Query 003958
Match_columns 784
No_of_seqs 348 out of 3731
Neff 10.0
Searched_HMMs 46136
Date Thu Mar 28 15:01:13 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/003958.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/003958hhsearch_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 1.2E-84 2.5E-89 656.2 42.6 703 28-784 23-765 (897)
2 KOG4440 NMDA selective glutama 100.0 1.1E-76 2.5E-81 601.1 42.1 673 26-784 30-779 (993)
3 KOG1053 Glutamate-gated NMDA-t 100.0 8.7E-74 1.9E-78 601.5 47.6 652 79-784 82-780 (1258)
4 KOG1052 Glutamate-gated kainat 100.0 1.1E-53 2.4E-58 492.1 44.3 520 213-784 5-546 (656)
5 cd06364 PBP1_CaSR Ligand-bindi 100.0 1.8E-48 3.9E-53 431.6 42.0 377 27-420 8-494 (510)
6 cd06375 PBP1_mGluR_groupII Lig 100.0 1.4E-48 3E-53 428.3 40.3 369 30-419 1-454 (458)
7 cd06374 PBP1_mGluR_groupI Liga 100.0 1.7E-48 3.6E-53 431.8 39.0 379 27-425 5-469 (472)
8 cd06365 PBP1_Pheromone_recepto 100.0 1.8E-48 3.9E-53 429.2 38.9 371 30-420 1-453 (469)
9 cd06362 PBP1_mGluR Ligand bind 100.0 5.3E-48 1.2E-52 427.7 39.9 374 30-422 1-449 (452)
10 cd06376 PBP1_mGluR_groupIII Li 100.0 2.9E-47 6.2E-52 421.3 41.0 371 30-419 1-452 (463)
11 cd06361 PBP1_GPC6A_like Ligand 100.0 3.7E-47 8E-52 409.9 39.7 346 33-422 1-396 (403)
12 cd06393 PBP1_iGluR_Kainate_Glu 100.0 4.6E-45 1E-49 394.3 38.0 370 31-424 2-382 (384)
13 KOG1056 Glutamate-gated metabo 100.0 6E-45 1.3E-49 399.0 36.2 398 26-463 26-495 (878)
14 cd06379 PBP1_iGluR_NMDA_NR1 N- 100.0 6.4E-44 1.4E-48 385.3 37.9 336 29-420 17-364 (377)
15 cd06392 PBP1_iGluR_delta_1 N-t 100.0 9.3E-44 2E-48 375.9 37.8 366 33-423 1-398 (400)
16 cd06386 PBP1_NPR_C_like Ligand 100.0 6.5E-44 1.4E-48 385.0 36.7 359 35-420 3-379 (387)
17 cd06390 PBP1_iGluR_AMPA_GluR1 100.0 1.1E-43 2.4E-48 376.1 36.7 360 33-423 1-363 (364)
18 cd06363 PBP1_Taste_receptor Li 100.0 2.3E-43 4.9E-48 384.6 39.3 352 27-420 2-396 (410)
19 cd06385 PBP1_NPR_A Ligand-bind 100.0 1.4E-43 3.1E-48 386.5 33.4 362 33-421 1-392 (405)
20 cd06367 PBP1_iGluR_NMDA N-term 100.0 3.3E-43 7.2E-48 378.0 34.8 339 31-419 2-351 (362)
21 cd06380 PBP1_iGluR_AMPA N-term 100.0 1.4E-42 3.1E-47 376.0 39.5 375 33-423 1-381 (382)
22 cd06370 PBP1_Speract_GC_like L 100.0 4.2E-43 9.2E-48 381.7 35.2 356 32-415 1-390 (404)
23 cd06366 PBP1_GABAb_receptor Li 100.0 1.1E-42 2.3E-47 372.9 35.2 342 33-424 1-347 (350)
24 cd06387 PBP1_iGluR_AMPA_GluR3 100.0 3.9E-42 8.5E-47 362.8 38.3 365 34-423 2-371 (372)
25 cd06373 PBP1_NPR_like Ligand b 100.0 7.8E-43 1.7E-47 379.8 33.7 363 33-421 1-390 (396)
26 cd06372 PBP1_GC_G_like Ligand- 100.0 2.2E-42 4.8E-47 375.5 37.1 360 33-421 1-387 (391)
27 cd06391 PBP1_iGluR_delta_2 N-t 100.0 9.9E-42 2.1E-46 365.0 38.1 368 33-423 1-398 (400)
28 cd06371 PBP1_sensory_GC_DEF_li 100.0 1.7E-41 3.7E-46 365.2 36.9 353 33-417 1-369 (382)
29 cd06352 PBP1_NPR_GC_like Ligan 100.0 1.2E-41 2.6E-46 370.4 36.0 364 33-421 1-383 (389)
30 cd06388 PBP1_iGluR_AMPA_GluR4 100.0 2.5E-41 5.5E-46 359.9 37.5 364 33-423 1-369 (371)
31 cd06389 PBP1_iGluR_AMPA_GluR2 100.0 4.4E-41 9.5E-46 359.2 37.8 362 33-423 1-368 (370)
32 cd06384 PBP1_NPR_B Ligand-bind 100.0 7.8E-41 1.7E-45 363.6 35.9 362 33-421 1-393 (399)
33 cd06382 PBP1_iGluR_Kainate N-t 100.0 2.6E-40 5.6E-45 350.8 30.6 321 33-423 1-326 (327)
34 PF01094 ANF_receptor: Recepto 100.0 4E-39 8.6E-44 346.1 31.2 339 48-407 2-348 (348)
35 cd06394 PBP1_iGluR_Kainate_KA1 100.0 1.6E-39 3.6E-44 337.5 26.9 325 33-424 1-332 (333)
36 PRK15404 leucine ABC transport 100.0 1.6E-37 3.5E-42 332.7 36.8 337 28-410 22-363 (369)
37 cd06342 PBP1_ABC_LIVBP_like Ty 100.0 9.9E-37 2.1E-41 325.2 33.6 328 33-406 1-334 (334)
38 cd06368 PBP1_iGluR_non_NMDA_li 100.0 1.7E-36 3.8E-41 321.5 31.4 320 33-422 1-322 (324)
39 cd06350 PBP1_GPCR_family_C_lik 100.0 1.9E-36 4.2E-41 324.7 31.7 308 33-420 1-340 (348)
40 cd06338 PBP1_ABC_ligand_bindin 100.0 7.6E-36 1.6E-40 319.6 31.5 329 33-406 1-345 (345)
41 cd06345 PBP1_ABC_ligand_bindin 100.0 1.8E-35 3.9E-40 316.0 33.0 321 33-398 1-338 (344)
42 cd06346 PBP1_ABC_ligand_bindin 100.0 1.6E-35 3.4E-40 311.6 29.4 282 33-332 1-288 (312)
43 cd06381 PBP1_iGluR_delta_like 100.0 1E-34 2.2E-39 307.5 35.3 336 33-423 1-362 (363)
44 cd06348 PBP1_ABC_ligand_bindin 100.0 9.2E-35 2E-39 310.7 33.3 334 33-403 1-343 (344)
45 cd06378 PBP1_iGluR_NMDA_NR2 N- 100.0 2.2E-34 4.8E-39 304.4 29.9 303 78-425 43-355 (362)
46 cd06355 PBP1_FmdD_like Peripla 100.0 1.4E-33 3.1E-38 300.9 34.6 337 33-414 1-345 (348)
47 cd06340 PBP1_ABC_ligand_bindin 100.0 3.5E-34 7.5E-39 306.0 29.8 324 33-399 1-342 (347)
48 cd06344 PBP1_ABC_ligand_bindin 100.0 1.1E-33 2.3E-38 300.7 29.9 320 33-399 1-327 (332)
49 COG0683 LivK ABC-type branched 100.0 3.5E-33 7.5E-38 298.6 34.0 338 29-409 8-355 (366)
50 TIGR03669 urea_ABC_arch urea A 100.0 6.3E-33 1.4E-37 296.2 35.3 341 32-418 1-349 (374)
51 cd06383 PBP1_iGluR_AMPA_Like N 100.0 4.2E-34 9E-39 303.5 25.5 333 41-400 7-354 (368)
52 cd06329 PBP1_SBP_like_3 Peripl 100.0 2.8E-33 6.1E-38 298.5 31.2 314 33-393 1-331 (342)
53 cd06347 PBP1_ABC_ligand_bindin 100.0 6.9E-33 1.5E-37 295.6 32.1 321 33-400 1-330 (334)
54 cd06343 PBP1_ABC_ligand_bindin 100.0 1.3E-32 2.9E-37 296.2 34.2 342 28-411 3-362 (362)
55 cd06377 PBP1_iGluR_NMDA_NR3 N- 100.0 9.1E-32 2E-36 278.9 37.5 342 27-423 14-374 (382)
56 cd06331 PBP1_AmiC_like Type I 100.0 1.8E-32 4E-37 291.4 32.4 322 33-399 1-328 (333)
57 TIGR03407 urea_ABC_UrtA urea A 100.0 4.3E-32 9.3E-37 290.6 35.2 331 32-407 1-338 (359)
58 cd06349 PBP1_ABC_ligand_bindin 100.0 2.8E-32 6.1E-37 291.1 33.0 329 33-410 1-339 (340)
59 KOG1055 GABA-B ion channel rec 100.0 2.9E-34 6.2E-39 303.9 15.4 373 27-421 37-431 (865)
60 cd06327 PBP1_SBP_like_1 Peripl 100.0 1.6E-32 3.5E-37 292.0 29.1 318 33-397 1-328 (334)
61 cd06330 PBP1_Arsenic_SBP_like 100.0 3.2E-32 7E-37 291.5 31.0 326 33-399 1-339 (346)
62 cd06359 PBP1_Nba_like Type I p 100.0 7.5E-32 1.6E-36 286.6 32.7 325 33-405 1-332 (333)
63 cd06336 PBP1_ABC_ligand_bindin 100.0 2.6E-32 5.6E-37 291.6 29.2 322 33-399 1-342 (347)
64 cd06357 PBP1_AmiC Periplasmic 100.0 3.1E-31 6.7E-36 284.1 36.1 340 33-415 1-347 (360)
65 cd06328 PBP1_SBP_like_2 Peripl 100.0 2.9E-31 6.2E-36 281.6 32.5 316 33-395 1-325 (333)
66 cd06351 PBP1_iGluR_N_LIVBP_lik 100.0 3.5E-31 7.7E-36 281.8 31.9 317 33-419 1-322 (328)
67 cd06360 PBP1_alkylbenzenes_lik 100.0 5E-31 1.1E-35 281.4 32.6 324 33-400 1-331 (336)
68 PF13458 Peripla_BP_6: Peripla 100.0 1.7E-31 3.7E-36 286.0 27.8 332 31-407 1-339 (343)
69 cd06358 PBP1_NHase Type I peri 100.0 1E-30 2.2E-35 277.9 32.5 316 33-395 1-324 (333)
70 cd06356 PBP1_Amide_Urea_BP_lik 100.0 1.8E-30 3.8E-35 275.6 32.9 317 33-395 1-325 (334)
71 cd06334 PBP1_ABC_ligand_bindin 100.0 8E-31 1.7E-35 278.9 29.7 333 33-393 1-345 (351)
72 cd06335 PBP1_ABC_ligand_bindin 100.0 1.9E-30 4.2E-35 277.1 31.9 323 33-395 1-337 (347)
73 cd06332 PBP1_aromatic_compound 100.0 9.5E-30 2E-34 271.3 32.9 323 33-403 1-330 (333)
74 PF13433 Peripla_BP_5: Peripla 100.0 2.3E-29 4.9E-34 254.4 28.3 318 32-395 1-327 (363)
75 cd06337 PBP1_ABC_ligand_bindin 100.0 3.7E-29 8E-34 268.0 27.3 331 33-410 1-356 (357)
76 cd06326 PBP1_STKc_like Type I 100.0 2E-27 4.3E-32 253.6 31.4 317 32-392 1-326 (336)
77 cd06339 PBP1_YraM_LppC_lipopro 100.0 4.8E-28 1E-32 256.7 25.1 302 33-396 1-329 (336)
78 cd06269 PBP1_glutamate_recepto 100.0 9.2E-27 2E-31 244.1 27.8 224 33-262 1-235 (298)
79 TIGR03863 PQQ_ABC_bind ABC tra 100.0 6.4E-27 1.4E-31 246.1 25.5 298 45-406 10-315 (347)
80 cd04509 PBP1_ABC_transporter_G 99.9 6.3E-26 1.4E-30 237.8 25.6 280 33-328 1-290 (299)
81 cd06333 PBP1_ABC-type_HAAT_lik 99.9 1.5E-25 3.3E-30 236.1 28.4 279 33-330 1-293 (312)
82 cd06341 PBP1_ABC_ligand_bindin 99.9 1.9E-25 4.1E-30 238.6 28.8 308 33-386 1-318 (341)
83 cd06369 PBP1_GC_C_enterotoxin_ 99.9 3.7E-24 8E-29 215.6 28.5 325 45-421 17-366 (380)
84 cd06268 PBP1_ABC_transporter_L 99.9 1.1E-23 2.4E-28 220.7 27.7 280 33-330 1-287 (298)
85 PRK10797 glutamate and asparta 99.7 9.6E-17 2.1E-21 166.4 18.1 195 467-783 39-243 (302)
86 PRK11917 bifunctional adhesin/ 99.7 1.6E-16 3.4E-21 161.4 18.7 194 466-783 36-233 (259)
87 PRK09495 glnH glutamine ABC tr 99.7 7.4E-16 1.6E-20 156.2 19.0 190 467-782 24-215 (247)
88 PRK11260 cystine transporter s 99.7 1.8E-15 3.9E-20 155.1 18.0 194 466-783 39-233 (266)
89 PRK15007 putative ABC transpor 99.7 4.1E-15 8.8E-20 150.6 18.4 190 467-783 20-214 (243)
90 PF00060 Lig_chan: Ligand-gate 99.6 4E-17 8.6E-22 151.2 -0.5 107 588-694 1-115 (148)
91 PF00497 SBP_bac_3: Bacterial 99.6 3E-15 6.5E-20 149.6 13.1 193 470-782 1-195 (225)
92 PRK15010 ABC transporter lysin 99.6 2.7E-14 5.9E-19 145.8 19.1 195 466-783 24-226 (260)
93 cd01391 Periplasmic_Binding_Pr 99.6 1.9E-13 4.1E-18 140.2 24.0 216 33-260 1-220 (269)
94 TIGR01096 3A0103s03R lysine-ar 99.6 4.4E-14 9.6E-19 143.7 18.6 192 468-783 24-223 (250)
95 TIGR02995 ectoine_ehuB ectoine 99.6 2.9E-14 6.3E-19 146.8 16.9 196 466-783 31-233 (275)
96 PRK15437 histidine ABC transpo 99.6 4.4E-14 9.5E-19 144.2 17.9 194 466-782 24-225 (259)
97 PRK10859 membrane-bound lytic 99.5 9.1E-14 2E-18 153.6 17.0 192 466-781 41-235 (482)
98 TIGR03870 ABC_MoxJ methanol ox 99.5 1E-13 2.3E-18 139.9 15.8 184 470-783 2-217 (246)
99 COG0834 HisJ ABC-type amino ac 99.4 4.6E-12 1E-16 130.9 17.5 194 467-781 33-233 (275)
100 PRK09959 hybrid sensory histid 99.4 2.9E-12 6.3E-17 159.9 16.6 194 466-783 54-250 (1197)
101 TIGR03871 ABC_peri_MoxJ_2 quin 99.4 1.2E-11 2.6E-16 124.2 17.0 186 470-783 2-203 (232)
102 TIGR02285 conserved hypothetic 99.4 8.8E-12 1.9E-16 127.8 15.4 201 466-782 16-230 (268)
103 PRK09959 hybrid sensory histid 99.4 6.7E-12 1.5E-16 156.7 17.1 188 469-783 303-493 (1197)
104 smart00062 PBPb Bacterial peri 99.3 5.2E-11 1.1E-15 117.7 17.3 188 470-783 2-192 (219)
105 cd00134 PBPb Bacterial peripla 99.3 9.9E-11 2.1E-15 115.7 17.9 186 471-782 2-190 (218)
106 PF04348 LppC: LppC putative l 99.3 1.8E-10 3.9E-15 127.4 18.3 307 30-406 218-533 (536)
107 PF10613 Lig_chan-Glu_bd: Liga 99.0 2.3E-10 5E-15 85.5 3.1 50 487-536 13-65 (65)
108 smart00079 PBPe Eukaryotic hom 98.8 1.7E-08 3.7E-13 91.5 9.0 97 683-784 1-107 (134)
109 COG4623 Predicted soluble lyti 98.8 3.5E-08 7.6E-13 98.1 11.4 192 467-782 22-217 (473)
110 cd01537 PBP1_Repressors_Sugar_ 98.8 3.6E-07 7.9E-12 93.4 19.8 202 33-252 1-208 (264)
111 cd01536 PBP1_ABC_sugar_binding 98.8 2E-06 4.3E-11 88.2 23.6 198 33-247 1-206 (267)
112 cd06267 PBP1_LacI_sugar_bindin 98.7 1.3E-06 2.8E-11 89.4 19.7 204 33-254 1-209 (264)
113 cd06300 PBP1_ABC_sugar_binding 98.7 3E-06 6.5E-11 87.3 22.5 202 33-249 1-211 (272)
114 TIGR01098 3A0109s03R phosphate 98.6 5.8E-07 1.3E-11 91.5 14.7 184 468-781 32-238 (254)
115 COG2984 ABC-type uncharacteriz 98.5 5.3E-05 1.2E-09 75.4 24.3 204 27-246 26-240 (322)
116 cd06325 PBP1_ABC_uncharacteriz 98.5 1.1E-05 2.4E-10 83.5 20.5 201 33-246 1-208 (281)
117 cd06320 PBP1_allose_binding Pe 98.5 4.8E-05 1E-09 78.4 23.7 199 33-247 1-207 (275)
118 COG3107 LppC Putative lipoprot 98.4 2.2E-05 4.8E-10 82.2 19.2 254 30-302 256-539 (604)
119 cd06282 PBP1_GntR_like_2 Ligan 98.3 5.3E-05 1.2E-09 77.6 20.4 199 34-252 2-206 (266)
120 PRK10653 D-ribose transporter 98.3 0.00034 7.4E-09 72.9 26.3 200 30-246 25-231 (295)
121 cd06323 PBP1_ribose_binding Pe 98.2 0.00027 5.9E-09 72.4 23.0 203 34-256 2-213 (268)
122 cd06317 PBP1_ABC_sugar_binding 98.2 0.00026 5.6E-09 72.9 21.6 200 34-247 2-212 (275)
123 cd06273 PBP1_GntR_like_1 This 98.1 0.00021 4.5E-09 73.3 20.0 201 33-251 1-207 (268)
124 PRK00489 hisG ATP phosphoribos 98.1 1.6E-05 3.5E-10 81.7 11.4 135 526-780 52-188 (287)
125 cd06319 PBP1_ABC_sugar_binding 98.1 0.00067 1.5E-08 69.9 22.7 199 33-247 1-210 (277)
126 cd06312 PBP1_ABC_sugar_binding 98.1 0.00096 2.1E-08 68.5 23.1 199 33-247 1-208 (271)
127 cd06305 PBP1_methylthioribose_ 98.1 0.00074 1.6E-08 69.4 22.2 207 33-256 1-216 (273)
128 cd06301 PBP1_rhizopine_binding 98.1 0.00096 2.1E-08 68.5 22.8 208 33-256 1-217 (272)
129 cd06310 PBP1_ABC_sugar_binding 98.0 0.002 4.4E-08 66.1 24.1 208 33-256 1-216 (273)
130 cd01545 PBP1_SalR Ligand-bindi 98.0 0.00067 1.4E-08 69.6 20.2 200 34-250 2-207 (270)
131 PRK10936 TMAO reductase system 98.0 0.0044 9.6E-08 66.0 26.7 202 27-246 42-254 (343)
132 cd06309 PBP1_YtfQ_like Peripla 97.9 0.0023 5E-08 65.7 22.9 208 33-255 1-218 (273)
133 PF13407 Peripla_BP_4: Peripla 97.9 0.0016 3.4E-08 66.3 20.9 201 34-248 1-208 (257)
134 COG1879 RbsB ABC-type sugar tr 97.8 0.01 2.2E-07 62.7 26.2 205 31-248 33-245 (322)
135 cd06289 PBP1_MalI_like Ligand- 97.8 0.002 4.3E-08 65.9 19.5 201 33-250 1-206 (268)
136 PRK15395 methyl-galactoside AB 97.8 0.013 2.7E-07 62.1 25.5 208 29-246 22-249 (330)
137 PRK09701 D-allose transporter 97.7 0.028 6E-07 59.0 27.6 204 33-247 26-241 (311)
138 cd06284 PBP1_LacI_like_6 Ligan 97.7 0.0035 7.7E-08 64.0 20.4 197 34-249 2-203 (267)
139 cd06298 PBP1_CcpA_like Ligand- 97.7 0.0037 7.9E-08 64.0 20.3 206 33-256 1-212 (268)
140 cd01539 PBP1_GGBP Periplasmic 97.7 0.0096 2.1E-07 62.2 23.4 208 33-249 1-228 (303)
141 cd06303 PBP1_LuxPQ_Quorum_Sens 97.7 0.012 2.6E-07 60.6 23.0 212 33-256 1-223 (280)
142 cd06311 PBP1_ABC_sugar_binding 97.6 0.018 4E-07 59.1 24.1 202 34-247 2-210 (274)
143 cd06275 PBP1_PurR Ligand-bindi 97.6 0.0065 1.4E-07 62.2 20.5 204 34-254 2-210 (269)
144 PRK10355 xylF D-xylose transpo 97.6 0.022 4.8E-07 60.2 24.8 202 29-247 23-236 (330)
145 PF00532 Peripla_BP_1: Peripla 97.6 0.0049 1.1E-07 63.4 19.3 202 33-252 3-211 (279)
146 cd01540 PBP1_arabinose_binding 97.6 0.013 2.8E-07 60.7 22.8 213 33-256 1-228 (289)
147 cd01542 PBP1_TreR_like Ligand- 97.6 0.0069 1.5E-07 61.6 20.2 200 34-256 2-207 (259)
148 cd06322 PBP1_ABC_sugar_binding 97.6 0.02 4.2E-07 58.5 23.6 194 34-246 2-203 (267)
149 cd06288 PBP1_sucrose_transcrip 97.6 0.0054 1.2E-07 62.7 19.5 205 33-256 1-211 (269)
150 TIGR01481 ccpA catabolite cont 97.6 0.0077 1.7E-07 63.8 20.9 203 30-250 58-264 (329)
151 cd06321 PBP1_ABC_sugar_binding 97.6 0.016 3.5E-07 59.3 22.7 205 33-256 1-213 (271)
152 PRK15408 autoinducer 2-binding 97.6 0.037 8E-07 58.5 25.5 199 33-246 25-233 (336)
153 cd01575 PBP1_GntR Ligand-bindi 97.6 0.0086 1.9E-07 61.2 20.5 201 34-252 2-207 (268)
154 cd06283 PBP1_RegR_EndR_KdgR_li 97.5 0.012 2.6E-07 60.0 21.1 202 34-253 2-209 (267)
155 cd06271 PBP1_AglR_RafR_like Li 97.5 0.0081 1.8E-07 61.4 19.4 200 34-252 2-211 (268)
156 cd06306 PBP1_TorT-like TorT-li 97.5 0.024 5.1E-07 58.0 22.5 196 33-246 1-207 (268)
157 cd06308 PBP1_sensor_kinase_lik 97.5 0.028 6.1E-07 57.5 23.1 207 33-257 1-216 (270)
158 cd06324 PBP1_ABC_sugar_binding 97.5 0.02 4.4E-07 59.8 22.1 209 34-255 2-236 (305)
159 cd06295 PBP1_CelR Ligand bindi 97.5 0.0097 2.1E-07 61.1 19.5 205 32-253 4-217 (275)
160 TIGR03431 PhnD phosphonate ABC 97.5 0.0014 3.1E-08 67.9 12.9 94 682-781 125-233 (288)
161 PRK10703 DNA-binding transcrip 97.4 0.013 2.9E-07 62.3 20.5 208 30-254 58-271 (341)
162 cd06285 PBP1_LacI_like_7 Ligan 97.4 0.016 3.5E-07 59.1 20.3 198 33-250 1-203 (265)
163 cd06270 PBP1_GalS_like Ligand 97.4 0.021 4.6E-07 58.3 21.1 200 33-250 1-205 (268)
164 cd06293 PBP1_LacI_like_11 Liga 97.4 0.022 4.7E-07 58.3 21.1 205 33-255 1-210 (269)
165 cd06316 PBP1_ABC_sugar_binding 97.4 0.041 9E-07 57.1 23.3 203 33-246 1-210 (294)
