccceEEcCCcHHHHHHHHHHHHHHhCCCCeEEEEECCCCcchhHHHHHHHHHHhh
Confidence 345678999999765321 111 112235666677778888887555 789999997432 2334456889999999
Q ss_pred CCceeeeeeecCCCCChHHHHHHHHHhhcC--CceEEEEEeChhhHHHHHHHHHHcCCcccceEEEEcCc
Q 003054 85 IDTRVPYRSVISPLATDDQIEKELYKLFTM--QTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDG 152 (852)
Q Consensus 85 ~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~--~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~ 152 (852)
.|+++... ...+.+...-...+.++.+. ++++|+.. +...+..+++.+++.|... +...++.++
T Consensus 155 ~~~~~~~~--~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~-~d~~a~g~~~al~~~g~~~-~~~ivg~d~ 220 (274)
T cd06311 155 YPIKILDR--QYANWNRDDAFSVMQDLLTKFPKIDAVWAH-DDDMAVGVLAAIKQAGRTD-IKFVVGGAG 220 (274)
T ss_pred CCcEEEec--cCCCCcHHHHHHHHHHHHHhCCCcCEEEEC-CCcHHHHHHHHHHHcCCCC-CceEEEeCC
Confidence 88776532 21111222233444454433 35665443 4445778899999999752 333444444
No 184
>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=93.38 E-value=1.3 Score=46.40 Aligned_cols=131 Identities=14% Similarity=0.061 Sum_probs=82.8
Q ss_pred CCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeCC--cccccHHHHHHHHHhCCcee
Q 003054 12 KSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDNQ--YGEEMIPSLTDALQAIDTRV 89 (852)
Q Consensus 12 ~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~~--~G~~~~~~l~~~l~~~g~~v 89 (852)
..++|+|......+. ...+ .+.+++...+..+++++.+.|-+++++|..+.. ......+.|++++++.|..+
T Consensus 76 ~~~~pvV~i~~~~~~---~~~~---~V~~d~~~~~~~~~~~L~~~G~~~i~~i~~~~~~~~~~~R~~Gf~~a~~~~~~~~ 149 (269)
T cd06293 76 NSYGNIVLVDEDVPG---AKVP---KVFCDNEQGGRLATRHLARAGHRRIAFVGGPDALISARERYAGYREALAEAHIPE 149 (269)
T ss_pred hcCCCEEEECCCCCC---CCCC---EEEECCHHHHHHHHHHHHHCCCceEEEEecCcccccHHHHHHHHHHHHHHcCCCC
Confidence 357999987653322 1122 355788888889999988889999999974333 23455788999999988754
Q ss_pred eeeeecCCCCChHHHHHHHHHhhc--CCceEEEEEeChhhHHHHHHHHHHcCCcccceEEEE
Q 003054 90 PYRSVISPLATDDQIEKELYKLFT--MQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIM 149 (852)
Q Consensus 90 ~~~~~~~~~~~~~d~~~~l~~l~~--~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~ 149 (852)
.....+..+.+.++-...+.++.+ ..+++|+.. +...+..+++.+++.|...|+-+-|+
T Consensus 150 ~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~-~d~~a~g~~~al~~~g~~vp~di~i~ 210 (269)
T cd06293 150 VPEYVCFGDYTREFGRAAAAQLLARGDPPTAIFAA-SDEIAIGLLEVLRERGLSIPGDMSLV 210 (269)
T ss_pred ChheEEecCCCHHHHHHHHHHHHcCCCCCCEEEEc-CcHHHHHHHHHHHHcCCCCccceEEE
Confidence 321111111122233345555543 346776654 56667789999999998666544443
No 185
>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=93.38 E-value=1.5 Score=46.10 Aligned_cols=137 Identities=12% Similarity=0.052 Sum_probs=80.0
Q ss_pred HhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHc-C--CcEEEEEEEeCC--cccccHHHHHHHH
Q 003054 8 QLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAF-G--WREAVPIYVDNQ--YGEEMIPSLTDAL 82 (852)
Q Consensus 8 ~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~-g--w~~vaii~~d~~--~G~~~~~~l~~~l 82 (852)
..+.+.++|+|......+. ... +..+..++...+..+++++.+. | -++++++..+.. ......+.|.+++
T Consensus 77 ~~~~~~~ipvV~~~~~~~~--~~~---~~~V~~d~~~~g~~~~~~l~~~~g~~~~~i~~i~~~~~~~~~~~R~~gf~~a~ 151 (275)
T cd06307 77 ARLAAAGVPVVTLVSDLPG--SPR---AGYVGIDNRAAGRTAAWLIGRFLGRRPGKVAVLAGSHRFRGHEEREMGFRSVL 151 (275)
T ss_pred HHHHHCCCcEEEEeCCCCC--Cce---eeEEccChHHHHHHHHHHHHHHhCCCCCeEEEEecCCCCcchHHHHHHHHHHH
Confidence 4455689999987543221 111 1224555566666777777554 5 469999975332 3345578899999
Q ss_pred HhCCceeeeeeecCCCCChHHHHHHHHHhhc--CCceEEEEEeChhhHHHHHHHHHHcCCcccceEEEEcCc
Q 003054 83 QAIDTRVPYRSVISPLATDDQIEKELYKLFT--MQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDG 152 (852)
Q Consensus 83 ~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~--~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~ 152 (852)
++.|..+.....+..+.+..+-...+.++.+ .++++|+..... +..+++.+++.|.. .+...++.|.
T Consensus 152 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~~d~--~~g~~~al~~~g~~-~di~Ivg~d~ 220 (275)
T cd06307 152 REEFPGLRVLETLEGLDDPARAYEATRKLLARHPDLVGIYNAGGG--NRGVIRALREAGRA-GKVVFVGHEL 220 (275)
T ss_pred HhhCCCcEEEeeccCCCChHHHHHHHHHHHHhCCCceEEEECCCC--hHHHHHHHHHcCCC-CCcEEEEecC
Confidence 9877654332222211122233345555543 357787777643 36899999999984 3445554443
No 186
>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=93.37 E-value=4.9 Score=39.15 Aligned_cols=69 Identities=16% Similarity=0.128 Sum_probs=45.7
Q ss_pred EeeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCcccEEEeeeeeecCcceeeeccccccccceEEEE
Q 003054 377 GYCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGEFDAVVGDITIVFNRSNYVDFTLPYTESGVSMIV 456 (852)
Q Consensus 377 G~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv 456 (852)
.+-.+++..+.++.+ .+++++.. ++..+++.++.+|++|+++..... ....+. +.++....+++++
T Consensus 13 ~~l~~~l~~~~~~~P-~i~l~i~~---------~~~~~~~~~l~~~~~D~~i~~~~~---~~~~~~-~~~l~~~~~~~v~ 78 (199)
T cd08426 13 ELLPSLIARFRQRYP-GVFFTVDV---------ASTADVLEAVLSGEADIGLAFSPP---PEPGIR-VHSRQPAPIGAVV 78 (199)
T ss_pred HHHHHHHHHHHHhCC-CeEEEEEe---------CCcHHHHHHHHCCCccEEEecCCC---CCCCeE-EEeeccCcEEEEe
Confidence 344678888888876 24555543 246789999999999999853221 122233 4677788888888
Q ss_pred Ecc
Q 003054 457 PIK 459 (852)
Q Consensus 457 ~~~ 459 (852)
+..
T Consensus 79 ~~~ 81 (199)
T cd08426 79 PPG 81 (199)
T ss_pred cCC
Confidence 754
No 187
>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=93.36 E-value=4.3 Score=39.42 Aligned_cols=70 Identities=16% Similarity=0.179 Sum_probs=47.7
Q ss_pred EEeeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCcccEEEeeeeeecCcceeeeccccccccceEEE
Q 003054 376 TGYCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGEFDAVVGDITIVFNRSNYVDFTLPYTESGVSMI 455 (852)
Q Consensus 376 ~G~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~~D~~~g~~~it~~r~~~vdft~p~~~~~~~~v 455 (852)
..+-.+++..+.++.+- +++++.. ++..+++.+|.+|++|+++... +.....+. ..|+....++++
T Consensus 12 ~~~l~~~l~~~~~~~P~-i~l~i~~---------~~~~~~~~~l~~~~~D~~i~~~---~~~~~~~~-~~~l~~~~~~~~ 77 (198)
T cd08412 12 PYYLPGLLRRFREAYPG-VEVRVVE---------GNQEELEEGLRSGELDLALTYD---LDLPEDIA-FEPLARLPPYVW 77 (198)
T ss_pred hhhhHHHHHHHHHHCCC-cEEEEEE---------CCHHHHHHHHHcCCCcEEEEcC---CCCCcccc-eeeeeccceEEE
Confidence 35567889999888872 4555543 3467899999999999987532 22222332 477777888888
Q ss_pred EEcc
Q 003054 456 VPIK 459 (852)
Q Consensus 456 v~~~ 459 (852)
++..
T Consensus 78 ~~~~ 81 (198)
T cd08412 78 LPAD 81 (198)
T ss_pred ecCC
Confidence 7754
No 188
>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=93.31 E-value=6.2 Score=39.03 Aligned_cols=70 Identities=16% Similarity=0.228 Sum_probs=47.6
Q ss_pred EeeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCcccEEEeeeeeecCcceeeeccccccccceEEEE
Q 003054 377 GYCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGEFDAVVGDITIVFNRSNYVDFTLPYTESGVSMIV 456 (852)
Q Consensus 377 G~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv 456 (852)
.+-.+++..+.++.+- +.+++.... +..+++++|.+|++|++++.... ....++ ..|+.+...++++
T Consensus 13 ~~~~~~l~~~~~~~P~-~~v~~~~~~--------~~~~l~~~L~~g~lDl~i~~~~~---~~~~l~-~~~l~~~~~~lv~ 79 (203)
T cd08463 13 LFLPELVARFRREAPG-ARLEIHPLG--------PDFDYERALASGELDLVIGNWPE---PPEHLH-LSPLFSDEIVCLM 79 (203)
T ss_pred HHhHHHHHHHHHHCCC-CEEEEEeCC--------cchhHHHHHhcCCeeEEEecccc---CCCCcE-EeEeecCceEEEE
Confidence 4567899999988872 455554322 35689999999999999863211 112233 3677788888888
Q ss_pred Ecc
Q 003054 457 PIK 459 (852)
Q Consensus 457 ~~~ 459 (852)
+..
T Consensus 80 ~~~ 82 (203)
T cd08463 80 RAD 82 (203)
T ss_pred eCC
Confidence 855
No 189
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=93.26 E-value=1.7 Score=47.28 Aligned_cols=131 Identities=11% Similarity=-0.007 Sum_probs=82.6
Q ss_pred cCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeC--CcccccHHHHHHHHHhCCc
Q 003054 10 GNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDN--QYGEEMIPSLTDALQAIDT 87 (852)
Q Consensus 10 ~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~--~~G~~~~~~l~~~l~~~g~ 87 (852)
+.+.++|+|...... .....++ ...++...+..+++++-..|-++++++.... ..+....+.|.+++++.|+
T Consensus 137 l~~~~iPvV~v~~~~---~~~~~~~---V~~d~~~~~~~a~~~L~~~G~r~I~~i~~~~~~~~~~~R~~Gf~~al~~~g~ 210 (328)
T PRK11303 137 LQNDGLPIIALDRAL---DREHFTS---VVSDDQDDAEMLAESLLKFPAESILLLGALPELSVSFEREQGFRQALKDDPR 210 (328)
T ss_pred HHhcCCCEEEECCCC---CCCCCCE---EEeCCHHHHHHHHHHHHHCCCCeEEEEeCccccccHHHHHHHHHHHHHHcCC
Confidence 345789998875422 1122333 3466777778888888888999999997433 3345667899999999987
Q ss_pred eeeeeeecCCCCChHHHHHHHHHhhcC--CceEEEEEeChhhHHHHHHHHHHcCCcccceEEEE
Q 003054 88 RVPYRSVISPLATDDQIEKELYKLFTM--QTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIM 149 (852)
Q Consensus 88 ~v~~~~~~~~~~~~~d~~~~l~~l~~~--~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~ 149 (852)
.+... ...+.+..+-...+.++.+. .|++|++. +...+..+++++++.|+..|+-+=|+
T Consensus 211 ~~~~~--~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~-~d~~A~g~~~al~~~g~~vP~disv~ 271 (328)
T PRK11303 211 EVHYL--YANSFEREAGAQLFEKWLETHPMPDALFTT-SYTLLQGVLDVLLERPGELPSDLAIA 271 (328)
T ss_pred CceEE--EeCCCChHHHHHHHHHHHcCCCCCCEEEEc-CcHHHHHHHHHHHHcCCCCCCceEEE
Confidence 64322 11111222233345555433 46777665 45567788999999998665544333
No 190
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=93.24 E-value=1.1 Score=48.60 Aligned_cols=130 Identities=9% Similarity=0.032 Sum_probs=79.1
Q ss_pred CCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEe--CCcccccHHHHHHHHHhCCceee
Q 003054 13 SQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVD--NQYGEEMIPSLTDALQAIDTRVP 90 (852)
Q Consensus 13 ~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d--~~~G~~~~~~l~~~l~~~g~~v~ 90 (852)
.++|+|...... .....+ ....++..-+..+++++...|-+++++|..+ ........+.|.+++++.|+++.
T Consensus 135 ~~iPvV~i~~~~---~~~~~~---~v~~d~~~~~~~a~~~L~~~G~~~I~~i~~~~~~~~~~~R~~Gf~~al~~~~~~~~ 208 (327)
T PRK10423 135 PSVPTVMMDWAP---FDGDSD---LIQDNSLLGGDLATQYLIDKGYTRIACITGPLDKTPARLRLEGYRAAMKRAGLNIP 208 (327)
T ss_pred CCCCEEEECCcc---CCCCCC---EEEEChHHHHHHHHHHHHHcCCCeEEEEeCCccccchHHHHHHHHHHHHHcCCCCC
Confidence 378988875321 111111 2334444557788888888899999999632 33455667899999999997653
Q ss_pred eeeecCCCCChHHHHHHHHHhhcC--CceEEEEEeChhhHHHHHHHHHHcCCcccceEEEE
Q 003054 91 YRSVISPLATDDQIEKELYKLFTM--QTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIM 149 (852)
Q Consensus 91 ~~~~~~~~~~~~d~~~~l~~l~~~--~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~ 149 (852)
....+..+.+...-...+.++.+. .|++|++ ++...+..+++.+++.|+..|+-+-|+
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 222221111122223445555433 4676555 456677889999999998766544443
No 191
>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=93.22 E-value=6.1 Score=38.81 Aligned_cols=72 Identities=13% Similarity=0.095 Sum_probs=47.4
Q ss_pred EeeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCcccEEEeeeeeecCcceeeeccccccccceEEEE
Q 003054 377 GYCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGEFDAVVGDITIVFNRSNYVDFTLPYTESGVSMIV 456 (852)
Q Consensus 377 G~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv 456 (852)
.+-.+++..+.++.+- +++++.. ++..+++++|.+|++|++++.......-...+. +.+......++++
T Consensus 13 ~~l~~~l~~~~~~~P~-v~i~~~~---------~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~~~-~~~l~~~~~~~~~ 81 (202)
T cd08468 13 AVMPRLMARLEELAPS-VRLNLVH---------AEQKLPLDALLAGEIDFALGYSHDDGAEPRLIE-ERDWWEDTYVVIA 81 (202)
T ss_pred HHhHHHHHHHHhhCCC-CEEEEEE---------CChHhHHHHHHCCCccEEEecccccccCCCCEE-EEEEecCcEEEEE
Confidence 4556889999888762 5565554 346899999999999998863321100012333 3567777788888
Q ss_pred Ecc
Q 003054 457 PIK 459 (852)
Q Consensus 457 ~~~ 459 (852)
+..
T Consensus 82 ~~~ 84 (202)
T cd08468 82 SRD 84 (202)
T ss_pred eCC
Confidence 755
No 192
>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=93.16 E-value=0.34 Score=50.81 Aligned_cols=103 Identities=14% Similarity=0.098 Sum_probs=67.5
Q ss_pred CCcCCHHHHHhcCCeEEEEeCchHHHHHHhcCCCCcceeecCCHhHHHHHhhcccccCceeEEEechhHHHHH-HhhcCC
Q 003054 568 PTITDVKMLIKRGDNVGYQKGSFVLGILKQLGFDERKLVVYNSPEDCHELFQKGSVNGGIAAAFDEIPYMKLL-IGQYCS 646 (852)
Q Consensus 568 ~~i~sl~dL~~~~~~vg~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~-~~~~~~ 646 (852)
.+|++++||. |+++.+..++.....++.++.. .+ ..+..|.+.+|++|. +|+.+........+ +.+..+
T Consensus 126 ~~i~s~~Dl~--G~kir~~~~~~~~~~~~~~Ga~---~v-~~~~~e~~~aL~~G~----vDg~~~~~~~~~~~~~~ev~~ 195 (257)
T TIGR00787 126 KPITKPEDLK--GLKIRIPNSPMNEAQFKALGAN---PE-PMAFSEVYTALQTGV----VDGQENPLSNVYSSKFYEVQK 195 (257)
T ss_pred CccCChHHhC--CCEEecCCCHHHHHHHHHcCCc---cc-ccCHHHHHHHHHcCC----cccccCCHHHHhhcchhhhcc
Confidence 4699999996 9999998777778888887543 22 566778999999999 99988765433221 112233
Q ss_pred ceEeecccccccceEEEecCC--CCchhhHHHHHHhcc
Q 003054 647 KYAMIEPKFKTAGFGFVFPLH--SPLVHDVSKAILNVT 682 (852)
Q Consensus 647 ~~~~v~~~~~~~~~~~~~~k~--spl~~~in~~il~l~ 682 (852)
.++..+ .......+++++. ..|-++..++|....
T Consensus 196 y~~~~~--~~~~~~~~~~n~~~~~~L~~e~q~~i~~a~ 231 (257)
T TIGR00787 196 YLSMTN--HGYLGYLVVVNKAFWKSLPPDLQAVVKEAA 231 (257)
T ss_pred hheecC--CcccceEEEEeHHHHhcCCHHHHHHHHHHH
Confidence 222222 2345567778776 336666666665543
No 193
>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=93.10 E-value=8.2 Score=37.51 Aligned_cols=69 Identities=17% Similarity=0.138 Sum_probs=45.7
Q ss_pred EeeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCcccEEEeeeeeecCcceeeeccccccccceEEEE
Q 003054 377 GYCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGEFDAVVGDITIVFNRSNYVDFTLPYTESGVSMIV 456 (852)
Q Consensus 377 G~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv 456 (852)
.+-.+++..+.+..+ .+.+++... +-.++...|.+|++|+++... +.....+ -..++....+++++
T Consensus 13 ~~l~~~l~~~~~~~P-~i~i~~~~~---------~~~~~~~~l~~~~~D~~i~~~---~~~~~~~-~~~~l~~~~~~~~~ 78 (198)
T cd08433 13 VLAVPLLRAVRRRYP-GIRLRIVEG---------LSGHLLEWLLNGRLDLALLYG---PPPIPGL-STEPLLEEDLFLVG 78 (198)
T ss_pred hcchHHHHHHHHHCC-CcEEEEEec---------CcHHHHHHHhCCCCcEEEEeC---CCCCCCe-eEEEeccccEEEEe
Confidence 345678888888876 355655432 346889999999999987532 2222222 24677778888888
Q ss_pred Ecc
Q 003054 457 PIK 459 (852)
Q Consensus 457 ~~~ 459 (852)
+..
T Consensus 79 ~~~ 81 (198)
T cd08433 79 PAD 81 (198)
T ss_pred cCC
Confidence 754
No 194
>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=93.10 E-value=6.1 Score=38.46 Aligned_cols=71 Identities=15% Similarity=0.192 Sum_probs=46.3
Q ss_pred EeeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCcccEEEeeeeeecCcceeeeccccccccceEEEE
Q 003054 377 GYCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGEFDAVVGDITIVFNRSNYVDFTLPYTESGVSMIV 456 (852)
Q Consensus 377 G~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv 456 (852)
.+-..++..+.++.+ .+.+++.. ++..++..+|.+|++|++++..... .....+. ..+.....+++++
T Consensus 13 ~~l~~~l~~~~~~~P-~i~l~i~~---------~~~~~~~~~l~~g~~Dl~i~~~~~~-~~~~~~~-~~~l~~~~~~~v~ 80 (201)
T cd08418 13 TLMPAVINRFKEQFP-DVQISIYE---------GQLSSLLPELRDGRLDFAIGTLPDE-MYLKELI-SEPLFESDFVVVA 80 (201)
T ss_pred hhhHHHHHHHHHHCC-CceEEEEe---------CcHHHHHHHHHcCCCcEEEEecCCC-CCCccee-EEeecCCceEEEe
Confidence 445678888888876 35565543 2467899999999999998632111 1112233 3666777888887
Q ss_pred Ecc
Q 003054 457 PIK 459 (852)
Q Consensus 457 ~~~ 459 (852)
+..
T Consensus 81 ~~~ 83 (201)
T cd08418 81 RKD 83 (201)
T ss_pred CCC
Confidence 744
No 195
>CHL00180 rbcR LysR transcriptional regulator; Provisional
Probab=93.07 E-value=5.8 Score=42.61 Aligned_cols=71 Identities=15% Similarity=0.236 Sum_probs=46.2
Q ss_pred eeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCcccEEEeeeeeecCcceeeeccccccccceEEEEE
Q 003054 378 YCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGEFDAVVGDITIVFNRSNYVDFTLPYTESGVSMIVP 457 (852)
Q Consensus 378 ~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv~ 457 (852)
+-.+++..+.+..+- +++++.. ++...++..|.+|++|+++..-....+....+ ...++....++++++
T Consensus 109 ~~~~~l~~~~~~~P~-v~i~~~~---------~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~~-~~~~l~~~~~~~v~~ 177 (305)
T CHL00180 109 LMPRLIGLFRQRYPQ-INVQLQV---------HSTRRIAWNVANGQIDIAIVGGEVPTELKKIL-EITPYVEDELALIIP 177 (305)
T ss_pred HHHHHHHHHHHHCCC-ceEEEEe---------CCHHHHHHHHHcCCccEEEEcCccCcccccce-eEEEeccCcEEEEEC
Confidence 445788888887763 4555543 24688999999999999986322111111122 246777888888888
Q ss_pred cc
Q 003054 458 IK 459 (852)
Q Consensus 458 ~~ 459 (852)
..
T Consensus 178 ~~ 179 (305)
T CHL00180 178 KS 179 (305)
T ss_pred CC
Confidence 65
No 196
>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=92.90 E-value=4.7 Score=39.47 Aligned_cols=69 Identities=14% Similarity=0.054 Sum_probs=46.6
Q ss_pred EeeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCcccEEEeeeeeecCcceeeeccccccccceEEEE
Q 003054 377 GYCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGEFDAVVGDITIVFNRSNYVDFTLPYTESGVSMIV 456 (852)
Q Consensus 377 G~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv 456 (852)
.+-.+++..+.++.+- +.+++.. ++.+++..+|.+|++|+++..... ....+. +.|.....+++++
T Consensus 13 ~~l~~~l~~~~~~~P~-v~v~i~~---------~~~~~~~~~l~~g~~D~~i~~~~~---~~~~l~-~~~l~~~~~~~v~ 78 (201)
T cd08459 13 YFLPRLLAALREVAPG-VRIETVR---------LPVDELEEALESGEIDLAIGYLPD---LGAGFF-QQRLFRERYVCLV 78 (201)
T ss_pred HHHHHHHHHHHHHCCC-CeEEEEe---------cCccCHHHHhhCCCceEEEEcCCC---Ccccce-EEEeecCceEEEE
Confidence 3456788888888763 4555543 245688999999999999853221 122333 4677788888888
Q ss_pred Ecc
Q 003054 457 PIK 459 (852)
Q Consensus 457 ~~~ 459 (852)
+..
T Consensus 79 ~~~ 81 (201)
T cd08459 79 RKD 81 (201)
T ss_pred cCC
Confidence 754
No 197
>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=92.85 E-value=1.3 Score=46.68 Aligned_cols=131 Identities=6% Similarity=-0.073 Sum_probs=80.8
Q ss_pred hcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeCC-------cccccHHHHHHH
Q 003054 9 LGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDNQ-------YGEEMIPSLTDA 81 (852)
Q Consensus 9 i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~~-------~G~~~~~~l~~~ 81 (852)
.+.+.++|+|...... .+...++ +..++...+..+++++.+.|-++++++..+.. ......+.|.++
T Consensus 69 ~~~~~~~pvV~~~~~~---~~~~~~~---v~~D~~~a~~~~~~~l~~~g~~~i~~i~~~~~~~~~~~~~~~~R~~gf~~~ 142 (270)
T cd01544 69 KLAKLNPNLVFVDSNP---APDGFDS---VVPDFEQAVEKALDYLLELGHTRIGFIGGEEKTTDGHEYIEDPRETAFREY 142 (270)
T ss_pred HHHhhCCCEEEECCCC---CCCCCCE---EEECHHHHHHHHHHHHHHcCCCcEEEECCCcccccccchhhhHHHHHHHHH
Confidence 3456789999875432 2223343 45677777888888888889999999985432 345557889999
Q ss_pred HHhCCceeeeeeecCCCCChHHHHHHHHHhhcC----CceEEEEEeChhhHHHHHHHHHHcCCcccceEE
Q 003054 82 LQAIDTRVPYRSVISPLATDDQIEKELYKLFTM----QTRVFILHMLPSLGSRIFEKANEIGLMNKGCVW 147 (852)
Q Consensus 82 l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~----~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vw 147 (852)
+++.|.. .....+.-..+..+-...+.++.+. .+++|+. ++...+..+++.+++.|+..++-+-
T Consensus 143 ~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~ai~~-~~d~~a~g~~~~l~~~g~~vp~di~ 210 (270)
T cd01544 143 MKEKGLY-DPELIYIGDFTVESGYQLMKEALKSLGDNLPTAFFI-ASDPMAIGALRALQEAGIKVPEDVS 210 (270)
T ss_pred HHHcCCC-ChheEeeCCCCHHHHHHHHHHHHhccCCCCCCEEEE-cCcHHHHHHHHHHHHcCCCCCCceE
Confidence 9998841 1111111111122223444454332 3676555 5677788999999999986554333
No 198
>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=92.85 E-value=1.3 Score=46.29 Aligned_cols=137 Identities=9% Similarity=0.108 Sum_probs=83.0
Q ss_pred HhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeCC-cccccHHHHHHHHHhCC
Q 003054 8 QLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDNQ-YGEEMIPSLTDALQAID 86 (852)
Q Consensus 8 ~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~~-~G~~~~~~l~~~l~~~g 86 (852)
..+.+.++|+|......+. +.+-.+..++..-+..+++++...|-++++++..... ......+.|++++++.|
T Consensus 65 ~~l~~~~~PvV~~~~~~~~------~~~~~v~~d~~~~g~~~~~~l~~~g~~~i~~i~~~~~~~~~~R~~gf~~~~~~~~ 138 (265)
T cd01543 65 EALQKLGIPVVDVSGSREK------PGIPRVTTDNAAIGRMAAEHFLERGFRHFAFYGLPGARWSDEREEAFRQLVAEAG 138 (265)
T ss_pred HHHhhCCCCEEEEeCccCC------CCCCEEeeCHHHHHHHHHHHHHHCCCcEEEEEcCCCCHHHHHHHHHHHHHHHHcC
Confidence 3345678999988653221 1233466777788888888888889999999874332 23345678999999999
Q ss_pred ceeeeeee--cCCCCChHHHHHHHHHhhcC--CceEEEEEeChhhHHHHHHHHHHcCCcccc-eEEEEcC
Q 003054 87 TRVPYRSV--ISPLATDDQIEKELYKLFTM--QTRVFILHMLPSLGSRIFEKANEIGLMNKG-CVWIMTD 151 (852)
Q Consensus 87 ~~v~~~~~--~~~~~~~~d~~~~l~~l~~~--~~~viv~~~~~~~~~~i~~~a~~~G~~~~~-~vwi~~~ 151 (852)
..+..... .....+..+-...+.++.+. .+++|+. ++...+..+++.+++.|+..++ ...++-|
T Consensus 139 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~-~~d~~a~g~~~~l~~~g~~vp~di~vigfd 207 (265)
T cd01543 139 YECSFFYRGLSTDAQSWEEEQEELAQWLQSLPKPVGIFA-CTDARARQLLEACRRAGIAVPEEVAVLGVD 207 (265)
T ss_pred CccccccCccccccccHHHHHHHHHHHHhcCCCCcEEEe-cChHHHHHHHHHHHHhCCCCCCceEEEeeC
Confidence 87521111 11001112223344554333 4666554 4666788899999999986443 3444433
No 199
>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=92.83 E-value=1.3 Score=46.53 Aligned_cols=130 Identities=15% Similarity=0.045 Sum_probs=78.3
Q ss_pred HHhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeCC--cccccHHHHHHHHHh
Q 003054 7 IQLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDNQ--YGEEMIPSLTDALQA 84 (852)
Q Consensus 7 ~~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~~--~G~~~~~~l~~~l~~ 84 (852)
...+.+.++|+|......+ ....+| +..++...++.+++++...|.++++++..+.. ......+.|.+++++
T Consensus 73 ~~~l~~~~ipvV~~~~~~~---~~~~~~---V~~d~~~~~~~a~~~l~~~g~~~i~~i~~~~~~~~~~~R~~gf~~~~~~ 146 (268)
T cd06277 73 IKEIKELGIPFVLVDHYIP---NEKADC---VLTDNYSGAYAATEYLIEKGHRKIGFVGDPLYSPSFEERYEGYKKALLD 146 (268)
T ss_pred HHHHhhcCCCEEEEccCCC---CCCCCE---EEecchHHHHHHHHHHHHCCCCcEEEECCCCCCcchHHHHHHHHHHHHH
Confidence 3445677899998754322 122333 34455566666777877779999999975543 234556789999999
Q ss_pred CCceeeeeeecCC-CCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHcCCcccc
Q 003054 85 IDTRVPYRSVISP-LATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEIGLMNKG 144 (852)
Q Consensus 85 ~g~~v~~~~~~~~-~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~ 144 (852)
.|+++.....+.. .....+....+.++. ..+++|++. +...+..+++.+++.|+..++
T Consensus 147 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~~-~~~~ai~~~-~d~~a~g~~~a~~~~g~~~p~ 205 (268)
T cd06277 147 HGIPFNEDYDITEKEEDEEDIGKFIDELK-PLPTAFFCS-NDGVAFLLIKVLKEMGIRVPE 205 (268)
T ss_pred cCCCCCcceEEEcchhHHHHHHHHHhcCC-CCCCEEEEC-CcHHHHHHHHHHHHcCCCCCC
Confidence 8876543222211 111223333333322 247765554 555667888899999986543
No 200
>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=92.79 E-value=9.5 Score=36.73 Aligned_cols=69 Identities=16% Similarity=0.182 Sum_probs=46.5
Q ss_pred EeeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCcccEEEeeeeeecCcceeeeccccccccceEEEE
Q 003054 377 GYCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGEFDAVVGDITIVFNRSNYVDFTLPYTESGVSMIV 456 (852)
Q Consensus 377 G~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv 456 (852)
.+-.+++..+.++.+ .+++++.. ++..++.+.|.+|++|+++.... .....+. +.++....+++++
T Consensus 13 ~~l~~~l~~~~~~~p-~v~i~i~~---------~~~~~~~~~l~~g~~D~~i~~~~---~~~~~~~-~~~l~~~~~~~~~ 78 (197)
T cd08440 13 TLLPPVLAAFRRRHP-GIRVRLRD---------VSAEQVIEAVRSGEVDFGIGSEP---EADPDLE-FEPLLRDPFVLVC 78 (197)
T ss_pred hHHHHHHHHHHHhCC-CcEEEEEe---------CChHHHHHHHHcCCccEEEEeCC---CCCCCee-EEEeecccEEEEe
Confidence 455688888888876 35555543 24678999999999999985322 2222232 3567778888888
Q ss_pred Ecc
Q 003054 457 PIK 459 (852)
Q Consensus 457 ~~~ 459 (852)
+..
T Consensus 79 ~~~ 81 (197)
T cd08440 79 PKD 81 (197)
T ss_pred cCC
Confidence 754
No 201
>PRK11233 nitrogen assimilation transcriptional regulator; Provisional
Probab=92.78 E-value=3.9 Score=43.98 Aligned_cols=69 Identities=14% Similarity=0.170 Sum_probs=44.0
Q ss_pred EeeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCcccEEEeeeeeecCcceeeeccccccccceEEEE
Q 003054 377 GYCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGEFDAVVGDITIVFNRSNYVDFTLPYTESGVSMIV 456 (852)
Q Consensus 377 G~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv 456 (852)
.+...++..+.++.+ .+.+.+.. +...++...|.+|++|+++..-. .....++ ..|+....+++++
T Consensus 105 ~~~~~~l~~~~~~~p-~i~l~~~~---------~~~~~~~~~l~~g~~Di~i~~~~---~~~~~~~-~~~l~~~~~~lv~ 170 (305)
T PRK11233 105 SLTMPLLQAVRAEFP-GIVLYLHE---------NSGATLNEKLMNGQLDMAVIYEH---SPVAGLS-SQPLLKEDLFLVG 170 (305)
T ss_pred HHHHHHHHHHHHHCC-CcEEEEEE---------CCcHHHHHHHHCCCCCEEEEcCC---cCCCCcE-EEEEeeeeEEEEE
Confidence 344568888888875 24554433 24568899999999999875321 1112232 4577777888777
Q ss_pred Ecc
Q 003054 457 PIK 459 (852)
Q Consensus 457 ~~~ 459 (852)
+..
T Consensus 171 ~~~ 173 (305)
T PRK11233 171 TQD 173 (305)
T ss_pred cCc
Confidence 744
No 202
>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=92.74 E-value=7.4 Score=37.79 Aligned_cols=68 Identities=19% Similarity=0.244 Sum_probs=46.2
Q ss_pred eeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCcccEEEeeeeeecCcceeeeccccccccceEEEEE
Q 003054 378 YCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGEFDAVVGDITIVFNRSNYVDFTLPYTESGVSMIVP 457 (852)
Q Consensus 378 ~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv~ 457 (852)
+-.+++..+.++.+ .+++++.. ++..+++++|.+|++|+++.... .....+. ..+.....++++++
T Consensus 14 ~l~~~l~~~~~~~P-~i~i~~~~---------~~~~~~~~~l~~~~~D~~i~~~~---~~~~~~~-~~~l~~~~~~~v~~ 79 (198)
T cd08421 14 FLPEDLASFLAAHP-DVRIDLEE---------RLSADIVRAVAEGRADLGIVAGN---VDAAGLE-TRPYRTDRLVVVVP 79 (198)
T ss_pred hhHHHHHHHHHHCC-CceEEEEe---------cCcHHHHHHHhcCCceEEEEecC---CCCCCcE-EEEeecCcEEEEeC
Confidence 44588888888876 25555543 24678999999999999885322 2223333 36777888888887
Q ss_pred cc
Q 003054 458 IK 459 (852)
Q Consensus 458 ~~ 459 (852)
+.
T Consensus 80 ~~ 81 (198)
T cd08421 80 RD 81 (198)
T ss_pred CC
Confidence 54
No 203
>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=92.74 E-value=1.6 Score=45.91 Aligned_cols=132 Identities=6% Similarity=-0.066 Sum_probs=82.3
Q ss_pred HhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHcCC-----cEEEEEEEeC--CcccccHHHHHH
Q 003054 8 QLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAFGW-----REAVPIYVDN--QYGEEMIPSLTD 80 (852)
Q Consensus 8 ~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~gw-----~~vaii~~d~--~~G~~~~~~l~~ 80 (852)
.-+.+.++|+|......+ +. .....+..++...++.+++++.+.|- ++++++.... .......+.|++
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 335668999998744221 11 12223566677777888888866665 8999997432 345666788999
Q ss_pred HHHhCCceeeeeeecCCCCChHHHHHHHHHhhcC--CceEEEEEeChhhHHHHHHHHHHcCCcccceEEEE
Q 003054 81 ALQAIDTRVPYRSVISPLATDDQIEKELYKLFTM--QTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIM 149 (852)
Q Consensus 81 ~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~--~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~ 149 (852)
++++.|+++... .....+.+.-...+.++.+. ++++|+. ....+..+++.+++.|+ +++...++
T Consensus 150 ~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~l~~~~~~~~i~~--~d~~a~~~~~~l~~~g~-p~di~vig 215 (268)
T cd06306 150 ALAGSAIEISAI--KYGDTGKEVQRKLVEEALEAHPDIDYIVG--SAVAAEAAVGILRQRGL-TDQIKIVS 215 (268)
T ss_pred HHhhcCcEEeee--ccCCccHHHHHHHHHHHHHhCCCcCEEee--cchhhhHHHHHHHhcCC-CCCeEEEe
Confidence 999999887542 11111223334455555433 4677764 36677889999999997 33333443
No 204
>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=92.70 E-value=0.76 Score=48.83 Aligned_cols=137 Identities=11% Similarity=0.030 Sum_probs=91.5
Q ss_pred HHHhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHcCCcE-EEEEEEeCCc--ccccHHHHHHHH
Q 003054 6 IIQLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAFGWRE-AVPIYVDNQY--GEEMIPSLTDAL 82 (852)
Q Consensus 6 v~~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~gw~~-vaii~~d~~~--G~~~~~~l~~~l 82 (852)
+..+.+. ++|+|........- ...|++ ..++..-+..+++++.+.|-++ ++++..+... +....+.+.+++
T Consensus 72 l~~~~~~-~iPvV~~~~~~~~~--~~~~~V---~~D~~~a~~~a~~~Li~~Gh~~~I~~i~~~~~~~~~~~R~~Gy~~Al 145 (279)
T PF00532_consen 72 LRRLIKS-GIPVVLIDRYIDNP--EGVPSV---YIDNYEAGYEATEYLIKKGHRRPIAFIGGPEDSSTSRERLQGYRDAL 145 (279)
T ss_dssp HHHHHHT-TSEEEEESS-SCTT--CTSCEE---EEEHHHHHHHHHHHHHHTTCCSTEEEEEESTTTHHHHHHHHHHHHHH
T ss_pred HHHHHHc-CCCEEEEEeccCCc--ccCCEE---EEcchHHHHHHHHHHHhcccCCeEEEEecCcchHHHHHHHHHHHHHH
Confidence 3444455 89998865532111 133444 2345666668888899999999 9999965544 566677899999
Q ss_pred HhCCceeeeeeecCCCCChHHHHHHHHHhhcCCce--EEEEEeChhhHHHHHHHHHHcC-CcccceEEEE
Q 003054 83 QAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTR--VFILHMLPSLGSRIFEKANEIG-LMNKGCVWIM 149 (852)
Q Consensus 83 ~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~--viv~~~~~~~~~~i~~~a~~~G-~~~~~~vwi~ 149 (852)
++.|+++........+.+..+=...++++.+.+|+ +| ++++...+..+++.+++.| +..++-+-+.
T Consensus 146 ~~~Gl~~~~~~i~~~~~~~~~g~~~~~~ll~~~p~idai-~~~nd~~A~ga~~~l~~~gr~~ip~di~~~ 214 (279)
T PF00532_consen 146 KEAGLPIDEEWIFEGDFDYESGYEAARELLESHPDIDAI-FCANDMMAIGAIRALRERGRLKIPEDIVSG 214 (279)
T ss_dssp HHTTSCEEEEEEEESSSSHHHHHHHHHHHHHTSTT-SEE-EESSHHHHHHHHHHHHHTT-TCTTTEEEEC
T ss_pred HHcCCCCCcccccccCCCHHHHHHHHHHHHhhCCCCEEE-EEeCHHHHHHHHHHHHHcCCcccChhheee
Confidence 99999665554433223344445666777777776 54 4567778899999999999 7777655433
No 205
>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=92.68 E-value=2 Score=45.26 Aligned_cols=133 Identities=11% Similarity=0.097 Sum_probs=83.5
Q ss_pred cCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEe--CCcccccHHHHHHHHHhCCc
Q 003054 10 GNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVD--NQYGEEMIPSLTDALQAIDT 87 (852)
Q Consensus 10 ~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d--~~~G~~~~~~l~~~l~~~g~ 87 (852)
+.+.++|+|......+. ....++ +..++..-+..+++.+.+.|-+++++|... ...+......|++++++.|+
T Consensus 75 l~~~~iPvV~i~~~~~~--~~~~~~---V~~d~~~~~~~a~~~L~~~G~~~I~~i~~~~~~~~~~~R~~gf~~a~~~~g~ 149 (269)
T cd06287 75 LRQRGIPVVSIGRPPGD--RTDVPY---VDLQSAATARMLLEHLRAQGARQIALIVGSARRNSYLEAEAAYRAFAAEHGM 149 (269)
T ss_pred HHHcCCCEEEeCCCCCC--CCCCCe---EeeCcHHHHHHHHHHHHHcCCCcEEEEeCCcccccHHHHHHHHHHHHHHcCC
Confidence 44568999987553210 122333 345666677788888888899999999632 23345567889999999987
Q ss_pred eeeeeeecCCCCChHHHHHHHHHhhcC--CceEEEEEeChhhHHHHHHHHHHcCCcccceEEEE
Q 003054 88 RVPYRSVISPLATDDQIEKELYKLFTM--QTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIM 149 (852)
Q Consensus 88 ~v~~~~~~~~~~~~~d~~~~l~~l~~~--~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~ 149 (852)
..... .+....+.++-...+.++.+. .+++|+. .+...+..+++.+++.|+..|+-+=|+
T Consensus 150 ~~~~~-~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~-~~d~~A~gvl~al~~~gl~vP~dvsvi 211 (269)
T cd06287 150 PPVVL-RVDEAGGEEAGYAACAQLLAQHPDLDALCV-PVDAFAVGAVRAATELGRAVPDQLRVV 211 (269)
T ss_pred Cccee-EecCCCChHHHHHHHHHHHhCCCCCCEEEE-cCcHHHHHHHHHHHHcCCCCCCceEEE
Confidence 64321 111111223333455555433 4677664 466788899999999999766544333
No 206
>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=92.64 E-value=3.8 Score=43.30 Aligned_cols=113 Identities=8% Similarity=0.030 Sum_probs=71.9
Q ss_pred EeccCCchhHHHHHHHHHHH--cCCcEEEEEEEeC-CcccccHHHHHHHHHhC-CceeeeeeecCCCCChHHHHHHHHHh
Q 003054 36 FRGSLNDSSQAGAITAIIKA--FGWREAVPIYVDN-QYGEEMIPSLTDALQAI-DTRVPYRSVISPLATDDQIEKELYKL 111 (852)
Q Consensus 36 fR~~p~d~~~~~aia~~l~~--~gw~~vaii~~d~-~~G~~~~~~l~~~l~~~-g~~v~~~~~~~~~~~~~d~~~~l~~l 111 (852)
-.+..++..-+..+++++.+ .|.+++++|.... ..+....+.|++++++. |+++... +..+.+..+-...+.++
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 33556666777888888766 7999999997432 23445678899999987 7664322 22122233334455555
Q ss_pred hcCC--ceEEEEEeChhhHHHHHHHHHHcCCcccceEEEEcCc
Q 003054 112 FTMQ--TRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDG 152 (852)
Q Consensus 112 ~~~~--~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~ 152 (852)
.+.. +++|+ +.+...+..+++.+++.|+. ++..+++-+.
T Consensus 185 l~~~~~~~ai~-~~nd~~A~g~l~al~~~G~~-~dv~vvg~d~ 225 (280)
T cd06303 185 LSNNPDVDFIY-ACSTDIALGASDALKELGRE-DDILINGWGG 225 (280)
T ss_pred HHhCCCCcEEE-ECCcHHHHHHHHHHHHcCCC-CCcEEEecCC
Confidence 5443 56554 55666788899999999985 4444554443
No 207
>PRK12684 transcriptional regulator CysB-like protein; Reviewed
Probab=92.64 E-value=4.6 Score=43.61 Aligned_cols=115 Identities=8% Similarity=-0.045 Sum_probs=66.5
Q ss_pred CCHHHHHhcCCeEEEEeCchHH----HHHHhcCCCCcceeecCCHhHHHHHhhcccccCceeEEEechhHHHHHHhhcCC
Q 003054 571 TDVKMLIKRGDNVGYQKGSFVL----GILKQLGFDERKLVVYNSPEDCHELFQKGSVNGGIAAAFDEIPYMKLLIGQYCS 646 (852)
Q Consensus 571 ~sl~dL~~~~~~vg~~~~s~~~----~~l~~~~~~~~~~~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~~~~ 646 (852)
-+++||.+.. -|.+..++..+ .++...++........++.+...+++..|. ..+++... ....... .
T Consensus 184 i~~~dL~~~~-~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~----Gv~~lp~~-~~~~~~~---~ 254 (313)
T PRK12684 184 LTLEDLAQYP-LITYDFAFAGRSKINKAFALRGLKPDIVLEAIDADVIKTYVELGL----GVGIVADM-AFDPERD---R 254 (313)
T ss_pred cCHHHHhcCC-cEecCCCCcHHHHHHHHHHHcCCCCCeEEEeCCHHHHHHHHHhCC----ceEEeehh-hcccccc---C
Confidence 3688887322 44554554333 344445555545567788999999999987 45555543 2222211 1
Q ss_pred ceEee--cccccccceEEEecCCCCchhhHHHHHHhccccChhHHHHHHHc
Q 003054 647 KYAMI--EPKFKTAGFGFVFPLHSPLVHDVSKAILNVTEGDKMKEIEDAWF 695 (852)
Q Consensus 647 ~~~~v--~~~~~~~~~~~~~~k~spl~~~in~~il~l~e~G~~~~i~~kw~ 695 (852)
.+..+ ........+.++.+++.++...+...+..+.+. +..++.++-+
T Consensus 255 ~l~~~~i~~~~~~~~~~l~~~~~~~~~~~~~~f~~~l~~~-~~~~~~~~~~ 304 (313)
T PRK12684 255 NLRAIDAGHLFGSSTTRLGLRRGAYLRGYVYTFIELFAPT-LNRKLVEQAL 304 (313)
T ss_pred CeEEEECCCCCcceeEEEEEECCCcCCHHHHHHHHHHHHH-hCHHHHHHHh
Confidence 23333 233344578899999987777766666655543 4455555444
No 208
>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=92.63 E-value=5.4 Score=38.88 Aligned_cols=69 Identities=22% Similarity=0.222 Sum_probs=45.9
Q ss_pred EeeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCcccEEEeeeeeecCcceeeeccccccccceEEEE
Q 003054 377 GYCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGEFDAVVGDITIVFNRSNYVDFTLPYTESGVSMIV 456 (852)
Q Consensus 377 G~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv 456 (852)
.+-.+++..+.++.+ .+++++.. ++...+...|.+|++|+++... +.....+. ..|+....+++++
T Consensus 13 ~~~~~~i~~~~~~~P-~i~l~~~~---------~~~~~~~~~l~~g~~D~~i~~~---~~~~~~~~-~~~l~~~~~~~v~ 78 (200)
T cd08417 13 LLLPPLLARLRQEAP-GVRLRFVP---------LDRDDLEEALESGEIDLAIGVF---PELPPGLR-SQPLFEDRFVCVA 78 (200)
T ss_pred HHHHHHHHHHHhhCC-CeEEEecc---------CCHHHHHHHHHcCCCCEEEeec---ccCCCccc-hhhhhcCceEEEe
Confidence 344577888888776 23444432 3567899999999999998532 22223332 4677888888888
Q ss_pred Ecc
Q 003054 457 PIK 459 (852)
Q Consensus 457 ~~~ 459 (852)
+..
T Consensus 79 ~~~ 81 (200)
T cd08417 79 RKD 81 (200)
T ss_pred cCC
Confidence 854
No 209
>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=92.57 E-value=1.5 Score=46.49 Aligned_cols=130 Identities=15% Similarity=0.166 Sum_probs=81.5
Q ss_pred HhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeC-------------------
Q 003054 8 QLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDN------------------- 68 (852)
Q Consensus 8 ~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~------------------- 68 (852)
..+...++|+|......+ ...+ .+..++...+..+++++.+.|-++++++..+.
T Consensus 73 ~~~~~~~ipvV~~~~~~~----~~~~---~v~~d~~~~g~~~~~~L~~~g~~~i~~i~~~~~~~~~~~~~~~~~~~~~~~ 145 (283)
T cd06279 73 AALLRRGLPVVVVDQPLP----PGVP---SVGIDDRAAAREAARHLLDLGHRRIGILGLRLGRDRNTGRVTDERLASATF 145 (283)
T ss_pred HHHHHcCCCEEEEecCCC----CCCC---EEeeCcHHHHHHHHHHHHHcCCCcEEEecCccccccccccccccccccccc
Confidence 345668899998765321 1122 34667777888888998888999999997432
Q ss_pred CcccccHHHHHHHHHhCCceeeeeeecC-CCCChHHHHHHHHHhhcC--CceEEEEEeChhhHHHHHHHHHHcCCcccce
Q 003054 69 QYGEEMIPSLTDALQAIDTRVPYRSVIS-PLATDDQIEKELYKLFTM--QTRVFILHMLPSLGSRIFEKANEIGLMNKGC 145 (852)
Q Consensus 69 ~~G~~~~~~l~~~l~~~g~~v~~~~~~~-~~~~~~d~~~~l~~l~~~--~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~ 145 (852)
.......+.+.+++++.|++......+. ...+.......+.++.+. .+++|+ +++...+..+++.+++.|+..++-
T Consensus 146 ~~~~~R~~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~-~~~d~~a~gv~~al~~~g~~ip~d 224 (283)
T cd06279 146 SVARERLEGYLEALEEAGIDISDVPIWEIPENDRASGEEAARELLDASPRPTAIL-CMSDVLALGALQVARELGLRVPED 224 (283)
T ss_pred ccHHHHHHHHHHHHHHcCCCCChheEEecCCCchHHHHHHHHHHHcCCCCCcEEE-ECCcHHHHHHHHHHHHcCCCCCCc
Confidence 1234457888999998886532211111 111223344556665544 356655 445667788999999999865543
No 210
>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=92.45 E-value=2.4 Score=45.50 Aligned_cols=144 Identities=8% Similarity=0.015 Sum_probs=77.4
Q ss_pred HhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHc--CCc---------EE--EEEEEeCC--ccc
Q 003054 8 QLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAF--GWR---------EA--VPIYVDNQ--YGE 72 (852)
Q Consensus 8 ~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~--gw~---------~v--aii~~d~~--~G~ 72 (852)
..+...++|+|......+...-...+-+..+.+++..-+..+++++... |-+ ++ +++..+.. ...
T Consensus 76 ~~~~~~giPvV~~~~~~~~~~~~~~~~~~~V~~d~~~~g~~~a~~l~~~~~~~~~~~~~~~~g~~~i~~~~g~~~~~~~~ 155 (303)
T cd01539 76 NKAKQKNIPVIFFNREPEEEDIKSYDKAYYVGTDAEQSGILQGKLIADYWNANKDALDKNGDGIIQYVMLKGEPGHPDAI 155 (303)
T ss_pred HHHHHCCCCEEEeCCCCcccccccccccceeeecHHHHHHHHHHHHHHHhhccccccccCCCCceEEEEEEcCCCCchhh
Confidence 4456679999988653221110111223345666666667777777443 221 23 44443222 234
Q ss_pred ccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcC---CceEEEEEeChhhHHHHHHHHHHcCCccc----ce
Q 003054 73 EMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTM---QTRVFILHMLPSLGSRIFEKANEIGLMNK----GC 145 (852)
Q Consensus 73 ~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~---~~~viv~~~~~~~~~~i~~~a~~~G~~~~----~~ 145 (852)
...+.+++++++.|.++........+.+.+.-...+.++.+. ++++|+. .+...+..+++++++.|...+ +.
T Consensus 156 ~R~~gf~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~~~~~~ai~~-~~d~~a~g~~~al~~~g~~~p~~~~di 234 (303)
T cd01539 156 ARTKYSIETLNDAGIKTEELASDTANWDRAQAKDKMDALLLKYGDKIEAVIA-NNDAMALGAIEALQKYGYNKGDKSKNI 234 (303)
T ss_pred hhhhhHHHHHHhcCCCeEEEEeecCCCCHHHHHHHHHHHHHhcCCCccEEEE-CCchHHHHHHHHHHHcCCCcCCCCCce
Confidence 457788999998887653322222122222333345555433 2566554 455566788899999998654 44
Q ss_pred EEEEcCc
Q 003054 146 VWIMTDG 152 (852)
Q Consensus 146 vwi~~~~ 152 (852)
.+++.++
T Consensus 235 ~iig~d~ 241 (303)
T cd01539 235 PVVGVDA 241 (303)
T ss_pred EEEccCC
Confidence 4454443
No 211
>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=92.23 E-value=2.7 Score=44.77 Aligned_cols=139 Identities=7% Similarity=0.027 Sum_probs=81.1
Q ss_pred HhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHc--CCcEEEEEEEeCCc--ccccHHHHHHHHH
Q 003054 8 QLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAF--GWREAVPIYVDNQY--GEEMIPSLTDALQ 83 (852)
Q Consensus 8 ~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~--gw~~vaii~~d~~~--G~~~~~~l~~~l~ 83 (852)
..+.+.++|+|.+....+.... ..+++.-+..++..-+..+++++... |-++++++..+.+. .....+.+.++++
T Consensus 75 ~~~~~~~iPvV~~~~~~~~~~~-~~~~~~~v~~d~~~~g~~~~~~l~~~~~g~~~i~~l~~~~~~~~~~~R~~gf~~~l~ 153 (294)
T cd06316 75 KKVAEAGIKLVFMDNVPSGLEH-GKDYAGIVTDDNYGNGQIAADALAKALPGKGKVGLIYHGADYFVTNQRDQGFKETIK 153 (294)
T ss_pred HHHHHcCCcEEEecCCCccccc-CcceEEEEccCcHHHHHHHHHHHHHHhCCCceEEEEeCCCCcccHHHHHHHHHHHHH
Confidence 4456679999987664332221 11333445566666678888888665 78999999754333 4455788888998
Q ss_pred hCCceeeeeeecCCCCChHHHHHHHHHhhcC--CceEEEEEeChhhHHHHHHHHHHcCCcccceEEEEcC
Q 003054 84 AIDTRVPYRSVISPLATDDQIEKELYKLFTM--QTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTD 151 (852)
Q Consensus 84 ~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~--~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~ 151 (852)
+.+..+......... +...-...+.++.+. .+++|+. .+...+..+++.+++.|+ ++..+++-+
T Consensus 154 ~~~~~~~~~~~~~~~-~~~~~~~~~~~~l~~~~~~~ai~~-~~d~~a~g~~~~l~~~g~--~di~vvg~d 219 (294)
T cd06316 154 KNYPDITIVAEKGID-GPSKAEDIANAMLTQNPDLKGIYA-VWDVPAEGVIAALRAAGR--DDIKVTTVD 219 (294)
T ss_pred HhCCCcEEEeecCCc-chhHHHHHHHHHHHhCCCeeEEEe-CCCchhHHHHHHHHHcCC--CCceEEEeC
Confidence 765432211111111 111223345554433 4566554 455678899999999997 344455444
No 212
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=92.23 E-value=1.6 Score=47.72 Aligned_cols=110 Identities=15% Similarity=0.077 Sum_probs=70.3
Q ss_pred ccCCchhHHHHHHHHHHHcCCcEEEEEEEeC--CcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcC-
Q 003054 38 GSLNDSSQAGAITAIIKAFGWREAVPIYVDN--QYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTM- 114 (852)
Q Consensus 38 ~~p~d~~~~~aia~~l~~~gw~~vaii~~d~--~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~- 114 (852)
...++..-+..+++++...|.+++++|..+. .....-.+.|++++++.|+.+........+.+..+-...+.++.+.
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 3456666667777888888999999997433 2345567889999999998653221111111122222345555443
Q ss_pred -CceEEEEEeChhhHHHHHHHHHHcCCcccceEEE
Q 003054 115 -QTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWI 148 (852)
Q Consensus 115 -~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi 148 (852)
.+++|+. .+...+..+++.++++|+..|+-+-|
T Consensus 236 ~~~~ai~~-~nD~~A~g~~~al~~~G~~vP~disV 269 (343)
T PRK10727 236 RNFTAVAC-YNDSMAAGAMGVLNDNGIDVPGEISL 269 (343)
T ss_pred CCCCEEEE-cCcHHHHHHHHHHHHcCCCCCcceeE
Confidence 3676654 56667889999999999976654433
No 213
>PRK11242 DNA-binding transcriptional regulator CynR; Provisional
Probab=92.18 E-value=6.7 Score=41.75 Aligned_cols=69 Identities=12% Similarity=0.028 Sum_probs=47.3
Q ss_pred EeeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCcccEEEeeeeeecCcceeeeccccccccceEEEE
Q 003054 377 GYCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGEFDAVVGDITIVFNRSNYVDFTLPYTESGVSMIV 456 (852)
Q Consensus 377 G~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv 456 (852)
.+..+++..+.++.+ .+.++... ++..+++.+|.+|++|+++... +.....+ .+.++....+++++
T Consensus 104 ~~l~~~l~~~~~~~p-~~~i~~~~---------~~~~~~~~~l~~g~~Dl~i~~~---~~~~~~l-~~~~l~~~~~~~~~ 169 (296)
T PRK11242 104 YLIGPLIDAFHARYP-GITLTIRE---------MSQERIEALLADDELDVGIAFA---PVHSPEI-EAQPLFTETLALVV 169 (296)
T ss_pred hhhHHHHHHHHHHCC-CCEEEEEe---------CCHHHHHHHHHCCCCcEEEEec---CCCCcce-eEEEeeeccEEEEE
Confidence 345688888888876 35555543 2467899999999999997532 2222233 34777788888888
Q ss_pred Ecc
Q 003054 457 PIK 459 (852)
Q Consensus 457 ~~~ 459 (852)
++.
T Consensus 170 ~~~ 172 (296)
T PRK11242 170 GRH 172 (296)
T ss_pred cCC
Confidence 865
No 214
>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=92.04 E-value=2 Score=45.13 Aligned_cols=134 Identities=11% Similarity=0.160 Sum_probs=83.1
Q ss_pred hcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEe-CCcccccHHHHHHHHHhCCc
Q 003054 9 LGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVD-NQYGEEMIPSLTDALQAIDT 87 (852)
Q Consensus 9 i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d-~~~G~~~~~~l~~~l~~~g~ 87 (852)
-+...++|+|......+. ... ..+..++..-+..+++++.+.|.++++++... +..+....+.+.+++++.|.
T Consensus 78 ~~~~~~ipvV~~~~~~~~---~~~---~~V~~D~~~~g~~~~~~l~~~G~~~i~~l~~~~~~~~~~r~~g~~~~l~~~~~ 151 (273)
T cd01541 78 KLEKLGIPYVFINASYEE---LNF---PSLVLDDEKGGYKATEYLIELGHRKIAGIFKADDLQGVKRMKGFIKAYREHGI 151 (273)
T ss_pred HHHHCCCCEEEEecCCCC---CCC---CEEEECcHHHHHHHHHHHHHcCCcCEEEecCCCcccHHHHHHHHHHHHHHcCC
Confidence 346678999988654221 112 23566777788888898888899999988732 22345556788999998887
Q ss_pred eeeeee--ecCCCCChHHHHHHHHHhhcC--CceEEEEEeChhhHHHHHHHHHHcCCcccceEEEE
Q 003054 88 RVPYRS--VISPLATDDQIEKELYKLFTM--QTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIM 149 (852)
Q Consensus 88 ~v~~~~--~~~~~~~~~d~~~~l~~l~~~--~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~ 149 (852)
++.... .+..+.........+.++.+. .+++|+. .+...+..+++.+++.|+..++-+-|+
T Consensus 152 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~av~~-~~d~~a~g~~~al~~~g~~~p~dv~vv 216 (273)
T cd01541 152 PFNPSNVITYTTEEKEEKLFEKIKEILKRPERPTAIVC-YNDEIALRVIDLLKELGLKIPEDISVV 216 (273)
T ss_pred CCChHHEEeccccchhhHHHHHHHHHHcCCCCCCEEEE-cCcHHHHHHHHHHHHcCCCCCCcEEEE
Confidence 532211 111111112334455555433 4676644 556677789999999998665444443
No 215
>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=91.91 E-value=9.1 Score=37.00 Aligned_cols=69 Identities=13% Similarity=0.128 Sum_probs=47.4
Q ss_pred EeeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCcccEEEeeeeeecCcceeeeccccccccceEEEE
Q 003054 377 GYCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGEFDAVVGDITIVFNRSNYVDFTLPYTESGVSMIV 456 (852)
Q Consensus 377 G~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv 456 (852)
.+..+++..+.+..+ .+++++.. +...++..+|.+|++|+++..... ....+ .+.|+.....++++
T Consensus 13 ~~l~~~l~~~~~~~P-~i~l~i~~---------~~~~~~~~~l~~~~~Dl~i~~~~~---~~~~~-~~~~l~~~~~~~v~ 78 (196)
T cd08415 13 SLLPRAIARFRARHP-DVRISLHT---------LSSSTVVEAVLSGQADLGLASLPL---DHPGL-ESEPLASGRAVCVL 78 (196)
T ss_pred cccHHHHHHHHHHCC-CcEEEEEe---------cchHHHHHHHHcCCccEEEEeCCC---CCCcc-eeeeecccceEEEE
Confidence 456789999988876 35555544 246789999999999999853222 12223 35677788888888
Q ss_pred Ecc
Q 003054 457 PIK 459 (852)
Q Consensus 457 ~~~ 459 (852)
+..
T Consensus 79 ~~~ 81 (196)
T cd08415 79 PPG 81 (196)
T ss_pred cCC
Confidence 754
No 216
>PRK09526 lacI lac repressor; Reviewed
Probab=91.88 E-value=2.6 Score=46.05 Aligned_cols=126 Identities=9% Similarity=0.044 Sum_probs=78.9
Q ss_pred CCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeC--CcccccHHHHHHHHHhCCceee
Q 003054 13 SQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDN--QYGEEMIPSLTDALQAIDTRVP 90 (852)
Q Consensus 13 ~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~--~~G~~~~~~l~~~l~~~g~~v~ 90 (852)
.++|+|..... + +...+ .+..++..-+..+++++...|.++++++..+. .......+.|++++++.|+++.
T Consensus 143 ~~iPvV~~d~~-~---~~~~~---~V~~d~~~~~~~a~~~L~~~G~~~I~~l~g~~~~~~~~~R~~Gf~~al~~~gi~~~ 215 (342)
T PRK09526 143 ADVPCLFLDVS-P---QSPVN---SVSFDPEDGTRLGVEHLVELGHQRIALLAGPESSVSARLRLAGWLEYLTDYQLQPI 215 (342)
T ss_pred CCCCEEEEecc-C---CCCCC---EEEECcHHHHHHHHHHHHHCCCCeEEEEeCCCccccHHHHHHHHHHHHHHcCCCcc
Confidence 57888877542 1 11122 34556667778888998888999999997432 2334567889999999998643
Q ss_pred eeeecCCCCChHHHHHHHHHhhcC--CceEEEEEeChhhHHHHHHHHHHcCCcccceEEE
Q 003054 91 YRSVISPLATDDQIEKELYKLFTM--QTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWI 148 (852)
Q Consensus 91 ~~~~~~~~~~~~d~~~~l~~l~~~--~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi 148 (852)
.. +..+.+..+-...+.++... .+++|+. .+...+..+++.+++.|+..|+-+-|
T Consensus 216 ~~--~~~~~~~~~~~~~~~~~l~~~~~~~ai~~-~~d~~A~g~~~al~~~g~~vP~disv 272 (342)
T PRK09526 216 AV--REGDWSAMSGYQQTLQMLREGPVPSAILV-ANDQMALGVLRALHESGLRVPGQISV 272 (342)
T ss_pred eE--EeCCCchHHHHHHHHHHhcCCCCCcEEEE-cCcHHHHHHHHHHHHcCCCCCCceEE
Confidence 22 11111122222344555433 4676664 56667888999999999976654433
No 217
>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=91.66 E-value=13 Score=35.77 Aligned_cols=68 Identities=13% Similarity=0.166 Sum_probs=44.6
Q ss_pred eeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCcccEEEeeeeeecCcceeeeccccccccceEEEEE
Q 003054 378 YCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGEFDAVVGDITIVFNRSNYVDFTLPYTESGVSMIVP 457 (852)
Q Consensus 378 ~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv~ 457 (852)
+...++..+.++.+- +++++.. +....+..+|.+|++|+++...... ...+ ...++....++++++
T Consensus 13 ~l~~~l~~~~~~~P~-i~l~i~~---------~~~~~~~~~l~~g~~Dl~i~~~~~~---~~~~-~~~~l~~~~~~~~~~ 78 (197)
T cd08419 13 FAPRLLGAFCRRHPG-VEVSLRV---------GNREQVLERLADNEDDLAIMGRPPE---DLDL-VAEPFLDNPLVVIAP 78 (197)
T ss_pred HhhHHHHHHHHHCCC-ceEEEEE---------CCHHHHHHHHhcCCccEEEecCCCC---CCCe-EEEEeccCCEEEEec
Confidence 445778888888752 4555543 2467899999999999998532211 1112 246777788888887
Q ss_pred cc
Q 003054 458 IK 459 (852)
Q Consensus 458 ~~ 459 (852)
..
T Consensus 79 ~~ 80 (197)
T cd08419 79 PD 80 (197)
T ss_pred CC
Confidence 44
No 218
>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=91.54 E-value=2.6 Score=45.76 Aligned_cols=129 Identities=9% Similarity=0.021 Sum_probs=80.2
Q ss_pred cCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeCC--cccccHHHHHHHHHhCCc
Q 003054 10 GNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDNQ--YGEEMIPSLTDALQAIDT 87 (852)
Q Consensus 10 ~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~~--~G~~~~~~l~~~l~~~g~ 87 (852)
+.+.++|+|......+. ...++ +..++..-+..+++++...|.++++++..... .+..-.+.|.+++++.|+
T Consensus 136 l~~~~iPvV~~~~~~~~---~~~~~---V~~dn~~~~~~~~~~L~~~G~~~I~~i~~~~~~~~~~~R~~Gf~~al~~~~~ 209 (327)
T TIGR02417 136 LQNEGLPVVALDRSLDD---EHFCS---VISDDVDAAAELIERLLSQHADEFWYLGAQPELSVSRDRLAGFRQALKQATL 209 (327)
T ss_pred HHhcCCCEEEEccccCC---CCCCE---EEeCcHHHHHHHHHHHHHCCCCeEEEEeCcccchhHHHHHHHHHHHHHHcCC
Confidence 34568898887553221 12233 34566666777778888889999999974332 345567889999999987
Q ss_pred eeeeeeecCCCCChHHHHHHHHHhhcC---CceEEEEEeChhhHHHHHHHHHHcCCcccceEEE
Q 003054 88 RVPYRSVISPLATDDQIEKELYKLFTM---QTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWI 148 (852)
Q Consensus 88 ~v~~~~~~~~~~~~~d~~~~l~~l~~~---~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi 148 (852)
++... +..+...++-...+.++.+. .|++|++. +...+..+++.+++.| ..|+-+-|
T Consensus 210 ~~~~~--~~~~~~~~~~~~~~~~ll~~~~~~~~Ai~~~-~D~~A~g~~~al~~~g-~vP~dvsv 269 (327)
T TIGR02417 210 EVEWV--YGGNYSRESGYQMFAKLCARLGRLPQALFTT-SYTLLEGVLDYMLERP-LLDSQLHL 269 (327)
T ss_pred ChHhE--EeCCCChHHHHHHHHHHHhcCCCCCcEEEEc-CcHHHHHHHHHHHHcC-CCCCcceE
Confidence 53221 11111122233455555443 36876664 4566788999999999 66644333
No 219
>PRK12679 cbl transcriptional regulator Cbl; Reviewed
Probab=91.53 E-value=11 Score=40.80 Aligned_cols=208 Identities=13% Similarity=0.107 Sum_probs=127.1
Q ss_pred CceEEEeeecccCcccceEEeeCCCCCCCceEEEeeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCc
Q 003054 344 EKKLRIGVPVKKGFSDFVNVTIDPKTQEPTSVTGYCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGE 423 (852)
Q Consensus 344 ~~~lrv~v~~~~~~~~~~~~~~d~~~~~~~~~~G~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~ 423 (852)
.+.+|||++ +. ....+-.++++.+.++.+- +.+++.. ++.++++++|.+|+
T Consensus 92 ~g~lrIg~~--~~-----------------~~~~~l~~~l~~f~~~~P~-i~l~l~~---------~~~~~~~~~L~~g~ 142 (316)
T PRK12679 92 SGVLTIATT--HT-----------------QARYSLPEVIKAFRELFPE-VRLELIQ---------GTPQEIATLLQNGE 142 (316)
T ss_pred CceEEEEec--hH-----------------hhhcchHHHHHHHHHHCCC-eEEEEec---------CCHHHHHHHHHcCC
Confidence 467999997 22 1224556888888888763 4555433 34678999999999
Q ss_pred ccEEEeeeeeecCcceeeeccccccccceEEEEEccCCCCCCceEeecccchhHHHHHHHHHHHHHhhhhheecccCCCC
Q 003054 424 FDAVVGDITIVFNRSNYVDFTLPYTESGVSMIVPIKDSKKRNAWVFLQPLTWDLWVTCFCFFIFIGFVVWVLEHRVNEDF 503 (852)
Q Consensus 424 ~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv~~~~~~~~~~~~~l~PF~~~lW~~i~~~~i~~~~v~~~l~~~~~~~~ 503 (852)
+|+++...... . ...+. +.++.....++++++.....