166 cd01574 PBP1_LacI Ligand-bindi 97.4 0.033 7.1E-07 56.7 22.1 200 33-252 1-204 (264)
167 cd01538 PBP1_ABC_xylose_bindin 97.4 0.04 8.7E-07 57.0 22.7 199 33-248 1-216 (288)
168 cd06281 PBP1_LacI_like_5 Ligan 97.4 0.012 2.5E-07 60.3 18.5 200 33-251 1-205 (269)
169 cd06299 PBP1_LacI_like_13 Liga 97.4 0.017 3.6E-07 59.0 19.5 204 33-254 1-207 (265)
170 cd06274 PBP1_FruR Ligand bindi 97.4 0.029 6.3E-07 57.2 21.3 205 34-255 2-211 (264)
171 cd06278 PBP1_LacI_like_2 Ligan 97.4 0.019 4.1E-07 58.5 20.0 191 34-245 2-197 (266)
172 PRK10014 DNA-binding transcrip 97.4 0.025 5.5E-07 60.2 21.4 203 30-249 63-270 (342)
173 cd06296 PBP1_CatR_like Ligand- 97.3 0.022 4.7E-07 58.3 19.9 201 34-252 2-208 (270)
174 cd06292 PBP1_LacI_like_10 Liga 97.3 0.034 7.3E-07 57.0 21.1 206 33-254 1-213 (273)
175 cd06313 PBP1_ABC_sugar_binding 97.3 0.079 1.7E-06 54.3 23.4 171 68-246 29-207 (272)
176 cd06318 PBP1_ABC_sugar_binding 97.3 0.074 1.6E-06 54.7 23.3 200 33-247 1-215 (282)
177 PRK11303 DNA-binding transcrip 97.3 0.053 1.1E-06 57.4 22.4 203 30-252 60-268 (328)
178 PRK10423 transcriptional repre 97.3 0.041 8.9E-07 58.1 21.4 205 30-253 55-266 (327)
179 cd06290 PBP1_LacI_like_9 Ligan 97.2 0.037 8.1E-07 56.4 20.1 199 33-250 1-204 (265)
180 cd06307 PBP1_uncharacterized_s 97.2 0.095 2.1E-06 53.7 22.8 208 33-255 1-217 (275)
181 COG1609 PurR Transcriptional r 97.2 0.057 1.2E-06 57.0 21.2 201 30-250 57-265 (333)
182 cd06294 PBP1_ycjW_transcriptio 97.2 0.039 8.3E-07 56.4 19.6 199 34-250 2-211 (270)
183 cd06314 PBP1_tmGBP Periplasmic 97.2 0.19 4.1E-06 51.4 24.6 197 33-247 1-204 (271)
184 cd06286 PBP1_CcpB_like Ligand- 97.1 0.033 7.2E-07 56.6 18.7 198 33-250 1-203 (260)
185 cd06354 PBP1_BmpA_PnrA_like Pe 97.1 0.065 1.4E-06 54.7 20.7 195 33-245 1-206 (265)
186 PF04392 ABC_sub_bind: ABC tra 97.1 0.038 8.2E-07 57.3 19.1 184 33-230 1-193 (294)
187 cd06291 PBP1_Qymf_like Ligand 97.1 0.058 1.2E-06 55.0 20.2 194 34-250 2-201 (265)
188 cd06304 PBP1_BmpA_like Peripla 97.1 0.046 1E-06 55.6 19.4 198 33-245 1-202 (260)
189 TIGR02417 fruct_sucro_rep D-fr 97.1 0.066 1.4E-06 56.6 21.2 202 30-252 59-267 (327)
190 PRK10727 DNA-binding transcrip 97.1 0.066 1.4E-06 57.0 20.8 204 30-252 58-267 (343)
191 cd06280 PBP1_LacI_like_4 Ligan 97.0 0.081 1.8E-06 53.8 20.5 200 33-254 1-204 (263)
192 cd06297 PBP1_LacI_like_12 Liga 97.0 0.06 1.3E-06 55.1 19.5 200 34-255 2-213 (269)
193 cd06272 PBP1_hexuronate_repres 97.0 0.048 1E-06 55.4 18.7 196 33-251 1-201 (261)
194 cd06302 PBP1_LsrB_Quorum_Sensi 97.0 0.25 5.4E-06 51.4 24.0 201 33-247 1-210 (298)
195 cd06277 PBP1_LacI_like_1 Ligan 97.0 0.091 2E-06 53.6 20.1 196 34-249 2-204 (268)
196 TIGR02955 TMAO_TorT TMAO reduc 97.0 0.17 3.6E-06 52.6 22.2 194 33-246 1-207 (295)
197 cd01541 PBP1_AraR Ligand-bindi 97.0 0.078 1.7E-06 54.3 19.5 204 34-254 2-215 (273)
198 PRK09526 lacI lac repressor; R 96.9 0.18 3.9E-06 53.6 22.2 202 30-252 62-270 (342)
199 cd06279 PBP1_LacI_like_3 Ligan 96.9 0.1 2.2E-06 53.8 19.6 194 34-250 2-223 (283)
200 cd01543 PBP1_XylR Ligand-bindi 96.7 0.094 2E-06 53.4 17.9 200 33-256 1-206 (265)
201 PRK09492 treR trehalose repres 96.7 0.21 4.6E-06 52.3 20.9 192 30-246 61-256 (315)
202 PRK11041 DNA-binding transcrip 96.7 0.25 5.5E-06 51.6 21.0 209 29-255 33-246 (309)
203 PRK10401 DNA-binding transcrip 96.6 0.28 6E-06 52.3 21.4 205 30-253 58-268 (346)
204 PRK14987 gluconate operon tran 96.6 0.32 7E-06 51.4 21.7 206 31-255 63-272 (331)
205 PRK11553 alkanesulfonate trans 96.4 0.032 7E-07 58.6 12.0 71 682-758 119-193 (314)
206 TIGR02634 xylF D-xylose ABC tr 96.4 0.91 2E-05 47.3 22.7 171 68-247 28-209 (302)
207 cd01544 PBP1_GalR Ligand-bindi 96.1 0.34 7.4E-06 49.4 17.7 195 33-252 1-209 (270)
208 TIGR02405 trehalos_R_Ecol treh 96.0 1.1 2.3E-05 47.0 21.2 191 30-246 58-253 (311)
209 TIGR01729 taurine_ABC_bnd taur 96.0 0.036 7.7E-07 57.8 10.0 71 682-758 90-164 (300)
210 TIGR02637 RhaS rhamnose ABC tr 95.8 3 6.5E-05 43.3 24.6 163 77-247 37-210 (302)
211 cd06315 PBP1_ABC_sugar_binding 95.3 3.4 7.4E-05 42.3 21.4 203 33-249 2-216 (280)
212 PF13379 NMT1_2: NMT1-like fam 95.3 0.11 2.4E-06 52.5 10.0 73 682-759 104-188 (252)
213 cd06353 PBP1_BmpA_Med_like Per 95.3 0.92 2E-05 45.9 16.7 192 33-245 1-200 (258)
214 TIGR02990 ectoine_eutA ectoine 94.7 0.68 1.5E-05 45.9 13.1 90 151-243 107-203 (239)
215 PF12974 Phosphonate-bd: ABC t 94.5 0.13 2.8E-06 51.7 8.0 101 674-781 88-201 (243)
216 TIGR02122 TRAP_TAXI TRAP trans 94.2 0.23 5E-06 52.2 9.6 60 682-748 131-197 (320)
217 PF07885 Ion_trans_2: Ion chan 93.6 0.082 1.8E-06 42.3 3.6 55 622-676 22-78 (79)
218 PF09084 NMT1: NMT1/THI5 like; 93.5 0.46 1E-05 46.6 9.7 59 682-746 83-145 (216)
219 cd06287 PBP1_LacI_like_8 Ligan 93.4 7.5 0.00016 39.5 18.8 151 94-252 54-208 (269)
220 TIGR01728 SsuA_fam ABC transpo 93.4 0.37 8E-06 49.7 9.1 71 682-758 91-165 (288)
221 COG1744 Med Uncharacterized AB 92.8 15 0.00032 38.9 21.3 156 82-246 83-244 (345)
222 COG4213 XylF ABC-type xylose t 92.7 12 0.00027 37.7 19.2 207 26-249 20-244 (341)
223 PRK10339 DNA-binding transcrip 92.1 10 0.00022 39.9 18.1 147 95-251 113-263 (327)
224 TIGR03427 ABC_peri_uca ABC tra 92.1 0.93 2E-05 47.5 9.9 68 684-758 98-170 (328)
225 KOG1419 Voltage-gated K+ chann 90.9 0.36 7.7E-06 51.8 5.2 87 590-676 235-323 (654)
226 cd06276 PBP1_FucR_like Ligand- 89.3 23 0.00049 35.5 16.9 143 89-250 45-190 (247)
227 cd05466 PBP2_LTTR_substrate Th 88.7 15 0.00034 33.9 14.7 69 494-574 13-81 (197)
228 PRK11480 tauA taurine transpor 88.4 3.2 7E-05 43.5 10.3 68 683-756 113-184 (320)
229 COG3473 Maleate cis-trans isom 88.4 16 0.00035 34.5 13.2 88 153-243 107-201 (238)
230 PF13377 Peripla_BP_3: Peripla 88.4 1.3 2.8E-05 40.9 6.6 97 156-254 1-100 (160)
231 COG3221 PhnD ABC-type phosphat 88.3 4 8.7E-05 41.9 10.4 96 681-782 133-243 (299)
232 cd08468 PBP2_Pa0477 The C-term 87.5 16 0.00035 34.6 14.1 71 494-574 13-84 (202)
233 PF03466 LysR_substrate: LysR 87.3 15 0.00033 34.9 13.8 69 494-574 19-87 (209)
234 cd06353 PBP1_BmpA_Med_like Per 87.2 8.7 0.00019 38.8 12.2 86 33-127 122-207 (258)
235 PF02608 Bmp: Basic membrane p 87.0 41 0.0009 34.9 18.8 197 32-246 2-212 (306)
236 cd08421 PBP2_LTTR_like_1 The C 86.8 27 0.00058 32.7 15.2 68 494-574 13-81 (198)
237 PRK09860 putative alcohol dehy 86.2 3.3 7.1E-05 44.7 8.9 86 153-238 20-107 (383)
238 COG1454 EutG Alcohol dehydroge 85.9 4.8 0.0001 42.7 9.6 91 153-243 18-110 (377)
239 TIGR00035 asp_race aspartate r 85.4 8.1 0.00018 38.2 10.7 44 82-126 60-104 (229)
240 PF03808 Glyco_tran_WecB: Glyc 84.9 15 0.00032 34.4 11.6 99 151-259 36-136 (172)
241 cd08190 HOT Hydroxyacid-oxoaci 84.7 4.5 9.8E-05 44.1 9.2 79 153-231 12-90 (414)
242 PRK15454 ethanol dehydrogenase 84.5 3.9 8.5E-05 44.2 8.5 79 153-231 38-116 (395)
243 cd08192 Fe-ADH7 Iron-containin 84.4 4.7 0.0001 43.3 9.1 88 153-240 13-102 (370)
244 cd08440 PBP2_LTTR_like_4 TThe 83.6 37 0.00081 31.5 15.0 69 494-574 13-81 (197)
245 PRK10624 L-1,2-propanediol oxi 83.5 5 0.00011 43.3 8.9 78 153-230 19-96 (382)
246 cd08442 PBP2_YofA_SoxR_like Th 83.3 39 0.00084 31.4 15.0 68 494-574 13-81 (193)
247 cd08193 HVD 5-hydroxyvalerate 82.6 5.8 0.00013 42.7 8.9 87 153-239 15-103 (376)
248 cd08420 PBP2_CysL_like C-termi 82.4 42 0.00092 31.2 15.2 69 493-574 12-81 (201)
249 cd08459 PBP2_DntR_NahR_LinR_li 82.0 23 0.0005 33.4 12.3 69 494-574 13-81 (201)
250 cd08189 Fe-ADH5 Iron-containin 81.9 6.9 0.00015 42.1 9.2 89 153-241 15-105 (374)
251 cd08551 Fe-ADH iron-containing 81.9 6.9 0.00015 42.0 9.2 87 153-239 12-100 (370)
252 cd08194 Fe-ADH6 Iron-containin 81.8 6.9 0.00015 42.1 9.1 79 153-231 12-90 (375)
253 PRK11151 DNA-binding transcrip 81.4 51 0.0011 34.1 15.4 69 494-574 104-172 (305)
254 KOG3713 Voltage-gated K+ chann 81.2 2.4 5.1E-05 45.4 5.0 62 601-666 358-421 (477)
255 COG0715 TauA ABC-type nitrate/ 80.9 6.8 0.00015 41.4 8.7 73 681-759 125-202 (335)
256 TIGR02638 lactal_redase lactal 80.8 6.8 0.00015 42.2 8.7 79 153-231 18-96 (379)
257 cd08419 PBP2_CbbR_RubisCO_like 80.0 51 0.0011 30.6 15.7 68 494-574 12-80 (197)
258 KOG3857 Alcohol dehydrogenase, 80.0 13 0.00027 38.0 9.3 95 137-231 39-137 (465)
259 CHL00180 rbcR LysR transcripti 79.9 61 0.0013 33.5 15.4 71 495-574 109-179 (305)
260 cd08460 PBP2_DntR_like_1 The C 79.8 25 0.00055 33.1 11.8 69 493-574 12-80 (200)
261 PF12727 PBP_like: PBP superfa 79.6 20 0.00044 34.3 10.5 91 681-781 80-178 (193)
262 TIGR01256 modA molybdenum ABC 79.4 18 0.00038 35.3 10.6 56 723-783 135-191 (216)
263 PF13407 Peripla_BP_4: Peripla 78.8 6.1 0.00013 39.7 7.3 78 167-246 1-81 (257)
264 cd08433 PBP2_Nac The C-teminal 78.7 57 0.0012 30.4 15.0 69 494-574 13-81 (198)
265 cd08185 Fe-ADH1 Iron-containin 78.7 11 0.00023 40.7 9.3 85 153-238 15-102 (380)
266 TIGR00787 dctP tripartite ATP- 78.6 7 0.00015 39.5 7.5 59 682-751 126-184 (257)
267 cd08426 PBP2_LTTR_like_5 The C 78.0 60 0.0013 30.3 14.7 69 494-574 13-81 (199)
268 cd08438 PBP2_CidR The C-termin 77.9 59 0.0013 30.2 15.3 69 494-574 13-81 (197)
269 cd08411 PBP2_OxyR The C-termin 77.5 63 0.0014 30.2 14.3 68 495-574 15-82 (200)
270 PRK12684 transcriptional regul 77.4 79 0.0017 32.9 15.4 90 685-783 184-279 (313)
271 PF02608 Bmp: Basic membrane p 77.0 20 0.00044 37.2 10.6 89 33-128 128-221 (306)
272 cd08188 Fe-ADH4 Iron-containin 77.0 12 0.00026 40.3 9.1 79 153-231 17-95 (377)
273 cd08417 PBP2_Nitroaromatics_li 76.7 51 0.0011 30.8 12.8 69 494-574 13-81 (200)
274 cd08434 PBP2_GltC_like The sub 76.6 64 0.0014 29.8 14.4 68 494-574 13-81 (195)
275 cd08181 PPD-like 1,3-propanedi 75.8 14 0.00029 39.5 9.1 77 154-231 16-93 (357)
276 cd08463 PBP2_DntR_like_4 The C 75.7 74 0.0016 30.1 15.4 71 493-574 12-82 (203)
277 PRK11242 DNA-binding transcrip 75.6 1E+02 0.0022 31.6 15.6 69 494-574 104-172 (296)
278 COG1464 NlpA ABC-type metal io 75.5 15 0.00032 36.5 8.3 75 1-87 1-75 (268)
279 cd08176 LPO Lactadehyde:propan 75.1 11 0.00025 40.4 8.3 79 153-231 17-95 (377)
280 cd06533 Glyco_transf_WecG_TagA 74.9 37 0.0008 31.7 10.7 101 150-258 33-133 (171)
281 PRK11233 nitrogen assimilation 74.7 57 0.0012 33.8 13.4 67 495-574 106-173 (305)
282 PF12683 DUF3798: Protein of u 74.4 98 0.0021 30.9 17.1 206 31-246 2-224 (275)
283 PF00465 Fe-ADH: Iron-containi 74.3 6.8 0.00015 42.0 6.4 89 153-243 12-102 (366)
284 PRK10200 putative racemase; Pr 74.2 31 0.00067 34.1 10.5 86 81-195 59-146 (230)
285 cd08191 HHD 6-hydroxyhexanoate 73.9 17 0.00036 39.3 9.2 86 153-239 12-99 (386)
286 cd08170 GlyDH Glycerol dehydro 73.8 12 0.00025 39.9 8.0 76 153-231 12-87 (351)
287 PF13685 Fe-ADH_2: Iron-contai 73.6 16 0.00036 36.4 8.3 99 154-257 9-108 (250)
288 COG1794 RacX Aspartate racemas 73.4 73 0.0016 30.9 12.0 86 81-196 59-146 (230)
289 cd08466 PBP2_LeuO The C-termin 72.8 83 0.0018 29.4 13.6 69 494-574 13-81 (200)
290 cd08461 PBP2_DntR_like_3 The C 72.0 85 0.0018 29.2 13.2 69 493-574 12-81 (198)
291 cd08467 PBP2_SyrM The C-termin 71.8 67 0.0015 30.2 12.3 69 494-574 13-81 (200)
292 PF13531 SBP_bac_11: Bacterial 71.6 24 0.00053 34.7 9.3 97 682-783 91-203 (230)
293 COG1880 CdhB CO dehydrogenase/ 71.5 65 0.0014 29.1 10.3 121 88-217 27-167 (170)
294 cd08414 PBP2_LTTR_aromatics_li 71.4 86 0.0019 29.0 14.7 69 494-574 13-81 (197)
295 cd08182 HEPD Hydroxyethylphosp 71.3 20 0.00043 38.5 9.0 85 153-240 12-98 (367)
296 PRK07475 hypothetical protein; 71.1 29 0.00063 34.7 9.5 119 81-231 62-206 (245)
297 cd08462 PBP2_NodD The C-termin 71.0 93 0.002 29.2 13.6 67 495-574 14-80 (200)
298 COG1910 Periplasmic molybdate- 70.3 75 0.0016 30.5 11.2 70 681-754 86-163 (223)
299 cd08412 PBP2_PAO1_like The C-t 70.1 93 0.002 28.8 14.7 69 493-574 12-81 (198)
300 cd08186 Fe-ADH8 Iron-containin 70.0 21 0.00046 38.5 9.0 87 153-239 12-104 (383)
301 cd08171 GlyDH-like2 Glycerol d 69.8 19 0.00041 38.2 8.3 84 153-238 12-97 (345)
302 PRK12681 cysB transcriptional 69.7 1.2E+02 0.0026 31.8 14.4 70 494-574 106-175 (324)
303 cd07766 DHQ_Fe-ADH Dehydroquin 69.7 23 0.0005 37.3 9.0 86 154-241 13-100 (332)
304 COG1744 Med Uncharacterized AB 69.5 70 0.0015 33.8 12.4 75 31-111 161-235 (345)
305 cd08441 PBP2_MetR The C-termin 69.4 98 0.0021 28.8 15.2 67 495-574 14-81 (198)
306 PRK10537 voltage-gated potassi 68.7 7.9 0.00017 41.6 5.2 56 621-676 165-222 (393)
307 PRK00945 acetyl-CoA decarbonyl 68.7 41 0.00089 31.3 9.1 91 90-188 28-133 (171)
308 cd08415 PBP2_LysR_opines_like 68.7 99 0.0021 28.6 14.4 69 493-574 12-81 (196)
309 PF06506 PrpR_N: Propionate ca 68.3 1.1E+02 0.0023 28.8 12.4 128 80-247 17-145 (176)
310 cd08187 BDH Butanol dehydrogen 67.8 22 0.00047 38.4 8.5 78 153-231 18-96 (382)
311 cd08456 PBP2_LysR The C-termin 67.3 1.1E+02 0.0023 28.4 13.9 69 494-574 13-81 (196)
312 TIGR02424 TF_pcaQ pca operon t 66.9 1.4E+02 0.0031 30.6 14.3 70 495-574 107-176 (300)
313 cd08418 PBP2_TdcA The C-termin 66.5 1.1E+02 0.0024 28.4 15.2 71 494-574 13-83 (201)
314 cd06301 PBP1_rhizopine_binding 66.4 22 0.00048 35.9 7.9 78 166-246 1-82 (272)
315 cd08423 PBP2_LTTR_like_6 The C 66.3 1.1E+02 0.0024 28.3 14.3 72 494-574 13-86 (200)
316 PRK09423 gldA glycerol dehydro 65.6 23 0.00051 37.9 8.1 83 153-238 19-103 (366)
317 PF01177 Asp_Glu_race: Asp/Glu 65.5 1.3E+02 0.0029 29.0 14.1 123 91-243 60-198 (216)
318 cd08413 PBP2_CysB_like The C-t 65.4 1.2E+02 0.0026 28.4 13.9 70 494-574 13-82 (198)
319 cd01537 PBP1_Repressors_Sugar_ 65.2 27 0.00058 34.8 8.3 77 166-245 1-79 (264)
320 cd08427 PBP2_LTTR_like_2 The C 65.2 1.2E+02 0.0025 28.1 14.7 70 494-574 13-83 (195)
321 cd08443 PBP2_CysB The C-termin 64.9 1.2E+02 0.0027 28.3 15.0 70 493-574 12-82 (198)
322 cd06305 PBP1_methylthioribose_ 64.6 28 0.00061 35.1 8.3 78 166-246 1-81 (273)
323 cd08183 Fe-ADH2 Iron-containin 64.2 31 0.00067 37.1 8.8 80 154-238 13-94 (374)
324 cd08486 PBP2_CbnR The C-termin 63.6 1.3E+02 0.0028 28.2 14.1 69 494-574 14-82 (198)
325 PLN03192 Voltage-dependent pot 63.5 5.6 0.00012 47.8 3.2 53 625-677 251-305 (823)
326 cd06267 PBP1_LacI_sugar_bindin 63.3 31 0.00067 34.4 8.3 76 167-246 2-79 (264)
327 COG0078 ArgF Ornithine carbamo 63.2 1.8E+02 0.004 29.7 16.1 162 31-227 44-212 (310)
328 PRK03692 putative UDP-N-acetyl 63.0 93 0.002 31.0 11.1 88 150-243 92-179 (243)
329 PF03480 SBP_bac_7: Bacterial 62.7 23 0.0005 36.4 7.2 87 681-779 125-212 (286)
330 cd08469 PBP2_PnbR The C-termin 62.6 1.4E+02 0.003 28.6 12.6 69 494-574 13-81 (221)
331 TIGR00696 wecB_tagA_cpsF bacte 62.6 93 0.002 29.2 10.5 86 150-243 35-122 (177)
332 cd08444 PBP2_Cbl The C-termina 62.3 1.4E+02 0.003 28.0 15.0 70 493-574 12-82 (198)
333 cd06289 PBP1_MalI_like Ligand- 62.3 39 0.00085 33.9 8.9 77 167-246 2-80 (268)
334 cd08429 PBP2_NhaR The C-termin 60.6 1.5E+02 0.0033 28.0 14.9 72 494-574 13-84 (204)
335 KOG0025 Zn2+-binding dehydroge 60.5 58 0.0013 32.8 8.8 97 138-245 161-257 (354)
336 cd01538 PBP1_ABC_xylose_bindin 60.3 41 0.00089 34.4 8.7 77 167-246 2-81 (288)
337 cd08550 GlyDH-like Glycerol_de 59.8 36 0.00079 36.1 8.3 76 153-231 12-87 (349)
338 PRK09508 leuO leucine transcri 59.4 94 0.002 32.3 11.3 68 494-574 125-193 (314)
339 TIGR00315 cdhB CO dehydrogenas 59.3 78 0.0017 29.2 9.1 86 95-187 28-124 (162)
340 cd08425 PBP2_CynR The C-termin 59.2 1.5E+02 0.0032 27.4 14.1 69 494-574 14-82 (197)
341 PRK11063 metQ DL-methionine tr 58.7 39 0.00084 34.4 7.8 78 6-101 8-85 (271)
342 PRK12683 transcriptional regul 58.6 2.3E+02 0.0049 29.3 15.5 68 495-574 107-175 (309)
343 PRK10837 putative DNA-binding 58.5 2.1E+02 0.0046 29.0 15.9 68 494-574 102-170 (290)
344 PRK15116 sulfur acceptor prote 58.5 2E+02 0.0043 29.1 12.7 114 45-174 82-208 (268)
345 cd08465 PBP2_ToxR The C-termin 58.4 1.3E+02 0.0028 28.2 11.4 70 493-574 12-81 (200)
346 cd06306 PBP1_TorT-like TorT-li 57.9 39 0.00085 34.1 7.9 80 166-246 1-82 (268)
347 PRK15408 autoinducer 2-binding 57.7 42 0.00091 35.4 8.3 82 163-246 22-106 (336)
348 cd01536 PBP1_ABC_sugar_binding 57.5 46 0.001 33.2 8.4 77 166-245 1-80 (267)
349 COG2358 Imp TRAP-type uncharac 57.5 93 0.002 32.2 10.2 80 681-766 126-214 (321)
350 cd06282 PBP1_GntR_like_2 Ligan 57.5 55 0.0012 32.7 9.0 77 167-246 2-80 (266)
351 COG2247 LytB Putative cell wal 56.8 2.4E+02 0.0052 29.0 12.5 78 96-197 77-159 (337)
352 cd06299 PBP1_LacI_like_13 Liga 56.7 63 0.0014 32.3 9.3 76 167-246 2-79 (265)
353 cd06303 PBP1_LuxPQ_Quorum_Sens 56.3 36 0.00078 34.6 7.4 80 166-245 1-84 (280)
354 cd01545 PBP1_SalR Ligand-bindi 55.8 62 0.0013 32.4 9.1 77 167-245 2-80 (270)
355 cd08178 AAD_C C-terminal alcoh 55.7 34 0.00074 37.1 7.3 78 162-239 19-98 (398)
356 cd06318 PBP1_ABC_sugar_binding 55.6 49 0.0011 33.5 8.3 78 166-246 1-81 (282)
357 PRK10341 DNA-binding transcrip 55.4 2.6E+02 0.0056 28.9 14.2 70 495-574 111-180 (312)
358 cd06277 PBP1_LacI_like_1 Ligan 55.4 68 0.0015 32.2 9.3 74 167-245 2-80 (268)
359 TIGR00249 sixA phosphohistidin 55.1 84 0.0018 28.6 8.7 98 145-243 24-121 (152)
360 PRK11303 DNA-binding transcrip 54.9 88 0.0019 32.6 10.3 79 164-245 61-141 (328)
361 cd06312 PBP1_ABC_sugar_binding 54.7 48 0.001 33.4 8.0 78 166-245 1-82 (271)
362 cd08175 G1PDH Glycerol-1-phosp 54.5 51 0.0011 35.0 8.3 77 153-231 12-90 (348)
363 cd06310 PBP1_ABC_sugar_binding 53.9 51 0.0011 33.2 8.0 79 166-245 1-82 (273)
364 cd08436 PBP2_LTTR_like_3 The C 53.8 1.8E+02 0.0039 26.7 15.1 70 494-574 13-82 (194)
365 PRK00865 glutamate racemase; P 53.8 2E+02 0.0043 29.1 12.0 35 91-125 62-96 (261)
366 cd06304 PBP1_BmpA_like Peripla 52.9 1.9E+02 0.0041 28.9 12.0 129 31-168 120-248 (260)
367 TIGR00854 pts-sorbose PTS syst 52.8 58 0.0013 29.7 7.1 82 150-239 12-93 (151)
368 cd06281 PBP1_LacI_like_5 Ligan 52.8 73 0.0016 32.0 9.0 76 167-245 2-79 (269)
369 PRK12682 transcriptional regul 52.7 2.8E+02 0.0061 28.6 14.8 71 493-574 105-175 (309)
370 cd00755 YgdL_like Family of ac 52.4 2.4E+02 0.0053 27.8 12.2 116 43-174 61-182 (231)
371 PRK10014 DNA-binding transcrip 52.4 98 0.0021 32.5 10.2 79 164-245 64-144 (342)
372 PRK09791 putative DNA-binding 52.2 2.8E+02 0.0061 28.4 14.5 84 468-574 95-178 (302)
373 TIGR02667 moaB_proteo molybden 52.1 1.6E+02 0.0034 27.3 10.0 78 164-243 4-90 (163)
374 PRK09756 PTS system N-acetylga 52.0 64 0.0014 29.7 7.3 81 150-239 16-97 (158)
375 PF00448 SRP54: SRP54-type pro 51.9 2E+02 0.0044 27.5 11.1 76 164-243 29-107 (196)
376 cd02071 MM_CoA_mut_B12_BD meth 51.8 1.2E+02 0.0025 26.5 8.7 72 169-246 4-79 (122)
377 PRK05452 anaerobic nitric oxid 51.8 3.8E+02 0.0083 29.9 15.4 140 100-259 198-348 (479)
378 PRK15395 methyl-galactoside AB 51.2 1.7E+02 0.0037 30.6 11.7 124 29-161 160-293 (330)
379 cd00001 PTS_IIB_man PTS_IIB, P 51.1 63 0.0014 29.5 7.1 82 150-239 11-92 (151)
380 cd08177 MAR Maleylacetate redu 50.9 47 0.001 35.1 7.3 76 153-231 12-87 (337)
381 COG0563 Adk Adenylate kinase a 50.5 39 0.00084 31.8 5.9 102 98-201 3-113 (178)
382 PF04273 DUF442: Putative phos 50.3 1.3E+02 0.0028 25.7 8.5 81 158-238 22-103 (110)
383 cd01391 Periplasmic_Binding_Pr 50.1 58 0.0013 32.1 7.7 78 166-246 1-83 (269)
384 cd06322 PBP1_ABC_sugar_binding 50.0 70 0.0015 32.1 8.3 77 167-246 2-81 (267)
385 COG0725 ModA ABC-type molybdat 49.1 2.9E+02 0.0064 27.8 12.3 95 683-783 123-228 (258)
386 cd06296 PBP1_CatR_like Ligand- 48.7 92 0.002 31.2 9.0 75 167-245 2-78 (270)
387 TIGR00363 lipoprotein, YaeC fa 48.6 1.3E+02 0.0028 30.3 9.6 68 681-755 105-196 (258)
388 TIGR02417 fruct_sucro_rep D-fr 48.2 1.4E+02 0.0031 31.0 10.6 80 163-245 59-140 (327)
389 cd06270 PBP1_GalS_like Ligand 48.2 99 0.0021 31.0 9.1 75 167-245 2-78 (268)
390 cd01539 PBP1_GGBP Periplasmic 48.0 72 0.0016 32.9 8.1 78 166-246 1-83 (303)
391 PRK11425 PTS system N-acetylga 47.8 80 0.0017 29.0 7.3 81 150-239 14-94 (157)
392 cd08549 G1PDH_related Glycerol 47.7 80 0.0017 33.3 8.4 84 154-239 13-100 (332)
393 cd08448 PBP2_LTTR_aromatics_li 47.7 2.3E+02 0.0049 26.0 15.2 68 494-574 13-81 (197)
394 PRK12679 cbl transcriptional r 47.6 3.4E+02 0.0074 28.1 14.0 70 494-574 106-175 (316)
395 cd08179 NADPH_BDH NADPH-depend 47.5 41 0.00089 36.2 6.3 70 162-231 21-91 (375)
396 PF14503 YhfZ_C: YhfZ C-termin 47.5 61 0.0013 31.8 6.7 51 694-750 114-166 (232)
397 TIGR02122 TRAP_TAXI TRAP trans 47.4 3.4E+02 0.0074 28.0 14.7 40 1-41 1-41 (320)
398 cd08416 PBP2_MdcR The C-termin 47.4 2.3E+02 0.005 26.1 15.0 71 493-574 12-83 (199)
399 cd06316 PBP1_ABC_sugar_binding 47.2 75 0.0016 32.5 8.1 79 166-246 1-82 (294)
400 COG1179 Dinucleotide-utilizing 47.2 1.1E+02 0.0023 30.2 8.1 100 43-158 80-180 (263)
401 cd06317 PBP1_ABC_sugar_binding 47.0 84 0.0018 31.6 8.4 77 167-246 2-82 (275)
402 cd08180 PDD 1,3-propanediol de 46.9 43 0.00092 35.3 6.2 71 160-231 18-88 (332)
403 PRK00002 aroB 3-dehydroquinate 46.8 1.2E+02 0.0025 32.4 9.6 92 153-245 20-118 (358)
404 PF00625 Guanylate_kin: Guanyl 46.3 1.5E+02 0.0032 27.9 9.3 129 96-244 3-135 (183)
405 cd01542 PBP1_TreR_like Ligand- 45.7 1.1E+02 0.0024 30.3 9.0 75 167-245 2-78 (259)
406 PF00205 TPP_enzyme_M: Thiamin 45.5 26 0.00056 31.3 3.7 57 87-144 2-62 (137)
407 cd08453 PBP2_IlvR The C-termin 45.4 2.5E+02 0.0055 25.9 15.7 71 494-574 13-84 (200)
408 cd06302 PBP1_LsrB_Quorum_Sensi 45.4 83 0.0018 32.4 8.1 78 167-246 2-82 (298)
409 PF13380 CoA_binding_2: CoA bi 45.3 28 0.0006 30.1 3.7 85 165-257 1-88 (116)
410 cd03770 SR_TndX_transposase Se 45.3 2.3E+02 0.0049 25.3 10.1 20 149-168 21-40 (140)
411 TIGR02370 pyl_corrinoid methyl 45.2 1.5E+02 0.0033 28.4 9.2 87 165-257 85-175 (197)
412 PRK10653 D-ribose transporter 45.2 96 0.0021 31.8 8.5 80 164-246 26-108 (295)
413 PRK10355 xylF D-xylose transpo 45.1 1E+02 0.0022 32.4 8.7 79 164-245 25-106 (330)
414 cd06285 PBP1_LacI_like_7 Ligan 44.2 1.4E+02 0.0029 29.9 9.4 75 167-245 2-78 (265)
415 PRK10936 TMAO reductase system 44.1 92 0.002 32.9 8.3 81 164-246 46-129 (343)
416 PF12683 DUF3798: Protein of u 44.0 96 0.0021 31.0 7.5 80 148-233 15-98 (275)
417 cd00423 Pterin_binding Pterin 43.9 2.5E+02 0.0055 28.2 11.0 18 153-171 110-127 (258)
418 cd06295 PBP1_CelR Ligand bindi 43.9 1.4E+02 0.0029 30.1 9.4 77 164-246 3-88 (275)
419 cd00338 Ser_Recombinase Serine 43.6 2.3E+02 0.0049 24.9 10.4 26 147-172 15-40 (137)
420 cd06319 PBP1_ABC_sugar_binding 43.4 93 0.002 31.3 8.1 76 167-245 2-80 (277)
421 cd06271 PBP1_AglR_RafR_like Li 43.4 1.2E+02 0.0026 30.3 8.8 75 167-245 2-82 (268)
422 cd06274 PBP1_FruR Ligand bindi 43.3 1.3E+02 0.0029 29.9 9.1 75 167-245 2-78 (264)
423 cd06278 PBP1_LacI_like_2 Ligan 43.2 1.2E+02 0.0027 30.1 8.9 75 167-246 2-78 (266)
424 cd01540 PBP1_arabinose_binding 43.2 88 0.0019 31.8 7.9 77 166-246 1-80 (289)
425 cd06273 PBP1_GntR_like_1 This 43.2 1.4E+02 0.0029 29.9 9.2 75 167-245 2-78 (268)
426 TIGR00177 molyb_syn molybdenum 43.1 1.4E+02 0.003 26.9 8.1 60 180-242 28-88 (144)
427 cd06292 PBP1_LacI_like_10 Liga 42.8 1.3E+02 0.0029 30.1 9.1 77 167-246 2-84 (273)
428 cd06324 PBP1_ABC_sugar_binding 42.8 1E+02 0.0022 31.8 8.4 77 167-246 2-83 (305)
429 cd06315 PBP1_ABC_sugar_binding 42.7 1.3E+02 0.0028 30.6 8.9 78 165-245 1-81 (280)
430 cd06300 PBP1_ABC_sugar_binding 42.6 1E+02 0.0023 30.9 8.3 79 166-245 1-85 (272)
431 cd00758 MoCF_BD MoCF_BD: molyb 42.5 1.3E+02 0.0029 26.5 7.8 61 179-242 19-80 (133)
432 cd01575 PBP1_GntR Ligand-bindi 42.3 1.3E+02 0.0027 30.1 8.8 75 167-245 2-78 (268)
433 PF03830 PTSIIB_sorb: PTS syst 42.0 29 0.00063 31.6 3.5 83 151-241 13-95 (151)
434 cd06320 PBP1_allose_binding Pe 42.0 99 0.0021 31.1 8.0 80 166-246 1-83 (275)
435 COG1419 FlhF Flagellar GTP-bin 41.9 1.8E+02 0.004 31.1 9.6 84 151-243 220-305 (407)
436 PRK10677 modA molybdate transp 41.8 1.9E+02 0.0041 29.1 9.7 92 684-783 127-229 (257)
437 PF07302 AroM: AroM protein; 41.7 1.8E+02 0.0039 28.4 8.9 74 165-242 126-201 (221)
438 cd02067 B12-binding B12 bindin 41.3 2.1E+02 0.0046 24.5 8.8 67 173-245 8-78 (119)
439 TIGR01744 XPRTase xanthine pho 41.3 74 0.0016 30.4 6.2 71 55-126 4-79 (191)
440 PF02310 B12-binding: B12 bind 41.3 2.3E+02 0.0049 24.2 9.8 17 180-196 16-32 (121)
441 cd03364 TOPRIM_DnaG_primases T 41.1 56 0.0012 25.8 4.7 42 155-197 35-76 (79)
442 cd06321 PBP1_ABC_sugar_binding 40.9 1E+02 0.0022 31.0 7.8 76 167-245 2-82 (271)
443 cd08173 Gro1PDH Sn-glycerol-1- 40.5 1.2E+02 0.0026 32.1 8.4 81 154-238 14-97 (339)
444 PRK09701 D-allose transporter 40.5 1.2E+02 0.0026 31.4 8.4 84 162-246 22-108 (311)
445 cd06286 PBP1_CcpB_like Ligand- 40.5 1.4E+02 0.0031 29.6 8.8 73 167-243 2-76 (260)
446 PF02602 HEM4: Uroporphyrinoge 40.4 23 0.0005 34.9 2.9 92 145-243 97-189 (231)
447 TIGR01098 3A0109s03R phosphate 40.4 68 0.0015 32.0 6.3 19 210-228 183-201 (254)
448 cd08435 PBP2_GbpR The C-termin 40.3 3E+02 0.0064 25.3 15.8 70 495-574 14-83 (201)
449 cd06323 PBP1_ribose_binding Pe 40.2 1E+02 0.0022 30.8 7.7 76 167-245 2-80 (268)
450 PF00532 Peripla_BP_1: Peripla 40.2 1.1E+02 0.0024 31.3 7.8 76 165-245 2-79 (279)
451 cd08184 Fe-ADH3 Iron-containin 39.9 1.4E+02 0.0029 31.7 8.6 75 153-231 12-91 (347)
452 cd00886 MogA_MoaB MogA_MoaB fa 39.8 1.5E+02 0.0031 27.1 7.8 63 166-230 2-70 (152)
453 PRK11063 metQ DL-methionine tr 39.7 1.6E+02 0.0035 29.9 8.8 39 497-543 46-85 (271)
454 PF07172 GRP: Glycine rich pro 39.7 28 0.00061 28.8 2.7 20 1-20 1-20 (95)
455 PRK05928 hemD uroporphyrinogen 39.6 85 0.0018 31.1 6.9 87 153-245 112-200 (249)
456 PRK15421 DNA-binding transcrip 39.4 4.6E+02 0.0099 27.2 14.4 68 495-574 103-170 (317)
457 cd06167 LabA_like LabA_like pr 39.0 2.9E+02 0.0062 24.7 12.7 92 154-246 28-124 (149)
458 cd06298 PBP1_CcpA_like Ligand- 38.8 1.5E+02 0.0032 29.6 8.7 75 167-245 2-78 (268)
459 TIGR00640 acid_CoA_mut_C methy 38.8 2E+02 0.0044 25.4 8.2 74 167-246 5-82 (132)
460 KOG1545 Voltage-gated shaker-l 38.4 23 0.0005 36.4 2.3 40 622-661 391-432 (507)
461 PRK14987 gluconate operon tran 38.2 2.5E+02 0.0055 29.2 10.6 79 164-246 63-143 (331)
462 COG1638 DctP TRAP-type C4-dica 38.2 2.1E+02 0.0045 30.2 9.5 170 498-753 48-217 (332)
463 cd06354 PBP1_BmpA_PnrA_like Pe 38.0 4.2E+02 0.0092 26.4 13.7 122 31-158 121-242 (265)
464 KOG0498 K+-channel ERG and rel 37.8 21 0.00045 41.3 2.2 53 625-677 295-349 (727)
465 cd06578 HemD Uroporphyrinogen- 37.5 3.9E+02 0.0086 25.9 13.3 117 118-244 76-195 (239)
466 cd08450 PBP2_HcaR The C-termin 37.5 3.3E+02 0.0071 25.0 14.2 69 494-574 13-81 (196)
467 cd08432 PBP2_GcdR_TrpI_HvrB_Am 37.4 1.7E+02 0.0036 26.9 8.4 90 686-782 87-181 (194)
468 PF01936 NYN: NYN domain; Int 37.3 2.3E+02 0.0051 25.1 8.9 99 152-256 22-126 (146)
469 PF00072 Response_reg: Respons 37.2 2.1E+02 0.0046 23.6 8.2 58 179-245 9-69 (112)
470 cd06287 PBP1_LacI_like_8 Ligan 37.0 4.4E+02 0.0096 26.4 12.2 119 33-160 120-245 (269)
471 COG1922 WecG Teichoic acid bio 36.8 2.5E+02 0.0055 28.0 9.2 99 151-258 96-195 (253)
472 PRK05569 flavodoxin; Provision 36.8 2.4E+02 0.0051 25.0 8.7 85 165-260 2-95 (141)
473 TIGR00067 glut_race glutamate 36.6 2.6E+02 0.0057 28.0 9.7 126 90-231 54-182 (251)
474 PRK09189 uroporphyrinogen-III 36.5 86 0.0019 31.1 6.3 114 120-243 75-191 (240)
475 TIGR02637 RhaS rhamnose ABC tr 36.4 1.2E+02 0.0026 31.2 7.6 77 168-246 2-82 (302)
476 TIGR03339 phn_lysR aminoethylp 36.4 4.5E+02 0.0098 26.3 15.4 68 495-574 98-165 (279)
477 cd06283 PBP1_RegR_EndR_KdgR_li 36.1 2E+02 0.0043 28.6 9.1 75 167-245 2-78 (267)
478 TIGR02634 xylF D-xylose ABC tr 36.0 1.3E+02 0.0028 31.0 7.8 71 173-246 9-80 (302)
479 PF02401 LYTB: LytB protein; 35.7 2.1E+02 0.0045 29.2 8.7 55 72-126 185-241 (281)
480 cd01574 PBP1_LacI Ligand-bindi 35.6 2.2E+02 0.0047 28.3 9.3 76 167-245 2-79 (264)
481 cd08437 PBP2_MleR The substrat 35.5 3.6E+02 0.0077 24.8 14.7 71 494-574 13-83 (198)
482 PRK00843 egsA NAD(P)-dependent 35.5 1.6E+02 0.0034 31.3 8.4 82 153-238 22-106 (350)
483 cd08449 PBP2_XapR The C-termin 35.5 3.5E+02 0.0076 24.7 14.0 71 494-574 13-83 (197)
484 PF13155 Toprim_2: Toprim-like 35.0 51 0.0011 27.0 3.7 41 152-192 35-75 (96)
485 TIGR03850 bind_CPR_0540 carboh 35.0 1.2E+02 0.0026 33.3 7.7 24 50-76 48-71 (437)
486 cd06309 PBP1_YtfQ_like Peripla 34.8 1.2E+02 0.0026 30.5 7.2 71 173-246 10-81 (273)
487 cd06293 PBP1_LacI_like_11 Liga 34.5 2E+02 0.0043 28.7 8.8 62 167-231 2-65 (269)
488 cd08169 DHQ-like Dehydroquinat 34.3 3E+02 0.0065 29.1 10.1 91 154-245 13-109 (344)
489 PLN02821 1-hydroxy-2-methyl-2- 34.2 1.8E+02 0.0038 31.7 8.2 57 69-125 334-393 (460)
490 COG5510 Predicted small secret 34.1 51 0.0011 22.5 2.6 21 1-21 2-22 (44)
491 cd03522 MoeA_like MoeA_like. T 34.1 2.5E+02 0.0054 29.2 9.2 80 162-243 157-242 (312)
492 cd06308 PBP1_sensor_kinase_lik 34.0 1.7E+02 0.0036 29.4 8.1 77 167-246 2-82 (270)
493 cd08197 DOIS 2-deoxy-scyllo-in 33.9 3.8E+02 0.0083 28.5 10.9 99 154-256 13-118 (355)
494 cd02070 corrinoid_protein_B12- 33.9 3.4E+02 0.0073 26.0 9.7 86 165-256 83-172 (201)
495 cd06294 PBP1_ycjW_transcriptio 33.8 2.2E+02 0.0047 28.4 9.0 68 174-246 16-84 (270)
496 TIGR01481 ccpA catabolite cont 33.6 3.4E+02 0.0074 28.1 10.7 79 163-245 58-138 (329)
497 PRK10481 hypothetical protein; 33.6 3E+02 0.0064 27.0 9.1 75 156-234 120-195 (224)
498 cd06307 PBP1_uncharacterized_s 33.6 1.3E+02 0.0029 30.2 7.3 80 166-246 1-84 (275)
499 PRK07377 hypothetical protein; 33.5 1.1E+02 0.0024 28.5 5.7 63 468-546 75-137 (184)
500 cd06313 PBP1_ABC_sugar_binding 33.4 1.3E+02 0.0027 30.4 7.1 70 174-246 11-81 (272)
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=1.2e-84 Score=656.22 Aligned_cols=703 Identities=18% Similarity=0.302 Sum_probs=568.0
Q ss_pred CCceEEEEEEeecCCcchhhHHHHHHHHHHHHhcCCCCCC-CCEEEEEEecCC-CCHHHHHHHHHHHHhcCceEEEccCc
Q 003958 28 RPSVVNIGALLSFSTNVGKVAKLAIKAAVDDVNSDPTTLG-GTKLKLQMQDCN-HSGFLALAEALHLMEGQTVAIIGPQD 105 (784)
Q Consensus 28 ~~~~i~IG~i~~~~~~~g~~~~~a~~~Ave~IN~~~~il~-g~~l~~~~~D~~-~~~~~a~~~~~~li~~~v~aiiGp~~ 105 (784)
-+..|.||++||-+.. +...|+++|+-..|.+..--+ -.+|..++..-. .+....+.+.|+..++||.||+|-.+
T Consensus 23 f~~tiqigglF~~n~~---qe~~Afr~~~~~~~~~~~~~~~pf~L~~~~d~~e~a~Sf~~tnafCsq~s~Gv~Aifg~yd 99 (897)
T KOG1054|consen 23 FPNTIQIGGLFPRNTD---QEHSAFRFAVQLYNTNQNTTEKPFKLNPHVDNLESANSFAVTNAFCSQFSRGVYAIFGFYD 99 (897)
T ss_pred CCCceeeccccCCcch---HHHHHHHHHHHHhhcCCCCCCCCcccccccchhhhhhhHHHHHHHHHHHhhhHhhheeccc
Confidence 4568999999998753 456778888877665432110 134444443222 47777788999999999999999998
Q ss_pred hhhHHHHHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcCCCcchhHHHHH
Q 003958 106 AVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDDDHGRNGIAALG 185 (784)
Q Consensus 106 s~~~~~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~ 185 (784)
-.....+..+|+..++|.|+++... +...++.+++.|+-. .++++++.|++|.++.++| |.+-|...++.+.