T Consensus 143 ~Dl~i~~~~~~-~-~~~l~-~~~l~~~~~~~v~~~~hpl~---------------------------------------- 179 (316)
T PRK12679 143 ADIGIASERLS-N-DPQLV-AFPWFRWHHSLLVPHDHPLT---------------------------------------- 179 (316)
T ss_pred CCEEEecccCC-C-CCCce-EEEccCCcEEEEecCCCccc----------------------------------------
Confidence 99987532211 1 12233 35777888888887552110
Q ss_pred CCCcccccchhHHHHHHHhhhccccccccchhhHHHHHHHHHHHHHHHHhhhhccceeeecccCCCcCCHHHHHhcCCe-
Q 003054 504 RGPAGQQVGTSFWFSFSTMVFSQRERVISNLARIVVIVWCFVVLILTQSYTASLTSLLTVQQLQPTITDVKMLIKRGDN- 582 (852)
Q Consensus 504 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~s~~~R~v~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~i~sl~dL~~~~~~- 582 (852)
....-+++||. +.+
T Consensus 180 ---------------------------------------------------------------~~~~i~~~~L~--~~~~ 194 (316)
T PRK12679 180 ---------------------------------------------------------------QITPLTLESIA--KWPL 194 (316)
T ss_pred ---------------------------------------------------------------cCCCCCHHHHh--CCCe
Confidence 00123788887 333
Q ss_pred EEEEeCch----HHHHHHhcCCCCcceeecCCHhHHHHHhhcccccCceeEEEechhHHHHHHhhcCCceEee--ccccc
Q 003054 583 VGYQKGSF----VLGILKQLGFDERKLVVYNSPEDCHELFQKGSVNGGIAAAFDEIPYMKLLIGQYCSKYAMI--EPKFK 656 (852)
Q Consensus 583 vg~~~~s~----~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~~~~~~~~v--~~~~~ 656 (852)
+....+.. ...++...+.........++.+...+++..|. ..+++-... ... . +.. .+..+ .....
T Consensus 195 i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~g~----Gi~~lp~~~-~~~-~-~~~-~L~~~~~~~~~~ 266 (316)
T PRK12679 195 ITYRQGITGRSRIDDAFARKGLLADIVLSAQDSDVIKTYVALGL----GIGLVAEQS-SGE-Q-EES-NLIRLDTRHLFD 266 (316)
T ss_pred EEecCCCcHHHHHHHHHHHcCCCceEEEEeccHHHHHHHHHcCC----cEEEecccc-ccc-c-cCC-cEEEEECcccCC
Confidence 44444433 33445555555444566788888999999987 455554432 222 1 112 23333 22334
Q ss_pred ccceEEEecCCCCchhhHHHHHHhccccChhHHHHHHHcc
Q 003054 657 TAGFGFVFPLHSPLVHDVSKAILNVTEGDKMKEIEDAWFK 696 (852)
Q Consensus 657 ~~~~~~~~~k~spl~~~in~~il~l~e~G~~~~i~~kw~~ 696 (852)
...+.++.+++.++...+..++..+.+.--...+.++...
T Consensus 267 ~~~~~l~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~ 306 (316)
T PRK12679 267 ANTVWLGLKRGQLQRNYVWRFLELCNAGLSVEDIKRQVME 306 (316)
T ss_pred CceEEEEEeCCchhhHHHHHHHHHHhcccCHHHHHHHHhh
Confidence 4578899999988888888888777666566777777664
No 220
>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=91.43 E-value=4.5 Score=42.23 Aligned_cols=124 Identities=7% Similarity=0.043 Sum_probs=76.1
Q ss_pred HhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHc--CCcEEEEEEEeC-CcccccHHHHHHHHHh
Q 003054 8 QLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAF--GWREAVPIYVDN-QYGEEMIPSLTDALQA 84 (852)
Q Consensus 8 ~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~--gw~~vaii~~d~-~~G~~~~~~l~~~l~~ 84 (852)
..+.+.++|+|.+....+ ..+.+.....++..-+..+++++.+. |-+++++++..+ .......+.|++++++
T Consensus 74 ~~~~~~~ipvV~~~~~~~-----~~~~~~~v~~d~~~~g~~~~~~l~~~~~g~~~i~~i~~~~~~~~~~R~~gf~~~~~~ 148 (267)
T cd06322 74 AKAKKAGIPVITVDIAAE-----GVAVVSHVATDNYAGGVLAGELAAKVLNGKGQVAIIDYPTVQSVVDRVRGFKEALAD 148 (267)
T ss_pred HHHHHCCCCEEEEcccCC-----CCceEEEEecChHHHHHHHHHHHHHHhCCCceEEEEecCCCccHHHHHHHHHHHHHh
Confidence 445678999999854211 11223345666667777888887664 888999997432 2344567889999999
Q ss_pred C-CceeeeeeecCCCCChHHHHHHHHHhhcC--CceEEEEEeChhhHHHHHHHHHHcCC
Q 003054 85 I-DTRVPYRSVISPLATDDQIEKELYKLFTM--QTRVFILHMLPSLGSRIFEKANEIGL 140 (852)
Q Consensus 85 ~-g~~v~~~~~~~~~~~~~d~~~~l~~l~~~--~~~viv~~~~~~~~~~i~~~a~~~G~ 140 (852)
. |+++.... .. ...+.-...+.++.+. ++++|+. .+...+..+++.+++.|.
T Consensus 149 ~~~~~~~~~~-~~--~~~~~~~~~~~~~l~~~~~~~ai~~-~~d~~a~~~~~al~~~g~ 203 (267)
T cd06322 149 YPNIKIVAVQ-PG--ITRAEALTAAQNILQANPDLDGIFA-FGDDAALGAVSAIKAAGR 203 (267)
T ss_pred CCCcEEEEec-CC--CChHHHHHHHHHHHHhCCCCCEEEE-cCCcHHHHHHHHHHHCCC
Confidence 8 88764221 11 1122233344454433 4565444 455567788899999998
No 221
>PRK09492 treR trehalose repressor; Provisional
Probab=91.38 E-value=2.5 Score=45.61 Aligned_cols=99 Identities=12% Similarity=0.012 Sum_probs=67.7
Q ss_pred ccCCchhHHHHHHHHHHHcCCcEEEEEEEe---CCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcC
Q 003054 38 GSLNDSSQAGAITAIIKAFGWREAVPIYVD---NQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTM 114 (852)
Q Consensus 38 ~~p~d~~~~~aia~~l~~~gw~~vaii~~d---~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~ 114 (852)
+..++..-+..+++++...|-++++++... ...+....+.|.+++++.|+++... .. ..+...-...+.++.+.
T Consensus 155 V~~D~~~~~~~a~~~L~~~G~~~I~~i~~~~~~~~~~~~R~~Gf~~al~~~g~~~~~~--~~-~~~~~~~~~~~~~~l~~ 231 (315)
T PRK09492 155 VCYDDEGAIKLLMQRLYDQGHRHISYLGVDHSDVTTGKRRHQAYLAFCKQHKLTPVAA--LG-GLSMQSGYELVAKVLTP 231 (315)
T ss_pred EEECcHHHHHHHHHHHHHcCCCeEEEEcCCcccchhHHHHHHHHHHHHHHcCCCceee--cC-CCCchHHHHHHHHHhhc
Confidence 455666777788888888899999999632 2345677889999999999875421 11 11112222345555556
Q ss_pred CceEEEEEeChhhHHHHHHHHHHcCC
Q 003054 115 QTRVFILHMLPSLGSRIFEKANEIGL 140 (852)
Q Consensus 115 ~~~viv~~~~~~~~~~i~~~a~~~G~ 140 (852)
+|++|++. +...+..+++.+++.|+
T Consensus 232 ~~~ai~~~-~D~~A~g~~~al~~~g~ 256 (315)
T PRK09492 232 ETTALVCA-TDTLALGASKYLQEQGR 256 (315)
T ss_pred CCCEEEEc-CcHHHHHHHHHHHHcCC
Confidence 78988754 45778889999999997
No 222
>PRK09860 putative alcohol dehydrogenase; Provisional
Probab=91.30 E-value=1.5 Score=48.79 Aligned_cols=90 Identities=10% Similarity=-0.004 Sum_probs=68.8
Q ss_pred HHHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeC
Q 003054 45 QAGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHML 124 (852)
Q Consensus 45 ~~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~ 124 (852)
....+.+.++.+|.+++.+++...-...+..+.+.+.|++.|+++.....+.++++.+++...+..+++.++|+||-.+-
T Consensus 18 ~~~~l~~~~~~~g~~~~livt~~~~~~~g~~~~v~~~L~~~~i~~~~f~~v~~np~~~~v~~~~~~~~~~~~D~IiaiGG 97 (383)
T PRK09860 18 SLTDAMNMMADYGFTRTLIVTDNMLTKLGMAGDVQKALEERNIFSVIYDGTQPNPTTENVAAGLKLLKENNCDSVISLGG 97 (383)
T ss_pred HHHHHHHHHHhcCCCEEEEEcCcchhhCccHHHHHHHHHHcCCeEEEeCCCCCCcCHHHHHHHHHHHHHcCCCEEEEeCC
Confidence 34557778899999999988854434456788999999999988755555666777888999999999999999996654
Q ss_pred h--hhHHHHHHH
Q 003054 125 P--SLGSRIFEK 134 (852)
Q Consensus 125 ~--~~~~~i~~~ 134 (852)
+ -|+.+.+..
T Consensus 98 GS~iD~AK~ia~ 109 (383)
T PRK09860 98 GSPHDCAKGIAL 109 (383)
T ss_pred chHHHHHHHHHH
Confidence 3 466666554
No 223
>PRK11151 DNA-binding transcriptional regulator OxyR; Provisional
Probab=91.27 E-value=11 Score=40.37 Aligned_cols=69 Identities=13% Similarity=0.140 Sum_probs=47.3
Q ss_pred EeeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCcccEEEeeeeeecCcceeeeccccccccceEEEE
Q 003054 377 GYCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGEFDAVVGDITIVFNRSNYVDFTLPYTESGVSMIV 456 (852)
Q Consensus 377 G~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv 456 (852)
++-..++..+.+..+- +++.+.. ++.++++++|.+|++|+++...... ...+ ...|+....+++++
T Consensus 104 ~~~~~~l~~~~~~~P~-v~i~~~~---------~~~~~~~~~l~~g~~Dl~i~~~~~~---~~~l-~~~~l~~~~~~~~~ 169 (305)
T PRK11151 104 YLLPHIIPMLHQTFPK-LEMYLHE---------AQTHQLLAQLDSGKLDCAILALVKE---SEAF-IEVPLFDEPMLLAV 169 (305)
T ss_pred HHHHHHHHHHHHHCCC-cEEEEEe---------CCHHHHHHHHHcCCccEEEEecCCC---CCCe-EEEEeccCcEEEEe
Confidence 3445778888887763 5555544 2468999999999999998643222 1122 35788888999988
Q ss_pred Ecc
Q 003054 457 PIK 459 (852)
Q Consensus 457 ~~~ 459 (852)
++.
T Consensus 170 ~~~ 172 (305)
T PRK11151 170 YED 172 (305)
T ss_pred cCC
Confidence 855
No 224
>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=91.27 E-value=2.2 Score=44.82 Aligned_cols=128 Identities=7% Similarity=-0.001 Sum_probs=72.4
Q ss_pred HHHhcCCC-CccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHH-cCCcEEEEEEEeCCcc-cccHHHHHHHH
Q 003054 6 IIQLGNKS-QVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKA-FGWREAVPIYVDNQYG-EEMIPSLTDAL 82 (852)
Q Consensus 6 v~~i~~~~-~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~-~gw~~vaii~~d~~~G-~~~~~~l~~~l 82 (852)
+..+..++ ++|++......+.. +.+-....++..-+..++.++.. .|-++++++..+..-. ....+.+++++
T Consensus 72 ~~~~~~~~~~~PiV~i~~~~~~~-----~~~~~v~~d~~~a~~~a~~ll~~~~G~~~I~~i~~~~~~~~~~r~~gf~~~~ 146 (265)
T cd06354 72 LKEVAKQYPDQKFAIIDAVVDDP-----PNVASIVFKEEEGSFLAGYLAALMTKTGKVGFIGGMDIPLIRRFEAGFEAGV 146 (265)
T ss_pred HHHHHHHCCCCEEEEEecccCCC-----CcEEEEEecchhHHHHHHHHHHhhcCCCeEEEEecccChHHHHHHHHHHHHH
Confidence 34455555 89999875422110 11222333444444444555554 3999999997432211 22236788899
Q ss_pred HhCC---ceeeeeeecCCCCC-hHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHcC
Q 003054 83 QAID---TRVPYRSVISPLAT-DDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEIG 139 (852)
Q Consensus 83 ~~~g---~~v~~~~~~~~~~~-~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~G 139 (852)
++.| ..+..........+ ..+-...+.++.+.+||+|+.. +...+..+++.+++.|
T Consensus 147 ~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~pdaI~~~-nd~~A~gv~~al~~~g 206 (265)
T cd06354 147 KYVNPGVPDIEVLVQYAGSFNDPAKGKEIAQAMYDQGADVIFAA-AGGTGNGVFQAAKEAG 206 (265)
T ss_pred HHHhccCCCceEEEEEcCcccCHHHHHHHHHHHHHCCCcEEEEC-CCCCchHHHHHHHhcC
Confidence 8888 65432222211111 1233345666665568875554 6667788999999998
No 225
>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=91.25 E-value=12 Score=37.18 Aligned_cols=103 Identities=12% Similarity=-0.039 Sum_probs=57.9
Q ss_pred CHHHHHhcCCeEEE-EeCch----HHHHHHhcCCCCcceeecCCHhHHHHHhhcccccCceeEEEechhHHHHHHhhcCC
Q 003054 572 DVKMLIKRGDNVGY-QKGSF----VLGILKQLGFDERKLVVYNSPEDCHELFQKGSVNGGIAAAFDEIPYMKLLIGQYCS 646 (852)
Q Consensus 572 sl~dL~~~~~~vg~-~~~s~----~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~~~~ 646 (852)
+++||. +.++.. ..++. ...++++.+.........++.+...+++..|. ..+++-+.. ........
T Consensus 93 ~~~dL~--~~~~i~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~v~~G~----Gv~~lp~~~-~~~~~~~~-- 163 (204)
T cd08429 93 FPASLD--EAPLLLPGEDSALRRKLLQWFERQGLRPQIVGEFDDSALMKAFGQAGA----GIFAAPTVI-ADEVARQY-- 163 (204)
T ss_pred CHhHhc--cCCeeecCCCCcHHHHHHHHHHHcCCCcceEEEeCCHHHHHHHHHcCC----CeEeccHHH-HHHHHhcC--
Confidence 678886 433333 34443 33455556665545556788899999999998 455555433 33222221
Q ss_pred ceEeec-ccccccceEEEecCCCCchhhHHHHHHhccc
Q 003054 647 KYAMIE-PKFKTAGFGFVFPLHSPLVHDVSKAILNVTE 683 (852)
Q Consensus 647 ~~~~v~-~~~~~~~~~~~~~k~spl~~~in~~il~l~e 683 (852)
.+..+. ..-....++++.+|+......+...+..+++
T Consensus 164 ~l~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f~~~~~~ 201 (204)
T cd08429 164 GVVEIGRTDEVVEEFYAISVERRITHPAVVAISEAARS 201 (204)
T ss_pred CeEeeccCccceeeEEEEeecccCCCHHHHHHHHhhcc
Confidence 233332 1113446788888876666666555555443
No 226
>PRK09791 putative DNA-binding transcriptional regulator; Provisional
Probab=91.22 E-value=6 Score=42.34 Aligned_cols=85 Identities=14% Similarity=0.180 Sum_probs=55.7
Q ss_pred CceEEEeeecccCcccceEEeeCCCCCCCceEEEeeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCc
Q 003054 344 EKKLRIGVPVKKGFSDFVNVTIDPKTQEPTSVTGYCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGE 423 (852)
Q Consensus 344 ~~~lrv~v~~~~~~~~~~~~~~d~~~~~~~~~~G~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~ 423 (852)
.+.++||++.. + ...+-.+++..+.+..+ .+++++.. ++..++..+|.+|+
T Consensus 94 ~g~l~I~~~~~--~-----------------~~~~l~~~l~~~~~~~p-~i~~~~~~---------~~~~~~~~~l~~g~ 144 (302)
T PRK09791 94 AGQINIGMGAS--I-----------------ARSLMPAVISRFHQQHP-QVKVRIME---------GQLVSMINELRQGE 144 (302)
T ss_pred ceEEEEEechH--H-----------------HHhhhHHHHHHHHHHCC-CeEEEEEe---------CChHHHHHHHHCCC
Confidence 57899998722 1 12344688888888887 34555443 24679999999999
Q ss_pred ccEEEeeeeeecCcceeeeccccccccceEEEEEcc
Q 003054 424 FDAVVGDITIVFNRSNYVDFTLPYTESGVSMIVPIK 459 (852)
Q Consensus 424 ~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv~~~ 459 (852)
+|+++..... ......+.+ .|+....+++++++.
T Consensus 145 ~Di~i~~~~~-~~~~~~~~~-~~l~~~~~~l~~~~~ 178 (302)
T PRK09791 145 LDFTINTYYQ-GPYDHEFTF-EKLLEKQFAVFCRPG 178 (302)
T ss_pred ccEEEEecCC-cccccceeE-EEeccceEEEEEcCC
Confidence 9998752111 111223443 678888888888855
No 227
>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=91.14 E-value=7.4 Score=38.12 Aligned_cols=67 Identities=19% Similarity=0.182 Sum_probs=43.6
Q ss_pred eeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCcccEEEeeeeeecCcceeeeccccccccceEEEEE
Q 003054 378 YCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGEFDAVVGDITIVFNRSNYVDFTLPYTESGVSMIVP 457 (852)
Q Consensus 378 ~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv~ 457 (852)
+-..++..+.++.+- +.++... ++. ++++.|.+|++|++++.-.. ....+. ..|+....++++++
T Consensus 14 ~l~~~i~~~~~~~P~-i~l~i~~---------~~~-~~~~~l~~g~~D~~i~~~~~---~~~~~~-~~~l~~~~~~~v~~ 78 (200)
T cd08462 14 LLPPVIERVAREAPG-VRFELLP---------PDD-QPHELLERGEVDLLIAPERF---MSDGHP-SEPLFEEEFVCVVW 78 (200)
T ss_pred HHHHHHHHHHHHCCC-CEEEEec---------CCh-hHHHHHhcCCeeEEEecCCC---CCCCce-eeeeeccceEEEEc
Confidence 345778888888762 4555543 234 89999999999999863211 112233 35677788888877
Q ss_pred cc
Q 003054 458 IK 459 (852)
Q Consensus 458 ~~ 459 (852)
..
T Consensus 79 ~~ 80 (200)
T cd08462 79 AD 80 (200)
T ss_pred CC
Confidence 54
No 228
>PRK11063 metQ DL-methionine transporter substrate-binding subunit; Provisional
Probab=91.12 E-value=5.2 Score=42.18 Aligned_cols=120 Identities=14% Similarity=0.133 Sum_probs=63.5
Q ss_pred CcCCHHHHHhcCCeEEEEeCc-hH---HHHHHhcCC------------------CCcceeecC-CHhHHHHHhhcccccC
Q 003054 569 TITDVKMLIKRGDNVGYQKGS-FV---LGILKQLGF------------------DERKLVVYN-SPEDCHELFQKGSVNG 625 (852)
Q Consensus 569 ~i~sl~dL~~~~~~vg~~~~s-~~---~~~l~~~~~------------------~~~~~~~~~-~~~~~~~~l~~g~~~~ 625 (852)
.|++++||. .|++|++..+. .. ..+|++.++ .+.++...+ ...+...++.+|+
T Consensus 120 ~i~si~DL~-~Gk~IAip~d~~n~~r~L~lL~~~Gli~l~~~~~~~~t~~di~~n~~~v~~v~~~~~~~~~al~~g~--- 195 (271)
T PRK11063 120 KIKSLDELQ-DGSQVAVPNDPTNLGRSLLLLQKVGLIKLKDGVGLLPTVLDIVENPKNLKIVELEAPQLPRSLDDAQ--- 195 (271)
T ss_pred CCCCHHHhc-CCCEEEecCCCccHHHHHHHHHHCCCEEecCCCCCCCCHHHHhcCCCCCEEEECcHHHHHHhccccc---
Confidence 499999994 58899997532 11 123455443 111222222 3456778899998
Q ss_pred ceeEEEechhHHHHHHhhc-CCceEeecccccccceEEEecCCCCchhhHHHHHHhccccChhHHHHHHH
Q 003054 626 GIAAAFDEIPYMKLLIGQY-CSKYAMIEPKFKTAGFGFVFPLHSPLVHDVSKAILNVTEGDKMKEIEDAW 694 (852)
Q Consensus 626 g~~a~~~~~~~~~~~~~~~-~~~~~~v~~~~~~~~~~~~~~k~spl~~~in~~il~l~e~G~~~~i~~kw 694 (852)
+++++...+++...-... -+.+ ...+.-...-..+++++...--+.+.+.+.-++....-+.|.++|
T Consensus 196 -vDaa~i~~~~a~~a~~~~~~~~l-~~e~~~~~~~~~~~v~~~~~~~~~~~~l~~a~~s~~v~~~i~~~~ 263 (271)
T PRK11063 196 -IALAVINTTYASQIGLTPAKDGI-FVEDKDSPYVNLIVAREDNKDAENVKKFVQAYQSDEVYEAANKVF 263 (271)
T ss_pred -ccEEEEChHHHHHcCCCCCCCee-EECCCCCCeEEEEEECCcccCCHHHHHHHHHHcCHHHHHHHHHHc
Confidence 999998877766432211 1122 222211122235556655333344555555455554555555554
No 229
>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=91.08 E-value=2.7 Score=43.81 Aligned_cols=128 Identities=16% Similarity=0.192 Sum_probs=80.5
Q ss_pred CCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEe-CCcccccHHHHHHHHHhCCcee
Q 003054 11 NKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVD-NQYGEEMIPSLTDALQAIDTRV 89 (852)
Q Consensus 11 ~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d-~~~G~~~~~~l~~~l~~~g~~v 89 (852)
...++|+|......+ ....+++ ..++..-+..+++++.+.|-++++++..+ ........+.|++++++.|+..
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 356788888755332 2233443 35666777788888888899999998743 2233455788999999988765
Q ss_pred eeeeecCCCCChHHHHHHHHHhhcC--CceEEEEEeChhhHHHHHHHHHHcCCcccceEEE
Q 003054 90 PYRSVISPLATDDQIEKELYKLFTM--QTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWI 148 (852)
Q Consensus 90 ~~~~~~~~~~~~~d~~~~l~~l~~~--~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi 148 (852)
.... +.. +..+-...+.++... .|++|+ +.+...+..+++.+++.|+..++-+.|
T Consensus 148 ~~~~-~~~--~~~~~~~~~~~~l~~~~~~~ai~-~~~d~~a~g~~~~l~~~g~~~p~di~i 204 (263)
T cd06280 148 DARF-VAP--TAEAAEAALAAWLAAPERPEALV-ASNGLLLLGALRAVRAAGLRIPQDLAL 204 (263)
T ss_pred Chhh-ccc--CHHHHHHHHHHHhcCCCCCcEEE-ECCcHHHHHHHHHHHHcCCCCCCcEEE
Confidence 3221 121 122333445554433 467654 456667888999999999865544433
No 230
>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=91.05 E-value=5.8 Score=41.78 Aligned_cols=136 Identities=10% Similarity=0.030 Sum_probs=80.2
Q ss_pred HhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHH-cCCc--EEEEEEEe--CCcccccHHHHHHHH
Q 003054 8 QLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKA-FGWR--EAVPIYVD--NQYGEEMIPSLTDAL 82 (852)
Q Consensus 8 ~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~-~gw~--~vaii~~d--~~~G~~~~~~l~~~l 82 (852)
..+.+.++|+|......+ + ..+.+..+..++...+..+++++-+ .|-+ +++++..+ ...+....+.|++++
T Consensus 74 ~~~~~~~iPvV~~~~~~~---~-~~~~~~~v~~d~~~~g~~~~~~l~~~~g~~~~~i~~i~~~~~~~~~~~R~~gf~~~l 149 (282)
T cd06318 74 AAAKAAGVPVVVVDSSIN---L-EAGVVTQVQSSNAKNGNLVGEWVVGELGDKPMKIILLSGDAGNLVGQARRDGFLLGV 149 (282)
T ss_pred HHHHHCCCCEEEecCCCC---C-CcCeEEEEecCcHHHHHHHHHHHHHHhCCCCceEEEEECCCCCchHhHHHHhHHHHH
Confidence 444568999999865321 1 0123344667777888889988744 6865 89888743 345667788899999
Q ss_pred HhCCcee------eeeeecCCCCChHHHHHHHHHhhcC--CceEEEEEeChhhHHHHHHHHHHcCCcccceEEEE
Q 003054 83 QAIDTRV------PYRSVISPLATDDQIEKELYKLFTM--QTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIM 149 (852)
Q Consensus 83 ~~~g~~v------~~~~~~~~~~~~~d~~~~l~~l~~~--~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~ 149 (852)
++.|... ..........+..+-...+.++... ++++|+. .+...+..+++.+++.|+. .+...++
T Consensus 150 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~-~~d~~a~g~~~al~~~g~~-~dv~vvg 222 (282)
T cd06318 150 SEAQLRKYGKTNFTIVAQGYGDWTREGGLKAMEDLLVAHPDINVVYS-ENDDMALGAMRVLAEAGKT-DDVKVAA 222 (282)
T ss_pred hhCcccccccCCeEEEecCCCCCCHHHHHHHHHHHHHhCCCcCEEEE-CCcchHHHHHHHHHHcCCC-CCeEEEe
Confidence 9886421 1111011111222333445554433 4565554 4555677889999999984 3333443
No 231
>PRK09701 D-allose transporter subunit; Provisional
Probab=91.00 E-value=5.7 Score=42.80 Aligned_cols=138 Identities=9% Similarity=0.018 Sum_probs=81.6
Q ss_pred cCCCCccEEeeecCCCC--CCCCCCCceEeccCCchhHHHHHHHHH-HHcCC--cEEEEEEEeC--CcccccHHHHHHHH
Q 003054 10 GNKSQVPILSFSATSPS--LTSIRSPYFFRGSLNDSSQAGAITAII-KAFGW--REAVPIYVDN--QYGEEMIPSLTDAL 82 (852)
Q Consensus 10 ~~~~~vP~Is~~ats~~--lt~~~~py~fR~~p~d~~~~~aia~~l-~~~gw--~~vaii~~d~--~~G~~~~~~l~~~l 82 (852)
+.+.+||++.+....+. +.........-+..++...+..+++++ +..|- ++++++..+. .......+.|++++
T Consensus 103 ~~~~giPvV~~~~~~~~~~~~~~~~~~~~~V~~d~~~~g~~aa~~L~~~~g~~~~~i~~l~g~~~~~~~~~R~~Gf~~al 182 (311)
T PRK09701 103 AWKKGIYLVNLDEKIDMDNLKKAGGNVEAFVTTDNVAVGAKGASFIIDKLGAEGGEVAIIEGKAGNASGEARRNGATEAF 182 (311)
T ss_pred HHHCCCcEEEeCCCCCcccccccCCceEEEeccchHHHHHHHHHHHHHHhCCCCCEEEEEECCCCCccHHHHHHHHHHHH
Confidence 45688999998654321 111111122335677778888888887 44564 7999886433 33456678899999
Q ss_pred HhCC-ceeeeeeecCCCCChHHHHHHHHHhhcC--CceEEEEEeChhhHHHHHHHHHHcCCcccceEEEEcC
Q 003054 83 QAID-TRVPYRSVISPLATDDQIEKELYKLFTM--QTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTD 151 (852)
Q Consensus 83 ~~~g-~~v~~~~~~~~~~~~~d~~~~l~~l~~~--~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~ 151 (852)
++.| +++..... ......+-...+.++.+. ++++|+ +.+...+..+++.+++.|.. .+...++-+
T Consensus 183 ~~~~~~~~~~~~~--~~~~~~~~~~~~~~ll~~~~~~~~I~-~~~d~~A~g~~~al~~~G~~-~dv~vvg~d 250 (311)
T PRK09701 183 KKASQIKLVASQP--ADWDRIKALDVATNVLQRNPNIKAIY-CANDTMAMGVAQAVANAGKT-GKVLVVGTD 250 (311)
T ss_pred HhCCCcEEEEecC--CCCCHHHHHHHHHHHHHhCCCCCEEE-ECCcchHHHHHHHHHHcCCC-CCEEEEEeC
Confidence 8887 76543211 111222233455555433 356544 55666788899999999984 333344333
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=90.95 E-value=4.3 Score=43.16 Aligned_cols=128 Identities=8% Similarity=0.061 Sum_probs=76.3
Q ss_pred HhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHc------CCcEEEEEEEeC--CcccccHHHHH
Q 003054 8 QLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAF------GWREAVPIYVDN--QYGEEMIPSLT 79 (852)
Q Consensus 8 ~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~------gw~~vaii~~d~--~~G~~~~~~l~ 79 (852)
..+...++|+|......+. ...++. +..++...++.+++++... |-++++++..+. .......+.|+
T Consensus 74 ~~l~~~~ipvV~~~~~~~~---~~~~~~--v~~d~~~~g~~~~~~l~~~~~~~~~g~~~i~~l~g~~~~~~~~~R~~gf~ 148 (288)
T cd01538 74 EKAADAGIPVIAYDRLILN---SNVDYY--VSFDNEKVGELQGQALVDGLGAKGKPPGNIELIAGSPTDNNAKLFFNGAM 148 (288)
T ss_pred HHHHHCCCCEEEECCCCCC---CCcceE--EEeChHHHHHHHHHHHHHHHhhcCCCCceEEEEECCCCCchHHHHHHHHH
Confidence 3455679999998654322 112222 3456566677777776444 889999997433 23445578889
Q ss_pred HHHHhCC----ceeeeeeecCCCCChHHHHHHHHHhhcC---CceEEEEEeChhhHHHHHHHHHHcCCcc
Q 003054 80 DALQAID----TRVPYRSVISPLATDDQIEKELYKLFTM---QTRVFILHMLPSLGSRIFEKANEIGLMN 142 (852)
Q Consensus 80 ~~l~~~g----~~v~~~~~~~~~~~~~d~~~~l~~l~~~---~~~viv~~~~~~~~~~i~~~a~~~G~~~ 142 (852)
+++++.| +++.... +..+.+..+-...+.++.+. .+++|+.. +...+..+++.+++.|+..
T Consensus 149 ~~l~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~l~~~~~~~~~I~~~-~d~~a~g~~~al~~~g~~~ 216 (288)
T cd01538 149 SVLKPLIDSGKITIVGEV-ATPDWDPETAQKRMENALTANYNKVDGVLAA-NDGTAGGAIAALKAAGLAG 216 (288)
T ss_pred HHHHhccccCCeeEEecc-ccCCCCHHHHHHHHHHHHHhCCCCccEEEeC-CcHHHHHHHHHHHHcCCCC
Confidence 9999887 5543221 11111222233445555433 35665544 4667788899999999865
No 233
>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=90.69 E-value=6.3 Score=38.59 Aligned_cols=69 Identities=20% Similarity=0.210 Sum_probs=46.4
Q ss_pred EEeeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCcccEEEeeeeeecCcceeeeccccccccceEEE
Q 003054 376 TGYCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGEFDAVVGDITIVFNRSNYVDFTLPYTESGVSMI 455 (852)
Q Consensus 376 ~G~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~~D~~~g~~~it~~r~~~vdft~p~~~~~~~~v 455 (852)
..+-.+++..+.++.+ .++++... ++. +++++|.+|++|++++.... ....+. ..|+....++++
T Consensus 12 ~~~l~~~l~~~~~~~P-~v~v~l~~---------~~~-~~~~~l~~g~~D~~i~~~~~---~~~~~~-~~~l~~~~~~~v 76 (200)
T cd08460 12 AAFGPALLAAVAAEAP-GVRLRFVP---------ESD-KDVDALREGRIDLEIGVLGP---TGPEIR-VQTLFRDRFVGV 76 (200)
T ss_pred HHHHHHHHHHHHHHCC-CCEEEEec---------Cch-hHHHHHHCCCccEEEecCCC---CCcchh-eeeeeccceEEE
Confidence 3556788888888876 35565543 234 78899999999999863221 122233 467778888888
Q ss_pred EEcc
Q 003054 456 VPIK 459 (852)
Q Consensus 456 v~~~ 459 (852)
++..
T Consensus 77 ~~~~ 80 (200)
T cd08460 77 VRAG 80 (200)
T ss_pred EeCC
Confidence 8854
No 234
>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=90.62 E-value=5.3 Score=42.69 Aligned_cols=127 Identities=7% Similarity=-0.051 Sum_probs=74.6
Q ss_pred HhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHc-CC-cEEEEEEEeCC--cccccHHHHHHHHH
Q 003054 8 QLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAF-GW-REAVPIYVDNQ--YGEEMIPSLTDALQ 83 (852)
Q Consensus 8 ~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~-gw-~~vaii~~d~~--~G~~~~~~l~~~l~ 83 (852)
..+.+.++|+|......+. . ..-++....++...+..+++++.+. +- ++++++..+.. ......+.|+++++
T Consensus 75 ~~~~~~~iPvV~v~~~~~~---~-~~~~~~v~~D~~~~g~~a~~~l~~~~~~~~~I~~l~g~~~~~~~~~R~~Gf~~~l~ 150 (298)
T cd06302 75 KKAREAGIKVVTHDSDVQP---D-NRDYDIEQADNKAIGETLMDSLAEQMGGKGEYAIFVGSLTATNQNAWIDAAKAYQK 150 (298)
T ss_pred HHHHHCCCeEEEEcCCCCC---C-cceeEEeccCHHHHHHHHHHHHHHHcCCCCEEEEEeCCCCCcchHHHHHHHHHHHh
Confidence 3456789999987643211 0 1113334567777778888887554 43 69999874332 23445688999999
Q ss_pred hCC---ceeeeeeecCCCCChHHHHHHHHHhhcC--CceEEEEEeChhhHHHHHHHHHHcCCc
Q 003054 84 AID---TRVPYRSVISPLATDDQIEKELYKLFTM--QTRVFILHMLPSLGSRIFEKANEIGLM 141 (852)
Q Consensus 84 ~~g---~~v~~~~~~~~~~~~~d~~~~l~~l~~~--~~~viv~~~~~~~~~~i~~~a~~~G~~ 141 (852)
+.| .++.. .+....+...-...+.++.+. .+++|+. .+...+..+++.+++.|+.
T Consensus 151 ~~g~~~~~~~~--~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~-~~D~~A~g~~~al~~~g~~ 210 (298)
T cd06302 151 EKYYPMLELVD--RQYGDDDADKSYQTAQELLKAYPDLKGIIG-PTSVGIPGAARAVEEAGLK 210 (298)
T ss_pred hcCCCCeEEeC--cccCCCCHHHHHHHHHHHHHhCCCceEEEE-CCCcchhHHHHHHHhcCCC
Confidence 987 23211 111111222222344444333 3555554 3456788899999999985
No 235
>PRK11041 DNA-binding transcriptional regulator CytR; Provisional
Probab=90.53 E-value=1.9 Score=46.33 Aligned_cols=111 Identities=13% Similarity=0.086 Sum_probs=71.2
Q ss_pred ccCCchhHHHHHHHHHHHcCCcEEEEEEEeCC--cccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcC-
Q 003054 38 GSLNDSSQAGAITAIIKAFGWREAVPIYVDNQ--YGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTM- 114 (852)
Q Consensus 38 ~~p~d~~~~~aia~~l~~~gw~~vaii~~d~~--~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~- 114 (852)
+..++...+..+++++.+.|-+++++|..+.. ......+.|++++++.|+++.....+..+.+.......+.++.+.
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 34566677777888887789999999974332 344568889999999988753221111111223334455666543
Q ss_pred -CceEEEEEeChhhHHHHHHHHHHcCCcccceEEEE
Q 003054 115 -QTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIM 149 (852)
Q Consensus 115 -~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~ 149 (852)
.+++|++ ++...+..+++.+++.|+..++-+.|+
T Consensus 212 ~~~~ai~~-~~d~~a~gv~~al~~~g~~ip~di~vv 246 (309)
T PRK11041 212 QPPTAVFC-HSDVMALGALSQAKRMGLRVPQDLSII 246 (309)
T ss_pred CCCCEEEE-cCcHHHHHHHHHHHHcCCCCCcceEEE
Confidence 3688775 466667789999999998654434433
No 236
>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=90.51 E-value=18 Score=35.12 Aligned_cols=69 Identities=14% Similarity=0.124 Sum_probs=44.8
Q ss_pred EeeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCcccEEEeeeeeecCcceeeeccccccccceEEEE
Q 003054 377 GYCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGEFDAVVGDITIVFNRSNYVDFTLPYTESGVSMIV 456 (852)
Q Consensus 377 G~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv 456 (852)
.+-..++..+.++.+ .+++++... .-.++...|.+|++|+++... +.....+. ..++....+++++
T Consensus 13 ~~l~~~l~~~~~~~P-~i~l~~~~~---------~~~~~~~~l~~~~~Dl~i~~~---~~~~~~~~-~~~l~~~~~~~~~ 78 (196)
T cd08457 13 GFLPRFLAAFLRLRP-NLHLSLMGL---------SSSQVLEAVASGRADLGIADG---PLEERQGF-LIETRSLPAVVAV 78 (196)
T ss_pred cccHHHHHHHHHHCC-CeEEEEEec---------CcHHHHHHHHcCCccEEEecc---CCCCCCcE-EEEeccCCeEEEe
Confidence 455689999998887 255555442 346888999999999987532 22222232 3556677777777
Q ss_pred Ecc
Q 003054 457 PIK 459 (852)
Q Consensus 457 ~~~ 459 (852)
+..
T Consensus 79 ~~~ 81 (196)
T cd08457 79 PMG 81 (196)
T ss_pred eCC
Confidence 743
No 237
>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=90.48 E-value=4.5 Score=42.34 Aligned_cols=133 Identities=8% Similarity=-0.015 Sum_probs=80.7
Q ss_pred hcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHc--CCcEEEEEEEeC-CcccccHHHHHHHHHhC
Q 003054 9 LGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAF--GWREAVPIYVDN-QYGEEMIPSLTDALQAI 85 (852)
Q Consensus 9 i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~--gw~~vaii~~d~-~~G~~~~~~l~~~l~~~ 85 (852)
.+.+.++|+|......+ + .. ..+..++...++.+++++... |.++++++..+. .......+.+++++++.
T Consensus 77 ~~~~~~ipvv~~~~~~~---~-~~---~~V~~d~~~~g~~~~~~l~~~~~g~~~i~~i~g~~~~~~~~R~~g~~~~~~~~ 149 (271)
T cd06321 77 RAQAAGIVVVAVDVAAE---G-AD---ATVTTDNVQAGEISCQYLADRLGGKGNVAILNGPPVSAVLDRVAGCKAALAKY 149 (271)
T ss_pred HHHHCCCeEEEecCCCC---C-cc---ceeeechHHHHHHHHHHHHHHhCCCceEEEEeCCCCchHHHHHHHHHHHHHhC
Confidence 34567899999865332 1 11 235667777888888888766 999999997432 23455568888899987
Q ss_pred -CceeeeeeecCCCCChHHHHHHHHHhhcC--CceEEEEEeChhhHHHHHHHHHHcCCcccceEEEEcCc
Q 003054 86 -DTRVPYRSVISPLATDDQIEKELYKLFTM--QTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDG 152 (852)
Q Consensus 86 -g~~v~~~~~~~~~~~~~d~~~~l~~l~~~--~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~ 152 (852)
+++.... ......+...-...+.++.+. .+++|++ .+...+..+++.+++.|+ .+..+++.+.
T Consensus 150 ~~~~~~~~-~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~-~~d~~a~g~~~al~~~g~--~di~v~g~d~ 215 (271)
T cd06321 150 PGIKLLSD-DQNGKGSRDGGLRVMQGLLTRFPKLDGVFA-INDPTAIGADLAAKQAGR--NDIKITSVDG 215 (271)
T ss_pred CCcEEEee-ecCCCCChhhHHHHHHHHHHhCCCCCEEEE-CCchhHHHHHHHHHHcCC--CCcEEEEecC
Confidence 5653221 111111111112344554433 4577555 455567788899999998 3455555444
No 238
>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=90.44 E-value=14 Score=35.90 Aligned_cols=69 Identities=17% Similarity=0.122 Sum_probs=46.7
Q ss_pred EeeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCcccEEEeeeeeecCcceeeeccccccccceEEEE
Q 003054 377 GYCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGEFDAVVGDITIVFNRSNYVDFTLPYTESGVSMIV 456 (852)
Q Consensus 377 G~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv 456 (852)
.+-.+++..+.++.+ .+++++.. ++..++..+|.+|++|+++... +.....+. +.|+....+++++
T Consensus 13 ~~l~~~l~~f~~~~P-~v~l~~~~---------~~~~~~~~~l~~g~~Dl~i~~~---~~~~~~~~-~~~l~~~~~~lv~ 78 (200)
T cd08466 13 LLLPRLLARLKQLAP-NISLRESP---------SSEEDLFEDLRLQEVDLVIDYV---PFRDPSFK-SELLFEDELVCVA 78 (200)
T ss_pred HHHHHHHHHHHHHCC-CCEEEEec---------CchHhHHHHHHcCCccEEEecc---cCCCCCce-eeeecccceEEEE
Confidence 344678888888876 35555543 3567899999999999998532 22222232 4677788888888
Q ss_pred Ecc
Q 003054 457 PIK 459 (852)
Q Consensus 457 ~~~ 459 (852)
+..
T Consensus 79 ~~~ 81 (200)
T cd08466 79 RKD 81 (200)
T ss_pred eCC
Confidence 855
No 239
>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=90.24 E-value=2.2 Score=44.39 Aligned_cols=108 Identities=10% Similarity=0.009 Sum_probs=70.9
Q ss_pred ccCCchhHHHHHHHHHHHcCCcEEEEEEEe--CCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhc--
Q 003054 38 GSLNDSSQAGAITAIIKAFGWREAVPIYVD--NQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFT-- 113 (852)
Q Consensus 38 ~~p~d~~~~~aia~~l~~~gw~~vaii~~d--~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~-- 113 (852)
+..+....+..+++++...|-++++++..+ +.......+.|.+++++.|+++.....+....+..+-...+.++.+
T Consensus 94 v~~d~~~~~~~~~~~l~~~g~~~i~~i~~~~~~~~~~~R~~Gf~~~l~~~~~~~~~~~i~~~~~~~~~~~~~~~~~l~~~ 173 (260)
T cd06286 94 VYIDHYEAFYEALKYLIQKGYRKIAYCIGRKKSLNSQSRKKAYKDALEEYGLTPDEEWIFEGCFTIEDGERIGHQLLKMK 173 (260)
T ss_pred EEECChHHHHHHHHHHHHCCCceEEEEcCCcccchhHHHHHHHHHHHHHcCCCCChHheEeCCCCHHHHHHHHHHHHcCC
Confidence 456777788888898888899999999743 3345566788999999998765322111111122233344455543
Q ss_pred CCceEEEEEeChhhHHHHHHHHHHcCCcccceE
Q 003054 114 MQTRVFILHMLPSLGSRIFEKANEIGLMNKGCV 146 (852)
Q Consensus 114 ~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~v 146 (852)
..+++|+ +++...+..+++.+++.|+..++-+
T Consensus 174 ~~~~ai~-~~~d~~a~~~~~~l~~~g~~ip~di 205 (260)
T cd06286 174 DRPDAIF-TGSDEVAAGIITEAKKQGIRVPEDL 205 (260)
T ss_pred CCCCEEE-EcchHHHHHHHHHHHHcCCCCCcce
Confidence 3567655 5566678889999999998654433
No 240
>COG2984 ABC-type uncharacterized transport system, periplasmic component [General function prediction only]
Probab=90.23 E-value=6.5 Score=41.57 Aligned_cols=123 Identities=13% Similarity=0.146 Sum_probs=84.8
Q ss_pred CCccEEeeecCCCCC---CC-CCCCceEeccCCchhHHHHHHHHHHHc--CCcEEEEEEEe-CCcccccHHHHHHHHHhC
Q 003054 13 SQVPILSFSATSPSL---TS-IRSPYFFRGSLNDSSQAGAITAIIKAF--GWREAVPIYVD-NQYGEEMIPSLTDALQAI 85 (852)
Q Consensus 13 ~~vP~Is~~ats~~l---t~-~~~py~fR~~p~d~~~~~aia~~l~~~--gw~~vaii~~d-~~~G~~~~~~l~~~l~~~ 85 (852)
.++|+|-.+.++|.= .. -.-|----|.-+|..-...-.+++++. +.++++++|.. .+......+.+++.+++.
T Consensus 108 ~~iPVV~aavtd~v~a~Lv~~~~~pg~NvTGvsD~~~v~q~i~lik~~~Pnak~Igv~Y~p~E~ns~~l~eelk~~A~~~ 187 (322)
T COG2984 108 KTIPVVFAAVTDPVGAKLVKSLEQPGGNVTGVSDLLPVAQQIELIKALLPNAKSIGVLYNPGEANSVSLVEELKKEARKA 187 (322)
T ss_pred CCCCEEEEccCchhhccCCccccCCCCceeecCCcchHHHHHHHHHHhCCCCeeEEEEeCCCCcccHHHHHHHHHHHHHC
Confidence 348998877776642 21 111222235567777666667777663 89999999954 458889999999999999
Q ss_pred CceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChh---hHHHHHHHHHHcCC
Q 003054 86 DTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPS---LGSRIFEKANEIGL 140 (852)
Q Consensus 86 g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~---~~~~i~~~a~~~G~ 140 (852)
|++|+... ++ + ..|....++.+. -++|+|++.++.. ....+++.|.+.+.
T Consensus 188 Gl~vve~~-v~-~--~ndi~~a~~~l~-g~~d~i~~p~dn~i~s~~~~l~~~a~~~ki 240 (322)
T COG2984 188 GLEVVEAA-VT-S--VNDIPRAVQALL-GKVDVIYIPTDNLIVSAIESLLQVANKAKI 240 (322)
T ss_pred CCEEEEEe-cC-c--ccccHHHHHHhc-CCCcEEEEecchHHHHHHHHHHHHHHHhCC
Confidence 99986443 32 2 344555555554 7899999998764 45677888888776
No 241
>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=90.18 E-value=14 Score=35.80 Aligned_cols=69 Identities=17% Similarity=0.098 Sum_probs=45.7
Q ss_pred EeeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCcccEEEeeeeeecCcceeeeccccccccceEEEE
Q 003054 377 GYCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGEFDAVVGDITIVFNRSNYVDFTLPYTESGVSMIV 456 (852)
Q Consensus 377 G~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv 456 (852)
.+-.+++..+.++.+ .+++++.. ++...+..++.+|++|+++... ......+. +.++....+++++
T Consensus 13 ~~l~~~l~~f~~~~P-~v~i~i~~---------~~~~~~~~~l~~~~~Di~i~~~---~~~~~~~~-~~~l~~~~~~lv~ 78 (198)
T cd08461 13 AILPPLLAALRQEAP-GVRVAIRD---------LESDNLEAQLERGEVDLALTTP---EYAPDGLR-SRPLFEERYVCVT 78 (198)
T ss_pred HHhHHHHHHHHHHCC-CcEEEEee---------CCcccHHHHHhcCCCcEEEecC---ccCCccce-eeeeecCcEEEEE
Confidence 445688888888876 24555543 2346789999999999987532 11122232 5677778888888
Q ss_pred Ecc
Q 003054 457 PIK 459 (852)
Q Consensus 457 ~~~ 459 (852)
+..
T Consensus 79 ~~~ 81 (198)
T cd08461 79 RRG 81 (198)
T ss_pred cCC
Confidence 754
No 242
>PRK15454 ethanol dehydrogenase EutG; Provisional
Probab=90.08 E-value=2.2 Score=47.71 Aligned_cols=91 Identities=9% Similarity=-0.074 Sum_probs=68.3
Q ss_pred HHHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeC
Q 003054 45 QAGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHML 124 (852)
Q Consensus 45 ~~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~ 124 (852)
..+.+.++++.+|.+++.++....-...+..+.+.+.|++.|+++.....+.++.+.+++...+...++.++|+||-.+-
T Consensus 36 ~~~~l~~~~~~~g~~~~lvv~~~~~~~~g~~~~v~~~L~~~gi~~~~~~~v~~~P~~~~v~~~~~~~r~~~~D~IiavGG 115 (395)
T PRK15454 36 AVSSCGQQAQTRGLKHLFVMADSFLHQAGMTAGLTRSLAVKGIAMTLWPCPVGEPCITDVCAAVAQLRESGCDGVIAFGG 115 (395)
T ss_pred HHHHHHHHHHhcCCCEEEEEcCcchhhCccHHHHHHHHHHcCCeEEEECCCCCCcCHHHHHHHHHHHHhcCcCEEEEeCC
Confidence 44567778889998888877654444567788899999999998765545666667788889999999999999998866
Q ss_pred hh--hHHHHHHHH
Q 003054 125 PS--LGSRIFEKA 135 (852)
Q Consensus 125 ~~--~~~~i~~~a 135 (852)
+. |+.+.+...
T Consensus 116 GS~iD~AKaia~~ 128 (395)
T PRK15454 116 GSVLDAAKAVALL 128 (395)
T ss_pred hHHHHHHHHHHHH
Confidence 53 555554443
No 243
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=90.02 E-value=3.8 Score=44.50 Aligned_cols=133 Identities=10% Similarity=-0.013 Sum_probs=80.4
Q ss_pred hcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeC-CcccccHHHHHHHHHhCCc
Q 003054 9 LGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDN-QYGEEMIPSLTDALQAIDT 87 (852)
Q Consensus 9 i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~-~~G~~~~~~l~~~l~~~g~ 87 (852)
.+.+.++|+|....... + .... -+..++..-+..+++++...|.++++++.... .......+.|.+++++.|+
T Consensus 137 ~l~~~~iPvV~~~~~~~---~-~~~~--~V~~Dn~~~~~~a~~~L~~~Gh~~I~~i~~~~~~~~~~R~~Gf~~al~~~g~ 210 (331)
T PRK14987 137 MIEVAGIPVVELMDSQS---P-CLDI--AVGFDNFEAARQMTTAIIARGHRHIAYLGARLDERTIIKQKGYEQAMLDAGL 210 (331)
T ss_pred HHHhCCCCEEEEecCCC---C-CCCc--eEEeCcHHHHHHHHHHHHHCCCceEEEEcCCCcccHHHHHHHHHHHHHHcCC
Confidence 34567899987532111 1 1112 25566777778888888888999999996322 2233457889999999986
Q ss_pred eeeeeeecCCCCChHHHHHHHHHhhcC--CceEEEEEeChhhHHHHHHHHHHcCCcccceEEEE
Q 003054 88 RVPYRSVISPLATDDQIEKELYKLFTM--QTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIM 149 (852)
Q Consensus 88 ~v~~~~~~~~~~~~~d~~~~l~~l~~~--~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~ 149 (852)
... ...+....+...-...+.++.+. .+++|+. .+...+..+++.+++.|+..|+-+-|+
T Consensus 211 ~~~-~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~-~nD~~A~g~~~al~~~g~~vP~disvi 272 (331)
T PRK14987 211 VPY-SVMVEQSSSYSSGIELIRQARREYPQLDGVFC-TNDDLAVGAAFECQRLGLKVPDDMAIA 272 (331)
T ss_pred Ccc-ceeecCCCChhhHHHHHHHHHhcCCCCCEEEE-CCcHHHHHHHHHHHHcCCCCCCccEEE
Confidence 321 11111111111222345555443 4677664 566678889999999999776554443
No 244
>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=90.01 E-value=19 Score=34.76 Aligned_cols=69 Identities=14% Similarity=0.165 Sum_probs=46.2
Q ss_pred eeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCcccEEEeeeeeecCcceeeeccccccccceEEEEE
Q 003054 378 YCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGEFDAVVGDITIVFNRSNYVDFTLPYTESGVSMIVP 457 (852)
Q Consensus 378 ~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv~ 457 (852)
+..++++.+.++.+- +++++.. ++..++..++.+|++|+++...... ....+ .+.++....++++++
T Consensus 15 ~l~~~l~~~~~~~P~-i~l~i~~---------~~~~~~~~~l~~g~~Dl~i~~~~~~--~~~~~-~~~~l~~~~~~~v~~ 81 (199)
T cd08451 15 LVPGLIRRFREAYPD-VELTLEE---------ANTAELLEALREGRLDAAFVRPPVA--RSDGL-VLELLLEEPMLVALP 81 (199)
T ss_pred ccHHHHHHHHHHCCC-cEEEEec---------CChHHHHHHHHCCCccEEEEecCCC--CCCce-eEEEeecccEEEEec
Confidence 556789999988872 4555543 2467899999999999998532211 11222 246677788888887
Q ss_pred cc
Q 003054 458 IK 459 (852)
Q Consensus 458 ~~ 459 (852)
..
T Consensus 82 ~~ 83 (199)
T cd08451 82 AG 83 (199)
T ss_pred CC
Confidence 54
No 245
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=89.84 E-value=3.7 Score=44.56 Aligned_cols=131 Identities=8% Similarity=-0.046 Sum_probs=78.7
Q ss_pred HhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeC--CcccccHHHHHHHHHhC
Q 003054 8 QLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDN--QYGEEMIPSLTDALQAI 85 (852)
Q Consensus 8 ~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~--~~G~~~~~~l~~~l~~~ 85 (852)
..+.+.++|++......+ ....++ +..++..-+..+++++...|.++++++..+. .........+.+++++.
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 344567889888654221 122332 4556666667888888888999999996433 23445567888888888
Q ss_pred CceeeeeeecCCCCChHHHHHHHHHhhc--CCceEEEEEeChhhHHHHHHHHHHcCCcccceE
Q 003054 86 DTRVPYRSVISPLATDDQIEKELYKLFT--MQTRVFILHMLPSLGSRIFEKANEIGLMNKGCV 146 (852)
Q Consensus 86 g~~v~~~~~~~~~~~~~d~~~~l~~l~~--~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~v 146 (852)
|+ +.....+..+.+.++-...+.++.+ ..|++|++ ++...+..+++.++++|+..|+-+
T Consensus 204 g~-~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~-~~D~~A~g~~~al~~~g~~vP~di 264 (327)
T PRK10339 204 QV-VREEDIWRGGFSSSSGYELAKQMLAREDYPKALFV-ASDSIAIGVLRAIHERGLNIPQDI 264 (327)
T ss_pred CC-CChhheeecCcChhHHHHHHHHHHhCCCCCCEEEE-CCcHHHHHHHHHHHHcCCCCCCce
Confidence 86 1111111111112223344555543 24676554 456678899999999998655433
No 246
>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=89.84 E-value=4.4 Score=43.60 Aligned_cols=118 Identities=10% Similarity=-0.006 Sum_probs=75.9
Q ss_pred CCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEE---eCCcccccHHHHHHHHHhCCc
Q 003054 11 NKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYV---DNQYGEEMIPSLTDALQAIDT 87 (852)
Q Consensus 11 ~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~---d~~~G~~~~~~l~~~l~~~g~ 87 (852)
.+.++|++..+... ...+ .+..++..-+..+++++...|-+++++|.. +...+....+.|++++++.|+
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 34567777665311 1122 245566677778888888889999999973 223456678899999999998
Q ss_pred eeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHcCC
Q 003054 88 RVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEIGL 140 (852)
Q Consensus 88 ~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~G~ 140 (852)
+... .....+..+-...+.++.+.+|++|| +.+...+..+++.++++|.
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 6321 11111122223345554445688775 5566678888999999996
No 247
>PRK12681 cysB transcriptional regulator CysB; Reviewed
Probab=89.83 E-value=8 Score=42.00 Aligned_cols=104 Identities=11% Similarity=0.049 Sum_probs=58.0
Q ss_pred cCCHHHHHhcCCeE-EEEeCchHHH----HHHhcCCCCcceeecCCHhHHHHHhhcccccCceeEEEechhHHHHHHhhc
Q 003054 570 ITDVKMLIKRGDNV-GYQKGSFVLG----ILKQLGFDERKLVVYNSPEDCHELFQKGSVNGGIAAAFDEIPYMKLLIGQY 644 (852)
Q Consensus 570 i~sl~dL~~~~~~v-g~~~~s~~~~----~l~~~~~~~~~~~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~~ 644 (852)
..+++||. +.++ ....++.... ++.+.+.........++.+....++..|. ..+++-.. .......
T Consensus 183 ~~~~~~L~--~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~g~----Gi~~lp~~-~~~~~~~-- 253 (324)
T PRK12681 183 KLTIEELA--QYPLVTYVFGFTGRSELDTAFNRAGLTPRIVFTATDADVIKTYVRLGL----GVGVIASM-AVDPVAD-- 253 (324)
T ss_pred CcCHHHHh--CCCeEeccCCCchHHHHHHHHHHcCCCCceEEEeCCHHHHHHHHHhCC----CEEEeehh-hcccccC--
Confidence 35688886 4433 3334443333 33444554444456788899999999998 44555432 2222111
Q ss_pred CCceEee--cccccccceEEEecCCCCchhhHHHHHHhccc
Q 003054 645 CSKYAMI--EPKFKTAGFGFVFPLHSPLVHDVSKAILNVTE 683 (852)
Q Consensus 645 ~~~~~~v--~~~~~~~~~~~~~~k~spl~~~in~~il~l~e 683 (852)
..+..+ .+......++++.+|+.++...+..++..+.+
T Consensus 254 -~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~fi~~~~~ 293 (324)
T PRK12681 254 -PDLVAIDASHLFSHSTTKIGFRRGTFLRSYMYDFIERFAP 293 (324)
T ss_pred -CceEEeecCCCCCceEEEEEEECCchhhHHHHHHHHHHHH
Confidence 123322 23334557889999997766666665554433
No 248
>COG1454 EutG Alcohol dehydrogenase, class IV [Energy production and conversion]
Probab=89.77 E-value=2.6 Score=46.25 Aligned_cols=94 Identities=12% Similarity=0.026 Sum_probs=76.3
Q ss_pred HHHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeC
Q 003054 45 QAGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHML 124 (852)
Q Consensus 45 ~~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~ 124 (852)
..+.+.+.++.+|++++-|+.+-.-...+..+.+.+.|++.|+++.....+.++.+.+.....+..+++.++|.||-.+-
T Consensus 16 ~l~~l~~~~~~~g~~r~liVTd~~~~~~g~~~~v~~~L~~~~i~~~if~~v~p~P~~~~v~~~~~~~~~~~~D~iIalGG 95 (377)
T COG1454 16 SLKELGEEVKRLGAKRALIVTDRGLAKLGLLDKVLDSLDAAGIEYEVFDEVEPEPTIETVEAGAEVAREFGPDTIIALGG 95 (377)
T ss_pred hHHHHHHHHHhcCCCceEEEECCccccchhHHHHHHHHHhcCCeEEEecCCCCCCCHHHHHHHHHHHHhcCCCEEEEeCC
Confidence 34566777888999999999876667778899999999999988877778888888889999999999999999998755
Q ss_pred h--hhHHHHHHHHHHc
Q 003054 125 P--SLGSRIFEKANEI 138 (852)
Q Consensus 125 ~--~~~~~i~~~a~~~ 138 (852)
+ -|+.+.+.-..+.
T Consensus 96 GS~~D~AK~i~~~~~~ 111 (377)
T COG1454 96 GSVIDAAKAIALLAEN 111 (377)
T ss_pred ccHHHHHHHHHHHhhC
Confidence 4 4666665555543
No 249
>PRK12683 transcriptional regulator CysB-like protein; Reviewed
Probab=89.71 E-value=13 Score=39.95 Aligned_cols=105 Identities=7% Similarity=-0.031 Sum_probs=60.9
Q ss_pred CCHHHHHhcCCeEEEEeCchHH----HHHHhcCCCCcceeecCCHhHHHHHhhcccccCceeEEEechhHHHHHHhhcCC
Q 003054 571 TDVKMLIKRGDNVGYQKGSFVL----GILKQLGFDERKLVVYNSPEDCHELFQKGSVNGGIAAAFDEIPYMKLLIGQYCS 646 (852)
Q Consensus 571 ~sl~dL~~~~~~vg~~~~s~~~----~~l~~~~~~~~~~~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~~~~ 646 (852)
-+++||.+.. -+....++..+ .++.+.+.........++.+...+.+..|. ..+++... ...... ..
T Consensus 184 ~~~~~L~~~~-~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~----Gi~~lp~~-~~~~~~--~~- 254 (309)
T PRK12683 184 LTLEAIAEYP-IITYDQGFTGRSRIDQAFAEAGLVPDIVLTALDADVIKTYVELGM----GVGIVAAM-AYDPQR--DT- 254 (309)
T ss_pred cCHHHHhcCC-eEeccCCCcHHHHHHHHHHHCCCCceeEEEeccHHHHHHHHHhCC----CeEEeehh-hccccC--CC-
Confidence 4688887322 34444454433 344555555544556778888899999988 45555432 222111 12
Q ss_pred ceEeec--ccccccceEEEecCCCCchhhHHHHHHhcccc
Q 003054 647 KYAMIE--PKFKTAGFGFVFPLHSPLVHDVSKAILNVTEG 684 (852)
Q Consensus 647 ~~~~v~--~~~~~~~~~~~~~k~spl~~~in~~il~l~e~ 684 (852)
.+..+. +......++++.+|+.++.......+..+.+.
T Consensus 255 ~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~fi~~l~~~ 294 (309)
T PRK12683 255 GLVALDTDHLFEANTTRVGLRRGAYLRGYAYRFIELFAPH 294 (309)
T ss_pred ceEEEeCCCCcccceEEEEEECCCcCCHHHHHHHHHHHhh
Confidence 244332 23335578899999988777766666655543
No 250
>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=89.70 E-value=12 Score=36.51 Aligned_cols=70 Identities=21% Similarity=0.232 Sum_probs=46.9
Q ss_pred EeeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCcccEEEeeeeeecCcceeeeccccccccceEEEE
Q 003054 377 GYCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGEFDAVVGDITIVFNRSNYVDFTLPYTESGVSMIV 456 (852)
Q Consensus 377 G~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv 456 (852)
.+-.+++..+.++.+- +++++.. +....+.++|.+|++|+++..... .....+. +.+.....+++++
T Consensus 13 ~~l~~~l~~~~~~~P~-i~v~~~~---------~~~~~~~~~l~~g~~D~~i~~~~~--~~~~~~~-~~~l~~~~~~~v~ 79 (198)
T cd08413 13 YVLPPVIAAFRKRYPK-VKLSLHQ---------GTPSQIAEMVLKGEADIAIATEAL--DDHPDLV-TLPCYRWNHCVIV 79 (198)
T ss_pred hhccHHHHHHHHhCCc-eEEEEEe---------CCHHHHHHHHHcCCCCEEEEccCC--CCCCCcE-EEEeeeeeEEEEe
Confidence 3456888999998873 4555543 246789999999999999852211 1112233 3667778888888
Q ss_pred Ecc
Q 003054 457 PIK 459 (852)
Q Consensus 457 ~~~ 459 (852)
+..
T Consensus 80 ~~~ 82 (198)
T cd08413 80 PPG 82 (198)
T ss_pred cCC
Confidence 754
No 251
>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=89.69 E-value=4.8 Score=40.02 Aligned_cols=101 Identities=16% Similarity=0.091 Sum_probs=65.4
Q ss_pred CcCCHHHHHhcCCeEEE-EeCchHHHHHHh----cCCCCcceeec----CCHhHHHHHhhcccccCceeEEEechhHHHH
Q 003054 569 TITDVKMLIKRGDNVGY-QKGSFVLGILKQ----LGFDERKLVVY----NSPEDCHELFQKGSVNGGIAAAFDEIPYMKL 639 (852)
Q Consensus 569 ~i~sl~dL~~~~~~vg~-~~~s~~~~~l~~----~~~~~~~~~~~----~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~ 639 (852)
.|++++||.+.+.++.- +.||-.+.+|.+ .+.+...+..| .+-.+...++..|. .|+-+.....+..
T Consensus 82 ~i~~~~dL~~~~~r~vnR~~GSGtR~l~d~~l~~~gi~~~~i~gy~~~~~th~~vA~aVa~G~----AD~G~g~~~~A~~ 157 (193)
T PF12727_consen 82 GITSLEDLADPGLRFVNRQPGSGTRILFDQLLAEEGIDPEDIPGYAQEANTHLAVAAAVASGK----ADAGIGIRAAAEE 157 (193)
T ss_pred cCCCHHHhccCCcEEEECCCCCHHHHHHHHHHHHcCCChhhCCCccccccChHHHHHHHHcCC----CCEEeehHHHHHh
Confidence 49999999877775544 678877776654 44555455544 35567889999999 8888876544432
Q ss_pred HHhhcCCceEeecccccccceEEEecCCCCchhhHHHHHHh
Q 003054 640 LIGQYCSKYAMIEPKFKTAGFGFVFPLHSPLVHDVSKAILN 680 (852)
Q Consensus 640 ~~~~~~~~~~~v~~~~~~~~~~~~~~k~spl~~~in~~il~ 680 (852)
+ ..- .+. ++....|-+++++..-..+.+.+.|.-
T Consensus 158 ~--~gL-~Fv----pl~~E~~dlv~~~~~~~~~~vq~ll~~ 191 (193)
T PF12727_consen 158 F--YGL-DFV----PLAEERYDLVIRREDLEDPAVQALLDF 191 (193)
T ss_pred h--cCC-CcE----EccccceEEEEEhhHcCCHHHHHHHHH
Confidence 1 111 122 223467788999887666666666543
No 252
>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=89.67 E-value=20 Score=34.50 Aligned_cols=69 Identities=14% Similarity=0.196 Sum_probs=45.7
Q ss_pred EeeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCcccEEEeeeeeecCcceeeeccccccccceEEEE
Q 003054 377 GYCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGEFDAVVGDITIVFNRSNYVDFTLPYTESGVSMIV 456 (852)
Q Consensus 377 G~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv 456 (852)
.+-.+++..+.++.+ .+++++... +-.+++.+|.+|++|+++..... ....+. +.+.....+++++
T Consensus 13 ~~l~~~l~~~~~~~P-~~~l~~~~~---------~~~~~~~~l~~g~~D~~i~~~~~---~~~~~~-~~~l~~~~~~~v~ 78 (201)
T cd08420 13 YLLPRLLARFRKRYP-EVRVSLTIG---------NTEEIAERVLDGEIDLGLVEGPV---DHPDLI-VEPFAEDELVLVV 78 (201)
T ss_pred hhhHHHHHHHHHHCC-CceEEEEeC---------CcHHHHHHHHCCCccEEEecCCC---CCcceE-EEeecCccEEEEe
Confidence 445688888888876 345555432 35688999999999998864322 122232 3667777888887
Q ss_pred Ecc
Q 003054 457 PIK 459 (852)
Q Consensus 457 ~~~ 459 (852)
+..