T Consensus 100 ~ks~~~ltsfc~aLh~~~vtpsfp~----~~~~~Fviq~RP~l~---~al~s~i~hy~W~~fv~ly-D~~rg~s~Lqai~ 171 (897)
T KOG1054|consen 100 KKSVNTLTSFCGALHVSFVTPSFPT----DGDNQFVIQMRPALK---GALLSLIDHYKWEKFVYLY-DTDRGLSILQAIM 171 (897)
T ss_pred ccchhhhhhhccceeeeeecccCCc----CCCceEEEEeCchHH---HHHHHHHHhcccceEEEEE-cccchHHHHHHHH
Confidence 8888999999999999999986522 233567888888754 6999999999999999999 5567888899999
Q ss_pred HHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHcCCCCCCeEEEecCcccccccc
Q 003958 186 DTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIATSWLSTALDT 265 (784)
Q Consensus 186 ~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~ 265 (784)
+.+.++++.|.....-.+ .+...++.+++.+...+.+-|++.|..+....++.++.+.+....+|++|+.+..-...|.
T Consensus 172 ~~a~~~nw~VtA~~v~~~-~d~~~yr~~f~~l~~r~e~rv~iDce~~~~~~il~q~i~~~k~~~~YHYvlaNl~f~d~dl 250 (897)
T KOG1054|consen 172 EAAAQNNWQVTAINVGNI-NDVKEYRMLFEMLDRRQENRVLIDCESERRNRILLQVIELGKHVKGYHYVLANLGFTDIDL 250 (897)
T ss_pred HHHHhcCceEEEEEcCCc-ccHHHHHHHHHHHhccccceEEEEcccHHHHHHHHHHHHHhhhccceEEEEeeCCCchhhH
Confidence 999999999987654332 3666799999999999999999999999999999999988888899999998754333332
Q ss_pred CCCCCCCccccceeeEEEeeecCCchhHHHHHHHHHhhccC-CCCCCCCCCChhHHHHhhHHHHHHHHHHHHhhcCCccc
Q 003958 266 NSPFPSDVMDDIQGVLTLRTYTPDSVLKRKFISRWRNLTDA-KTPNGYIGLNAYGFYAYDTVWLLARAINSFFKQGGNLS 344 (784)
Q Consensus 266 ~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~f~~~~~~~~~~-~~~~~~~~~~~~~~~~YDAv~~~a~Al~~~~~~~~~~~ 344 (784)
........++.++...+.+++..++|.++|++.... .++.....+...++..|||+.+.++|++.++++..+..
T Consensus 251 -----~~f~~g~aNitgFqivn~~~~~~~k~~~~~~~l~~~~~~g~~~~~~k~tsAlthDailV~~eaf~~~~~q~~~~~ 325 (897)
T KOG1054|consen 251 -----ERFQHGGANITGFQIVNKNNPMVKKFIQRWKELDEREYPGASNDPIKYTSALTHDAILVMAEAFRSLRRQRIDIS 325 (897)
T ss_pred -----HHHhcCCcceeEEEEecCCChHHHHHHHHHhhhcccccCCCCCCCcchhhhhhhhHHHHHHHHHHHHHHhhhchh
Confidence 223345566889999999999999999999986543 33334345667789999999999999999987754432
Q ss_pred cccCCccccccCCcccc--cccccCCchHHHHHHHhccccceeeeEEEecCCCCcCCcEEEEEeeccceEEEEEecCCCC
Q 003958 345 FSKDSRLSDIQGHLRLD--SLRIFNGGNLLRDSILQANMTGTAGPARFNSHGDLINPAYEIINVIGTGYRRIGYWSNYSG 422 (784)
Q Consensus 345 ~~~~~~~~~~~g~~~~~--~~~~~~~~~~l~~~l~~~~f~g~tG~v~Fd~~g~~~~~~~~I~~~~~~~~~~VG~w~~~~~ 422 (784)
.. +....|. +..+|.+|..+.++++++.++|++|.|+||..|.|.+.+.+|+++..++.+++|.|+...+
T Consensus 326 rR--------G~~GD~~an~~~p~~qG~~I~ralk~v~~eGLTGniqFd~~G~R~Nyt~~i~elk~~~~rk~~~W~e~~~ 397 (897)
T KOG1054|consen 326 RR--------GNAGDCLANPAVPWEQGIDIERALKQVQVEGLTGNIQFDKYGRRTNYTIDIVELKSNGSRKVGYWNEGEG 397 (897)
T ss_pred cc--------CCCccccCCCCCchhcchhHHHHHHheeecccccceeecccCccccceEEEEEeccCCcceeeeecccCc
Confidence 11 0022443 4568889999999999999999999999999999999999999999999999999999887
Q ss_pred CceecCccccCCCCCCCCCccccceeecCCCCCCCCCceeccCCCccEEEEecCCCccceeEe----eCCCcceeeeeHH
Q 003958 423 LSVVRPETLYSKPPNRSSSNQRLYSVIWPGQTTQKPRGWVFPNNGRHLRIGVPNRVSFREFVS----VKGSEMTSGFCID 498 (784)
Q Consensus 423 l~~~~~~~~~~~~~~~~~~~~~~~~i~W~~~~~~~p~~~c~~~~~~~l~v~~~~~~~~~~~~~----~~~~~~~~G~~~d 498 (784)
+...... + +.. ..+ .....++.++.+....||.++.+ ..++.++.|||+|
T Consensus 398 fv~~~t~----------a---~~~-------~d~------~~~~n~tvvvttiL~spyvm~kkn~~~~egn~ryEGyCvd 451 (897)
T KOG1054|consen 398 FVPGSTV----------A---QSR-------NDQ------ASKENRTVVVTTILESPYVMLKKNHEQLEGNERYEGYCVD 451 (897)
T ss_pred eeecccc----------c---ccc-------ccc------cccccceEEEEEecCCchhHHHhhHHHhcCCcccceeHHH
Confidence 5432110 0 000 000 00123455666666667776655 4689999999999
Q ss_pred HHHHHHHHCCCccceEEeeC---CCCCCCCC-hhHHHHHHHcCcccEEEeeEEeecCccccceeccccccccEEEEEecc
Q 003958 499 VFTAAINLLPYAVPYKLIPF---GDGHNNPS-CTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPVR 574 (784)
Q Consensus 499 l~~~l~~~l~f~~~~~~~~~---~~~~~~~~-~~g~i~~l~~~~~D~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~~ 574 (784)
|+.+||++.++++++.++.. +..+..++ |+||+|+|..|+||+++++++||-+|++++|||.|++.+|+++|+++|
T Consensus 452 La~~iAkhi~~~Y~l~iv~dgkyGardaD~k~WnGMvGeLv~grAdiavApLTIt~~REeviDFSKPfMslGISIMIKKP 531 (897)
T KOG1054|consen 452 LAAEIAKHIGIKYKLFIVGDGKYGARDADTKIWNGMVGELVYGRADIAVAPLTITLVREEVIDFSKPFMSLGISIMIKKP 531 (897)
T ss_pred HHHHHHHhcCceEEEEEecCCcccccCCCcccccchhHHHhcCccceEEeeeeeehhhhhhhccccchhhcCeEEEEeCc
Confidence 99999999999844444432 23345666 999999999999999999999999999999999999999999999999
Q ss_pred C-CccccccccccccHHHHHHHHHHHHHHHHHhhheecccCCCCCCC-------------ccCCceeehhhhhhhhhccc
Q 003958 575 K-LDSNAWAFLSPFTPMMWGVTAIFFLAVGAVVWILEHRLNDEFRGP-------------PKRQVVTIFWFSFSTMFFAH 640 (784)
Q Consensus 575 ~-~~~~~~~~~~pf~~~~W~~i~~~~~~~~~~~~~~~~~~~~~~~~~-------------~~~~~~~~~~~~~~~~~~~~ 640 (784)
. ..+..++|+.|....+|+||+.+++-+++++++..|++|+||+.. +.+++.||+|++++++++||
T Consensus 532 qKsk~gVFSFldPLa~eIWm~ivfaYiGVSvvlFLVSrFSPYEwh~Ee~~rg~~t~~~~~NeFgifNsLWFsLgAFMQQG 611 (897)
T KOG1054|consen 532 QKSKPGVFSFLDPLAYEIWMCIVFAYIGVSVVLFLVSRFSPYEWHTEEFERGRFTPSDPPNEFGIFNSLWFSLGAFMQQG 611 (897)
T ss_pred ccCCCCeeeecchhHHHHHHHHHHHHhcceEEEEEEeccCchheeccccccCCCCCCCCCccchhhHHHHHHHHHHHhcC
Confidence 9 789999999999999999999999999999999999999988532 23558899999999999999
Q ss_pred cc-ccccchhhHHHHHHHHHHHHHHhhccccceeeEeeccccCCCCChHhhhhCCCc-eEEeeCchHHHHHHhhcccCcc
Q 003958 641 KE-KTVSALGRLVLIIWLFVVLIINSSYTASLTSILTVQKLSSPIKGIDSLRSSNYP-IGYQVNSFARNYLVDELNIDES 718 (784)
Q Consensus 641 ~~-~p~~~~~R~~~~~w~~~~lvl~~~Yta~L~s~l~~~~~~~~i~~~~dl~~~~~~-i~~~~~~~~~~~~~~~~~~~~~ 718 (784)
+. .||+.|+||+.++||||+||++++|||||+||||++++.+||.|.+||++|... +|+.++.++.+||++..-....
T Consensus 612 ~DI~PRslSGRIvggvWWFFTlIIiSSYTANLAAFLTvErMvsPIESaEDLAkQteIaYGt~~~GSTkeFFr~Skiavy~ 691 (897)
T KOG1054|consen 612 CDISPRSLSGRIVGGVWWFFTLIIISSYTANLAAFLTVERMVSPIESAEDLAKQTEIAYGTLDSGSTKEFFRRSKIAVYE 691 (897)
T ss_pred CCCCccccccceeccchhhhhhhhhhhhhhHHHHHHhHHhhcCcchhHHHHhhcceeeeeecCCCchHHHHhhhhHHHHH
Confidence 88 899999999999999999999999999999999999999999999999998875 8888888899999764332334
Q ss_pred CceeC----------CCHHHHHHHHhcCCcCCCeeEEEechhhhHHHHcC-CCCeEEeCCccccceEEEEeeCCCCC
Q 003958 719 RLVPL----------NSPEEYAKALKDGPHKGGVAAVVDDRAYAELFLST-RCEFSIVGQVFTKNGWGFVSIVSSFY 784 (784)
Q Consensus 719 ~~~~~----------~~~~~~~~~l~~~~~~~~~~a~~~~~~~~~~~~~~-~c~l~~~~~~~~~~~~~~~~~k~s~~ 784 (784)
+|+.| .+..|++..+++ ++|.|||+.|....+|..++ .|+-+.+|..+.+.|||+|.||||-+
T Consensus 692 kMW~yM~SaepsVFv~t~aeGv~rVRk---sKGkyAfLLEsTmNey~eqRkPCDTMKVGgNLds~GYGiATp~Gssl 765 (897)
T KOG1054|consen 692 KMWTYMKSAEPSVFVRTTAEGVARVRK---SKGKYAFLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGIATPKGSSL 765 (897)
T ss_pred HHHHHHhcCCcceeeehhhhHHHHHHh---cCCceEeehHhhhhhhhhccCCccceecccccCCcceeecCCCCccc
Confidence 55543 356677777665 48999999999999998865 79999999999999999999999853
No 2
>KOG4440 consensus NMDA selective glutamate-gated ion channel receptor subunit GRIN1 [Inorganic ion transport and metabolism; Amino acid transport and metabolism; Signal transduction mechanisms]
Probab=100.00 E-value=1.1e-76 Score=601.07 Aligned_cols=673 Identities=23% Similarity=0.382 Sum_probs=547.8
Q ss_pred cCCCceEEEEEEeecCCcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEec--CCCCHHHHHHHHH-HHHhcCceEEEc
Q 003958 26 SGRPSVVNIGALLSFSTNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQD--CNHSGFLALAEAL-HLMEGQTVAIIG 102 (784)
Q Consensus 26 ~~~~~~i~IG~i~~~~~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D--~~~~~~~a~~~~~-~li~~~v~aiiG 102 (784)
+..++.++||.+..-. ..+.-+.-++..+|++.+ ..++.+.-.- ...++.+.+..+| ++++..|.+|+-
T Consensus 30 ~~np~t~nig~Vlst~-----~~ee~F~~t~~hln~~~~---s~k~~~~aksv~~d~n~i~t~~~VC~~li~~~vyav~v 101 (993)
T KOG4440|consen 30 ACNPKTVNIGAVLSTR-----KHEEMFRETVNHLNKRHG---SWKIQLNAKSVTHDPNAIQTALSVCEDLISSQVYAVLV 101 (993)
T ss_pred CCCccceeeeeeeech-----hHHHHHHHHHHHhhcccc---ceEEEEccccccCCCcHHHHHHHHHHHHHhhheeEEEe
Confidence 3567899999998764 456778889999997753 2444442211 2335555555666 577778887764
Q ss_pred -c-Cchh---hHHHHHHhhhcCCccEEecccCCCCCCc-CCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcCCC
Q 003958 103 -P-QDAV---TSHVVSHVANELQVPLLSFSATDPTLSS-LQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDDDH 176 (784)
Q Consensus 103 -p-~~s~---~~~~va~~~~~~~ip~Is~~a~~~~l~~-~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~~~ 176 (784)
| ..|. .-.+++--++.+.||++.....+..++| +-++.|.|++|+..+|+....+.|.+|.|++|.++.+||..
T Consensus 102 Sh~~Ts~d~f~p~~vSYT~gFY~iPV~G~~~Rda~fSdKnIh~sFlRtvpPyshqa~VwleMl~~~~y~~vi~l~s~d~~ 181 (993)
T KOG4440|consen 102 SHPPTSNDHFTPTPVSYTAGFYRIPVLGLTTRDAIFSDKNIHLSFLRTVPPYSHQASVWLEMLRVYSYNHVILLVSDDHE 181 (993)
T ss_pred cCCCCCCcccccccceeeccceeeeeeeeeehhhhhccCceeeeEeecCCCccchhHHHHHHHHHhhcceEEEEEccccc
Confidence 2 2222 2344566788899999999888999999 57999999999999999999999999999999999999999
Q ss_pred cchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHcCCCCCCeEEEec
Q 003958 177 GRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIAT 256 (784)
Q Consensus 177 g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~wi~~ 256 (784)
|+.....++..+++..-++.....+. +...+++..+-+.|..++|||++..+.+++..+++.|-.++|++.+|+||.+
T Consensus 182 gra~~~r~qt~~e~~~~~~e~v~~f~--p~~~~~t~~l~~~k~~~~rv~~~~as~dDA~~ifr~Ag~lnmTG~G~VWiV~ 259 (993)
T KOG4440|consen 182 GRAAQKRLQTLLEERESKAEKVLQFD--PGTKNVTALLMEAKELEARVIILSASEDDAATIFRAAGMLNMTGSGYVWIVG 259 (993)
T ss_pred chhHHhHHHHHHHHHhhhhhhheecC--cccchHHHHHhhhhhhhheeEEeecccchHHHHHHhhhhhcccCceEEEEEe
Confidence 98887788777776555544444455 4567788999999999999999999999999999999999999999999998
Q ss_pred CccccccccCCCCCCCccccceeeEEEeeecCCchhHHHHHHHHHhhccCCCCCCCCCCChhHHHHhhHHHHHHHHHHHH
Q 003958 257 SWLSTALDTNSPFPSDVMDDIQGVLTLRTYTPDSVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTVWLLARAINSF 336 (784)
Q Consensus 257 ~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~~~a~Al~~~ 336 (784)
+..... .....|+++...-... ...+..-|++.+++.|++.+
T Consensus 260 E~a~~~-----------nn~PdG~LGlqL~~~~---------------------------~~~~hirDsv~vlasAv~e~ 301 (993)
T KOG4440|consen 260 ERAISG-----------NNLPDGILGLQLINGK---------------------------NESAHIRDSVGVLASAVHEL 301 (993)
T ss_pred cccccc-----------CCCCCceeeeEeecCc---------------------------cccceehhhHHHHHHHHHHH
Confidence 754322 2346788888764321 11346679999999999999
Q ss_pred hhcCCccccccCCccccccCCcccccccccCCchHHHHHHHhcc-ccceeeeEEEecCCCCcCCcEEEEEee-ccceEEE
Q 003958 337 FKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQAN-MTGTAGPARFNSHGDLINPAYEIINVI-GTGYRRI 414 (784)
Q Consensus 337 ~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~l~~~l~~~~-f~g~tG~v~Fd~~g~~~~~~~~I~~~~-~~~~~~V 414 (784)
++...-.... +.||++...|..+..+.+.+...+ ..|.+|+|.||++|||....|+|+|+. +.+.+-+
T Consensus 302 ~~~e~I~~~P----------~~c~d~~~~w~~g~~l~~~l~s~~~~~g~TgrV~Fnd~gdRi~a~YdiiN~hq~rk~Vg~ 371 (993)
T KOG4440|consen 302 LEKENITDPP----------RGCVDNTNIWKTGPLLKRVLMSSKYADGVTGRVEFNDDGDRIFANYDIINLHQNRKLVGV 371 (993)
T ss_pred HhhccCCCCC----------CcccCccchhcccHHHHHHHhhhcccCCcceeEEEcCCCceeeccceeEehhhhhhhhhh
Confidence 8754311111 457888889998888888887755 689999999999999999999999995 4455667
Q ss_pred EEecCCCCCceecCccccCCCCCCCCCccccceeecCCCCCCCCCceeccCCCccEEEEecCCCccceeEe---e-----
Q 003958 415 GYWSNYSGLSVVRPETLYSKPPNRSSSNQRLYSVIWPGQTTQKPRGWVFPNNGRHLRIGVPNRVSFREFVS---V----- 486 (784)
Q Consensus 415 G~w~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~i~W~~~~~~~p~~~c~~~~~~~l~v~~~~~~~~~~~~~---~----- 486 (784)
|.|+..- . ..+...|.|||+....|+++-+| .+||+.+.+++||....- .
T Consensus 372 ~~yd~~r---~----------------~~nd~~IiWpGg~~~KP~gi~~p---thLrivTi~~~PFVYv~p~~sd~~c~e 429 (993)
T KOG4440|consen 372 GIYDGTR---V----------------IPNDRKIIWPGGETEKPRGIQMP---THLRIVTIHQEPFVYVKPTLSDGTCKE 429 (993)
T ss_pred cccccee---e----------------ccCCceeecCCCCcCCCcccccc---ceeEEEEeccCCeEEEecCCCCcchhh
Confidence 7665431 1 11236899999999999999877 579999999888754431 0
Q ss_pred ----C-----------------------CCcceeeeeHHHHHHHHHHCCCccceEEeeCCC-------CC---CC-CChh
Q 003958 487 ----K-----------------------GSEMTSGFCIDVFTAAINLLPYAVPYKLIPFGD-------GH---NN-PSCT 528 (784)
Q Consensus 487 ----~-----------------------~~~~~~G~~~dl~~~l~~~l~f~~~~~~~~~~~-------~~---~~-~~~~ 528 (784)
+ ...||.|||+|||-+|+..+||+++..++..+. ++ .+ .+|+
T Consensus 430 ef~~~~d~~~k~~c~gpn~s~p~s~~~t~~fCC~G~cIDLLi~Ls~~~Nftyd~~l~~dg~fg~~~~vnnsseT~~kew~ 509 (993)
T KOG4440|consen 430 EFTVNGDPVKKVICTGPNDSSPGSPRHTVPFCCYGFCIDLLIKLSRTMNFTYDVHLVADGKFGTQERVNNSSETNKKEWN 509 (993)
T ss_pred hccccCCcccceeecCCCCCCCCCcccCcchhhhHHHHHHHHHHHHhhcceEEEEEeecccccceeeeecccccccceeh
Confidence 0 135899999999999999999998777776432 11 12 2799
Q ss_pred HHHHHHHcCcccEEEeeEEeecCccccceeccccccccEEEEEeccCCccccccccccccHHHHHHHHHHHHHHHHHhhh
Q 003958 529 ELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPVRKLDSNAWAFLSPFTPMMWGVTAIFFLAVGAVVWI 608 (784)
Q Consensus 529 g~i~~l~~~~~D~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~~~~~~~~~~~~~pf~~~~W~~i~~~~~~~~~~~~~ 608 (784)
||||+|.+|+|||++++++|++||.++++||.||...|++++.+++...+...+|+.||+..+|++++++++++++++++
T Consensus 510 G~iGEL~~~~ADMivaplTINpERa~yieFskPfkYqGitILeKk~~r~Stl~SFlQPfqstLW~lv~~SVhvVal~lYl 589 (993)
T KOG4440|consen 510 GMIGELLSGQADMIVAPLTINPERAQYIEFSKPFKYQGITILEKKEIRRSTLDSFLQPFQSTLWLLVGLSVHVVALMLYL 589 (993)
T ss_pred hhhhhhhCCccceEeeceeeChhhhhheeccCcccccceEEEeeCCCCCchHHHHHhHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eecccCCC-CCCC-------ccCCceeehhhhhhhhhcccc--cccccchhhHHHHHHHHHHHHHHhhccccceeeEeec
Q 003958 609 LEHRLNDE-FRGP-------PKRQVVTIFWFSFSTMFFAHK--EKTVSALGRLVLIIWLFVVLIINSSYTASLTSILTVQ 678 (784)
Q Consensus 609 ~~~~~~~~-~~~~-------~~~~~~~~~~~~~~~~~~~~~--~~p~~~~~R~~~~~w~~~~lvl~~~Yta~L~s~l~~~ 678 (784)
+++++|.+ |+.. ...+++.++|++||.++..|- ..|||.|.|++.++|+-|++|++++|||||+|||+.+
T Consensus 590 LDrfSPFgRFk~~ds~~~ee~alnlssAmWF~WGVLLNSGigEgtPRSfSARvLGmVWaGFaMIiVASYTANLAAFLVLd 669 (993)
T KOG4440|consen 590 LDRFSPFGRFKVNDSEEEEEDALNLSSAMWFSWGVLLNSGIGEGTPRSFSARVLGMVWAGFAMIIVASYTANLAAFLVLD 669 (993)
T ss_pred HHhcCcccceeeccCccchhhhcchhhhHHHHhHhhhccccCCCCCcchhHHHHHHHHhhhheeeehhhhhhhhhheeec
Confidence 99999873 4322 234599999999999998873 3799999999999999999999999999999999999
Q ss_pred cccCCCCChHhhhhCC----CceEEeeCchHHHHHHhhcccCccCce------eCCCHHHHHHHHhcCCcCCCeeEEEec
Q 003958 679 KLSSPIKGIDSLRSSN----YPIGYQVNSFARNYLVDELNIDESRLV------PLNSPEEYAKALKDGPHKGGVAAVVDD 748 (784)
Q Consensus 679 ~~~~~i~~~~dl~~~~----~~i~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~l~~~~~~~~~~a~~~~ 748 (784)
+.+..+.++.|-.-.+ ..++.+++|+...||++.-... .|+ .|.+.+|++++|++ |+.+||+.|
T Consensus 670 rPe~~ltGinDpRLRNps~nf~~aTVk~SsVd~YFrRqVELS--~MyR~ME~hNy~~A~eAiq~v~~----gkL~AFIWD 743 (993)
T KOG4440|consen 670 RPEERLTGINDPRLRNPSDNFIYATVKQSSVDIYFRRQVELS--TMYRHMEKHNYESAAEAIQAVRD----GKLHAFIWD 743 (993)
T ss_pred CccccccCCCCccccCcccceeEEEecCccHHHHHHHHhHHH--HHHHhhhhcchhhHHHHHHHHHc----CceeEEEee
Confidence 9999999998854322 3578899999999997754332 333 25678899999999 899999999
Q ss_pred hhhhHHHHcCCCCeEEeCCccccceEEEEeeCCCCC
Q 003958 749 RAYAELFLSTRCEFSIVGQVFTKNGWGFVSIVSSFY 784 (784)
Q Consensus 749 ~~~~~~~~~~~c~l~~~~~~~~~~~~~~~~~k~s~~ 784 (784)
...++|...++|+|...|+.|...+|||+++|||||
T Consensus 744 S~rLEfEAs~~CeLvT~GeLFgRSgyGIGlqK~SPW 779 (993)
T KOG4440|consen 744 SARLEFEASQKCELVTTGELFGRSGYGIGLQKDSPW 779 (993)
T ss_pred cceeeehhhcccceEeccccccccccccccccCCCC
Confidence 999999999999999999999999999999999998
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=8.7e-74 Score=601.49 Aligned_cols=652 Identities=20% Similarity=0.347 Sum_probs=497.9
Q ss_pred CCCHHHHHHHHHHHHhc-CceEEEccCchh---hHHHHHHhhhcCCccEEecccC-CCCCCcC-CCCceEeecCChHHHH
Q 003958 79 NHSGFLALAEALHLMEG-QTVAIIGPQDAV---TSHVVSHVANELQVPLLSFSAT-DPTLSSL-QFPYFVRTTQSDQYQM 152 (784)
Q Consensus 79 ~~~~~~a~~~~~~li~~-~v~aiiGp~~s~---~~~~va~~~~~~~ip~Is~~a~-~~~l~~~-~~p~~~r~~ps~~~~~ 152 (784)
..||...+...|+++.. +|.+|+-...|. ++..+--++...+||+|+..+. +..++++ .-..|+++.|+.++|+
T Consensus 82 ~tdPkSll~~vC~lvs~~~V~glvf~d~s~~~avaq~LDfiSs~t~iPIisi~gg~a~~~~~kd~gs~flQlg~Sieqqa 161 (1258)
T KOG1053|consen 82 TTDPKSLLTQVCDLVSGARVHGLVFEDDSDTEAVAQILDFISSQTHIPIISIHGGAAMVLTPKDLGSTFLQLGPSIEQQA 161 (1258)
T ss_pred CCCHHHHHHHHHhhhhhcceeEEEeecCccchHHHHHHHHHHHhcCCcEEEEecCccceecCCCCcceEEEeCCcHHHHH
Confidence 37999999999999976 899887655554 2333444677889999998654 4455553 3357999999999999
Q ss_pred HHHHHHHHHcCCcEEEEEEEcCCCcchhHHHHHHHHhcc--CcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEecc
Q 003958 153 AAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAK--RCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTH 230 (784)
Q Consensus 153 ~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~~l~~~--gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~ 230 (784)
++|.++|++|+|..+++|++..+..+.+...++...... |+.+.......+..+ +.......++|+-++.||+++|+
T Consensus 162 ~Vml~iL~~ydW~~Fs~vtt~~pg~~~f~~~ir~~~d~s~vgwe~i~v~~l~~s~~-d~~a~~q~qLkki~a~VillyC~ 240 (1258)
T KOG1053|consen 162 QVMLKILEEYDWYNFSLVTTQFPGNRTFVSLIRQTNDNSHVGWEMINVLTLDPSTD-DLLAKLQAQLKKIQAPVILLYCS 240 (1258)
T ss_pred HHHHHHHHHcCcceeEEEEeecCchHHHHHHHHHhhhhccccceeeeeeecCCCCC-chHHHHHHHHHhcCCcEEEEEec
Confidence 999999999999999999999888888888888877653 555554444443222 22233334455666999999999
Q ss_pred CCcHHHHHHHHHHcCCCCCCeEEEecCccccccccCCCCCCCccccceeeEEEeeecCCchhHHHHHHHHHhhccCCCCC
Q 003958 231 YNRGPVVFHVAQYLGMLGTGYVWIATSWLSTALDTNSPFPSDVMDDIQGVLTLRTYTPDSVLKRKFISRWRNLTDAKTPN 310 (784)
Q Consensus 231 ~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~ 310 (784)
.+++..++..|.+.|+++++|+||++...... + +.-.+...|.+.+... .|+
T Consensus 241 ~eea~~IF~~A~q~Gl~g~~y~Wi~pqlv~g~-~------~~pa~~P~GLisv~~~------------~w~--------- 292 (1258)
T KOG1053|consen 241 REEAERIFEEAEQAGLTGPGYVWIVPQLVEGL-E------PRPAEFPLGLISVSYD------------TWR--------- 292 (1258)
T ss_pred HHHHHHHHHHHHhcCCcCCceEEEeehhccCC-C------CCCccCccceeeeecc------------chh---------
Confidence 99999999999999999999999996643331 1 1123456677776542 222
Q ss_pred CCCCCChhHHHHhhHHHHHHHHHHHHhhcCCccccccCCccccccCCccccccc--ccCCchHHHHHHHhccccceeeeE
Q 003958 311 GYIGLNAYGFYAYDTVWLLARAINSFFKQGGNLSFSKDSRLSDIQGHLRLDSLR--IFNGGNLLRDSILQANMTGTAGPA 388 (784)
Q Consensus 311 ~~~~~~~~~~~~YDAv~~~a~Al~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~--~~~~~~~l~~~l~~~~f~g~tG~v 388 (784)
..+...+-|++.++|.|.+.++...+..+.. ...|...+ ....+..+..+|.|++|+| +++
T Consensus 293 -----~~l~~rVrdgvaiva~aa~s~~~~~~~lp~~----------~~~C~~~~~~~~~~~~~l~r~l~NvT~~g--~~l 355 (1258)
T KOG1053|consen 293 -----YSLEARVRDGVAIVARAASSMLRIHGFLPEP----------KMDCREQEETRLTSGETLHRFLANVTWDG--RDL 355 (1258)
T ss_pred -----hhHHHHHhhhHHHHHHHHHHHHhhcccCCCc----------ccccccccCccccchhhhhhhhheeeecc--cce
Confidence 2345677899999999999998776544321 23454322 3335788999999999999 789
Q ss_pred EEecCCCCcCCcEEEEEeec-cceEEEEEecCCCCCceecC-ccccCCCCCCCCCccccceeecCCCCCCCCCceeccCC
Q 003958 389 RFNSHGDLINPAYEIINVIG-TGYRRIGYWSNYSGLSVVRP-ETLYSKPPNRSSSNQRLYSVIWPGQTTQKPRGWVFPNN 466 (784)
Q Consensus 389 ~Fd~~g~~~~~~~~I~~~~~-~~~~~VG~w~~~~~l~~~~~-~~~~~~~~~~~~~~~~~~~i~W~~~~~~~p~~~c~~~~ 466 (784)
+|+++|-.+++...++.+.. ..|.+||.|...+ |.|..+ |.++.++.+..+...+++.++-....... ..-+.|..
T Consensus 356 sf~~~g~~v~p~lvvI~l~~~r~We~VG~We~~~-L~M~y~vWPr~~~~~q~~~d~~HL~VvTLeE~PFVi-ve~vDP~t 433 (1258)
T KOG1053|consen 356 SFNEDGYLVHPNLVVIDLNRDRTWERVGSWENGT-LVMKYPVWPRYHKFLQPVPDKLHLTVVTLEERPFVI-VEDVDPLT 433 (1258)
T ss_pred eecCCceeeccceEEEecCCCcchheeceecCCe-EEEeccccccccCccCCCCCcceeEEEEeccCCeEE-EecCCCCc
Confidence 99999987888888887764 5699999998765 555444 44444444444444444433311100000 00001233
Q ss_pred CccEEEEecCCCccce-eEe-----eCCCcceeeeeHHHHHHHHHHCCCccceEEeeCCCCC----CCCChhHHHHHHHc
Q 003958 467 GRHLRIGVPNRVSFRE-FVS-----VKGSEMTSGFCIDVFTAAINLLPYAVPYKLIPFGDGH----NNPSCTELVRLITA 536 (784)
Q Consensus 467 ~~~l~v~~~~~~~~~~-~~~-----~~~~~~~~G~~~dl~~~l~~~l~f~~~~~~~~~~~~~----~~~~~~g~i~~l~~ 536 (784)
+.|++-.+++...... +.. ..-+.||+|||||||++|++.+||+ |++..+++++ .||.|+|||+++..
T Consensus 434 ~~C~~ntvpc~s~~~~t~ss~~~~~~tvKkCCkGfCIDiLkKlA~~v~Ft--YDLYlVtnGKhGkk~ng~WnGmIGev~~ 511 (1258)
T KOG1053|consen 434 QTCVRNTVPCRSQLNSTFSSGDEANRTVKKCCKGFCIDILKKLARDVKFT--YDLYLVTNGKHGKKINGVWNGMIGEVVY 511 (1258)
T ss_pred CcCCCCCCcchhhhhhccCCCccCCchHHhhhhhhhHHHHHHHHhhcCcc--eEEEEecCCcccceecCcchhhHHHHHh
Confidence 3333333322210000 000 1125799999999999999999999 5555554433 88999999999999
Q ss_pred CcccEEEeeEEeecCccccceeccccccccEEEEEeccCCccccccccccccHHHHHHHHHHHHHH-HHHhhheecccCC
Q 003958 537 GVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPVRKLDSNAWAFLSPFTPMMWGVTAIFFLAV-GAVVWILEHRLND 615 (784)
Q Consensus 537 ~~~D~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~~~~~~~~~~~~~pf~~~~W~~i~~~~~~~-~~~~~~~~~~~~~ 615 (784)
++|||++++++|++||+++||||.||..+++.+||++.+...++.+|+.||++.+|+++++.++++ ++.++++|++++.
T Consensus 512 ~rA~MAVgSltINeeRSevVDFSvPFveTgIsVmV~rsngtvspsAFLePfs~svWVmmFVm~livaai~vFlFEy~SPv 591 (1258)
T KOG1053|consen 512 QRADMAVGSLTINEERSEVVDFSVPFVETGISVMVARSNGTVSPSAFLEPFSPSVWVMMFVMCLIVAAITVFLFEYFSPV 591 (1258)
T ss_pred hhhheeeeeeEechhhhccccccccccccceEEEEEecCCccCchhhcCCcchHHHHHHHHHHHHHHHHHHHHHhhcCcc
Confidence 999999999999999999999999999999999999999999999999999999999999888866 5667799999876
Q ss_pred CCC---------CCccCCceeehhhhhhhhhccccc--ccccchhhHHHHHHHHHHHHHHhhccccceeeEeeccccCCC
Q 003958 616 EFR---------GPPKRQVVTIFWFSFSTMFFAHKE--KTVSALGRLVLIIWLFVVLIINSSYTASLTSILTVQKLSSPI 684 (784)
Q Consensus 616 ~~~---------~~~~~~~~~~~~~~~~~~~~~~~~--~p~~~~~R~~~~~w~~~~lvl~~~Yta~L~s~l~~~~~~~~i 684 (784)
.+. +.+.+.++.++|..|+.+|.+..+ .|+++.+||++.+|.+|++++.++|||||||||+++++...+
T Consensus 592 gyn~~l~~gkkpggp~FtigkaiwllwaLvFnnsVpv~nPKgtTskiMv~VWAfFavifLAsYTANLAAfMIqE~~~d~v 671 (1258)
T KOG1053|consen 592 GYNRNLANGKKPGGPSFTIGKAIWLLWALVFNNSVPVENPKGTTSKIMVLVWAFFAVIFLASYTANLAAFMIQEEYYDTV 671 (1258)
T ss_pred cccccccCCCCCCCcceehhhHHHHHHHHHhCCCcCCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhc
Confidence 542 235788999999999999999754 899999999999999999999999999999999999999999
Q ss_pred CChHhhhhC-------CCceEEeeCchHHHHHHhhcccCccCceeCC--CHHHHHHHHhcCCcCCCeeEEEechhhhHHH
Q 003958 685 KGIDSLRSS-------NYPIGYQVNSFARNYLVDELNIDESRLVPLN--SPEEYAKALKDGPHKGGVAAVVDDRAYAELF 755 (784)
Q Consensus 685 ~~~~dl~~~-------~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~l~~~~~~~~~~a~~~~~~~~~~~ 755 (784)
.++.|-+-| ..++|++.+++++.+.+++...-...|+.|+ .+++++..||+ ++.||||.|..+|+|.
T Consensus 672 SGlsD~KfqrP~dq~PpFRFGTVpngSTE~niR~Nyp~MHeYM~kyNq~~v~dal~sLK~----gKLDAFIyDaAVLnY~ 747 (1258)
T KOG1053|consen 672 SGLSDPKFQRPHDQYPPFRFGTVPNGSTERNIRSNYPEMHEYMVKYNQPGVEDALESLKN----GKLDAFIYDAAVLNYM 747 (1258)
T ss_pred cccCcccccCccccCCCcccccCCCCchhhhHHhccHHHHHHHHHhccCchHHHHHHHhc----ccchhHHHHHHHHHHh
Confidence 999997754 3479999988899999654433335666664 67999999999 8999999999999999
Q ss_pred HcC--CCCeEEeC--CccccceEEEEeeCCCCC
Q 003958 756 LST--RCEFSIVG--QVFTKNGWGFVSIVSSFY 784 (784)
Q Consensus 756 ~~~--~c~l~~~~--~~~~~~~~~~~~~k~s~~ 784 (784)
..+ .|+|..+| +.|.+.||||++||||||
T Consensus 748 agkDegCKLvTIGsgKvFAttGYGIal~k~Spw 780 (1258)
T KOG1053|consen 748 AGKDEGCKLVTIGSGKVFATTGYGIALPKNSPW 780 (1258)
T ss_pred hccCCCceEEEecCCceeeecceeeecCCCCcc
Confidence 877 79999999 999999999999999996
No 4
>KOG1052 consensus Glutamate-gated kainate-type ion channel receptor subunit GluR5 and related subunits [Inorganic ion transport and metabolism; Amino acid transport and metabolism; Signal transduction mechanisms]
Probab=100.00 E-value=1.1e-53 Score=492.05 Aligned_cols=520 Identities=35% Similarity=0.596 Sum_probs=438.5
Q ss_pred HHHHhhcCCceEEEEeccCCcHHHHHHHHHHcCCCCCCeEEEecCccccccccCCCCCCCccccceeeEEEeeecCCchh
Q 003958 213 LLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIATSWLSTALDTNSPFPSDVMDDIQGVLTLRTYTPDSVL 292 (784)
Q Consensus 213 ~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~ 292 (784)
.+.+.+....+++++.+.+..+..++.++.+.|+...+|+|+.+.+.....+.... ....+..+|.+....+.+....
T Consensus 5 ~~~~~~~~~~~~~v~~~~~~~~~~~~~~a~~~~~~~~~~~~i~t~~~~~~~~~~~~--~~~~~~~~~~l~~~~~~~~s~~ 82 (656)
T KOG1052|consen 5 LLLKLKAMRTRVFVLHMFPILALAIFSQAEELGMMQFGYVWILTNLLTDALDLDEL--YSLIDVMNGVLGLRGHIPRSEL 82 (656)
T ss_pred HHHHhhccCceEEEEeCCHHHHHHHHHHHHHhCccccCeEEEEEecchhhhccccc--ccchhheeeEEeeccCCCccHH
Confidence 34445557788999988888899999999999999999999999977665554322 2334667788888888888888
Q ss_pred HHHHHHHHHhhccCCCCCCCCCCChhHHHHhhHHHHHHHHHHHHhhcCCccccccCCccccccCCcccccccccCCchHH
Q 003958 293 KRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTVWLLARAINSFFKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLL 372 (784)
Q Consensus 293 ~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~~~a~Al~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~l 372 (784)
.+.|..+|+.. . .....++..+||++++++.|++++.. .... +..|.....|.++..+
T Consensus 83 ~~~~~~~~~~~-~-------~~~~~~~~~~~D~~~~~a~~~~~~~~-~~~~-------------~~~~~~~~~~~~~~~~ 140 (656)
T KOG1052|consen 83 LQNFVTRWQTS-N-------VELLVYALWAYDAIQALARAVESLLN-IGNL-------------SLSCGRNNSWLDALGV 140 (656)
T ss_pred HHHHHHHHhhc-c-------ccccchhhHHHHHHHHHHHHHHHhhc-CCCC-------------ceecCCCCcccchhHH
Confidence 88999988865 1 23456789999999999999999864 1111 3456655667778889
Q ss_pred HHHHHhccccc---eeeeEEEecCCCCcCCcEEEEEeeccceEEEEEecCCCCCceecCccccCCCCCCCCCccccceee
Q 003958 373 RDSILQANMTG---TAGPARFNSHGDLINPAYEIINVIGTGYRRIGYWSNYSGLSVVRPETLYSKPPNRSSSNQRLYSVI 449 (784)
Q Consensus 373 ~~~l~~~~f~g---~tG~v~Fd~~g~~~~~~~~I~~~~~~~~~~VG~w~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~i~ 449 (784)
.+.++.....+ .+|.+.++.++.+....++|++........||.|++..| ..|.
T Consensus 141 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~n~~~~~~~~ig~W~~~~~-----------------------~~i~ 197 (656)
T KOG1052|consen 141 FNFGKKLLVVNLSGVTGQFQFFRGGLLEYFKYEILNLNGSGERRIGYWYPRGG-----------------------ENIS 197 (656)
T ss_pred HHHHHhhhhhccccceeEEEecCCCccccceEEEEEecCcCceeEEEecCCCC-----------------------ceee
Confidence 99888876554 456777777888889999999999888888999988752 4688
Q ss_pred cCCCCCCCCCceeccCCCccEEEEecCCCccceeEee----CCCcceeeeeHHHHHHHHHHCCCccceEEeeCCCCC--C
Q 003958 450 WPGQTTQKPRGWVFPNNGRHLRIGVPNRVSFREFVSV----KGSEMTSGFCIDVFTAAINLLPYAVPYKLIPFGDGH--N 523 (784)
Q Consensus 450 W~~~~~~~p~~~c~~~~~~~l~v~~~~~~~~~~~~~~----~~~~~~~G~~~dl~~~l~~~l~f~~~~~~~~~~~~~--~ 523 (784)
||+.....|.++-.+.+|++++|++...+||..+... .++.++.|+|+||++++++.|||++++..++.+.+. +
T Consensus 198 ~~~~~~~~~~~~~~~~~~~~l~v~~~~~~P~~~~~~~~~~~~~~~~~~G~~idll~~l~~~l~f~~~~~~~~~~~g~~~~ 277 (656)
T KOG1052|consen 198 WPGKDYFVPKGWFFPTNGKPLRVGVVTEPPFVDLVEDLAILNGNDRIEGFEIDLLQALAKRLNFSYEIIFVPDGSGSRDP 277 (656)
T ss_pred ccCCcccCcCCccccCCCceEEEEEeccCCceeeeecccccCCCCccceEEehHHHHHHHhCCCceEEEEcCCCCCCCCC
Confidence 9999999999888777899999999999888776663 256799999999999999999999777777765443 5
Q ss_pred CCChhHHHHHHHcCcccEEEeeEEeecCccccceeccccccccEEEEEeccCCccccccccccccHHHHHHHHHHHHHHH
Q 003958 524 NPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPVRKLDSNAWAFLSPFTPMMWGVTAIFFLAVG 603 (784)
Q Consensus 524 ~~~~~g~i~~l~~~~~D~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~~~~~~~~~~~~~pf~~~~W~~i~~~~~~~~ 603 (784)
+|+|+|++++|.+|++|++ ++++++.+|++++|||.||+..+++++++++...+..+.|+.||++++|+++++++++++
T Consensus 278 ~g~~~g~v~~l~~~~advg-~~~tit~~R~~~vdfT~p~~~~~~~i~~~~~~~~~~~~~fl~Pf~~~vW~~i~~~~l~~~ 356 (656)
T KOG1052|consen 278 NGNWDGLVGQLVDGEADVG-ADITITPERSKYVDFTIPYLQFGIVIIVRKPDSRSKLWNFLAPFSPEVWLLILASLLLVG 356 (656)
T ss_pred CCChhHHHHHHhcCccccc-cceEEeecccccEEeccceEeccEEEEEEecCCcccceEEecCCcHHHHHHHHHHHHHHH
Confidence 5799999999999999999 999999999999999999999999999999995555999999999999999999999999
Q ss_pred HHhhheecccCCCCCCCc-----cCCceeehhhhhhhhhccccc-ccccchhhHHHHHHHHHHHHHHhhccccceeeEee
Q 003958 604 AVVWILEHRLNDEFRGPP-----KRQVVTIFWFSFSTMFFAHKE-KTVSALGRLVLIIWLFVVLIINSSYTASLTSILTV 677 (784)
Q Consensus 604 ~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~-~p~~~~~R~~~~~w~~~~lvl~~~Yta~L~s~l~~ 677 (784)
+++|+++|+.+.++ .++ .....+++|+++++++.|+.. .|++.++|++.++||+|+++++++|||+|+|+||+
T Consensus 357 ~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~q~~~~~p~~~~~Rll~~~w~~~~lil~ssYTa~L~a~Lt~ 435 (656)
T KOG1052|consen 357 LLLWILERLSPYEL-PPRQIVTSLFSLLNCLWLTVGSLLQQGSDEIPRSLSTRLLLGAWWLFVLILISSYTANLTAFLTV 435 (656)
T ss_pred HHHHHHhccccccC-CccccceeEeecccchhhhhHHHhccCCCccccchhhhHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 99999999999888 222 122557889999999999865 89999999999999999999999999999999999
Q ss_pred ccccCCCCChHhhhh-CCCceEEeeCchHHHHHHhh---cccCcc-CceeCCCHHHHHHHHhcCCcCCCeeEEEechhhh
Q 003958 678 QKLSSPIKGIDSLRS-SNYPIGYQVNSFARNYLVDE---LNIDES-RLVPLNSPEEYAKALKDGPHKGGVAAVVDDRAYA 752 (784)
Q Consensus 678 ~~~~~~i~~~~dl~~-~~~~i~~~~~~~~~~~~~~~---~~~~~~-~~~~~~~~~~~~~~l~~~~~~~~~~a~~~~~~~~ 752 (784)
+++.++|++++||.+ .+..+|...+++.+.|+++. ...... +...+.+++++++.++++.. +.++++.+...+
T Consensus 436 ~~~~~~i~~~~dL~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~v~~~~~--~~~~~~~~~~~~ 513 (656)
T KOG1052|consen 436 PRLRSPIDSLDDLADQSNIPYGTQRGSFTRIYLEESEDMWAFKVSQRSVPLASPEEGVERVRKGPS--GGYAFASDELYL 513 (656)
T ss_pred cccCCcccCHHHHHHhcCCeEEEEecchHHHHHHHHHHHHhhhccCCCccCCCHHHHHHHHHcCCC--CceEEEeccHHH
Confidence 999999999999995 77789999999999999765 223333 66778999999999999422 368888888888
Q ss_pred HHHHcCC--CCeEEeCCccccceEEEEeeCCCCC
Q 003958 753 ELFLSTR--CEFSIVGQVFTKNGWGFVSIVSSFY 784 (784)
Q Consensus 753 ~~~~~~~--c~l~~~~~~~~~~~~~~~~~k~s~~ 784 (784)
.|....+ |+++++++.+...+|| ++||||||
T Consensus 514 ~~~~~~~~~c~~~~v~~~~~~~~~~-~~~~~Spl 546 (656)
T KOG1052|consen 514 AYLFLRDEICDLTEVGEPFLYKGYG-AFPKGSPL 546 (656)
T ss_pred HHHHhhcCCCceEEeCCcccCCCcc-eecCCCcc
Confidence 8887765 9999999999999999 99999997
No 5
>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=1.8e-48 Score=431.57 Aligned_cols=377 Identities=22% Similarity=0.334 Sum_probs=312.9
Q ss_pred CCCceEEEEEEeecCC----------------------cchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHH
Q 003958 27 GRPSVVNIGALLSFST----------------------NVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFL 84 (784)
Q Consensus 27 ~~~~~i~IG~i~~~~~----------------------~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~ 84 (784)
..+|++.||++||.|. ..|.+...|+.+|+|+||+++++||+++|++.++|+|+++..