T Consensus 79 ~~~ 81 (201)
T cd08420 79 PPD 81 (201)
T ss_pred cCC
Confidence 754
No 253
>PRK12680 transcriptional regulator CysB-like protein; Reviewed
Probab=89.61 E-value=15 Score=40.00 Aligned_cols=84 Identities=11% Similarity=0.043 Sum_probs=55.3
Q ss_pred CceEEEeeecccCcccceEEeeCCCCCCCceEEEeeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCc
Q 003054 344 EKKLRIGVPVKKGFSDFVNVTIDPKTQEPTSVTGYCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGE 423 (852)
Q Consensus 344 ~~~lrv~v~~~~~~~~~~~~~~d~~~~~~~~~~G~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~ 423 (852)
.+.+|||+.. . ....+-.++++.+.++.+- +++++.. +..++++.+|.+|+
T Consensus 92 ~g~lrIg~~~--~-----------------~~~~~l~~~l~~f~~~~P~-v~i~l~~---------~~~~~~~~~l~~g~ 142 (327)
T PRK12680 92 QGQLTLTTTH--T-----------------QARFVLPPAVAQIKQAYPQ-VSVHLQQ---------AAESAALDLLGQGD 142 (327)
T ss_pred ceEEEEEecc--h-----------------hHHHhhHHHHHHHHHHCCC-cEEEEEe---------CChHHHHHHHHCCC
Confidence 4679999872 2 1123456889999988873 5555544 34689999999999
Q ss_pred ccEEEeeeeeecCcceeeeccccccccceEEEEEcc
Q 003054 424 FDAVVGDITIVFNRSNYVDFTLPYTESGVSMIVPIK 459 (852)
Q Consensus 424 ~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv~~~ 459 (852)
+|+++..... ....... ..|+.....+++++..
T Consensus 143 ~Dl~i~~~~~--~~~~~~~-~~~l~~~~~~l~~~~~ 175 (327)
T PRK12680 143 ADIAIVSTAG--GEPSAGI-AVPLYRWRRLVVVPRG 175 (327)
T ss_pred CcEEEEecCC--CCCCcce-EEEeeccceEEEEeCC
Confidence 9998753211 1111222 4677788888888854
No 254
>PRK15395 methyl-galactoside ABC transporter galactose-binding periplasmic protein MglB; Provisional
Probab=89.58 E-value=7 Score=42.59 Aligned_cols=135 Identities=9% Similarity=0.023 Sum_probs=72.2
Q ss_pred HhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHc------------CCcEEEEEEEe--CCcccc
Q 003054 8 QLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAF------------GWREAVPIYVD--NQYGEE 73 (852)
Q Consensus 8 ~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~------------gw~~vaii~~d--~~~G~~ 73 (852)
..+...++|+|......+.-.-...+-...+..++..-++.+++++.++ |-.++++|... ......
T Consensus 100 ~~l~~~giPvV~vd~~~~~~~~~~~~~~~~V~~D~~~ag~~a~~~l~~~~~~~~~~~~~~~g~~~i~~i~g~~~~~~~~~ 179 (330)
T PRK15395 100 EKARGQDVPVVFFNKEPSRKALDSYDKAYYVGTDSKESGIIQGDLIAKHWKANPAWDLNKDGKIQYVLLKGEPGHPDAEA 179 (330)
T ss_pred HHHHHCCCcEEEEcCCccccccccccceeEEccChHHHHHHHHHHHHHHHhhccccccCCCCceEEEEEecCCCCchHHH
Confidence 3455679999998763211000001112234556666666666655331 33344545432 223345
Q ss_pred cHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcC----CceEEEEEeChhhHHHHHHHHHHcCC-ccc
Q 003054 74 MIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTM----QTRVFILHMLPSLGSRIFEKANEIGL-MNK 143 (852)
Q Consensus 74 ~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~----~~~viv~~~~~~~~~~i~~~a~~~G~-~~~ 143 (852)
....+++++++.|+.+..........+.++-...+.++.+. .+++|+ +++...+..+++.+++.|+ ..+
T Consensus 180 R~~G~~~al~~~g~~~~~~~~~~~~~~~~~a~~~~~~~l~~~~~~~~~ai~-~~~d~~A~gvl~al~~~Gl~~vp 253 (330)
T PRK15395 180 RTTYVIKELNDKGIKTEQLQLDTAMWDTAQAKDKMDAWLSGPNANKIEVVI-ANNDAMAMGAVEALKAHNKSSIP 253 (330)
T ss_pred HHHHHHHHHHhcCCCeeeeecccCCcCHHHHHHHHHHHHhhCcCCCeeEEE-ECCchHHHHHHHHHHhcCCCCCe
Confidence 67888999999887654321111111122223445555433 356655 4566677889999999998 444
No 255
>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=89.54 E-value=14 Score=39.34 Aligned_cols=85 Identities=19% Similarity=0.228 Sum_probs=55.1
Q ss_pred CceEEEeeecccCcccceEEeeCCCCCCCceEEEeeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCc
Q 003054 344 EKKLRIGVPVKKGFSDFVNVTIDPKTQEPTSVTGYCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGE 423 (852)
Q Consensus 344 ~~~lrv~v~~~~~~~~~~~~~~d~~~~~~~~~~G~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~ 423 (852)
.+.++||++ +.. ...+-.+++..+.++.+ .+.+.+.. ++..+++.+|.+|+
T Consensus 92 ~~~l~I~~~--~~~-----------------~~~~~~~~l~~~~~~~P-~~~i~~~~---------~~~~~~~~~l~~g~ 142 (300)
T TIGR02424 92 GPTVRIGAL--PTV-----------------AARLMPEVVKRFLARAP-RLRVRIMT---------GPNAYLLDQLRVGA 142 (300)
T ss_pred CceEEEecc--cHH-----------------HHhhhHHHHHHHHHhCC-CcEEEEEe---------CchHHHHHHHHCCC
Confidence 568999987 221 11234578888888887 35555544 24678999999999
Q ss_pred ccEEEeeeeeecCcceeeeccccccccceEEEEEcc
Q 003054 424 FDAVVGDITIVFNRSNYVDFTLPYTESGVSMIVPIK 459 (852)
Q Consensus 424 ~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv~~~ 459 (852)
+|++++.... ......+. ..|......+++++..
T Consensus 143 ~D~~i~~~~~-~~~~~~~~-~~~l~~~~~~~~~~~~ 176 (300)
T TIGR02424 143 LDLVVGRLGA-PETMQGLS-FEHLYNEPVVFVVRAG 176 (300)
T ss_pred CCEEEEecCC-ccccccee-eeeecCCceEEEEcCC
Confidence 9999853322 11122232 3577778888888754
No 256
>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=89.51 E-value=17 Score=35.27 Aligned_cols=68 Identities=16% Similarity=0.194 Sum_probs=44.7
Q ss_pred eeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCcccEEEeeeeeecCcceeeeccccccccceEEEEE
Q 003054 378 YCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGEFDAVVGDITIVFNRSNYVDFTLPYTESGVSMIVP 457 (852)
Q Consensus 378 ~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv~ 457 (852)
+..+++..+.++.+ .+++++.. ++..+++..|.+|++|+++.... .....+. ..++....++++++
T Consensus 15 ~l~~~l~~~~~~~P-~i~i~i~~---------~~~~~~~~~l~~~~~Dl~i~~~~---~~~~~~~-~~~l~~~~~~~v~~ 80 (200)
T cd08411 15 LLPRLLPALRQAYP-KLRLYLRE---------DQTERLLEKLRSGELDAALLALP---VDEPGLE-EEPLFDEPFLLAVP 80 (200)
T ss_pred hhHHHHHHHHHHCC-CcEEEEEe---------CcHHHHHHHHHcCCccEEEEecc---CCCCCce-EEEeeccceEEEec
Confidence 45678888888876 24555543 24678999999999999975321 1112222 35566777788877
Q ss_pred cc
Q 003054 458 IK 459 (852)
Q Consensus 458 ~~ 459 (852)
..
T Consensus 81 ~~ 82 (200)
T cd08411 81 KD 82 (200)
T ss_pred CC
Confidence 54
No 257
>PRK10837 putative DNA-binding transcriptional regulator; Provisional
Probab=89.50 E-value=27 Score=36.83 Aligned_cols=104 Identities=7% Similarity=-0.069 Sum_probs=56.5
Q ss_pred CCHHHHHhcCCeEEEEeCchHHHHH----HhcCCCCcceeecCCHhHHHHHhhcccccCceeEEEechhHHHHHHhhcCC
Q 003054 571 TDVKMLIKRGDNVGYQKGSFVLGIL----KQLGFDERKLVVYNSPEDCHELFQKGSVNGGIAAAFDEIPYMKLLIGQYCS 646 (852)
Q Consensus 571 ~sl~dL~~~~~~vg~~~~s~~~~~l----~~~~~~~~~~~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~~~~ 646 (852)
-+++||.+.. -+....++.....+ ...+.........++.+...+++..|. ..+++.+. .+........
T Consensus 178 i~~~~L~~~~-~i~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~----gi~~~p~~-~~~~~~~~~~- 250 (290)
T PRK10837 178 VTLEQLAAAP-WILRERGSGTREIVDYLLLSHLPRFELAMELGNSEAIKHAVRHGL----GISCLSRR-VIADQLQAGT- 250 (290)
T ss_pred CCHHHHhcCC-eEEecCCCcHHHHHHHHHHHcCCCCceEEEeCCHHHHHHHHHhCC----cEEEeeHH-HHHHHHhCCc-
Confidence 4688887322 33334444333333 333333334456688888999999987 45555543 3333222221
Q ss_pred ceEee--cccccccceEEEecCCCCchhhHHHHHHhcc
Q 003054 647 KYAMI--EPKFKTAGFGFVFPLHSPLVHDVSKAILNVT 682 (852)
Q Consensus 647 ~~~~v--~~~~~~~~~~~~~~k~spl~~~in~~il~l~ 682 (852)
+..+ +.......+.++.+++.+....+.+.+..+.
T Consensus 251 -l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~ 287 (290)
T PRK10837 251 -LVEVAVPLPRLMRTLYRIHHRQKHLSNALQRFLSYCQ 287 (290)
T ss_pred -EEEEEcCCccceEEEEEEEeCCCCCCHHHHHHHHHHH
Confidence 3222 2222345677788888776666666655443
No 258
>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=89.44 E-value=22 Score=34.71 Aligned_cols=71 Identities=20% Similarity=0.191 Sum_probs=46.9
Q ss_pred EEeeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCcccEEEeeeeeecCcceeeeccccccccceEEE
Q 003054 376 TGYCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGEFDAVVGDITIVFNRSNYVDFTLPYTESGVSMI 455 (852)
Q Consensus 376 ~G~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~~D~~~g~~~it~~r~~~vdft~p~~~~~~~~v 455 (852)
..+-.+++..+.++.+- +++++.. ++..++...+.+|++|+++..... .....+. +.++.....+++
T Consensus 12 ~~~l~~~l~~f~~~~P~-~~i~i~~---------~~~~~~~~~l~~g~~Dl~i~~~~~--~~~~~~~-~~~l~~~~~~~v 78 (198)
T cd08443 12 RYVLPPVIKGFIERYPR-VSLQMHQ---------GSPTQIAEMVSKGLVDFAIATEAL--HDYDDLI-TLPCYHWNRCVV 78 (198)
T ss_pred eeECcHHHHHHHHHCCC-eEEEEEe---------CCHHHHHHHHHCCCccEEEEeccc--cccCCce-EeeeeeceEEEE
Confidence 35567889999888762 4555543 346789999999999999853211 1112233 466777788888
Q ss_pred EEcc
Q 003054 456 VPIK 459 (852)
Q Consensus 456 v~~~ 459 (852)
++..
T Consensus 79 ~~~~ 82 (198)
T cd08443 79 VKRD 82 (198)
T ss_pred EcCC
Confidence 7754
No 259
>COG3473 Maleate cis-trans isomerase [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=89.42 E-value=7.1 Score=38.36 Aligned_cols=135 Identities=15% Similarity=0.077 Sum_probs=88.2
Q ss_pred hhHHHHhcCCCCccEEeeecCCCCCCC-CCCCc--eEec----cCCchhHHHHHHHHHHHcCCcEEEEEEEeCCcccccH
Q 003054 3 TNFIIQLGNKSQVPILSFSATSPSLTS-IRSPY--FFRG----SLNDSSQAGAITAIIKAFGWREAVPIYVDNQYGEEMI 75 (852)
Q Consensus 3 a~~v~~i~~~~~vP~Is~~ats~~lt~-~~~py--~fR~----~p~d~~~~~aia~~l~~~gw~~vaii~~d~~~G~~~~ 75 (852)
+...+......++=+|+|++++.++.. .+|.- --|+ .-....-+.|..+-++.+|.+++.++. +|-.+..
T Consensus 56 t~~aAl~Lada~vdvI~Y~CtsgS~i~G~~~d~ei~~~ie~~~~v~vvTts~Avv~aL~al~a~ri~vlT---PY~~evn 132 (238)
T COG3473 56 TERAALELADAGVDVIVYGCTSGSLIGGPGYDKEIAQRIEEAKGVPVVTTSTAVVEALNALGAQRISVLT---PYIDEVN 132 (238)
T ss_pred HHHHHHhcCccccCEEEEeccceeeecCCchhHHHHHHHHhccCCceeechHHHHHHHHhhCcceEEEec---cchhhhh
Confidence 445567788889999999999988864 22210 0000 001112345677778999999999987 4667888
Q ss_pred HHHHHHHHhCCceeeeeeecCCCC-------ChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHH-HHcCC
Q 003054 76 PSLTDALQAIDTRVPYRSVISPLA-------TDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKA-NEIGL 140 (852)
Q Consensus 76 ~~l~~~l~~~g~~v~~~~~~~~~~-------~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a-~~~G~ 140 (852)
+.-.+.++++|.+|+....+.... ..........++..-++|.||+.|..--+..++... ++.|.
T Consensus 133 ~~e~ef~~~~Gfeiv~~~~Lgi~dn~eigr~~P~~~y~lAk~~~~~~~DaiFiSCTnlRt~eii~~lE~~~G~ 205 (238)
T COG3473 133 QREIEFLEANGFEIVDFKGLGITDNLEIGRQEPWAVYRLAKEVFTPDADAIFISCTNLRTFEIIEKLERDTGV 205 (238)
T ss_pred hHHHHHHHhCCeEEEEeeccCCcccchhcccChHHHHHHHHHhcCCCCCeEEEEeeccccHHHHHHHHHHhCC
Confidence 889999999999998776543221 112233444566678899999988765555555444 34554
No 260
>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=89.41 E-value=9.8 Score=39.79 Aligned_cols=132 Identities=12% Similarity=0.089 Sum_probs=75.1
Q ss_pred CCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHc--CCcEEEEEEEeC--CcccccHHHHHHHHHhCC
Q 003054 11 NKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAF--GWREAVPIYVDN--QYGEEMIPSLTDALQAID 86 (852)
Q Consensus 11 ~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~--gw~~vaii~~d~--~~G~~~~~~l~~~l~~~g 86 (852)
.+ ++|+|......+. ....+| +..++..-+..+++++.+. +-.+++++..+. .......+.+++++++.|
T Consensus 77 ~~-~ipvV~~~~~~~~--~~~~~~---V~~D~~~~g~~a~~~l~~~~~~g~~~~~~~~~~~~~~~~~R~~gf~~~~~~~~ 150 (271)
T cd06314 77 AA-GIKLITTDSDAPD--SGRYVY---IGTDNYAAGRTAGEIMKKALPGGGKVAIFVGSLGADNAKERIQGIKDAIKDSK 150 (271)
T ss_pred hc-CCCEEEecCCCCc--cceeEE---EccChHHHHHHHHHHHHHHcCCCCEEEEEecCCCCCCHHHHHHHHHHHHhcCC
Confidence 45 9999998643221 111122 3456666667888887553 234666666432 234566788999999999
Q ss_pred ceeeeeeecCCCCChHHHHHHHHHhhcC--CceEEEEEeChhhHHHHHHHHHHcCCcccceEEEEcCc
Q 003054 87 TRVPYRSVISPLATDDQIEKELYKLFTM--QTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDG 152 (852)
Q Consensus 87 ~~v~~~~~~~~~~~~~d~~~~l~~l~~~--~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~ 152 (852)
+++.... . .+.+..+-...+.++.+. .+++|+.. +...+..+++.+++.|.. ++...++-++
T Consensus 151 ~~~~~~~-~-~~~~~~~~~~~~~~~l~~~~~~~~i~~~-~d~~a~~~~~al~~~g~~-~di~vig~d~ 214 (271)
T cd06314 151 IEIVDTR-G-DEEDFAKAKSNAEDALNAHPDLKCMFGL-YAYNGPAIAEAVKAAGKL-GKVKIVGFDE 214 (271)
T ss_pred cEEEEEe-c-CccCHHHHHHHHHHHHHhCCCccEEEec-CCccHHHHHHHHHHcCCC-CceEEEEeCC
Confidence 8765422 1 111223334455565443 35666543 445556678888999985 3344444433
No 261
>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=89.28 E-value=4.2 Score=45.19 Aligned_cols=92 Identities=10% Similarity=0.043 Sum_probs=69.1
Q ss_pred HHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeC-
Q 003054 46 AGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHML- 124 (852)
Q Consensus 46 ~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~- 124 (852)
.+.+.+.++.+|-+++.+++....+..+..+.+.+.|++.|+++.....+.++.+.+++...+..+++.++|+||-.+-
T Consensus 14 l~~l~~~l~~~g~~~~lvvt~~~~~~~g~~~~v~~~L~~~g~~~~~~~~v~~~p~~~~v~~~~~~~~~~~~d~IIaiGGG 93 (374)
T cd08189 14 LAQLPAAISQLGVKKVLIVTDKGLVKLGLLDKVLEALEGAGIEYAVYDGVPPDPTIENVEAGLALYRENGCDAILAVGGG 93 (374)
T ss_pred HHHHHHHHHhcCCCeEEEEeCcchhhcccHHHHHHHHHhcCCeEEEeCCCCCCcCHHHHHHHHHHHHhcCCCEEEEeCCc
Confidence 4567778888998999988855545455678899999999988765555666677888999999999999999986654
Q ss_pred -hhhHHHHHHHHHH
Q 003054 125 -PSLGSRIFEKANE 137 (852)
Q Consensus 125 -~~~~~~i~~~a~~ 137 (852)
.-|+.+++.....
T Consensus 94 S~~D~aK~ia~~~~ 107 (374)
T cd08189 94 SVIDCAKAIAARAA 107 (374)
T ss_pred cHHHHHHHHHHHHh
Confidence 3466666554433
No 262
>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=89.22 E-value=21 Score=34.17 Aligned_cols=69 Identities=20% Similarity=0.377 Sum_probs=45.2
Q ss_pred EeeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCcccEEEeeeeeecCcceeeeccccccccceEEEE
Q 003054 377 GYCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGEFDAVVGDITIVFNRSNYVDFTLPYTESGVSMIV 456 (852)
Q Consensus 377 G~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv 456 (852)
.+-..++..+.++.+- ++++... +...+++.++.+|++|+++... +.....+. ..++....+++++
T Consensus 13 ~~l~~~l~~~~~~~P~-i~i~i~~---------~~~~~~~~~l~~~~~Dl~i~~~---~~~~~~l~-~~~l~~~~~~~v~ 78 (195)
T cd08434 13 SLVPDLIRAFRKEYPN-VTFELHQ---------GSTDELLDDLKNGELDLALCSP---VPDEPDIE-WIPLFTEELVLVV 78 (195)
T ss_pred hhhHHHHHHHHHhCCC-eEEEEec---------CcHHHHHHHHHcCCccEEEEcc---CCCCCCee-EEEeecceEEEEe
Confidence 3455788888888752 4555543 2457889999999999987532 22223333 3567777888888
Q ss_pred Ecc
Q 003054 457 PIK 459 (852)
Q Consensus 457 ~~~ 459 (852)
+..
T Consensus 79 ~~~ 81 (195)
T cd08434 79 PKD 81 (195)
T ss_pred cCC
Confidence 754
No 263
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=89.02 E-value=3.2 Score=45.47 Aligned_cols=110 Identities=12% Similarity=0.026 Sum_probs=70.4
Q ss_pred ccCCchhHHHHHHHHHHHcCCcEEEEEEEeC--CcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcC-
Q 003054 38 GSLNDSSQAGAITAIIKAFGWREAVPIYVDN--QYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTM- 114 (852)
Q Consensus 38 ~~p~d~~~~~aia~~l~~~gw~~vaii~~d~--~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~- 114 (852)
+..++..-+..+++++...|-+++++|.... ..+....+.|++++++.|+.+........+.....-...+.++.+.
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 3445555566777888888999999997433 3456678899999999997643221111111112222345555433
Q ss_pred -CceEEEEEeChhhHHHHHHHHHHcCCcccceEEE
Q 003054 115 -QTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWI 148 (852)
Q Consensus 115 -~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~vwi 148 (852)
.|++|++ .+...+..+++.+++.|+..|+-+-|
T Consensus 236 ~~~~ai~~-~nd~~A~g~~~al~~~G~~vP~disv 269 (346)
T PRK10401 236 LQLTAVFA-YNDNMAAGALTALKDNGIAIPLHLSI 269 (346)
T ss_pred CCCcEEEE-CCcHHHHHHHHHHHHcCCCCCCceEE
Confidence 4677665 46667888999999999976654443
No 264
>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=88.95 E-value=22 Score=34.26 Aligned_cols=71 Identities=10% Similarity=0.024 Sum_probs=45.9
Q ss_pred EeeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCcccEEEeeeeeecCcceeeeccccccccceEEEE
Q 003054 377 GYCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGEFDAVVGDITIVFNRSNYVDFTLPYTESGVSMIV 456 (852)
Q Consensus 377 G~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv 456 (852)
.+...++..+.++.+ .+.+++.. +...+++..|.+|++|++++...... +...+. ..++....+++++
T Consensus 13 ~~l~~~l~~~~~~~P-~i~i~~~~---------~~~~~~~~~l~~~~~Dl~i~~~~~~~-~~~~~~-~~~l~~~~~~~v~ 80 (197)
T cd08449 13 GGLGPALRRFKRQYP-NVTVRFHE---------LSPEAQKAALLSKRIDLGFVRFADTL-NDPPLA-SELLWREPMVVAL 80 (197)
T ss_pred hhHHHHHHHHHHHCC-CeEEEEEE---------CCHHHHHHHHhCCCccEEEecccccC-CCCCce-EEEEEEeeEEEEe
Confidence 445688888888876 25555543 24678999999999999985322110 112232 3567777778887
Q ss_pred Ecc
Q 003054 457 PIK 459 (852)
Q Consensus 457 ~~~ 459 (852)
+..
T Consensus 81 ~~~ 83 (197)
T cd08449 81 PEE 83 (197)
T ss_pred cCC
Confidence 744
No 265
>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=88.88 E-value=3.2 Score=46.11 Aligned_cols=91 Identities=9% Similarity=-0.009 Sum_probs=68.5
Q ss_pred HHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeC-
Q 003054 46 AGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHML- 124 (852)
Q Consensus 46 ~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~- 124 (852)
...+.++++.+|.+++.+++....+..+..+.+.+.|++.|+++.....+.++.+.+++...+...+..++|+||-.+.
T Consensus 12 ~~~l~~~l~~~g~~~~liv~~~~~~~~~~~~~v~~~L~~~g~~~~~~~~v~~~p~~~~v~~~~~~~~~~~~d~IIaiGGG 91 (370)
T cd08192 12 IKELPAECAELGIKRPLIVTDPGLAALGLVARVLALLEDAGLAAALFDEVPPNPTEAAVEAGLAAYRAGGCDGVIAFGGG 91 (370)
T ss_pred HHHHHHHHHHcCCCeEEEEcCcchhhCccHHHHHHHHHHcCCeEEEeCCCCCCCCHHHHHHHHHHHHhcCCCEEEEeCCc
Confidence 3457778888999999988855544455788899999999988765545666677788999999999999999986654
Q ss_pred -hhhHHHHHHHHH
Q 003054 125 -PSLGSRIFEKAN 136 (852)
Q Consensus 125 -~~~~~~i~~~a~ 136 (852)
.-|+.+++....
T Consensus 92 SviD~aK~ia~~~ 104 (370)
T cd08192 92 SALDLAKAVALMA 104 (370)
T ss_pred hHHHHHHHHHHHH
Confidence 446666655543
No 266
>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=88.86 E-value=20 Score=34.72 Aligned_cols=68 Identities=12% Similarity=0.123 Sum_probs=45.9
Q ss_pred eeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCcccEEEeeeeeecCcceeeeccccccccceEEEEE
Q 003054 378 YCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGEFDAVVGDITIVFNRSNYVDFTLPYTESGVSMIVP 457 (852)
Q Consensus 378 ~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv~ 457 (852)
+...++..+.++.+ .+.+++... ...++...|.+|++|+++... +.....+. ..++....++++++
T Consensus 15 ~l~~~l~~~~~~~P-~v~i~i~~~---------~~~~~~~~l~~g~~Dl~i~~~---~~~~~~~~-~~~l~~~~~~~v~~ 80 (197)
T cd08425 15 LIGPLIDRFHARYP-GIALSLREM---------PQERIEAALADDRLDLGIAFA---PVRSPDID-AQPLFDERLALVVG 80 (197)
T ss_pred hhHHHHHHHHHHCC-CcEEEEEEC---------cHHHHHHHHHcCCccEEEEec---CCCCCCcE-EEEeccccEEEEec
Confidence 34688888888876 356666442 357899999999999997532 22222232 36677778888887
Q ss_pred cc
Q 003054 458 IK 459 (852)
Q Consensus 458 ~~ 459 (852)
..
T Consensus 81 ~~ 82 (197)
T cd08425 81 AT 82 (197)
T ss_pred CC
Confidence 55
No 267
>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=88.77 E-value=23 Score=34.50 Aligned_cols=69 Identities=12% Similarity=0.063 Sum_probs=45.6
Q ss_pred EeeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCcccEEEeeeeeecCcceeeeccccccccceEEEE
Q 003054 377 GYCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGEFDAVVGDITIVFNRSNYVDFTLPYTESGVSMIV 456 (852)
Q Consensus 377 G~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv 456 (852)
.+-.+++..+.++.+- +++++.. +...++.+.|.+|++|+++... +.....+. ..+.....+++++
T Consensus 13 ~~l~~~l~~~~~~~P~-i~l~~~~---------~~~~~~~~~l~~g~~D~~i~~~---~~~~~~~~-~~~l~~~~~~~v~ 78 (200)
T cd08467 13 ALLPRLAPRLRERAPG-LDLRLCP---------IGDDLAERGLEQGTIDLAVGRF---AVPPDGLV-VRRLYDDGFACLV 78 (200)
T ss_pred HHHHHHHHHHHhhCCC-CEEEEec---------CCcccHHHHhhCCCcCEEEecC---CCCCccce-eEEeeeccEEEEE
Confidence 4556788888888772 5555543 2456899999999999988532 11122233 3567778888888
Q ss_pred Ecc
Q 003054 457 PIK 459 (852)
Q Consensus 457 ~~~ 459 (852)
+..
T Consensus 79 ~~~ 81 (200)
T cd08467 79 RHG 81 (200)
T ss_pred cCC
Confidence 744
No 268
>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=88.73 E-value=8.1 Score=39.00 Aligned_cols=73 Identities=12% Similarity=0.049 Sum_probs=41.1
Q ss_pred eeecCCHhHHHHHhhcccccCceeEEEechhHHHHHHhhcCCceEeeccc-ccccceEEEecCCCCchhhHHHHHHhccc
Q 003054 605 LVVYNSPEDCHELFQKGSVNGGIAAAFDEIPYMKLLIGQYCSKYAMIEPK-FKTAGFGFVFPLHSPLVHDVSKAILNVTE 683 (852)
Q Consensus 605 ~~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~~~~~~~~v~~~-~~~~~~~~~~~k~spl~~~in~~il~l~e 683 (852)
+....+..+..+.+.+|+ +++.+......... ..... ...++.. .....+++++.|+++-.+.-.++|..+..
T Consensus 132 ~~~~~~~~~~~~~~~~Ge----~~~~~~~~~~~~~~-~~~~~-~~~~P~~~~~~~~~~~ai~k~a~~~~~A~~fi~fl~s 205 (216)
T TIGR01256 132 LVYGEDVRQALQFVETGN----APAGIVALSDVIPS-KKVGS-VATFPEDLYKPIRYPAVIVKGGKNNAAAKAFIDYLKS 205 (216)
T ss_pred eeecCcHHHHHHHHHcCC----CCEEeeehhhhccc-CCccE-EEEeCccccCCccccEEEEECCCChHHHHHHHHHHcC
Confidence 333446677888999999 78777654322211 11221 2223332 23345688999998866555555555443
No 269
>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=88.72 E-value=0.51 Score=50.38 Aligned_cols=103 Identities=13% Similarity=0.094 Sum_probs=64.4
Q ss_pred CCcCCHHHHHhcCCeEEEEeCchHHHHHHhcCCCCcceeecCCHhHHHHHhhcccccCceeEEEechhHHHHHH-hhcCC
Q 003054 568 PTITDVKMLIKRGDNVGYQKGSFVLGILKQLGFDERKLVVYNSPEDCHELFQKGSVNGGIAAAFDEIPYMKLLI-GQYCS 646 (852)
Q Consensus 568 ~~i~sl~dL~~~~~~vg~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~-~~~~~ 646 (852)
.+|++++||. |+++-+..+.....+++.++..+ ..-...|.+.+|++|. +|+...........- .+.++
T Consensus 126 ~pi~s~~Dlk--G~kiR~~~~~~~~~~~~~lGa~p----v~ip~~evy~aLq~G~----vDg~~~~~~~~~~~~~~ev~~ 195 (286)
T PF03480_consen 126 KPIRSPEDLK--GLKIRVPGSPVMSDFFEALGASP----VPIPWSEVYQALQQGV----VDGAENSASSIYSLGLYEVAK 195 (286)
T ss_dssp S--SSGGGGT--TEEEEETSSHHHHHHHHHCTSEE----EE-TGGGHHHHHHTTS----SSEEEEEHHHHHHTTGGGTSS
T ss_pred cCCccHhhHh--hCeEEecCCHHHHHHHHHcCCee----ecCcHHHHHHHHhcCC----cCeEecCHHHHHhcChhhhCC
Confidence 5799999997 88888876677778888887643 2224567999999999 999998765552221 22254
Q ss_pred ceEeecccccccceEEEecCCC--CchhhHHHHHHhcc
Q 003054 647 KYAMIEPKFKTAGFGFVFPLHS--PLVHDVSKAILNVT 682 (852)
Q Consensus 647 ~~~~v~~~~~~~~~~~~~~k~s--pl~~~in~~il~l~ 682 (852)
+..... +...++.+++.+.. -|-++..++|....
T Consensus 196 -y~~~~~-~~~~~~~~~~n~~~w~~L~~e~q~~l~~~~ 231 (286)
T PF03480_consen 196 -YFTDTN-HGWSPYAVIMNKDWWDSLPDEDQEALDDAA 231 (286)
T ss_dssp -EEEEEE-EEEEEEEEEEEHHHHHHS-HHHHHHHHHHH
T ss_pred -eeEeec-ccCcceEEEEcHHHHhcCCHHHHHHHHHHH
Confidence 333322 45566777777762 24455555554443
No 270
>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=88.72 E-value=24 Score=34.17 Aligned_cols=68 Identities=19% Similarity=0.246 Sum_probs=44.1
Q ss_pred eeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCcccEEEeeeeeecCcceeeeccccccccceEEEEE
Q 003054 378 YCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGEFDAVVGDITIVFNRSNYVDFTLPYTESGVSMIVP 457 (852)
Q Consensus 378 ~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv~ 457 (852)
+-..++..+.++.+- +++++.. ++..++..+|.+|++|+++..-.. ....+. ..++....++++++
T Consensus 14 ~~~~~l~~~~~~~P~-i~i~i~~---------~~~~~~~~~l~~g~~Dl~i~~~~~---~~~~~~-~~~l~~~~~~~~~~ 79 (198)
T cd08441 14 WLMPVLDQFRERWPD-VELDLSS---------GFHFDPLPALLRGELDLVITSDPL---PLPGIA-YEPLFDYEVVLVVA 79 (198)
T ss_pred hhHHHHHHHHHhCCC-eEEEEEe---------CCchhHHHHHHcCCceEEEecCCc---CCCCcE-EEEccCCcEEEEEc
Confidence 345788888888763 4555543 245789999999999999853211 112232 35666777777777
Q ss_pred cc
Q 003054 458 IK 459 (852)
Q Consensus 458 ~~ 459 (852)
..
T Consensus 80 ~~ 81 (198)
T cd08441 80 PD 81 (198)
T ss_pred CC
Confidence 54
No 271
>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=88.66 E-value=2.5 Score=43.30 Aligned_cols=193 Identities=15% Similarity=0.123 Sum_probs=112.7
Q ss_pred EEeeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcC-cccEEEeeeeeecCcc---eeee--ccccccc
Q 003054 376 TGYCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLG-EFDAVVGDITIVFNRS---NYVD--FTLPYTE 449 (852)
Q Consensus 376 ~G~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g-~~D~~~g~~~it~~r~---~~vd--ft~p~~~ 449 (852)
.+..-++.+.+.++.|+++++.+. .-..+..+|..| ++|+.+.+-....++. ..+. -..|+..
T Consensus 10 ~~~~~~l~~~f~~~~g~~v~v~~~-----------~s~~~~~~l~~g~~~Dv~~~~~~~~~~~l~~~g~~~~~~~~~~~~ 78 (230)
T PF13531_consen 10 APALEELAEAFEKQPGIKVEVSFG-----------GSGELVRRLQAGKKPDVFIPASSEWLERLAAAGLVDPGSPAPLAR 78 (230)
T ss_dssp HHHHHHHHHHHHHHHCEEEEEEEE-----------CHHHHHHHHHTT-S-SEEEESSHHHHHHHHHTTTCSGGGEEEEEE
T ss_pred HHHHHHHHHHHHhccCCeEEEEEC-----------ChHHHHHHHhcCCCceEEEECCHHHHHHHHhcccccCCccccccc
Confidence 345567888888888865544442 235788888876 7898876532222222 2333 5678888
Q ss_pred cceEEEEEccCCCCCCceEeecccchhHHHHHHHHHHHHHhhhhheecccCCCCCCCcccccchhHHHHHHHhhhccccc
Q 003054 450 SGVSMIVPIKDSKKRNAWVFLQPLTWDLWVTCFCFFIFIGFVVWVLEHRVNEDFRGPAGQQVGTSFWFSFSTMVFSQRER 529 (852)
Q Consensus 450 ~~~~~vv~~~~~~~~~~~~~l~PF~~~lW~~i~~~~i~~~~v~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ 529 (852)
+.+++++++....
T Consensus 79 ~~~vl~~~~~~~~------------------------------------------------------------------- 91 (230)
T PF13531_consen 79 SPLVLAVPKGNPK------------------------------------------------------------------- 91 (230)
T ss_dssp EEEEEEEETTSTT-------------------------------------------------------------------
T ss_pred CceEEEeccCccc-------------------------------------------------------------------
Confidence 9999999976421
Q ss_pred cccchhhHHHHHHHHHHHHHHHHhhhhccceeeecccCCCcCCHHHHHhcCCeEEEEeCc------hHHHHHHhcC---C
Q 003054 530 VISNLARIVVIVWCFVVLILTQSYTASLTSLLTVQQLQPTITDVKMLIKRGDNVGYQKGS------FVLGILKQLG---F 600 (852)
Q Consensus 530 ~~s~~~R~v~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~i~sl~dL~~~~~~vg~~~~s------~~~~~l~~~~---~ 600 (852)
.+++++||.+.+.+|++.... .....+.+.+ +
T Consensus 92 ---------------------------------------~~~~~~dL~~~~~~i~~~dP~~s~~g~~~~~~l~~~g~~~~ 132 (230)
T PF13531_consen 92 ---------------------------------------GIRSWADLAQPGLRIAIPDPSTSPSGLAALQVLAAAGGQEL 132 (230)
T ss_dssp ---------------------------------------STTCHHHHCSTT--EEEE-TTTTHHHHHHHHHHHHHTHCHH
T ss_pred ---------------------------------------ccCCHHHHhhccCEEEecCcccChhhHHHHHHHHHcccHHH
Confidence 278888888776688886531 1223333332 0
Q ss_pred C---Cccee-ecCCHhHHHHHhhcccccCceeEEEechhHHHHHHhhcCCceE--eeccccc--ccceEEEecCCCCchh
Q 003054 601 D---ERKLV-VYNSPEDCHELFQKGSVNGGIAAAFDEIPYMKLLIGQYCSKYA--MIEPKFK--TAGFGFVFPLHSPLVH 672 (852)
Q Consensus 601 ~---~~~~~-~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~~~~~~~--~v~~~~~--~~~~~~~~~k~spl~~ 672 (852)
- ..++. ..++..+....+.+|+ +++.+.....+.+. ..-..+. .+++.+. ...+.+++.++++-.+
T Consensus 133 ~~~l~~~~~~~~~~~~~~~~~v~~g~----~d~~~~~~s~~~~~--~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~ 206 (230)
T PF13531_consen 133 LDALQKNIVQYVPSTSQVLSAVASGE----ADAGIVYESQAIFA--RQGDPLSYVYPPDGVNSPPIDYPIAILKNAPHPE 206 (230)
T ss_dssp HHHHHHTEEEEESSHHHHHHHHHTTS----SSEEEEEHHHHHHC--TSHTTEEEEE-STTTSSSEEEEEEEEBTTCTTHH
T ss_pred HHHHHHhCcccccchHHHHHHHHcCC----CcceeeHHHHHHHh--hcCCCeEEEECCchhcCCCEEEEEEEecCCCCHH
Confidence 0 11333 5567788899999998 88888765544222 1211233 3344444 3457888888887666
Q ss_pred hHHHHHHhccccChhHHHHH
Q 003054 673 DVSKAILNVTEGDKMKEIED 692 (852)
Q Consensus 673 ~in~~il~l~e~G~~~~i~~ 692 (852)
.-..++..|... .-+++..
T Consensus 207 ~a~~f~~~L~s~-~~q~~l~ 225 (230)
T PF13531_consen 207 AARAFIDFLLSP-EGQQILA 225 (230)
T ss_dssp HHHHHHHHHTSH-HHHHHHH
T ss_pred HHHHHHHHHCCH-HHHHHHH
Confidence 666666666554 3344433
No 272
>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=88.65 E-value=24 Score=34.05 Aligned_cols=70 Identities=11% Similarity=0.205 Sum_probs=45.9
Q ss_pred eeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCcccEEEeeeeeecCcceeeeccccccccceEEEEE
Q 003054 378 YCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGEFDAVVGDITIVFNRSNYVDFTLPYTESGVSMIVP 457 (852)
Q Consensus 378 ~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv~ 457 (852)
+-.+++..+.+..+ .+++++.. ++..++.+++.+|++|+++..... ..+...+. ..|+....++++++
T Consensus 14 ~l~~~l~~~~~~~P-~v~i~i~~---------~~~~~~~~~l~~~~~Dl~i~~~~~-~~~~~~~~-~~~l~~~~~~~~~~ 81 (201)
T cd08435 14 LLPPAIARLLARHP-RLTVRVVE---------GTSDELLEGLRAGELDLAIGRLAD-DEQPPDLA-SEELADEPLVVVAR 81 (201)
T ss_pred HHHHHHHHHHHHCC-CeEEEEEe---------CCHHHHHHHHHcCCccEEEEecCc-ccCCCCcE-EEEcccCcEEEEEe
Confidence 34578888888876 35555543 246789999999999998753211 11122232 35777888888888
Q ss_pred cc
Q 003054 458 IK 459 (852)
Q Consensus 458 ~~ 459 (852)
..
T Consensus 82 ~~ 83 (201)
T cd08435 82 PG 83 (201)
T ss_pred CC
Confidence 55
No 273
>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=88.62 E-value=3.2 Score=46.83 Aligned_cols=89 Identities=12% Similarity=0.015 Sum_probs=68.0
Q ss_pred HHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeCh
Q 003054 46 AGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLP 125 (852)
Q Consensus 46 ~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~ 125 (852)
.+.+.++++.+|.+++.+++....+..+..+.+.+.|++.|+++.....+.++.+.+.+...+..+++.++|+||-.+-+
T Consensus 11 ~~~l~~~l~~~g~~~vlivt~~~~~~~g~~~~v~~~L~~~gi~~~~f~~v~~~p~~~~v~~~~~~~~~~~~D~IIaiGGG 90 (414)
T cd08190 11 TAEVGMDLKNLGARRVCLVTDPNLAQLPPVKVVLDSLEAAGINFEVYDDVRVEPTDESFKDAIAFAKKGQFDAFVAVGGG 90 (414)
T ss_pred HHHHHHHHHHcCCCeEEEEECcchhhcchHHHHHHHHHHcCCcEEEeCCCCCCcCHHHHHHHHHHHHhcCCCEEEEeCCc
Confidence 45567788899999999998666565667788999999999887655455566677888888999999999999887654
Q ss_pred --hhHHHHHHH
Q 003054 126 --SLGSRIFEK 134 (852)
Q Consensus 126 --~~~~~i~~~ 134 (852)
-|+.+.+..
T Consensus 91 SviD~AKaia~ 101 (414)
T cd08190 91 SVIDTAKAANL 101 (414)
T ss_pred cHHHHHHHHHH
Confidence 355555543
No 274
>PRK10624 L-1,2-propanediol oxidoreductase; Provisional
Probab=88.28 E-value=3.8 Score=45.69 Aligned_cols=89 Identities=15% Similarity=0.103 Sum_probs=66.7
Q ss_pred HHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeCh
Q 003054 46 AGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLP 125 (852)
Q Consensus 46 ~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~ 125 (852)
...+.+.++.+|.+++.|+....-+-.+..+.+.+.|++.|+++.....+.++.+.++....+..+++.++|+||-.+-+
T Consensus 18 l~~l~~~~~~~g~~~~lvvtd~~~~~~g~~~~v~~~L~~~g~~~~~~~~v~~~p~~~~v~~~~~~~~~~~~D~IIaiGGG 97 (382)
T PRK10624 18 IGALTDEVKRRGFKKALIVTDKTLVKCGVVAKVTDVLDAAGLAYEIYDGVKPNPTIEVVKEGVEVFKASGADYLIAIGGG 97 (382)
T ss_pred HHHHHHHHHhcCCCEEEEEeCcchhhCcchHHHHHHHHHCCCeEEEeCCCCCCcCHHHHHHHHHHHHhcCCCEEEEeCCh
Confidence 45677888889999999888655455567888999999999887654455556667888888899999999999866543
Q ss_pred --hhHHHHHHH
Q 003054 126 --SLGSRIFEK 134 (852)
Q Consensus 126 --~~~~~i~~~ 134 (852)
-|+.+.+..
T Consensus 98 S~iD~aK~ia~ 108 (382)
T PRK10624 98 SPQDTCKAIGI 108 (382)
T ss_pred HHHHHHHHHHH
Confidence 355655443
No 275
>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=88.13 E-value=3.8 Score=45.58 Aligned_cols=90 Identities=10% Similarity=0.028 Sum_probs=68.1
Q ss_pred HHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeCh
Q 003054 46 AGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLP 125 (852)
Q Consensus 46 ~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~ 125 (852)
...+.++++.+|.+++.+++...-...+..+.+.+.|++.|+++.....+.++.+.+++...+..+++.++|+||-.+.+
T Consensus 14 l~~l~~~l~~~~~~~~livt~~~~~~~~~~~~v~~~L~~~~~~~~~~~~v~~~p~~~~v~~~~~~~~~~~~D~IIaiGGG 93 (376)
T cd08193 14 LARLGELLAALGAKRVLVVTDPGILKAGLIDPLLASLEAAGIEVTVFDDVEADPPEAVVEAAVEAARAAGADGVIGFGGG 93 (376)
T ss_pred HHHHHHHHHHcCCCeEEEEcCcchhhCccHHHHHHHHHHcCCeEEEECCCCCCcCHHHHHHHHHHHHhcCCCEEEEeCCc
Confidence 35567778888999999888554444557888999999999887655556666778889999999999999999887654
Q ss_pred --hhHHHHHHHH
Q 003054 126 --SLGSRIFEKA 135 (852)
Q Consensus 126 --~~~~~i~~~a 135 (852)
-|+.+++...
T Consensus 94 s~iD~aK~ia~~ 105 (376)
T cd08193 94 SSMDVAKLVAVL 105 (376)
T ss_pred hHHHHHHHHHHH
Confidence 3566665544
No 276
>PRK12682 transcriptional regulator CysB-like protein; Reviewed
Probab=88.11 E-value=29 Score=37.21 Aligned_cols=70 Identities=23% Similarity=0.256 Sum_probs=46.2
Q ss_pred EeeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCcccEEEeeeeeecCcceeeeccccccccceEEEE
Q 003054 377 GYCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGEFDAVVGDITIVFNRSNYVDFTLPYTESGVSMIV 456 (852)
Q Consensus 377 G~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv 456 (852)
.+-.+++..+.++.+- +++++.. ++.++++..|.+|++|++++.... .....++ +.|+.....++++
T Consensus 106 ~~l~~~l~~~~~~~P~-i~i~i~~---------~~~~~~~~~l~~g~~D~~i~~~~~--~~~~~l~-~~~l~~~~~~~~~ 172 (309)
T PRK12682 106 YVLPRVVAAFRKRYPK-VNLSLHQ---------GSPDEIARMVISGEADIGIATESL--ADDPDLA-TLPCYDWQHAVIV 172 (309)
T ss_pred HHHHHHHHHHHHhCCC-eEEEEec---------CCHHHHHHHHHcCCccEEEecCcc--cCCCcce-EEEeeeeeEEEEe
Confidence 3456788888888762 4454433 246789999999999999863221 1122333 3577788888888
Q ss_pred Ecc
Q 003054 457 PIK 459 (852)
Q Consensus 457 ~~~ 459 (852)
+..
T Consensus 173 ~~~ 175 (309)
T PRK12682 173 PPD 175 (309)
T ss_pred cCC
Confidence 855
No 277
>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=88.09 E-value=6.3 Score=41.11 Aligned_cols=126 Identities=6% Similarity=0.022 Sum_probs=72.0
Q ss_pred HhcCCC-CccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHc-CCcEEEEEEEeC-CcccccHHHHHHHHHh
Q 003054 8 QLGNKS-QVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAF-GWREAVPIYVDN-QYGEEMIPSLTDALQA 84 (852)
Q Consensus 8 ~i~~~~-~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~-gw~~vaii~~d~-~~G~~~~~~l~~~l~~ 84 (852)
...++. ++|++......+. +...+ ....++..-++.++.++..+ |-+++++|..+. .......+.|.+++++
T Consensus 73 ~~~~~~~~ipvv~~~~~~~~--~~~~~---~v~~d~~~~~~~a~~l~~~~~g~~~I~~i~~~~~~~~~~R~~Gf~~~~~~ 147 (260)
T cd06304 73 KVAKEYPDVKFAIIDGVVDA--PPNVA---SYVFREYEGSYLAGVLAALMTKTGKVGFVGGMPIPEVNRFINGFAAGAKS 147 (260)
T ss_pred HHHHHCCCCEEEEecCccCC--CCCee---eeecchHHHHHHHHHHHHHhccCCceEEEeccccHHHHHHHHHHHHHHHH
Confidence 444433 7888876543211 01112 12333333344444455554 999999997432 2334457789999999
Q ss_pred CCceeeeeeecCCCCC-hHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHcC
Q 003054 85 IDTRVPYRSVISPLAT-DDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEIG 139 (852)
Q Consensus 85 ~g~~v~~~~~~~~~~~-~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~G 139 (852)
.|..+..........+ .+.-...+.++.+..|++| ++.+...+..+++++++.|
T Consensus 148 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~ai-~~~~d~~A~gv~~al~~~g 202 (260)
T cd06304 148 VNPDITVLVIYTGSFFDPAKGKEAALALIDQGADVI-FAAAGGTGPGVIQAAKEAG 202 (260)
T ss_pred hCCCcEEEEEEecCccCcHHHHHHHHHHHhCCCCEE-EEcCCCCchHHHHHHHHcC
Confidence 8865432222211111 1223345666666678876 5667777888999999998
No 278
>PRK10936 TMAO reductase system periplasmic protein TorT; Provisional
Probab=87.98 E-value=7.5 Score=42.59 Aligned_cols=122 Identities=7% Similarity=-0.022 Sum_probs=74.8
Q ss_pred cCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHc-----CCcEEEEEEEeC--CcccccHHHHHHHH
Q 003054 10 GNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAF-----GWREAVPIYVDN--QYGEEMIPSLTDAL 82 (852)
Q Consensus 10 ~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~-----gw~~vaii~~d~--~~G~~~~~~l~~~l 82 (852)
+.+.++|+|....... .+. ....+..++...+...++++... |-++++++..+. .......+.|++++
T Consensus 124 ~~~~giPvV~~~~~~~--~~~---~~~~V~~D~~~~g~~aa~~L~~~~~~~~g~~~i~~i~g~~~~~~~~~R~~Gf~~~l 198 (343)
T PRK10936 124 LQAANIPVIALVNGID--SPQ---VTTRVGVSWYQMGYQAGRYLAQWHPKGSKPLNVALLPGPEGAGGSKAVEQGFRAAI 198 (343)
T ss_pred HHHCCCCEEEecCCCC--Ccc---ceEEEecChHHHHHHHHHHHHHHHHhcCCCceEEEEECCCCCchHHHHHHHHHHHH
Confidence 4567899997643221 111 12235567777778888876443 578999997432 23344578899999
Q ss_pred HhCCceeeeeeecCCCCChHHHHHHHHHhhcC--CceEEEEEeChhhHHHHHHHHHHcCC
Q 003054 83 QAIDTRVPYRSVISPLATDDQIEKELYKLFTM--QTRVFILHMLPSLGSRIFEKANEIGL 140 (852)
Q Consensus 83 ~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~--~~~viv~~~~~~~~~~i~~~a~~~G~ 140 (852)
++.|+++.... .. +.+.+.-...+.++.+. ++++|+ +....+..+++.+++.|+
T Consensus 199 ~~~~i~~~~~~-~~-~~~~~~~~~~~~~~l~~~~~~~ai~--~~d~~A~ga~~al~~~g~ 254 (343)
T PRK10936 199 AGSDVRIVDIA-YG-DNDKELQRNLLQELLERHPDIDYIA--GSAVAAEAAIGELRGRNL 254 (343)
T ss_pred hcCCCEEEEee-cC-CCcHHHHHHHHHHHHHhCCCccEEE--eCCHHHHHHHHHHHhcCC
Confidence 98898875421 11 11222223445554433 468776 345667788899999997
No 279
>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=87.95 E-value=3.9 Score=45.40 Aligned_cols=91 Identities=12% Similarity=0.026 Sum_probs=68.5
Q ss_pred HHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeCh
Q 003054 46 AGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLP 125 (852)
Q Consensus 46 ~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~ 125 (852)
.+.+.+.++.+|.+++.+++....+.....+.+.+.|++.|+++.....+..+.+.+++...+..++..++|+||-.+.+
T Consensus 11 l~~l~~~l~~~~~~~~lvv~~~~~~~~~~~~~v~~~L~~~~~~~~~~~~~~~~p~~~~v~~~~~~~~~~~~d~IiaiGGG 90 (370)
T cd08551 11 IEKLGEEIKNLGGRKALIVTDPGLVKTGVLDKVIDSLKEAGIEVVIFDGVEPNPTLSNVDAAVAAYREEGCDGVIAVGGG 90 (370)
T ss_pred HHHHHHHHHHcCCCeEEEEeCcchhhCccHHHHHHHHHHcCCeEEEECCCCCCCCHHHHHHHHHHHHhcCCCEEEEeCCc
Confidence 45677778888999999998555444477788999999999877644445556678889999999999999999876554
Q ss_pred --hhHHHHHHHHH
Q 003054 126 --SLGSRIFEKAN 136 (852)
Q Consensus 126 --~~~~~i~~~a~ 136 (852)
-|+.+++....
T Consensus 91 s~~D~AK~va~~~ 103 (370)
T cd08551 91 SVLDTAKAIALLA 103 (370)
T ss_pred hHHHHHHHHHHHH
Confidence 46666665443
No 280
>PRK10341 DNA-binding transcriptional activator TdcA; Provisional
Probab=87.58 E-value=17 Score=39.18 Aligned_cols=70 Identities=11% Similarity=0.211 Sum_probs=46.9
Q ss_pred eeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCcccEEEeeeeeecCcceeeeccccccccceEEEEE
Q 003054 378 YCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGEFDAVVGDITIVFNRSNYVDFTLPYTESGVSMIVP 457 (852)
Q Consensus 378 ~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv~ 457 (852)
+-.+++..+.+..+- +++++.. +...+++.+|.+|++|+++...... .....+ ...|+....++++++
T Consensus 111 ~l~~~l~~~~~~~p~-v~i~~~~---------~~~~~~~~~l~~g~~Dl~i~~~~~~-~~~~~l-~~~~l~~~~~~lv~~ 178 (312)
T PRK10341 111 FMSDMINKFKEVFPK-AQVSMYE---------AQLSSFLPAIRDGRLDFAIGTLSNE-MKLQDL-HVEPLFESEFVLVAS 178 (312)
T ss_pred hHHHHHHHHHHhCCC-CEEEEEe---------CCHHHHHHHHHcCCCcEEEecCCcc-cccCCe-eEEEEecccEEEEEc
Confidence 345788888887763 5565544 2478999999999999998532111 111223 247788888888887
Q ss_pred cc
Q 003054 458 IK 459 (852)
Q Consensus 458 ~~ 459 (852)
..
T Consensus 179 ~~ 180 (312)
T PRK10341 179 KS 180 (312)
T ss_pred CC
Confidence 54
No 281
>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=87.39 E-value=24 Score=35.12 Aligned_cols=69 Identities=16% Similarity=0.146 Sum_probs=46.5
Q ss_pred EeeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCcccEEEeeeeeecCcceeeeccccccccceEEEE
Q 003054 377 GYCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGEFDAVVGDITIVFNRSNYVDFTLPYTESGVSMIV 456 (852)
Q Consensus 377 G~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv 456 (852)
.+..+++..+.++.+ .+++++.. ++..++.+.|.+|++|++++.. ......+. ..|......++++
T Consensus 13 ~~l~~~l~~f~~~~P-~v~l~i~~---------~~~~~~~~~l~~g~~Di~i~~~---~~~~~~l~-~~~l~~~~~~~v~ 78 (221)
T cd08469 13 VLLPALVRRLETEAP-GIDLRIRP---------VTRLDLAEQLDLGRIDLVIGIF---EQIPPRFR-RRTLFDEDEVWVM 78 (221)
T ss_pred HHHHHHHHHHHHHCC-CcEEEEee---------CChhhHHHHHHCCCccEEEecC---CCCCccce-eeeeeccceEEEE
Confidence 345678888888876 35555543 2467899999999999998632 22223343 4677788888888
Q ss_pred Ecc
Q 003054 457 PIK 459 (852)
Q Consensus 457 ~~~ 459 (852)
+..
T Consensus 79 ~~~ 81 (221)
T cd08469 79 RKD 81 (221)
T ss_pred eCC
Confidence 854
No 282
>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=87.26 E-value=29 Score=33.35 Aligned_cols=71 Identities=20% Similarity=0.246 Sum_probs=45.9
Q ss_pred EeeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCcccEEEeeeeeecCcceeeeccccccccceEEEE
Q 003054 377 GYCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGEFDAVVGDITIVFNRSNYVDFTLPYTESGVSMIV 456 (852)
Q Consensus 377 G~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv 456 (852)
.+-.+++..+.++.+- +++++.. ++.+++++.+.+|++|+++..-... .....+. +.+.....+++++
T Consensus 13 ~~l~~~l~~~~~~~P~-i~l~~~~---------~~~~~~~~~l~~g~~Dl~i~~~~~~-~~~~~~~-~~~l~~~~~~~v~ 80 (195)
T cd08427 13 GLLPRALARLRRRHPD-LEVHIVP---------GLSAELLARVDAGELDAAIVVEPPF-PLPKDLV-WTPLVREPLVLIA 80 (195)
T ss_pred HHhHHHHHHHHHHCCC-ceEEEEe---------CCcHHHHHHHHCCCCCEEEEcCCCC-ccccCce-EEEcccCcEEEEE
Confidence 4456788888888762 4555543 2467899999999999997532111 1012232 4567778888888
Q ss_pred Ecc
Q 003054 457 PIK 459 (852)
Q Consensus 457 ~~~ 459 (852)
+..
T Consensus 81 ~~~ 83 (195)
T cd08427 81 PAE 83 (195)
T ss_pred CCC
Confidence 754
No 283
>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=87.10 E-value=30 Score=33.36 Aligned_cols=70 Identities=19% Similarity=0.246 Sum_probs=45.9
Q ss_pred EeeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCcccEEEeeeeeecCcceeeeccccccccceEEEE
Q 003054 377 GYCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGEFDAVVGDITIVFNRSNYVDFTLPYTESGVSMIV 456 (852)
Q Consensus 377 G~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv 456 (852)
.+-.+++..+.++.+ .++++... ++..+++.+|.+|++|+++...... ....+. ..++....+++++
T Consensus 13 ~~l~~~l~~~~~~~P-~v~l~~~~---------~~~~~~~~~l~~g~~Dl~i~~~~~~--~~~~l~-~~~l~~~~~~~~~ 79 (199)
T cd08430 13 SFLPPILERFRAQHP-QVEIKLHT---------GDPADAIDKVLNGEADIAIAARPDK--LPARLA-FLPLATSPLVFIA 79 (199)
T ss_pred eeccHHHHHHHHHCC-CceEEEEe---------CCHHHHHHHHHCCCCCEEEEecCCC--CCcccE-EEeeccceEEEEE
Confidence 455688999999986 25565544 2577899999999999987532111 112232 3566677777777
Q ss_pred Ecc
Q 003054 457 PIK 459 (852)
Q Consensus 457 ~~~ 459 (852)
+..
T Consensus 80 ~~~ 82 (199)
T cd08430 80 PNI 82 (199)
T ss_pred eCC
Confidence 744
No 284
>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=86.92 E-value=4.8 Score=44.82 Aligned_cols=89 Identities=11% Similarity=0.028 Sum_probs=66.3
Q ss_pred HHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeCh
Q 003054 46 AGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLP 125 (852)
Q Consensus 46 ~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~ 125 (852)
...+.+.++.+|.+++.|++.....-.+..+.+.+.|++.|+++.....+.++.+.+++...+..+++.++|+||-.+-+
T Consensus 17 l~~l~~~l~~~g~~r~lvvt~~~~~~~g~~~~v~~~L~~~~i~~~~~~~v~~~p~~~~v~~~~~~~~~~~~D~IiaiGGG 96 (379)
T TIGR02638 17 IEDIVDEVKRRGFKKALVVTDKDLIKFGVADKVTDLLDEAGIAYELFDEVKPNPTITVVKAGVAAFKASGADYLIAIGGG 96 (379)
T ss_pred HHHHHHHHHhcCCCEEEEEcCcchhhccchHHHHHHHHHCCCeEEEECCCCCCcCHHHHHHHHHHHHhcCCCEEEEeCCh
Confidence 45567778889999999888554444457888999999999887655455556667888888899999999999977554
Q ss_pred --hhHHHHHHH
Q 003054 126 --SLGSRIFEK 134 (852)
Q Consensus 126 --~~~~~i~~~ 134 (852)
-|+.+.+..
T Consensus 97 SviD~aKaia~ 107 (379)
T TIGR02638 97 SPIDTAKAIGI 107 (379)
T ss_pred HHHHHHHHHHH
Confidence 355555443
No 285
>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=86.84 E-value=2.8 Score=46.41 Aligned_cols=90 Identities=11% Similarity=0.068 Sum_probs=70.9
Q ss_pred HHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeCh
Q 003054 46 AGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLP 125 (852)
Q Consensus 46 ~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~ 125 (852)
.+.+.+.++.+| ++.+|+...-...+..+.+.+.|++.|+++.....+..+.+.+++...+..+++.++|+||-.+.+
T Consensus 11 l~~l~~~l~~~g--r~lvVt~~~~~~~~~~~~v~~~L~~~~i~~~~~~~~~~~p~~~~v~~~~~~~~~~~~D~IIaiGGG 88 (366)
T PF00465_consen 11 LEELGEELKRLG--RVLVVTDPSLSKSGLVDRVLDALEEAGIEVQVFDGVGPNPTLEDVDEAAEQARKFGADCIIAIGGG 88 (366)
T ss_dssp GGGHHHHHHCTT--EEEEEEEHHHHHHTHHHHHHHHHHHTTCEEEEEEEESSS-BHHHHHHHHHHHHHTTSSEEEEEESH
T ss_pred HHHHHHHHHhcC--CEEEEECchHHhCccHHHHHHHHhhCceEEEEEecCCCCCcHHHHHHHHHHHHhcCCCEEEEcCCC
Confidence 345667777787 999998663344557899999999999999777777777888999999999999999999988776
Q ss_pred h--hHHHHHHHHHH
Q 003054 126 S--LGSRIFEKANE 137 (852)
Q Consensus 126 ~--~~~~i~~~a~~ 137 (852)
. ++.+++..+..
T Consensus 89 S~~D~aK~va~~~~ 102 (366)
T PF00465_consen 89 SVMDAAKAVALLLA 102 (366)
T ss_dssp HHHHHHHHHHHHHT
T ss_pred CcCcHHHHHHhhcc
Confidence 4 66777666655
No 286
>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=86.78 E-value=25 Score=34.29 Aligned_cols=69 Identities=14% Similarity=0.239 Sum_probs=45.9
Q ss_pred EeeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCcccEEEeeeeeecCcceeeeccccccccceEEEE
Q 003054 377 GYCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGEFDAVVGDITIVFNRSNYVDFTLPYTESGVSMIV 456 (852)
Q Consensus 377 G~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv 456 (852)
++..+++..+.++.+ .+++++.. ++..+++.+|.+|++|++++..... ...+. +.|+....+++++
T Consensus 14 ~~l~~~l~~~~~~~P-~i~l~i~~---------~~~~~~~~~l~~~~~Dl~i~~~~~~---~~~~~-~~~l~~~~~~~v~ 79 (203)
T cd08445 14 GLLPELIRRFRQAAP-DVEIELIE---------MTTVQQIEALKEGRIDVGFGRLRIE---DPAIR-RIVLREEPLVVAL 79 (203)
T ss_pred hHHHHHHHHHHHHCC-CeEEEEEe---------CChHHHHHHHHcCCCcEEEecCCCC---CCCce-eEEEEeccEEEEe
Confidence 455688888888876 24555543 2467899999999999998532211 12232 4566777888888
Q ss_pred Ecc
Q 003054 457 PIK 459 (852)
Q Consensus 457 ~~~ 459 (852)
+..
T Consensus 80 ~~~ 82 (203)
T cd08445 80 PAG 82 (203)
T ss_pred eCC
Confidence 754
No 287
>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=86.74 E-value=31 Score=33.21 Aligned_cols=71 Identities=13% Similarity=0.109 Sum_probs=46.0
Q ss_pred eeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCcccEEEeeeeee--cCcceeeeccccccccceEEE
Q 003054 378 YCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGEFDAVVGDITIV--FNRSNYVDFTLPYTESGVSMI 455 (852)
Q Consensus 378 ~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~~D~~~g~~~it--~~r~~~vdft~p~~~~~~~~v 455 (852)
+-.+++..+.+..+ .+++++.. ++..++..++.+|++|+++...... ......+ ...+.....++++
T Consensus 14 ~l~~~l~~~~~~~P-~i~i~~~~---------~~~~~~~~~l~~~~~Dl~i~~~~~~~~~~~~~~~-~~~~l~~~~~~~~ 82 (200)
T cd08423 14 LLPPALAALRARHP-GLEVRLRE---------AEPPESLDALRAGELDLAVVFDYPVTPPPDDPGL-TRVPLLDDPLDLV 82 (200)
T ss_pred hhhHHHHHHHHhCC-CCeEEEEe---------CCHHHHHHHHhcCCccEEEEeccccccCCCCCCc-EEEEeccCcEEEE
Confidence 45678888888876 35555544 2457899999999999987532110 0122223 2566777888888
Q ss_pred EEcc
Q 003054 456 VPIK 459 (852)
Q Consensus 456 v~~~ 459 (852)
++..
T Consensus 83 ~~~~ 86 (200)
T cd08423 83 LPAD 86 (200)
T ss_pred ecCC
Confidence 8754
No 288
>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=86.51 E-value=5.4 Score=44.33 Aligned_cols=88 Identities=13% Similarity=0.055 Sum_probs=67.0
Q ss_pred HHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeCh
Q 003054 46 AGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLP 125 (852)
Q Consensus 46 ~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~ 125 (852)
...+.++++.++.+++.+++....+..+..+.+.+.|++.|+++.....+.++.+.+++...+..++..++|+||-.+.+
T Consensus 11 ~~~l~~~~~~~~~~r~livt~~~~~~~g~~~~v~~~L~~~gi~~~~~~~v~~~p~~~~v~~~~~~~~~~~~D~IIaiGGG 90 (375)
T cd08194 11 VDETGAVLADLGGKRPLIVTDKVMVKLGLVDKLTDSLKKEGIESAIFDDVVSEPTDESVEEGVKLAKEGGCDVIIALGGG 90 (375)
T ss_pred HHHHHHHHHHcCCCeEEEEcCcchhhcchHHHHHHHHHHCCCeEEEECCCCCCcCHHHHHHHHHHHHhcCCCEEEEeCCc
Confidence 34566777778889999998555555557788999999999987655556667778889999999999999999877554
Q ss_pred --hhHHHHHH
Q 003054 126 --SLGSRIFE 133 (852)
Q Consensus 126 --~~~~~i~~ 133 (852)
-|+.+.+.
T Consensus 91 S~~D~AKaia 100 (375)
T cd08194 91 SPIDTAKAIA 100 (375)
T ss_pred hHHHHHHHHH
Confidence 35555554
No 289
>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=86.13 E-value=33 Score=32.97 Aligned_cols=69 Identities=10% Similarity=0.035 Sum_probs=45.9
Q ss_pred EeeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCcccEEEeeeeeecCcceeeeccccccccceEEEE
Q 003054 377 GYCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGEFDAVVGDITIVFNRSNYVDFTLPYTESGVSMIV 456 (852)
Q Consensus 377 G~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv 456 (852)
.+-.+++..+.++.+ .+++++.. +....+++++.+|++|+++..... ....+. +.+.....+++++
T Consensus 13 ~~l~~~l~~~~~~~P-~i~~~i~~---------~~~~~~~~~l~~g~~Dl~i~~~~~---~~~~~~-~~~l~~~~~~~~~ 78 (196)
T cd08456 13 SFLPRAIKAFLQRHP-DVTISIHT---------RDSPTVEQWLSAQQCDLGLVSTLH---EPPGIE-RERLLRIDGVCVL 78 (196)
T ss_pred hhHHHHHHHHHHHCC-CcEEEEEe---------CCHHHHHHHHHcCCccEEEEecCC---CCCCee-EEEeeccCeEEEe
Confidence 455688889988886 35666654 246788999999999998753211 112222 4566677788777
Q ss_pred Ecc
Q 003054 457 PIK 459 (852)
Q Consensus 457 ~~~ 459 (852)
+..