T Consensus 8 ~~~Gd~~igglFpvh~~~~~~~~~~~~~~~~~~c~~~~~~g~~~~~am~~AieeIN~~~~lLp~i~Lg~~i~Dtc~~~~~ 87 (510)
T cd06364 8 QKKGDIILGGLFPIHFGVAAKDQDLKSRPESVECIRYNFRGFRWLQAMIFAIEEINNSPTLLPNITLGYRIFDTCNTVSK 87 (510)
T ss_pred eecCCEEEEEEEECcccccccccccccCCCCCcccccChhhHHHHHHHHHHHHHHhCCCccCCCCEEeEEEEccCCchHH
Confidence 5789999999999983 236677899999999999999999999999999999999999
Q ss_pred HHHHHHHHHhc-------------------CceEEEccCchhhHHHHHHhhhcCCccEEecccCCCCCCc-CCCCceEee
Q 003958 85 ALAEALHLMEG-------------------QTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSS-LQFPYFVRT 144 (784)
Q Consensus 85 a~~~~~~li~~-------------------~v~aiiGp~~s~~~~~va~~~~~~~ip~Is~~a~~~~l~~-~~~p~~~r~ 144 (784)
|++.+.+++.+ ++.+||||.+|..+.++++++..++||+|+++++++.+++ ..||+|||+
T Consensus 88 a~~~a~~li~~~~~~~~~~~~~c~~~~~~~~v~aVIG~~sS~~s~ava~~~~~~~IP~IS~~sss~~ls~~~~yp~ffRt 167 (510)
T cd06364 88 ALEATLSFVAQNKIDSLNLDEFCNCSEHIPSTIAVVGATGSGVSTAVANLLGLFYIPQVSYASSSRLLSNKNQFKSFLRT 167 (510)
T ss_pred HHHHHHHHHhcccccccccccccccCCCCCceEEEECCCchhHHHHHHHHhccccccccccccCCcccCCccccCCeeEc
Confidence 99999999864 2469999999999999999999999999999999999998 589999999
Q ss_pred cCChHHHHHHHHHHHHHcCCcEEEEEEEcCCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceE
Q 003958 145 TQSDQYQMAAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRI 224 (784)
Q Consensus 145 ~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~v 224 (784)
.|++..++.++++++++|+|++|++|+.|++||+...+.+++.+++.|+||+..+.++......++..++++++++++|+
T Consensus 168 ~psd~~q~~Ai~~l~~~f~wk~VaiI~~dd~yG~~~~~~~~~~~~~~Gi~I~~~~~i~~~~~~~d~~~~l~klk~~~a~v 247 (510)
T cd06364 168 IPNDEHQATAMADIIEYFRWNWVGTIAADDDYGRPGIEKFREEAEERDICIDFSELISQYSDEEEIQRVVEVIQNSTAKV 247 (510)
T ss_pred CCChHHHHHHHHHHHHHcCCeEEEEEEecCcchHHHHHHHHHHHHHCCcEEEEEEEeCCCCCHHHHHHHHHHHHhcCCeE
Confidence 99999999999999999999999999999999999999999999999999998887765346789999999999999999
Q ss_pred EEEeccCCcHHHHHHHHHHcCCCCCCeEEEecCccccccccCCCCCCCccccceeeEEEeeecCCchhHHHHHH------
Q 003958 225 IVVHTHYNRGPVVFHVAQYLGMLGTGYVWIATSWLSTALDTNSPFPSDVMDDIQGVLTLRTYTPDSVLKRKFIS------ 298 (784)
Q Consensus 225 Ivl~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~f~~------ 298 (784)
||+++...++..++++++++|+. +++||+++.|........ ....+.+.|++++.+.....+++++|++
T Consensus 248 Vvl~~~~~~~~~ll~qa~~~g~~--~~iwI~s~~w~~~~~~~~---~~~~~~~gg~lg~~~~~~~i~~f~~~l~~l~p~~ 322 (510)
T cd06364 248 IVVFSSGPDLEPLIKEIVRRNIT--GKIWLASEAWASSSLIAM---PEYFDVMGGTIGFALKAGQIPGFREFLQKVHPKK 322 (510)
T ss_pred EEEEeCcHHHHHHHHHHHHhCCC--CcEEEEEchhhccccccc---CCccceeeEEEEEEECCCcCccHHHHHHhCCccc
Confidence 99999999999999999999986 469999987764322211 2345678899999888776666655553
Q ss_pred ---------HHHhhcc-----------------------------------CCCCCCCCC----------CChhHHHHhh
Q 003958 299 ---------RWRNLTD-----------------------------------AKTPNGYIG----------LNAYGFYAYD 324 (784)
Q Consensus 299 ---------~~~~~~~-----------------------------------~~~~~~~~~----------~~~~~~~~YD 324 (784)
.|+..++ .|.+.+... ...+++.+||
T Consensus 323 ~~~~~~~~~~we~~f~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~~~~~~~~~~~~~~~~~~~~~~~v~~ 402 (510)
T cd06364 323 SSHNGFAKEFWEETFNCYLEDSPKNALPVDTFLGHEESGDDSENGSTAFRPLCTGDENIASVETPYLDYTHLRISYNVYL 402 (510)
T ss_pred CCCChHHHHHHHHhcCCCCCCCcccccccccccccccccccccccccccCCCCCChhhhcccCCccccccchhhHHHHHH
Confidence 4554443 122111110 1245678999
Q ss_pred HHHHHHHHHHHHhhcCCcc-ccccCCccccccCCcccccccccCCchHHHHHHHhccccceee-eEEEecCCCCcCCcEE
Q 003958 325 TVWLLARAINSFFKQGGNL-SFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANMTGTAG-PARFNSHGDLINPAYE 402 (784)
Q Consensus 325 Av~~~a~Al~~~~~~~~~~-~~~~~~~~~~~~g~~~~~~~~~~~~~~~l~~~l~~~~f~g~tG-~v~Fd~~g~~~~~~~~ 402 (784)
||+++|+|||+++.|..+. +.. ...|...... ++++|.++|++++|+|.+| .|.||+||+. ...|+
T Consensus 403 AVyAvAhaLh~~~~c~~~~~~~~----------~~~c~~~~~~-~~~~l~~~L~~v~F~~~~g~~v~Fd~~Gd~-~~~Yd 470 (510)
T cd06364 403 AVYSIAHALQDIYTCTPGKGLFT----------NGSCADIKKV-EAWQVLKHLRHLNFTDNMGEQVRFDEGGDL-VGNYS 470 (510)
T ss_pred HHHHHHHHHHHHhcCCCCCCCcc----------CCCCCCCCCC-CHHHHHHHHHhcEEecCCCCEEEEecCCCC-cccee
Confidence 9999999999999885321 110 1246554444 4899999999999999988 5999999995 78999
Q ss_pred EEEeec---c---ceEEEEEecCC
Q 003958 403 IINVIG---T---GYRRIGYWSNY 420 (784)
Q Consensus 403 I~~~~~---~---~~~~VG~w~~~ 420 (784)
|+||+. + .+++||.|++.
T Consensus 471 I~n~q~~~~~~~~~~v~VG~~~~~ 494 (510)
T cd06364 471 IINWHLSPEDGSVVFKEVGYYNVY 494 (510)
T ss_pred EEEeeecCCCCcEEEEEEEEEcCC
Confidence 999994 2 26899999753
No 6
>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=1.4e-48 Score=428.27 Aligned_cols=369 Identities=22% Similarity=0.363 Sum_probs=309.8
Q ss_pred ceEEEEEEeecCC-------------cchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHh--
Q 003958 30 SVVNIGALLSFST-------------NVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLME-- 94 (784)
Q Consensus 30 ~~i~IG~i~~~~~-------------~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~-- 94 (784)
|++.||++||.|. ..|.+...||.+|||+||+++++|||++|++.++|+|+++..|++.+.+++.
T Consensus 1 Gd~~igglFp~h~~~~~~~~C~~~~~~~g~~~~~Am~~AIe~IN~~~~lLp~~~Lg~~i~Dtc~~~~~a~~~~~~~i~~~ 80 (458)
T cd06375 1 GDLVLGGLFPVHEKGEGTEECGRINEDRGIQRLEAMLFAIDRINNDPRILPGIKLGVHILDTCSRDTYALEQSLEFVRAS 80 (458)
T ss_pred CCEEEEEEEEeeeCCCCCCCCcCccccchHHHHHHHHHHHHHHhCCCCCCCCceeccEEEecCCCcHHHHHHHHHHHhhh
Confidence 5899999999982 2477889999999999999999999999999999999999999999988873
Q ss_pred -----------------------cCceEEEccCchhhHHHHHHhhhcCCccEEecccCCCCCCc-CCCCceEeecCChHH
Q 003958 95 -----------------------GQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSS-LQFPYFVRTTQSDQY 150 (784)
Q Consensus 95 -----------------------~~v~aiiGp~~s~~~~~va~~~~~~~ip~Is~~a~~~~l~~-~~~p~~~r~~ps~~~ 150 (784)
++|.+||||.+|..+.+++++++.++||+|+++++++.|++ .+||+|||+.|++..
T Consensus 81 ~~~~~~~~~~C~~~~~~~~~~~~~~V~aVIG~~~S~~s~ava~~~~~~~IP~Is~~sts~~Ls~~~~~~~ffRt~psd~~ 160 (458)
T cd06375 81 LTKVDTSEYECPDGSYAVQENSPLAIAGVIGGSYSSVSIQVANLLRLFQIPQISYASTSAKLSDKSRYDYFARTVPPDFY 160 (458)
T ss_pred hhcccccccccccCCccccccCCCCeEEEEcCCCchHHHHHHHHhhhccccceeeccCChhhcccccCCCeEEecCCcHH
Confidence 27999999999999999999999999999999999999998 579999999999999
Q ss_pred HHHHHHHHHHHcCCcEEEEEEEcCCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhc-CCceEEEEec
Q 003958 151 QMAAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVAL-TESRIIVVHT 229 (784)
Q Consensus 151 ~~~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~-~~~~vIvl~~ 229 (784)
++.|+++++++|+|++|++||+|++||+...+.+++.+++.|+||+..+.++...+..|+..+++++++ .++|+||+++
T Consensus 161 qa~ai~~ll~~~~W~~Vaii~~~~~yG~~~~~~~~~~~~~~gi~i~~~~~i~~~~~~~d~~~~l~~l~~~~~a~vVvl~~ 240 (458)
T cd06375 161 QAKAMAEILRFFNWTYVSTVASEGDYGETGIEAFEQEARLRNICIATSEKVGRSADRKSYDSVIRKLLQKPNARVVVLFT 240 (458)
T ss_pred HHHHHHHHHHHCCCeEEEEEEeCchHHHHHHHHHHHHHHHCCeeEEEEEEecCCCCHHHHHHHHHHHhccCCCEEEEEec
Confidence 999999999999999999999999999999999999999999999998888755567899999999875 6999999999
Q ss_pred cCCcHHHHHHHHHHcCCCCCCeEEEecCccccccccCCCCCCCccccceeeEEEeeecCCchhHHHHHH-----------
Q 003958 230 HYNRGPVVFHVAQYLGMLGTGYVWIATSWLSTALDTNSPFPSDVMDDIQGVLTLRTYTPDSVLKRKFIS----------- 298 (784)
Q Consensus 230 ~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~f~~----------- 298 (784)
..+++..++++|+++|++ +.||+++.|....... .......+|++++.+.....+++++|++
T Consensus 241 ~~~~~~~ll~~a~~~g~~---~~wigs~~~~~~~~~~----~~~~~~~~G~i~~~~~~~~i~~f~~yl~~l~p~~~~~n~ 313 (458)
T cd06375 241 RSEDARELLAAAKRLNAS---FTWVASDGWGAQESIV----KGSEDVAEGAITIELASHPIPDFDRYFQSLTPETNTRNP 313 (458)
T ss_pred ChHHHHHHHHHHHHcCCc---EEEEEeccccccchhh----hccchhhceEEEEEeccccchhHHHHHHhCCcCcCCCCc
Confidence 999999999999999975 7899999876432211 1233578899999998887777776664
Q ss_pred ----HHHhhcc-----------CCCCCCCC------CCChhHHHHhhHHHHHHHHHHHHhhcCCccccccCCccccccCC
Q 003958 299 ----RWRNLTD-----------AKTPNGYI------GLNAYGFYAYDTVWLLARAINSFFKQGGNLSFSKDSRLSDIQGH 357 (784)
Q Consensus 299 ----~~~~~~~-----------~~~~~~~~------~~~~~~~~~YDAv~~~a~Al~~~~~~~~~~~~~~~~~~~~~~g~ 357 (784)
.|+..|+ .|++.+.. .....+.++||||+++|||||++++++.+.. +
T Consensus 314 w~~e~w~~~f~c~~~~~~~~~~~C~~~~~~~~~~~~~~~~~~~~v~~AVyA~AhaLh~~l~~~c~~~------------~ 381 (458)
T cd06375 314 WFKDFWEQKFQCSLQNRDCANTTTNDKERLLDKVNYEQESKIMFVVNAVYAMAHALHNMQRDLCPNT------------T 381 (458)
T ss_pred HHHHHHHHHcCCCCCCCCccCCCCCchhcccccCcccccchHHHHHHHHHHHHHHHHHHHHhcCCCC------------C
Confidence 4655553 13221111 1245788999999999999999996532211 1
Q ss_pred cccccccccCCchHHH-HHHHhcccc-----ceee-eEEEecCCCCcCCcEEEEEeec--c--c--eEEEEEecC
Q 003958 358 LRLDSLRIFNGGNLLR-DSILQANMT-----GTAG-PARFNSHGDLINPAYEIINVIG--T--G--YRRIGYWSN 419 (784)
Q Consensus 358 ~~~~~~~~~~~~~~l~-~~l~~~~f~-----g~tG-~v~Fd~~g~~~~~~~~I~~~~~--~--~--~~~VG~w~~ 419 (784)
..|.....+ ++++|. ++|++++|+ |.+| +|.||+||+. ...|+|+||+. + . +++||.|+.
T Consensus 382 ~~c~~~~~~-~~~~l~~~~L~~v~F~~~~~~~~~g~~v~Fd~nGd~-~~~YdI~n~q~~~~~~~~~~~~VG~w~~ 454 (458)
T cd06375 382 KLCDAMKPL-DGKKLYKEYLLNVSFTAPFRPDLADSEVKFDSQGDG-LGRYNIFNYQRTGNSYGYRYVGVGAWAN 454 (458)
T ss_pred CCCCCCCCC-CHHHHHHHHHHhccccccccCCCCCCeeEECCCCCC-CcceEEEEEEEcCCCCcEEEEEEEEEec
Confidence 246554445 589999 599999999 9988 5999999994 78999999993 3 2 689999964
No 7
>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=1.7e-48 Score=431.81 Aligned_cols=379 Identities=21% Similarity=0.337 Sum_probs=310.8
Q ss_pred CCCceEEEEEEeecCC-----------------cchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHH
Q 003958 27 GRPSVVNIGALLSFST-----------------NVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEA 89 (784)
Q Consensus 27 ~~~~~i~IG~i~~~~~-----------------~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~ 89 (784)
..+|++.||++||.|. ..|.+...|+.+|+|+||++++||||++|++.++|+|+++..|++.+
T Consensus 5 ~~~Gd~~igglfpvh~~~~~~~~~~~~c~~~~~~~g~~~~~Am~~Aie~IN~~~~lLp~~~Lg~~i~Dtc~~~~~a~~~~ 84 (472)
T cd06374 5 RMDGDIIIGALFSVHHQPAAEKVPERKCGEIREQYGIQRVEAMFHTLDRINADPVLLPNITLGCEIRDSCWHSSVALEQS 84 (472)
T ss_pred EecCCEEEEEEEecccccccCCCCCCCccccCcchhHHHHHHHHHHHHHHhCCcccCCCceeccEEEEcCCCchHHHHHH
Confidence 5689999999999983 13667789999999999999999999999999999999999999999
Q ss_pred HHHHh--------------------------cCceEEEccCchhhHHHHHHhhhcCCccEEecccCCCCCCc-CCCCceE
Q 003958 90 LHLME--------------------------GQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSS-LQFPYFV 142 (784)
Q Consensus 90 ~~li~--------------------------~~v~aiiGp~~s~~~~~va~~~~~~~ip~Is~~a~~~~l~~-~~~p~~~ 142 (784)
.+++. ++|.+||||.+|..+.+++++++.+++|+|+++++++.+++ ..||++|
T Consensus 85 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~aiiGp~~S~~~~ava~~~~~~~iP~Is~~ats~~ls~~~~~p~~f 164 (472)
T cd06374 85 IEFIRDSLISIRDEKDGVNPDGQSPGPNKSKKPIVGVIGPGSSSVAIQVQNLLQLFNIPQIAYSATSIDLSDKTLFKYFL 164 (472)
T ss_pred HHHHhhcccccccccccccccCCCcccccCCCCeEEEECCCcchHHHHHHHHhhhhcccccccccCchhhcccccCCceE
Confidence 99885 27999999999999999999999999999999999999998 4799999
Q ss_pred eecCChHHHHHHHHHHHHHcCCcEEEEEEEcCCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcC--
Q 003958 143 RTTQSDQYQMAAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALT-- 220 (784)
Q Consensus 143 r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~-- 220 (784)
|+.|++..++.++++++++|+|++|++|+++++||+...+.+++.+++.|+||+..+.++......++..++++|++.
T Consensus 165 Rt~p~d~~~~~al~~l~~~~~W~~Vaii~~~~~yg~~~~~~~~~~~~~~gi~i~~~~~i~~~~~~~d~~~~l~~lk~~~~ 244 (472)
T cd06374 165 RVVPSDTLQARAMLDIVKRYNWTYVSAVHTEGNYGESGMEAFKELAAHEGLCIAHSDKIYSNAGEQSFDRLLRKLRSRLP 244 (472)
T ss_pred EcCCChHHHHHHHHHHHHHCCCcEEEEEEecchHHHHHHHHHHHHHHHCCeeEEEEEEecCCCchHHHHHHHHHHHhcCC
Confidence 999999999999999999999999999999999999999999999999999999888776445678999999999965
Q ss_pred CceEEEEeccCCcHHHHHHHHHHcCCCCCCeEEEecCccccccccCCCCCCCccccceeeEEEeeecCCchhHHHHH---
Q 003958 221 ESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIATSWLSTALDTNSPFPSDVMDDIQGVLTLRTYTPDSVLKRKFI--- 297 (784)
Q Consensus 221 ~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~f~--- 297 (784)
+++||++++....++.++++++++|+. .+++||+++.|....... ....+..+|.+++.+..+..+.+++|+
T Consensus 245 da~vvv~~~~~~~~~~~l~~a~~~g~~-~~~~wi~s~~~~~~~~~~----~~~~~~~~G~l~~~~~~~~~~~F~~~l~~l 319 (472)
T cd06374 245 KARVVVCFCEGMTVRGLLMAMRRLGVG-GEFQLIGSDGWADRDDVV----EGYEEEAEGGITIKLQSPEVPSFDDYYLKL 319 (472)
T ss_pred CcEEEEEEechHHHHHHHHHHHHhcCC-CceEEEEecccccchHhh----hcchhhhheeEEEEecCCCCccHHHHHHhC
Confidence 566777777777899999999999986 468999998776432111 223466799999998887777776654
Q ss_pred ------------HHHHhhccC---------------CCCCCCC----CCChhHHHHhhHHHHHHHHHHHHhhcCCccccc
Q 003958 298 ------------SRWRNLTDA---------------KTPNGYI----GLNAYGFYAYDTVWLLARAINSFFKQGGNLSFS 346 (784)
Q Consensus 298 ------------~~~~~~~~~---------------~~~~~~~----~~~~~~~~~YDAv~~~a~Al~~~~~~~~~~~~~ 346 (784)
+.|+..+.. |++.+.. ....++.++|||||++|+|||+++.+.....
T Consensus 320 ~~~~~~~~~~~~~~w~~~f~c~~~~~~~~~~~~~~~c~~~~~~~~~~~~~~~~~~vyDAVyaiA~ALh~~~~~~~~~~-- 397 (472)
T cd06374 320 RPETNTRNPWFREFWQHRFQCRLPGHPQENPNYIKICTGNESLDEQYVQDSKMGFVINAIYAMAHGLHNMHQDLCPGH-- 397 (472)
T ss_pred CcccCCCChHHHHHHHHhcCCCcCCccCcCCccCCCCCCcccccccccccceeHHHHHHHHHHHHHHHHHHHhhCCCC--
Confidence 456655531 2111111 1124566899999999999999986542111
Q ss_pred cCCccccccCCcccccccccCCchHHHHHHHhccccceee-eEEEecCCCCcCCcEEEEEeec-----cceEEEEEecCC
Q 003958 347 KDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANMTGTAG-PARFNSHGDLINPAYEIINVIG-----TGYRRIGYWSNY 420 (784)
Q Consensus 347 ~~~~~~~~~g~~~~~~~~~~~~~~~l~~~l~~~~f~g~tG-~v~Fd~~g~~~~~~~~I~~~~~-----~~~~~VG~w~~~ 420 (784)
...|..... .++++|.++|++++|+|++| +|.||++|++ ...|+|+|++. ..+++||.|++.
T Consensus 398 ----------~~~c~~~~~-~~~~~l~~~l~~v~F~g~tG~~v~Fd~~G~~-~~~ydI~n~~~~~~~~~~~~~VG~w~~~ 465 (472)
T cd06374 398 ----------VGLCDAMKP-IDGRKLLEYLLKTSFSGVSGEEVYFDENGDS-PGRYDIMNLQYTEDLRFDYINVGSWHEG 465 (472)
T ss_pred ----------CCCCcCCCC-CCHHHHHHHHHhCcccCCCCCeEEEcCCCCC-CCceEEEEEEECCCCCEEEEEEEEEeCC
Confidence 113443332 36999999999999999999 6999999997 56899999994 247999999753
Q ss_pred CCCce
Q 003958 421 SGLSV 425 (784)
Q Consensus 421 ~~l~~ 425 (784)
+|.+
T Consensus 466 -~l~~ 469 (472)
T cd06374 466 -DLGI 469 (472)
T ss_pred -cccc
Confidence 4543
No 8
>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=1.8e-48 Score=429.21 Aligned_cols=371 Identities=19% Similarity=0.291 Sum_probs=306.2
Q ss_pred ceEEEEEEeecCC----------------------cchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHH
Q 003958 30 SVVNIGALLSFST----------------------NVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALA 87 (784)
Q Consensus 30 ~~i~IG~i~~~~~----------------------~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~ 87 (784)
|+|.||++||.|. ..|.+...|+.+|+|+||++..+|||++|++.++|+||++..|++
T Consensus 1 Gdi~igglf~vh~~~~~~~~~~~~~~~~~~c~~~~~~~~~~~~Am~~Ai~~IN~~~~lLp~~~Lg~~i~dtc~~~~~a~~ 80 (469)
T cd06365 1 GDLVIGGFFPLYTLSGPFETDDWHPFSADLDFRLLLKNYQHVLALLFAIEEINKNPHLLPNISLGFHIYNVLHSDRKALE 80 (469)
T ss_pred CCeeEeceEEEEEeccccccccccCccccccccccchhhHHHHHHHHHHHHHhCCCCCCCCceEEEEEECCCCccHHHHH
Confidence 5799999999972 125567899999999999999999999999999999999999999
Q ss_pred HHHHHHh--------------cCceEEEccCchhhHHHHHHhhhcCCccEEecccCCCCCCc-CCCCceEeecCChHHHH
Q 003958 88 EALHLME--------------GQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSS-LQFPYFVRTTQSDQYQM 152 (784)
Q Consensus 88 ~~~~li~--------------~~v~aiiGp~~s~~~~~va~~~~~~~ip~Is~~a~~~~l~~-~~~p~~~r~~ps~~~~~ 152 (784)
.+.+++. +++++||||.+|..+.+++++++.++||+|+++++++.+++ .+||||||+.|++..++
T Consensus 81 ~~~~~~~~~~~~~~~~~C~~~~~vvavIG~~~S~~s~~va~i~~~~~IP~Is~~sts~~lsd~~~yp~ffRt~psd~~q~ 160 (469)
T cd06365 81 SSLMWLSGEGETIPNYSCRRQRKSVAVIGGPSWALSATIATLLGLYKFPQLTYGPFDPLLSDRVQFPSLYQMAPKDTSLP 160 (469)
T ss_pred HHHHHHhCCCcccCCccCCCCCceEEEEcCCccHHHHHHHHHhhhhcccceeeccCCccccchhhCCcceEecCCchhHH
Confidence 9999985 36999999999999999999999999999999999999998 57999999999999999
Q ss_pred HHHHHHHHHcCCcEEEEEEEcCCCcchhHHHHHHHHhccCcEEEEeeccCCCCC--hhHHHHHHHHhhcCCceEEEEecc
Q 003958 153 AAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEAT--EDEITDLLVKVALTESRIIVVHTH 230 (784)
Q Consensus 153 ~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~--~~d~~~~l~~l~~~~~~vIvl~~~ 230 (784)
.|+++++++|+|++|++|+.|++||+...+.+.+.+++.|+||+..+.++.... ..++..++++|+++++|+||+++.