T Consensus 79 ~~~ 81 (196)
T cd08456 79 PPG 81 (196)
T ss_pred cCC
Confidence 754
No 290
>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=86.10 E-value=34 Score=33.11 Aligned_cols=68 Identities=15% Similarity=0.117 Sum_probs=45.0
Q ss_pred eeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCcccEEEeeeeeecCcceeeeccccccccceEEEEE
Q 003054 378 YCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGEFDAVVGDITIVFNRSNYVDFTLPYTESGVSMIVP 457 (852)
Q Consensus 378 ~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv~ 457 (852)
+-.+++..+.++.+- +++++.. ++..++...|.+|++|+++...... ...+. +.++.....+++++
T Consensus 14 ~l~~~l~~f~~~~P~-v~i~~~~---------~~~~~~~~~l~~g~~Dl~i~~~~~~---~~~~~-~~~l~~~~~~~v~~ 79 (196)
T cd08458 14 FMSGVIQTFIADRPD-VSVYLDT---------VPSQTVLELVSLQHYDLGISILAGD---YPGLT-TEPVPSFRAVCLLP 79 (196)
T ss_pred hhHHHHHHHHHHCCC-cEEEEec---------cChHHHHHHHHcCCCCEEEEeccCC---CCCce-EEEeccCceEEEec
Confidence 446888999888873 5555543 2467899999999999988632211 12222 35667777788777
Q ss_pred cc
Q 003054 458 IK 459 (852)
Q Consensus 458 ~~ 459 (852)
..
T Consensus 80 ~~ 81 (196)
T cd08458 80 PG 81 (196)
T ss_pred CC
Confidence 44
No 291
>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=85.96 E-value=35 Score=33.01 Aligned_cols=70 Identities=16% Similarity=0.163 Sum_probs=46.7
Q ss_pred eeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCcccEEEeeeeeecCcceeeeccccccccceEEEEE
Q 003054 378 YCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGEFDAVVGDITIVFNRSNYVDFTLPYTESGVSMIVP 457 (852)
Q Consensus 378 ~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv~ 457 (852)
+-..++..+.++.+ .+++++.. ++...+++.|.+|++|+++.... .......++ ..++....++++++
T Consensus 14 ~l~~~l~~~~~~~P-~v~i~~~~---------~~~~~~~~~l~~g~~Dl~i~~~~-~~~~~~~l~-~~~l~~~~~~~~~~ 81 (198)
T cd08437 14 YFPKLAKDLIKTGL-MIQIDTYE---------GGSAELLEQLLQGDLDIALLGSL-TPLENSALH-SKIIKTQHFMIIVS 81 (198)
T ss_pred HhHHHHHHHHHhCC-ceEEEEEE---------cCHHHHHHHHHcCCCCEEEecCC-CCCCcccce-EEEeecceEEEEec
Confidence 45688888888877 35666544 24678999999999999875321 111223343 35677788888887
Q ss_pred cc
Q 003054 458 IK 459 (852)
Q Consensus 458 ~~ 459 (852)
..
T Consensus 82 ~~ 83 (198)
T cd08437 82 KD 83 (198)
T ss_pred CC
Confidence 54
No 292
>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=85.82 E-value=36 Score=33.08 Aligned_cols=70 Identities=19% Similarity=0.226 Sum_probs=46.9
Q ss_pred EeeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCcccEEEeeeeeecCcceeeeccccccccceEEEE
Q 003054 377 GYCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGEFDAVVGDITIVFNRSNYVDFTLPYTESGVSMIV 456 (852)
Q Consensus 377 G~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv 456 (852)
++..+++..+.++.+- ++++... ++..++++.|.+|++|+++..-.. .....+. +.|+....+++++
T Consensus 13 ~~l~~~l~~~~~~~P~-v~l~i~~---------~~~~~~~~~l~~g~~Dl~i~~~~~--~~~~~~~-~~~l~~~~~~~~~ 79 (198)
T cd08444 13 YALPWVVQAFKEQFPN-VHLVLHQ---------GSPEEIASMLANGQADIGIATEAL--ENHPELV-SFPYYDWHHHIIV 79 (198)
T ss_pred hhhhHHHHHHHHHCCC-eEEEEEe---------CCHHHHHHHHHCCCccEEEecccc--CCCcCcE-EeeccccceeEEe
Confidence 4567889999998762 5555543 246789999999999998752111 1112232 4677777888888
Q ss_pred Ecc
Q 003054 457 PIK 459 (852)
Q Consensus 457 ~~~ 459 (852)
+..
T Consensus 80 ~~~ 82 (198)
T cd08444 80 PVG 82 (198)
T ss_pred cCC
Confidence 755
No 293
>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=85.74 E-value=10 Score=36.95 Aligned_cols=105 Identities=10% Similarity=0.041 Sum_probs=71.7
Q ss_pred CchhHHHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHHHHHhC--CceeeeeeecCCCCChHHHHHHHHHhhcCCceE
Q 003054 41 NDSSQAGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTDALQAI--DTRVPYRSVISPLATDDQIEKELYKLFTMQTRV 118 (852)
Q Consensus 41 ~d~~~~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~~l~~~--g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~v 118 (852)
+.......+.+.+...+ .++.++..+.+ ..+.+.+.|++. |+.|+....-+ .+..+....++.|++++||+
T Consensus 32 ~g~dl~~~l~~~~~~~~-~~ifllG~~~~----~~~~~~~~l~~~yP~l~ivg~~~g~--f~~~~~~~i~~~I~~~~pdi 104 (172)
T PF03808_consen 32 TGSDLFPDLLRRAEQRG-KRIFLLGGSEE----VLEKAAANLRRRYPGLRIVGYHHGY--FDEEEEEAIINRINASGPDI 104 (172)
T ss_pred CHHHHHHHHHHHHHHcC-CeEEEEeCCHH----HHHHHHHHHHHHCCCeEEEEecCCC--CChhhHHHHHHHHHHcCCCE
Confidence 33455666666666666 48888885543 456666667665 77777654322 24677888999999999999
Q ss_pred EEEEeChhhHHHHHHHHHHcCCcccceEEEEcCcccc
Q 003054 119 FILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTN 155 (852)
Q Consensus 119 iv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~~~~ 155 (852)
|++.+..+.-..++...++..- .+ +++..++..+
T Consensus 105 v~vglG~PkQE~~~~~~~~~l~--~~-v~i~vG~~~d 138 (172)
T PF03808_consen 105 VFVGLGAPKQERWIARHRQRLP--AG-VIIGVGGAFD 138 (172)
T ss_pred EEEECCCCHHHHHHHHHHHHCC--CC-EEEEECchhh
Confidence 9999988877777777665431 22 6776665443
No 294
>KOG3857 consensus Alcohol dehydrogenase, class IV [Energy production and conversion]
Probab=85.67 E-value=4.6 Score=42.61 Aligned_cols=96 Identities=14% Similarity=0.015 Sum_probs=78.2
Q ss_pred CCCCceEeccCCchhHHHHH----HHHHHHcCCcEEEEEEEeCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHH
Q 003054 30 IRSPYFFRGSLNDSSQAGAI----TAIIKAFGWREAVPIYVDNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIE 105 (852)
Q Consensus 30 ~~~py~fR~~p~d~~~~~ai----a~~l~~~gw~~vaii~~d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~ 105 (852)
...+|-|-+.|+....++.. +..++.+|.|++.++.+-+---....+...+.|+++|+++.....+.++.++..+.
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 45678888888877666543 34578999999999997777777788889999999999987776677777888999
Q ss_pred HHHHHhhcCCceEEEEEeCh
Q 003054 106 KELYKLFTMQTRVFILHMLP 125 (852)
Q Consensus 106 ~~l~~l~~~~~~viv~~~~~ 125 (852)
..|.=+|..+.|.+|..+.+
T Consensus 118 ~alefak~~~fDs~vaiGGG 137 (465)
T KOG3857|consen 118 AALEFAKKKNFDSFVAIGGG 137 (465)
T ss_pred HHHHHHHhcccceEEEEcCc
Confidence 99999999999999877654
No 295
>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=85.59 E-value=36 Score=32.92 Aligned_cols=71 Identities=13% Similarity=0.108 Sum_probs=45.2
Q ss_pred eeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCcccEEEeeeeeecCcceeeeccccccccceEEEEE
Q 003054 378 YCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGEFDAVVGDITIVFNRSNYVDFTLPYTESGVSMIVP 457 (852)
Q Consensus 378 ~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv~ 457 (852)
+-..++..+.++.+- +++++.. +...++..+|.+|++|+++............+. +.|.....++++++
T Consensus 14 ~l~~~l~~~~~~~P~-i~l~i~~---------~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~~~~-~~~l~~~~~~~v~~ 82 (200)
T cd08453 14 VLPELVRRFREAYPD-VELQLRE---------ATSDVQLEALLAGEIDAGIVIPPPGASAPPALA-YRPLLSEPLVLAVP 82 (200)
T ss_pred HHHHHHHHHHHhCCC-ceEEEEe---------CCHHHHHHHHHcCCCCEEEEecCcccCCCccee-EEEeeeCceEEEEE
Confidence 456788888888762 5555543 246789999999999998753211110112222 46677778888887
Q ss_pred cc
Q 003054 458 IK 459 (852)
Q Consensus 458 ~~ 459 (852)
..
T Consensus 83 ~~ 84 (200)
T cd08453 83 AA 84 (200)
T ss_pred CC
Confidence 54
No 296
>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=85.40 E-value=24 Score=34.50 Aligned_cols=69 Identities=14% Similarity=0.128 Sum_probs=45.8
Q ss_pred EeeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCcccEEEeeeeeecCcceeeeccccccccceEEEE
Q 003054 377 GYCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGEFDAVVGDITIVFNRSNYVDFTLPYTESGVSMIV 456 (852)
Q Consensus 377 G~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv 456 (852)
++-.+++..+.++.+ .++++... ++..+++++|.+|++|++++..... ...+.. .+......++++
T Consensus 13 ~~l~~~l~~f~~~~P-~i~l~i~~---------~~~~~~~~~L~~g~~Dl~i~~~~~~---~~~~~~-~~l~~~~~~lv~ 78 (200)
T cd08465 13 LVLPALMRQLRAEAP-GIDLAVSQ---------ASREAMLAQVADGEIDLALGVFPEL---PEELHA-ETLFEERFVCLA 78 (200)
T ss_pred HhhhHHHHHHHHHCC-CcEEEEec---------CChHhHHHHHHCCCccEEEeccccC---CcCeeE-EEeeeccEEEEE
Confidence 455688888888876 24555543 3578999999999999988532211 122333 466677788888
Q ss_pred Ecc
Q 003054 457 PIK 459 (852)
Q Consensus 457 ~~~ 459 (852)
+..
T Consensus 79 ~~~ 81 (200)
T cd08465 79 DRA 81 (200)
T ss_pred eCC
Confidence 754
No 297
>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=85.17 E-value=7.2 Score=43.37 Aligned_cols=89 Identities=9% Similarity=-0.014 Sum_probs=65.7
Q ss_pred HHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeCh
Q 003054 46 AGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLP 125 (852)
Q Consensus 46 ~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~ 125 (852)
...+.++++.+|.+++.+++.......+..+.+.+.|++.|+++.....+.++.+.++....+..+++.++|+||-.+-+
T Consensus 16 l~~l~~~l~~~g~~~~livt~~~~~~~~~~~~v~~~L~~~~~~~~~~~~v~~~p~~~~v~~~~~~~~~~~~d~IIaiGGG 95 (377)
T cd08188 16 LKLAGRYARRLGAKKVLLVSDPGVIKAGWVDRVIESLEEAGLEYVVFSDVSPNPRDEEVMAGAELYLENGCDVIIAVGGG 95 (377)
T ss_pred HHHHHHHHHHcCCCeEEEEeCcchhhCccHHHHHHHHHHcCCeEEEeCCCCCCCCHHHHHHHHHHHHhcCCCEEEEeCCc
Confidence 45677778888999999988544444456788999999999877654445556667788888999999999999877654
Q ss_pred --hhHHHHHHH
Q 003054 126 --SLGSRIFEK 134 (852)
Q Consensus 126 --~~~~~i~~~ 134 (852)
-|+.+.+..
T Consensus 96 sviD~AK~ia~ 106 (377)
T cd08188 96 SPIDCAKGIGI 106 (377)
T ss_pred hHHHHHHHHHH
Confidence 355555443
No 298
>PRK11482 putative DNA-binding transcriptional regulator; Provisional
Probab=85.03 E-value=38 Score=36.54 Aligned_cols=66 Identities=9% Similarity=0.099 Sum_probs=44.5
Q ss_pred eeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCcccEEEeeeeeecCcceeeeccccccccceEEEEE
Q 003054 378 YCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGEFDAVVGDITIVFNRSNYVDFTLPYTESGVSMIVP 457 (852)
Q Consensus 378 ~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv~ 457 (852)
+-..++..+.+..+ .++++.. ..++++..|.+|++|+++.... .....+. +.|+....++++++
T Consensus 131 ~l~~~l~~f~~~~P-~i~i~~~-----------~~~~~~~~l~~g~~Dl~i~~~~---~~~~~~~-~~~l~~~~~~lv~~ 194 (317)
T PRK11482 131 VMPVIYQAIKTHYP-QLLLRNI-----------PISDAENQLSQFQTDLIIDTHS---CSNRTIQ-HHVLFTDNVVLVCR 194 (317)
T ss_pred HHHHHHHHHHHHCC-CCEEEEe-----------cchhHHHHHHCCCcCEEEeccC---CCCCceE-EEEEecCcEEEEEe
Confidence 45678888888877 2444321 2457899999999999986432 2223343 36777888888887
Q ss_pred cc
Q 003054 458 IK 459 (852)
Q Consensus 458 ~~ 459 (852)
..
T Consensus 195 ~~ 196 (317)
T PRK11482 195 QG 196 (317)
T ss_pred CC
Confidence 55
No 299
>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=85.00 E-value=6.2 Score=38.39 Aligned_cols=103 Identities=9% Similarity=0.002 Sum_probs=68.2
Q ss_pred CchhHHHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHHHHHhC--CceeeeeeecCCCCChHHHHHHHHHhhcCCceE
Q 003054 41 NDSSQAGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTDALQAI--DTRVPYRSVISPLATDDQIEKELYKLFTMQTRV 118 (852)
Q Consensus 41 ~d~~~~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~~l~~~--g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~v 118 (852)
+.......+.+.+...+ .+|.++....+ .++.+.+.+++. |++|+....-+. ...+-...+.+|++.+||+
T Consensus 30 ~g~dl~~~ll~~~~~~~-~~v~llG~~~~----~~~~~~~~l~~~yp~l~i~g~~~g~~--~~~~~~~i~~~I~~~~pdi 102 (171)
T cd06533 30 TGSDLMPALLELAAQKG-LRVFLLGAKPE----VLEKAAERLRARYPGLKIVGYHHGYF--GPEEEEEIIERINASGADI 102 (171)
T ss_pred CcHHHHHHHHHHHHHcC-CeEEEECCCHH----HHHHHHHHHHHHCCCcEEEEecCCCC--ChhhHHHHHHHHHHcCCCE
Confidence 44556677777776655 68888875543 455555556654 788876433232 2444455889999999999
Q ss_pred EEEEeChhhHHHHHHHHHHcCCcccceEEEEcCcc
Q 003054 119 FILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGM 153 (852)
Q Consensus 119 iv~~~~~~~~~~i~~~a~~~G~~~~~~vwi~~~~~ 153 (852)
|++.+..+.-..++...++.. +.-+++..++.
T Consensus 103 v~vglG~PkQE~~~~~~~~~l---~~~v~~~vG~~ 134 (171)
T cd06533 103 LFVGLGAPKQELWIARHKDRL---PVPVAIGVGGS 134 (171)
T ss_pred EEEECCCCHHHHHHHHHHHHC---CCCEEEEecee
Confidence 999999888888887776654 23345654443
No 300
>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=84.82 E-value=6.6 Score=43.77 Aligned_cols=89 Identities=7% Similarity=-0.046 Sum_probs=66.3
Q ss_pred HHHHHHHHHHcCCcEEEEEEEeCCc-ccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeC
Q 003054 46 AGAITAIIKAFGWREAVPIYVDNQY-GEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHML 124 (852)
Q Consensus 46 ~~aia~~l~~~gw~~vaii~~d~~~-G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~ 124 (852)
...+.++++.+| +++.+++....+ ..+..+.+.+.|++.|+++.....+.++.+.++....+..+++.++|+||-.+.
T Consensus 14 l~~l~~~~~~~g-~r~livt~~~~~~~~g~~~~v~~~L~~~~~~~~~~~~v~~~p~~~~v~~~~~~~~~~~~D~IiavGG 92 (380)
T cd08185 14 LNELGEEALKPG-KKALIVTGNGSSKKTGYLDRVIELLKQAGVEVVVFDKVEPNPTTTTVMEGAALAREEGCDFVVGLGG 92 (380)
T ss_pred HHHHHHHHHhcC-CeEEEEeCCCchhhccHHHHHHHHHHHcCCeEEEeCCccCCCCHHHHHHHHHHHHHcCCCEEEEeCC
Confidence 345677777788 899888854442 567788899999999988765555666777888888889999999999996654
Q ss_pred --hhhHHHHHHHH
Q 003054 125 --PSLGSRIFEKA 135 (852)
Q Consensus 125 --~~~~~~i~~~a 135 (852)
.-|+.+.+...
T Consensus 93 GS~iD~aK~ia~~ 105 (380)
T cd08185 93 GSSMDTAKAIAFM 105 (380)
T ss_pred ccHHHHHHHHHHH
Confidence 34666665543
No 301
>COG1910 Periplasmic molybdate-binding protein/domain [Inorganic ion transport and metabolism]
Probab=84.49 E-value=16 Score=36.36 Aligned_cols=104 Identities=13% Similarity=0.133 Sum_probs=63.8
Q ss_pred cCCHHHHHhcCCeEEE-EeCchHHHHHH----hcCCCCcceeecC----CHhHHHHHhhcccccCceeEEEechhHHHHH
Q 003054 570 ITDVKMLIKRGDNVGY-QKGSFVLGILK----QLGFDERKLVVYN----SPEDCHELFQKGSVNGGIAAAFDEIPYMKLL 640 (852)
Q Consensus 570 i~sl~dL~~~~~~vg~-~~~s~~~~~l~----~~~~~~~~~~~~~----~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~ 640 (852)
|++++||.+.+.++.- ++||-.+..|. +.+..+..+.-|. +-.....++..|+ .||-+.-+ +.
T Consensus 89 i~~~edl~~~d~~fVNR~rGSGTR~LlD~~L~~~~~~~~~I~GY~~e~~th~avA~aVa~G~----AD~GvGlr----~~ 160 (223)
T COG1910 89 ISSLEDLLRKDLRFVNRNRGSGTRILLDELLGELNILPDSIKGYSDEATTHDAVASAVASGR----ADAGVGLR----HA 160 (223)
T ss_pred cccHHHHhhcCcEEEecCCCccHHHHHHHHHHHcCcCchhcCCccccccccHHHHHHHHcCC----CCccccHH----HH
Confidence 8999999966654332 57787776554 3555555666665 3345678899999 88888744 33
Q ss_pred HhhcCCceEeecccccccceEEEecCCCCchhhHHHHHHhccccC
Q 003054 641 IGQYCSKYAMIEPKFKTAGFGFVFPLHSPLVHDVSKAILNVTEGD 685 (852)
Q Consensus 641 ~~~~~~~~~~v~~~~~~~~~~~~~~k~spl~~~in~~il~l~e~G 685 (852)
..++-=++. ++....|-|+.+|..-=.+.+...+..|...+
T Consensus 161 A~~~gL~Fi----pl~~E~YD~virke~~~~~~vr~fi~~L~s~~ 201 (223)
T COG1910 161 AEKYGLDFI----PLGDEEYDFVIRKERLDKPVVRAFIKALKSEG 201 (223)
T ss_pred HHHcCCceE----EcccceEEEEEehhHccCHHHHHHHHHhcccc
Confidence 444421233 34556788999997444444444444444433
No 302
>PRK11062 nhaR transcriptional activator NhaR; Provisional
Probab=84.39 E-value=30 Score=36.80 Aligned_cols=72 Identities=15% Similarity=0.184 Sum_probs=43.0
Q ss_pred EeeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCcccEEEeeeeeecCcceeeeccccccccceEEEE
Q 003054 377 GYCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGEFDAVVGDITIVFNRSNYVDFTLPYTESGVSMIV 456 (852)
Q Consensus 377 G~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv 456 (852)
++-.+++..+.++.+ .++++... ++..++..+|.+|++|+++............+ ...|+.....++++
T Consensus 106 ~~l~~~l~~f~~~~P-~i~l~~~~---------~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~~l-~~~~l~~~~~~~~~ 174 (296)
T PRK11062 106 RLVSRVLLTAVPEDE-SIHLRCFE---------STHEMLLEQLSQHKLDMILSDCPVDSTQQEGL-FSKKLGECGVSFFC 174 (296)
T ss_pred hhHHHHHHHHHhcCC-ceEEEEEe---------CCHHHHHHHHHcCCCCEEEecCCCccccccch-hhhhhhccCcceEe
Confidence 455677888877665 24444432 25788999999999999875322111111222 23566666666666
Q ss_pred Ecc
Q 003054 457 PIK 459 (852)
Q Consensus 457 ~~~ 459 (852)
+.+
T Consensus 175 ~~~ 177 (296)
T PRK11062 175 TNP 177 (296)
T ss_pred cCC
Confidence 543
No 303
>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=84.36 E-value=40 Score=32.33 Aligned_cols=68 Identities=9% Similarity=0.101 Sum_probs=45.2
Q ss_pred eeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCcccEEEeeeeeecCcceeeeccccccccceEEEEE
Q 003054 378 YCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGEFDAVVGDITIVFNRSNYVDFTLPYTESGVSMIVP 457 (852)
Q Consensus 378 ~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv~ 457 (852)
+..+++..+.++.+ .+++++.. ++..++..+|.+|++|+++..... ....+. ..|+....++++++
T Consensus 14 ~l~~~l~~~~~~~p-~i~i~i~~---------~~~~~~~~~l~~~~~Dl~i~~~~~---~~~~~~-~~~l~~~~~~~v~~ 79 (197)
T cd08414 14 LLPRLLRRFRARYP-DVELELRE---------MTTAEQLEALRAGRLDVGFVRPPP---DPPGLA-SRPLLREPLVVALP 79 (197)
T ss_pred HHHHHHHHHHHHCC-CcEEEEec---------CChHHHHHHHHcCCccEEEEcCCC---CCCCee-EEEEeeccEEEEec
Confidence 44678888888876 24555543 246789999999999999853222 122232 36677788888887
Q ss_pred cc
Q 003054 458 IK 459 (852)
Q Consensus 458 ~~ 459 (852)
..
T Consensus 80 ~~ 81 (197)
T cd08414 80 AD 81 (197)
T ss_pred CC
Confidence 54
No 304
>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=84.22 E-value=18 Score=38.56 Aligned_cols=118 Identities=6% Similarity=-0.021 Sum_probs=70.9
Q ss_pred CCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHcC------CcEEEEEEEeC--CcccccHHHHHHHHHh
Q 003054 13 SQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAFG------WREAVPIYVDN--QYGEEMIPSLTDALQA 84 (852)
Q Consensus 13 ~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~g------w~~vaii~~d~--~~G~~~~~~l~~~l~~ 84 (852)
.++|+|....... .. ..+-.+..++..-+..+++++.+ + -++++++.... .......+.+++++++
T Consensus 80 ~~iPvV~~~~~~~--~~---~~~~~V~~D~~~~g~~~~~~L~~-~~~~~~g~~~I~~i~g~~~~~~~~~R~~Gf~~al~~ 153 (295)
T TIGR02955 80 KSIPVFALVNQID--SN---QVKGRVGVDWYQMGYQAGEYLAQ-RHPKGSGPTTLAWLPGPKNRGGTKPVTQGFRAALEG 153 (295)
T ss_pred cCCCEEEEecCCC--cc---ceeEEEeecHHHHHHHHHHHHHH-hcccCCCCeeEEEEeCCCcCCchhHHHHHHHHHHhc
Confidence 4899987643211 11 11233455666667778887755 3 34699997433 3456678899999999
Q ss_pred CCceeeeeeecCCCCChHHHHHHHHHhhcC--CceEEEEEeChhhHHHHHHHHHHcCC
Q 003054 85 IDTRVPYRSVISPLATDDQIEKELYKLFTM--QTRVFILHMLPSLGSRIFEKANEIGL 140 (852)
Q Consensus 85 ~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~--~~~viv~~~~~~~~~~i~~~a~~~G~ 140 (852)
.|+++... ...+.+..+-...+.++.+. .+|+| ++....+..+++.+++.|.
T Consensus 154 ~g~~~~~~--~~~~~~~~~~~~~~~~~L~~~~~~d~i--~~~d~~a~g~l~al~~~g~ 207 (295)
T TIGR02955 154 SDVEISAI--LWADNDKELQRNLLQDLLKKHPDIDYL--VGSAVAAEAAISELRSLHM 207 (295)
T ss_pred CCcEEEEE--ecCCCcHHHHHHHHHHHHHhCCCcCEE--EeccHHHHHHHHHHHhhCc
Confidence 99877532 22112222333445555433 45764 4556667888999988886
No 305
>COG0725 ModA ABC-type molybdate transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=84.10 E-value=23 Score=36.98 Aligned_cols=115 Identities=15% Similarity=0.214 Sum_probs=68.6
Q ss_pred cCCHHHHHhc-CCeEEEE------eCchHHHHHHhcCCC---CcceeecCCHhHHHHHhhcccccCceeEEEechhHHHH
Q 003054 570 ITDVKMLIKR-GDNVGYQ------KGSFVLGILKQLGFD---ERKLVVYNSPEDCHELFQKGSVNGGIAAAFDEIPYMKL 639 (852)
Q Consensus 570 i~sl~dL~~~-~~~vg~~------~~s~~~~~l~~~~~~---~~~~~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~ 639 (852)
+..+++|.+. +.++++- -|.+..+.|++.+.- ..+++.-.+.++.+..+..|. +++.+.-...+..
T Consensus 124 ~~~~~~l~~~~~~~lai~~p~~~P~G~ya~~~l~~~g~~~~~~~k~v~~~~v~~~l~~V~~G~----ad~g~vy~sd~~~ 199 (258)
T COG0725 124 IESLEDLLERPDVRLAIGDPKTVPAGKYAKEALELLGLWYTLKDKLVLATNVRQALAYVETGE----ADAGFVYVSDALL 199 (258)
T ss_pred cccHHHHhcCcCcEEEecCCCCCCchHHHHHHHHHhchhhhccccEEecCcHHHHHHHHHcCC----CCeEEEEEEhhhc
Confidence 4447778764 4578873 466777777775443 336777788899999999999 7776654432222
Q ss_pred HHhhcCCceEeecccc-cccceEEEecCCCCc---hhhHHHHHHhccccChhHHHHHHH
Q 003054 640 LIGQYCSKYAMIEPKF-KTAGFGFVFPLHSPL---VHDVSKAILNVTEGDKMKEIEDAW 694 (852)
Q Consensus 640 ~~~~~~~~~~~v~~~~-~~~~~~~~~~k~spl---~~~in~~il~l~e~G~~~~i~~kw 694 (852)
. ..-+.+..++... .+..|.+++.+++.- ...|-+.++. ..-+++.++|
T Consensus 200 ~--~~~~~~~~~~~~~~~Pi~y~iav~~~~~~~~~A~~f~~fl~s----~~a~~il~~~ 252 (258)
T COG0725 200 S--KKVKIVGVFPEDLHSPIVYPIAVLKNAKNPELAKEFVDFLLS----PEAQEILEKY 252 (258)
T ss_pred c--CCceEEEEcccccCCCeEEEEEEEcCCCCHHHHHHHHHHHhC----HHHHHHHHHc
Confidence 1 1222233344333 346778888887664 5555555544 2334455444
No 306
>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=83.72 E-value=42 Score=32.07 Aligned_cols=70 Identities=13% Similarity=0.124 Sum_probs=45.7
Q ss_pred EeeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCcccEEEeeeeeecCcceeeeccccccccceEEEE
Q 003054 377 GYCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGEFDAVVGDITIVFNRSNYVDFTLPYTESGVSMIV 456 (852)
Q Consensus 377 G~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv 456 (852)
.+-.+++..+.++.+ ++.+++.. ++..++..+|.+|++|+++..... .....+. ..++....+++++
T Consensus 13 ~~l~~~l~~~~~~~P-~v~i~i~~---------~~~~~~~~~l~~~~~Dl~i~~~~~--~~~~~~~-~~~l~~~~~~~~~ 79 (194)
T cd08436 13 VDLPELLARFHRRHP-GVDIRLRQ---------AGSDDLLAAVREGRLDLAFVGLPE--RRPPGLA-SRELAREPLVAVV 79 (194)
T ss_pred HHHHHHHHHHHHHCC-CcEEEEec---------CCHHHHHHHHHcCCccEEEEecCC--CCCCCcE-EEEeecceEEEEe
Confidence 445678888888876 35555543 246789999999999999864322 1222232 3566677777777
Q ss_pred Ecc
Q 003054 457 PIK 459 (852)
Q Consensus 457 ~~~ 459 (852)
+..
T Consensus 80 ~~~ 82 (194)
T cd08436 80 APD 82 (194)
T ss_pred cCC
Confidence 754
No 307
>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=83.54 E-value=7.9 Score=43.07 Aligned_cols=89 Identities=12% Similarity=0.057 Sum_probs=65.4
Q ss_pred HHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeCh
Q 003054 46 AGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLP 125 (852)
Q Consensus 46 ~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~ 125 (852)
...+.+.++.+|-+++.+++....+-.+..+.+.+.|++.|+++.....+.++.+.+.+...+..+++.++|+||-.+.+
T Consensus 16 l~~l~~~l~~~g~~~~lvv~~~~~~~~~~~~~v~~~L~~~~~~~~~f~~v~~~p~~~~v~~~~~~~~~~~~D~IIavGGG 95 (377)
T cd08176 16 IKEIGDELKNLGFKKALIVTDKGLVKIGVVEKVTDVLDEAGIDYVIYDGVKPNPTITNVKDGLAVFKKEGCDFIISIGGG 95 (377)
T ss_pred HHHHHHHHHHhCCCeEEEECCchHhhcCcHHHHHHHHHHcCCeEEEeCCCCCCCCHHHHHHHHHHHHhcCCCEEEEeCCc
Confidence 45567778888888998887544333467888999999999887655455556677888889999999999999976554
Q ss_pred --hhHHHHHHH
Q 003054 126 --SLGSRIFEK 134 (852)
Q Consensus 126 --~~~~~i~~~ 134 (852)
-|+.+.+..
T Consensus 96 S~iD~aK~ia~ 106 (377)
T cd08176 96 SPHDCAKAIGI 106 (377)
T ss_pred HHHHHHHHHHH
Confidence 355555543
No 308
>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=83.50 E-value=40 Score=35.88 Aligned_cols=124 Identities=6% Similarity=-0.026 Sum_probs=64.1
Q ss_pred cCCCCccEEeeecCCCCCCCCCCCceEeccCCch-hHHHHHHHHH-HHc-CCcEEEEEEEeCCc--ccccHHHHHHHHHh
Q 003054 10 GNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDS-SQAGAITAII-KAF-GWREAVPIYVDNQY--GEEMIPSLTDALQA 84 (852)
Q Consensus 10 ~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~-~~~~aia~~l-~~~-gw~~vaii~~d~~~--G~~~~~~l~~~l~~ 84 (852)
+.+.+||+|......+. + +....+...|. ..++..++.+ +++ +-++|++|..+... .....+.+++.+++
T Consensus 77 ~~~~giPvV~~~~~~~~--~---~~~~~v~~~Dn~~~g~~aa~~l~~~l~~~~~I~~i~g~~~~~~~~~r~~g~~~~~~~ 151 (302)
T TIGR02637 77 AMKRGIKVVTWDSGVAP--E---GRNLFLNQASADLIGRTQVQLAAEQIGNGGEIAILSAASTATNQNAWIEIMKKELKD 151 (302)
T ss_pred HHHCCCEEEEeCCCCCC--C---ceeEEEecCCHHHHHHHHHHHHHHHcCCCcEEEEEECCCCCccHHHHHHHHHHHHhh
Confidence 55679999987643221 1 12233333343 3344445544 332 23799998744321 22345677777776
Q ss_pred CC---ceeeeeeecCCCCChHHHHHHHHHhhcCC--ceEEEEEeChhhHHHHHHHHHHcCCc
Q 003054 85 ID---TRVPYRSVISPLATDDQIEKELYKLFTMQ--TRVFILHMLPSLGSRIFEKANEIGLM 141 (852)
Q Consensus 85 ~g---~~v~~~~~~~~~~~~~d~~~~l~~l~~~~--~~viv~~~~~~~~~~i~~~a~~~G~~ 141 (852)
.| .++.... ....+.++-...+.++.+.. +++|+. .....+..+++.+++.|..
T Consensus 152 ~~~~~~~~~~~~--~~~~~~~~~~~~~~~~L~~~~~~~ai~~-~~d~~a~ga~~al~~~g~~ 210 (302)
T TIGR02637 152 PKYPKVKLVATV--YGDDDAQKSYQEAQGLLKSYPNLKGIIA-PTTVGIKAAAQAVSDAKLI 210 (302)
T ss_pred ccCCCCEEEeee--cCCchHHHHHHHHHHHHHhCCCccEEEe-CCCchHHHHHHHHHhcCCC
Confidence 53 3433221 11112223334455544444 456665 3455667788888888874
No 309
>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=83.48 E-value=2.3 Score=44.22 Aligned_cols=78 Identities=15% Similarity=0.208 Sum_probs=61.1
Q ss_pred EEEEE--EeCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeC-hhhHHHHHHHHHH
Q 003054 61 AVPIY--VDNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHML-PSLGSRIFEKANE 137 (852)
Q Consensus 61 vaii~--~d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~-~~~~~~i~~~a~~ 137 (852)
|+++. .++.|.....+.+++++++.|.++... .+...+.......+.++.+.++|.|++... +.....+++++++
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 45555 456688889999999999999988765 222344667778888888999999988855 4567899999999
Q ss_pred cCC
Q 003054 138 IGL 140 (852)
Q Consensus 138 ~G~ 140 (852)
.|+
T Consensus 79 ~gI 81 (257)
T PF13407_consen 79 AGI 81 (257)
T ss_dssp TTS
T ss_pred cCc
Confidence 998
No 310
>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=83.46 E-value=9.3 Score=42.13 Aligned_cols=86 Identities=10% Similarity=0.028 Sum_probs=63.8
Q ss_pred HHHHHHHHHcCCcEEEEEEEeCCcc-cccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeCh
Q 003054 47 GAITAIIKAFGWREAVPIYVDNQYG-EEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLP 125 (852)
Q Consensus 47 ~aia~~l~~~gw~~vaii~~d~~~G-~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~ 125 (852)
+.+.++++.+| +++.+++....+- .+..+.+.+.|++.|+++.....+.++.+.++....+..+++.++|+||-.+-+
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 44667788888 8988887544433 345688999999999887655456666778889999999999999999988655
Q ss_pred h--hHHHHHH
Q 003054 126 S--LGSRIFE 133 (852)
Q Consensus 126 ~--~~~~i~~ 133 (852)
. |+.+.+.
T Consensus 94 SviD~aK~ia 103 (357)
T cd08181 94 SPLDAAKAIA 103 (357)
T ss_pred hHHHHHHHHH
Confidence 3 5555544
No 311
>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=83.44 E-value=9.4 Score=42.63 Aligned_cols=89 Identities=13% Similarity=0.025 Sum_probs=63.2
Q ss_pred HHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeCh-
Q 003054 47 GAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLP- 125 (852)
Q Consensus 47 ~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~- 125 (852)
..+.++++.+| +++.+++....+..+..+.+.+.|++.|+++.....+.++....+....+...++.++|+||-.+.+
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 45677788889 8998888444344577888999999999887544444434456677777888888999999877654
Q ss_pred -hhHHHHHHHHH
Q 003054 126 -SLGSRIFEKAN 136 (852)
Q Consensus 126 -~~~~~i~~~a~ 136 (852)
-|+.+++....
T Consensus 91 ~iD~aK~ia~~~ 102 (386)
T cd08191 91 CIDLAKIAGLLL 102 (386)
T ss_pred HHHHHHHHHHHH
Confidence 36666655443
No 312
>COG0715 TauA ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]
Probab=83.25 E-value=3.8 Score=44.63 Aligned_cols=70 Identities=24% Similarity=0.233 Sum_probs=50.3
Q ss_pred CcCCHHHHHhcCCeEEEEeCch-HH----HHHHhcCCCCccee-ecCCHhHHHHHhhcccccCceeEEEechhHHHHHHh
Q 003054 569 TITDVKMLIKRGDNVGYQKGSF-VL----GILKQLGFDERKLV-VYNSPEDCHELFQKGSVNGGIAAAFDEIPYMKLLIG 642 (852)
Q Consensus 569 ~i~sl~dL~~~~~~vg~~~~s~-~~----~~l~~~~~~~~~~~-~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~ 642 (852)
+|++++||. |++||+..++. .. ..|.+.+.+.+.+. ..-.+.+...++..|+ ++|+....++......
T Consensus 127 ~i~~~adlk--Gk~vg~~~~~~~~~~~l~~~L~~~Gl~~~dv~~v~~~~~~~~~al~~g~----vda~~~~ep~~~~~~~ 200 (335)
T COG0715 127 GIKSVADLK--GKKVGVPFGGSTSDFLLRYALAKAGLDPDDVELVNLPPADAVAALAAGQ----VDAFVVWEPWNAAAEG 200 (335)
T ss_pred CcccccCCC--CceEEEeCCCchHHHHHHHHHHHcCCCcccceEEeeCcHHHHHHHhcCC----cceEEecCCchhhhhc
Confidence 388899996 99999988874 33 33455666665554 3335558889999999 9998887777666655
Q ss_pred hc
Q 003054 643 QY 644 (852)
Q Consensus 643 ~~ 644 (852)
+.
T Consensus 201 ~~ 202 (335)
T COG0715 201 EG 202 (335)
T ss_pred cC
Confidence 54
No 313
>PF14503 YhfZ_C: YhfZ C-terminal domain; PDB: 2OZZ_B.
Probab=83.19 E-value=1.5 Score=44.33 Aligned_cols=105 Identities=16% Similarity=0.209 Sum_probs=52.8
Q ss_pred CCeEEEEeCchHHHHHHhcCCCCcceeecC-CHhHHHHHhhcccccCceeEEEechhHHHHHHhhcCCceEee--cc---
Q 003054 580 GDNVGYQKGSFVLGILKQLGFDERKLVVYN-SPEDCHELFQKGSVNGGIAAAFDEIPYMKLLIGQYCSKYAMI--EP--- 653 (852)
Q Consensus 580 ~~~vg~~~~s~~~~~l~~~~~~~~~~~~~~-~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~~~~~~~~v--~~--- 653 (852)
|.+||+...|.-...|.+..+...++..++ +..++++.+.+|. +||.+.... . ...+.- .+..+ ..
T Consensus 114 GmRVGiD~~S~Dq~~LT~~~~~gk~Ve~Vei~Y~q~~~~l~~g~----IDA~IWN~d--~-i~~~~~-~l~~~~l~~~~~ 185 (232)
T PF14503_consen 114 GMRVGIDPSSIDQKILTEAEFEGKNVEFVEIPYNQLLELLRSGE----IDAAIWNYD--E-IEDKNF-GLKYVPLKDDPM 185 (232)
T ss_dssp --EEEE-TT-HHHHHHHHHHHTTS--EEEE--HHHHHHHHHHTS------EEEEE----H-HCCHHC-TEEEEE--SSCH
T ss_pred eeEeecCCCCccHHHHHHHHhCCCceEEEEecHHHHHHHHHCCC----ccEEEECCc--c-cccccC-CeeEEeCCchHH
Confidence 789999999988888876545555543333 4568999999999 999998854 1 111111 23222 11
Q ss_pred cccccceEEEecCCCCchhhHHHHHHhccccChhHHHHHHHc
Q 003054 654 KFKTAGFGFVFPLHSPLVHDVSKAILNVTEGDKMKEIEDAWF 695 (852)
Q Consensus 654 ~~~~~~~~~~~~k~spl~~~in~~il~l~e~G~~~~i~~kw~ 695 (852)
......-.++.+|+.+....+-+. +.....+..+.++-.
T Consensus 186 ~~~~seAVivi~~~~~~i~~ll~~---~id~~~vl~iQ~~V~ 224 (232)
T PF14503_consen 186 SKDASEAVIVIRKDNEPIKALLRK---LIDVEKVLEIQKKVL 224 (232)
T ss_dssp HHHTT-EEEEEETT-HHHHHHHHH---H--HHHHHHHHHHHH
T ss_pred HHhcCeeEEEEeCCCHHHHHHHHH---hcCHHHHHHHHHHHH
Confidence 112345577888887644333332 222334555666655
No 314
>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=83.10 E-value=63 Score=33.69 Aligned_cols=66 Identities=12% Similarity=0.144 Sum_probs=44.0
Q ss_pred HHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCcccEEEeeeeeecCcceeeeccccccccceEEEEEcc
Q 003054 380 VDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGEFDAVVGDITIVFNRSNYVDFTLPYTESGVSMIVPIK 459 (852)
Q Consensus 380 ~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv~~~ 459 (852)
.+++..+.+..+- ++++... ++..+++..|.+|++|+++...... ...+. ..|+....++++++..
T Consensus 100 ~~~l~~~~~~~p~-v~l~i~~---------~~~~~~~~~l~~g~~Dl~i~~~~~~---~~~~~-~~~l~~~~~~lv~s~~ 165 (279)
T TIGR03339 100 LDLVARFRQRYPG-IEVSVRI---------GNSQEVLQALQSYRVDVAVSSEVVD---DPRLD-RVVLGNDPLVAVVHRQ 165 (279)
T ss_pred HHHHHHHHHHCCC-cEEEEEE---------CCHHHHHHHHHcCCCcEEEEecccC---CCceE-EEEcCCceEEEEECCC
Confidence 4677888887762 4555543 2467899999999999998532222 12232 3667778888888755
No 315
>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=82.80 E-value=47 Score=32.00 Aligned_cols=69 Identities=14% Similarity=0.119 Sum_probs=44.9
Q ss_pred EeeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCcccEEEeeeeeecCcceeeeccccccccceEEEE
Q 003054 377 GYCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGEFDAVVGDITIVFNRSNYVDFTLPYTESGVSMIV 456 (852)
Q Consensus 377 G~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv 456 (852)
++-..++..+.++.+ .+++++.. ++..+++..|.+|++|+++.... .....+. ..+.....+++++
T Consensus 13 ~~l~~~l~~~~~~~P-~v~l~i~~---------~~~~~~~~~l~~g~~D~~i~~~~---~~~~~~~-~~~l~~~~~~~v~ 78 (200)
T cd08464 13 WLAPPLLAALRAEAP-GVRLVFRQ---------VDPFNVGDMLDRGEIDLAIGVFG---ELPAWLK-REVLYTEGYACLF 78 (200)
T ss_pred HHHHHHHHHHHHHCC-CcEEEEec---------CCcccHHHHHhcCcccEEEecCC---CCcccce-eeeecccceEEEE
Confidence 445678888888876 25555543 24568899999999999975321 1122232 4677777887777
Q ss_pred Ecc
Q 003054 457 PIK 459 (852)
Q Consensus 457 ~~~ 459 (852)
+..
T Consensus 79 ~~~ 81 (200)
T cd08464 79 DPQ 81 (200)
T ss_pred eCC
Confidence 644
No 316
>PRK15421 DNA-binding transcriptional regulator MetR; Provisional
Probab=82.65 E-value=42 Score=36.20 Aligned_cols=67 Identities=16% Similarity=0.147 Sum_probs=44.6
Q ss_pred eHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCcccEEEeeeeeecCcceeeeccccccccceEEEEEc
Q 003054 379 CVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGEFDAVVGDITIVFNRSNYVDFTLPYTESGVSMIVPI 458 (852)
Q Consensus 379 ~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv~~ 458 (852)
-.+++..+.+..+ .+.+++... .-.++...|.+|++|+++..- +.....+. ..++....++++++.
T Consensus 104 l~~~l~~~~~~~P-~i~l~~~~~---------~~~~~~~~L~~g~~Dl~i~~~---~~~~~~~~-~~~l~~~~~~lv~~~ 169 (317)
T PRK15421 104 LTPALENFHKNWP-QVEMDFKSG---------VTFDPQPALQQGELDLVMTSD---ILPRSGLH-YSPMFDYEVRLVLAP 169 (317)
T ss_pred HHHHHHHHHHHCC-CceEEEEeC---------ccHHHHHHHHCCCcCEEEecC---cccCCCce-EEEeccceEEEEEcC
Confidence 3577888888776 355555432 356889999999999997532 22222343 367778888888875
Q ss_pred c
Q 003054 459 K 459 (852)
Q Consensus 459 ~ 459 (852)
.
T Consensus 170 ~ 170 (317)
T PRK15421 170 D 170 (317)
T ss_pred C
Confidence 5
No 317
>PRK11013 DNA-binding transcriptional regulator LysR; Provisional
Probab=82.57 E-value=49 Score=35.45 Aligned_cols=102 Identities=12% Similarity=0.121 Sum_probs=56.7
Q ss_pred CCHHHHHhcCC-eEEEEeCchHH----HHHHhcCCCCcceeecCCHhHHHHHhhcccccCceeEEEechhHHHHHHhhcC
Q 003054 571 TDVKMLIKRGD-NVGYQKGSFVL----GILKQLGFDERKLVVYNSPEDCHELFQKGSVNGGIAAAFDEIPYMKLLIGQYC 645 (852)
Q Consensus 571 ~sl~dL~~~~~-~vg~~~~s~~~----~~l~~~~~~~~~~~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~~~ 645 (852)
-+++||. +. .|....++..+ .++...+.........++.....+++..|. ..+++.... .......
T Consensus 184 i~~~dL~--~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~----Gv~~~p~~~-~~~~~~~-- 254 (309)
T PRK11013 184 LTPDDFA--GENFISLSRTDSYRQLLDQLFAEHGVKRRMVVETHSAASVCAMVRAGV----GVSIVNPLT-ALDYAGS-- 254 (309)
T ss_pred cCHHHHC--CCcEEeecCCCcHHHHHHHHHHHcCCCcceEEEeccHHHHHHHHHcCC----eEEEeChhh-hccccCC--
Confidence 4688886 44 34444454433 344555555444556678888888998887 445553332 2222221
Q ss_pred CceEeeccc-ccccceEEEecCCCCchhhHHHHHHhcc
Q 003054 646 SKYAMIEPK-FKTAGFGFVFPLHSPLVHDVSKAILNVT 682 (852)
Q Consensus 646 ~~~~~v~~~-~~~~~~~~~~~k~spl~~~in~~il~l~ 682 (852)
.+.+++.. -....+.++.+|+.+....+...+..+.
T Consensus 255 -~l~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f~~~i~ 291 (309)
T PRK11013 255 -GLVVRRFSISVPFTVSLIRPLHRPASALVDAFSEHLQ 291 (309)
T ss_pred -CEEEEeCCCCCceeEEEEecCCCCCCHHHHHHHHHHH
Confidence 23333211 1234678888888777766666655543
No 318
>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=82.50 E-value=25 Score=34.37 Aligned_cols=69 Identities=10% Similarity=0.160 Sum_probs=45.7
Q ss_pred EeeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCcccEEEeeeeeecCcceeeeccccccccceEEEE
Q 003054 377 GYCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGEFDAVVGDITIVFNRSNYVDFTLPYTESGVSMIV 456 (852)
Q Consensus 377 G~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv 456 (852)
.+-.+++..+.++.+ .++++... ++..+++++|.+|++|+++... ......++ +.++....+++++
T Consensus 14 ~~l~~~l~~f~~~~P-~v~i~i~~---------~~~~~l~~~l~~g~~D~~~~~~---~~~~~~~~-~~~l~~~~~~lv~ 79 (198)
T cd08486 14 RSLPLLLRAFLTSTP-TATVSLTH---------MTKDEQVEGLLAGTIHVGFSRF---FPRHPGIE-IVNIAQEDLYLAV 79 (198)
T ss_pred HHHHHHHHHHHHhCC-CeEEEEEE---------CCHHHHHHHHHcCCceEEEecC---CCCCCceE-EEEEeeccEEEEe
Confidence 345678888888876 24555543 3578999999999999998522 11112232 4566677888888
Q ss_pred Ecc
Q 003054 457 PIK 459 (852)
Q Consensus 457 ~~~ 459 (852)
+..
T Consensus 80 ~~~ 82 (198)
T cd08486 80 HRS 82 (198)
T ss_pred cCC
Confidence 754
No 319
>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=81.93 E-value=50 Score=31.74 Aligned_cols=71 Identities=18% Similarity=0.235 Sum_probs=45.7
Q ss_pred EeeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCcccEEEeeeeeecCcceeeeccccccccceEEEE
Q 003054 377 GYCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGEFDAVVGDITIVFNRSNYVDFTLPYTESGVSMIV 456 (852)
Q Consensus 377 G~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv 456 (852)
++-.+++..+.++.+- +++++.. +...++..++.+|++|+++..... +.....+. +.++....+++++
T Consensus 13 ~~l~~~l~~~~~~~P~-i~l~i~~---------~~~~~~~~~l~~~~~Dl~i~~~~~-~~~~~~l~-~~~l~~~~~~~v~ 80 (199)
T cd08416 13 NTVPRIIMGLKLRRPE-LDIELTL---------GSNKDLLKKLKDGELDAILVATPE-GLNDPDFE-VVPLFEDDIFLAV 80 (199)
T ss_pred hhhHHHHHHHHHhCCC-eEEEEEE---------cCcHHHHHHHhCCCCCEEEEecCC-cCCCCCeE-EEEeecceEEEEE
Confidence 4566888888888862 4555543 235678999999999998863221 00112222 4567777888888
Q ss_pred Ecc
Q 003054 457 PIK 459 (852)
Q Consensus 457 ~~~ 459 (852)
+..
T Consensus 81 ~~~ 83 (199)
T cd08416 81 PAT 83 (199)
T ss_pred CCC
Confidence 754
No 320
>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=81.83 E-value=50 Score=31.61 Aligned_cols=69 Identities=12% Similarity=0.060 Sum_probs=46.5
Q ss_pred EeeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCcccEEEeeeeeecCcceeeeccccccccceEEEE
Q 003054 377 GYCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGEFDAVVGDITIVFNRSNYVDFTLPYTESGVSMIV 456 (852)
Q Consensus 377 G~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv 456 (852)
.+-.+++..+.++.+ .+++++.. ++..++..++.+|++|+++... ......+. +.++....+++++
T Consensus 13 ~~l~~~l~~~~~~~P-~i~i~i~~---------~~~~~~~~~l~~~~~Di~i~~~---~~~~~~~~-~~~l~~~~~~~~~ 78 (197)
T cd08448 13 RGLPRILRAFRAEYP-GIEVALHE---------MSSAEQIEALLRGELDLGFVHS---RRLPAGLS-ARLLHREPFVCCL 78 (197)
T ss_pred HHHHHHHHHHHHHCC-CCeEEEEe---------CCHHHHHHHHHcCCcceEEEeC---CCCCcCce-EEEEecCcEEEEe
Confidence 455688889988886 35565544 2478899999999999987532 22222232 4667777888777
Q ss_pred Ecc
Q 003054 457 PIK 459 (852)
Q Consensus 457 ~~~ 459 (852)
+..
T Consensus 79 ~~~ 81 (197)
T cd08448 79 PAG 81 (197)
T ss_pred eCC
Confidence 744
No 321
>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=81.68 E-value=11 Score=41.86 Aligned_cols=86 Identities=12% Similarity=0.114 Sum_probs=63.3
Q ss_pred HHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeCh-
Q 003054 47 GAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLP- 125 (852)
Q Consensus 47 ~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~- 125 (852)
..+.+.++.+|.+++.+++....+ ..+.+.+.+++.|+++.....+.++.+.++....+..+++.++|+||-.+.+
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 456677888898999999855444 4567788888888776555456666667788888888999999999876554
Q ss_pred -hhHHHHHHHH
Q 003054 126 -SLGSRIFEKA 135 (852)
Q Consensus 126 -~~~~~i~~~a 135 (852)
-|+.+++...
T Consensus 89 ~~D~aK~ia~~ 99 (367)
T cd08182 89 VLDTAKALAAL 99 (367)
T ss_pred HHHHHHHHHHH
Confidence 4666666544
No 322
>PRK09508 leuO leucine transcriptional activator; Reviewed
Probab=81.31 E-value=28 Score=37.45 Aligned_cols=69 Identities=10% Similarity=0.130 Sum_probs=47.2
Q ss_pred EeeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCcccEEEeeeeeecCcceeeeccccccccceEEEE
Q 003054 377 GYCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGEFDAVVGDITIVFNRSNYVDFTLPYTESGVSMIV 456 (852)
Q Consensus 377 G~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv 456 (852)
++-.+++..+.++.+- +.+++.. ++...++.+|.+|++|+++.... .....+. ..++.....++++
T Consensus 125 ~~l~~~l~~f~~~~P~-i~l~i~~---------~~~~~~~~~l~~g~~Di~i~~~~---~~~~~l~-~~~l~~~~~~lv~ 190 (314)
T PRK09508 125 RLTSQIYNRIEQIAPN-IHVVFKS---------SLNQNIEHQLRYQETEFVISYEE---FDRPEFT-SVPLFKDELVLVA 190 (314)
T ss_pred HHHHHHHHHHHHhCCC-cEEEEEe---------CcchhHHHHHhcCCccEEEecCC---CCccccc-eeeeecCceEEEE
Confidence 4557889999998873 5555543 24678999999999999986432 1122333 3467778888888
Q ss_pred Ecc
Q 003054 457 PIK 459 (852)
Q Consensus 457 ~~~ 459 (852)
+..
T Consensus 191 ~~~ 193 (314)
T PRK09508 191 SKN 193 (314)
T ss_pred cCC
Confidence 754
No 323
>COG1879 RbsB ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]
Probab=81.22 E-value=35 Score=36.86 Aligned_cols=133 Identities=12% Similarity=0.124 Sum_probs=78.6
Q ss_pred HHHhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHH-HHcCC-cEEEEEEEe--CCcccccHHHHHHH
Q 003054 6 IIQLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAII-KAFGW-REAVPIYVD--NQYGEEMIPSLTDA 81 (852)
Q Consensus 6 v~~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l-~~~gw-~~vaii~~d--~~~G~~~~~~l~~~ 81 (852)
+..-+.+.+||+|.+.+..+.- .....-...+....++..++++ +.++- -+++++... ........+.+++.
T Consensus 108 ~v~~a~~aGIpVv~~d~~~~~~----~~~~~~vg~dn~~~G~~~a~~l~~~~~~~g~v~~~~g~~~~~~~~~R~~G~~~~ 183 (322)
T COG1879 108 AVKKAKAAGIPVVTVDSDIPGP----GDRVAYVGSDNYKAGRLAAEYLAKALGGKGKVVVLVGSPGNSSAEERVKGFRDA 183 (322)
T ss_pred HHHHHHHCCCcEEEEecCCCCC----CceeEEEecCcHHHHHHHHHHHHHHhCCCCeEEEEecCCCCchHHHHHhhHHHH
Confidence 3455677899999987654432 1222333335555556667766 44432 346666632 34456678899999
Q ss_pred HHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeCh-hhHHHHHHHHHHcCCcc
Q 003054 82 LQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLP-SLGSRIFEKANEIGLMN 142 (852)
Q Consensus 82 l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~-~~~~~i~~~a~~~G~~~ 142 (852)
+++.+.++........+.+.+.-...+..+.+..||+-.+++.. ..+....+.+++.|...
T Consensus 184 l~~~~~~~~v~~~~~~~~~~~~a~~~~~~~L~~~pdi~~i~~~~d~~a~ga~~A~~~~g~~~ 245 (322)
T COG1879 184 LKEHPPDIEVVDVQTGDWDRDKALEVMEDLLAANPDIDGIYAANDGMALGAIQALKAAGRKG 245 (322)
T ss_pred HHhCCCcEEEeeccCCcccHHHHHHHHHHHHHhCCCceEEEECCchhHHHHHHHHHHcCCCC
Confidence 99988532222222222223334456677777888877666554 44556667777888754
No 324
>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=80.53 E-value=11 Score=41.88 Aligned_cols=88 Identities=7% Similarity=0.079 Sum_probs=63.8
Q ss_pred HHHHHHHHHHcCCcEEEEEEEeCCc-ccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeC
Q 003054 46 AGAITAIIKAFGWREAVPIYVDNQY-GEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHML 124 (852)
Q Consensus 46 ~~aia~~l~~~gw~~vaii~~d~~~-G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~ 124 (852)
.+.+.+.++.++ +++.++.....+ ..+..+.+.+.|++.|+++.....+.++.+.++....+..+++.++|+||-.+.
T Consensus 17 ~~~l~~~~~~~~-~r~livt~~~~~~~~~~~~~v~~~L~~~g~~~~~~~~v~~~p~~~~v~~~~~~~~~~~~D~IIaiGG 95 (382)
T cd08187 17 ESELGKELKKYG-KKVLLVYGGGSIKKNGLYDRVIASLKEAGIEVVELGGVEPNPRLETVREGIELCKEEKVDFILAVGG 95 (382)
T ss_pred HHHHHHHHHHhC-CEEEEEeCCcHHHhcCcHHHHHHHHHHcCCeEEEECCccCCCCHHHHHHHHHHHHHcCCCEEEEeCC
Confidence 345667777776 898888744333 345678899999999988765555666666788889999999999999987655
Q ss_pred h--hhHHHHHHH
Q 003054 125 P--SLGSRIFEK 134 (852)
Q Consensus 125 ~--~~~~~i~~~ 134 (852)
+ -|+.+++..
T Consensus 96 GS~iD~aK~ia~ 107 (382)
T cd08187 96 GSVIDSAKAIAA 107 (382)
T ss_pred hHHHHHHHHHHh
Confidence 4 355555543
No 325
>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=80.34 E-value=12 Score=41.67 Aligned_cols=90 Identities=14% Similarity=0.096 Sum_probs=64.9
Q ss_pred HHHHHHHHHHc---CCcEEEEEEEeCCcc-cccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEE
Q 003054 46 AGAITAIIKAF---GWREAVPIYVDNQYG-EEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFIL 121 (852)
Q Consensus 46 ~~aia~~l~~~---gw~~vaii~~d~~~G-~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~ 121 (852)
.+.+.++++.+ |.+++.+++....+. .+..+.+.+.|++.|+++.....+.++.+.+++...+..+++.++|+||-
T Consensus 11 ~~~l~~~l~~~~~~g~kr~livtd~~~~~~~g~~~~v~~~L~~~gi~~~~f~~v~~~p~~~~v~~~~~~~~~~~~D~IIa 90 (383)
T cd08186 11 IEKIGEILKDLKSKGISKVLLVTGKSAYKKSGAWDKVEPALDEHGIEYVLYNKVTPNPTVDQVDEAAKLGREFGAQAVIA 90 (383)
T ss_pred HHHHHHHHHHhcccCCCEEEEEcCccHHhhcChHHHHHHHHHHcCCeEEEeCCCCCCCCHHHHHHHHHHHHHcCCCEEEE
Confidence 34566677776 789998888544443 44578899999999987765555666667788889999999999999986
Q ss_pred EeC--hhhHHHHHHHH
Q 003054 122 HML--PSLGSRIFEKA 135 (852)
Q Consensus 122 ~~~--~~~~~~i~~~a 135 (852)
.+- .-|+.+++...
T Consensus 91 iGGGS~iD~aK~ia~~ 106 (383)
T cd08186 91 IGGGSPIDSAKSAAIL 106 (383)
T ss_pred eCCccHHHHHHHHHHH
Confidence 654 34666665543
No 326
>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=79.67 E-value=6.2 Score=43.44 Aligned_cols=85 Identities=13% Similarity=0.051 Sum_probs=62.9
Q ss_pred HHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChh
Q 003054 47 GAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPS 126 (852)
Q Consensus 47 ~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~ 126 (852)
..+.++++.++ +++.+++....+. +..+.+.+.|++.|+.+.+. .+..+.+.+++...+..+++.++|+||-.+.+.
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 45667777777 8998888444444 77888899999999987643 455566778888888999999999998876543
Q ss_pred --hHHHHHHH
Q 003054 127 --LGSRIFEK 134 (852)
Q Consensus 127 --~~~~i~~~ 134 (852)
|+.+++..
T Consensus 89 ~iD~aK~ia~ 98 (351)
T cd08170 89 TLDTAKAVAD 98 (351)
T ss_pred hhHHHHHHHH
Confidence 55555543
No 327
>PRK11074 putative DNA-binding transcriptional regulator; Provisional
Probab=79.55 E-value=63 Score=34.41 Aligned_cols=85 Identities=11% Similarity=0.041 Sum_probs=53.6
Q ss_pred CceEEEeeecccCcccceEEeeCCCCCCCceEEEeeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCc
Q 003054 344 EKKLRIGVPVKKGFSDFVNVTIDPKTQEPTSVTGYCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGE 423 (852)
Q Consensus 344 ~~~lrv~v~~~~~~~~~~~~~~d~~~~~~~~~~G~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~ 423 (852)
.+.++||+. +.+ ...+..+++..+.++.+- +++.... ++-.+++.+|.+|+
T Consensus 91 ~g~l~Ig~~--~~~-----------------~~~~l~~~l~~~~~~~p~-i~i~i~~---------~~~~~~~~~l~~g~ 141 (300)
T PRK11074 91 RGQLSIAVD--NIV-----------------RPDRTRQLIVDFYRHFDD-VELIIRQ---------EVFNGVWDALADGR 141 (300)
T ss_pred CceEEEEEc--Ccc-----------------chhHHHHHHHHHHHhCCC-ceEEEEe---------hhhhHHHHHHHCCC
Confidence 468999986 221 113345888888888873 4555543 24578999999999
Q ss_pred ccEEEeeeeeecCcceeeeccccccccceEEEEEcc
Q 003054 424 FDAVVGDITIVFNRSNYVDFTLPYTESGVSMIVPIK 459 (852)
Q Consensus 424 ~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv~~~ 459 (852)
+|++++.... ......+. ..++....+++++++.
T Consensus 142 ~Dl~i~~~~~-~~~~~~l~-~~~l~~~~~~~v~~~~ 175 (300)
T PRK11074 142 VDIAIGATRA-IPVGGRFA-FRDMGMLSWACVVSSD 175 (300)
T ss_pred CCEEEecCcc-CCcccccc-eeecccceEEEEEcCC
Confidence 9999863211 11111222 3567777888888754
No 328
>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=79.08 E-value=21 Score=38.13 Aligned_cols=104 Identities=13% Similarity=0.143 Sum_probs=62.0
Q ss_pred ccEEeeecCCCCCCC----CCC--CceEeccCCchhHHHHHHHHHHHc--CCcEEEEEEEeCCc-ccccHHHHHHHHHhC
Q 003054 15 VPILSFSATSPSLTS----IRS--PYFFRGSLNDSSQAGAITAIIKAF--GWREAVPIYVDNQY-GEEMIPSLTDALQAI 85 (852)
Q Consensus 15 vP~Is~~ats~~lt~----~~~--py~fR~~p~d~~~~~aia~~l~~~--gw~~vaii~~d~~~-G~~~~~~l~~~l~~~ 85 (852)
+|+|-.+.++|.-.. ... +++.-+. +....+.-.++++++ +.++++++|.++.- +....+.+++++++.
T Consensus 82 iPVVf~~V~dp~~~~l~~~~~~~~~nvTGv~--~~~~~~~~l~l~~~l~P~~k~igvl~~~~~~~~~~~~~~~~~~a~~~ 159 (294)
T PF04392_consen 82 IPVVFCGVSDPVGAGLVDSLDRPGKNVTGVS--ERPPIEKQLELIKKLFPDAKRIGVLYDPSEPNSVAQIEQLRKAAKKL 159 (294)
T ss_dssp S-EEEECES-TTTTTS-S-SSS--SSEEEEE--E---HHHHHHHHHHHSTT--EEEEEEETT-HHHHHHHHHHHHHHHHT
T ss_pred cEEEEEeccChhhhhccccccCCCCCEEEEE--CCcCHHHHHHHHHHhCCCCCEEEEEecCCCccHHHHHHHHHHHHHHc
Confidence 999887777775432 222 3443333 555566666666654 57999999965543 466788888999999
Q ss_pred CceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeCh
Q 003054 86 DTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLP 125 (852)
Q Consensus 86 g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~ 125 (852)
|+++.... ++ +..++...+..+. .+.|++++..+.
T Consensus 160 g~~l~~~~-v~---~~~~~~~~~~~l~-~~~da~~~~~~~ 194 (294)
T PF04392_consen 160 GIELVEIP-VP---SSEDLEQALEALA-EKVDALYLLPDN 194 (294)
T ss_dssp T-EEEEEE-ES---SGGGHHHHHHHHC-TT-SEEEE-S-H
T ss_pred CCEEEEEe-cC---cHhHHHHHHHHhh-ccCCEEEEECCc
Confidence 99986543 32 3567888888875 567888887654
No 329
>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=78.82 E-value=14 Score=40.33 Aligned_cols=92 Identities=14% Similarity=0.090 Sum_probs=64.0
Q ss_pred HHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeCh-
Q 003054 47 GAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLP- 125 (852)
Q Consensus 47 ~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~- 125 (852)
..+.+.++.+|.+++.+++....+. ...+.+.+.|++. .++.......++.+.++....+..+++.++|+||-.+.+
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 3466677888999999998444433 6777888888876 655444344444567788888899998999999876544
Q ss_pred -hhHHHHHHHHHHcCC
Q 003054 126 -SLGSRIFEKANEIGL 140 (852)
Q Consensus 126 -~~~~~i~~~a~~~G~ 140 (852)
-|+.+++......|+
T Consensus 90 ~~D~aK~ia~~~~~~~ 105 (332)
T cd07766 90 TLDTAKAVAALLNRGL 105 (332)
T ss_pred HHHHHHHHHHHhcCCC
Confidence 466666655543343
No 330
>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=78.66 E-value=35 Score=36.43 Aligned_cols=128 Identities=7% Similarity=0.018 Sum_probs=74.4
Q ss_pred HHhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHcCCc-EEEEEEEe--CCcccccHHHHHHHHH
Q 003054 7 IQLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAFGWR-EAVPIYVD--NQYGEEMIPSLTDALQ 83 (852)
Q Consensus 7 ~~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~gw~-~vaii~~d--~~~G~~~~~~l~~~l~ 83 (852)
...+.+.++|+|......+. .+....+..++..-++.+++++.+.|-+ +++++..+ +.......+.++++++
T Consensus 72 l~~~~~~~iPvV~~d~~~~~-----~~~~~~V~~d~~~~g~~~~~~L~~~g~~~~i~~i~g~~~~~~~~~R~~g~~~~~~ 146 (302)
T TIGR02634 72 VQEAKDEGIKVVAYDRLIND-----ADIDFYLSFDNEKVGEMQARAVLEAAPKGNYFLMGGSPTDNNAKLLRGGQMKVLQ 146 (302)
T ss_pred HHHHHHCCCeEEEecCcCCC-----CCccEEEecCHHHHHHHHHHHHHhhCCCCCEEEEeCCCCCcchHHHHHHHHHHHh
Confidence 34456789999987653211 1222335567777778888888666655 78887633 2223334577888887
Q ss_pred hC----CceeeeeeecCCCCChHHHHHHHHHhhc---CCceEEEEEeChhhHHHHHHHHHHcCCc
Q 003054 84 AI----DTRVPYRSVISPLATDDQIEKELYKLFT---MQTRVFILHMLPSLGSRIFEKANEIGLM 141 (852)
Q Consensus 84 ~~----g~~v~~~~~~~~~~~~~d~~~~l~~l~~---~~~~viv~~~~~~~~~~i~~~a~~~G~~ 141 (852)
+. ++++.... +.......+-...+.++.. ..+++|++ .+...+..+++.+++.|+.
T Consensus 147 ~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~ll~~~~~~~~aI~~-~~D~~A~g~~~al~~~g~~ 209 (302)
T TIGR02634 147 PAIDSGDIKIVGDQ-WVDGWLPENALRIMENALTANDNKVDAVVA-SNDATAGGAIQALTAQGLA 209 (302)
T ss_pred hhccCCCeEEecCc-CCCCCCHHHHHHHHHHHHHhCCCCccEEEE-CCCchHHHHHHHHHHCCCC
Confidence 64 35543221 1111122333455666543 24676555 4555677889999999973
No 331
>PLN03192 Voltage-dependent potassium channel; Provisional
Probab=78.65 E-value=3 Score=51.72 Aligned_cols=55 Identities=18% Similarity=0.303 Sum_probs=47.6
Q ss_pred cccchhHHHHHHHhhhcc-cc-ccccchhhHHHHHHHHHHHHHHHHhhhhccceeee
Q 003054 509 QQVGTSFWFSFSTMVFSQ-RE-RVISNLARIVVIVWCFVVLILTQSYTASLTSLLTV 563 (852)
Q Consensus 509 ~~~~~~~~~~~~~l~~~~-~~-~~~s~~~R~v~~~w~~~~lil~~~Yta~L~s~Lt~ 563 (852)
.++..++||++.+|...| +. .|.+...|++.++|+++++++.++..+++++++..
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 356679999999999876 44 67899999999999999999999999999997654
No 332
>PRK15408 autoinducer 2-binding protein lsrB; Provisional
Probab=78.40 E-value=36 Score=37.19 Aligned_cols=128 Identities=4% Similarity=0.023 Sum_probs=67.6
Q ss_pred HHhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHH-c--CCcEEEEEEEeCC--cccccHHHHHHH
Q 003054 7 IQLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKA-F--GWREAVPIYVDNQ--YGEEMIPSLTDA 81 (852)
Q Consensus 7 ~~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~-~--gw~~vaii~~d~~--~G~~~~~~l~~~ 81 (852)
..-+.+.+||+|++.+..+. + ...++-...++...++.+++++.+ + +-.+|+++..... -.....+.+.+.
T Consensus 98 l~~a~~~gIpVV~~d~~~~~--~--~~~~~V~~~~~~~~G~~~~~~l~~~l~~g~gki~il~g~~~~~~~~~r~~g~~~~ 173 (336)
T PRK15408 98 LKRAMQRGVKVLTWDSDTKP--E--CRSYYINQGTPEQLGSMLVEMAAKQVGKDKAKVAFFYSSPTVTDQNQWVKEAKAK 173 (336)
T ss_pred HHHHHHCCCeEEEeCCCCCC--c--cceEEEecCCHHHHHHHHHHHHHHhcCCCCCEEEEEECCCCCccHHHHHHHHHHH
Confidence 34456779999998664321 1 112221112334566666676643 3 4568988873222 223345667777
Q ss_pred HHh--CCceeeeeeecCCCCChHHHHHHHHHhhcCCce--EEEEEeChhhHHHHHHHHHHcCCc
Q 003054 82 LQA--IDTRVPYRSVISPLATDDQIEKELYKLFTMQTR--VFILHMLPSLGSRIFEKANEIGLM 141 (852)
Q Consensus 82 l~~--~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~--viv~~~~~~~~~~i~~~a~~~G~~ 141 (852)
+++ .+++++... +. +.+...-...+.++.+..|| +|+.. ....+...++++++.|..
T Consensus 174 l~~~~p~~~vv~~~-~~-~~d~~~a~~~~~~lL~~~pdi~aI~~~-~~~~~~Ga~~Al~~~g~~ 234 (336)
T PRK15408 174 IAKEHPGWEIVTTQ-FG-YNDATKSLQTAEGILKAYPDLDAIIAP-DANALPAAAQAAENLKRD 234 (336)
T ss_pred HHhhCCCCEEEeec-CC-CCcHHHHHHHHHHHHHHCCCCcEEEEC-CCccHHHHHHHHHhCCCC
Confidence 754 356665332 11 11222223355666655665 54443 333344688888888863
No 333
>PRK09861 cytoplasmic membrane lipoprotein-28; Provisional
Probab=78.02 E-value=50 Score=34.81 Aligned_cols=121 Identities=13% Similarity=0.109 Sum_probs=63.2
Q ss_pred CCCcCCHHHHHhcCCeEEEEe--CchHHHH--HHhcC---------CC---------Ccceeec-CCHhHHHHHhhcccc
Q 003054 567 QPTITDVKMLIKRGDNVGYQK--GSFVLGI--LKQLG---------FD---------ERKLVVY-NSPEDCHELFQKGSV 623 (852)
Q Consensus 567 ~~~i~sl~dL~~~~~~vg~~~--~s~~~~~--l~~~~---------~~---------~~~~~~~-~~~~~~~~~l~~g~~ 623 (852)
...|++++||. .|.+|++.. +...+.+ |+..+ .. +.++... -...+...++.+|.
T Consensus 119 s~~iksl~DL~-~Ga~IAipnd~~n~~ral~lL~~agli~l~~~~g~~~t~~di~~np~~l~~ve~~~~q~~~al~dg~- 196 (272)
T PRK09861 119 SKKIKTVAQIK-EGATVAIPNDPTNLGRALLLLQKEKLITLKEGKGLLPTALDITDNPRHLQIMELEGAQLPRVLDDPK- 196 (272)
T ss_pred ccCCCCHHHcC-CCCEEEEeCCCccHHHHHHHHHHCCCEEEcCCCCCCCCHhHHhcCCCCCEEEEcCHHHhHhhccCcc-
Confidence 34599999995 688999986 3333332 23322 10 1122211 13456788888888
Q ss_pred cCceeEEEechhHHHHHHhhc-C-CceEeecccccccceEEEecCCCCchhhHHHHHHhccccChhHHHHHHH
Q 003054 624 NGGIAAAFDEIPYMKLLIGQY-C-SKYAMIEPKFKTAGFGFVFPLHSPLVHDVSKAILNVTEGDKMKEIEDAW 694 (852)
Q Consensus 624 ~~g~~a~~~~~~~~~~~~~~~-~-~~~~~v~~~~~~~~~~~~~~k~spl~~~in~~il~l~e~G~~~~i~~kw 694 (852)
+++++...+++.- ..- . +.-...+..-......++.+.+..=.+.+.+.+..++....-+.|.++|
T Consensus 197 ---vD~a~i~~~~~~~--ag~~~~~~~l~~e~~~~~~~n~~~~r~~~~~~~~~~~lv~~~~s~~v~~~i~~~~ 264 (272)
T PRK09861 197 ---VDVAIISTTYIQQ--TGLSPVHDSVFIEDKNSPYVNILVAREDNKNAENVKEFLQSYQSPEVAKAAETIF 264 (272)
T ss_pred ---cCEEEEchhHHHH--cCCCcccceeEEcCCCCCeEEEEEEcCCccCCHHHHHHHHHHcCHHHHHHHHHHc
Confidence 8888887666542 111 1 1111122111122234455544334455666666666655555665554
No 334
>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=77.12 E-value=74 Score=30.84 Aligned_cols=69 Identities=12% Similarity=0.051 Sum_probs=43.9
Q ss_pred EeeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCcccEEEeeeeeecCcceeeeccccccccceEEEE
Q 003054 377 GYCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGEFDAVVGDITIVFNRSNYVDFTLPYTESGVSMIV 456 (852)
Q Consensus 377 G~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv 456 (852)
.+-.+++..+.++.+ .+++++.. ++-++++.+|.+|++|+++..... . ...+. +.++....+++++
T Consensus 14 ~~l~~~l~~~~~~~P-~i~l~~~~---------~~~~~~~~~l~~~~~D~~i~~~~~-~--~~~l~-~~~l~~~~~~~~~ 79 (198)
T cd08485 14 HTLPLLLRQLLSVAP-SATVSLTQ---------MSKNRQIEALDAGTIDIGFGRFYP-Y--QEGVV-VRNVTNERLFLGA 79 (198)
T ss_pred HHHHHHHHHHHHhCC-CcEEEEEE---------CCHHHHHHHHHcCCccEEEecCCC-C--CCCeE-EEEeeccceEEEe
Confidence 345678888888876 35555543 245789999999999998863211 1 12232 3566667777666
Q ss_pred Ecc
Q 003054 457 PIK 459 (852)
Q Consensus 457 ~~~ 459 (852)
+..
T Consensus 80 ~~~ 82 (198)
T cd08485 80 QKS 82 (198)
T ss_pred CCC
Confidence 543
No 335
>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=76.89 E-value=14 Score=40.62 Aligned_cols=88 Identities=9% Similarity=0.025 Sum_probs=62.4
Q ss_pred HHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeCh
Q 003054 46 AGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLP 125 (852)
Q Consensus 46 ~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~ 125 (852)
...+.++++.+| +|+.+++....+ ....+.+.+.|++.|+++.....+..+.+.++....+...++.++|+||-.+.+
T Consensus 11 ~~~l~~~~~~~~-~r~liv~d~~~~-~~~~~~v~~~l~~~~~~~~~~~~~~~~p~~~~v~~~~~~~~~~~~d~iiavGGG 88 (345)
T cd08171 11 YKKIPEVCEKYG-KKVVVIGGKTAL-AAAKDKIKAALEQSGIEITDFIWYGGESTYENVERLKKNPAVQEADMIFAVGGG 88 (345)
T ss_pred HHHHHHHHHhcC-CEEEEEeCHHHH-HHHHHHHHHHHHHCCCeEEEEEecCCCCCHHHHHHHHHHHhhcCCCEEEEeCCc
Confidence 355667777788 898888754444 345677888898889877655555556667778888888888999999877654
Q ss_pred --hhHHHHHHHH
Q 003054 126 --SLGSRIFEKA 135 (852)
Q Consensus 126 --~~~~~i~~~a 135 (852)
-|+.+++...
T Consensus 89 s~~D~aK~ia~~ 100 (345)
T cd08171 89 KAIDTVKVLADK 100 (345)
T ss_pred HHHHHHHHHHHH
Confidence 3566665543
No 336
>COG1638 DctP TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]
Probab=76.02 E-value=4.4 Score=44.02 Aligned_cols=101 Identities=12% Similarity=0.215 Sum_probs=67.7
Q ss_pred CcCCHHHHHhcCCeEEEEeCchHHHHHHhcCCCCcceeecCCHhHHHHHhhcccccCceeEEEechhHHH----HHHhhc
Q 003054 569 TITDVKMLIKRGDNVGYQKGSFVLGILKQLGFDERKLVVYNSPEDCHELFQKGSVNGGIAAAFDEIPYMK----LLIGQY 644 (852)
Q Consensus 569 ~i~sl~dL~~~~~~vg~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~----~~~~~~ 644 (852)
||++.+||. |.++=+.........++.++..+..+ ...|.+.+|+.|. +|+.-.....+. |-.++|
T Consensus 158 PI~~peDlk--GlkiRv~~s~~~~~~~~a~GA~P~pm----~f~Evy~aLqtGv----VDGqEnp~~~i~~~k~~EVqky 227 (332)
T COG1638 158 PIKTPEDLK--GLKIRVPQSPLLLAMFKALGANPTPM----PFAEVYTALQTGV----VDGQENPLSNIYSAKLYEVQKY 227 (332)
T ss_pred CCCChHHhC--CCeeecCCCHHHHHHHHHcCCCCCCC----CHHHHHHHHHcCC----cccccCCHHHHhhccHHHHhHH
Confidence 799999997 99998988888888888887765432 4568899999999 888776654322 112233
Q ss_pred CCceEeecccccccceEEEecCC--CCchhhHHHHHHhcccc
Q 003054 645 CSKYAMIEPKFKTAGFGFVFPLH--SPLVHDVSKAILNVTEG 684 (852)
Q Consensus 645 ~~~~~~v~~~~~~~~~~~~~~k~--spl~~~in~~il~l~e~ 684 (852)
+. +.+ ....++.+.+.+. .-|-+...++|++..+.
T Consensus 228 ~t---~tn--H~~~~~~~~~s~~~w~~L~~e~q~il~~aa~e 264 (332)
T COG1638 228 LT---LTN--HIYLPLAVLVSKAFWDSLPEEDQTILLEAAKE 264 (332)
T ss_pred hh---hcc--ccccceeeEEcHHHHhcCCHHHHHHHHHHHHH
Confidence 21 121 2334556667765 33777777777766544
No 337
>PF12683 DUF3798: Protein of unknown function (DUF3798); InterPro: IPR024258 This entry represents functionally uncharacterised proteins that are found in bacteria. They are typically between 247 and 417 amino acids in length. Most of the proteins in this entry have an N-terminal lipoprotein attachment site. These proteins have distant similarity to periplasmic ligand binding families suggesting that this family has a similar role.; PDB: 3QI7_A.
Probab=75.85 E-value=79 Score=32.79 Aligned_cols=168 Identities=15% Similarity=0.194 Sum_probs=86.2
Q ss_pred HHHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHHHHH---hCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEE
Q 003054 45 QAGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTDALQ---AIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFIL 121 (852)
Q Consensus 45 ~~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~~l~---~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~ 121 (852)
.-++.=+++++||-..|.-++--+.|..+.-..+.+.+. ...++..... .......+.++++|...||++++
T Consensus 18 ~~r~Ae~l~~~Yg~~~I~h~tyPdnf~~e~EttIskI~~lAdDp~mKaIVv~-----q~vpGt~~af~kIkekRpDIl~i 92 (275)
T PF12683_consen 18 EYRGAEELIKKYGDVMIKHVTYPDNFMSEQETTISKIVSLADDPDMKAIVVS-----QAVPGTAEAFRKIKEKRPDILLI 92 (275)
T ss_dssp HHHHHHHHHHHHHHHEEEEEE--TTGGGCHHHHHHHHHGGGG-TTEEEEEEE------SS---HHHHHHHHHH-TTSEEE
T ss_pred HHHHHHHHHHHhCcceEEEEeCCCcccchHHHHHHHHHHhccCCCccEEEEe-----CCCcchHHHHHHHHhcCCCeEEE
Confidence 334445567788865666666667788776666666665 3444433222 12334678899999999999888
Q ss_pred EeChh--------------------hHHHHHHHHHHcCCcccceEEE-EcCccccccccCCchhhcc---cceEEEE--E
Q 003054 122 HMLPS--------------------LGSRIFEKANEIGLMNKGCVWI-MTDGMTNLLRTLEPSVIDS---MQGVIGV--G 175 (852)
Q Consensus 122 ~~~~~--------------------~~~~i~~~a~~~G~~~~~~vwi-~~~~~~~~~~~~~~~~~~~---~~gv~~~--~ 175 (852)
.+.+. .+..+...|+++|- +.+|.+ ....+....-.......+. -.|+-.+ .
T Consensus 93 a~~~~EDp~~i~~~aDi~~~~D~~~~G~~i~~~Ak~mGA--ktFVh~sfprhms~~~l~~Rr~~M~~~C~~lGi~fv~~t 170 (275)
T PF12683_consen 93 AGEPHEDPEVISSAADIVVNPDEISRGYTIVWAAKKMGA--KTFVHYSFPRHMSYELLARRRDIMEEACKDLGIKFVEVT 170 (275)
T ss_dssp ESS--S-HHHHHHHSSEEEE--HHHHHHHHHHHHHHTT---S-EEEEEETTGGGSHHHHHHHHHHHHHHHHCT--EEEEE
T ss_pred cCCCcCCHHHHhhccCeEeccchhhccHHHHHHHHHcCC--ceEEEEechhhcchHHHHHHHHHHHHHHHHcCCeEEEEe
Confidence 87642 34678889999985 667766 4444442211100001111 1233222 2
Q ss_pred ecCCCC----hHHHHHHH----HHHHhccccCCCCcccccchhhHhHhhHHHHHHHHHHH
Q 003054 176 PHVPKT----KALENFRV----RWKRNFLQENPSIVDVELNIFGLLAYDATRALAEAVEK 227 (852)
Q Consensus 176 ~~~~~~----~~~~~F~~----~~~~~~~~~~~~~~~~~~~~~a~~aYDAv~~lA~Al~~ 227 (852)
..+|.+ ...+.|.. +|-++||. ....|+-...-.--+|.++++.
T Consensus 171 aPDP~sd~gv~gaqqfIlE~vp~~i~kYGk--------dtaff~TN~a~~epllk~~~~~ 222 (275)
T PF12683_consen 171 APDPTSDVGVAGAQQFILEDVPKWIKKYGK--------DTAFFCTNDAMTEPLLKQALEY 222 (275)
T ss_dssp E---SSTCHHHHHHHHHHHHHHHHHHHH-S----------EEEESSHHHHHHHHHHHHHH
T ss_pred CCCCCCCCCcHHHHHHHHHHHHHHHHHhCC--------ceeEEecCccccHHHHHHHHHc
Confidence 334432 56777754 69999987 3444444333333456666665
No 338
>PRK10355 xylF D-xylose transporter subunit XylF; Provisional
Probab=75.76 E-value=35 Score=37.07 Aligned_cols=127 Identities=6% Similarity=-0.004 Sum_probs=75.4
Q ss_pred HhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEe---CCcccccHHHHHHHHHh
Q 003054 8 QLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVD---NQYGEEMIPSLTDALQA 84 (852)
Q Consensus 8 ~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d---~~~G~~~~~~l~~~l~~ 84 (852)
..+.+.++|+|...... .+. +....+..++...++.++++|...|-++++++... ...+....+.+++++++
T Consensus 100 ~~~~~~~iPvV~id~~~---~~~--~~~~~V~~D~~~~g~~a~~~L~~~g~~~i~~i~~g~~~~~~~~~R~~gf~~~l~~ 174 (330)
T PRK10355 100 KEAKQEGIKVLAYDRMI---NNA--DIDFYISFDNEKVGELQAKALVDKVPQGNYFLMGGSPVDNNAKLFRAGQMKVLKP 174 (330)
T ss_pred HHHHHCCCeEEEECCCC---CCC--CccEEEecCHHHHHHHHHHHHHHhcCCCCEEEEeCCCCCccHHHHHHHHHHHHhh
Confidence 44567789999975432 111 12234677888888999999877787887765432 22334557778888876
Q ss_pred C---C-ceeeeeeecCCCCChHHHHHHHHHhh-c--CCceEEEEEeChhhHHHHHHHHHHcCCc
Q 003054 85 I---D-TRVPYRSVISPLATDDQIEKELYKLF-T--MQTRVFILHMLPSLGSRIFEKANEIGLM 141 (852)
Q Consensus 85 ~---g-~~v~~~~~~~~~~~~~d~~~~l~~l~-~--~~~~viv~~~~~~~~~~i~~~a~~~G~~ 141 (852)
. | +++....... ..+..+-...+.++. + ..+++|+. .+...+..+++.++++|+.
T Consensus 175 ~~~~~~i~~~~~~~~~-~~~~~~~~~~~~~lL~~~~~~~~aI~~-~nD~~A~g~l~al~~~g~~ 236 (330)
T PRK10355 175 YIDSGKIKVVGDQWVD-GWLPENALKIMENALTANNNKIDAVVA-SNDATAGGAIQALSAQGLS 236 (330)
T ss_pred hccCCCeEEecccCCC-CCCHHHHHHHHHHHHHhCCCCccEEEE-CCCchHHHHHHHHHHCCCC
Confidence 3 4 4432221111 111222234444443 2 34676544 5666777899999999985
No 339
>PRK10094 DNA-binding transcriptional activator AllS; Provisional
Probab=75.72 E-value=1.2e+02 Score=32.49 Aligned_cols=69 Identities=9% Similarity=0.158 Sum_probs=45.6
Q ss_pred eHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCcccEEEeeeeeecCcceeeeccccccccceEEEEEc
Q 003054 379 CVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGEFDAVVGDITIVFNRSNYVDFTLPYTESGVSMIVPI 458 (852)
Q Consensus 379 ~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv~~ 458 (852)
-.+++..+.++.+. +++.+.. ++..++.++|.+|++|++++... .......+. ..++....++++++.
T Consensus 108 l~~~l~~~~~~~P~-i~l~l~~---------~~~~~~~~~l~~g~~D~~i~~~~-~~~~~~~l~-~~~l~~~~~~~v~~~ 175 (308)
T PRK10094 108 VAQLLAWLNERYPF-TQFHISR---------QIYMGVWDSLLYEGFSLAIGVTG-TEALANTFS-LDPLGSVQWRFVMAA 175 (308)
T ss_pred HHHHHHHHHHhCCC-cEEEEEe---------ehhhhHHHHHhCCCccEEEeccc-CccccCCee-EEEecceeEEEEECC
Confidence 35788899888884 5665544 24678899999999999886211 111122233 357777888888875
Q ss_pred c
Q 003054 459 K 459 (852)
Q Consensus 459 ~ 459 (852)
.
T Consensus 176 ~ 176 (308)
T PRK10094 176 D 176 (308)
T ss_pred C
Confidence 4
No 340
>PRK09986 DNA-binding transcriptional activator XapR; Provisional
Probab=75.47 E-value=1.1e+02 Score=32.14 Aligned_cols=71 Identities=17% Similarity=0.123 Sum_probs=46.0
Q ss_pred EeeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCcccEEEeeeeeecCcceeeeccccccccceEEEE
Q 003054 377 GYCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGEFDAVVGDITIVFNRSNYVDFTLPYTESGVSMIV 456 (852)
Q Consensus 377 G~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv 456 (852)
.+..++++.+.++.+- +.++.... +-++++.+|.+|++|+++.... .......+.+ .|+....+++++
T Consensus 110 ~~l~~~l~~f~~~~p~-i~l~i~~~---------~~~~~~~~l~~g~~D~~i~~~~-~~~~~~~l~~-~~l~~~~~~~v~ 177 (294)
T PRK09986 110 GRLRPAMRHFLKENPN-VEWLLREL---------SPSMQMAALERRELDAGIWRMA-DLEPNPGFTS-RRLHESAFAVAV 177 (294)
T ss_pred HHHHHHHHHHHHhCCC-eEEEEEeC---------CHHHHHHHHHcCCCCEEEecCC-ccCCCCCeEE-EEeecccEEEEE
Confidence 3446778888888772 45555432 3468899999999999874211 0112233443 677778888888
Q ss_pred Ecc
Q 003054 457 PIK 459 (852)
Q Consensus 457 ~~~ 459 (852)
+..
T Consensus 178 ~~~ 180 (294)
T PRK09986 178 PEE 180 (294)
T ss_pred cCC
Confidence 865
No 341
>PRK09906 DNA-binding transcriptional regulator HcaR; Provisional
Probab=74.58 E-value=97 Score=32.74 Aligned_cols=68 Identities=15% Similarity=0.141 Sum_probs=47.1
Q ss_pred eeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCcccEEEeeeeeecCcceeeeccccccccceEEEEE
Q 003054 378 YCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGEFDAVVGDITIVFNRSNYVDFTLPYTESGVSMIVP 457 (852)
Q Consensus 378 ~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv~ 457 (852)
+..+++..+.++.+ .+.+.+.. ++..+++..|.+|++|+++.... .....+. +.|+....++++++
T Consensus 104 ~l~~~~~~~~~~~p-~v~i~~~~---------~~~~~~~~~l~~~~~D~~i~~~~---~~~~~l~-~~~l~~~~~~~v~~ 169 (296)
T PRK09906 104 LLPKVLPMFRLRHP-DTLIELVS---------LITTQQEEKLRRGELDVGFMRHP---VYSDEID-YLELLDEPLVVVLP 169 (296)
T ss_pred HHHHHHHHHHHHCC-CeEEEEEe---------CCcHHHHHHHHcCCeeEEEecCC---CCCCCce-EEEEecccEEEEec
Confidence 34578888888876 34555443 23578999999999999986332 2233344 36888889999988
Q ss_pred cc
Q 003054 458 IK 459 (852)
Q Consensus 458 ~~ 459 (852)
+.
T Consensus 170 ~~ 171 (296)
T PRK09906 170 VD 171 (296)
T ss_pred CC
Confidence 55
No 342
>PRK03692 putative UDP-N-acetyl-D-mannosaminuronic acid transferase; Provisional
Probab=74.18 E-value=26 Score=36.19 Aligned_cols=90 Identities=8% Similarity=0.010 Sum_probs=59.0
Q ss_pred chhHHHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHHHHHh-CCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEE
Q 003054 42 DSSQAGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTDALQA-IDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFI 120 (852)
Q Consensus 42 d~~~~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~~l~~-~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv 120 (852)
.......+.+.....| .+|.++..+.+ .++.+.+.+++ .|++|+....=.. +.++....+.+|.+++||+++
T Consensus 90 G~dl~~~ll~~~~~~~-~~v~llG~~~~----v~~~a~~~l~~~y~l~i~g~~~Gyf--~~~e~~~i~~~I~~s~~dil~ 162 (243)
T PRK03692 90 GADLWEALMARAGKEG-TPVFLVGGKPE----VLAQTEAKLRTQWNVNIVGSQDGYF--TPEQRQALFERIHASGAKIVT 162 (243)
T ss_pred hHHHHHHHHHHHHhcC-CeEEEECCCHH----HHHHHHHHHHHHhCCEEEEEeCCCC--CHHHHHHHHHHHHhcCCCEEE
Confidence 3445556666666666 68888875443 45555555544 3788765432122 244566789999999999999
Q ss_pred EEeChhhHHHHHHHHHHc
Q 003054 121 LHMLPSLGSRIFEKANEI 138 (852)
Q Consensus 121 ~~~~~~~~~~i~~~a~~~ 138 (852)
+.+..+.--.++...++.
T Consensus 163 VglG~PkQE~~~~~~~~~ 180 (243)
T PRK03692 163 VAMGSPKQEIFMRDCRLV 180 (243)
T ss_pred EECCCcHHHHHHHHHHHh
Confidence 999887777777665544
No 343
>PF13685 Fe-ADH_2: Iron-containing alcohol dehydrogenase; PDB: 3CE9_C.
Probab=73.80 E-value=21 Score=37.03 Aligned_cols=99 Identities=16% Similarity=0.178 Sum_probs=57.3
Q ss_pred HHHHHHHHcCCcEEEEEEEeCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChh-
Q 003054 48 AITAIIKAFGWREAVPIYVDNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPS- 126 (852)
Q Consensus 48 aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~- 126 (852)
.+.+++++++.+++.++...+.| ....+.+.+.|+..|+++.........++..+......+++..++|+|+-.+.+.
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 45677888888999999865544 3355678888999999887443222234455566667777778899998888764
Q ss_pred -hHHHHHHHHHHcCCcccceEEEEcCc
Q 003054 127 -LGSRIFEKANEIGLMNKGCVWIMTDG 152 (852)
Q Consensus 127 -~~~~i~~~a~~~G~~~~~~vwi~~~~ 152 (852)
|..+.+ |.++|. .|+-+-|..
T Consensus 88 ~D~~K~~--A~~~~~---p~isVPTa~ 109 (250)
T PF13685_consen 88 IDIAKYA--AFELGI---PFISVPTAA 109 (250)
T ss_dssp HHHHHHH--HHHHT-----EEEEES--
T ss_pred HHHHHHH--HHhcCC---CEEEecccc
Confidence 334443 556664 466665543
No 344
>PLN02245 ATP phosphoribosyl transferase
Probab=73.36 E-value=28 Score=38.38 Aligned_cols=102 Identities=17% Similarity=0.069 Sum_probs=59.9
Q ss_pred cCCHHHHHh-------cCCeEEEEeCchHHHHHHhcCCCCcceeecC-CHhHHHHHhhcccccCceeEEEechhHHHHHH
Q 003054 570 ITDVKMLIK-------RGDNVGYQKGSFVLGILKQLGFDERKLVVYN-SPEDCHELFQKGSVNGGIAAAFDEIPYMKLLI 641 (852)
Q Consensus 570 i~sl~dL~~-------~~~~vg~~~~s~~~~~l~~~~~~~~~~~~~~-~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~ 641 (852)
+++++||.. ..++|+..--...+.||++.+.....++... +.| . +-..|- .|++++-.....-+.
T Consensus 179 ~~s~~dL~g~~~~~~~~~~RIATkYp~ltr~ff~~~Gv~~v~Iv~l~GAvE-~--AP~lGl----ADaIvDIVsTGtTLr 251 (403)
T PLN02245 179 INSLKELAQMPQWTEERPLRVVTGFTYLGPKFMKDNGFKHVTFSTADGALE-A--APAMGI----ADAILDLVSSGTTLR 251 (403)
T ss_pred cCCHHHhcccccccccCceEEEeCCHHHHHHHHHHcCCCeEEEEECcCcee-c--ccccCc----hhhhcchhccHHHHH
Confidence 788999973 1168988777888999999887544444333 443 2 344455 666666544444443
Q ss_pred hhcCCceEeec-ccccccceEEEecCCCC-----chhhHHHHHHhc
Q 003054 642 GQYCSKYAMIE-PKFKTAGFGFVFPLHSP-----LVHDVSKAILNV 681 (852)
Q Consensus 642 ~~~~~~~~~v~-~~~~~~~~~~~~~k~sp-----l~~~in~~il~l 681 (852)
.+ ++.+++ +.+....-.++.++++. -.+.+.+.+.+|
T Consensus 252 aN---gLk~i~~~~Il~S~A~LIan~~sl~~~~~~~~~i~~ll~rl 294 (403)
T PLN02245 252 EN---NLKEIEGGVVLESQAVLVASRRALLERKGALEVVHEILERL 294 (403)
T ss_pred HC---CCEEccCceEEEEEEEEEEecchhhcchhHHHHHHHHHHHH
Confidence 33 366775 45555556666677754 222444444444
No 345
>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=73.35 E-value=23 Score=39.34 Aligned_cols=84 Identities=12% Similarity=0.069 Sum_probs=60.5
Q ss_pred HHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeCh-
Q 003054 47 GAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLP- 125 (852)
Q Consensus 47 ~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~- 125 (852)
..+.++++.+| +++.|++..... ..+.+.+.|++.|+++.... +..+.+.+++...+..++..++|+||-.+.+
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 45667777776 899888744333 67778889999998865443 4445667788888889999999999887654
Q ss_pred -hhHHHHHHHH
Q 003054 126 -SLGSRIFEKA 135 (852)
Q Consensus 126 -~~~~~i~~~a 135 (852)
-|+.+++...
T Consensus 87 ~~D~aK~ia~~ 97 (374)
T cd08183 87 VIDAGKAIAAL 97 (374)
T ss_pred HHHHHHHHHHH
Confidence 3666665443
No 346
>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=73.31 E-value=18 Score=37.74 Aligned_cols=85 Identities=15% Similarity=0.171 Sum_probs=56.3
Q ss_pred EEEEEEE----eCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHH
Q 003054 60 EAVPIYV----DNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKA 135 (852)
Q Consensus 60 ~vaii~~----d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a 135 (852)
||+++++ |..|.....+.+.++-++.|+++.+.+..+ +.+++...+.++.+.++|+||.++. .....+.+.|
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 4777774 445666667888888888899988776542 3678999999999899999998432 2223334444
Q ss_pred HHcCCcccceEEEEcCc
Q 003054 136 NEIGLMNKGCVWIMTDG 152 (852)
Q Consensus 136 ~~~G~~~~~~vwi~~~~ 152 (852)
++- |+..|+..++
T Consensus 77 ~~~----p~~~F~~~d~ 89 (258)
T cd06353 77 KEY----PDVKFEHCSG 89 (258)
T ss_pred HHC----CCCEEEECCC
Confidence 443 3444555443
No 347
>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=72.64 E-value=32 Score=33.61 Aligned_cols=88 Identities=5% Similarity=-0.102 Sum_probs=60.5
Q ss_pred chhHHHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHHHHHhC--CceeeeeeecCCCCChHHHHHHHHHhhcCCceEE
Q 003054 42 DSSQAGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTDALQAI--DTRVPYRSVISPLATDDQIEKELYKLFTMQTRVF 119 (852)
Q Consensus 42 d~~~~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~~l~~~--g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vi 119 (852)
....+..+.+.....+ .+|.++.... +.++.+.+.+++. |++|+....+ .++++-...+.+|.+++||++
T Consensus 33 G~dl~~~l~~~~~~~~-~~vfllG~~~----~v~~~~~~~l~~~yP~l~i~g~~g~---f~~~~~~~i~~~I~~s~~dil 104 (177)
T TIGR00696 33 GPDLMEELCQRAGKEK-LPIFLYGGKP----DVLQQLKVKLIKEYPKLKIVGAFGP---LEPEERKAALAKIARSGAGIV 104 (177)
T ss_pred hHHHHHHHHHHHHHcC-CeEEEECCCH----HHHHHHHHHHHHHCCCCEEEEECCC---CChHHHHHHHHHHHHcCCCEE
Confidence 3456666666666666 5888887443 3566666666664 7887765222 234455678899999999999
Q ss_pred EEEeChhhHHHHHHHHHH
Q 003054 120 ILHMLPSLGSRIFEKANE 137 (852)
Q Consensus 120 v~~~~~~~~~~i~~~a~~ 137 (852)
++.+..+.-..++.+.++
T Consensus 105 ~VglG~PkQE~~~~~~~~ 122 (177)
T TIGR00696 105 FVGLGCPKQEIWMRNHRH 122 (177)
T ss_pred EEEcCCcHhHHHHHHhHH
Confidence 999888877777765544
No 348
>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=72.54 E-value=14 Score=38.51 Aligned_cols=77 Identities=6% Similarity=0.128 Sum_probs=55.7
Q ss_pred EEEEEE--eCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeC-hhhHHHHHHHHHH
Q 003054 61 AVPIYV--DNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHML-PSLGSRIFEKANE 137 (852)
Q Consensus 61 vaii~~--d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~-~~~~~~i~~~a~~ 137 (852)
|+++.. ++.|.....+.+.+++++.|.++..... ..+.......+..+.+.++|.||+... ......+++++++
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 566654 5778888999999999999998775421 223444566777777789999998754 3344667788888
Q ss_pred cCC
Q 003054 138 IGL 140 (852)
Q Consensus 138 ~G~ 140 (852)
.|+
T Consensus 79 ~~i 81 (273)
T cd06305 79 AGI 81 (273)
T ss_pred cCC
Confidence 886
No 349
>PRK09423 gldA glycerol dehydrogenase; Provisional
Probab=72.33 E-value=14 Score=41.03 Aligned_cols=85 Identities=13% Similarity=0.067 Sum_probs=61.6
Q ss_pred HHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeCh
Q 003054 46 AGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLP 125 (852)
Q Consensus 46 ~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~ 125 (852)
...+.+.++.+| +++.+|+....+ ....+.+.+.|++.|+++.+. .+..+.+.+++...+..+++.++|+||-.+.+
T Consensus 18 ~~~l~~~l~~~g-~~~livtd~~~~-~~~~~~v~~~l~~~~~~~~~~-~~~~ep~~~~v~~~~~~~~~~~~d~IIavGGG 94 (366)
T PRK09423 18 LARLGEYLKPLG-KRALVIADEFVL-GIVGDRVEASLKEAGLTVVFE-VFNGECSDNEIDRLVAIAEENGCDVVIGIGGG 94 (366)
T ss_pred HHHHHHHHHHcC-CEEEEEEChhHH-HHHHHHHHHHHHhCCCeEEEE-EeCCCCCHHHHHHHHHHHHhcCCCEEEEecCh
Confidence 455667788889 999888844444 336778888899889887543 45556667788888888988999999877654
Q ss_pred --hhHHHHHH
Q 003054 126 --SLGSRIFE 133 (852)
Q Consensus 126 --~~~~~i~~ 133 (852)
-|+.+++.
T Consensus 95 sv~D~aK~iA 104 (366)
T PRK09423 95 KTLDTAKAVA 104 (366)
T ss_pred HHHHHHHHHH
Confidence 35666655
No 350
>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=72.20 E-value=41 Score=34.69 Aligned_cols=120 Identities=8% Similarity=0.029 Sum_probs=76.3
Q ss_pred HhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHH--cCCcEEEEEEEeC-CcccccHHHHHHHHHh
Q 003054 8 QLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKA--FGWREAVPIYVDN-QYGEEMIPSLTDALQA 84 (852)
Q Consensus 8 ~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~--~gw~~vaii~~d~-~~G~~~~~~l~~~l~~ 84 (852)
...++.++|++...-..+. ....++ ...++..-+..+++.+.. .|-+++++|.... ..++...+.+++++++
T Consensus 70 ~~~~~~~~PvV~i~~~~~~--~~~~~~---V~~D~~~~~~~a~~~L~~~~~G~~~Ia~i~~~~~~~~~~R~~gf~~~l~~ 144 (247)
T cd06276 70 LLKKIPKEKLLILDHSIPE--GGEYSS---VAQDFEKAIYNALQEGLEKLKKYKKLILVFPNKTAIPKEIKRGFERFCKD 144 (247)
T ss_pred HHhccCCCCEEEEcCcCCC--CCCCCe---EEEccHHHHHHHHHHHHHHhcCCCEEEEEecCccHhHHHHHHHHHHHHHH
Confidence 3445567888876543211 112232 445666777778888877 8999999997432 4566778899999999
Q ss_pred CCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHcCCcccceE
Q 003054 85 IDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEIGLMNKGCV 146 (852)
Q Consensus 85 ~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~~v 146 (852)
.|++... .. . ..+ ... .++++ |++++...+..+++.+++.|+..|+-+
T Consensus 145 ~g~~~~~---~~-~--~~~------~~~-~~~~a-i~~~~d~~A~g~~~~l~~~g~~iP~di 192 (247)
T cd06276 145 YNIETEI---IN-D--YEN------REI-EKGDL-YIILSDTDLVFLIKKARESGLLLGKDI 192 (247)
T ss_pred cCCCccc---cc-c--cch------hhc-cCCcE-EEEeCHHHHHHHHHHHHHcCCcCCcee
Confidence 9986532 11 1 111 001 13465 555677788999999999998666443
No 351
>PRK15408 autoinducer 2-binding protein lsrB; Provisional
Probab=70.84 E-value=16 Score=39.86 Aligned_cols=82 Identities=10% Similarity=0.024 Sum_probs=60.7
Q ss_pred CCcEEEEEE--EeCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChh-hHHHHHH
Q 003054 57 GWREAVPIY--VDNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPS-LGSRIFE 133 (852)
Q Consensus 57 gw~~vaii~--~d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~-~~~~i~~ 133 (852)
.-.+++++. .+++|.....+.+++++++.|.++.... +...+...-...+..+.+.++|.|++....+ .....++
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 346888888 4678888899999999999999886532 2222333345677888889999999975443 3477889
Q ss_pred HHHHcCC
Q 003054 134 KANEIGL 140 (852)
Q Consensus 134 ~a~~~G~ 140 (852)
+|++.|.
T Consensus 100 ~a~~~gI 106 (336)
T PRK15408 100 RAMQRGV 106 (336)
T ss_pred HHHHCCC
Confidence 9999986
No 352
>PRK11716 DNA-binding transcriptional regulator IlvY; Provisional
Probab=70.73 E-value=1.1e+02 Score=31.44 Aligned_cols=69 Identities=22% Similarity=0.218 Sum_probs=44.4
Q ss_pred eeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCcccEEEeeeeeecCcceeeeccccccccceEEEEE
Q 003054 378 YCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGEFDAVVGDITIVFNRSNYVDFTLPYTESGVSMIVP 457 (852)
Q Consensus 378 ~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv~ 457 (852)
+..+++..+.++.+- +++++.. ++..+++.+|.+|++|+++..... .....+. ..+.....++++++
T Consensus 81 ~~~~~l~~~~~~~p~-i~l~i~~---------~~~~~~~~~l~~~~~D~~i~~~~~--~~~~~~~-~~~l~~~~~~~v~~ 147 (269)
T PRK11716 81 HLPPILDRFRAEHPL-VEIKLTT---------GDAADAVEKVQSGEADLAIAAKPE--TLPASVA-FSPIDEIPLVLIAP 147 (269)
T ss_pred HHHHHHHHHHHHCCC-eEEEEEE---------CCHHHHHHHHHCCCccEEEEecCC--CCCcceE-EEEcccceEEEEEc
Confidence 456888888888762 4555544 246789999999999999753221 1111222 35666777777776
Q ss_pred cc
Q 003054 458 IK 459 (852)
Q Consensus 458 ~~ 459 (852)
..
T Consensus 148 ~~ 149 (269)
T PRK11716 148 AL 149 (269)
T ss_pred CC
Confidence 44
No 353
>KOG1419 consensus Voltage-gated K+ channel KCNQ [Inorganic ion transport and metabolism]
Probab=70.51 E-value=5.7 Score=44.60 Aligned_cols=89 Identities=15% Similarity=0.262 Sum_probs=69.5
Q ss_pred hhHHHHHHHHHHHHHhhhhheecccCCCCCCCcccccchhHHHHHHHhhhcc--ccccccchhhHHHHHHHHHHHHHHHH
Q 003054 475 WDLWVTCFCFFIFIGFVVWVLEHRVNEDFRGPAGQQVGTSFWFSFSTMVFSQ--RERVISNLARIVVIVWCFVVLILTQS 552 (852)
Q Consensus 475 ~~lW~~i~~~~i~~~~v~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~--~~~~~s~~~R~v~~~w~~~~lil~~~ 552 (852)
...|..-++.+++.++++|+.|.....+=......++-.++||..-++...| ...|..+.+|++..++.++++-+.+.
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 3678888899999999999999883222111122367889999999999877 45789999999999999999888888
Q ss_pred hhhhccceeee
Q 003054 553 YTASLTSLLTV 563 (852)
Q Consensus 553 Yta~L~s~Lt~ 563 (852)
=.+-|-|=++.
T Consensus 314 PAGILGSGfAL 324 (654)
T KOG1419|consen 314 PAGILGSGFAL 324 (654)
T ss_pred ccccccchhhh
Confidence 77777776554
No 354
>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=70.39 E-value=14 Score=38.10 Aligned_cols=76 Identities=14% Similarity=0.121 Sum_probs=56.7
Q ss_pred EEEEEE--eCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHc
Q 003054 61 AVPIYV--DNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEI 138 (852)
Q Consensus 61 vaii~~--d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~ 138 (852)
++++.. +++|.....+.+++++++.|+++.... .+.+.......++++.+.++|+|++......... ++.+.+.
T Consensus 2 i~~v~~~~~~~~~~~~~~g~~~~~~~~g~~~~~~~---~~~~~~~~~~~~~~~~~~~~d~iii~~~~~~~~~-~~~~~~~ 77 (264)
T cd06267 2 IGVIVPDISNPFFAELLRGIEEAAREAGYSVLLCN---SDEDPEKEREALELLLSRRVDGIILAPSRLDDEL-LEELAAL 77 (264)
T ss_pred EEEEECCCCCHHHHHHHHHHHHHHHHcCCEEEEEc---CCCCHHHHHHHHHHHHHcCcCEEEEecCCcchHH-HHHHHHc
Confidence 566663 478899999999999999998876442 2223445667788888889999998877665555 7778888
Q ss_pred CC
Q 003054 139 GL 140 (852)
Q Consensus 139 G~ 140 (852)
|+
T Consensus 78 ~i 79 (264)
T cd06267 78 GI 79 (264)
T ss_pred CC
Confidence 86
No 355
>PRK11119 proX glycine betaine transporter periplasmic subunit; Provisional
Probab=70.05 E-value=30 Score=37.67 Aligned_cols=63 Identities=11% Similarity=0.155 Sum_probs=42.5
Q ss_pred ccCCCceEEEeeecccCcccceEEeeCCCCCCCceEEEeeHHHHHHHHHHCCCcc-ceEEEecCCCCCCCCCChhHHHHH
Q 003054 340 VPTNEKKLRIGVPVKKGFSDFVNVTIDPKTQEPTSVTGYCVDVFKAVIQELPYAV-AYDFVPYGQPDGSSSGSYNDLVYQ 418 (852)
Q Consensus 340 ~~~~~~~lrv~v~~~~~~~~~~~~~~d~~~~~~~~~~G~~~dl~~~ia~~l~~~~-~~~~~~~~~~~g~~ngs~~~li~~ 418 (852)
+|.+++++++|+. +|.. . -+.-.|++.+.+.+||++ +++ +. +-.-+...
T Consensus 24 ~~~~~~~V~~~~~---~W~~------------~----~~~t~v~~~iLe~~GY~V~e~~--~~---------~~~~~~~a 73 (331)
T PRK11119 24 LPGKGITVQPAQS---TIAE------------E----TFQTLLVSRALEKLGYDVNKPK--EV---------DYNVFYTS 73 (331)
T ss_pred CCCCCeEEEEeec---CccH------------H----HHHHHHHHHHHHHcCCceeeec--cc---------CcHHHHHH
Confidence 3567889999887 2321 1 233478888888899865 443 32 23677899
Q ss_pred HhcCcccEEEeeee
Q 003054 419 VFLGEFDAVVGDIT 432 (852)
Q Consensus 419 l~~g~~D~~~g~~~ 432 (852)
|.+|++|+.+..-.
T Consensus 74 la~GdiDv~~~~W~ 87 (331)
T PRK11119 74 IANGDATFTAVNWF 87 (331)
T ss_pred HHcCCCeEehhhcc
Confidence 99999999775433
No 356
>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=69.38 E-value=1.1e+02 Score=29.33 Aligned_cols=69 Identities=10% Similarity=0.120 Sum_probs=46.0
Q ss_pred EeeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCcccEEEeeeeeecCcceeeeccccccccceEEEE
Q 003054 377 GYCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGEFDAVVGDITIVFNRSNYVDFTLPYTESGVSMIV 456 (852)
Q Consensus 377 G~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv 456 (852)
++-.+++..+.++.+ .++++... +...++..+|.+|++|+++..... ....+. +.++....+++++
T Consensus 14 ~~l~~~i~~~~~~~P-~v~l~i~~---------~~~~~~~~~l~~~~~Dl~i~~~~~---~~~~~~-~~~l~~~~~~~v~ 79 (198)
T cd08446 14 DTVPRLLRAFLTARP-DVTVSLHN---------MTKDEQIEALRAGRIHIGFGRFYP---VEPDIA-VENVAQERLYLAV 79 (198)
T ss_pred HHHHHHHHHHHHHCC-CeEEEEee---------CCHHHHHHHHHCCCccEEEEecCC---CCCCce-eEEeeeccEEEEE
Confidence 345678888888877 35555543 357789999999999999853211 112222 4567777888888
Q ss_pred Ecc
Q 003054 457 PIK 459 (852)
Q Consensus 457 ~~~ 459 (852)
+..
T Consensus 80 ~~~ 82 (198)
T cd08446 80 PKS 82 (198)
T ss_pred eCC
Confidence 754
No 357
>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=68.72 E-value=1.1e+02 Score=29.16 Aligned_cols=69 Identities=14% Similarity=0.193 Sum_probs=46.1
Q ss_pred EeeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCcccEEEeeeeeecCcceeeeccccccccceEEEE
Q 003054 377 GYCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGEFDAVVGDITIVFNRSNYVDFTLPYTESGVSMIV 456 (852)
Q Consensus 377 G~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv 456 (852)
.+-.++++.+.++.+- +++++.. ++..+++..|.+|++|+++..... . ...+. ..++....+++++
T Consensus 13 ~~l~~~l~~~~~~~P~-i~l~i~~---------~~~~~~~~~l~~~~~Dl~i~~~~~--~-~~~~~-~~~l~~~~~~~~~ 78 (196)
T cd08450 13 QWLPEVLPILREEHPD-LDVELSS---------LFSPQLAEALMRGKLDVAFMRPEI--Q-SDGID-YQLLLKEPLIVVL 78 (196)
T ss_pred hhHHHHHHHHHhhCCC-cEEEEEe---------cChHHHHHHHhcCCccEEEEeCCC--C-CCCcE-EEEEEccceEEEe
Confidence 4556888888888873 5555544 246789999999999998753211 1 12232 4667777888888
Q ss_pred Ecc
Q 003054 457 PIK 459 (852)
Q Consensus 457 ~~~ 459 (852)
+..
T Consensus 79 ~~~ 81 (196)
T cd08450 79 PAD 81 (196)
T ss_pred cCC
Confidence 754
No 358
>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=68.71 E-value=14 Score=38.01 Aligned_cols=78 Identities=14% Similarity=0.136 Sum_probs=56.1
Q ss_pred EEEEEEEe--CCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHH
Q 003054 60 EAVPIYVD--NQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANE 137 (852)
Q Consensus 60 ~vaii~~d--~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~ 137 (852)
+++++... +.|+......+++++++.|+++..... ..+.+.....++++.+.++|++|+..........++.+.+
T Consensus 1 ~ig~v~~~~~~~~~~~~~~g~~~~~~~~g~~l~~~~~---~~~~~~~~~~~~~~~~~~~d~ii~~~~~~~~~~~~~~l~~ 77 (264)
T cd01537 1 TIGVLVPDLDNPFFAQVLKGIEEAAKAAGYQVLLANS---QNDAEKQLSALENLIARGVDGIIIAPSDLTAPTIVKLARK 77 (264)
T ss_pred CeEEEEcCCCChHHHHHHHHHHHHHHHcCCeEEEEeC---CCCHHHHHHHHHHHHHcCCCEEEEecCCCcchhHHHHhhh
Confidence 36777743 678899999999999999988764432 2234556777888888899999887655444335777777
Q ss_pred cCC
Q 003054 138 IGL 140 (852)
Q Consensus 138 ~G~ 140 (852)
.|.
T Consensus 78 ~~i 80 (264)
T cd01537 78 AGI 80 (264)
T ss_pred cCC
Confidence 775
No 359
>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=67.94 E-value=16 Score=38.04 Aligned_cols=78 Identities=8% Similarity=0.103 Sum_probs=57.2
Q ss_pred EEEEEEE--eCCcccccHHHHHHHHHh-CCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChh-hHHHHHHHH
Q 003054 60 EAVPIYV--DNQYGEEMIPSLTDALQA-IDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPS-LGSRIFEKA 135 (852)
Q Consensus 60 ~vaii~~--d~~~G~~~~~~l~~~l~~-~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~-~~~~i~~~a 135 (852)
+|+++.. +++|.....+.+.+++++ .|.++..... ..+.......+.++.+.++|.+++..... ....+++++
T Consensus 1 ~igvi~~~~~~~~~~~~~~gi~~~~~~~~~~~~~~~~~---~~~~~~~~~~i~~l~~~~vdgiii~~~~~~~~~~~~~~l 77 (272)
T cd06301 1 KIGVSMANFDDNFLTLLRNAMKEHAKVLGGVELQFEDA---KNDVATQLSQVENFIAQGVDAIIVVPVDTAATAPIVKAA 77 (272)
T ss_pred CeeEeecccCCHHHHHHHHHHHHHHHHcCCcEEEEeCC---CCCHHHHHHHHHHHHHcCCCEEEEecCchhhhHHHHHHH
Confidence 4677774 467888999999999999 8988876432 12345566778888888999998876443 345677888
Q ss_pred HHcCC
Q 003054 136 NEIGL 140 (852)
Q Consensus 136 ~~~G~ 140 (852)
.+.|+
T Consensus 78 ~~~~i 82 (272)
T cd06301 78 NAAGI 82 (272)
T ss_pred HHCCC
Confidence 88776
No 360
>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=67.42 E-value=86 Score=32.85 Aligned_cols=133 Identities=12% Similarity=0.106 Sum_probs=70.0
Q ss_pred HhcCCCCccEEeeecCCCCCCCCCCC-ceEeccCCchhHHHHHHHHHHHc--CCcEEEEEEEeCCcccc--cHHHHHHHH
Q 003054 8 QLGNKSQVPILSFSATSPSLTSIRSP-YFFRGSLNDSSQAGAITAIIKAF--GWREAVPIYVDNQYGEE--MIPSLTDAL 82 (852)
Q Consensus 8 ~i~~~~~vP~Is~~ats~~lt~~~~p-y~fR~~p~d~~~~~aia~~l~~~--gw~~vaii~~d~~~G~~--~~~~l~~~l 82 (852)
..+.+.++|+|......+. .....+ .+-.+..++...++.++++|... |-++++++... ..... ..+.+...+
T Consensus 75 ~~~~~~~iPvV~~d~~~~~-~~~~~~~~~~~v~~D~~~~~~~~~~~L~~~~~G~~~i~~i~~~-~~~~~~~r~~~~~~~~ 152 (280)
T cd06315 75 ELAQKAGIPVVGWHAGPEP-GPIEEPGIFYNVTTDPLAVAEVAALYAIANSGGKAGVVIFTDS-RFSIAKAKANAMKEII 152 (280)
T ss_pred HHHHHCCCCEEEecCCCCC-CcccCCceeEEecCCHHHHHHHHHHHHHHHcCCCceEEEEeCC-CCccHHHHHHHHHHHH
Confidence 3345679999987653211 100011 13345666777778888888665 89999988632 22111 123444444
Q ss_pred HhC-CceeeeeeecCCCCChHHHHHHHHHhhcC---CceEEEEEeChhhHHHHHHHHHHcCCccc
Q 003054 83 QAI-DTRVPYRSVISPLATDDQIEKELYKLFTM---QTRVFILHMLPSLGSRIFEKANEIGLMNK 143 (852)
Q Consensus 83 ~~~-g~~v~~~~~~~~~~~~~d~~~~l~~l~~~---~~~viv~~~~~~~~~~i~~~a~~~G~~~~ 143 (852)
+.. +..+..................+.++.+. .+++|+ +.+...+..+++.+++.|+..+
T Consensus 153 ~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~ai~-~~~D~~A~g~~~~l~~~g~~~p 216 (280)
T cd06315 153 EACKGCTVLSIEDVPISRTATRMPALTARLLQRYGDKWTHSL-AINDLYFDYMAPPLASAGRKAD 216 (280)
T ss_pred HhCCCCEEEEecccCcchhhhhhHHHHHHHHHhcCcccceec-ccchhhhHHhHHHHHHhcccCC
Confidence 443 33332111111111111112344444432 367544 4566677888899999998654
No 361
>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=67.40 E-value=17 Score=37.91 Aligned_cols=79 Identities=9% Similarity=0.108 Sum_probs=56.4
Q ss_pred EEEEEEE---eCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChh-hHHHHHHHH
Q 003054 60 EAVPIYV---DNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPS-LGSRIFEKA 135 (852)
Q Consensus 60 ~vaii~~---d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~-~~~~i~~~a 135 (852)
||+++.. ++.|.....+.+.+++++.|..+..... . +.+.......+.++...++|.+++..... .....++.+
T Consensus 1 ~i~~i~~~~~~~~~~~~~~~g~~~~~~~~g~~v~~~~~-~-~~~~~~~~~~i~~l~~~~vdgiii~~~~~~~~~~~l~~~ 78 (271)
T cd06312 1 KIAFVTHGPAGDPFWTVVKNGAEDAAKDLGVDVEYRGP-E-TFDVADMARLIEAAIAAKPDGIVVTIPDPDALDPAIKRA 78 (271)
T ss_pred CEEEecCCCCCCcHHHHHHHHHHHHHHHhCCEEEEECC-C-CCCHHHHHHHHHHHHHhCCCEEEEeCCChHHhHHHHHHH
Confidence 4677774 4578889999999999999998765422 1 11345566778888888999998876433 345567888
Q ss_pred HHcCC
Q 003054 136 NEIGL 140 (852)
Q Consensus 136 ~~~G~ 140 (852)
++.|+
T Consensus 79 ~~~~i 83 (271)
T cd06312 79 VAAGI 83 (271)
T ss_pred HHCCC
Confidence 88775
No 362
>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=67.11 E-value=26 Score=39.23 Aligned_cols=80 Identities=14% Similarity=0.052 Sum_probs=59.2
Q ss_pred HcCCcEEEEEEEeCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeC--hhhHHHHH
Q 003054 55 AFGWREAVPIYVDNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHML--PSLGSRIF 132 (852)
Q Consensus 55 ~~gw~~vaii~~d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~--~~~~~~i~ 132 (852)
..+.+++.+++.......+..+.+.+.|++.|+++.....+.++.+.+.+...+..+++.++|+||-.+- .-|+.+++
T Consensus 18 ~~~~~k~liVtd~~~~~~g~~~~v~~~L~~~gi~~~~f~~v~~~p~~~~v~~~~~~~~~~~~D~IIaiGGGS~iD~AK~i 97 (398)
T cd08178 18 LKGKKRAFIVTDRFMVKLGYVDKVIDVLKRRGVETEVFSDVEPDPSLETVRKGLELMNSFKPDTIIALGGGSPMDAAKIM 97 (398)
T ss_pred hcCCCeEEEEcChhHHhCccHHHHHHHHHHCCCeEEEecCCCCCcCHHHHHHHHHHHHhcCCCEEEEeCCccHHHHHHHH
Confidence 3466899888844434455788899999999988765555666677788889999999999999996654 34666665
Q ss_pred HH
Q 003054 133 EK 134 (852)
Q Consensus 133 ~~ 134 (852)
..
T Consensus 98 A~ 99 (398)
T cd08178 98 WL 99 (398)
T ss_pred HH
Confidence 53
No 363
>PRK10677 modA molybdate transporter periplasmic protein; Provisional
Probab=66.44 E-value=66 Score=33.54 Aligned_cols=70 Identities=16% Similarity=0.142 Sum_probs=39.9
Q ss_pred eHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCc-ccEEEeeeeeecCcc---eee-ecc-ccccccce
Q 003054 379 CVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGE-FDAVVGDITIVFNRS---NYV-DFT-LPYTESGV 452 (852)
Q Consensus 379 ~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~-~D~~~g~~~it~~r~---~~v-dft-~p~~~~~~ 452 (852)
.-++.+.+.++.|.++.+++ . ++ ..+..++.+|. +|+.+.+-.-..++. ..+ ..+ .+|....+
T Consensus 41 ~~~l~~~Fe~~~g~~v~~~~--~--------~S-g~l~~qi~~g~~~Dv~~~a~~~~~~~l~~~gl~~~~~~~~~a~n~l 109 (257)
T PRK10677 41 LQDIAAQYKKEKGVDVVSSF--A--------SS-STLARQIEQGAPADLFISADQKWMDYAVDKKAIDTATRYTLLGNSL 109 (257)
T ss_pred HHHHHHHHHhhhCCeEEEEe--c--------cc-HHHHHHHHcCCCCCEEEECCHHHHHHHHHCCCCCCcchheeecCEE
Confidence 34566666666665444443 1 12 36778888877 899876532211121 122 111 35777888
Q ss_pred EEEEEcc
Q 003054 453 SMIVPIK 459 (852)
Q Consensus 453 ~~vv~~~ 459 (852)
++++++.
T Consensus 110 vl~~~~~ 116 (257)
T PRK10677 110 VVVAPKA 116 (257)
T ss_pred EEEEECC
Confidence 8888865
No 364
>PRK10537 voltage-gated potassium channel; Provisional
Probab=65.79 E-value=13 Score=41.55 Aligned_cols=56 Identities=20% Similarity=0.254 Sum_probs=43.6
Q ss_pred CcccccchhHHHHHHHhhhcc--ccccccchhhHHHHHHHHHHHHHHHHhhhhcccee
Q 003054 506 PAGQQVGTSFWFSFSTMVFSQ--RERVISNLARIVVIVWCFVVLILTQSYTASLTSLL 561 (852)
Q Consensus 506 ~~~~~~~~~~~~~~~~l~~~~--~~~~~s~~~R~v~~~w~~~~lil~~~Yta~L~s~L 561 (852)
+...++.+++||++.++...| ...|.+..+|++.++++++++.+..+..+.++..+
T Consensus 164 ~~~~s~~dA~y~svvt~tTvGyGdi~p~t~~grl~~i~~ii~Gi~vf~~~is~i~~p~ 221 (393)
T PRK10537 164 PPIESLSTAFYFSIVTMSTVGYGDIVPVSESARLFTISVIILGITVFATSISAIFGPV 221 (393)
T ss_pred cCCCCHHHHHHhhheeeecccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455689999999999988766 33578888999999999999887766555555433
No 365
>PRK00002 aroB 3-dehydroquinate synthase; Reviewed
Probab=65.51 E-value=71 Score=35.23 Aligned_cols=104 Identities=10% Similarity=-0.008 Sum_probs=66.0
Q ss_pred CceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHHHHHhCCceeeee--eecCCCCChHHHHHHHHH
Q 003054 33 PYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTDALQAIDTRVPYR--SVISPLATDDQIEKELYK 110 (852)
Q Consensus 33 py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~~l~~~g~~v~~~--~~~~~~~~~~d~~~~l~~ 110 (852)
|+-+..... ..+.+.++++.++.+++.+++.... .....+.+.+.|++.|+++... ....++.+.+++...+..
T Consensus 9 ~~~v~~G~g---~~~~l~~~l~~~~~~~~livtd~~~-~~~~~~~v~~~L~~~gi~~~~~~~~~~e~~~~~~~v~~~~~~ 84 (358)
T PRK00002 9 SYPIIIGKG---LLSELGELLAPLKGKKVAIVTDETV-APLYLEKLRASLEAAGFEVDVVVLPDGEQYKSLETLEKIYDA 84 (358)
T ss_pred CCcEEEeCC---hHHHHHHHHHhcCCCeEEEEECCch-HHHHHHHHHHHHHhcCCceEEEEeCCCCCCCCHHHHHHHHHH
Confidence 444444443 2345666777778899999984444 3457777888898888866421 122333456777778888
Q ss_pred hhcCCc---eEEEEEeCh--hhHHHHHHHHHHcCC
Q 003054 111 LFTMQT---RVFILHMLP--SLGSRIFEKANEIGL 140 (852)
Q Consensus 111 l~~~~~---~viv~~~~~--~~~~~i~~~a~~~G~ 140 (852)
+++.++ |+||..+.+ -|+.+++......|.
T Consensus 85 ~~~~~~~r~d~IIavGGGsv~D~aK~iA~~~~~gi 119 (358)
T PRK00002 85 LLEAGLDRSDTLIALGGGVIGDLAGFAAATYMRGI 119 (358)
T ss_pred HHHcCCCCCCEEEEEcCcHHHHHHHHHHHHhcCCC
Confidence 877655 888876554 466666665454553
No 366
>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=65.49 E-value=90 Score=27.80 Aligned_cols=84 Identities=15% Similarity=0.143 Sum_probs=44.2
Q ss_pred HHHcCCcEEEEEEEeCC-cccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHH
Q 003054 53 IKAFGWREAVPIYVDNQ-YGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRI 131 (852)
Q Consensus 53 l~~~gw~~vaii~~d~~-~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i 131 (852)
++..|.|.|.-+-.|.+ -+......+.++.++.|+..++.-......+.+++......+.+..--|++.|.++.-+..+
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 45589999988877654 45666777889999999987655333323345555555555554443455555566666665
Q ss_pred HHHHH
Q 003054 132 FEKAN 136 (852)
Q Consensus 132 ~~~a~ 136 (852)
...++
T Consensus 103 ~~l~~ 107 (110)
T PF04273_consen 103 WALAQ 107 (110)
T ss_dssp HHHHH
T ss_pred HHHHh
Confidence 54443
No 367
>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=65.42 E-value=1.3e+02 Score=28.86 Aligned_cols=68 Identities=13% Similarity=0.137 Sum_probs=44.6
Q ss_pred eeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCcccEEEeeeeeecCcceeeeccccccccceEEEEE
Q 003054 378 YCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGEFDAVVGDITIVFNRSNYVDFTLPYTESGVSMIVP 457 (852)
Q Consensus 378 ~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv~ 457 (852)
+-.+++..+.++.+ .++++... ++..++..+|.+|++|+++.. .......+. +.++....++++++
T Consensus 14 ~l~~~l~~~~~~~P-~v~i~i~~---------~~~~~~~~~l~~~~~Dl~i~~---~~~~~~~~~-~~~l~~~~~~lv~~ 79 (197)
T cd08452 14 FLPPIVREYRKKFP-SVKVELRE---------LSSPDQVEELLKGRIDIGFLH---PPIQHTALH-IETVQSSPCVLALP 79 (197)
T ss_pred HHHHHHHHHHHHCC-CcEEEEEe---------cChHHHHHHHHCCCccEEEee---CCCCCCCee-EEEeeeccEEEEEe
Confidence 44678888888876 25555543 246789999999999998752 222222233 35666777777777
Q ss_pred cc
Q 003054 458 IK 459 (852)
Q Consensus 458 ~~ 459 (852)
..
T Consensus 80 ~~ 81 (197)
T cd08452 80 KQ 81 (197)
T ss_pred CC
Confidence 54
No 368
>PRK14498 putative molybdopterin biosynthesis protein MoeA/LysR substrate binding-domain-containing protein; Provisional
Probab=64.79 E-value=51 Score=39.57 Aligned_cols=66 Identities=12% Similarity=0.135 Sum_probs=47.0
Q ss_pred CCcEEEEEEEeCCc---------c---cccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeC
Q 003054 57 GWREAVPIYVDNQY---------G---EEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHML 124 (852)
Q Consensus 57 gw~~vaii~~d~~~---------G---~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~ 124 (852)
..-+|++|...|+- | ......+...+++.|.++.....++ .+.+++...|.++.+ ++|+||+.+.
T Consensus 185 ~~prv~vi~tG~El~~~~~~~~~g~i~dsn~~~l~~~l~~~g~~~~~~~~v~--Dd~~~i~~~l~~~~~-~~D~iIttGG 261 (633)
T PRK14498 185 KKPRVGIISTGDELVEPGEPLKPGKIYDVNSYTLAAAVEEAGGEPVRYGIVP--DDEEELEAALRKALK-ECDLVLLSGG 261 (633)
T ss_pred cCcEEEEEecCccccCCCCCCCCCEEEEChHHHHHHHHHHCCCEEEEEEEeC--CCHHHHHHHHHHHHh-cCCEEEECCC
Confidence 34588888765541 2 2346678888999999988777665 335677888877754 7899998865
Q ss_pred h
Q 003054 125 P 125 (852)
Q Consensus 125 ~ 125 (852)
.
T Consensus 262 ~ 262 (633)
T PRK14498 262 T 262 (633)
T ss_pred C
Confidence 4
No 369
>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=64.36 E-value=24 Score=38.79 Aligned_cols=85 Identities=15% Similarity=0.067 Sum_probs=57.6
Q ss_pred HHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeCh
Q 003054 46 AGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLP 125 (852)
Q Consensus 46 ~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~ 125 (852)
...+.++++.+| +++.+++....+- ...+.+.+.|++.|+.+.... +..+.+.+.+...+..+++.++|+||-.+.+
T Consensus 11 ~~~l~~~~~~~g-~~~liv~~~~~~~-~~~~~v~~~l~~~~i~~~~~~-~~~~p~~~~v~~~~~~~~~~~~d~IIavGGG 87 (349)
T cd08550 11 IKEIAAILSTFG-SKVAVVGGKTVLK-KSRPRFEAALAKSIIVVDVIV-FGGECSTEEVVKALCGAEEQEADVIIGVGGG 87 (349)
T ss_pred HHHHHHHHHHcC-CeEEEEEChHHHH-HHHHHHHHHHHhcCCeeEEEE-cCCCCCHHHHHHHHHHHHhcCCCEEEEecCc
Confidence 345667788889 8887777433332 556788888988887653332 4434456677888888888999999876554
Q ss_pred --hhHHHHHH
Q 003054 126 --SLGSRIFE 133 (852)
Q Consensus 126 --~~~~~i~~ 133 (852)
-|+.+++.