T Consensus 161 ~ai~~li~~f~W~~Vaiv~~d~~yg~~~~~~~~~~~~~~gi~I~~~~~i~~~~~~~~~~~~~~l~~i~~~~arvIvl~~~ 240 (469)
T cd06365 161 LGMVSLMLHFSWTWVGLVISDDDRGEQFLSDLREEMQRNGICLAFVEKIPVNMQLYLTRAEKYYNQIMTSSAKVIIIYGD 240 (469)
T ss_pred HHHHHHHHhcCCeEEEEEEecChhHHHHHHHHHHHHHHCCeEEEEEEEecCCchhhHHHHHHHHHHhhcCCCeEEEEEcC
Confidence 999999999999999999999999999999999999999999999888875432 247889999999999999999999
Q ss_pred CCcHHHHHHHHHHcCCCCCCeEEEecCccccccccCCCCCCCccccceeeEEEeeecCCchhHHHHHHH-----------
Q 003958 231 YNRGPVVFHVAQYLGMLGTGYVWIATSWLSTALDTNSPFPSDVMDDIQGVLTLRTYTPDSVLKRKFISR----------- 299 (784)
Q Consensus 231 ~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~f~~~----------- 299 (784)
.+.+..++.++.+.+. .+++||+++.|....... ....+.++|+++++++.+..+++++|.++
T Consensus 241 ~~~~~~l~~~~~~~~~--~~~~wi~s~~w~~~~~~~----~~~~~~~~G~lg~~~~~~~~~~f~~fl~~l~~~~~~~npw 314 (469)
T cd06365 241 TDSLLEVSFRLWQYLL--IGKVWITTSQWDVTTSPK----DFTLNSFHGTLIFSHHHSEIPGFKDFLQTVNPSKYPEDIF 314 (469)
T ss_pred cHHHHHHHHHHHHhcc--CceEEEeecccccccccc----ccccceeeEEEEEEeccCcCcchHHHhhccCcccCCCccH
Confidence 8888777766666543 468999998776433221 23456789999999998888888777654
Q ss_pred ----HHhhcc------------CCCCCCCCC----------CChhHHHHhhHHHHHHHHHHHHhhcCCccccccCCcccc
Q 003958 300 ----WRNLTD------------AKTPNGYIG----------LNAYGFYAYDTVWLLARAINSFFKQGGNLSFSKDSRLSD 353 (784)
Q Consensus 300 ----~~~~~~------------~~~~~~~~~----------~~~~~~~~YDAv~~~a~Al~~~~~~~~~~~~~~~~~~~~ 353 (784)
|+..|+ .|+...... ....+.++||||+++|+|||++++|+....
T Consensus 315 ~~efwe~~f~c~~~~~~~~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~v~dAVya~AhALh~~l~c~~~~~--------- 385 (469)
T cd06365 315 LEKLWWIYFNCSLSKSSCKTLKNCLSNASLEWLPLHYFDMAMSEESYNVYNAVYAVAHALHEMLLQQVETQ--------- 385 (469)
T ss_pred HHhhHhHhcCcccCcCCccccCCCCCCccccccccccccchhhhhHHHHHHHHHHHHHHHHHHHHhhccCC---------
Confidence 444442 133222111 234678899999999999999998854210
Q ss_pred ccCCcccccccccCCchHHHHHHHhccccceeee-EEEecCCCCcCCcEEEEEeec--c---ceEEEEEecCC
Q 003958 354 IQGHLRLDSLRIFNGGNLLRDSILQANMTGTAGP-ARFNSHGDLINPAYEIINVIG--T---GYRRIGYWSNY 420 (784)
Q Consensus 354 ~~g~~~~~~~~~~~~~~~l~~~l~~~~f~g~tG~-v~Fd~~g~~~~~~~~I~~~~~--~---~~~~VG~w~~~ 420 (784)
...+|.. ... ++++|.++|++++|+|.+|. |.||+|||+ ...|+|+|++. + .+++||.|+..
T Consensus 386 --~~~~~~~-~~~-~~~~l~~~l~~v~F~~~~g~~v~Fd~nGd~-~~~YdI~n~q~~~~~~~~~~~VG~~~~~ 453 (469)
T cd06365 386 --SENNGKR-LIF-LPWQLHSFLKNIQFKNPAGDEVNLNQKRKL-DTEYDILNYWNFPQGLGLKVKVGEFSPQ 453 (469)
T ss_pred --CcCCCCC-CCc-cHHHHHHHHHhccccCCCCCEEEecCCCCc-CceeeEEEEEECCCCCEEEEEEEEEeCC
Confidence 0123332 233 58899999999999999995 999999995 77999999983 2 36999999753
No 9
>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=5.3e-48 Score=427.66 Aligned_cols=374 Identities=22% Similarity=0.358 Sum_probs=310.0
Q ss_pred ceEEEEEEeecCC-------------cchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHh--
Q 003958 30 SVVNIGALLSFST-------------NVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLME-- 94 (784)
Q Consensus 30 ~~i~IG~i~~~~~-------------~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~-- 94 (784)
|++.||++||+|. ..|.....|+++|+|+||+++++|||++|++.++|+|+++..|+..+.+++.
T Consensus 1 Gd~~igglfp~h~~~~~~~~c~~~~~~~G~~~~~a~~~Aie~IN~~~~iLpg~~L~~~i~D~~~~~~~a~~~a~~li~~~ 80 (452)
T cd06362 1 GDIILGGLFPVHSKGTGGEPCGEIKEQRGIQRLEAMLFALDEINNDPTLLPGITLGAHILDTCSRDTYALEQSLEFVRAS 80 (452)
T ss_pred CCeEEEEEEecccCCCCCCCCcCccccchHHHHHHHHHHHHHhhCCCCCCCCCeeCcEEEEeCCCchHHHHHHHHHHhhh
Confidence 5799999999983 2466678999999999999999999999999999999999999999988884
Q ss_pred ---------------------cCceEEEccCchhhHHHHHHhhhcCCccEEecccCCCCCCc-CCCCceEeecCChHHHH
Q 003958 95 ---------------------GQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSS-LQFPYFVRTTQSDQYQM 152 (784)
Q Consensus 95 ---------------------~~v~aiiGp~~s~~~~~va~~~~~~~ip~Is~~a~~~~l~~-~~~p~~~r~~ps~~~~~ 152 (784)
++|.+||||.+|.++.++++++..+++|+|+++++++.+++ .+||++||+.|++..++
T Consensus 81 ~~~~~~~~~~~~~~~~~~~~~~~v~aviG~~~S~~~~av~~~~~~~~ip~Is~~sts~~ls~~~~~~~~fR~~p~d~~~~ 160 (452)
T cd06362 81 LTKIDDCVYCDGGSPPPNNSPKPVAGVIGASYSSVSIQVANLLRLFKIPQISYASTSPELSDKTRYDYFSRTVPPDSFQA 160 (452)
T ss_pred hhcCCccccccCCCcccccCCCCeEEEECCCCCchHHHHHHHhccccCcccccccCchhhccccccCCEEEecCChHHHH
Confidence 38999999999999999999999999999999999999988 58999999999999999
Q ss_pred HHHHHHHHHcCCcEEEEEEEcCCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhc-CCceEEEEeccC
Q 003958 153 AAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVAL-TESRIIVVHTHY 231 (784)
Q Consensus 153 ~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~-~~~~vIvl~~~~ 231 (784)
.++++++++++|++|++|+++++||+...+.+++.+++.|+||+..+.++...+..|+..++++|++ .++|+||+++..
T Consensus 161 ~a~~~~l~~~~w~~vaii~~~~~~G~~~~~~~~~~~~~~gi~i~~~~~~~~~~~~~d~~~~l~~l~~~~~a~viil~~~~ 240 (452)
T cd06362 161 QAMVDIVKAFNWTYVSTVASEGNYGEKGIEAFEKLAAERGICIAGSEKIPSSATEEEFDNIIRKLLSKPNARVVVLFCRE 240 (452)
T ss_pred HHHHHHHHHCCCcEEEEEEeCCHHHHHHHHHHHHHHHHCCeeEEEEEEcCCCCCHHHHHHHHHHHhhcCCCeEEEEEcCh
Confidence 9999999999999999999999999999999999999999999988888754567899999999987 579999999999
Q ss_pred CcHHHHHHHHHHcCCCCCCeEEEecCccccccccCCCCCCCccccceeeEEEeeecCCchhHHHHH--------------
Q 003958 232 NRGPVVFHVAQYLGMLGTGYVWIATSWLSTALDTNSPFPSDVMDDIQGVLTLRTYTPDSVLKRKFI-------------- 297 (784)
Q Consensus 232 ~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~f~-------------- 297 (784)
.++..++++|+++|++ .+++||+++.|....... .......+|++++.+.....+.+++|+
T Consensus 241 ~~~~~~~~~a~~~g~~-~~~~~i~~~~~~~~~~~~----~~~~~~~~g~~~~~~~~~~i~~f~~~l~~l~~~~~~~~~~~ 315 (452)
T cd06362 241 DDIRGLLAAAKRLNAE-GHFQWIASDGWGARNSVV----EGLEDVAEGAITIELQSAEVPGFDEYFLSLTPENNSRNPWF 315 (452)
T ss_pred HHHHHHHHHHHHcCCc-CceEEEEeccccccchhh----cccccccceEEEEEecccccccHHHHhhhCCcCcCCCChHH
Confidence 9999999999999997 468999998775432211 234467888888887776655555443
Q ss_pred -HHHHhhcc-------------CCCCCCC----CCCChhHHHHhhHHHHHHHHHHHHhhcCCccccccCCccccccCCcc
Q 003958 298 -SRWRNLTD-------------AKTPNGY----IGLNAYGFYAYDTVWLLARAINSFFKQGGNLSFSKDSRLSDIQGHLR 359 (784)
Q Consensus 298 -~~~~~~~~-------------~~~~~~~----~~~~~~~~~~YDAv~~~a~Al~~~~~~~~~~~~~~~~~~~~~~g~~~ 359 (784)
+.|+..+. .|+.... .....+++++||||+++|+|||+++.++.... ...
T Consensus 316 ~~~w~~~~~c~~~~~~~~~~~~~c~~~~~~~~~~~~~~~~~~vyDAV~a~A~AL~~~l~~~~~~~------------~~~ 383 (452)
T cd06362 316 REFWEQKFNCKLTGNGSTKDNTCCTERILLLSNYEQESKVQFVIDAVYAMAHALHNMHRDLCPGT------------TGL 383 (452)
T ss_pred HHHHHHhcCCCcCCCCccccCCCCccccccccccccccchhHHHHHHHHHHHHHHHHHHhhCCCC------------CCC
Confidence 34444332 1111111 12345789999999999999999986642211 112
Q ss_pred cccccccCCchHHHHHHHhccccceee-eEEEecCCCCcCCcEEEEEeec----cceEEEEEecCCCC
Q 003958 360 LDSLRIFNGGNLLRDSILQANMTGTAG-PARFNSHGDLINPAYEIINVIG----TGYRRIGYWSNYSG 422 (784)
Q Consensus 360 ~~~~~~~~~~~~l~~~l~~~~f~g~tG-~v~Fd~~g~~~~~~~~I~~~~~----~~~~~VG~w~~~~~ 422 (784)
|.... +.++++|.++|++++|+|++| .|.||++|++ ...|+|++++. ..+++||.|++..|
T Consensus 384 c~~~~-~~~~~~l~~~l~~v~f~g~tg~~v~Fd~~G~~-~~~y~I~~~~~~~~~~~~~~VG~w~~~~~ 449 (452)
T cd06362 384 CDAMK-PIDGRKLLFYLRNVSFSGLAGGPVRFDANGDG-PGRYDIFNYQRTNGKYDYVKVGSWKGELS 449 (452)
T ss_pred CcCcc-CCCHHHHHHHHHhCCcCCCCCceEEECCCCCC-CCceEEEEEEEcCCceEEEEEEEEecccc
Confidence 44332 457999999999999999998 7999999997 56899999984 35899999987654
No 10
>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=2.9e-47 Score=421.26 Aligned_cols=371 Identities=22% Similarity=0.369 Sum_probs=301.7
Q ss_pred ceEEEEEEeecC--C-----------cchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHH----H
Q 003958 30 SVVNIGALLSFS--T-----------NVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALH----L 92 (784)
Q Consensus 30 ~~i~IG~i~~~~--~-----------~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~----l 92 (784)
|+|+||++||.| . ..|.....|+++|+|+||+++++|||++|+++++|+|+++..+.+.+.. +
T Consensus 1 Gdi~igglfp~h~~~~~~~~c~~~~~~~g~~~~~a~~~Aie~IN~~~~iLpg~~L~~~i~D~~~~~~~~~~~a~~~~~~l 80 (463)
T cd06376 1 GDITLGGLFPVHARGPAGVPCGDIKKENGIHRLEAMLYALDQINSDPDLLPNVTLGARILDTCSRDTYALEQSLTFVQAL 80 (463)
T ss_pred CCeEEEEEEeeeeCCCCCCCccccccchhHHHHHHHHHHHHHhhCCCCCCCCceEccEEEeccCCcHHHHHHHHHHHhhh
Confidence 589999999998 1 1466678999999999999999999999999999999987655554443 3
Q ss_pred Hh-------------------cCceEEEccCchhhHHHHHHhhhcCCccEEecccCCCCCCc-CCCCceEeecCChHHHH
Q 003958 93 ME-------------------GQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSS-LQFPYFVRTTQSDQYQM 152 (784)
Q Consensus 93 i~-------------------~~v~aiiGp~~s~~~~~va~~~~~~~ip~Is~~a~~~~l~~-~~~p~~~r~~ps~~~~~ 152 (784)
++ ++|.|||||.+|..+.+++++++.++||+|+++++++.+++ ..||+|||+.|++..++
T Consensus 81 ~~~~~~~~~C~~~~~~~~~~~~~V~aviG~~~S~~t~ava~i~~~~~iP~Is~~ats~~ls~~~~~~~ffR~~p~d~~~~ 160 (463)
T cd06376 81 IQKDTSDVRCTNGEPPVFVKPEKVVGVIGASASSVSIMVANILRLFQIPQISYASTAPELSDDRRYDFFSRVVPPDSFQA 160 (463)
T ss_pred hhcccccCcCCCCCccccCCCCCeEEEECCCCchHHHHHHHHhccccCcccccccCChhhcccccCCceEEccCCHHHHH
Confidence 32 37999999999999999999999999999999999999988 57999999999999999
Q ss_pred HHHHHHHHHcCCcEEEEEEEcCCCcchhHHHHHHHHhcc-CcEEEEeeccCCCCChhHHHHHHHHhhc-CCceEEEEecc
Q 003958 153 AAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAK-RCRISFKAPLSVEATEDEITDLLVKVAL-TESRIIVVHTH 230 (784)
Q Consensus 153 ~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~~l~~~-gi~v~~~~~~~~~~~~~d~~~~l~~l~~-~~~~vIvl~~~ 230 (784)
+++++++++|+|++|++|+.+++||....+.+.+.+++. ++||...+.++......|+..++++|++ .++|+||+.+.
T Consensus 161 ~ai~~~i~~~~w~~Vaii~~~~~yg~~~~~~~~~~~~~~g~~~v~~~~~i~~~~~~~d~~~~l~~ik~~~~~~vIvl~~~ 240 (463)
T cd06376 161 QAMVDIVKALGWNYVSTLASEGNYGESGVEAFTQISREAGGVCIAQSIKIPREPRPGEFDKIIKRLLETPNARAVIIFAN 240 (463)
T ss_pred HHHHHHHHHcCCeEEEEEEeCChHHHHHHHHHHHHHHHcCCceEEEEEecCCCCCHHHHHHHHHHHhccCCCeEEEEecC
Confidence 999999999999999999999999999999999999887 4788776666555567899999999987 79999999999
Q ss_pred CCcHHHHHHHHHHcCCCCCCeEEEecCccccccccCCCCCCCccccceeeEEEeeecCCchhHHHHHH------------
Q 003958 231 YNRGPVVFHVAQYLGMLGTGYVWIATSWLSTALDTNSPFPSDVMDDIQGVLTLRTYTPDSVLKRKFIS------------ 298 (784)
Q Consensus 231 ~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~f~~------------ 298 (784)
.+++..++++|+++|+.+ .|+||+++.|....... ........|.+++.+.....+.+++|..
T Consensus 241 ~~~~~~ll~~a~~~~~~g-~~~wig~d~~~~~~~~~----~~~~~~~~G~~~~~~~~~~~~~F~~~~~~l~~~~~~~~~~ 315 (463)
T cd06376 241 EDDIRRVLEAAKRANQVG-HFLWVGSDSWGAKISPI----LQQEDVAEGAITILPKRASIEGFDAYFTSRTLENNRRNVW 315 (463)
T ss_pred hHHHHHHHHHHHhcCCcC-ceEEEEecccccccccc----ccCcceeeeEEEEEeccccchhHHHHHHhCCcccCCCCcH
Confidence 999999999999999875 59999999876432221 1123568899999888777776666554
Q ss_pred ---HHHhhcc---------------CCCCCCCC------CCChhHHHHhhHHHHHHHHHHHHhhcCCccccccCCccccc
Q 003958 299 ---RWRNLTD---------------AKTPNGYI------GLNAYGFYAYDTVWLLARAINSFFKQGGNLSFSKDSRLSDI 354 (784)
Q Consensus 299 ---~~~~~~~---------------~~~~~~~~------~~~~~~~~~YDAv~~~a~Al~~~~~~~~~~~~~~~~~~~~~ 354 (784)
.|+..|+ .|.+.+.. .....++++||||+++|+|||++++++...+
T Consensus 316 ~~~~w~~~f~c~~~~~~~~~~~~~~~C~~~~~~~~~~~~~~~~~~~~v~dAVyaiA~ALh~l~~~~c~~~---------- 385 (463)
T cd06376 316 FAEFWEENFNCKLTISGSKKEDTDRKCTGQERIGRDSTYEQEGKVQFVIDAVYAMAHALHSMHKDLCPGY---------- 385 (463)
T ss_pred HHHHHHHhCCCcccCCCCccccccCcCcchhhccccCcccccchhHHHHHHHHHHHHHHHHHHHhhCCCC----------
Confidence 5665543 12221111 1133688999999999999999986532110
Q ss_pred cCCcccccccccCCchHHHHHHHhccccceee-eEEEecCCCCcCCcEEEEEeec-----cceEEEEEecC
Q 003958 355 QGHLRLDSLRIFNGGNLLRDSILQANMTGTAG-PARFNSHGDLINPAYEIINVIG-----TGYRRIGYWSN 419 (784)
Q Consensus 355 ~g~~~~~~~~~~~~~~~l~~~l~~~~f~g~tG-~v~Fd~~g~~~~~~~~I~~~~~-----~~~~~VG~w~~ 419 (784)
...|.... +.++++|.++|++++|+|.+| +|.||++|++ ...|+|.+++. .++++||.|++
T Consensus 386 --~~~C~~~~-~~~~~~l~~~L~~v~F~g~tg~~v~Fd~~G~~-~~~Ydi~n~q~~~~~~~~~~~VG~w~~ 452 (463)
T cd06376 386 --TGVCPEME-PADGKKLLKYIRAVNFNGSAGTPVMFNENGDA-PGRYDIFQYQITNTSSPGYRLIGQWTD 452 (463)
T ss_pred --CCCCccCC-CCCHHHHHHHHHhCCccCCCCCeEEeCCCCCC-CCceEEEEEEecCCCceeEEEEEEECC
Confidence 11355433 446999999999999999999 6999999996 56799999983 34799999975
No 11
>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=3.7e-47 Score=409.88 Aligned_cols=346 Identities=24% Similarity=0.290 Sum_probs=292.3
Q ss_pred EEEEEeecCCc---------------------chhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHH
Q 003958 33 NIGALLSFSTN---------------------VGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALH 91 (784)
Q Consensus 33 ~IG~i~~~~~~---------------------~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~ 91 (784)
.||++||.|.. .|.+...|+.+|+|+||+++ +|||++|+++++|+|+++..|+.++.+
T Consensus 1 ~lgglf~vh~~~~~~~~~~~~~~~~~c~~~~~~g~~~~~am~~AieeIN~~~-~Lpg~~L~~~i~Dt~~~~~~a~~~a~~ 79 (403)
T cd06361 1 IIGGLFAIHEAMLSVEDTPSRPQIQECVGFEIKGFLQTLAMIHAIEMINNST-LLLGVTLGYEIYDTCSEVTTAMAAVLR 79 (403)
T ss_pred CEEEEEECcccccccccccCCCCCCcccccChhHHHHHHHHHHHHHHHhCCC-CCCCCEEceEEEeCCCChHHHHHHHHH
Confidence 37899998742 26678899999999999999 668999999999999999999999999
Q ss_pred HHhc-------------------CceEEEccCchhhHHHHHHhhhcCCccEEecccCCCCCCc-CCCCceEeecCChHHH
Q 003958 92 LMEG-------------------QTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSS-LQFPYFVRTTQSDQYQ 151 (784)
Q Consensus 92 li~~-------------------~v~aiiGp~~s~~~~~va~~~~~~~ip~Is~~a~~~~l~~-~~~p~~~r~~ps~~~~ 151 (784)
|+++ +|.+||||.+|..+.+++++++.++||+|+|+++++.|++ .+||||||+.|++..|
T Consensus 80 li~~~~~~~~~~~~~c~~~~~~~~V~aVIG~~~S~~s~ava~v~~~~~IP~IS~~ats~~Ls~~~~~~~ffRt~p~D~~q 159 (403)
T cd06361 80 FLSKFNCSRSTVEFKCDYSQYVPRIKAVIGAGYSEISMAVSRMLNLQLIPQVSYASTAEILSDKIRFPSFLRTVPSDFYQ 159 (403)
T ss_pred HHhhcccccccccccccCCCCCCCeEEEECCCcchHHHHHHHHhccCCcceEecCcCCcccCCcccCCCeeECCCchHhH
Confidence 9873 7999999999999999999999999999999999999998 6899999999999999
Q ss_pred HHHHHHHHHHcCCcEEEEEEEcCCCcchhHHHHHHHHhccCcEEEEeeccCCCCC-----hhHHHHHHHHhhcCCceEEE
Q 003958 152 MAAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEAT-----EDEITDLLVKVALTESRIIV 226 (784)
Q Consensus 152 ~~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~-----~~d~~~~l~~l~~~~~~vIv 226 (784)
++++++++++|+|+||++|++|++||+...+.+++.+++.|+||+..+.++.... ..++..+++.++++++|+||
T Consensus 160 a~ai~~li~~~~w~~Vaii~~~d~yG~~~~~~f~~~~~~~GicIa~~e~~~~~~~~~~~~~~~~~~~~~~ik~~~a~vVv 239 (403)
T cd06361 160 TKAMAHLIKKSGWNWVGIIITDDDYGRSALETFIIQAEANGVCIAFKEILPASLSDNTKLNRIIRTTEKIIEENKVNVIV 239 (403)
T ss_pred HHHHHHHHHHcCCcEEEEEEecCchHHHHHHHHHHHHHHCCeEEEEEEEecCccCcchhHHHHHHHHHHHHhcCCCeEEE
Confidence 9999999999999999999999999999999999999999999999988875321 14666777778899999999
Q ss_pred EeccCCcHHHHHHHHHHcCCCCCCeEEEecCccccccccCCCCCCCccccceeeEEEeeecCCchhHHHHHHHHHhhccC
Q 003958 227 VHTHYNRGPVVFHVAQYLGMLGTGYVWIATSWLSTALDTNSPFPSDVMDDIQGVLTLRTYTPDSVLKRKFISRWRNLTDA 306 (784)
Q Consensus 227 l~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~f~~~~~~~~~~ 306 (784)
+.+...++..++++|+++|+ +++||+++.|........ ........|.+++.+..+..+++ .+.+++.+
T Consensus 240 v~~~~~~~~~l~~~a~~~g~---~~~wigs~~w~~~~~~~~---~~~~~~~~g~ig~~~~~~~~~~F---~~~~~~~~-- 308 (403)
T cd06361 240 VFARQFHVFLLFNKAIERNI---NKVWIASDNWSTAKKILT---DPNVKKIGKVVGFTFKSGNISSF---HQFLKNLL-- 308 (403)
T ss_pred EEeChHHHHHHHHHHHHhCC---CeEEEEECcccCcccccc---CCcccccceEEEEEecCCccchH---HHHHHHhh--
Confidence 99999999999999999998 589999998865322211 12235677899998877555554 44455432
Q ss_pred CCCCCCCCCChhHHHHhhHHHHHHHHHHHHhhcCCccccccCCccccccCCcccccccccCCchHHHHHHHhccccceee
Q 003958 307 KTPNGYIGLNAYGFYAYDTVWLLARAINSFFKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANMTGTAG 386 (784)
Q Consensus 307 ~~~~~~~~~~~~~~~~YDAv~~~a~Al~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~l~~~l~~~~f~g~tG 386 (784)
...+||||+++|+|||++..+. .|...... ++++|+++|++++|+|.+|
T Consensus 309 ------------~~~v~~AVyaiA~Al~~~~~~~------------------~c~~~~~~-~~~~l~~~L~~~~f~g~~~ 357 (403)
T cd06361 309 ------------IHSIQLAVFALAHAIRDLCQER------------------QCQNPNAF-QPWELLGQLKNVTFEDGGN 357 (403)
T ss_pred ------------HHHHHHHHHHHHHHHHHhccCC------------------CCCCCCCc-CHHHHHHHHheeEEecCCc
Confidence 3468999999999999974431 24332223 5899999999999999988
Q ss_pred eEEEecCCCCcCCcEEEEEeeccc----eEEEEEecCCCC
Q 003958 387 PARFNSHGDLINPAYEIINVIGTG----YRRIGYWSNYSG 422 (784)
Q Consensus 387 ~v~Fd~~g~~~~~~~~I~~~~~~~----~~~VG~w~~~~~ 422 (784)
++.||++||. ...|+|.++++++ +++||.|++...