T Consensus 88 s~~D~aK~ia 97 (349)
T cd08550 88 KTLDTAKAVA 97 (349)
T ss_pred HHHHHHHHHH
Confidence 35555554
No 370
>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=64.12 E-value=21 Score=37.23 Aligned_cols=80 Identities=6% Similarity=0.034 Sum_probs=55.1
Q ss_pred EEEEEEE--eCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHH
Q 003054 60 EAVPIYV--DNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANE 137 (852)
Q Consensus 60 ~vaii~~--d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~ 137 (852)
+|+++.. ++.|.......+.+++++.|.++.....-. ..+.++....+..+.+.++|.|++.....+....++++++
T Consensus 1 ~Igvi~~~~~~~f~~~~~~gi~~~a~~~g~~~~~~~~~~-~~~~~~~~~~i~~~~~~~vdgiI~~~~~~~~~~~~~~~~~ 79 (268)
T cd06306 1 KLCVLYPHLKDAYWLSVNYGMVEEAKRLGVSLKLLEAGG-YPNLAKQIAQLEDCAAWGADAILLGAVSPDGLNEILQQVA 79 (268)
T ss_pred CeEEEcCCCCCHHHHHHHHHHHHHHHHcCCEEEEecCCC-CCCHHHHHHHHHHHHHcCCCEEEEcCCChhhHHHHHHHHH
Confidence 3667774 467888889999999999999876542211 1123445567888888999999987654443225677888
Q ss_pred cCC
Q 003054 138 IGL 140 (852)
Q Consensus 138 ~G~ 140 (852)
.|+
T Consensus 80 ~gi 82 (268)
T cd06306 80 ASI 82 (268)
T ss_pred CCC
Confidence 776
No 371
>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=64.10 E-value=34 Score=37.58 Aligned_cols=86 Identities=16% Similarity=0.170 Sum_probs=57.6
Q ss_pred HHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHHHHHhCCceeeeeeecCCC--CChHHHHHHHHHhhcCCceEEEEEe
Q 003054 46 AGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTDALQAIDTRVPYRSVISPL--ATDDQIEKELYKLFTMQTRVFILHM 123 (852)
Q Consensus 46 ~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~--~~~~d~~~~l~~l~~~~~~viv~~~ 123 (852)
.+.+.++++.+|.+++.+++....+... .+.+.+.|++.|+++........+ .+.+.+...+..+++ ++|+||-.+
T Consensus 11 l~~l~~~~~~~~~~~~livtd~~~~~~~-~~~v~~~l~~~~i~~~~~~~~~~~~~pt~~~v~~~~~~~~~-~~d~IIaIG 88 (348)
T cd08175 11 LERLPEILKEFGYKKALIVADENTYAAA-GKKVEALLKRAGVVVLLIVLPAGDLIADEKAVGRVLKELER-DTDLIIAVG 88 (348)
T ss_pred HHHHHHHHHhcCCCcEEEEECCcHHHHH-HHHHHHHHHHCCCeeEEeecCCCcccCCHHHHHHHHHHhhc-cCCEEEEEC
Confidence 3456777888888999888743333222 577888899999866433333332 456667777777777 999998765
Q ss_pred Ch--hhHHHHHH
Q 003054 124 LP--SLGSRIFE 133 (852)
Q Consensus 124 ~~--~~~~~i~~ 133 (852)
-+ -|+.+++.
T Consensus 89 GGs~~D~aK~vA 100 (348)
T cd08175 89 SGTINDITKYVS 100 (348)
T ss_pred CcHHHHHHHHHH
Confidence 44 46666665
No 372
>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=63.73 E-value=19 Score=37.85 Aligned_cols=81 Identities=15% Similarity=0.174 Sum_probs=53.3
Q ss_pred EEEEEEEe---CCcccccHHHHHHHHHhCCceeeeeeecCCC-CChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHH
Q 003054 60 EAVPIYVD---NQYGEEMIPSLTDALQAIDTRVPYRSVISPL-ATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKA 135 (852)
Q Consensus 60 ~vaii~~d---~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~-~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a 135 (852)
+|++|..+ ++|.....+.+.+++++.|.++......... .+.......+.++.+.++|.||+..........++.+
T Consensus 1 ~Igvi~~~~~~~~~~~~~~~~i~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~i~~l~~~~vDgiIv~~~~~~~~~~~~~l 80 (280)
T cd06303 1 KIAVIYPGQQISDYWVRNIASFTARLEELNIPYELTQFSSRPGIDHRLQSQQLNEALQSKPDYLIFTLDSLRHRKLIERV 80 (280)
T ss_pred CeeEEecCccHHHHHHHHHHHHHHHHHHcCCcEEEEEeccCcccCHHHHHHHHHHHHHcCCCEEEEcCCchhhHHHHHHH
Confidence 36777754 4677888899999999999877654221111 1234455677788889999998875433334556666
Q ss_pred HHcCC
Q 003054 136 NEIGL 140 (852)
Q Consensus 136 ~~~G~ 140 (852)
.+.+.
T Consensus 81 ~~~~~ 85 (280)
T cd06303 81 LASGK 85 (280)
T ss_pred HhCCC
Confidence 66654
No 373
>COG2358 Imp TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]
Probab=63.56 E-value=16 Score=39.14 Aligned_cols=75 Identities=21% Similarity=0.291 Sum_probs=45.8
Q ss_pred cCCHHHHHhcCCeEEE-EeCc----hHHHHHHhcCCCCcceeecC--CHhHHHHHhhcccccCceeEEEechhH---HHH
Q 003054 570 ITDVKMLIKRGDNVGY-QKGS----FVLGILKQLGFDERKLVVYN--SPEDCHELFQKGSVNGGIAAAFDEIPY---MKL 639 (852)
Q Consensus 570 i~sl~dL~~~~~~vg~-~~~s----~~~~~l~~~~~~~~~~~~~~--~~~~~~~~l~~g~~~~g~~a~~~~~~~---~~~ 639 (852)
|++++||. |+||.+ ..|| ..+..|+..++....+.... ...+..+++++|+ +||++.-... .-.
T Consensus 129 Ikti~DL~--GKrV~iG~~gSgt~~~a~~il~a~Gi~~~~~~~~~~~~~a~~~~~l~~g~----iDA~~~~~G~p~~ai~ 202 (321)
T COG2358 129 IKTIADLK--GKRVAIGPPGSGTEATARQILEALGITYDDYELDLGLGDAESADALKNGT----IDAAFYVAGVPNPAIS 202 (321)
T ss_pred cceehhcC--CCEEeecCCCCccHHHHHHHHHHcCCCCcchhhhhhcCchhhHHHhhCCc----ccEEEEecCCCCccHH
Confidence 99999997 999988 3444 34455666666554433211 2334578899999 9998864321 223
Q ss_pred HHhhcCCceEee
Q 003054 640 LIGQYCSKYAMI 651 (852)
Q Consensus 640 ~~~~~~~~~~~v 651 (852)
.+...|+ +.++
T Consensus 203 el~~~~~-i~lv 213 (321)
T COG2358 203 ELATTCD-IVLV 213 (321)
T ss_pred HHHhhCC-eEEE
Confidence 3344463 5554
No 374
>PRK13348 chromosome replication initiation inhibitor protein; Provisional
Probab=63.41 E-value=2e+02 Score=30.26 Aligned_cols=101 Identities=11% Similarity=0.058 Sum_probs=53.6
Q ss_pred CCHHHHHhcCCe-EEEEeCch-HHHHHHhc-C--CCCcceeecCCHhHHHHHhhcccccCceeEEEechhHHHHHHhhcC
Q 003054 571 TDVKMLIKRGDN-VGYQKGSF-VLGILKQL-G--FDERKLVVYNSPEDCHELFQKGSVNGGIAAAFDEIPYMKLLIGQYC 645 (852)
Q Consensus 571 ~sl~dL~~~~~~-vg~~~~s~-~~~~l~~~-~--~~~~~~~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~~~ 645 (852)
-+++||. +.+ |.+..+.. ...++... + .........++.....+++..|. ..+++-+. .+.......+
T Consensus 180 v~~~~l~--~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~----gi~~lp~~-~~~~~~~~~~ 252 (294)
T PRK13348 180 LTRHSAL--KAPAVAFNRKDTLQDSFLEQLFGLPVGAYPRHYVPSTHAHLAAIRHGL----GYGMVPEL-LIGPLLAAGR 252 (294)
T ss_pred CCHHHHc--CCCEEEecCCchHHHHHHHHHHhccccccceEEeCcHHHHHHHHHcCC----eeEeCCHH-HHHHHHhcCe
Confidence 3688887 443 34444433 33444332 1 11122335678888899999998 44555444 3333222222
Q ss_pred CceEeecccccccceEEEecCCCCchhhHHHHHHhc
Q 003054 646 SKYAMIEPKFKTAGFGFVFPLHSPLVHDVSKAILNV 681 (852)
Q Consensus 646 ~~~~~v~~~~~~~~~~~~~~k~spl~~~in~~il~l 681 (852)
+..+... ....++++.+|+.+....+...+..+
T Consensus 253 --l~~l~~~-~~~~~~l~~~~~~~~~~~~~~~~~~i 285 (294)
T PRK13348 253 --LVDLAPG-HPVDVALYWHHWEVESPTMEALSQRV 285 (294)
T ss_pred --eeecCCC-CCCCceeEEeeccccChHHHHHHHHH
Confidence 3334333 34567888888876655554444433
No 375
>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=63.16 E-value=65 Score=35.45 Aligned_cols=100 Identities=11% Similarity=-0.006 Sum_probs=64.8
Q ss_pred HHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHHHHHhCCceeeeee--ecCCCCChHHHHHHHHHhhcCCce---EEEE
Q 003054 47 GAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTDALQAIDTRVPYRS--VISPLATDDQIEKELYKLFTMQTR---VFIL 121 (852)
Q Consensus 47 ~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~~l~~~g~~v~~~~--~~~~~~~~~d~~~~l~~l~~~~~~---viv~ 121 (852)
..+.++++.+|-+++.+++..+.+ ....+.+.+.|++.|.++.... ....+.+.+.+...+..+++.++| +||.
T Consensus 12 ~~l~~~l~~~g~~rvlvVtd~~v~-~~~~~~l~~~L~~~g~~~~~~~~~~~e~~k~~~~v~~~~~~~~~~~~dr~~~IIA 90 (355)
T cd08197 12 DSVLGYLPELNADKYLLVTDSNVE-DLYGHRLLEYLREAGAPVELLSVPSGEEHKTLSTLSDLVERALALGATRRSVIVA 90 (355)
T ss_pred HHHHHHHHhcCCCeEEEEECccHH-HHHHHHHHHHHHhcCCceEEEEeCCCCCCCCHHHHHHHHHHHHHcCCCCCcEEEE
Confidence 445667777888999888855544 3366778889998887653221 222334456788888888888888 7776
Q ss_pred EeCh--hhHHHHHHHHHHcCCcccceEEEEc
Q 003054 122 HMLP--SLGSRIFEKANEIGLMNKGCVWIMT 150 (852)
Q Consensus 122 ~~~~--~~~~~i~~~a~~~G~~~~~~vwi~~ 150 (852)
.+.+ -|+..++......|+ .++.|-|
T Consensus 91 vGGGsv~D~ak~~A~~~~rgi---p~I~IPT 118 (355)
T cd08197 91 LGGGVVGNIAGLLAALLFRGI---RLVHIPT 118 (355)
T ss_pred ECCcHHHHHHHHHHHHhccCC---CEEEecC
Confidence 6543 466666655444443 4555555
No 376
>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=62.64 E-value=1.4e+02 Score=28.25 Aligned_cols=98 Identities=9% Similarity=0.004 Sum_probs=51.8
Q ss_pred CCHHHHHhcCCeEEEEe-C-chHHHHHHhcCCCCc---ceeecCCHhHHHHHhhcccccCceeEEEechhHHHHHHhhcC
Q 003054 571 TDVKMLIKRGDNVGYQK-G-SFVLGILKQLGFDER---KLVVYNSPEDCHELFQKGSVNGGIAAAFDEIPYMKLLIGQYC 645 (852)
Q Consensus 571 ~sl~dL~~~~~~vg~~~-~-s~~~~~l~~~~~~~~---~~~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~~~ 645 (852)
-+++||. +.++.... . .....++.+.+.... ....+++.+...+++..|. ..+++.+.. +.......
T Consensus 86 ~~~~dl~--~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~----Gi~~~p~~~-~~~~~~~~- 157 (194)
T cd08481 86 AAPADLA--HLPLLQQTTRPEAWRDWFEEVGLEVPTAYRGMRFEQFSMLAQAAVAGL----GVALLPRFL-IEEELARG- 157 (194)
T ss_pred CcHHHHh--hCceEecCCCCcCHHHHHHHcCCCCCCccCceEeccHHHHHHHHHhCC----CeEEecHHH-HHHHHHCC-
Confidence 3688887 33333221 1 234556666555321 1234578888899999988 455555533 33322221
Q ss_pred CceEee--cccccccceEEEecCCCCchhhHHHH
Q 003054 646 SKYAMI--EPKFKTAGFGFVFPLHSPLVHDVSKA 677 (852)
Q Consensus 646 ~~~~~v--~~~~~~~~~~~~~~k~spl~~~in~~ 677 (852)
. +... .+......++++.+++.+....+...
T Consensus 158 ~-l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~ 190 (194)
T cd08481 158 R-LVVPFNLPLTSDKAYYLVYPEDKAESPPVQAF 190 (194)
T ss_pred C-EEeecCccccCCCeEEEEeCcccccCHHHHHH
Confidence 1 2221 22223457888888886655544443
No 377
>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=61.76 E-value=34 Score=38.00 Aligned_cols=79 Identities=8% Similarity=-0.045 Sum_probs=56.9
Q ss_pred cCCcEEEEEEEeCCcc-cccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeCh--hhHHHHH
Q 003054 56 FGWREAVPIYVDNQYG-EEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLP--SLGSRIF 132 (852)
Q Consensus 56 ~gw~~vaii~~d~~~G-~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~--~~~~~i~ 132 (852)
++.+++.+++....+- .+..+.+.+.|++.|+++.....+.++.+.+.+...+..+++.++|+||-.+.+ -|+.+.+
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 3458888887443332 456678889999999887655555566777888899999999999999877654 3555555
Q ss_pred HH
Q 003054 133 EK 134 (852)
Q Consensus 133 ~~ 134 (852)
..
T Consensus 101 a~ 102 (375)
T cd08179 101 WI 102 (375)
T ss_pred HH
Confidence 43
No 378
>PRK11139 DNA-binding transcriptional activator GcvA; Provisional
Probab=61.45 E-value=1.6e+02 Score=31.21 Aligned_cols=102 Identities=10% Similarity=0.025 Sum_probs=53.9
Q ss_pred cCCHHHHHhcCCe-EEEEeCchHHHHHHhcCCC---CcceeecCCHhHHHHHhhcccccCceeEEEechhHHHHHHhhcC
Q 003054 570 ITDVKMLIKRGDN-VGYQKGSFVLGILKQLGFD---ERKLVVYNSPEDCHELFQKGSVNGGIAAAFDEIPYMKLLIGQYC 645 (852)
Q Consensus 570 i~sl~dL~~~~~~-vg~~~~s~~~~~l~~~~~~---~~~~~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~~~ 645 (852)
.-+++||. +.+ |....+.....++...+.. ......+++.+...+++..|. ..+++.+. ..........
T Consensus 180 ~i~~~dL~--~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~----gi~~lp~~-~~~~~~~~~~ 252 (297)
T PRK11139 180 LKTPEDLA--RHTLLHDDSREDWRAWFRAAGLDDLNVQQGPIFSHSSMALQAAIHGQ----GVALGNRV-LAQPEIEAGR 252 (297)
T ss_pred CCCHHHhh--cCceEeecCcccHHHHHHHhCCCCcCcccceeeCCHHHHHHHHHhCC----CeEecchh-hhHHHHHCCc
Confidence 34788887 443 3333334455666654442 112345678888888888887 44555443 3333333221
Q ss_pred CceEeecccc-cccceEEEecCCCCchhhHHHHHH
Q 003054 646 SKYAMIEPKF-KTAGFGFVFPLHSPLVHDVSKAIL 679 (852)
Q Consensus 646 ~~~~~v~~~~-~~~~~~~~~~k~spl~~~in~~il 679 (852)
....+.+.. ....+.++.+|+.+....+...+.
T Consensus 253 -l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f~~ 286 (297)
T PRK11139 253 -LVCPFDTVLPSPNAFYLVCPDSQAELPKVAAFRQ 286 (297)
T ss_pred -eecccccCcCCCccEEEEeccccccChhHHHHHH
Confidence 111222222 235688888887665555544443
No 379
>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=61.41 E-value=57 Score=29.57 Aligned_cols=61 Identities=21% Similarity=0.196 Sum_probs=41.3
Q ss_pred cHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeCh----hhHHHHHHHHHHcCC
Q 003054 74 MIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLP----SLGSRIFEKANEIGL 140 (852)
Q Consensus 74 ~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~----~~~~~i~~~a~~~G~ 140 (852)
....+...|+..|.+|.+--.. ... ...+..+.+.+||+|.+++.. +.+..+++++++.|.
T Consensus 15 G~~~~~~~l~~~G~~vi~lG~~---vp~---e~~~~~a~~~~~d~V~iS~~~~~~~~~~~~~~~~L~~~~~ 79 (122)
T cd02071 15 GAKVIARALRDAGFEVIYTGLR---QTP---EEIVEAAIQEDVDVIGLSSLSGGHMTLFPEVIELLRELGA 79 (122)
T ss_pred HHHHHHHHHHHCCCEEEECCCC---CCH---HHHHHHHHHcCCCEEEEcccchhhHHHHHHHHHHHHhcCC
Confidence 3456667788899998765432 122 345556667899999988754 345777888888876
No 380
>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=61.09 E-value=1.3e+02 Score=28.13 Aligned_cols=68 Identities=16% Similarity=0.124 Sum_probs=48.7
Q ss_pred ccHHHHHHHHHhCCceeeeeeec----CCCCChHHHH-HHHHHhhcCCceEEEEEeChhhHHHHHHHHHHcCC
Q 003054 73 EMIPSLTDALQAIDTRVPYRSVI----SPLATDDQIE-KELYKLFTMQTRVFILHMLPSLGSRIFEKANEIGL 140 (852)
Q Consensus 73 ~~~~~l~~~l~~~g~~v~~~~~~----~~~~~~~d~~-~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~G~ 140 (852)
.....+.++|++.|.++...... ..+..|..+. ..+..+...++|.|++.+...+...+++++++.|.
T Consensus 52 ~~~~~~~~~L~~~g~~~~~~~~~~~~~~~~~~D~~l~~d~~~~~~~~~~d~ivLvSgD~Df~~~i~~lr~~G~ 124 (149)
T cd06167 52 ERQRGFLDALRRLGFEPIQKPLRTRGSGKKGVDVALAIDALELAYKRRIDTIVLVSGDSDFVPLVERLRELGK 124 (149)
T ss_pred hhHHHHHHHHHHCCcEEEEEcceecCCcccCccHHHHHHHHHHhhhcCCCEEEEEECCccHHHHHHHHHHcCC
Confidence 45688999999999998766532 1223333443 33334444578999999999999999999999986
No 381
>PRK03635 chromosome replication initiation inhibitor protein; Validated
Probab=60.93 E-value=2.2e+02 Score=29.98 Aligned_cols=65 Identities=12% Similarity=0.007 Sum_probs=42.8
Q ss_pred HHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCcccEEEeeeeeecCcceeeeccccccccceEEEEEcc
Q 003054 380 VDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGEFDAVVGDITIVFNRSNYVDFTLPYTESGVSMIVPIK 459 (852)
Q Consensus 380 ~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv~~~ 459 (852)
..++..+.++. .+++++... .-.+++.++.+|++|+++..- ......+ .+.|+....++++++..
T Consensus 106 ~~~l~~f~~~~--~i~i~l~~~---------~~~~~~~~l~~~~~d~~i~~~---~~~~~~l-~~~~l~~~~~~lv~~~~ 170 (294)
T PRK03635 106 LPALAPVLARS--GVLLDLVVE---------DQDHTAELLRRGEVVGAVTTE---PQPVQGC-RVDPLGAMRYLAVASPA 170 (294)
T ss_pred HHHHHHHHhCC--CcEEEEEec---------CcHHHHHHHhCCCceEEEecc---CCCCCCc-eeeecccceEEEEEcch
Confidence 45677777653 456666543 346789999999999987532 2222233 35778888888888744
No 382
>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=60.81 E-value=34 Score=37.33 Aligned_cols=87 Identities=8% Similarity=-0.079 Sum_probs=59.7
Q ss_pred HHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeCh
Q 003054 46 AGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLP 125 (852)
Q Consensus 46 ~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~ 125 (852)
.+.+.+.++.+|.+++.+++....+-. ..+.+.+.|++.+..+ ...+.++.+.+.+...+..+++.++|+||-.+.+
T Consensus 11 l~~l~~~l~~~g~~~~livt~~~~~~~-~~~~v~~~l~~~~~~~--~~~~~~~p~~~~v~~~~~~~~~~~~d~IIaiGGG 87 (337)
T cd08177 11 LAALAAELERLGASRALVLTTPSLATK-LAERVASALGDRVAGT--FDGAVMHTPVEVTEAAVAAAREAGADGIVAIGGG 87 (337)
T ss_pred HHHHHHHHHHcCCCeEEEEcChHHHHH-HHHHHHHHhccCCcEE--eCCCCCCCCHHHHHHHHHHHHhcCCCEEEEeCCc
Confidence 456777889999999998885444443 6667777887765433 2234445567778888888888999999877654
Q ss_pred --hhHHHHHHHH
Q 003054 126 --SLGSRIFEKA 135 (852)
Q Consensus 126 --~~~~~i~~~a 135 (852)
-|..+++...
T Consensus 88 s~iD~aK~ia~~ 99 (337)
T cd08177 88 STIDLAKAIALR 99 (337)
T ss_pred HHHHHHHHHHHH
Confidence 3566665543
No 383
>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=60.79 E-value=73 Score=33.94 Aligned_cols=65 Identities=9% Similarity=0.115 Sum_probs=40.1
Q ss_pred EEEEEEE-eCCcccccHHHHHHHHHhCCcee---eeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeCh
Q 003054 60 EAVPIYV-DNQYGEEMIPSLTDALQAIDTRV---PYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLP 125 (852)
Q Consensus 60 ~vaii~~-d~~~G~~~~~~l~~~l~~~g~~v---~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~ 125 (852)
+|+|+.. +.+-=.+..+.|++.|++.|... .+. ....+.+.......++++++.++|+|+..+..
T Consensus 1 ~v~i~~~~~~~~~~~~~~gf~~~L~~~g~~~~~~~~~-~~~a~~d~~~~~~~~~~l~~~~~DlIi~~gt~ 69 (294)
T PF04392_consen 1 KVGILQFISHPALDDIVRGFKDGLKELGYDEKNVEIE-YKNAEGDPEKLRQIARKLKAQKPDLIIAIGTP 69 (294)
T ss_dssp EEEEEESS--HHHHHHHHHHHHHHHHTT--CCCEEEE-EEE-TT-HHHHHHHHHHHCCTS-SEEEEESHH
T ss_pred CeEEEEEeccHHHHHHHHHHHHHHHHcCCccccEEEE-EecCCCCHHHHHHHHHHHhcCCCCEEEEeCcH
Confidence 4666662 22233566889999999998765 222 22333445678888889999999998877544
No 384
>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=60.52 E-value=13 Score=35.80 Aligned_cols=100 Identities=13% Similarity=0.060 Sum_probs=58.5
Q ss_pred cCCHHHHHhcCCeEEEEeCchHHHHHHhcCCCCcceeecCCHhHHHHHhhcccccCceeEEEechhHHHHHHhhcCCceE
Q 003054 570 ITDVKMLIKRGDNVGYQKGSFVLGILKQLGFDERKLVVYNSPEDCHELFQKGSVNGGIAAAFDEIPYMKLLIGQYCSKYA 649 (852)
Q Consensus 570 i~sl~dL~~~~~~vg~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~~~~~~~ 649 (852)
+++++||.. +++|+..--...+.||++.+.+-.-+....+.|-. ...|- .+++++-.....-+.++. +.
T Consensus 58 ~~~~~~l~~-~~rIATkyp~l~~~yf~~~g~~~~ii~l~GsvE~a---p~~gl----AD~IvDiv~TG~TLr~Ng---L~ 126 (163)
T PF01634_consen 58 YKSVEDLKA-GLRIATKYPNLTRRYFAEKGINVEIIKLSGSVELA---PPLGL----ADAIVDIVETGTTLRANG---LK 126 (163)
T ss_dssp GCCGGGGSS-TEEEEES-HHHHHHHHHHCT-EEEEEE-SS-TTHH---HHTTS----SSEEEEEESSSHHHHHTT---EE
T ss_pred CCCHHHhcc-CCEEEECCHHHHHHHHHHcCCcEEEEEccCCcccc---CCCCC----CCEEEEeccCcHHHHHCC---CE
Confidence 678888853 67999877778889999887655445555566533 44565 788887665554444443 55
Q ss_pred eecccccccceEEEecCCCC--chhhHHHHHHhc
Q 003054 650 MIEPKFKTAGFGFVFPLHSP--LVHDVSKAILNV 681 (852)
Q Consensus 650 ~v~~~~~~~~~~~~~~k~sp--l~~~in~~il~l 681 (852)
.++..+. ....++.++.+- -.+.+++.+.+|
T Consensus 127 ~i~~i~~-s~a~LI~n~~~~~~k~~~i~~l~~~l 159 (163)
T PF01634_consen 127 EIETILE-SSARLIANKASLKEKEEKIDELVTRL 159 (163)
T ss_dssp EEEEEEE-EEEEEEEEHHHHHHCHHHHHHHHHHH
T ss_pred EeEEEEE-EEEEEEEcCccchhhHHHHHHHHHHH
Confidence 6655444 455555555543 223355555544
No 385
>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=60.22 E-value=28 Score=35.41 Aligned_cols=78 Identities=13% Similarity=0.092 Sum_probs=56.7
Q ss_pred EEEEEEEe---CCcccccHHHHHHHHHh--CCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHH
Q 003054 60 EAVPIYVD---NQYGEEMIPSLTDALQA--IDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEK 134 (852)
Q Consensus 60 ~vaii~~d---~~~G~~~~~~l~~~l~~--~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~ 134 (852)
+|++|..+ +.|+....+.+.+++++ .|+++..... ..+..+....+.++...++|+++..........+.+.
T Consensus 1 ~Ig~i~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~d~ii~~~~~~~~~~~~~~ 77 (269)
T cd01391 1 KIGVLLPLSGSAPFGAQLLAGIELAAEEIGRGLEVILADS---QSDPERALEALRDLIQQGVDGIIGPPSSSSALAVVEL 77 (269)
T ss_pred CceEEeecCCCcHHHHHHHHHHHHHHHHhCCceEEEEecC---CCCHHHHHHHHHHHHHcCCCEEEecCCCHHHHHHHHH
Confidence 46777743 57888889999999999 7777654432 2234467778888888899999988776665557777
Q ss_pred HHHcCC
Q 003054 135 ANEIGL 140 (852)
Q Consensus 135 a~~~G~ 140 (852)
+.+.|.
T Consensus 78 ~~~~~i 83 (269)
T cd01391 78 AAAAGI 83 (269)
T ss_pred HHHcCC
Confidence 887775
No 386
>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=60.22 E-value=30 Score=35.71 Aligned_cols=77 Identities=9% Similarity=0.058 Sum_probs=54.3
Q ss_pred EEEEEE--eCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHc
Q 003054 61 AVPIYV--DNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEI 138 (852)
Q Consensus 61 vaii~~--d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~ 138 (852)
|+++.. +++|.....+.+.+++++.|..+..... ..+.......+.++.+.++|.|++..........++++.+.
T Consensus 2 igvv~~~~~~~~~~~~~~~i~~~~~~~g~~~~~~~~---~~~~~~~~~~~~~l~~~~vdgiii~~~~~~~~~~~~~~~~~ 78 (266)
T cd06282 2 VGVVLPSLANPVFAECVQGIQEEARAAGYSLLLATT---DYDAEREADAVETLLRQRVDGLILTVADAATSPALDLLDAE 78 (266)
T ss_pred eEEEeCCCCcchHHHHHHHHHHHHHHCCCEEEEeeC---CCCHHHHHHHHHHHHhcCCCEEEEecCCCCchHHHHHHhhC
Confidence 455553 4567788899999999999998865432 22345566778888888999999864433334477888888
Q ss_pred CC
Q 003054 139 GL 140 (852)
Q Consensus 139 G~ 140 (852)
|.
T Consensus 79 ~i 80 (266)
T cd06282 79 RV 80 (266)
T ss_pred CC
Confidence 86
No 387
>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=60.10 E-value=32 Score=35.62 Aligned_cols=77 Identities=9% Similarity=0.086 Sum_probs=54.1
Q ss_pred EEEEEEe--CCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhh-HHHHHHHHHH
Q 003054 61 AVPIYVD--NQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSL-GSRIFEKANE 137 (852)
Q Consensus 61 vaii~~d--~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~-~~~i~~~a~~ 137 (852)
|+++..| +.|-....+.+.+++++.|.++..... ..+.......+.++.+.++|.+++...... ....++++++
T Consensus 2 i~~~~~~~~~~~~~~~~~~i~~~~~~~g~~~~i~~~---~~~~~~~~~~~~~~~~~~vdgiii~~~~~~~~~~~~~~~~~ 78 (267)
T cd06322 2 IGASLLTQQHPFYIELANAMKEEAKKQKVNLIVSIA---NQDLNKQLSDVEDFITKKVDAIVLSPVDSKGIRAAIAKAKK 78 (267)
T ss_pred eeEeecCcccHHHHHHHHHHHHHHHhcCCEEEEecC---CCCHHHHHHHHHHHHHcCCCEEEEcCCChhhhHHHHHHHHH
Confidence 4555533 668888899999999999988754321 123445667778888889999998654333 4566788888
Q ss_pred cCC
Q 003054 138 IGL 140 (852)
Q Consensus 138 ~G~ 140 (852)
.|+
T Consensus 79 ~~i 81 (267)
T cd06322 79 AGI 81 (267)
T ss_pred CCC
Confidence 775
No 388
>PRK07377 hypothetical protein; Provisional
Probab=59.61 E-value=21 Score=34.38 Aligned_cols=62 Identities=19% Similarity=0.252 Sum_probs=45.0
Q ss_pred CceEEEeeecccCcccceEEeeCCCCCCCceEEEeeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCc
Q 003054 344 EKKLRIGVPVKKGFSDFVNVTIDPKTQEPTSVTGYCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGE 423 (852)
Q Consensus 344 ~~~lrv~v~~~~~~~~~~~~~~d~~~~~~~~~~G~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~ 423 (852)
...+|+|+.... + ..+ ..-+-.++.++.+.++++. .+++++++ +-..+.+++.+|+
T Consensus 74 s~~~Rlgv~~~~--------~-----~~~-~~~~~l~~~l~~~~~~y~~--rlElv~y~--------~~~~l~~aL~~~e 129 (184)
T PRK07377 74 SLVMRLGVLEIE--------T-----ETS-SVFDQLIDQLRTILDKYHL--RLELVVYP--------DLQALEQALRDKE 129 (184)
T ss_pred ccEEEEEEEecc--------c-----ccc-ccHHHHHHHHHHHHHHhCc--eeeEEecC--------CHHHHHHHHhcCC
Confidence 346889987330 0 122 3334467788888998884 77888887 6889999999999
Q ss_pred ccEEEe
Q 003054 424 FDAVVG 429 (852)
Q Consensus 424 ~D~~~g 429 (852)
+|++.+
T Consensus 130 Vh~~c~ 135 (184)
T PRK07377 130 VHAICL 135 (184)
T ss_pred ccEEec
Confidence 998765
No 389
>PF12683 DUF3798: Protein of unknown function (DUF3798); InterPro: IPR024258 This entry represents functionally uncharacterised proteins that are found in bacteria. They are typically between 247 and 417 amino acids in length. Most of the proteins in this entry have an N-terminal lipoprotein attachment site. These proteins have distant similarity to periplasmic ligand binding families suggesting that this family has a similar role.; PDB: 3QI7_A.
Probab=59.42 E-value=95 Score=32.24 Aligned_cols=101 Identities=12% Similarity=0.070 Sum_probs=63.6
Q ss_pred CCchhHHHHHHHHHHHcCCcEEEEEEEeCCccccc----HHHHHHHHHhCCceeeeeeecCCCCC-----hHHHH--HHH
Q 003054 40 LNDSSQAGAITAIIKAFGWREAVPIYVDNQYGEEM----IPSLTDALQAIDTRVPYRSVISPLAT-----DDQIE--KEL 108 (852)
Q Consensus 40 p~d~~~~~aia~~l~~~gw~~vaii~~d~~~G~~~----~~~l~~~l~~~g~~v~~~~~~~~~~~-----~~d~~--~~l 108 (852)
+.....+..++...+++|.+.++-+.....-+... .+.++++.++.|++.+....=.|..+ ..+|. ..-
T Consensus 113 ~D~~~~G~~i~~~Ak~mGAktFVh~sfprhms~~~l~~Rr~~M~~~C~~lGi~fv~~taPDP~sd~gv~gaqqfIlE~vp 192 (275)
T PF12683_consen 113 PDEISRGYTIVWAAKKMGAKTFVHYSFPRHMSYELLARRRDIMEEACKDLGIKFVEVTAPDPTSDVGVAGAQQFILEDVP 192 (275)
T ss_dssp --HHHHHHHHHHHHHHTT-S-EEEEEETTGGGSHHHHHHHHHHHHHHHHCT--EEEEEE---SSTCHHHHHHHHHHHHHH
T ss_pred cchhhccHHHHHHHHHcCCceEEEEechhhcchHHHHHHHHHHHHHHHHcCCeEEEEeCCCCCCCCCcHHHHHHHHHHHH
Confidence 45557788899999999999999887655555433 34566777889999887754322211 12222 233
Q ss_pred HHhhcCCceEEEEEeChhhHHHHHHHHHHcCC
Q 003054 109 YKLFTMQTRVFILHMLPSLGSRIFEKANEIGL 140 (852)
Q Consensus 109 ~~l~~~~~~viv~~~~~~~~~~i~~~a~~~G~ 140 (852)
+++++.+.|+-|.+++......+++++.+.|.
T Consensus 193 ~~i~kYGkdtaff~TN~a~~epllk~~~~~g~ 224 (275)
T PF12683_consen 193 KWIKKYGKDTAFFCTNDAMTEPLLKQALEYGG 224 (275)
T ss_dssp HHHHHH-S--EEEESSHHHHHHHHHHHHHH--
T ss_pred HHHHHhCCceeEEecCccccHHHHHHHHHcCC
Confidence 56778899999999999999999999999875
No 390
>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=59.19 E-value=75 Score=34.86 Aligned_cols=86 Identities=9% Similarity=-0.028 Sum_probs=56.9
Q ss_pred HHHHHHHHHHcCC--cEEEEEEEeCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcC---CceEEE
Q 003054 46 AGAITAIIKAFGW--REAVPIYVDNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTM---QTRVFI 120 (852)
Q Consensus 46 ~~aia~~l~~~gw--~~vaii~~d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~---~~~viv 120 (852)
...+.++++.+|. +++.++. |...-. +.+.+.|++.|+++.....+.++.+.++....+...++. ++|+||
T Consensus 11 l~~l~~~~~~~g~~~~~~lvvt-d~~~~~---~~v~~~L~~~g~~~~~f~~v~~nPt~~~v~~~~~~~~~~~~~~~D~II 86 (347)
T cd08184 11 FDQLNDLLAPKRKNKDPAVFFV-DDVFQG---KDLISRLPVESEDMIIWVDATEEPKTDQIDALTAQVKSFDGKLPCAIV 86 (347)
T ss_pred HHHHHHHHHHcCCCCCeEEEEE-Ccchhh---hHHHHHHHhcCCcEEEEcCCCCCcCHHHHHHHHHHHHhhCCCCCCEEE
Confidence 3456677777763 5566666 432211 567788888888765545566677778888888888877 899998
Q ss_pred EEeCh--hhHHHHHHHH
Q 003054 121 LHMLP--SLGSRIFEKA 135 (852)
Q Consensus 121 ~~~~~--~~~~~i~~~a 135 (852)
-.+-+ -|+.+.+...
T Consensus 87 aiGGGS~iD~AKaia~~ 103 (347)
T cd08184 87 GIGGGSTLDVAKAVSNM 103 (347)
T ss_pred EeCCcHHHHHHHHHHHH
Confidence 76544 3555555443
No 391
>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=58.90 E-value=27 Score=37.01 Aligned_cols=79 Identities=9% Similarity=0.178 Sum_probs=53.9
Q ss_pred EEEEEEE--eCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhh-HHHHHHHHH
Q 003054 60 EAVPIYV--DNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSL-GSRIFEKAN 136 (852)
Q Consensus 60 ~vaii~~--d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~-~~~i~~~a~ 136 (852)
||++|.. ++.|-......+.+++++.|.++.... ....+.......+..+.+.++|.|++...... ....++++.
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 4666663 355767788889999999999876321 11223444566777777889999888654332 467788888
Q ss_pred HcCC
Q 003054 137 EIGL 140 (852)
Q Consensus 137 ~~G~ 140 (852)
+.|.
T Consensus 79 ~~~i 82 (294)
T cd06316 79 EAGI 82 (294)
T ss_pred HcCC
Confidence 8886
No 392
>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=58.68 E-value=33 Score=35.44 Aligned_cols=77 Identities=14% Similarity=0.149 Sum_probs=53.6
Q ss_pred EEEEEE--eCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHc
Q 003054 61 AVPIYV--DNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEI 138 (852)
Q Consensus 61 vaii~~--d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~ 138 (852)
++++.. .+.|-....+.+.+++++.|.++... ....+.......+.++.+.++|.+++..........++++.+.
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 455553 46677888899999999999887533 1112234456677888888999998886544444577888887
Q ss_pred CC
Q 003054 139 GL 140 (852)
Q Consensus 139 G~ 140 (852)
|.
T Consensus 79 ~i 80 (268)
T cd06289 79 GI 80 (268)
T ss_pred CC
Confidence 76
No 393
>PRK13583 hisG ATP phosphoribosyltransferase catalytic subunit; Provisional
Probab=58.62 E-value=1.3e+02 Score=30.69 Aligned_cols=90 Identities=13% Similarity=0.108 Sum_probs=52.4
Q ss_pred cCCHHHHHh--------cC--CeEEEEeCchHHHHHHhcCCCCccee-ecCCHhHHHHHhhcccccCceeEEEechhHHH
Q 003054 570 ITDVKMLIK--------RG--DNVGYQKGSFVLGILKQLGFDERKLV-VYNSPEDCHELFQKGSVNGGIAAAFDEIPYMK 638 (852)
Q Consensus 570 i~sl~dL~~--------~~--~~vg~~~~s~~~~~l~~~~~~~~~~~-~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~ 638 (852)
+++++||.. .| ++|+..--...+.|+.+.+.+...++ .+.+.|- +-..|- .+++++-...-.
T Consensus 111 ~~~~~dl~~~~~~~~~~~g~~~RIATkYp~it~~yf~~~Gv~~~~Iv~l~GsvEl---aP~~Gl----AD~IvDivsTG~ 183 (228)
T PRK13583 111 VDTMADLDDVAADFRARHGRRLRIATKYWRLTQQFLSQKGVQDYRIVESLGATEG---APANGS----AEIIVDITSTGE 183 (228)
T ss_pred cCCHHHhhhhhhhhhhccCCceEEEeCCHHHHHHHHHHcCCceeEEEECCCceec---ccccCc----chhhhhhhchhH
Confidence 677777751 13 58888777788899998877642333 3445542 233344 556665544444
Q ss_pred HHHhhcCCceEeec-ccccccceEEEecCCCC
Q 003054 639 LLIGQYCSKYAMIE-PKFKTAGFGFVFPLHSP 669 (852)
Q Consensus 639 ~~~~~~~~~~~~v~-~~~~~~~~~~~~~k~sp 669 (852)
-+.++ .+.+++ +.+......++.++.|.
T Consensus 184 TLr~N---gL~~i~~~~Il~SsA~LI~n~~s~ 212 (228)
T PRK13583 184 TLRAN---HLKILSDGVILRSQACLVRARKAD 212 (228)
T ss_pred HHHHC---CCEEecCceEEEEEEEEEEecccc
Confidence 33332 366775 35555566666677764
No 394
>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=58.23 E-value=42 Score=35.46 Aligned_cols=77 Identities=12% Similarity=0.107 Sum_probs=56.6
Q ss_pred EEEEEE--eCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeC-hhhHHHHHHHHHH
Q 003054 61 AVPIYV--DNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHML-PSLGSRIFEKANE 137 (852)
Q Consensus 61 vaii~~--d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~-~~~~~~i~~~a~~ 137 (852)
|+++.. ++.|-....+.+.+++++.|.++..... ..+.......++.+.+.++|.|++... .......++++++
T Consensus 2 I~vi~~~~~~~~~~~~~~gi~~~a~~~g~~~~~~~~---~~~~~~~~~~i~~~~~~~vdgiii~~~~~~~~~~~l~~l~~ 78 (288)
T cd01538 2 IGLSLPTKTEERWIRDRPNFEAALKELGAEVIVQNA---NGDPAKQISQIENMIAKGVDVLVIAPVDGEALASAVEKAAD 78 (288)
T ss_pred eEEEEeCCCcHHHHHHHHHHHHHHHHcCCEEEEECC---CCCHHHHHHHHHHHHHcCCCEEEEecCChhhHHHHHHHHHH
Confidence 566664 4677888899999999999998765432 223445667788888899999988754 3445678888888
Q ss_pred cCC
Q 003054 138 IGL 140 (852)
Q Consensus 138 ~G~ 140 (852)
.|.
T Consensus 79 ~~i 81 (288)
T cd01538 79 AGI 81 (288)
T ss_pred CCC
Confidence 775
No 395
>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=57.74 E-value=2.2e+02 Score=30.33 Aligned_cols=40 Identities=15% Similarity=0.188 Sum_probs=29.8
Q ss_pred HHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCcccEEEee
Q 003054 380 VDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGEFDAVVGD 430 (852)
Q Consensus 380 ~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~~D~~~g~ 430 (852)
..|++.+.+.+||++++. .. +-.-+...|.+|++|+.+..
T Consensus 24 ~~i~~~iLE~~Gy~Ve~~--~~---------~~~~~~~al~~GdiD~~~e~ 63 (290)
T TIGR03414 24 TALASVLLEGLGYQPKVT--LL---------SVPVTYAGLKDGDLDVFLGN 63 (290)
T ss_pred HHHHHHHHHHcCCcceeE--Ec---------cHHHHHHHHHcCCceEeccc
Confidence 478888888889877653 22 34677889999999997753
No 396
>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=57.39 E-value=44 Score=34.61 Aligned_cols=75 Identities=15% Similarity=0.052 Sum_probs=51.5
Q ss_pred EEEEEEe-----CCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHH
Q 003054 61 AVPIYVD-----NQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKA 135 (852)
Q Consensus 61 vaii~~d-----~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a 135 (852)
|+++..+ +.|-....+.+.+++++.|.++..... . ..+.+....+..+.+.++|.|++.....+. .++.+
T Consensus 2 vgv~~~~~~~~~~~~~~~~~~~i~~~~~~~g~~~~~~~~-~--~~~~~~~~~~~~l~~~~vdgiii~~~~~~~--~~~~l 76 (268)
T cd06277 2 IGLIASKRILNSPAFYSEIYRAIEEEAKKYGYNLILKFV-S--DEDEEEFELPSFLEDGKVDGIILLGGISTE--YIKEI 76 (268)
T ss_pred eEEEEeccccccCCcHHHHHHHHHHHHHHcCCEEEEEeC-C--CChHHHHHHHHHHHHCCCCEEEEeCCCChH--HHHHH
Confidence 5666655 778888899999999999988765432 2 223334455566777899999987654332 37777
Q ss_pred HHcCC
Q 003054 136 NEIGL 140 (852)
Q Consensus 136 ~~~G~ 140 (852)
.+.|.
T Consensus 77 ~~~~i 81 (268)
T cd06277 77 KELGI 81 (268)
T ss_pred hhcCC
Confidence 77775
No 397
>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=57.28 E-value=35 Score=35.10 Aligned_cols=78 Identities=12% Similarity=0.102 Sum_probs=54.4
Q ss_pred EEEEEEEe--CCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeCh-hhHHHHHHHHH
Q 003054 60 EAVPIYVD--NQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLP-SLGSRIFEKAN 136 (852)
Q Consensus 60 ~vaii~~d--~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~-~~~~~i~~~a~ 136 (852)
+|++|..+ +.|.....+.+.+++++.|.++..... ..+.......++++...++|.|++.... +.....++.++
T Consensus 1 ~ig~i~p~~~~~~~~~~~~~~~~~a~~~g~~~~~~~~---~~~~~~~~~~~~~l~~~~vdgvi~~~~~~~~~~~~~~~l~ 77 (267)
T cd01536 1 KIGLVVPSLNNPFWQAMNKGAEAAAKELGVELIVLDA---QNDVSKQIQQIEDLIAQGVDGIIISPVDSAALTPALKKAN 77 (267)
T ss_pred CEEEEeccccCHHHHHHHHHHHHHHHhcCceEEEECC---CCCHHHHHHHHHHHHHcCCCEEEEeCCCchhHHHHHHHHH
Confidence 46777753 678888999999999999988765422 1234445677788888899999887544 33344667777
Q ss_pred HcCC
Q 003054 137 EIGL 140 (852)
Q Consensus 137 ~~G~ 140 (852)
+.|.
T Consensus 78 ~~~i 81 (267)
T cd01536 78 AAGI 81 (267)
T ss_pred HCCC
Confidence 7664
No 398
>PF07287 DUF1446: Protein of unknown function (DUF1446); InterPro: IPR010839 This family consists of several bacterial and plant proteins of around 400 residues in length. The function of this family is unknown.
Probab=57.13 E-value=72 Score=35.03 Aligned_cols=114 Identities=12% Similarity=0.144 Sum_probs=62.5
Q ss_pred HHHHhcCCCCccEEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHcCCc-EEEEEEEeCCcccccHHHHHHHHH
Q 003054 5 FIIQLGNKSQVPILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAFGWR-EAVPIYVDNQYGEEMIPSLTDALQ 83 (852)
Q Consensus 5 ~v~~i~~~~~vP~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~gw~-~vaii~~d~~~G~~~~~~l~~~l~ 83 (852)
.+.+.+.+.+||+|+-++.. +....++.+.+++++.|++ ||++|+.|+. .+.+.+.++
T Consensus 62 ~~L~~~~~~gIkvI~NaGg~----------------np~~~a~~v~eia~e~Gl~lkvA~V~gDd~-----~~~v~~~~~ 120 (362)
T PF07287_consen 62 PLLPAAAEKGIKVITNAGGL----------------NPAGCADIVREIARELGLSLKVAVVYGDDL-----KDEVKELLA 120 (362)
T ss_pred HHHHHHHhCCCCEEEeCCCC----------------CHHHHHHHHHHHHHhcCCCeeEEEEECccc-----hHhHHHHHh
Confidence 45677888999999843311 1222777888888887775 8888886665 445554444
Q ss_pred hCCceeeeeeecCCC-------------CChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHcCCcccc
Q 003054 84 AIDTRVPYRSVISPL-------------ATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEIGLMNKG 144 (852)
Q Consensus 84 ~~g~~v~~~~~~~~~-------------~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~G~~~~~ 144 (852)
+ |..+..-..-++. .+. .+.+..|+ .++||||..=..+.+.-+--.+.+.|+...+
T Consensus 121 ~-g~~~~~l~~~~~l~~~~~~~~~a~aylGa---~pI~~AL~-~GADIVI~GR~~D~Al~~a~~~~~~GW~~~d 189 (362)
T PF07287_consen 121 E-GETIRPLDTGPPLSEWDDRIVSANAYLGA---EPIVEALE-AGADIVITGRVADPALFAAPAIHEFGWSEDD 189 (362)
T ss_pred C-CCCCccCCCCCCcchhccccceEEEecCh---HHHHHHHH-cCCCEEEeCcccchHHHHhHHHHHcCCCccc
Confidence 2 2111100000000 112 23333333 6899877654444444444456678875443
No 399
>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=56.52 E-value=15 Score=33.07 Aligned_cols=87 Identities=15% Similarity=0.137 Sum_probs=46.6
Q ss_pred cEEEEEEEeCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhh--cCCceEEEEEeChhhHHHHHHHHH
Q 003054 59 REAVPIYVDNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLF--TMQTRVFILHMLPSLGSRIFEKAN 136 (852)
Q Consensus 59 ~~vaii~~d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~--~~~~~viv~~~~~~~~~~i~~~a~ 136 (852)
|++|++...+.-++- ...+.+.|.+.|.+|... .+..+.-+=......|. -..+|.++++..+.....+++++.
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 KSIAVVGASDNPGKF-GYRVLRNLKAAGYEVYPV---NPKGGEILGIKCYPSLAEIPEPIDLAVVCVPPDKVPEIVDEAA 76 (116)
T ss_dssp -EEEEET--SSTTSH-HHHHHHHHHHTT-EEEEE---STTCSEETTEE-BSSGGGCSST-SEEEE-S-HHHHHHHHHHHH
T ss_pred CEEEEEcccCCCCCh-HHHHHHHHHhCCCEEEEE---CCCceEECcEEeeccccCCCCCCCEEEEEcCHHHHHHHHHHHH
Confidence 578888754443332 233444455577666432 22221100001222333 368899999999999999999999
Q ss_pred HcCCcccceEEEEcCc
Q 003054 137 EIGLMNKGCVWIMTDG 152 (852)
Q Consensus 137 ~~G~~~~~~vwi~~~~ 152 (852)
++|. +.+|+.++.
T Consensus 77 ~~g~---~~v~~~~g~ 89 (116)
T PF13380_consen 77 ALGV---KAVWLQPGA 89 (116)
T ss_dssp HHT----SEEEE-TTS
T ss_pred HcCC---CEEEEEcch
Confidence 9984 578988773
No 400
>COG0040 HisG ATP phosphoribosyltransferase [Amino acid transport and metabolism]
Probab=56.39 E-value=85 Score=33.11 Aligned_cols=102 Identities=13% Similarity=0.046 Sum_probs=59.4
Q ss_pred cCCHHHHHhcCCeEEEEeCchHHHHHHhcCCCCcceeecCCHhHHHHHhhcccccCceeEEEechhHHHHHHhhcCCceE
Q 003054 570 ITDVKMLIKRGDNVGYQKGSFVLGILKQLGFDERKLVVYNSPEDCHELFQKGSVNGGIAAAFDEIPYMKLLIGQYCSKYA 649 (852)
Q Consensus 570 i~sl~dL~~~~~~vg~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~~~~~~~ 649 (852)
+++.+||... .+|+..--...++|+++.+.+-.-+....+.| -+-..|- .||+++-...-.-+..+.+ .
T Consensus 107 ~~~~~~l~~~-~rIATkYp~l~~~yf~~~g~~~~Ii~l~GsvE---~aP~~Gl----ADaIvDivsTG~TLkaNgL---~ 175 (290)
T COG0040 107 YTSPEDLKGR-LRIATKYPNLARKYFAEKGIDVEIIKLSGSVE---LAPALGL----ADAIVDIVSTGTTLKANGL---K 175 (290)
T ss_pred ccChhHhcCC-ceEEEccHHHHHHHHHHcCceEEEEEccCcEe---eccccCc----cceEEEeecCCHhHHHCCC---E
Confidence 6788888622 48888777778889988766543344444444 2334465 7888877666666555544 4
Q ss_pred eecccccccceEEEecCCCCch---hhHHHHHHhccc
Q 003054 650 MIEPKFKTAGFGFVFPLHSPLV---HDVSKAILNVTE 683 (852)
Q Consensus 650 ~v~~~~~~~~~~~~~~k~spl~---~~in~~il~l~e 683 (852)
.+ +.+....-+++..+...+. +.+++.+.+++.
T Consensus 176 ~i-d~i~~ssa~LI~n~~~~~~~k~~~i~~l~~rl~g 211 (290)
T COG0040 176 EI-EVIYDSSARLIVNAKASLKDKQELIDQLVTRLKG 211 (290)
T ss_pred EE-EEEEeeEEEEEeccccccchhHHHHHHHHHHHHH
Confidence 45 3334444455555332222 346666666543
No 401
>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=56.05 E-value=39 Score=35.96 Aligned_cols=78 Identities=13% Similarity=0.088 Sum_probs=54.6
Q ss_pred EEEEE--EeCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeCh-hhHHHHHHHHHH
Q 003054 61 AVPIY--VDNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLP-SLGSRIFEKANE 137 (852)
Q Consensus 61 vaii~--~d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~-~~~~~i~~~a~~ 137 (852)
|+++. .++.|-......+.+++++.|.++.... +.+.+.......+..+...++|.|++.... +....+++++++
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 55555 3567888889999999999998876421 112234556677777878899999987543 334677788888
Q ss_pred cCC
Q 003054 138 IGL 140 (852)
Q Consensus 138 ~G~ 140 (852)
.|+
T Consensus 80 ~~i 82 (298)
T cd06302 80 AGI 82 (298)
T ss_pred CCC
Confidence 776
No 402
>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=56.01 E-value=35 Score=35.73 Aligned_cols=77 Identities=9% Similarity=0.028 Sum_probs=54.1
Q ss_pred EEEEEE--eCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhh-HHHHHHHHHH
Q 003054 61 AVPIYV--DNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSL-GSRIFEKANE 137 (852)
Q Consensus 61 vaii~~--d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~-~~~i~~~a~~ 137 (852)
|+++.. .+.|.......+.+++++.|.++.... ...+.......+..+...++|.|++.....+ ....++.+.+
T Consensus 2 igv~~~~~~~~~~~~~~~~i~~~~~~~g~~v~~~~---~~~~~~~~~~~i~~~~~~~~Dgiii~~~~~~~~~~~i~~~~~ 78 (282)
T cd06318 2 IGFSQYTLNSPFFAALTEAAKAHAKALGYELISTD---AQGDLTKQIADVEDLLTRGVNVLIINPVDPEGLVPAVAAAKA 78 (282)
T ss_pred eeEEeccccCHHHHHHHHHHHHHHHHcCCEEEEEc---CCCCHHHHHHHHHHHHHcCCCEEEEecCCccchHHHHHHHHH
Confidence 555553 467788889999999999999876432 1223444556788888899999998754333 3456788887
Q ss_pred cCC
Q 003054 138 IGL 140 (852)
Q Consensus 138 ~G~ 140 (852)
.|.
T Consensus 79 ~~i 81 (282)
T cd06318 79 AGV 81 (282)
T ss_pred CCC
Confidence 775
No 403
>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=55.21 E-value=46 Score=34.39 Aligned_cols=76 Identities=14% Similarity=0.085 Sum_probs=54.8
Q ss_pred EEEEEE--eCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHc
Q 003054 61 AVPIYV--DNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEI 138 (852)
Q Consensus 61 vaii~~--d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~ 138 (852)
|+++.. +++|-....+.+.+++++.|..+..... ..+.+.....+..+.+.++|.||+....... ..++++++.
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 566664 5677788889999999999998775432 1234456677888888999999987654333 357888887
Q ss_pred CC
Q 003054 139 GL 140 (852)
Q Consensus 139 G~ 140 (852)
|.
T Consensus 78 ~i 79 (265)
T cd06299 78 GI 79 (265)
T ss_pred CC
Confidence 75
No 404
>PRK01741 cell division protein ZipA; Provisional
Probab=55.11 E-value=34 Score=36.48 Aligned_cols=14 Identities=36% Similarity=0.667 Sum_probs=10.7
Q ss_pred eecceeecCCCccc
Q 003054 833 IVSAVELTIPDQEI 846 (852)
Q Consensus 833 ~~~~~~~~~~~~~~ 846 (852)
-|+.|.++.|++|.
T Consensus 97 sv~~IKI~LP~~~~ 110 (332)
T PRK01741 97 SVDEIKITLPNQEP 110 (332)
T ss_pred hHhheEEeCCCCCc
Confidence 46778899999663
No 405
>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=54.99 E-value=38 Score=35.19 Aligned_cols=80 Identities=9% Similarity=0.074 Sum_probs=54.1
Q ss_pred EEEEEEE--eCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhh-HHHHHHHHH
Q 003054 60 EAVPIYV--DNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSL-GSRIFEKAN 136 (852)
Q Consensus 60 ~vaii~~--d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~-~~~i~~~a~ 136 (852)
||++|.. +++|-......+.+++++.|.++.....-. ..+.......+.++...++|.+|+...... ....++.+.
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 4677764 366778889999999999999876543211 122344556777778889999988654433 245677777
Q ss_pred HcCC
Q 003054 137 EIGL 140 (852)
Q Consensus 137 ~~G~ 140 (852)
+.|+
T Consensus 80 ~~~i 83 (273)
T cd06310 80 DAGI 83 (273)
T ss_pred HCCC
Confidence 7665
No 406
>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=54.77 E-value=1.3e+02 Score=31.62 Aligned_cols=128 Identities=19% Similarity=0.236 Sum_probs=74.8
Q ss_pred eeeecccCCCcCCHHHHHhc-----C-CeEEEE-eCchHH---H-HHHhcCCCCcceeecCCHhHHHHHhhcccccCcee
Q 003054 560 LLTVQQLQPTITDVKMLIKR-----G-DNVGYQ-KGSFVL---G-ILKQLGFDERKLVVYNSPEDCHELFQKGSVNGGIA 628 (852)
Q Consensus 560 ~Lt~~~~~~~i~sl~dL~~~-----~-~~vg~~-~~s~~~---~-~l~~~~~~~~~~~~~~~~~~~~~~l~~g~~~~g~~ 628 (852)
.|.+.. ..+++|++||++- + ..+|.. .|+..+ . +.+..+.+ .+.++|+.-.+.+.+|..|. ++
T Consensus 81 vl~v~~-dsp~~t~~eli~~ak~~p~~~~~g~~g~g~~~hl~~~~l~~~~G~~-~~~Vpy~G~~~~~~allgG~----vd 154 (274)
T PF03401_consen 81 VLVVRA-DSPYKTLEELIEYAKANPGKLTFGSSGPGSSDHLAAALLAKAAGIK-FTHVPYDGGAEALTALLGGH----VD 154 (274)
T ss_dssp EEEEET-TSS-SSHHHHHHHHHCSCCC-EEEESSTTSHHHHHHHHHHHHHT----EEEE-SSHHHHHHHHHTTS----SS
T ss_pred EEEEeC-CCccccHHHHHHHHHhCCCCeEEEecCCCchHHHHHHHHHHHhCCc-eEEEEeCCccHHHHHHhCCe----ee
Confidence 344433 5679999999732 2 266654 233222 2 22345553 36789999999999999999 99
Q ss_pred EEEechhHHHHHHh-hcCC--------ce------Eeecc----cc-cccceEEEecCCCC--chhhHHHHHHhccccCh
Q 003054 629 AAFDEIPYMKLLIG-QYCS--------KY------AMIEP----KF-KTAGFGFVFPLHSP--LVHDVSKAILNVTEGDK 686 (852)
Q Consensus 629 a~~~~~~~~~~~~~-~~~~--------~~------~~v~~----~~-~~~~~~~~~~k~sp--l~~~in~~il~l~e~G~ 686 (852)
+.+.......-+++ ...+ +. -.+.+ .+ .....+++.|||-| .++.+..++.+..++-.
T Consensus 155 ~~~~~~~~~~~~~~~G~~k~Lav~~~~r~~~~pdvPT~~E~G~~d~~~~~~~g~~~p~gtp~~~~~~l~~a~~~~~~~pe 234 (274)
T PF03401_consen 155 AAFGSPGEALPYVEAGDLKPLAVFSDERSPALPDVPTFKEQGYPDIVFGSWRGLFAPKGTPDEIVDKLADAIKKALEDPE 234 (274)
T ss_dssp EEEEEHHHHHHHHHTTSEEEEEECSSS-BTTCTTS-BTTTTT-TTG--EEEEEEEEETTS-HHHHHHHHHHHHHHHT-HH
T ss_pred EEeecHHHHHHHHhCCCceEEEEecCccccccCCCCCHHHhCccceeeeeeeeeecCCCCCHHHHHHHHHHHHHHhCCHH
Confidence 98877544443333 2211 01 01111 11 22344889999977 89999999999998877
Q ss_pred hHHHHHH
Q 003054 687 MKEIEDA 693 (852)
Q Consensus 687 ~~~i~~k 693 (852)
+++..++
T Consensus 235 ~~~~~~~ 241 (274)
T PF03401_consen 235 FQEFLEK 241 (274)
T ss_dssp HHHHHHH
T ss_pred HHHHHHH
Confidence 7665554
No 407
>cd01540 PBP1_arabinose_binding Periplasmic L-arabinose-binding protein (ABP), a member of a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily. Periplasmic L-arabinose-binding protein (ABP), a member of a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily. ABP is only involved in transport contrary to other related sugar-binding proteins such as the glucose/galactose-binding protein (GGBP) and the ribose-binding protein (RBP), both of which are involved in chemotaxis as well as transport. The periplasmic ABP consists of two alpha/beta globular domains connected by a three-stranded hinge, a Venus flytrap-like domain, which undergoes a transition from an open to a closed conformational state upon ligand binding. Moreover, ABP is homologous to the ligand-binding domain of eukaryotic receptors such as metabotropic glutamate receptor (mGluR) and DNA-binding transcriptional repressors such a
Probab=54.49 E-value=34 Score=35.99 Aligned_cols=76 Identities=13% Similarity=0.080 Sum_probs=54.5
Q ss_pred EEEEEE--eCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeCh-hhHHHHHHHHHH
Q 003054 61 AVPIYV--DNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLP-SLGSRIFEKANE 137 (852)
Q Consensus 61 vaii~~--d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~-~~~~~i~~~a~~ 137 (852)
|+++.. ++.|-....+.+.+++++.|.++... ... +.......+.++...++|.|++.... +....+++++++
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 566663 45677888899999999999887643 222 24445567788888999999887543 345667888888
Q ss_pred cCC
Q 003054 138 IGL 140 (852)
Q Consensus 138 ~G~ 140 (852)
.|.
T Consensus 78 ~~i 80 (289)
T cd01540 78 YNM 80 (289)
T ss_pred CCC
Confidence 876
No 408
>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=54.39 E-value=41 Score=34.82 Aligned_cols=78 Identities=17% Similarity=0.099 Sum_probs=52.1
Q ss_pred EEEEE--EeCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHc
Q 003054 61 AVPIY--VDNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEI 138 (852)
Q Consensus 61 vaii~--~d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~ 138 (852)
|+++. .++.|.....+.+.+++++.|.++.....- ...+......+..+.+.++|.|++..........++.+.+.
T Consensus 2 I~vi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~~--~~~~~~~~~~~~~l~~~~vdgiii~~~~~~~~~~~~~~~~~ 79 (270)
T cd01545 2 IGLLYDNPSPGYVSEIQLGALDACRDTGYQLVIEPCD--SGSPDLAERVRALLQRSRVDGVILTPPLSDNPELLDLLDEA 79 (270)
T ss_pred EEEEEcCCCcccHHHHHHHHHHHHHhCCCeEEEEeCC--CCchHHHHHHHHHHHHCCCCEEEEeCCCCCccHHHHHHHhc
Confidence 45666 346789999999999999999887654321 11122445556667788999988864432335566777777
Q ss_pred CC
Q 003054 139 GL 140 (852)
Q Consensus 139 G~ 140 (852)
|+
T Consensus 80 ~i 81 (270)
T cd01545 80 GV 81 (270)
T ss_pred CC
Confidence 75
No 409
>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=53.29 E-value=93 Score=33.97 Aligned_cols=82 Identities=11% Similarity=-0.063 Sum_probs=56.5
Q ss_pred HHHHHHH-HcCCcEEEEEEEeCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeCh-
Q 003054 48 AITAIIK-AFGWREAVPIYVDNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLP- 125 (852)
Q Consensus 48 aia~~l~-~~gw~~vaii~~d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~- 125 (852)
.+.++++ ..+.+++.++.....+ +...+.+.+.|++.| .+... +.++.+.+.+...+..+++.++|+||..+.+
T Consensus 14 ~l~~~l~~~~~~~~~liv~d~~~~-~~~~~~v~~~l~~~~-~~~~~--~~~~~~~~~v~~~~~~~~~~~~d~iIaiGGGs 89 (339)
T cd08173 14 KIPNVLRDLLLGGRVLVVTGPTTK-SIAGKKVEALLEDEG-EVDVV--IVEDATYEEVEKVESSARDIGADFVIGVGGGR 89 (339)
T ss_pred HHHHHHHHhCCCCeEEEEECCchH-HHHHHHHHHHHHhcC-CeEEE--EeCCCCHHHHHHHHHHhhhcCCCEEEEeCCch
Confidence 4556676 3567899888844333 356677888898888 54332 3345567788888888988899999877554
Q ss_pred -hhHHHHHH
Q 003054 126 -SLGSRIFE 133 (852)
Q Consensus 126 -~~~~~i~~ 133 (852)
-|+.+++.
T Consensus 90 ~~D~aK~~a 98 (339)
T cd08173 90 VIDVAKVAA 98 (339)
T ss_pred HHHHHHHHH
Confidence 46666665
No 410
>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=53.27 E-value=46 Score=34.59 Aligned_cols=80 Identities=13% Similarity=0.133 Sum_probs=53.8
Q ss_pred EEEEEE--EeCCcccccHHHHHHHHHhC---CceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhh-HHHHHH
Q 003054 60 EAVPIY--VDNQYGEEMIPSLTDALQAI---DTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSL-GSRIFE 133 (852)
Q Consensus 60 ~vaii~--~d~~~G~~~~~~l~~~l~~~---g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~-~~~i~~ 133 (852)
||+++. .++.|-....+.+.+++++. |.++.... +..+.+.+.....+.++...++|.||+...... ....++
T Consensus 1 ~Ig~i~~~~~~~~~~~~~~~i~~~~~~~~~~g~~~~l~i-~~~~~~~~~~~~~~~~~~~~~vdgiIi~~~~~~~~~~~l~ 79 (272)
T cd06300 1 KIGLSNSYAGNTWRAQMLDEFKAQAKELKKAGLISEFIV-TSADGDVAQQIADIRNLIAQGVDAIIINPASPTALNPVIE 79 (272)
T ss_pred CeEEeccccCChHHHHHHHHHHHHHHhhhccCCeeEEEE-ecCCCCHHHHHHHHHHHHHcCCCEEEEeCCChhhhHHHHH
Confidence 456665 34567778888999999998 87432222 122223455778888888889999999765433 345677
Q ss_pred HHHHcCC
Q 003054 134 KANEIGL 140 (852)
Q Consensus 134 ~a~~~G~ 140 (852)
.+++.|.
T Consensus 80 ~~~~~~i 86 (272)
T cd06300 80 EACEAGI 86 (272)
T ss_pred HHHHCCC
Confidence 8888775
No 411
>COG4521 TauA ABC-type taurine transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=53.12 E-value=85 Score=31.90 Aligned_cols=108 Identities=20% Similarity=0.198 Sum_probs=68.2
Q ss_pred CcCCHHHHHhcCCeEEEEeCchHHH-H---HHhcCCCCcceeecC-CHhHHHHHhhcccccCceeEEEechhHHHHHHhh
Q 003054 569 TITDVKMLIKRGDNVGYQKGSFVLG-I---LKQLGFDERKLVVYN-SPEDCHELFQKGSVNGGIAAAFDEIPYMKLLIGQ 643 (852)
Q Consensus 569 ~i~sl~dL~~~~~~vg~~~~s~~~~-~---l~~~~~~~~~~~~~~-~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~ 643 (852)
.|...+||+ |++|++..-|+.+- + |+..+.++.++...+ .+-+...+.++|. +|+.....+.+.-+...
T Consensus 121 gI~kpeDL~--GK~iavPFvSTtHysLLaaLkhw~idp~~V~IlNl~Pp~IaAAwqRGD----IDgAyVW~PAl~el~ks 194 (334)
T COG4521 121 GIEKPEDLI--GKRIAVPFVSTTHYSLLAALKHWGIDPGQVEILNLQPPAIAAAWQRGD----IDGAYVWAPALSELKKS 194 (334)
T ss_pred CcCChHHhc--cCeeccceeehhHHHHHHHHHHcCCCccceeEeccCCHHHHHHHHcCC----CCceeeccHhHHHHhhc
Confidence 389999998 99999865554432 2 355677777766665 5678899999999 88887777766655433
Q ss_pred cC--CceEeecccccccceEEEecCC----CC-chhhHHHHHHhcc
Q 003054 644 YC--SKYAMIEPKFKTAGFGFVFPLH----SP-LVHDVSKAILNVT 682 (852)
Q Consensus 644 ~~--~~~~~v~~~~~~~~~~~~~~k~----sp-l~~~in~~il~l~ 682 (852)
.- ..-..++..-.+..-+++.+|+ .| .+..|-+..+.-.
T Consensus 195 GkVltDs~qvgqwgaPTfdvwVvrkdfAekhPe~v~aFakv~~da~ 240 (334)
T COG4521 195 GKVLTDSEQVGQWGAPTFDVWVVRKDFAEKHPEVVAAFAKVALDAQ 240 (334)
T ss_pred CcEeccHHHhhccCCCceeeEEeehHhhHhChHHHHHHHHHHHHhh
Confidence 21 0111233333333446777775 34 6666666655443
No 412
>KOG1420 consensus Ca2+-activated K+ channel Slowpoke, alpha subunit [Inorganic ion transport and metabolism; Signal transduction mechanisms]
Probab=53.11 E-value=9.5 Score=42.73 Aligned_cols=53 Identities=17% Similarity=0.231 Sum_probs=44.1
Q ss_pred CCCCcccccchhHHHHHHHhhhccccc--cccchhhHHHHHHHHHHHHHHHHhhh
Q 003054 503 FRGPAGQQVGTSFWFSFSTMVFSQRER--VISNLARIVVIVWCFVVLILTQSYTA 555 (852)
Q Consensus 503 ~~~~~~~~~~~~~~~~~~~l~~~~~~~--~~s~~~R~v~~~w~~~~lil~~~Yta 555 (852)
|..+.+..+++|+++.+.+|-..+--. -....+|+++++++++++-+.++|.-
T Consensus 281 f~n~hrltyw~cvyfl~vtmstvgygdvyc~t~lgrlfmvffil~glamfasyvp 335 (1103)
T KOG1420|consen 281 FQNNHRLTYWECVYFLMVTMSTVGYGDVYCKTTLGRLFMVFFILGGLAMFASYVP 335 (1103)
T ss_pred ccCcccchhhheeeeeEEEeeeccccceeehhhhhHHHHHHHHHHHHHHHHhhhH
Confidence 667777889999999888887776333 37888999999999999999999943
No 413
>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=53.06 E-value=92 Score=33.91 Aligned_cols=85 Identities=13% Similarity=0.060 Sum_probs=56.3
Q ss_pred HHHHHHHHHcCC-cEEEEEEEeCCcccccHHHHHHHHHhCCceeeeee-ecCCCCChHHHHHHHHHhhcCCceEEEEEeC
Q 003054 47 GAITAIIKAFGW-REAVPIYVDNQYGEEMIPSLTDALQAIDTRVPYRS-VISPLATDDQIEKELYKLFTMQTRVFILHML 124 (852)
Q Consensus 47 ~aia~~l~~~gw-~~vaii~~d~~~G~~~~~~l~~~l~~~g~~v~~~~-~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~ 124 (852)
..+.++++.++. +++.+|.....+... .+.+.+.|++.|.++.... ....+.+.+.+...+..+++ ++|+||-.+.
T Consensus 12 ~~l~~~~~~~~~~~kvlivtd~~~~~~~-~~~i~~~L~~~~~~~~i~~~~~~~~p~~~~v~~~~~~~~~-~~d~IIaiGG 89 (332)
T cd08549 12 NDIGPIINKIGVNSKIMIVCGNNTYKVA-GKEIIERLESNNFTKEVLERDSLLIPDEYELGEVLIKLDK-DTEFLLGIGS 89 (332)
T ss_pred HHHHHHHHHcCCCCcEEEEECCcHHHHH-HHHHHHHHHHcCCeEEEEecCCCCCCCHHHHHHHHHHhhc-CCCEEEEECC
Confidence 456667777775 788888855544332 3778888988887654321 22333456777788888887 9999987765
Q ss_pred h--hhHHHHHH
Q 003054 125 P--SLGSRIFE 133 (852)
Q Consensus 125 ~--~~~~~i~~ 133 (852)
+ -|+.+++.
T Consensus 90 Gsv~D~aK~iA 100 (332)
T cd08549 90 GTIIDLVKFVS 100 (332)
T ss_pred cHHHHHHHHHH
Confidence 4 46666665
No 414
>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=52.97 E-value=13 Score=27.60 Aligned_cols=28 Identities=29% Similarity=0.710 Sum_probs=23.0
Q ss_pred hHHHHHHHHHHHHHhhhhheecccCCCC
Q 003054 476 DLWVTCFCFFIFIGFVVWVLEHRVNEDF 503 (852)
Q Consensus 476 ~lW~~i~~~~i~~~~v~~~l~~~~~~~~ 503 (852)
++|.++..+.+++|+++|.+..+..+.|
T Consensus 12 ~~~~l~~~~~~Figiv~wa~~p~~k~~f 39 (48)
T cd01324 12 DSWGLLYLALFFLGVVVWAFRPGRKKAF 39 (48)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCCcchhH
Confidence 6789999899999999999987655443
No 415
>PF14981 FAM165: FAM165 family
Probab=52.87 E-value=29 Score=24.98 Aligned_cols=33 Identities=18% Similarity=0.218 Sum_probs=28.4
Q ss_pred ccchhHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q 003054 715 LNSFWGLFLIAGVAAILALIIFMAVFIHQHWNV 747 (852)
Q Consensus 715 l~~~~g~f~il~ig~~lsl~vf~~e~~~~~r~~ 747 (852)
++++--++||+..-.++.++.|..--+|++++.
T Consensus 3 L~~vPlLlYILaaKtlilClaFAgvK~yQ~krl 35 (51)
T PF14981_consen 3 LDNVPLLLYILAAKTLILCLAFAGVKMYQRKRL 35 (51)
T ss_pred hhhchHHHHHHHHHHHHHHHHHhhHHHHHHHHH
Confidence 567888999999999999999999888987765
No 416
>PRK00843 egsA NAD(P)-dependent glycerol-1-phosphate dehydrogenase; Reviewed
Probab=52.59 E-value=1.1e+02 Score=33.59 Aligned_cols=84 Identities=13% Similarity=-0.027 Sum_probs=57.8
Q ss_pred HHHHHHHHHHcCC-cEEEEEEEeCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeC
Q 003054 46 AGAITAIIKAFGW-REAVPIYVDNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHML 124 (852)
Q Consensus 46 ~~aia~~l~~~gw-~~vaii~~d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~ 124 (852)
...+.++++.++. +++.+|.....+.. ..+.+.+.+++.| ++... +.++.+.+.+...+.++++.++|+||..+.
T Consensus 21 l~~l~~~l~~~~~~~~~livtd~~~~~~-~~~~l~~~l~~~~-~~~~~--~~~~~t~~~v~~~~~~~~~~~~d~IIaiGG 96 (350)
T PRK00843 21 LDDIGDVCSDLKLTGRALIVTGPTTKKI-AGDRVEENLEDAG-DVEVV--IVDEATMEEVEKVEEKAKDVNAGFLIGVGG 96 (350)
T ss_pred HHHHHHHHHHhCCCCeEEEEECCcHHHH-HHHHHHHHHHhcC-CeeEE--eCCCCCHHHHHHHHHHhhccCCCEEEEeCC
Confidence 3456677777775 78888885554433 4567788888877 54322 344566778888889999889999987655
Q ss_pred h--hhHHHHHH
Q 003054 125 P--SLGSRIFE 133 (852)
Q Consensus 125 ~--~~~~~i~~ 133 (852)
+ -|..+++.
T Consensus 97 Gsv~D~ak~vA 107 (350)
T PRK00843 97 GKVIDVAKLAA 107 (350)
T ss_pred chHHHHHHHHH
Confidence 4 46666664
No 417
>PF06506 PrpR_N: Propionate catabolism activator; InterPro: IPR010524 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 [, ]. This entry represents a domain found at the N terminus of several sigma54- dependent transcriptional activators including PrpR, which activates catabolism of propionate. In Salmonella enterica subsp. enterica serovar Typhimurium, PrpR acts as a sensor of 2-methylcitrate (2-MC), an intermediate of the 2-methylcitric acid cycle used by this bacterium to convert propionate to pyruvate []. ; GO: 0000156 two-component response regulator activity, 0003677 DNA binding, 0005524 ATP binding, 0000160 two-component signal transduction system (phosphorelay); PDB: 2Q5C_A 2PJU_A.
Probab=52.33 E-value=39 Score=32.94 Aligned_cols=107 Identities=15% Similarity=0.128 Sum_probs=66.8
Q ss_pred EEeeecCCCCCCCCCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHHHHHhCCceeeeeeecC
Q 003054 17 ILSFSATSPSLTSIRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTDALQAIDTRVPYRSVIS 96 (852)
Q Consensus 17 ~Is~~ats~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~ 96 (852)
+||-++|...|.+.-.--+..+.++.....+++...- .++ ++++++...+.. .....+.+.| |.++.....
T Consensus 38 iIsRG~ta~~lr~~~~iPVV~I~~s~~Dil~al~~a~-~~~-~~Iavv~~~~~~--~~~~~~~~ll---~~~i~~~~~-- 108 (176)
T PF06506_consen 38 IISRGGTAELLRKHVSIPVVEIPISGFDILRALAKAK-KYG-PKIAVVGYPNII--PGLESIEELL---GVDIKIYPY-- 108 (176)
T ss_dssp EEEEHHHHHHHHCC-SS-EEEE---HHHHHHHHHHCC-CCT-SEEEEEEESS-S--CCHHHHHHHH---T-EEEEEEE--
T ss_pred EEECCHHHHHHHHhCCCCEEEECCCHhHHHHHHHHHH-hcC-CcEEEEeccccc--HHHHHHHHHh---CCceEEEEE--
Confidence 5777777776665323346667777777777776644 444 899999866554 2255665555 566654432
Q ss_pred CCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHcCC
Q 003054 97 PLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEIGL 140 (852)
Q Consensus 97 ~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~G~ 140 (852)
.+.+|+...+.++++.+.|+|+-.+ ...+.|++.|+
T Consensus 109 --~~~~e~~~~i~~~~~~G~~viVGg~------~~~~~A~~~gl 144 (176)
T PF06506_consen 109 --DSEEEIEAAIKQAKAEGVDVIVGGG------VVCRLARKLGL 144 (176)
T ss_dssp --SSHHHHHHHHHHHHHTT--EEEESH------HHHHHHHHTTS
T ss_pred --CCHHHHHHHHHHHHHcCCcEEECCH------HHHHHHHHcCC
Confidence 2477899999999999999988543 23667788898
No 418
>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=52.07 E-value=40 Score=36.73 Aligned_cols=79 Identities=14% Similarity=0.091 Sum_probs=54.1
Q ss_pred HHcCCcEEEEEEEeCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeCh--hhHHHH
Q 003054 54 KAFGWREAVPIYVDNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLP--SLGSRI 131 (852)
Q Consensus 54 ~~~gw~~vaii~~d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~--~~~~~i 131 (852)
+.++.+++.+++....+..+..+.+.+.|++. +++.....+.++.+.+.+...+..+++.++|+||-.+-+ -|+.+.
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 44556899888854444445778888888876 555433344555667778888899999999999966543 355555
Q ss_pred HH
Q 003054 132 FE 133 (852)
Q Consensus 132 ~~ 133 (852)
+.
T Consensus 97 ~a 98 (332)
T cd08180 97 II 98 (332)
T ss_pred HH
Confidence 43
No 419
>COG1879 RbsB ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]
Probab=51.98 E-value=51 Score=35.51 Aligned_cols=81 Identities=11% Similarity=0.119 Sum_probs=56.1
Q ss_pred cEEEEEE--EeCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEe-ChhhHHHHHHHH
Q 003054 59 REAVPIY--VDNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHM-LPSLGSRIFEKA 135 (852)
Q Consensus 59 ~~vaii~--~d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~-~~~~~~~i~~~a 135 (852)
.++++++ .+++|-....+.++++.++.|.... ....+...+...-...+..+...++|.|++.. ++......+++|
T Consensus 34 ~~i~~~~~~~~~~f~~~~~~g~~~~a~~~g~~~~-~~~~~~~~d~~~Q~~~i~~~ia~~~daIiv~~~d~~~~~~~v~~a 112 (322)
T COG1879 34 KTIGVVVPTLGNPFFQAVRKGAEAAAKKLGVVVA-VVIADAQNDVAKQIAQIEDLIAQGVDAIIINPVDPDALTPAVKKA 112 (322)
T ss_pred ceEEEEeccCCChHHHHHHHHHHHHHHHcCCcEE-EEecccccChHHHHHHHHHHHHcCCCEEEEcCCChhhhHHHHHHH
Confidence 5677777 5677888899999999999996211 11122122233344556666678999998875 556679999999
Q ss_pred HHcCC
Q 003054 136 NEIGL 140 (852)
Q Consensus 136 ~~~G~ 140 (852)
.+.|.
T Consensus 113 ~~aGI 117 (322)
T COG1879 113 KAAGI 117 (322)
T ss_pred HHCCC
Confidence 99997
No 420
>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=51.77 E-value=48 Score=35.63 Aligned_cols=88 Identities=18% Similarity=0.265 Sum_probs=59.2
Q ss_pred cEEEEEE----EeCCcccccHHHHHHHHHhC-CceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHH
Q 003054 59 REAVPIY----VDNQYGEEMIPSLTDALQAI-DTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFE 133 (852)
Q Consensus 59 ~~vaii~----~d~~~G~~~~~~l~~~l~~~-g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~ 133 (852)
++++++. .|..|.....+.+.+.-++. |+++...+..+. ++.++...+..+.+.+.|+||.++.. ..-.+.+
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 4566665 46678888888999998998 999888776542 36789999999999999999997653 2223333
Q ss_pred HHHHcCCcccceEEEEcCcc
Q 003054 134 KANEIGLMNKGCVWIMTDGM 153 (852)
Q Consensus 134 ~a~~~G~~~~~~vwi~~~~~ 153 (852)
.|++- |+-.|+..++.
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 44332 45556665543
No 421
>PRK09189 uroporphyrinogen-III synthase; Validated
Probab=51.76 E-value=75 Score=32.65 Aligned_cols=89 Identities=12% Similarity=0.006 Sum_probs=53.9
Q ss_pred hhHHHHHHHHHHHc--CCcEEEEEEEeCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEE
Q 003054 43 SSQAGAITAIIKAF--GWREAVPIYVDNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFI 120 (852)
Q Consensus 43 ~~~~~aia~~l~~~--gw~~vaii~~d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv 120 (852)
...++.+++++... .-++|.++. |....+.+.+.|++.|.+|.....|.......+-......+++.+.|+|+
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 35577888876432 345665555 34456788899999998876665553211111222334455666778776
Q ss_pred EEeChhhHHHHHHHHHH
Q 003054 121 LHMLPSLGSRIFEKANE 137 (852)
Q Consensus 121 ~~~~~~~~~~i~~~a~~ 137 (852)
+. ++..+..+++...+
T Consensus 176 f~-S~~~~~~f~~~~~~ 191 (240)
T PRK09189 176 LY-SRVAARRFFALMRL 191 (240)
T ss_pred Ee-CHHHHHHHHHHHhh
Confidence 65 45567788777644
No 422
>COG1794 RacX Aspartate racemase [Cell envelope biogenesis, outer membrane]
Probab=51.72 E-value=60 Score=32.70 Aligned_cols=86 Identities=15% Similarity=0.100 Sum_probs=49.9
Q ss_pred hHHHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHH-hhcCCceEEEEE
Q 003054 44 SQAGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYK-LFTMQTRVFILH 122 (852)
Q Consensus 44 ~~~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~-l~~~~~~viv~~ 122 (852)
+..++-++-+++.|.++|+++..... -.....++.|++.|++++ +|.+.....+...+.. |+. -.+.-
T Consensus 103 hIidaTa~~ik~~g~kkvgLLgT~~T---m~~~fY~~~l~~~gievv----vPdd~~q~~v~~iIy~El~~----G~~~~ 171 (230)
T COG1794 103 HIIDATAKAIKAAGAKKVGLLGTRFT---MEQGFYRKRLEEKGIEVV----VPDDDEQAEVNRIIYEELCQ----GIVKD 171 (230)
T ss_pred hHHHHHHHHHHhcCCceeEEeeccch---HHhHHHHHHHHHCCceEe----cCCHHHHHHHHHHHHHHHhc----ccchH
Confidence 46677788888889999999985432 234456789999998764 3322112222233322 332 12222
Q ss_pred eChhhHHHHHHHHHHcCC
Q 003054 123 MLPSLGSRIFEKANEIGL 140 (852)
Q Consensus 123 ~~~~~~~~i~~~a~~~G~ 140 (852)
.+.+....+.+.+.+.|-
T Consensus 172 ~sr~~~~~ii~~l~~~Ga 189 (230)
T COG1794 172 ASRELYLAVIERLAERGA 189 (230)
T ss_pred HHHHHHHHHHHHHHHcCC
Confidence 334445666677776664
No 423
>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=51.03 E-value=31 Score=35.14 Aligned_cols=93 Identities=13% Similarity=0.132 Sum_probs=61.5
Q ss_pred cCCchhHHHHHHHHHHH-cCCcEEEEEEEeCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCce
Q 003054 39 SLNDSSQAGAITAIIKA-FGWREAVPIYVDNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTR 117 (852)
Q Consensus 39 ~p~d~~~~~aia~~l~~-~gw~~vaii~~d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~ 117 (852)
.|.....++.+++.+.. ..-++|.++. |....+.|.+.|++.|.+|.....|.. .....-......+...+.+
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 56656677888888764 4447777765 444577899999999999887777654 2233334445555566777
Q ss_pred EEEEEeChhhHHHHHHHHHHc
Q 003054 118 VFILHMLPSLGSRIFEKANEI 138 (852)
Q Consensus 118 viv~~~~~~~~~~i~~~a~~~ 138 (852)
+|++ +++..+..+++...+.
T Consensus 171 ~v~f-tS~~~~~~~~~~~~~~ 190 (231)
T PF02602_consen 171 AVVF-TSPSAVRAFLELLKKN 190 (231)
T ss_dssp EEEE-SSHHHHHHHHHHSSGH
T ss_pred EEEE-CCHHHHHHHHHHhHhh
Confidence 6554 6777777787776654
No 424
>TIGR02370 pyl_corrinoid methyltransferase cognate corrinoid proteins, Methanosarcina family. This model describes a subfamily of the B12 binding domain (pfam02607, pfam02310) proteins. Members of the seed alignment include corrinoid proteins specific to four different, mutally non-homologous enzymes of the genus Methanosarcina. Three of the four cognate enzymes (trimethylamine, dimethylamine, and monomethylamine methyltransferases) all have the unusual, ribosomally incorporated amino acid pyrrolysine at the active site. All act in systems in which a methyl group is transferred to the corrinoid protein to create methylcobalamin, from which the methyl group is later transferred elsewhere.
Probab=50.89 E-value=97 Score=30.83 Aligned_cols=89 Identities=11% Similarity=-0.085 Sum_probs=59.5
Q ss_pred cEEEEEEEeCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeC----hhhHHHHHHH
Q 003054 59 REAVPIYVDNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHML----PSLGSRIFEK 134 (852)
Q Consensus 59 ~~vaii~~d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~----~~~~~~i~~~ 134 (852)
.+|.+....++.=.-....+...|+..|.+|.+-- .+... ...+..+++.+||+|.+.+. ......++++
T Consensus 85 ~~vv~~t~~gd~H~lG~~~v~~~l~~~G~~vi~LG---~~vp~---e~~v~~~~~~~pd~v~lS~~~~~~~~~~~~~i~~ 158 (197)
T TIGR02370 85 GKVVCGVAEGDVHDIGKNIVVTMLRANGFDVIDLG---RDVPI---DTVVEKVKKEKPLMLTGSALMTTTMYGQKDINDK 158 (197)
T ss_pred CeEEEEeCCCchhHHHHHHHHHHHHhCCcEEEECC---CCCCH---HHHHHHHHHcCCCEEEEccccccCHHHHHHHHHH
Confidence 46666665555544556777778999999987542 22223 44556667789999987754 3467888999
Q ss_pred HHHcCCcccceEEEEcCcc
Q 003054 135 ANEIGLMNKGCVWIMTDGM 153 (852)
Q Consensus 135 a~~~G~~~~~~vwi~~~~~ 153 (852)
+++.|...+-.+|+++...
T Consensus 159 l~~~~~~~~v~i~vGG~~~ 177 (197)
T TIGR02370 159 LKEEGYRDSVKFMVGGAPV 177 (197)
T ss_pred HHHcCCCCCCEEEEEChhc
Confidence 9999875554566665444
No 425
>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=50.46 E-value=62 Score=33.65 Aligned_cols=77 Identities=14% Similarity=0.042 Sum_probs=50.6
Q ss_pred CcEEEEEEE---------eCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhH
Q 003054 58 WREAVPIYV---------DNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLG 128 (852)
Q Consensus 58 w~~vaii~~---------d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~ 128 (852)
.+.|++|.. ++.|.....+.+.+++++.|.++..... +. + +.......+.+.++|.|++......
T Consensus 3 s~~i~vi~p~~~~~~~~~~~~~~~~~~~gi~~~~~~~g~~~~v~~~---~~-~-~~~~~~~~l~~~~~dgiii~~~~~~- 76 (275)
T cd06295 3 TDTIALVVPEPHERDQSFSDPFFLSLLGGIADALAERGYDLLLSFV---SS-P-DRDWLARYLASGRADGVILIGQHDQ- 76 (275)
T ss_pred ceEEEEEecCccccccccCCchHHHHHHHHHHHHHHcCCEEEEEeC---Cc-h-hHHHHHHHHHhCCCCEEEEeCCCCC-
Confidence 467888884 3456777888899999999988765421 11 1 2333444566688999988654322
Q ss_pred HHHHHHHHHcCC
Q 003054 129 SRIFEKANEIGL 140 (852)
Q Consensus 129 ~~i~~~a~~~G~ 140 (852)
...++++.+.|.
T Consensus 77 ~~~~~~~~~~~i 88 (275)
T cd06295 77 DPLPERLAETGL 88 (275)
T ss_pred hHHHHHHHhCCC
Confidence 244777888776
No 426
>COG0134 TrpC Indole-3-glycerol phosphate synthase [Amino acid transport and metabolism]
Probab=50.44 E-value=47 Score=34.28 Aligned_cols=88 Identities=16% Similarity=0.151 Sum_probs=68.8
Q ss_pred HHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEe---
Q 003054 47 GAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHM--- 123 (852)
Q Consensus 47 ~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~--- 123 (852)
..+|+..+++|..-+.|+. |..|-.+..+.+++.-+...+.|.-+..+. + ..++...+..++|+|++..
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 4477778888988888887 778889999999988888888877665442 2 2367788889999986653
Q ss_pred ChhhHHHHHHHHHHcCCcc
Q 003054 124 LPSLGSRIFEKANEIGLMN 142 (852)
Q Consensus 124 ~~~~~~~i~~~a~~~G~~~ 142 (852)
...+...++..|+++||..
T Consensus 141 ~~~~l~el~~~A~~LGm~~ 159 (254)
T COG0134 141 DDEQLEELVDRAHELGMEV 159 (254)
T ss_pred CHHHHHHHHHHHHHcCCee
Confidence 3455899999999999943
No 427
>KOG3713 consensus Voltage-gated K+ channel KCNB/KCNC [Inorganic ion transport and metabolism]
Probab=50.22 E-value=19 Score=40.30 Aligned_cols=62 Identities=13% Similarity=0.250 Sum_probs=48.8
Q ss_pred HHHhhhhheecccCCCCCCCcccccchhHHHHHHHhhhcc--ccccccchhhHHHHHHHHHHHHHHHH
Q 003054 487 FIGFVVWVLEHRVNEDFRGPAGQQVGTSFWFSFSTMVFSQ--RERVISNLARIVVIVWCFVVLILTQS 552 (852)
Q Consensus 487 ~~~~v~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~--~~~~~s~~~R~v~~~w~~~~lil~~~ 552 (852)
+.+.++|++|+-.+. ++-.++.-++||+.-+|...| ...|.+.++|++....+++++++.+.
T Consensus 358 iFStlvY~~Ek~~~~----~~FtSIPa~~WWaiVTMTTVGYGDm~P~T~~Gklvas~cil~GVLvlAl 421 (477)
T KOG3713|consen 358 IFSTLVYFAEKDEPD----TKFTSIPAGFWWAVVTMTTVGYGDMVPVTVLGKLVASLCILCGVLVLAL 421 (477)
T ss_pred HHHHHHHHhhhcCCC----CCCccccchhheeeEEEeeecccCccccccchHHHHHHHHHHhHHHhhc
Confidence 346677888876543 235578889999999999887 34689999999999999998887764
No 428
>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=50.07 E-value=1.1e+02 Score=33.56 Aligned_cols=100 Identities=6% Similarity=-0.047 Sum_probs=61.9
Q ss_pred HHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHHHHHh-CCceeeeeeecCCCCChHHHHHHHHHhhcCC---ceEEEEE
Q 003054 47 GAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTDALQA-IDTRVPYRSVISPLATDDQIEKELYKLFTMQ---TRVFILH 122 (852)
Q Consensus 47 ~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~~l~~-~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~---~~viv~~ 122 (852)
..+.++++.++-+++.++.....+. ...+.+.+.|++ .++++........+.+.+.+...+..+++.+ +|+||..
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 4456677778888998887444333 566777788876 5665543323333445666777777777544 8988876
Q ss_pred eCh--hhHHHHHHHHHHcCCcccceEEEEc
Q 003054 123 MLP--SLGSRIFEKANEIGLMNKGCVWIMT 150 (852)
Q Consensus 123 ~~~--~~~~~i~~~a~~~G~~~~~~vwi~~ 150 (852)
+.+ -|...++......|+ .++-|-|
T Consensus 91 GGGsv~D~ak~vA~~~~rgi---p~i~VPT 117 (344)
T cd08169 91 GGGATGDVAGFVASTLFRGI---AFIRVPT 117 (344)
T ss_pred CCcHHHHHHHHHHHHhccCC---cEEEecC
Confidence 554 466666665544454 3444444
No 429
>TIGR00249 sixA phosphohistidine phosphatase SixA.
Probab=50.06 E-value=66 Score=30.48 Aligned_cols=98 Identities=11% Similarity=0.029 Sum_probs=58.7
Q ss_pred ccCCchhHHHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCce
Q 003054 38 GSLNDSSQAGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTR 117 (852)
Q Consensus 38 ~~p~d~~~~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~ 117 (852)
..+....|++.+++.++..+..--.|+.+.-.-....++.+.+.+.. ..++.....+.++.+..++...|.++...+.+
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 34455678999999998766433344444444445555555444321 12333333344344455677777777654566
Q ss_pred EEEEEeChhhHHHHHHHHH
Q 003054 118 VFILHMLPSLGSRIFEKAN 136 (852)
Q Consensus 118 viv~~~~~~~~~~i~~~a~ 136 (852)
.+++.+..+....++.++-
T Consensus 102 ~vliVgH~P~i~~l~~~l~ 120 (152)
T TIGR00249 102 SVLLVSHLPLVGYLVAELC 120 (152)
T ss_pred EEEEEeCCCCHHHHHHHHh
Confidence 7777888888888887774
No 430
>PRK01686 hisG ATP phosphoribosyltransferase catalytic subunit; Reviewed
Probab=50.01 E-value=1.5e+02 Score=29.90 Aligned_cols=92 Identities=13% Similarity=0.028 Sum_probs=54.6
Q ss_pred cCCeEEEEeCchHHHHHHhcCCCCcceeecCCHhHHHHHhhcccccCceeEEEechhHHHHHHhhcCCceEeeccccccc
Q 003054 579 RGDNVGYQKGSFVLGILKQLGFDERKLVVYNSPEDCHELFQKGSVNGGIAAAFDEIPYMKLLIGQYCSKYAMIEPKFKTA 658 (852)
Q Consensus 579 ~~~~vg~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~~~~~~~~v~~~~~~~ 658 (852)
.+++|+..--...+.||.+.+.+-.-+....+.| . +-..|- .|++++-...-.-+..+. +.++...+. .
T Consensus 114 ~~~rIATkYp~it~~yf~~~gv~~~iv~l~GsvE-~--aP~~Gl----AD~IvDivsTG~TLr~Ng---L~~ie~Il~-s 182 (215)
T PRK01686 114 PRLRVATKYPNIARRYFAEKGEQVEIIKLYGSVE-L--APLVGL----ADAIVDIVETGNTLRANG---LVEVEEIMD-I 182 (215)
T ss_pred CCCEEEeCCHHHHHHHHHHcCCeEEEEECcCcee-e--ccccCC----ccEEEEeecChHHHHHCc---CEEeeEEEe-e
Confidence 4679998777888899988877532233333444 2 334455 778877665555554443 455654444 4
Q ss_pred ceEEEecCCCC--chhhHHHHHHhc
Q 003054 659 GFGFVFPLHSP--LVHDVSKAILNV 681 (852)
Q Consensus 659 ~~~~~~~k~sp--l~~~in~~il~l 681 (852)
.-.++.++.|. -.+.+++.+.++
T Consensus 183 ~A~LI~n~~s~~~k~~~i~~l~~~l 207 (215)
T PRK01686 183 SARLIVNRASLKLKREEIRPLIEKL 207 (215)
T ss_pred EEEEEEecccchhhHHHHHHHHHHH
Confidence 55666677765 224555555555
No 431
>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=49.86 E-value=56 Score=33.91 Aligned_cols=77 Identities=12% Similarity=0.011 Sum_probs=54.1
Q ss_pred EEEEEE---eCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChh-hHHHHHHHHH
Q 003054 61 AVPIYV---DNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPS-LGSRIFEKAN 136 (852)
Q Consensus 61 vaii~~---d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~-~~~~i~~~a~ 136 (852)
|++|.. +++|.....+.+.+++++.|..+..... ..+.+.....+..+...++|.|++..... .....+++++
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 455663 4678899999999999999988765421 22344455667777788999998876433 3356678888
Q ss_pred HcCC
Q 003054 137 EIGL 140 (852)
Q Consensus 137 ~~G~ 140 (852)
+.|.
T Consensus 79 ~~~i 82 (275)
T cd06317 79 QAGI 82 (275)
T ss_pred HCCC
Confidence 8776
No 432
>PRK10355 xylF D-xylose transporter subunit XylF; Provisional
Probab=49.80 E-value=67 Score=34.87 Aligned_cols=80 Identities=8% Similarity=0.056 Sum_probs=59.1
Q ss_pred CcEEEEEE--EeCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhh-HHHHHHH
Q 003054 58 WREAVPIY--VDNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSL-GSRIFEK 134 (852)
Q Consensus 58 w~~vaii~--~d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~-~~~i~~~ 134 (852)
-.+|+++. .+++|.....+.+.+++++.|..+..... ..+..+....+..+.+.++|.|++...... ....++.
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 36777777 56789999999999999999998765422 223455667888888899999998765432 3456677
Q ss_pred HHHcCC
Q 003054 135 ANEIGL 140 (852)
Q Consensus 135 a~~~G~ 140 (852)
+.+.|.
T Consensus 102 ~~~~~i 107 (330)
T PRK10355 102 AKQEGI 107 (330)
T ss_pred HHHCCC
Confidence 777775
No 433
>PRK10936 TMAO reductase system periplasmic protein TorT; Provisional
Probab=49.76 E-value=60 Score=35.47 Aligned_cols=81 Identities=5% Similarity=0.026 Sum_probs=56.4
Q ss_pred CcEEEEEEEe--CCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhh-HHHHHHH
Q 003054 58 WREAVPIYVD--NQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSL-GSRIFEK 134 (852)
Q Consensus 58 w~~vaii~~d--~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~-~~~i~~~ 134 (852)
-++|+++..+ +.|-....+.+.+++++.|.++.....-. ..+.+.....+..+.+.++|.|++.....+ ....+ +
T Consensus 46 t~~Igvv~p~~~~~f~~~~~~gi~~aa~~~G~~l~i~~~~~-~~~~~~q~~~i~~l~~~~vdgIIl~~~~~~~~~~~l-~ 123 (343)
T PRK10936 46 AWKLCALYPHLKDSYWLSVNYGMVEEAKRLGVDLKVLEAGG-YYNLAKQQQQLEQCVAWGADAILLGAVTPDGLNPDL-E 123 (343)
T ss_pred CeEEEEEecCCCchHHHHHHHHHHHHHHHhCCEEEEEcCCC-CCCHHHHHHHHHHHHHhCCCEEEEeCCChHHhHHHH-H
Confidence 3788888844 67778888999999999998876653211 112344556788888899999988764433 33455 7
Q ss_pred HHHcCC
Q 003054 135 ANEIGL 140 (852)
Q Consensus 135 a~~~G~ 140 (852)
+++.|.
T Consensus 124 ~~~~gi 129 (343)
T PRK10936 124 LQAANI 129 (343)
T ss_pred HHHCCC
Confidence 777775
No 434
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=49.40 E-value=73 Score=34.53 Aligned_cols=79 Identities=18% Similarity=0.143 Sum_probs=56.0
Q ss_pred cEEEEEEE--eCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHH
Q 003054 59 REAVPIYV--DNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKAN 136 (852)
Q Consensus 59 ~~vaii~~--d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~ 136 (852)
+.++++.. +++|.....+.+.+++++.|..+.... ...+.......+..+.+.++|.||+..........++.++
T Consensus 65 ~~Igvv~~~~~~~~~~~i~~gi~~~a~~~g~~~~~~~---~~~~~~~~~~~~~~l~~~~vdgiIi~~~~~~~~~~~~~l~ 141 (342)
T PRK10014 65 GVIGLIVRDLSAPFYAELTAGLTEALEAQGRMVFLLQ---GGKDGEQLAQRFSTLLNQGVDGVVIAGAAGSSDDLREMAE 141 (342)
T ss_pred CEEEEEeCCCccchHHHHHHHHHHHHHHcCCEEEEEe---CCCCHHHHHHHHHHHHhCCCCEEEEeCCCCCcHHHHHHHh
Confidence 46888884 467888889999999999998765432 1123445567778888889999998754433446677777
Q ss_pred HcCC
Q 003054 137 EIGL 140 (852)
Q Consensus 137 ~~G~ 140 (852)
+.|.
T Consensus 142 ~~~i 145 (342)
T PRK10014 142 EKGI 145 (342)
T ss_pred hcCC
Confidence 7775
No 435
>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=49.02 E-value=73 Score=33.40 Aligned_cols=79 Identities=11% Similarity=0.057 Sum_probs=55.4
Q ss_pred cEEEEEEE--eCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhh-HHHHHHHH
Q 003054 59 REAVPIYV--DNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSL-GSRIFEKA 135 (852)
Q Consensus 59 ~~vaii~~--d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~-~~~i~~~a 135 (852)
|+|+++.. ++.|-....+.+.+++++.|.++..... ..+.+.....+..+.+.++|.||+.....+ ....++++
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 46777774 3567778889999999999988765421 223455667888888899999998754333 23555667
Q ss_pred HHcCC
Q 003054 136 NEIGL 140 (852)
Q Consensus 136 ~~~G~ 140 (852)
++.|.
T Consensus 78 ~~~~i 82 (280)
T cd06315 78 QKAGI 82 (280)
T ss_pred HHCCC
Confidence 77665
No 436
>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=48.98 E-value=1.1e+02 Score=30.89 Aligned_cols=74 Identities=11% Similarity=0.081 Sum_probs=55.8
Q ss_pred cEEEEEEEeCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEe--ChhhHHHHHHHHH
Q 003054 59 REAVPIYVDNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHM--LPSLGSRIFEKAN 136 (852)
Q Consensus 59 ~~vaii~~d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~--~~~~~~~i~~~a~ 136 (852)
.++++|....+ ..+...+.++..+..+.+...-|+..+.+++...-.+|++.++|+|++.| |....+.+++++-
T Consensus 126 ~~vGVivP~~e----Q~~~~~~kW~~l~~~~~~a~asPy~~~~~~l~~Aa~~L~~~gadlIvLDCmGYt~~~r~~~~~~~ 201 (221)
T PF07302_consen 126 HQVGVIVPLPE----QIAQQAEKWQPLGNPVVVAAASPYEGDEEELAAAARELAEQGADLIVLDCMGYTQEMRDIVQRAL 201 (221)
T ss_pred CeEEEEecCHH----HHHHHHHHHHhcCCCeEEEEeCCCCCCHHHHHHHHHHHHhcCCCEEEEECCCCCHHHHHHHHHHh
Confidence 79999996543 34555667777777776666555545688999999999999999999996 5566777777653
No 437
>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=48.78 E-value=60 Score=33.49 Aligned_cols=77 Identities=12% Similarity=0.084 Sum_probs=53.6
Q ss_pred EEEEE--EeCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChh-hHHHHHHHHHH
Q 003054 61 AVPIY--VDNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPS-LGSRIFEKANE 137 (852)
Q Consensus 61 vaii~--~d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~-~~~~i~~~a~~ 137 (852)
+++|. .++.|.......+.+++++.|..+.... ...+..+....+.++.+.++|.|++..... .....++++++
T Consensus 2 I~vv~~~~~~~~~~~~~~~i~~~~~~~g~~v~~~~---~~~~~~~~~~~~~~~~~~~~dgii~~~~~~~~~~~~l~~l~~ 78 (268)
T cd06323 2 IGLSVSTLNNPFFVTLKDGAQKEAKELGYELTVLD---AQNDAAKQLNDIEDLITRGVDAIIINPTDSDAVVPAVKAANE 78 (268)
T ss_pred eeEecccccCHHHHHHHHHHHHHHHHcCceEEecC---CCCCHHHHHHHHHHHHHcCCCEEEEcCCChHHHHHHHHHHHH
Confidence 44555 3577888899999999999998875432 222345566788888888999988764333 23457777777
Q ss_pred cCC
Q 003054 138 IGL 140 (852)
Q Consensus 138 ~G~ 140 (852)
.|.
T Consensus 79 ~~i 81 (268)
T cd06323 79 AGI 81 (268)
T ss_pred CCC
Confidence 765
No 438
>TIGR00288 conserved hypothetical protein TIGR00288. This family of orthologs is restricted to but universal among the completed archaeal genomes so far. Eubacterial proteins showing at least local homology include slr1870 from Synechocystis PCC6803 and two proteins from Aquifex aeolicusr, none of which is characterized.
Probab=48.71 E-value=2.5e+02 Score=26.88 Aligned_cols=85 Identities=14% Similarity=0.086 Sum_probs=60.3
Q ss_pred HHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhh---cCCceEEEEE
Q 003054 46 AGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLF---TMQTRVFILH 122 (852)
Q Consensus 46 ~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~---~~~~~viv~~ 122 (852)
.+.+.+.+..+|-=.+.-+|.|- |. .+.|.+.+...|.+.... .+ +.|+.-.+.-+. +.+.|.+++.
T Consensus 43 ~~~i~~~ls~~G~i~~~R~Y~~a-~a---~~~l~~~l~~~Gf~pv~~----kG--~~Dv~laIDame~~~~~~iD~~vLv 112 (160)
T TIGR00288 43 LDEIREILSEYGDIKIGKVLLNQ-YA---SDKLIEAVVNQGFEPIIV----AG--DVDVRMAVEAMELIYNPNIDAVALV 112 (160)
T ss_pred HHHHHHHHHhcCCeEEEEEEech-hc---cHHHHHHHHHCCceEEEe----cC--cccHHHHHHHHHHhccCCCCEEEEE
Confidence 46777778888855566666442 32 246789999999986532 22 445544444433 4678999999
Q ss_pred eChhhHHHHHHHHHHcCC
Q 003054 123 MLPSLGSRIFEKANEIGL 140 (852)
Q Consensus 123 ~~~~~~~~i~~~a~~~G~ 140 (852)
+...+...++..+++.|.
T Consensus 113 SgD~DF~~Lv~~lre~G~ 130 (160)
T TIGR00288 113 TRDADFLPVINKAKENGK 130 (160)
T ss_pred eccHhHHHHHHHHHHCCC
Confidence 999999999999999986
No 439
>PRK13957 indole-3-glycerol-phosphate synthase; Provisional
Probab=48.60 E-value=1.5e+02 Score=30.62 Aligned_cols=88 Identities=15% Similarity=0.165 Sum_probs=63.5
Q ss_pred HHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeC--
Q 003054 47 GAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHML-- 124 (852)
Q Consensus 47 ~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~-- 124 (852)
..+|......|..-+.|+. |..|-.+..+.+++.-+...+.|..+..+- + ..++.+.+..++|+|++...
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 4566667788988888777 555666778888887777677666554332 1 23666777799999987754
Q ss_pred -hhhHHHHHHHHHHcCCcc
Q 003054 125 -PSLGSRIFEKANEIGLMN 142 (852)
Q Consensus 125 -~~~~~~i~~~a~~~G~~~ 142 (852)
..+...++..|.++||..
T Consensus 136 ~~~~l~~l~~~a~~lGle~ 154 (247)
T PRK13957 136 TPSQIKSFLKHASSLGMDV 154 (247)
T ss_pred CHHHHHHHHHHHHHcCCce
Confidence 346899999999999943
No 440
>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=48.46 E-value=58 Score=34.63 Aligned_cols=72 Identities=13% Similarity=0.115 Sum_probs=49.5
Q ss_pred eCCcccccHHHHHHHHHhCC-ceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeCh-hhHHHHHHHHHHcCC
Q 003054 67 DNQYGEEMIPSLTDALQAID-TRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLP-SLGSRIFEKANEIGL 140 (852)
Q Consensus 67 d~~~G~~~~~~l~~~l~~~g-~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~-~~~~~i~~~a~~~G~ 140 (852)
++.|-....+.+.+++++.| ..+.... +...+.......+..+.+.++|.|++.... +.....++++++.|.
T Consensus 9 ~~~f~~~~~~gi~~~a~~~g~~~~i~~~--~~~~d~~~q~~~i~~l~~~~vdgiIi~~~~~~~~~~~l~~~~~~gi 82 (302)
T TIGR02637 9 GNPFFEAANKGAEEAAKELGSVYIIYTG--PTGTTAEGQIEVVNSLIAQKVDAIAISANDPDALVPALKKAMKRGI 82 (302)
T ss_pred CCHHHHHHHHHHHHHHHHhCCeeEEEEC--CCCCCHHHHHHHHHHHHHcCCCEEEEeCCChHHHHHHHHHHHHCCC
Confidence 46677888889999999999 4443321 111234455677888888899999887543 334567888888886
No 441
>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=48.26 E-value=84 Score=30.80 Aligned_cols=73 Identities=19% Similarity=0.126 Sum_probs=47.2
Q ss_pred cCCHHHHHhcCCeEEEEeCchHHHHHHhcCCCCcceeecCCHhHHHHHhhcccccCceeEEEechhHHHHHHhhcCCceE
Q 003054 570 ITDVKMLIKRGDNVGYQKGSFVLGILKQLGFDERKLVVYNSPEDCHELFQKGSVNGGIAAAFDEIPYMKLLIGQYCSKYA 649 (852)
Q Consensus 570 i~sl~dL~~~~~~vg~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~~~~~~~ 649 (852)
+++.+||. +++|+..-....+.||.+.+.+-.-+....+.|- +-..|- .+++++-......+..+. +.
T Consensus 101 ~~~~~~l~--~~rIATkyp~i~~~~f~~~Gi~v~ii~l~GsvE~---aP~~Gl----aD~IvDiv~TG~TL~~Ng---L~ 168 (182)
T TIGR00070 101 ISSVEDLK--GKRIATKYPNLARRYFEKKGIDVEIIKLNGSVEL---APLLGL----ADAIVDIVSTGTTLRENG---LR 168 (182)
T ss_pred CCChHHhC--CCEEEECCHHHHHHHHHHcCCeEEEEECcceeec---ccCCCc----eeEEEEEeCCHHHHHHCC---CE
Confidence 77889996 8899997778899999988875333333334442 233566 788877665555554443 44
Q ss_pred eeccc
Q 003054 650 MIEPK 654 (852)
Q Consensus 650 ~v~~~ 654 (852)
++++.
T Consensus 169 ~ie~i 173 (182)
T TIGR00070 169 IIEVI 173 (182)
T ss_pred EeeEE
Confidence 44443
No 442
>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=48.26 E-value=69 Score=34.12 Aligned_cols=78 Identities=6% Similarity=0.143 Sum_probs=53.8
Q ss_pred EEEEEEE--eCCcccccHHHHHHHHHh--CCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeCh-hhHHHHHHH
Q 003054 60 EAVPIYV--DNQYGEEMIPSLTDALQA--IDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLP-SLGSRIFEK 134 (852)
Q Consensus 60 ~vaii~~--d~~~G~~~~~~l~~~l~~--~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~-~~~~~i~~~ 134 (852)
+|+++.. ++.|-....+.+.+++++ .|.++.... .+.+.+.....+.++.+.++|.|++.... ......+++
T Consensus 1 ~Igviv~~~~~~~~~~~~~gi~~~a~~~~~g~~~~~~~---~~~~~~~q~~~i~~l~~~~vdgiii~~~~~~~~~~~~~~ 77 (303)
T cd01539 1 KIGVFLYKFDDTFISLVRKNLEDIQKENGGKVEFTFYD---AKNNQSTQNEQIDTALAKGVDLLAVNLVDPTAAQTVINK 77 (303)
T ss_pred CeEEEeeCCCChHHHHHHHHHHHHHHhhCCCeeEEEec---CCCCHHHHHHHHHHHHHcCCCEEEEecCchhhHHHHHHH
Confidence 3566663 356777788899999999 777765432 22234445567888888999998886433 334677888
Q ss_pred HHHcCC
Q 003054 135 ANEIGL 140 (852)
Q Consensus 135 a~~~G~ 140 (852)
+++.|+
T Consensus 78 ~~~~gi 83 (303)
T cd01539 78 AKQKNI 83 (303)
T ss_pred HHHCCC
Confidence 888886
No 443
>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=48.23 E-value=70 Score=33.11 Aligned_cols=76 Identities=7% Similarity=0.030 Sum_probs=52.6
Q ss_pred EEEEE--EeCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHc
Q 003054 61 AVPIY--VDNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEI 138 (852)
Q Consensus 61 vaii~--~d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~ 138 (852)
+++|. .++.|-....+.+.+++++.|.++..... ..+.+.-...+..+.+.++|.|++....... ..++++.+.
T Consensus 2 igvi~p~~~~~~~~~~~~g~~~~a~~~g~~~~~~~~---~~~~~~~~~~i~~~~~~~vdgii~~~~~~~~-~~~~~~~~~ 77 (268)
T cd06270 2 IGLVVSDLDGPFFGPLLSGVESVARKAGKHLIITAG---HHSAEKEREAIEFLLERRCDALILHSKALSD-DELIELAAQ 77 (268)
T ss_pred EEEEEccccCcchHHHHHHHHHHHHHCCCEEEEEeC---CCchHHHHHHHHHHHHcCCCEEEEecCCCCH-HHHHHHhhC
Confidence 44554 45778888999999999999998764322 1223445567778888999999987643222 237777777
Q ss_pred CC
Q 003054 139 GL 140 (852)
Q Consensus 139 G~ 140 (852)
|.
T Consensus 78 ~i 79 (268)
T cd06270 78 VP 79 (268)
T ss_pred CC
Confidence 75
No 444
>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=48.10 E-value=89 Score=29.57 Aligned_cols=63 Identities=16% Similarity=0.206 Sum_probs=43.7
Q ss_pred EEEEEEEeCC--cc---cccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhc-CCceEEEEEeC
Q 003054 60 EAVPIYVDNQ--YG---EEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFT-MQTRVFILHML 124 (852)
Q Consensus 60 ~vaii~~d~~--~G---~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~-~~~~viv~~~~ 124 (852)
++++|...|+ .| ......+.+.+++.|.++.....++. +.+++...|.+..+ .++|+|+..+.
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 5777765553 22 22355788889999999887777763 36678888877654 37899988754
No 445
>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=48.02 E-value=1.1e+02 Score=29.43 Aligned_cols=65 Identities=12% Similarity=0.090 Sum_probs=45.8
Q ss_pred CcEEEEEEEeCCcc---cccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhc-CCceEEEEEeC
Q 003054 58 WREAVPIYVDNQYG---EEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFT-MQTRVFILHML 124 (852)
Q Consensus 58 w~~vaii~~d~~~G---~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~-~~~~viv~~~~ 124 (852)
..++++|...|+-+ ......+...+++.|.++.....++. +.+.+...+.+..+ .+.|+|+..+.
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 45788887555332 22355777889999999888777763 36678888877653 57899988754
No 446
>PRK09701 D-allose transporter subunit; Provisional
Probab=47.65 E-value=71 Score=34.24 Aligned_cols=84 Identities=13% Similarity=0.053 Sum_probs=58.5
Q ss_pred cCCcEEEEEEE--eCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChh-hHHHHH
Q 003054 56 FGWREAVPIYV--DNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPS-LGSRIF 132 (852)
Q Consensus 56 ~gw~~vaii~~--d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~-~~~~i~ 132 (852)
+--.+|+++.. ++.|-....+.+.+++++.|.++..... +...+..+....+..+.+.++|.||+..... .....+
T Consensus 22 ~~~~~Igvi~~~~~~~f~~~~~~gi~~~a~~~g~~v~~~~~-~~~~~~~~~~~~i~~l~~~~vDgiIi~~~~~~~~~~~l 100 (311)
T PRK09701 22 FAAAEYAVVLKTLSNPFWVDMKKGIEDEAKTLGVSVDIFAS-PSEGDFQSQLQLFEDLSNKNYKGIAFAPLSSVNLVMPV 100 (311)
T ss_pred ccCCeEEEEeCCCCCHHHHHHHHHHHHHHHHcCCeEEEecC-CCCCCHHHHHHHHHHHHHcCCCEEEEeCCChHHHHHHH
Confidence 44579999984 5678888999999999999988764321 1112234456677788888999998876543 333446
Q ss_pred HHHHHcCC
Q 003054 133 EKANEIGL 140 (852)
Q Consensus 133 ~~a~~~G~ 140 (852)
.++.+.|+
T Consensus 101 ~~~~~~gi 108 (311)
T PRK09701 101 ARAWKKGI 108 (311)
T ss_pred HHHHHCCC
Confidence 77777775
No 447
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=47.23 E-value=85 Score=33.75 Aligned_cols=80 Identities=13% Similarity=0.045 Sum_probs=53.2
Q ss_pred CcEEEEEEE--eCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHH
Q 003054 58 WREAVPIYV--DNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKA 135 (852)
Q Consensus 58 w~~vaii~~--d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a 135 (852)
-+.|+++.. ++.|-..+...+.+++++.|..+..... ..+.+.-...+..+.+.++|.||+..........++++
T Consensus 61 ~~~Igvv~~~~~~~~~~~l~~gi~~~~~~~g~~~~~~~~---~~~~~~~~~~~~~l~~~~vdgiIi~~~~~~~~~~~~~l 137 (328)
T PRK11303 61 TRSIGLIIPDLENTSYARIAKYLERQARQRGYQLLIACS---DDQPDNEMRCAEHLLQRQVDALIVSTSLPPEHPFYQRL 137 (328)
T ss_pred CceEEEEeCCCCCchHHHHHHHHHHHHHHcCCEEEEEeC---CCCHHHHHHHHHHHHHcCCCEEEEcCCCCCChHHHHHH
Confidence 346888774 4567777888999999999998765422 11233344566777788999998875432223456667
Q ss_pred HHcCC
Q 003054 136 NEIGL 140 (852)
Q Consensus 136 ~~~G~ 140 (852)
.+.|+
T Consensus 138 ~~~~i 142 (328)
T PRK11303 138 QNDGL 142 (328)
T ss_pred HhcCC
Confidence 77775
No 448
>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=47.21 E-value=1.5e+02 Score=26.36 Aligned_cols=59 Identities=14% Similarity=0.063 Sum_probs=29.3
Q ss_pred cHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEe-Chh---hHHHHHHHHHHc
Q 003054 74 MIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHM-LPS---LGSRIFEKANEI 138 (852)
Q Consensus 74 ~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~-~~~---~~~~i~~~a~~~ 138 (852)
.+..+...|++.|.+|..... +... ...+..+++.+||+|.+.+ ... .+..+.+.+++.
T Consensus 16 Gl~~la~~l~~~G~~v~~~d~---~~~~---~~l~~~~~~~~pd~V~iS~~~~~~~~~~~~l~~~~k~~ 78 (121)
T PF02310_consen 16 GLLYLAAYLRKAGHEVDILDA---NVPP---EELVEALRAERPDVVGISVSMTPNLPEAKRLARAIKER 78 (121)
T ss_dssp HHHHHHHHHHHTTBEEEEEES---SB-H---HHHHHHHHHTTCSEEEEEESSSTHHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHHHCCCeEEEECC---CCCH---HHHHHHHhcCCCcEEEEEccCcCcHHHHHHHHHHHHhc
Confidence 345566666666766653321 1111 3334455556777776665 332 334445444443
No 449
>PLN02428 lipoic acid synthase
Probab=47.02 E-value=4.2e+02 Score=28.99 Aligned_cols=108 Identities=16% Similarity=0.199 Sum_probs=64.8
Q ss_pred CCchhHHHHHHHHHHHcCCcEEEEEEEe----CCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCC
Q 003054 40 LNDSSQAGAITAIIKAFGWREAVPIYVD----NQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQ 115 (852)
Q Consensus 40 p~d~~~~~aia~~l~~~gw~~vaii~~d----~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~ 115 (852)
+.+......+++.+..+|.+.|.++..| .+.|.+....+.+++.+....+......+....+ ...|.+|++++
T Consensus 129 ~~d~~Ep~~vA~~v~~~Glk~vvltSg~rddl~D~ga~~~~elir~Ir~~~P~i~Ie~L~pdf~~d---~elL~~L~eAG 205 (349)
T PLN02428 129 PPDPDEPENVAEAIASWGVDYVVLTSVDRDDLPDGGSGHFAETVRRLKQLKPEILVEALVPDFRGD---LGAVETVATSG 205 (349)
T ss_pred CCChhhHHHHHHHHHHcCCCEEEEEEcCCCCCCcccHHHHHHHHHHHHHhCCCcEEEEeCccccCC---HHHHHHHHHcC
Confidence 4455555677777888999998777653 2445555555566666654333323222211112 45788888899
Q ss_pred ceEEEEEe---------------ChhhHHHHHHHHHHc--CCcccceEEEEc
Q 003054 116 TRVFILHM---------------LPSLGSRIFEKANEI--GLMNKGCVWIMT 150 (852)
Q Consensus 116 ~~viv~~~---------------~~~~~~~i~~~a~~~--G~~~~~~vwi~~ 150 (852)
+|++-... ..++...+++.|++. |+....+..++-
T Consensus 206 ~d~i~hnlETv~rL~~~Ir~~~~sye~~Le~L~~ak~~~pGi~tkSg~MvGL 257 (349)
T PLN02428 206 LDVFAHNIETVERLQRIVRDPRAGYKQSLDVLKHAKESKPGLLTKTSIMLGL 257 (349)
T ss_pred CCEEccCccCcHHHHHHhcCCCCCHHHHHHHHHHHHHhCCCCeEEEeEEEec
Confidence 99854332 224556788888888 876554444443
No 450
>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=46.98 E-value=53 Score=35.04 Aligned_cols=77 Identities=9% Similarity=0.100 Sum_probs=53.3
Q ss_pred EEEEEE---eCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcC--CceEEEEEeChhhHHHHHHHH
Q 003054 61 AVPIYV---DNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTM--QTRVFILHMLPSLGSRIFEKA 135 (852)
Q Consensus 61 vaii~~---d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~--~~~viv~~~~~~~~~~i~~~a 135 (852)
|+++.. ++.|.......+.+++++.|.++..... ..+.+.....+..+.+. ++|.|++.........+++.+
T Consensus 2 Igvi~~~~~~~~~~~~~~~gi~~~~~~~g~~v~~~~~---~~~~~~~~~~i~~~~~~~~~vdgiIi~~~~~~~~~~~~~~ 78 (305)
T cd06324 2 VVFLNPGKSDEPFWNSVARFMQAAADDLGIELEVLYA---ERDRFLMLQQARTILQRPDKPDALIFTNEKSVAPELLRLA 78 (305)
T ss_pred eEEecCCCCCCcHHHHHHHHHHHHHHhcCCeEEEEeC---CCCHHHHHHHHHHHHHhccCCCEEEEcCCccchHHHHHHH
Confidence 556652 4567788889999999999998765422 22344455677778888 999999865433345667788
Q ss_pred HHcCC
Q 003054 136 NEIGL 140 (852)
Q Consensus 136 ~~~G~ 140 (852)
++.|+
T Consensus 79 ~~~gi 83 (305)
T cd06324 79 EGAGV 83 (305)
T ss_pred HhCCC
Confidence 88776
No 451
>cd08447 PBP2_LTTR_aromatics_like_1 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=46.75 E-value=2.6e+02 Score=26.49 Aligned_cols=69 Identities=16% Similarity=0.083 Sum_probs=44.8
Q ss_pred EeeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCcccEEEeeeeeecCcceeeeccccccccceEEEE
Q 003054 377 GYCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGEFDAVVGDITIVFNRSNYVDFTLPYTESGVSMIV 456 (852)
Q Consensus 377 G~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv 456 (852)
.+-.+++..+.++.+- +.+++.. ++..++..++.+|++|+++... +.....+. +.++.....++++
T Consensus 13 ~~l~~~l~~~~~~~P~-i~v~~~~---------~~~~~~~~~l~~g~~D~~i~~~---~~~~~~~~-~~~l~~~~~~~v~ 78 (198)
T cd08447 13 SFLPRLLAAARAALPD-VDLVLRE---------MVTTDQIEALESGRIDLGLLRP---PFARPGLE-TRPLVREPLVAAV 78 (198)
T ss_pred HHHHHHHHHHHHHCCC-eEEEEEe---------CCHHHHHHHHHcCCceEEEecC---CCCCCCee-EEEeecCceEEEe
Confidence 4556888888888773 4454433 3578899999999999987521 21122222 3566677777777
Q ss_pred Ecc
Q 003054 457 PIK 459 (852)
Q Consensus 457 ~~~ 459 (852)
+..
T Consensus 79 ~~~ 81 (198)
T cd08447 79 PAG 81 (198)
T ss_pred cCC
Confidence 643
No 452
>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=46.44 E-value=51 Score=34.28 Aligned_cols=72 Identities=11% Similarity=0.190 Sum_probs=53.3
Q ss_pred EeCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhh-HHHHHHHHHHcCC
Q 003054 66 VDNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSL-GSRIFEKANEIGL 140 (852)
Q Consensus 66 ~d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~-~~~i~~~a~~~G~ 140 (852)
.++.|-....+.+.+++++.|.++..... ..+.......++.+.+.++|.|++.....+ ....++++.+.|+
T Consensus 9 ~~~~~~~~~~~~~~~~a~~~g~~~~~~~~---~~~~~~~~~~i~~l~~~~vdgiIi~~~~~~~~~~~i~~~~~~~i 81 (273)
T cd06309 9 AESPWRTAETKSIKDAAEKRGFDLKFADA---QQKQENQISAIRSFIAQGVDVIILAPVVETGWDPVLKEAKAAGI 81 (273)
T ss_pred CCCHHHHHHHHHHHHHHHhcCCEEEEeCC---CCCHHHHHHHHHHHHHcCCCEEEEcCCccccchHHHHHHHHCCC
Confidence 36778888999999999999999876432 123445667788888889999988654433 3567788888776
No 453
>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=46.39 E-value=64 Score=33.18 Aligned_cols=75 Identities=17% Similarity=0.211 Sum_probs=52.0
Q ss_pred EEEEE--EeCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHc
Q 003054 61 AVPIY--VDNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEI 138 (852)
Q Consensus 61 vaii~--~d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~ 138 (852)
|+++. .++.|-....+.+.+++++.|.++..... +... +....+.++.+.++|.|++....... ..++.+.+.
T Consensus 2 I~~i~~~~~~~~~~~~~~~i~~~~~~~g~~~~~~~~---~~~~-~~~~~i~~~~~~~vdgiii~~~~~~~-~~~~~~~~~ 76 (266)
T cd06278 2 IGVVVADLDNPFYSELLEALSRALQARGYQPLLINT---DDDE-DLDAALRQLLQYRVDGVIVTSGTLSS-ELAEECRRN 76 (266)
T ss_pred EEEEeCCCCCchHHHHHHHHHHHHHHCCCeEEEEcC---CCCH-HHHHHHHHHHHcCCCEEEEecCCCCH-HHHHHHhhc
Confidence 44555 35678888889999999999998764422 1223 66677888888999998886543222 447777777
Q ss_pred CC
Q 003054 139 GL 140 (852)
Q Consensus 139 G~ 140 (852)
|.
T Consensus 77 ~i 78 (266)
T cd06278 77 GI 78 (266)
T ss_pred CC
Confidence 75
No 454
>PRK11070 ssDNA exonuclease RecJ; Provisional
Probab=46.32 E-value=94 Score=36.59 Aligned_cols=87 Identities=10% Similarity=0.003 Sum_probs=60.7
Q ss_pred cEEEEEEEeCCcccccHHHHHHHHHhCCc-eeeeeee--cCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHH
Q 003054 59 REAVPIYVDNQYGEEMIPSLTDALQAIDT-RVPYRSV--ISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKA 135 (852)
Q Consensus 59 ~~vaii~~d~~~G~~~~~~l~~~l~~~g~-~v~~~~~--~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a 135 (852)
++|.|...-|.-|......+.+.|++.|. .+.+... +.-+.+- -...+.++.+.+++.||..-.+.....-++.|
T Consensus 70 e~I~I~gDyD~DGitstail~~~L~~~g~~~~~~~IP~R~~eGYGl--~~~~i~~~~~~~~~LiItvD~Gi~~~e~i~~a 147 (575)
T PRK11070 70 TRIIVVGDFDADGATSTALSVLALRSLGCSNVDYLVPNRFEDGYGL--SPEVVDQAHARGAQLIVTVDNGISSHAGVAHA 147 (575)
T ss_pred CEEEEEEecCccHHHHHHHHHHHHHHcCCCceEEEeCCCCcCCCCC--CHHHHHHHHhcCCCEEEEEcCCcCCHHHHHHH
Confidence 67777766677788888889999999998 4544321 0001011 01356667777889998888888888888889
Q ss_pred HHcCCcccceEEEEcCc
Q 003054 136 NEIGLMNKGCVWIMTDG 152 (852)
Q Consensus 136 ~~~G~~~~~~vwi~~~~ 152 (852)
+++|+ . .|++|.
T Consensus 148 ~~~gi--d---vIVtDH 159 (575)
T PRK11070 148 HALGI--P---VLVTDH 159 (575)
T ss_pred HHCCC--C---EEEECC
Confidence 99998 4 467664
No 455
>cd02067 B12-binding B12 binding domain (B12-BD). This domain binds different cobalamid derivates, like B12 (adenosylcobamide) or methylcobalamin or methyl-Co(III) 5-hydroxybenzimidazolylcobamide, it is found in several enzymes, such as glutamate mutase, methionine synthase and methylmalonyl-CoA mutase. Cobalamin undergoes a conformational change on binding the protein; the dimethylbenzimidazole group, which is coordinated to the cobalt in the free cofactor, moves away from the corrin and is replaced by a histidine contributed by the protein. The sequence Asp-X-His-X-X-Gly, which contains this histidine ligand, is conserved in many cobalamin-binding proteins.
Probab=46.18 E-value=1.9e+02 Score=25.85 Aligned_cols=66 Identities=14% Similarity=-0.007 Sum_probs=41.5
Q ss_pred CCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeCh----hhHHHHHHHHHHcC
Q 003054 68 NQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLP----SLGSRIFEKANEIG 139 (852)
Q Consensus 68 ~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~----~~~~~i~~~a~~~G 139 (852)
.+.=.-....+...|+..|.+|.+-. .+...+ ..+..+.+.+||+|.+.+.. ..+..+++++++.+
T Consensus 9 ~e~H~lG~~~~~~~l~~~G~~V~~lg---~~~~~~---~l~~~~~~~~pdvV~iS~~~~~~~~~~~~~i~~l~~~~ 78 (119)
T cd02067 9 GDGHDIGKNIVARALRDAGFEVIDLG---VDVPPE---EIVEAAKEEDADAIGLSGLLTTHMTLMKEVIEELKEAG 78 (119)
T ss_pred CchhhHHHHHHHHHHHHCCCEEEECC---CCCCHH---HHHHHHHHcCCCEEEEeccccccHHHHHHHHHHHHHcC
Confidence 33333445677778888998885432 112233 34555667899999888652 35577777888775
No 456
>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=46.12 E-value=62 Score=33.66 Aligned_cols=80 Identities=6% Similarity=0.068 Sum_probs=53.1
Q ss_pred EEEEEEE--eCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeCh-hhHHHHHHHHH
Q 003054 60 EAVPIYV--DNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLP-SLGSRIFEKAN 136 (852)
Q Consensus 60 ~vaii~~--d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~-~~~~~i~~~a~ 136 (852)
++++|.. ++.|-....+.+.+++++.|.++..... ....+...-...+.++...++|.|++.... +.....++.++
T Consensus 1 ~igvi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~-~~~~~~~~~~~~i~~l~~~~vdgiIi~~~~~~~~~~~~~~~~ 79 (275)
T cd06320 1 KYGVVLKTLSNEFWRSLKEGYENEAKKLGVSVDIQAA-PSEGDQQGQLSIAENMINKGYKGLLFSPISDVNLVPAVERAK 79 (275)
T ss_pred CeeEEEecCCCHHHHHHHHHHHHHHHHhCCeEEEEcc-CCCCCHHHHHHHHHHHHHhCCCEEEECCCChHHhHHHHHHHH
Confidence 3566663 5667788889999999999988764422 111223344566777888899998876543 33345677777
Q ss_pred HcCC
Q 003054 137 EIGL 140 (852)
Q Consensus 137 ~~G~ 140 (852)
+.|.
T Consensus 80 ~~~i 83 (275)
T cd06320 80 KKGI 83 (275)
T ss_pred HCCC
Confidence 7775
No 457
>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=45.79 E-value=78 Score=32.65 Aligned_cols=76 Identities=17% Similarity=0.084 Sum_probs=51.7
Q ss_pred EEEEEE--eCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHc
Q 003054 61 AVPIYV--DNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEI 138 (852)
Q Consensus 61 vaii~~--d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~ 138 (852)
|+++.. ++.|.......+.+++++.|..+.... .+.+.......++++.+.++|.+++..... ....++.+++.
T Consensus 2 i~vv~p~~~~~~~~~~~~~i~~~~~~~g~~~~~~~---~~~~~~~~~~~~~~l~~~~vdgiii~~~~~-~~~~~~~l~~~ 77 (268)
T cd06273 2 IGAIVPTLDNAIFARVIQAFQETLAAHGYTLLVAS---SGYDLDREYAQARKLLERGVDGLALIGLDH-SPALLDLLARR 77 (268)
T ss_pred eEEEeCCCCCchHHHHHHHHHHHHHHCCCEEEEec---CCCCHHHHHHHHHHHHhcCCCEEEEeCCCC-CHHHHHHHHhC
Confidence 566663 467788888999999999998876532 222334456777888888899988764432 23445666776
Q ss_pred CC
Q 003054 139 GL 140 (852)
Q Consensus 139 G~ 140 (852)
|.
T Consensus 78 ~i 79 (268)
T cd06273 78 GV 79 (268)
T ss_pred CC
Confidence 65
No 458
>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=45.77 E-value=66 Score=34.33 Aligned_cols=72 Identities=11% Similarity=0.120 Sum_probs=53.7
Q ss_pred EeCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeCh-hhHHHHHHHHHHcCC
Q 003054 66 VDNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLP-SLGSRIFEKANEIGL 140 (852)
Q Consensus 66 ~d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~-~~~~~i~~~a~~~G~ 140 (852)
.+++|.....+.+.+++++.|.++.... ...+.......+..+.+.++|.|++.... ......++.+++.|+
T Consensus 8 ~~~~~~~~~~~~i~~~a~~~g~~v~~~~---~~~~~~~q~~~i~~l~~~~vDgIIi~~~~~~~~~~~l~~~~~~~i 80 (302)
T TIGR02634 8 LRLERWQKDRDIFVAAAESLGAKVFVQS---ANGNEAKQISQIENLIARGVDVLVIIPQNGQVLSNAVQEAKDEGI 80 (302)
T ss_pred cchhhHHHHHHHHHHHHHhcCCEEEEEe---CCCCHHHHHHHHHHHHHcCCCEEEEeCCChhHHHHHHHHHHHCCC
Confidence 4677888889999999999999886542 22234455678888888999999887643 334677888888876
No 459
>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=45.62 E-value=70 Score=33.08 Aligned_cols=76 Identities=13% Similarity=0.094 Sum_probs=52.6
Q ss_pred EEEEE--EeCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHc
Q 003054 61 AVPIY--VDNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEI 138 (852)
Q Consensus 61 vaii~--~d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~ 138 (852)
++++. .+++|-......+.+++++.|.++..... ..+.......+..+.+.++|.|++....... ..++++.+.
T Consensus 2 i~vi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~---~~~~~~~~~~i~~l~~~~~dgiii~~~~~~~-~~~~~~~~~ 77 (270)
T cd06296 2 IGLVFPDLDSPWASEVLRGVEEAAAAAGYDVVLSES---GRRTSPERQWVERLSARRTDGVILVTPELTS-AQRAALRRT 77 (270)
T ss_pred eEEEECCCCCccHHHHHHHHHHHHHHcCCeEEEecC---CCchHHHHHHHHHHHHcCCCEEEEecCCCCh-HHHHHHhcC
Confidence 45555 35788899999999999999998765432 1223445567788888899988876543332 347777776
Q ss_pred CC
Q 003054 139 GL 140 (852)
Q Consensus 139 G~ 140 (852)
|.
T Consensus 78 ~i 79 (270)
T cd06296 78 GI 79 (270)
T ss_pred CC
Confidence 65
No 460
>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=45.46 E-value=2.7e+02 Score=26.24 Aligned_cols=64 Identities=3% Similarity=-0.071 Sum_probs=38.9
Q ss_pred eeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCcccEEEeeeeeecCcceeeeccccccccceEEEEE
Q 003054 378 YCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGEFDAVVGDITIVFNRSNYVDFTLPYTESGVSMIVP 457 (852)
Q Consensus 378 ~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv~ 457 (852)
+...++..+.++.+ .++++.... . .+..+.+|++|+++... +.....+ .+.+.....++++++
T Consensus 14 ~l~~~l~~~~~~~P-~v~i~~~~~---------~---~~~~l~~g~~D~~i~~~---~~~~~~~-~~~~l~~~~~~~v~~ 76 (194)
T cd08432 14 WLIPRLARFQARHP-DIDLRLSTS---------D---RLVDFAREGIDLAIRYG---DGDWPGL-EAERLMDEELVPVCS 76 (194)
T ss_pred HHHHHhHHHHHHCC-CeEEEEEec---------C---CccccccccccEEEEec---CCCCCCc-ceEEccCCcEEEecC
Confidence 34566777877776 355555431 1 35678899999987522 1112222 256677778887777
Q ss_pred c
Q 003054 458 I 458 (852)
Q Consensus 458 ~ 458 (852)
.
T Consensus 77 ~ 77 (194)
T cd08432 77 P 77 (194)
T ss_pred H
Confidence 4
No 461
>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=45.25 E-value=67 Score=33.36 Aligned_cols=77 Identities=10% Similarity=0.012 Sum_probs=52.6
Q ss_pred EEEEE--EeCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhh-HHHHHHHHHH
Q 003054 61 AVPIY--VDNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSL-GSRIFEKANE 137 (852)
Q Consensus 61 vaii~--~d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~-~~~i~~~a~~ 137 (852)
+++|. .++.|-....+.+.+++++.|.++... ....+...-...+.++.+.++|.|++...... ....++.+.+
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 55555 356788888999999999999887543 21222334456777777889999987654333 3456777777
Q ss_pred cCC
Q 003054 138 IGL 140 (852)
Q Consensus 138 ~G~ 140 (852)
.|.
T Consensus 79 ~~i 81 (277)
T cd06319 79 AKI 81 (277)
T ss_pred CCC
Confidence 775
No 462
>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=45.13 E-value=95 Score=27.67 Aligned_cols=71 Identities=15% Similarity=0.047 Sum_probs=47.3
Q ss_pred HHHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHHHHHhCCceeeeeee-cCCCCChHHHHHHHHHhhcCCceEEEEEe
Q 003054 45 QAGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTDALQAIDTRVPYRSV-ISPLATDDQIEKELYKLFTMQTRVFILHM 123 (852)
Q Consensus 45 ~~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~~l~~~g~~v~~~~~-~~~~~~~~d~~~~l~~l~~~~~~viv~~~ 123 (852)
-...++.++++.|| +|.++-.+. ..+.+.+.+.+.+.+++.... +. .+-......++.+|+..|++.++.+
T Consensus 16 Gl~~la~~l~~~G~-~v~~~d~~~-----~~~~l~~~~~~~~pd~V~iS~~~~--~~~~~~~~l~~~~k~~~p~~~iv~G 87 (121)
T PF02310_consen 16 GLLYLAAYLRKAGH-EVDILDANV-----PPEELVEALRAERPDVVGISVSMT--PNLPEAKRLARAIKERNPNIPIVVG 87 (121)
T ss_dssp HHHHHHHHHHHTTB-EEEEEESSB------HHHHHHHHHHTTCSEEEEEESSS--THHHHHHHHHHHHHTTCTTSEEEEE
T ss_pred HHHHHHHHHHHCCC-eEEEECCCC-----CHHHHHHHHhcCCCcEEEEEccCc--CcHHHHHHHHHHHHhcCCCCEEEEE
Confidence 34577788899898 555443221 137888888888888877765 33 2355667777888888888555444
No 463
>PRK15138 aldehyde reductase; Provisional
Probab=45.12 E-value=1.2e+02 Score=33.89 Aligned_cols=84 Identities=14% Similarity=0.103 Sum_probs=55.7
Q ss_pred HHHHHHHHHcCCcEEEEEEEeCCc-ccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeCh
Q 003054 47 GAITAIIKAFGWREAVPIYVDNQY-GEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLP 125 (852)
Q Consensus 47 ~aia~~l~~~gw~~vaii~~d~~~-G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~ 125 (852)
+.+.++++. + +++.+++.+..+ ..+..+.+.+.|+ |.++.....+.++.+.++....+...++.++|+||-.+-+
T Consensus 20 ~~l~~~l~~-~-~~~livt~~~~~~~~g~~~~v~~~L~--~~~~~~f~~v~~~p~~~~v~~~~~~~~~~~~D~IIaiGGG 95 (387)
T PRK15138 20 AGLREQIPA-D-ARVLITYGGGSVKKTGVLDQVLDALK--GMDVLEFGGIEPNPTYETLMKAVKLVREEKITFLLAVGGG 95 (387)
T ss_pred HHHHHHHhc-C-CeEEEECCCchHHhcCcHHHHHHHhc--CCeEEEECCccCCCCHHHHHHHHHHHHHcCCCEEEEeCCh
Confidence 444555665 4 888888743332 3455677888885 6665544455666677888888999999999999966543
Q ss_pred --hhHHHHHHH
Q 003054 126 --SLGSRIFEK 134 (852)
Q Consensus 126 --~~~~~i~~~ 134 (852)
-|+.+.+..
T Consensus 96 S~iD~AK~ia~ 106 (387)
T PRK15138 96 SVLDGTKFIAA 106 (387)
T ss_pred HHHHHHHHHHH
Confidence 355555543
No 464
>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=44.87 E-value=76 Score=32.86 Aligned_cols=77 Identities=10% Similarity=0.047 Sum_probs=53.1
Q ss_pred EEEEEE--eCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHc
Q 003054 61 AVPIYV--DNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEI 138 (852)
Q Consensus 61 vaii~~--d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~ 138 (852)
|+++.. ++.|-....+.+.+++++.|..+..... ..+.+.....+..+.+.+.|.|++.........+++++++.
T Consensus 2 Igvv~~~~~~~~~~~~~~~i~~~a~~~g~~~~~~~~---~~~~~~~~~~i~~l~~~~vdgii~~~~~~~~~~~~~~~~~~ 78 (269)
T cd06281 2 IGCLVSDITNPLLAQLFSGAEDRLRAAGYSLLIANS---LNDPERELEILRSFEQRRMDGIIIAPGDERDPELVDALASL 78 (269)
T ss_pred EEEEecCCccccHHHHHHHHHHHHHHcCCEEEEEeC---CCChHHHHHHHHHHHHcCCCEEEEecCCCCcHHHHHHHHhC
Confidence 556663 4677788889999999999998765432 12234456677788888999998875433344566777776
Q ss_pred CC
Q 003054 139 GL 140 (852)
Q Consensus 139 G~ 140 (852)
|.
T Consensus 79 ~i 80 (269)
T cd06281 79 DL 80 (269)
T ss_pred CC
Confidence 64
No 465
>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=44.28 E-value=1.4e+02 Score=30.95 Aligned_cols=89 Identities=15% Similarity=0.160 Sum_probs=61.0
Q ss_pred HHHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeC
Q 003054 45 QAGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHML 124 (852)
Q Consensus 45 ~~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~ 124 (852)
....++......|..-+.|+. |..|..+..+.+...-+..++.+..+..+- + .-++.+.+..++|+|++...
T Consensus 69 d~~~~a~~y~~~GA~aiSVlT-e~~~F~Gs~~dL~~v~~~~~~PvL~KDFIi-d------~~QI~eA~~~GADaVLLI~~ 140 (254)
T PF00218_consen 69 DPAEIAKAYEEAGAAAISVLT-EPKFFGGSLEDLRAVRKAVDLPVLRKDFII-D------PYQIYEARAAGADAVLLIAA 140 (254)
T ss_dssp SHHHHHHHHHHTT-SEEEEE---SCCCHHHHHHHHHHHHHSSS-EEEES----S------HHHHHHHHHTT-SEEEEEGG
T ss_pred CHHHHHHHHHhcCCCEEEEEC-CCCCCCCCHHHHHHHHHHhCCCcccccCCC-C------HHHHHHHHHcCCCEeehhHH
Confidence 456667777778988888887 667778888888888888888776654332 1 23677888899999988754
Q ss_pred ---hhhHHHHHHHHHHcCCc
Q 003054 125 ---PSLGSRIFEKANEIGLM 141 (852)
Q Consensus 125 ---~~~~~~i~~~a~~~G~~ 141 (852)
......++..|+++||.
T Consensus 141 ~L~~~~l~~l~~~a~~lGle 160 (254)
T PF00218_consen 141 ILSDDQLEELLELAHSLGLE 160 (254)
T ss_dssp GSGHHHHHHHHHHHHHTT-E
T ss_pred hCCHHHHHHHHHHHHHcCCC
Confidence 33458999999999993
No 466
>TIGR00640 acid_CoA_mut_C methylmalonyl-CoA mutase C-terminal domain. Methylmalonyl-CoA mutase (EC 5.4.99.2) catalyzes a reversible isomerization between L-methylmalonyl-CoA and succinyl-CoA. The enzyme uses an adenosylcobalamin cofactor. It may be a homodimer, as in mitochondrion, or a heterodimer with partially homologous beta chain that does not bind the adenosylcobalamin cofactor, as in Propionibacterium freudenreichii. The most similar archaeal sequences are separate chains, such as AF2215 and AF2219 of Archaeoglobus fulgidus, that correspond roughly to the first 500 and last 130 residues, respectively of known methylmalonyl-CoA mutases. This model describes the C-terminal domain subfamily. In a neighbor-joining tree (methylaspartate mutase S chain as the outgroup), AF2219 branches with a coenzyme B12-dependent enzyme known not to be 5.4.99.2.
Probab=44.25 E-value=2.2e+02 Score=26.23 Aligned_cols=60 Identities=12% Similarity=0.117 Sum_probs=42.3
Q ss_pred HHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChh----hHHHHHHHHHHcCC
Q 003054 75 IPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPS----LGSRIFEKANEIGL 140 (852)
Q Consensus 75 ~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~----~~~~i~~~a~~~G~ 140 (852)
.+.+...|+..|.+|...-... .....+...++.++|+|.+++... ....++++.++.|.
T Consensus 19 ~~iv~~~l~~~GfeVi~lg~~~------s~e~~v~aa~e~~adii~iSsl~~~~~~~~~~~~~~L~~~g~ 82 (132)
T TIGR00640 19 AKVIATAYADLGFDVDVGPLFQ------TPEEIARQAVEADVHVVGVSSLAGGHLTLVPALRKELDKLGR 82 (132)
T ss_pred HHHHHHHHHhCCcEEEECCCCC------CHHHHHHHHHHcCCCEEEEcCchhhhHHHHHHHHHHHHhcCC
Confidence 4555667888999987654332 223456667778999999987553 55777888888886
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=44.13 E-value=73 Score=32.80 Aligned_cols=76 Identities=16% Similarity=0.175 Sum_probs=51.5
Q ss_pred EEEEEE--eCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHc
Q 003054 61 AVPIYV--DNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEI 138 (852)
Q Consensus 61 vaii~~--d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~ 138 (852)
|++|.. ++.|-....+.+.+++++.|.++..... ..+..+....+.++.+.++|.|++...... ...++.+.+.
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 455663 4566777888999999999988765322 223455677888888889999988764322 3455566666
Q ss_pred CC
Q 003054 139 GL 140 (852)
Q Consensus 139 G~ 140 (852)
|.
T Consensus 78 ~i 79 (268)
T cd01575 78 GI 79 (268)
T ss_pred CC
Confidence 65
No 468
>KOG0498 consensus K+-channel ERG and related proteins, contain PAS/PAC sensor domain [Inorganic ion transport and metabolism; Signal transduction mechanisms]
Probab=43.89 E-value=23 Score=42.37 Aligned_cols=71 Identities=15% Similarity=0.215 Sum_probs=55.5
Q ss_pred ccchhHHHHHHHhhhcc--ccccccchhhHHHHHHHHHHHHHHHHhhhhccceeee-----cccCCCcCCHHHHHhcC
Q 003054 510 QVGTSFWFSFSTMVFSQ--RERVISNLARIVVIVWCFVVLILTQSYTASLTSLLTV-----QQLQPTITDVKMLIKRG 580 (852)
Q Consensus 510 ~~~~~~~~~~~~l~~~~--~~~~~s~~~R~v~~~w~~~~lil~~~Yta~L~s~Lt~-----~~~~~~i~sl~dL~~~~ 580 (852)
.+..++||++++|...| ...+.+....++.++.++++++|.++.-+|++++|.. .++...++++++-.+..
T Consensus 294 kY~~aLyw~l~tLstvG~g~~~s~~~~E~iFsi~~mi~GllL~A~lIGNmt~~iqs~tsR~~~~r~k~rd~e~~m~~~ 371 (727)
T KOG0498|consen 294 KYVYALYWGLSTLSTVGYGLVHANNMGEKIFSIFIMLFGLLLFAYLIGNMTALLQSLTSRTEEMRDKMRDAEQWMSRR 371 (727)
T ss_pred HHHHHHHHHhhHhhhccCCccCCCCcHHHHHHHHHHHHhHHHHHHHHhhHHHhHHHHhHHHHHHHHHHHHHHHHHHhc
Confidence 55689999999999755 4566788889999999999999999999999998743 34444566666665443
No 469
>PRK05569 flavodoxin; Provisional
Probab=43.81 E-value=1.5e+02 Score=27.37 Aligned_cols=85 Identities=13% Similarity=0.152 Sum_probs=0.0
Q ss_pred cEEEEEE-EeCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeCh--------hhHH
Q 003054 59 REAVPIY-VDNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLP--------SLGS 129 (852)
Q Consensus 59 ~~vaii~-~d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~--------~~~~ 129 (852)
+++.++| +.....+.+++.+.+.+++.|.++.....-. .+..++. +.|.|++.+.. +...
T Consensus 2 ~ki~iiY~S~tGnT~~iA~~i~~~~~~~g~~v~~~~~~~--~~~~~~~---------~~d~iilgsPty~~~~~~~~~~~ 70 (141)
T PRK05569 2 KKVSIIYWSCGGNVEVLANTIADGAKEAGAEVTIKHVAD--AKVEDVL---------EADAVAFGSPSMDNNNIEQEEMA 70 (141)
T ss_pred CeEEEEEECCCCHHHHHHHHHHHHHHhCCCeEEEEECCc--CCHHHHh---------hCCEEEEECCCcCCCcCChHHHH
Q ss_pred HHHHHHHHcCCcccceEEEEcCccc
Q 003054 130 RIFEKANEIGLMNKGCVWIMTDGMT 154 (852)
Q Consensus 130 ~i~~~a~~~G~~~~~~vwi~~~~~~ 154 (852)
.++.........++..+.+++.+|.
T Consensus 71 ~~~~~l~~~~~~~K~v~~f~t~g~~ 95 (141)
T PRK05569 71 PFLDQFKLTPNENKKCILFGSYGWD 95 (141)
T ss_pred HHHHHhhccCcCCCEEEEEeCCCCC
No 470
>PRK10653 D-ribose transporter subunit RbsB; Provisional
Probab=43.77 E-value=88 Score=33.10 Aligned_cols=80 Identities=8% Similarity=0.028 Sum_probs=56.2
Q ss_pred CcEEEEEEE--eCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhh-HHHHHHH
Q 003054 58 WREAVPIYV--DNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSL-GSRIFEK 134 (852)
Q Consensus 58 w~~vaii~~--d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~-~~~i~~~ 134 (852)
-+.++++.. ++.|-......+.+++++.|.++..... ..+.+.....++++...++|.+++.....+ ....++.
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 567888884 4567888899999999999998765322 122344556777777788998887654433 3466778
Q ss_pred HHHcCC
Q 003054 135 ANEIGL 140 (852)
Q Consensus 135 a~~~G~ 140 (852)
+++.|.
T Consensus 103 ~~~~~i 108 (295)
T PRK10653 103 ANQANI 108 (295)
T ss_pred HHHCCC
Confidence 887775
No 471
>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=43.66 E-value=1.7e+02 Score=27.72 Aligned_cols=66 Identities=11% Similarity=0.047 Sum_probs=38.8
Q ss_pred EeeHHHHHHHHHHCCCccceEEEecCCCCCCCCCChhHHHHHHhcCcccEEEeeeeeecCcceeeeccccccccceEEEE
Q 003054 377 GYCVDVFKAVIQELPYAVAYDFVPYGQPDGSSSGSYNDLVYQVFLGEFDAVVGDITIVFNRSNYVDFTLPYTESGVSMIV 456 (852)
Q Consensus 377 G~~~dl~~~ia~~l~~~~~~~~~~~~~~~g~~ngs~~~li~~l~~g~~D~~~g~~~it~~r~~~vdft~p~~~~~~~~vv 456 (852)
++-..++..+.++.+ .++++.... +.+. .+.+|++|+++... +.....+. +.++....+++++
T Consensus 14 ~~l~~~l~~~~~~~P-~v~i~i~~~-----------~~~~-~l~~~~~D~~i~~~---~~~~~~~~-~~~l~~~~~~~v~ 76 (197)
T cd08422 14 LHLAPLLAEFLARYP-DVRLELVLS-----------DRLV-DLVEEGFDLAIRIG---ELPDSSLV-ARRLGPVRRVLVA 76 (197)
T ss_pred HHHHHHHHHHHHhCC-ceEEEEecC-----------cccc-chhhcCccEEEEeC---CCCCcchh-hhhhhccCcEEEE
Confidence 445678888888876 345555321 1233 45668899998532 22222232 4567777777777
Q ss_pred Ecc
Q 003054 457 PIK 459 (852)
Q Consensus 457 ~~~ 459 (852)
+..
T Consensus 77 ~~~ 79 (197)
T cd08422 77 SPA 79 (197)
T ss_pred CHH
Confidence 643
No 472
>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=43.21 E-value=36 Score=30.87 Aligned_cols=27 Identities=22% Similarity=0.233 Sum_probs=14.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhcc
Q 003054 721 LFLIAGVAAILALIIFMAVFIHQHWNV 747 (852)
Q Consensus 721 ~f~il~ig~~lsl~vf~~e~~~~~r~~ 747 (852)
..+|+|+.+++.++++++-++.+|+++
T Consensus 67 ~~Ii~gv~aGvIg~Illi~y~irR~~K 93 (122)
T PF01102_consen 67 IGIIFGVMAGVIGIILLISYCIRRLRK 93 (122)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHS-
T ss_pred eehhHHHHHHHHHHHHHHHHHHHHHhc
Confidence 455666666665565555555554444
No 473
>cd08195 DHQS Dehydroquinate synthase (DHQS) catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis. 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, which involves seven sequential enzymatic steps in the conversion of erythrose 4-phosphate and phosphoenolpyruvate into chorismate for subsequent synthesis of aromatic compounds, is found in bacteria, microbial eukaryotes, and plants, but not in mammals. Therefore, enzymes of this pathway are attractive targets for the development of non-toxic antimicrobial compounds, herbicides and anti-parasitic agents. The activity of DHQS requires nicotinamide adenine dinucleotide (NAD) as cofactor. A single active site in DHQS catalyzes five sequential reactions involving alcohol oxidation, phosphate elimination, carbonyl reduction, ring opening, and intramolecular aldol
Probab=43.08 E-value=2.3e+02 Score=31.04 Aligned_cols=92 Identities=12% Similarity=-0.003 Sum_probs=59.4
Q ss_pred HHHHHHHH-cCCcEEEEEEEeCCcccccHHHHHHHHHhCCceeeeee--ecCCCCChHHHHHHHHHhhcCCc---eEEEE
Q 003054 48 AITAIIKA-FGWREAVPIYVDNQYGEEMIPSLTDALQAIDTRVPYRS--VISPLATDDQIEKELYKLFTMQT---RVFIL 121 (852)
Q Consensus 48 aia~~l~~-~gw~~vaii~~d~~~G~~~~~~l~~~l~~~g~~v~~~~--~~~~~~~~~d~~~~l~~l~~~~~---~viv~ 121 (852)
.+.+++.. .+.+++.+++....+ ....+.+.+.|++.|+++.... ....+.+.+.+...+..+++.++ |+||.
T Consensus 13 ~l~~~~~~~~~~~~~livtd~~~~-~~~~~~l~~~L~~~g~~~~~~~~~~~e~~~~~~~v~~~~~~~~~~~~~r~d~IIa 91 (345)
T cd08195 13 ELGELLAKLPKGSKILIVTDENVA-PLYLEKLKAALEAAGFEVEVIVIPAGEASKSLETLEKLYDALLEAGLDRKSLIIA 91 (345)
T ss_pred HHHHHHHhccCCCeEEEEECCchH-HHHHHHHHHHHHhcCCceEEEEeCCCCCcCCHHHHHHHHHHHHHcCCCCCCeEEE
Confidence 34444443 456889888844443 4677888889998887654321 12223456778888888888766 88877
Q ss_pred EeCh--hhHHHHHHHHHHcCC
Q 003054 122 HMLP--SLGSRIFEKANEIGL 140 (852)
Q Consensus 122 ~~~~--~~~~~i~~~a~~~G~ 140 (852)
.+.+ -|...++......|.
T Consensus 92 iGGGsv~D~ak~vA~~~~rgi 112 (345)
T cd08195 92 LGGGVVGDLAGFVAATYMRGI 112 (345)
T ss_pred ECChHHHhHHHHHHHHHhcCC
Confidence 7654 466777766555564
No 474
>PF01936 NYN: NYN domain; InterPro: IPR021139 This highly conserved domain has no known function. However it contains many conserved aspartates, suggesting an enzymatic function such as an endonuclease or glycosyl hydrolase.; PDB: 2QIP_A.
Probab=42.69 E-value=1.2e+02 Score=27.98 Aligned_cols=94 Identities=16% Similarity=0.139 Sum_probs=46.5
Q ss_pred HHHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHHHHHhCCceeeeeeec-----CCCCChHHHHHHHHHhh-cCCceE
Q 003054 45 QAGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTDALQAIDTRVPYRSVI-----SPLATDDQIEKELYKLF-TMQTRV 118 (852)
Q Consensus 45 ~~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~~l~~~g~~v~~~~~~-----~~~~~~~d~~~~l~~l~-~~~~~v 118 (852)
....+.+.+...|--....+|.+ +.......+.+.|+..|+++...... ..+..+..+...+..+. ...+|.
T Consensus 21 ~~~~l~~~i~~~~~~~~~~~y~~--~~~~~~~~~~~~L~~~g~~v~~~~~~~~~~~~k~~~D~~l~~d~~~~~~~~~~d~ 98 (146)
T PF01936_consen 21 DFERLLEEIRKYGPLVRIRAYGN--WDDPNQKSFQEALQRAGIKVRHFPLRKRGGGGKKGVDVALAVDILELAYENPPDT 98 (146)
T ss_dssp -HHHHHHHHTTTEEEEEEEEEE------HHHHHHHHHHHHHT-EEEE------S---S---HHHHHHHHHHHG--GG-SE
T ss_pred CHHHHHHHHHhcCCeEEEEEEee--ccccchhhHHHHHHhCeeeEEeeecccccccccCCcHHHHHHHHHHHhhccCCCE
Confidence 34555555555442112333433 33344677889999999977554331 12223334444444333 344688
Q ss_pred EEEEeChhhHHHHHHHHHHcCC
Q 003054 119 FILHMLPSLGSRIFEKANEIGL 140 (852)
Q Consensus 119 iv~~~~~~~~~~i~~~a~~~G~ 140 (852)
+++.+...+...+++.+++.|.
T Consensus 99 ivLvSgD~Df~~~v~~l~~~g~ 120 (146)
T PF01936_consen 99 IVLVSGDSDFAPLVRKLRERGK 120 (146)
T ss_dssp EEEE---GGGHHHHHHHHHH--
T ss_pred EEEEECcHHHHHHHHHHHHcCC
Confidence 8888888999999999999885
No 475
>PF06305 DUF1049: Protein of unknown function (DUF1049); InterPro: IPR010445 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=42.22 E-value=71 Score=25.33 Aligned_cols=27 Identities=7% Similarity=0.215 Sum_probs=14.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhcc
Q 003054 721 LFLIAGVAAILALIIFMAVFIHQHWNV 747 (852)
Q Consensus 721 ~f~il~ig~~lsl~vf~~e~~~~~r~~ 747 (852)
++..+++|.+++.++.+...+..+++.
T Consensus 24 il~~f~~G~llg~l~~~~~~~~~r~~~ 50 (68)
T PF06305_consen 24 ILIAFLLGALLGWLLSLPSRLRLRRRI 50 (68)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334455666666665555554444433
No 476
>cd08487 PBP2_BlaA The C-terminal substrate-binding domain of LysR-type trnascriptional regulator BlaA which involved in control of the beta-lactamase gene expression; contains the type 2 periplasmic binding fold. This CD represents the C-terminal substrate binding domain of LysR-type transcriptional regulator, BlaA, that involved in control of the expression of beta-lactamase genes, blaA and blaB. Beta-lactamases are responsible for bacterial resistance to beta-lactam antibiotics such as penicillins. The blaA gene is located just upstream of blaB in the opposite direction and regulates the expression of the blaB. BlaA also negatively auto-regulates the expression of its own gene, blaA. BlaA (a constitutive class A penicllinase) belongs to the LysR family of transcriptional regulators, whereas BlaB (an inducible class C cephalosporinase or AmpC) can be referred to as a penicillin binding protein but it does not act as a beta-lactamase. The topology of this substrate-binding domain is
Probab=41.96 E-value=3e+02 Score=25.86 Aligned_cols=99 Identities=12% Similarity=0.031 Sum_probs=48.7
Q ss_pred CHHHHHhcCCeEEE-EeCchHHHHHHhcCCCCcce--eecCCHhHHHHHhhcccccCceeEEEechhHHHHHHhhcCCce
Q 003054 572 DVKMLIKRGDNVGY-QKGSFVLGILKQLGFDERKL--VVYNSPEDCHELFQKGSVNGGIAAAFDEIPYMKLLIGQYCSKY 648 (852)
Q Consensus 572 sl~dL~~~~~~vg~-~~~s~~~~~l~~~~~~~~~~--~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~~~~~~ 648 (852)
+++||. +.++.. ........++.+.+...... ...++.....+++..|. ..+++.+. .......... ..
T Consensus 85 ~~~~l~--~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~----Gi~~~p~~-~~~~~~~~~~-l~ 156 (189)
T cd08487 85 HPADLI--NETLLRSYRTDEWLQWFEAANMPPIKIRGPVFDSSRLMVEAAMQGA----GVALAPAK-MFSREIENGQ-LV 156 (189)
T ss_pred CHHHHh--cCceeecCCchHHHHHHHHcCCCCccccCCccccHHHHHHHHHhCC----CeEeehHH-HHHHHHhCCC-EE
Confidence 467776 333322 11122344555544432221 24567777888888887 44555443 3332222221 11
Q ss_pred EeecccccccceEEEecCCCCchhhHHHHH
Q 003054 649 AMIEPKFKTAGFGFVFPLHSPLVHDVSKAI 678 (852)
Q Consensus 649 ~~v~~~~~~~~~~~~~~k~spl~~~in~~i 678 (852)
..+........++++.+|+.+.-..+...+
T Consensus 157 ~~l~~~~~~~~~~~~~~~~~~~~~~~~~f~ 186 (189)
T cd08487 157 QPFKIEVETGSYWLTWLKSKPMTPAMELFR 186 (189)
T ss_pred cccCcccCCCcEEEEecccccCCHHHHHHH
Confidence 122222234567778888877655555444
No 477
>TIGR00288 conserved hypothetical protein TIGR00288. This family of orthologs is restricted to but universal among the completed archaeal genomes so far. Eubacterial proteins showing at least local homology include slr1870 from Synechocystis PCC6803 and two proteins from Aquifex aeolicusr, none of which is characterized.
Probab=41.93 E-value=1.5e+02 Score=28.38 Aligned_cols=79 Identities=11% Similarity=0.205 Sum_probs=49.6
Q ss_pred HHHHHHHHcCCcEEEEEEEeCCcccccHHHHHHHHHhC-CceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChh
Q 003054 48 AITAIIKAFGWREAVPIYVDNQYGEEMIPSLTDALQAI-DTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPS 126 (852)
Q Consensus 48 aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~~l~~~-g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~ 126 (852)
.+.+.+.+.|.+-+ +. -|..-+....++++-. ..++....-+ ++|.||.+.+.+|++.+.+|+++.....
T Consensus 70 ~l~~~l~~~Gf~pv---~~---kG~~Dv~laIDame~~~~~~iD~~vLv---SgD~DF~~Lv~~lre~G~~V~v~g~~~~ 140 (160)
T TIGR00288 70 KLIEAVVNQGFEPI---IV---AGDVDVRMAVEAMELIYNPNIDAVALV---TRDADFLPVINKAKENGKETIVIGAEPG 140 (160)
T ss_pred HHHHHHHHCCceEE---Ee---cCcccHHHHHHHHHHhccCCCCEEEEE---eccHhHHHHHHHHHHCCCEEEEEeCCCC
Confidence 45667788888733 22 2333345555565542 2233223223 4589999999999999999999986555
Q ss_pred hHHHHHHHH
Q 003054 127 LGSRIFEKA 135 (852)
Q Consensus 127 ~~~~i~~~a 135 (852)
....+.+++
T Consensus 141 ts~~L~~ac 149 (160)
T TIGR00288 141 FSTALQNSA 149 (160)
T ss_pred ChHHHHHhc
Confidence 555555554
No 478
>cd00758 MoCF_BD MoCF_BD: molybdenum cofactor (MoCF) binding domain (BD). This domain is found a variety of proteins involved in biosynthesis of molybdopterin cofactor, like MoaB, MogA, and MoeA. The domain is presumed to bind molybdopterin.
Probab=41.60 E-value=1.1e+02 Score=28.11 Aligned_cols=49 Identities=18% Similarity=0.205 Sum_probs=36.3
Q ss_pred ccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeC
Q 003054 73 EMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHML 124 (852)
Q Consensus 73 ~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~ 124 (852)
.....+.+.+++.|.++.....++ .+.+.+...+.++.+. +|+|+..+-
T Consensus 19 ~n~~~l~~~l~~~G~~v~~~~~v~--Dd~~~i~~~i~~~~~~-~DlvittGG 67 (133)
T cd00758 19 TNGPALEALLEDLGCEVIYAGVVP--DDADSIRAALIEASRE-ADLVLTTGG 67 (133)
T ss_pred chHHHHHHHHHHCCCEEEEeeecC--CCHHHHHHHHHHHHhc-CCEEEECCC
Confidence 345678888999999987776665 3366788888877654 899988754
No 479
>cd02070 corrinoid_protein_B12-BD B12 binding domain of corrinoid proteins. A family of small methanogenic corrinoid proteins that bind methyl-Co(III) 5-hydroxybenzimidazolylcobamide as a cofactor. They play a role on the methanogenesis from trimethylamine, dimethylamine or monomethylamine, which is initiated by a series of corrinoid-dependent methyltransferases.
Probab=41.36 E-value=2.1e+02 Score=28.45 Aligned_cols=88 Identities=15% Similarity=0.004 Sum_probs=55.0
Q ss_pred cEEEEEEEeCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeC----hhhHHHHHHH
Q 003054 59 REAVPIYVDNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHML----PSLGSRIFEK 134 (852)
Q Consensus 59 ~~vaii~~d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~----~~~~~~i~~~ 134 (852)
.+|.+.....+.=.-....+...|+..|.+|.+-- .+...++ .+..+++.+||+|.+.+. .+....++++
T Consensus 83 ~~vl~~~~~gd~H~lG~~~v~~~l~~~G~~vi~lG---~~~p~~~---l~~~~~~~~~d~v~lS~~~~~~~~~~~~~i~~ 156 (201)
T cd02070 83 GKVVIGTVEGDIHDIGKNLVATMLEANGFEVIDLG---RDVPPEE---FVEAVKEHKPDILGLSALMTTTMGGMKEVIEA 156 (201)
T ss_pred CeEEEEecCCccchHHHHHHHHHHHHCCCEEEECC---CCCCHHH---HHHHHHHcCCCEEEEeccccccHHHHHHHHHH
Confidence 46655554444434445667778999999985432 2222334 455566789999987763 2467888888
Q ss_pred HHHcCCcccceEEEEcCc
Q 003054 135 ANEIGLMNKGCVWIMTDG 152 (852)
Q Consensus 135 a~~~G~~~~~~vwi~~~~ 152 (852)
+++.+....-.+++++..
T Consensus 157 lr~~~~~~~~~i~vGG~~ 174 (201)
T cd02070 157 LKEAGLRDKVKVMVGGAP 174 (201)
T ss_pred HHHCCCCcCCeEEEECCc
Confidence 988875333345555544
No 480
>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=41.20 E-value=80 Score=32.83 Aligned_cols=80 Identities=11% Similarity=0.025 Sum_probs=52.4
Q ss_pred EEEEEEE--eCCcccccHHHHHHHHHhCCceeeeeeec-CCCCChHHHHHHHHHhhcCCceEEEEEeChh-hHHHHHHHH
Q 003054 60 EAVPIYV--DNQYGEEMIPSLTDALQAIDTRVPYRSVI-SPLATDDQIEKELYKLFTMQTRVFILHMLPS-LGSRIFEKA 135 (852)
Q Consensus 60 ~vaii~~--d~~~G~~~~~~l~~~l~~~g~~v~~~~~~-~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~-~~~~i~~~a 135 (852)
+|+++.. ++.|-....+.+.+++++.|..+...... ....+.......+..+.. ++|.+++..... .....++++
T Consensus 1 ~ig~v~~~~~~~~~~~~~~~i~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~i~~~~~-~vdgiii~~~~~~~~~~~i~~~ 79 (275)
T cd06307 1 RLGFLLPKGSNAFYRELAAALEAAAAAFPDARIRVRIHFVESFDPAALAAALLRLGA-RSDGVALVAPDHPQVRAAVARL 79 (275)
T ss_pred CeEEEeCCCCChHHHHHHHHHHHHHhhhhccCceEEEEEccCCCHHHHHHHHHHHHh-cCCEEEEeCCCcHHHHHHHHHH
Confidence 4667774 35677888899999999988654433221 111223445567777777 999998865443 335677888
Q ss_pred HHcCC
Q 003054 136 NEIGL 140 (852)
Q Consensus 136 ~~~G~ 140 (852)
.+.|.
T Consensus 80 ~~~~i 84 (275)
T cd06307 80 AAAGV 84 (275)
T ss_pred HHCCC
Confidence 88775
No 481
>cd06283 PBP1_RegR_EndR_KdgR_like Ligand-binding domain of DNA transcription repressor RegR and other putative regulators such as KdgR and EndR. Ligand-binding domain of DNA transcription repressor RegR and other putative regulators such as KdgR and EndR, all of which are members of the LacI-GalR family of bacterial transcription regulators. RegR regulates bacterial competence and the expression of virulence factors, including hyaluronidase. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA b
Probab=41.15 E-value=93 Score=31.99 Aligned_cols=76 Identities=13% Similarity=0.156 Sum_probs=51.5
Q ss_pred EEEEE--EeCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHc
Q 003054 61 AVPIY--VDNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEI 138 (852)
Q Consensus 61 vaii~--~d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~ 138 (852)
|+++. .++.|-....+.+.+++++.|..+.... ...+.......+.++.+.++|.|++....... ..++++++.
T Consensus 2 igvi~~~~~~~~~~~~~~~i~~~a~~~g~~~~~~~---~~~~~~~~~~~~~~l~~~~~dgiii~~~~~~~-~~l~~~~~~ 77 (267)
T cd06283 2 IGVIVADITNPFSSLVLKGIEDVCRAHGYQVLVCN---SDNDPEKEKEYLESLLAYQVDGLIVNPTGNNK-ELYQRLAKN 77 (267)
T ss_pred EEEEecCCccccHHHHHHHHHHHHHHcCCEEEEEc---CCCCHHHHHHHHHHHHHcCcCEEEEeCCCCCh-HHHHHHhcC
Confidence 44555 3567778889999999999998875432 12234445677788888899999887644333 236777776
Q ss_pred CC
Q 003054 139 GL 140 (852)
Q Consensus 139 G~ 140 (852)
|.
T Consensus 78 ~i 79 (267)
T cd06283 78 GK 79 (267)
T ss_pred CC
Confidence 65
No 482
>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=40.87 E-value=93 Score=32.22 Aligned_cols=77 Identities=10% Similarity=0.083 Sum_probs=52.1
Q ss_pred EEEEE--EeCCcccccHHHHHHHHHh--CCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhh-HHHHHHHH
Q 003054 61 AVPIY--VDNQYGEEMIPSLTDALQA--IDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSL-GSRIFEKA 135 (852)
Q Consensus 61 vaii~--~d~~~G~~~~~~l~~~l~~--~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~-~~~i~~~a 135 (852)
|+++. .++.|-......+.+++++ .|.++.... ...+.+.....+..+...++|.|++...... ....++.+
T Consensus 2 Ig~v~~~~~~~~~~~~~~gi~~~~~~~~~~~~~~~~~---~~~~~~~~~~~i~~~~~~~~dgiIi~~~~~~~~~~~i~~~ 78 (271)
T cd06321 2 IGVSVGDLGNPFFVALAKGAEAAAKKLNPGVKVTVVS---ADYDLNKQVSQIDNFIAAKVDLILLNAVDSKGIAPAVKRA 78 (271)
T ss_pred eEEEecccCCHHHHHHHHHHHHHHHHhCCCeEEEEcc---CCCCHHHHHHHHHHHHHhCCCEEEEeCCChhHhHHHHHHH
Confidence 55666 3567888899999999999 666654331 1223445566777778889999988754333 35667778
Q ss_pred HHcCC
Q 003054 136 NEIGL 140 (852)
Q Consensus 136 ~~~G~ 140 (852)
++.|.
T Consensus 79 ~~~~i 83 (271)
T cd06321 79 QAAGI 83 (271)
T ss_pred HHCCC
Confidence 77775
No 483
>TIGR00644 recJ single-stranded-DNA-specific exonuclease RecJ. All proteins in this family are 5'-3' single-strand DNA exonucleases. These proteins are used in some aspects of mismatch repair, recombination, and recombinational repair.
Probab=40.81 E-value=1.8e+02 Score=34.17 Aligned_cols=109 Identities=14% Similarity=0.108 Sum_probs=61.8
Q ss_pred CCCCCCCCCceEeccCCchhHHHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHHHHHhCCceeeeeeecC--CCCChH
Q 003054 25 PSLTSIRSPYFFRGSLNDSSQAGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTDALQAIDTRVPYRSVIS--PLATDD 102 (852)
Q Consensus 25 ~~lt~~~~py~fR~~p~d~~~~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~--~~~~~~ 102 (852)
|.+.+...|+.+ +.-..-++.+++.++. -++|.|+...|.-|.+....+...|.+.|.++.+...-. ...+-.
T Consensus 26 ~~l~~l~~p~~l---~~~~~a~~~i~~~i~~--~~~I~I~gh~D~DGi~S~~~L~~~L~~~g~~v~~~ip~r~~~~yg~~ 100 (539)
T TIGR00644 26 PDLIDLPDPFLL---KDMEKAVERIIEAIEN--NEKILIFGDYDVDGITSTAILVEFLKDLGVNVDYYIPNRITEGYGLS 100 (539)
T ss_pred cchhhcCChhhc---CCHHHHHHHHHHHHhc--CCeEEEEEccCCCcHHHHHHHHHHHHHCCCceEEEeCCCCcccCCCC
Confidence 444433456544 3333333444444544 368888876677799999999999999998875443211 110100
Q ss_pred HHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHcCC
Q 003054 103 QIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEIGL 140 (852)
Q Consensus 103 d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~G~ 140 (852)
...+.++...+++.+|+.-.+.....-...+++.|+
T Consensus 101 --~~~i~~~~~~~~~LiI~vD~G~~~~~~~~~~~~~g~ 136 (539)
T TIGR00644 101 --PEALREAIENGVSLIITVDNGISAHEEIDYAKELGI 136 (539)
T ss_pred --HHHHHHHHhcCCCEEEEeCCCcccHHHHHHHHhcCC
Confidence 123445554577887766554444333455666665
No 484
>PRK06703 flavodoxin; Provisional
Probab=40.79 E-value=1.3e+02 Score=28.18 Aligned_cols=82 Identities=20% Similarity=0.242 Sum_probs=45.7
Q ss_pred EEEEEEEeCCcc--cccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeC-------hhhHHH
Q 003054 60 EAVPIYVDNQYG--EEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHML-------PSLGSR 130 (852)
Q Consensus 60 ~vaii~~d~~~G--~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~-------~~~~~~ 130 (852)
++.|+| .+.+| +..++.+.+.+.+.|.++..... . +.+.. .+ .+.|.|++.++ ++.+..
T Consensus 3 kv~IiY-~S~tGnT~~iA~~ia~~l~~~g~~v~~~~~-~----~~~~~----~l--~~~d~viigspt~~~g~~p~~~~~ 70 (151)
T PRK06703 3 KILIAY-ASMSGNTEDIADLIKVSLDAFDHEVVLQEM-D----GMDAE----EL--LAYDGIILGSYTWGDGDLPYEAED 70 (151)
T ss_pred eEEEEE-ECCCchHHHHHHHHHHHHHhcCCceEEEeh-h----hCCHH----HH--hcCCcEEEEECCCCCCcCcHHHHH
Confidence 677888 33454 66778888888888877643321 1 11111 22 24456666543 234677
Q ss_pred HHHHHHHcCCcccceEEEEcCcc
Q 003054 131 IFEKANEIGLMNKGCVWIMTDGM 153 (852)
Q Consensus 131 i~~~a~~~G~~~~~~vwi~~~~~ 153 (852)
++....+..+..+.+..+++.++
T Consensus 71 f~~~l~~~~l~~k~~~vfg~g~~ 93 (151)
T PRK06703 71 FHEDLENIDLSGKKVAVFGSGDT 93 (151)
T ss_pred HHHHHhcCCCCCCEEEEEccCCC
Confidence 77777655554444445544443
No 485
>cd01574 PBP1_LacI Ligand-binding domain of DNA transcription repressor LacI specific for lactose, a member of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressor LacI specific for lactose, a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of LacI is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA b
Probab=40.66 E-value=1.1e+02 Score=31.50 Aligned_cols=77 Identities=8% Similarity=0.044 Sum_probs=49.9
Q ss_pred EEEEE--EeCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHc
Q 003054 61 AVPIY--VDNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEI 138 (852)
Q Consensus 61 vaii~--~d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~ 138 (852)
|++|. .++.|-....+.+.+++++.|..+..... ...+.......+..+.+.++|.+++........ .+.++.+.
T Consensus 2 i~vi~~~~~~~~~~~~~~gi~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~l~~~~vdgiii~~~~~~~~-~~~~~~~~ 78 (264)
T cd01574 2 IGVVTTDLALHGPSSTLAAIESAAREAGYAVTLSML--AEADEEALRAAVRRLLAQRVDGVIVNAPLDDAD-AALAAAPA 78 (264)
T ss_pred EEEEeCCCCcccHHHHHHHHHHHHHHCCCeEEEEeC--CCCchHHHHHHHHHHHhcCCCEEEEeCCCCChH-HHHHHHhc
Confidence 45555 45567788899999999999988765422 111224456677778888999998875543333 23445566
Q ss_pred CC
Q 003054 139 GL 140 (852)
Q Consensus 139 G~ 140 (852)
|.
T Consensus 79 ~i 80 (264)
T cd01574 79 DV 80 (264)
T ss_pred CC
Confidence 64
No 486
>TIGR01501 MthylAspMutase methylaspartate mutase, S subunit. This model represents the S (sigma) subunit of methylaspartate mutase (glutamate mutase), a cobalamin-dependent enzyme that catalyzes the first step in a pathway of glutamate fermentation.
Probab=40.65 E-value=2.9e+02 Score=25.56 Aligned_cols=70 Identities=14% Similarity=0.084 Sum_probs=46.6
Q ss_pred HHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeC----hhhHHHHHHHHHHcCCcccceEEEEc
Q 003054 75 IPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHML----PSLGSRIFEKANEIGLMNKGCVWIMT 150 (852)
Q Consensus 75 ~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~----~~~~~~i~~~a~~~G~~~~~~vwi~~ 150 (852)
.+.+...|+..|.+|.+--. +......+...++.++|+|-+... ......+.+.+++.|+.. ..|+.+
T Consensus 18 k~iv~~~l~~~GfeVi~LG~------~v~~e~~v~aa~~~~adiVglS~l~~~~~~~~~~~~~~l~~~gl~~--~~vivG 89 (134)
T TIGR01501 18 NKILDHAFTNAGFNVVNLGV------LSPQEEFIKAAIETKADAILVSSLYGHGEIDCKGLRQKCDEAGLEG--ILLYVG 89 (134)
T ss_pred HHHHHHHHHHCCCEEEECCC------CCCHHHHHHHHHHcCCCEEEEecccccCHHHHHHHHHHHHHCCCCC--CEEEec
Confidence 35566788999999875432 122344566777789999987653 235678888999999843 345554
Q ss_pred Cc
Q 003054 151 DG 152 (852)
Q Consensus 151 ~~ 152 (852)
+.
T Consensus 90 G~ 91 (134)
T TIGR01501 90 GN 91 (134)
T ss_pred CC
Confidence 43
No 487
>PRK02261 methylaspartate mutase subunit S; Provisional
Probab=40.15 E-value=2.5e+02 Score=26.11 Aligned_cols=85 Identities=14% Similarity=0.071 Sum_probs=50.7
Q ss_pred cEEEEEEEeCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeC----hhhHHHHHHH
Q 003054 59 REAVPIYVDNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHML----PSLGSRIFEK 134 (852)
Q Consensus 59 ~~vaii~~d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~----~~~~~~i~~~ 134 (852)
.+|.+.....+.=.-....+...|+..|.+|.+--. +...++ .+..+.+.+||+|.+.+. ...+..++++
T Consensus 4 ~~vl~~~~~gD~H~lG~~iv~~~lr~~G~eVi~LG~---~vp~e~---i~~~a~~~~~d~V~lS~~~~~~~~~~~~~~~~ 77 (137)
T PRK02261 4 KTVVLGVIGADCHAVGNKILDRALTEAGFEVINLGV---MTSQEE---FIDAAIETDADAILVSSLYGHGEIDCRGLREK 77 (137)
T ss_pred CEEEEEeCCCChhHHHHHHHHHHHHHCCCEEEECCC---CCCHHH---HHHHHHHcCCCEEEEcCccccCHHHHHHHHHH
Confidence 344444433333233345666788889999876532 122333 455566789999988753 3467888888
Q ss_pred HHHcCCcccceEEEEc
Q 003054 135 ANEIGLMNKGCVWIMT 150 (852)
Q Consensus 135 a~~~G~~~~~~vwi~~ 150 (852)
+++.|... -.+|+++
T Consensus 78 L~~~~~~~-~~i~vGG 92 (137)
T PRK02261 78 CIEAGLGD-ILLYVGG 92 (137)
T ss_pred HHhcCCCC-CeEEEEC
Confidence 88887733 2344444
No 488
>PRK11914 diacylglycerol kinase; Reviewed
Probab=39.90 E-value=1.3e+02 Score=32.25 Aligned_cols=78 Identities=6% Similarity=-0.079 Sum_probs=50.0
Q ss_pred HcCCcEEEEEEEeCCccc----ccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHH
Q 003054 55 AFGWREAVPIYVDNQYGE----EMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSR 130 (852)
Q Consensus 55 ~~gw~~vaii~~d~~~G~----~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~ 130 (852)
...-+++.+|+. -.-|. ...+.+.+.|++.|.++..... ....+......++...++|+||+.+-......
T Consensus 5 ~~~~~~~~iI~N-P~sG~g~~~~~~~~~~~~l~~~g~~~~~~~t----~~~~~~~~~a~~~~~~~~d~vvv~GGDGTi~e 79 (306)
T PRK11914 5 RHEIGKVTVLTN-PLSGHGAAPHAAERAIARLHHRGVDVVEIVG----TDAHDARHLVAAALAKGTDALVVVGGDGVISN 79 (306)
T ss_pred cCCCceEEEEEC-CCCCCCcHHHHHHHHHHHHHHcCCeEEEEEe----CCHHHHHHHHHHHHhcCCCEEEEECCchHHHH
Confidence 344578888883 22232 3355677789999987643322 12456666666776778898888877766677
Q ss_pred HHHHHHH
Q 003054 131 IFEKANE 137 (852)
Q Consensus 131 i~~~a~~ 137 (852)
++..+..
T Consensus 80 vv~~l~~ 86 (306)
T PRK11914 80 ALQVLAG 86 (306)
T ss_pred HhHHhcc
Confidence 7766543
No 489
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=39.68 E-value=2.3e+02 Score=32.67 Aligned_cols=90 Identities=10% Similarity=0.145 Sum_probs=55.1
Q ss_pred CCcEEEEEEEeCCcc--cccHHHHHHHHHhC--CceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeCh------h
Q 003054 57 GWREAVPIYVDNQYG--EEMIPSLTDALQAI--DTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLP------S 126 (852)
Q Consensus 57 gw~~vaii~~d~~~G--~~~~~~l~~~l~~~--g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~------~ 126 (852)
.-++|.|+| .+.|| +.+++.+.+.+++. |+++.... +. +.+....+..+ ..+|.|++.++. +
T Consensus 250 ~~~kv~IvY-~S~~GnTe~mA~~ia~gl~~~g~gv~v~~~~-v~----~~~~~~i~~~~--~~ad~vilGspT~~~~~~p 321 (479)
T PRK05452 250 QEDRITIFY-DTMSNNTRMMADAIAQGIAEVDPRVAVKIFN-VA----RSDKNEILTNV--FRSKGVLVGSSTMNNVMMP 321 (479)
T ss_pred CcCcEEEEE-ECCccHHHHHHHHHHHHHHhhCCCceEEEEE-CC----CCCHHHHHhHH--hhCCEEEEECCccCCcchH
Confidence 347899998 45555 67788888888876 45543322 22 22333344444 256778777543 3
Q ss_pred hHHHHHHHHHHcCCcccceEEEEcCccc
Q 003054 127 LGSRIFEKANEIGLMNKGCVWIMTDGMT 154 (852)
Q Consensus 127 ~~~~i~~~a~~~G~~~~~~vwi~~~~~~ 154 (852)
....++.......+.++....+++.+|.
T Consensus 322 ~~~~fl~~l~~~~l~gK~~~vFGSygw~ 349 (479)
T PRK05452 322 KIAGLLEEITGLRFRNKRASAFGSHGWS 349 (479)
T ss_pred HHHHHHHHhhccCcCCCEEEEEECCCcC
Confidence 4566777777777666655666666664
No 490
>TIGR00035 asp_race aspartate racemase.
Probab=39.47 E-value=59 Score=33.25 Aligned_cols=43 Identities=7% Similarity=-0.032 Sum_probs=29.8
Q ss_pred HHHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHHHHHhCCceee
Q 003054 45 QAGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTDALQAIDTRVP 90 (852)
Q Consensus 45 ~~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~~l~~~g~~v~ 90 (852)
..++.++.++..|.++|+++..... -....+.+.+++.|+++.
T Consensus 104 i~~~~~~~~~~~~~~~VgvLaT~~T---~~s~~y~~~l~~~g~~v~ 146 (229)
T TIGR00035 104 MIEETAEAVKEDGVKKAGLLGTKGT---MKDGVYEREMKKHGIEIV 146 (229)
T ss_pred hHHHHHHHHHHcCCCEEEEEecHHH---HHhHHHHHHHHHCCCEEE
Confidence 3455566667778999999974432 223558888999997764
No 491
>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=39.45 E-value=1e+02 Score=31.49 Aligned_cols=76 Identities=12% Similarity=-0.013 Sum_probs=51.7
Q ss_pred EEEEEE--eCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHc
Q 003054 61 AVPIYV--DNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEI 138 (852)
Q Consensus 61 vaii~~--d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~ 138 (852)
|+++.. ++.|.....+.+.+++++.|.++..... ..+.+.....+.++.+.++|.+++...... ..+++.+++.
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 455553 3567778899999999999998865422 223445567788888899999998755322 3455666666
Q ss_pred CC
Q 003054 139 GL 140 (852)
Q Consensus 139 G~ 140 (852)
|.
T Consensus 78 ~i 79 (259)
T cd01542 78 NV 79 (259)
T ss_pred CC
Confidence 64
No 492
>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=39.44 E-value=1.2e+02 Score=31.31 Aligned_cols=76 Identities=11% Similarity=0.043 Sum_probs=52.4
Q ss_pred EEEEEE--eCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeChhhHHHHHHHHHHc
Q 003054 61 AVPIYV--DNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEI 138 (852)
Q Consensus 61 vaii~~--d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~~~~~~i~~~a~~~ 138 (852)
|+++.. +++|-......+.+++++.|.++.... .+.+.......+..+.+.++|.|++....... ..++++.+.
T Consensus 2 igvi~p~~~~~~~~~~~~gi~~~~~~~~~~~~~~~---~~~~~~~~~~~i~~l~~~~~dgiii~~~~~~~-~~~~~~~~~ 77 (265)
T cd06285 2 IGVLVPRLTDTVMATMYEGIEEAAAERGYSTFVAN---TGDNPDAQRRAIEMLLDRRVDGLILGDARSDD-HFLDELTRR 77 (265)
T ss_pred EEEEeCCCCCccHHHHHHHHHHHHHHCCCEEEEEe---CCCCHHHHHHHHHHHHHcCCCEEEEecCCCCh-HHHHHHHHc
Confidence 566664 467888889999999999998875322 12223445567778888999988887543333 346777777
Q ss_pred CC
Q 003054 139 GL 140 (852)
Q Consensus 139 G~ 140 (852)
|.
T Consensus 78 ~i 79 (265)
T cd06285 78 GV 79 (265)
T ss_pred CC
Confidence 75
No 493
>COG0541 Ffh Signal recognition particle GTPase [Intracellular trafficking and secretion]
Probab=39.33 E-value=2.2e+02 Score=31.88 Aligned_cols=120 Identities=17% Similarity=0.196 Sum_probs=77.5
Q ss_pred CCCCceEeccCC----chhHHHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHH-
Q 003054 30 IRSPYFFRGSLN----DSSQAGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQI- 104 (852)
Q Consensus 30 ~~~py~fR~~p~----d~~~~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~- 104 (852)
.+.|+++-++.- -+.-+.-+|.++++.| ++|.++..| .|--...+.|+...++.|+.+-.. ..+.+..++
T Consensus 97 ~~~P~vImmvGLQGsGKTTt~~KLA~~lkk~~-~kvllVaaD-~~RpAA~eQL~~La~q~~v~~f~~---~~~~~Pv~Ia 171 (451)
T COG0541 97 KKPPTVILMVGLQGSGKTTTAGKLAKYLKKKG-KKVLLVAAD-TYRPAAIEQLKQLAEQVGVPFFGS---GTEKDPVEIA 171 (451)
T ss_pred CCCCeEEEEEeccCCChHhHHHHHHHHHHHcC-CceEEEecc-cCChHHHHHHHHHHHHcCCceecC---CCCCCHHHHH
Confidence 345776655542 2356778899998855 888888754 466667777777777778775332 112223344
Q ss_pred HHHHHHhhcCCceEEEEEeChhhH--HHHHHHHHHcC-CcccceEEEEcCccc
Q 003054 105 EKELYKLFTMQTRVFILHMLPSLG--SRIFEKANEIG-LMNKGCVWIMTDGMT 154 (852)
Q Consensus 105 ~~~l~~l~~~~~~viv~~~~~~~~--~~i~~~a~~~G-~~~~~~vwi~~~~~~ 154 (852)
...|.+.+....|++|+.+.+... ..++.++++.. ...|.-+.+..|...
T Consensus 172 k~al~~ak~~~~DvvIvDTAGRl~ide~Lm~El~~Ik~~~~P~E~llVvDam~ 224 (451)
T COG0541 172 KAALEKAKEEGYDVVIVDTAGRLHIDEELMDELKEIKEVINPDETLLVVDAMI 224 (451)
T ss_pred HHHHHHHHHcCCCEEEEeCCCcccccHHHHHHHHHHHhhcCCCeEEEEEeccc
Confidence 567888998999999999887643 45555555443 234556666666655
No 494
>TIGR00177 molyb_syn molybdenum cofactor synthesis domain. The Drosophila protein cinnamon, the Arabidopsis protein cnx1, and rat protein gephyrin each have one domain like MoeA and one like MoaB and Mog. These domains are, however, distantly related to each other, as captured by this model. Gephyrin is unusual in that it seems to be a tubulin-binding neuroprotein involved in the clustering of both blycine receptors and GABA receptors, rather than a protein of molybdenum cofactor biosynthesis.
Probab=39.21 E-value=1.3e+02 Score=28.18 Aligned_cols=49 Identities=16% Similarity=0.145 Sum_probs=37.3
Q ss_pred ccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeC
Q 003054 73 EMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHML 124 (852)
Q Consensus 73 ~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~ 124 (852)
.....+.+.|++.|.++.....++. +.+++...+.++.+ +.|+||+.+.
T Consensus 27 ~n~~~l~~~l~~~G~~v~~~~~v~D--d~~~i~~~l~~~~~-~~DliIttGG 75 (144)
T TIGR00177 27 SNGPLLAALLEEAGFNVSRLGIVPD--DPEEIREILRKAVD-EADVVLTTGG 75 (144)
T ss_pred CcHHHHHHHHHHCCCeEEEEeecCC--CHHHHHHHHHHHHh-CCCEEEECCC
Confidence 3456888899999999887776663 36678888877654 7899998864
No 495
>cd06275 PBP1_PurR Ligand-binding domain of purine repressor, PurR, which functions as the master regulatory protein of de novo purine nucleotide biosynthesis in Escherichia coli. Ligand-binding domain of purine repressor, PurR, which functions as the master regulatory protein of de novo purine nucleotide biosynthesis in Escherichia coli. This dimeric PurR belongs to the LacI-GalR family of transcription regulators and is activated to bind to DNA operator sites by initially binding either of high affinity corepressors, hypoxanthine or guanine. PurR is composed of two functional domains: aan N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the purine transcription repressor undergoes a
Probab=39.16 E-value=2.2e+02 Score=29.19 Aligned_cols=62 Identities=6% Similarity=-0.021 Sum_probs=44.3
Q ss_pred EEEEEE--eCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeCh
Q 003054 61 AVPIYV--DNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLP 125 (852)
Q Consensus 61 vaii~~--d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~ 125 (852)
|+++.. ++.|.....+.+.+++++.|.++.... .+.+.......+..+.+.++|.|++....
T Consensus 2 igvi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~---~~~~~~~~~~~i~~l~~~~vdgiii~~~~ 65 (269)
T cd06275 2 IGMLVTTSTNPFFAEVVRGVEQYCYRQGYNLILCN---TEGDPERQRSYLRMLAQKRVDGLLVMCSE 65 (269)
T ss_pred EEEEeCCCCcchHHHHHHHHHHHHHHcCCEEEEEe---CCCChHHHHHHHHHHHHcCCCEEEEecCC
Confidence 455653 467888889999999999998875432 22234455677788888899999887643
No 496
>PRK13805 bifunctional acetaldehyde-CoA/alcohol dehydrogenase; Provisional
Probab=39.16 E-value=1.8e+02 Score=36.47 Aligned_cols=78 Identities=14% Similarity=0.020 Sum_probs=57.7
Q ss_pred CCcEEEEEEEeCCcccccHHHHHHHHH--hCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeCh--hhHHHHH
Q 003054 57 GWREAVPIYVDNQYGEEMIPSLTDALQ--AIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLP--SLGSRIF 132 (852)
Q Consensus 57 gw~~vaii~~d~~~G~~~~~~l~~~l~--~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~--~~~~~i~ 132 (852)
+.+++.+++....+..+..+.+.+.|+ +.|+++.....+.++.+.+++...+..++..++|+||-.+-+ -|+.+++
T Consensus 479 ~~~~~lvVtd~~~~~~g~~~~v~~~L~~~~~~i~~~~~~~v~~np~~~~v~~~~~~~~~~~~D~IIaiGGGSviD~AK~i 558 (862)
T PRK13805 479 GKKRAFIVTDRFMVELGYVDKVTDVLKKRENGVEYEVFSEVEPDPTLSTVRKGAELMRSFKPDTIIALGGGSPMDAAKIM 558 (862)
T ss_pred CCCEEEEEECcchhhcchHHHHHHHHhcccCCCeEEEeCCCCCCcCHHHHHHHHHHHHhcCCCEEEEeCCchHHHHHHHH
Confidence 668998888544455557888999998 778776655556666677888899999999999999977554 4566555
Q ss_pred HH
Q 003054 133 EK 134 (852)
Q Consensus 133 ~~ 134 (852)
..
T Consensus 559 a~ 560 (862)
T PRK13805 559 WL 560 (862)
T ss_pred HH
Confidence 43
No 497
>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=39.13 E-value=29 Score=31.92 Aligned_cols=24 Identities=8% Similarity=0.358 Sum_probs=9.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhc
Q 003054 723 LIAGVAAILALIIFMAVFIHQHWN 746 (852)
Q Consensus 723 ~il~ig~~lsl~vf~~e~~~~~r~ 746 (852)
+++++.+++.+++|++-++..+||
T Consensus 3 ~l~~iii~~i~l~~~~~~~~~rRR 26 (130)
T PF12273_consen 3 VLFAIIIVAILLFLFLFYCHNRRR 26 (130)
T ss_pred eeHHHHHHHHHHHHHHHHHHHHHH
Confidence 344443334444443333333333
No 498
>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=38.97 E-value=83 Score=32.79 Aligned_cols=71 Identities=8% Similarity=0.020 Sum_probs=51.8
Q ss_pred eCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeCh-hhHHHHHHHHHHcCC
Q 003054 67 DNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLP-SLGSRIFEKANEIGL 140 (852)
Q Consensus 67 d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~~-~~~~~i~~~a~~~G~ 140 (852)
+++|.....+.+.+++++.|.++..... ..+.......+..+.+.++|.|++.... ......++++.+.|.
T Consensus 10 ~~~f~~~~~~gi~~~~~~~G~~~~~~~~---~~d~~~~~~~i~~~~~~~vdgiii~~~~~~~~~~~i~~~~~~~i 81 (272)
T cd06313 10 QATWCAQGKQAADEAGKLLGVDVTWYGG---ALDAVKQVAAIENMASQGWDFIAVDPLGIGTLTEAVQKAIARGI 81 (272)
T ss_pred CChHHHHHHHHHHHHHHHcCCEEEEecC---CCCHHHHHHHHHHHHHcCCCEEEEcCCChHHhHHHHHHHHHCCC
Confidence 4567778888999999999998876532 2234556677888888999999986543 334667788888776
No 499
>PRK00278 trpC indole-3-glycerol-phosphate synthase; Reviewed
Probab=38.80 E-value=2.7e+02 Score=29.06 Aligned_cols=88 Identities=16% Similarity=0.175 Sum_probs=61.5
Q ss_pred HHHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEeC
Q 003054 45 QAGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHML 124 (852)
Q Consensus 45 ~~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~~ 124 (852)
....+|......|..-+.++.+...| .+..+.+...-+...+.|.....+. + .+ ++...+..++|+|.+.+.
T Consensus 71 ~~~~~A~~~~~~GA~aisvlte~~~f-~g~~~~l~~v~~~v~iPvl~kdfi~----~-~~--qi~~a~~~GAD~VlLi~~ 142 (260)
T PRK00278 71 DPVEIAKAYEAGGAACLSVLTDERFF-QGSLEYLRAARAAVSLPVLRKDFII----D-PY--QIYEARAAGADAILLIVA 142 (260)
T ss_pred CHHHHHHHHHhCCCeEEEEecccccC-CCCHHHHHHHHHhcCCCEEeeeecC----C-HH--HHHHHHHcCCCEEEEEec
Confidence 34567777777888888777744444 4447777766666677776533221 1 12 788888999999988764
Q ss_pred h---hhHHHHHHHHHHcCC
Q 003054 125 P---SLGSRIFEKANEIGL 140 (852)
Q Consensus 125 ~---~~~~~i~~~a~~~G~ 140 (852)
. .....+++.++++|+
T Consensus 143 ~l~~~~l~~li~~a~~lGl 161 (260)
T PRK00278 143 ALDDEQLKELLDYAHSLGL 161 (260)
T ss_pred cCCHHHHHHHHHHHHHcCC
Confidence 3 468999999999997
No 500
>PF05368 NmrA: NmrA-like family; InterPro: IPR008030 NmrA is a negative transcriptional regulator involved in the post-translational modification of the transcription factor AreA. NmrA is part of a system controlling nitrogen metabolite repression in fungi []. This family only contains a few sequences as iteration results in significant matches to other Rossmann fold families.; PDB: 2ZCV_A 2ZCU_A 2R6J_B 3C3X_A 2QZZ_B 2QYS_A 2QX7_A 2QW8_A 2R2G_B 3E5M_B ....
Probab=38.72 E-value=2.6e+02 Score=28.20 Aligned_cols=86 Identities=13% Similarity=0.091 Sum_probs=0.0
Q ss_pred hHHHHHHHHHHHcCCcEEEEEEEeCCcccccHHHHHHHHHhCCceeeeeeecCCCCChHHHHHHHHHhhcCCceEEEEEe
Q 003054 44 SQAGAITAIIKAFGWREAVPIYVDNQYGEEMIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHM 123 (852)
Q Consensus 44 ~~~~aia~~l~~~gw~~vaii~~d~~~G~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~viv~~~ 123 (852)
.++..+++.|.. ..-+|.++..+. .....+.+++.|.+++ ...+ .+.+.+...++ +.|++++..
T Consensus 9 ~~G~~v~~~L~~-~~~~V~~l~R~~------~~~~~~~l~~~g~~vv-~~d~---~~~~~l~~al~-----g~d~v~~~~ 72 (233)
T PF05368_consen 9 NQGRSVVRALLS-AGFSVRALVRDP------SSDRAQQLQALGAEVV-EADY---DDPESLVAALK-----GVDAVFSVT 72 (233)
T ss_dssp HHHHHHHHHHHH-TTGCEEEEESSS------HHHHHHHHHHTTTEEE-ES-T---T-HHHHHHHHT-----TCSEEEEES
T ss_pred HHHHHHHHHHHh-CCCCcEEEEecc------chhhhhhhhcccceEe-eccc---CCHHHHHHHHc-----CCceEEeec
Q ss_pred C------hhhHHHHHHHHHHcCCcccceEE
Q 003054 124 L------PSLGSRIFEKANEIGLMNKGCVW 147 (852)
Q Consensus 124 ~------~~~~~~i~~~a~~~G~~~~~~vw 147 (852)
. ......++++|++.|. +.++.
T Consensus 73 ~~~~~~~~~~~~~li~Aa~~agV--k~~v~ 100 (233)
T PF05368_consen 73 PPSHPSELEQQKNLIDAAKAAGV--KHFVP 100 (233)
T ss_dssp SCSCCCHHHHHHHHHHHHHHHT---SEEEE
T ss_pred CcchhhhhhhhhhHHHhhhcccc--ceEEE
Done!