T Consensus 358 ~v~Fd~~gd~-~~~y~I~~~~~~~~~~~~~~vg~~~~~~~ 396 (403)
T cd06361 358 MYHFDANGDL-NLGYDVVLWKEDNGHMTVTIMAEYDPQND 396 (403)
T ss_pred eEEECCCCCC-CcceEEEEeEecCCcEEEEEEEEEeCCCC
Confidence 9999999995 7889999999632 699999988753
No 12
>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=4.6e-45 Score=394.27 Aligned_cols=370 Identities=20% Similarity=0.282 Sum_probs=305.6
Q ss_pred eEEEEEEee-cC---CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCC-CHHHHHHHHHHHHhcCceEEEccCc
Q 003958 31 VVNIGALLS-FS---TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNH-SGFLALAEALHLMEGQTVAIIGPQD 105 (784)
Q Consensus 31 ~i~IG~i~~-~~---~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~-~~~~a~~~~~~li~~~v~aiiGp~~ 105 (784)
.|+||++++ ++ +..|.....|+++|+++||+++++||+..|.+.+.+.++ ++..+...+|+++.++|.|||||.+
T Consensus 2 ~i~IG~i~~~~tg~~~~~g~~~~~a~~~Av~~IN~~~~il~~~~l~~~~~~~~~~d~~~~~~~~~~~l~~~V~AiiGp~~ 81 (384)
T cd06393 2 VIRIGGIFEYLDGPNNQVMSAEELAFRFSANIINRNRTLLPNTTLTYDIQRIHFHDSFEATKKACDQLALGVVAIFGPSQ 81 (384)
T ss_pred eeeEEEeecCCcccccccCcHHHHHHHHHHHHhcCCCccCCCceEEEEEEecccccchhHHHHhhcccccCcEEEECCCC
Confidence 589999999 55 455778899999999999999999999999999998665 6667788888887789999999999
Q ss_pred hhhHHHHHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcCCCcchhHHHHH
Q 003958 106 AVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDDDHGRNGIAALG 185 (784)
Q Consensus 106 s~~~~~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~ 185 (784)
|..+.+++++++.++||+|+++++++.++++. ++++|+.|++..++.++++++++|+|++|++||+++. |....+.+.
T Consensus 82 S~~~~av~~i~~~~~iP~Is~~~t~~~lt~~~-~~~~~~~~~~~~~~~a~~~~~~~~~wk~vaily~~~~-g~~~l~~~~ 159 (384)
T cd06393 82 GSCTNAVQSICNALEVPHIQLRWKHHPLDNKD-TFYVNLYPDYASLSHAILDLVQYLKWRSATVVYDDST-GLIRLQELI 159 (384)
T ss_pred hHHHHHHHHHHhccCCCeEeccCCCcccCccc-eeEEEeccCHHHHHHHHHHHHHHcCCcEEEEEEeCch-hHHHHHHHH
Confidence 99999999999999999999999988887643 5678888998889999999999999999999997654 666667788
Q ss_pred HHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHcCCCCCCeEEEecCcccccccc
Q 003958 186 DTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIATSWLSTALDT 265 (784)
Q Consensus 186 ~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~ 265 (784)
+.+++.|++|+.. .++ .+..|++.+|++||..++++||+.+..+++..+++||+++||+.+.|+|+.++......+.
T Consensus 160 ~~~~~~g~~v~~~-~~~--~~~~d~~~~L~~ik~~~~~~iil~~~~~~~~~il~qa~~~gm~~~~~~~~~~~~~~~~~~~ 236 (384)
T cd06393 160 MAPSRYNIRLKIR-QLP--TDSDDARPLLKEMKRGREFRIIFDCSHQMAAQILKQAMAMGMMTEYYHFIFTTLDLYALDL 236 (384)
T ss_pred HhhhccCceEEEE-ECC--CCchHHHHHHHHHhhcCceEEEEECCHHHHHHHHHHHHHhccccCceEEEEccCccccccc
Confidence 8888899999864 355 3568999999999999999999999999999999999999999999999988764433332
Q ss_pred CCCCCCCccccceeeEEEeeecCCchhHHHHHHHHHhh-ccCCCCCC----CCCCChhHHHHhhHHHHHHHHHHHHhhcC
Q 003958 266 NSPFPSDVMDDIQGVLTLRTYTPDSVLKRKFISRWRNL-TDAKTPNG----YIGLNAYGFYAYDTVWLLARAINSFFKQG 340 (784)
Q Consensus 266 ~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~f~~~~~~~-~~~~~~~~----~~~~~~~~~~~YDAv~~~a~Al~~~~~~~ 340 (784)
+........+.++....++.+.+++|.++|+.+ ++..+..+ ...++.+++.+||||+++++|++++....
T Consensus 237 -----~~~~~~~~~it~~~~~~~~~~~~~~f~~~~~~~~~~~~p~~~~~~~~~~~~~~aal~yDav~~~a~A~~~~~~~~ 311 (384)
T cd06393 237 -----EPYRYSGVNLTGFRILNVDNPHVSSIVEKWSMERLQAAPKPETGLLDGVMMTDAALLYDAVHMVSVCYQRAPQMT 311 (384)
T ss_pred -----hhhhcCcceEEEEEecCCCcHHHHHHHHHHHhhhhccccccccccccccccchhHHhhhhHHHHHHHHhhhhhcC
Confidence 111111222577777788889999999999854 54211000 01235679999999999999999753221
Q ss_pred CccccccCCccccccCCcccccccccCCchHHHHHHHhccccceeeeEEEec-CCCCcCCcEEEEEeeccceEEEEEecC
Q 003958 341 GNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANMTGTAGPARFNS-HGDLINPAYEIINVIGTGYRRIGYWSN 419 (784)
Q Consensus 341 ~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~l~~~l~~~~f~g~tG~v~Fd~-~g~~~~~~~~I~~~~~~~~~~VG~w~~ 419 (784)
.+ ++.|.....|.+|..|.++|++++|+|+||+++||+ +|.|.+..++|+++.++++++||.|++
T Consensus 312 ~~--------------~~~c~~~~~w~~G~~i~~~l~~~~~~GltG~i~Fd~~~g~r~~~~~~i~~~~~~g~~~vg~W~~ 377 (384)
T cd06393 312 VN--------------SLQCHRHKAWRFGGRFMNFIKEAQWEGLTGRIVFNKTSGLRTDFDLDIISLKEDGLEKVGVWNP 377 (384)
T ss_pred CC--------------CCCCCCCCCCcccHHHHHHHhheeecccccceEecCCCCeeeeeEEEEEEecCCcceeeEEEcC
Confidence 11 346777779999999999999999999999999996 678899999999999999999999999
Q ss_pred CCCCc
Q 003958 420 YSGLS 424 (784)
Q Consensus 420 ~~~l~ 424 (784)
..||.
T Consensus 378 ~~g~~ 382 (384)
T cd06393 378 NTGLN 382 (384)
T ss_pred CCCcC
Confidence 88753
No 13
>KOG1056 consensus Glutamate-gated metabotropic ion channel receptor subunit GRM2 and related subunits, G-protein coupled receptor superfamily [Inorganic ion transport and metabolism; Signal transduction mechanisms]
Probab=100.00 E-value=6e-45 Score=398.97 Aligned_cols=398 Identities=23% Similarity=0.412 Sum_probs=337.2
Q ss_pred cCCCceEEEEEEeecCC-------------cchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHH
Q 003958 26 SGRPSVVNIGALLSFST-------------NVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHL 92 (784)
Q Consensus 26 ~~~~~~i~IG~i~~~~~-------------~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~l 92 (784)
...+++|.||++||.|. ..|.+...||.+|+|+||+ +.+|||.||++.++|+|+.+..|+++..++
T Consensus 26 ~~~~gdi~lgglFpvh~k~~~~~~cg~~~~~~gi~r~eAml~al~~iN~-~~lLp~~kLG~~i~DTCs~~t~aleqsl~F 104 (878)
T KOG1056|consen 26 ARIPGDIILGGLFPVHEKGGGAPQCGRIREPRGIQRLEAMLFALDEINN-PDLLPNIKLGARILDTCSRSTYALEQSLSF 104 (878)
T ss_pred ccCCCCeEEcceeeecccCCCCCcccccccchhHHHHHHHHHHHHHhcC-cccCCCceeeeeEeeccCCcHHHHHhhHHH
Confidence 46789999999999972 2356778999999999999 999999999999999999999999999998
Q ss_pred Hhc-----------------CceEEEccCchhhHHHHHHhhhcCCccEEecccCCCCCCc-CCCCceEeecCChHHHHHH
Q 003958 93 MEG-----------------QTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSS-LQFPYFVRTTQSDQYQMAA 154 (784)
Q Consensus 93 i~~-----------------~v~aiiGp~~s~~~~~va~~~~~~~ip~Is~~a~~~~l~~-~~~p~~~r~~ps~~~~~~a 154 (784)
+.+ .|.++||+..|+.+.+++.+..-++||||+|+++++.|+| ++|++|.|++|+|..|++|
T Consensus 105 v~~~~~~~~~e~~c~~g~sp~v~~VIG~s~Ssvsi~vanlLrlf~ipQisyaSts~~LSdk~ry~~F~RtVP~D~~Qa~A 184 (878)
T KOG1056|consen 105 VRASLTSDDSEVRCPDGYSPPVVAVIGPSYSSVSIAVANLLRLFLIPQISYASTSPDLSDKTRYDYFLRTVPSDVFQAQA 184 (878)
T ss_pred HHhcccCCCcceecCCCCCCceeEEeCCCCchHHHHHHHHHHhhcCceeccccCCcccccchhhhceeeecCChHHHHHH
Confidence 752 5889999999999999999999999999999999999999 6999999999999999999
Q ss_pred HHHHHHHcCCcEEEEEEEcCCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhc-CCceEEEEeccCCc
Q 003958 155 IAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVAL-TESRIIVVHTHYNR 233 (784)
Q Consensus 155 i~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~-~~~~vIvl~~~~~~ 233 (784)
|++++++|+|++|..++++++||+.+.+.|++..+++|+||+..+.++....+.++...++++.+ .++++||+++..++
T Consensus 185 m~~il~~f~W~yVstv~s~~dYGE~Gieaf~~~a~~~~iCIa~s~ki~~~~~~~~~~~~l~kl~~~~~a~vvV~F~~~~~ 264 (878)
T KOG1056|consen 185 MVDILKKFNWNYVSTVASEGDYGESGIEAFKEEAAERGICIAFSEKIYQLSIEQEFDCVLRKLLETPNARVVVVFCRGED 264 (878)
T ss_pred HHHHHHHhCeeEeeehhcCccchhhhHHHHHHhHHhcCceEEehhhcccccchhHHHHHHHHHhhcCCCeEEEEecCcch
Confidence 99999999999999999999999999999999999999999999877766678889999999887 89999999999999
Q ss_pred HHHHHHHHHHcCCCCCCeEEEecCccccccccCCCCCCCccccceeeEEEeeecCCchhHHHHHHH--------------
Q 003958 234 GPVVFHVAQYLGMLGTGYVWIATSWLSTALDTNSPFPSDVMDDIQGVLTLRTYTPDSVLKRKFISR-------------- 299 (784)
Q Consensus 234 ~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~f~~~-------------- 299 (784)
++.++++|.++++++ .++||+++.|....+.. .......+|.+++....+..+.+++|.+.
T Consensus 265 ~r~~~~aa~~~n~~g-~~~wiaSd~W~~~~~~~----~~~e~~a~g~i~i~l~~~~v~~F~~y~~s~~p~nn~~n~w~~e 339 (878)
T KOG1056|consen 265 ARRLLKAARRANLTG-EFLWIASDGWASQNSPT----EAPEREAEGAITIKLASPQVPGFDRYFQSLHPENNRRNPWFAE 339 (878)
T ss_pred HHHHHHHHHHhCCCc-ceEEEecchhhccCChh----hhhhhhhceeEEEEecCCcchhHHHHHHhcCccccccCcccch
Confidence 999999999999876 68999999887644332 12234788999999998888877776654
Q ss_pred -HHhhcc---------------CCCCCCCC------CCChhHHHHhhHHHHHHHHHHHHhhcCCccccccCCccccccCC
Q 003958 300 -WRNLTD---------------AKTPNGYI------GLNAYGFYAYDTVWLLARAINSFFKQGGNLSFSKDSRLSDIQGH 357 (784)
Q Consensus 300 -~~~~~~---------------~~~~~~~~------~~~~~~~~~YDAv~~~a~Al~~~~~~~~~~~~~~~~~~~~~~g~ 357 (784)
|++.|. .|++.+.. ........++|||+++|+|||.+.++-.... .
T Consensus 340 ~w~~~f~C~l~~~~~~~~~~~~~Ct~~e~~~~~~~~~q~~k~~~Vi~aVya~A~aLh~m~~~lc~~~------------~ 407 (878)
T KOG1056|consen 340 FWEDKFNCSLPNSAFKNENLIRLCTAVERITLDSAYEQDSKVQFVIDAVYAMAHALHNMHQDLCPGT------------S 407 (878)
T ss_pred hhhhcccCCCCcccccchhhhhhcccchhhccccchhhhcccccHHHHHHHHHHHHHHHHHhhcCCc------------c
Confidence 444432 13333210 1123456799999999999999986632111 3
Q ss_pred cccccccccCCchHHHHHHHhccccceeeeEEEecCCCCcCCcEEEEEeec-c---ceEEEEEecCCCCCceecCccccC
Q 003958 358 LRLDSLRIFNGGNLLRDSILQANMTGTAGPARFNSHGDLINPAYEIINVIG-T---GYRRIGYWSNYSGLSVVRPETLYS 433 (784)
Q Consensus 358 ~~~~~~~~~~~~~~l~~~l~~~~f~g~tG~v~Fd~~g~~~~~~~~I~~~~~-~---~~~~VG~w~~~~~l~~~~~~~~~~ 433 (784)
..|...... +|+.|.+++++++|.+..|.+.||++|| ....|+|++++. + .+..||+|+....
T Consensus 408 ~~C~~m~~~-dg~~L~~~l~~vnF~~~~~~v~Fd~~gD-~~~~y~I~~~~~~~~~~~y~~vg~w~~~~~----------- 474 (878)
T KOG1056|consen 408 GLCSAMKAI-DGSLLLKYLLNVNFTGPAGSVRFDENGD-GPGRYDILNYQLTNGSYTYKEVGYWSEGLS----------- 474 (878)
T ss_pred ccCcCcccc-CHHHHHhhhheeEEecCCCceeecCCCC-CccceeEEEeeccCCCccceeeeeeccccc-----------
Confidence 357766665 6999999999999999999999999999 589999999984 2 5799999987642
Q ss_pred CCCCCCCCccccceeecCCCCCCCCCceec
Q 003958 434 KPPNRSSSNQRLYSVIWPGQTTQKPRGWVF 463 (784)
Q Consensus 434 ~~~~~~~~~~~~~~i~W~~~~~~~p~~~c~ 463 (784)
.+...+.|.++..++|.|.|.
T Consensus 475 ---------l~i~~~~w~~~~~~v~~S~CS 495 (878)
T KOG1056|consen 475 ---------LNIEDLDWTTKPSGVPKSVCS 495 (878)
T ss_pred ---------ccceeeeeccCCCCCcccccc
Confidence 234678999999999999994
No 14
>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=6.4e-44 Score=385.32 Aligned_cols=336 Identities=25% Similarity=0.363 Sum_probs=274.1
Q ss_pred CceEEEEEEeecCCcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHH-HHHHHHHHHhcCceEEEc-cC-c
Q 003958 29 PSVVNIGALLSFSTNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFL-ALAEALHLMEGQTVAIIG-PQ-D 105 (784)
Q Consensus 29 ~~~i~IG~i~~~~~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~-a~~~~~~li~~~v~aiiG-p~-~ 105 (784)
+.+|+||+++|. .....|+++|++++|++.+++++.+++-...+.++++.. +...+.+|++++|.+|+| +. +
T Consensus 17 ~~~i~IG~i~~~-----~~~~~~~~~Ai~~~N~~~~~~~~~~l~~~~i~~~~~~~~~a~~~~~~Li~~~V~aii~~~~~s 91 (377)
T cd06379 17 PKTVNIGAVLSN-----KKHEQEFKEAVNAANVERHGSRKIKLNATTITHDPNPIQTALSVCEQLISNQVYAVIVSHPPT 91 (377)
T ss_pred CcEEEEeEEecc-----hhHHHHHHHHHHHHhhhhcCCcceeeccceEeecCChhhHHHHHHHHHhhcceEEEEEeCCCC
Confidence 568999999984 357899999999999965543443333322222345555 444445678889999974 33 3
Q ss_pred hh---hHHHHHHhhhcCCccEEecccCCCCCCcC-CCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcCCCcchhH
Q 003958 106 AV---TSHVVSHVANELQVPLLSFSATDPTLSSL-QFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDDDHGRNGI 181 (784)
Q Consensus 106 s~---~~~~va~~~~~~~ip~Is~~a~~~~l~~~-~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~~~g~~~~ 181 (784)
+. .+.+++.+++.++||+|+++++++.++++ .||++||+.|++..++.++++++++++|++|++||++++||+...
T Consensus 92 s~~~~~~~~v~~~~~~~~iP~Is~~a~~~~ls~~~~~~~~~R~~psd~~~~~a~~~~l~~~~w~~vaii~~~~~~g~~~~ 171 (377)
T cd06379 92 SNDHLTPTSVSYTAGFYRIPVVGISTRDSIFSDKNIHLSFLRTVPPYSHQADVWLEMLRSFKWNKVILLVSDDHEGRAAQ 171 (377)
T ss_pred CcccccHHHHHHHhhCCCCcEEecccCCccccCccccccEEEecCCHHHHHHHHHHHHHHcCCeEEEEEEEcCcchhHHH
Confidence 32 46678889999999999999999988874 699999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhccCc----EEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHcCCCCCCeEEEecC
Q 003958 182 AALGDTLAAKRC----RISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIATS 257 (784)
Q Consensus 182 ~~l~~~l~~~gi----~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~ 257 (784)
+.+++.+++.|+ ||+..+.++ .+..|+..+++++++.++|+|++++..+++..++++++++|+++++|+||+++
T Consensus 172 ~~~~~~~~~~g~~~~~~v~~~~~~~--~~~~d~~~~l~~ik~~~~~vIvl~~~~~~~~~l~~qa~~~g~~~~~~~wi~t~ 249 (377)
T cd06379 172 KRFETLLEEREIEFKIKVEKVVEFE--PGEKNVTSLLQEAKELTSRVILLSASEDDAAVIYRNAGMLNMTGEGYVWIVSE 249 (377)
T ss_pred HHHHHHHHhcCCccceeeeEEEecC--CchhhHHHHHHHHhhcCCeEEEEEcCHHHHHHHHHHHHHcCCCCCCEEEEEec
Confidence 999999999999 888877776 45688999999999999999999999999999999999999999999999998
Q ss_pred ccccccccCCCCCCCccccceeeEEEeeecCCchhHHHHHHHHHhhccCCCCCCCCCCChhHHHHhhHHHHHHHHHHHHh
Q 003958 258 WLSTALDTNSPFPSDVMDDIQGVLTLRTYTPDSVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTVWLLARAINSFF 337 (784)
Q Consensus 258 ~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~~~a~Al~~~~ 337 (784)
.+... .....|++++++..+ ..+++.+||||+++|+|+++++
T Consensus 250 ~~~~~-----------~~~~~g~~g~~~~~~---------------------------~~~~~~~yDAV~~~A~Al~~~~ 291 (377)
T cd06379 250 QAGAA-----------RNAPDGVLGLQLING---------------------------KNESSHIRDAVAVLASAIQELF 291 (377)
T ss_pred ccccc-----------ccCCCceEEEEECCC---------------------------CCHHHHHHHHHHHHHHHHHHHH
Confidence 76321 134568888876532 1246789999999999999987
Q ss_pred hcCCccccccCCccccccCCcccccc-cccCCchHHHHHHHhccccceeeeEEEecCCCCcCCcEEEEEeeccceEEEEE
Q 003958 338 KQGGNLSFSKDSRLSDIQGHLRLDSL-RIFNGGNLLRDSILQANMTGTAGPARFNSHGDLINPAYEIINVIGTGYRRIGY 416 (784)
Q Consensus 338 ~~~~~~~~~~~~~~~~~~g~~~~~~~-~~~~~~~~l~~~l~~~~f~g~tG~v~Fd~~g~~~~~~~~I~~~~~~~~~~VG~ 416 (784)
++... +.. +..|... ..|.+|..+.++|++++|+|++|++.||++|+|....|+|+++++.++++||.
T Consensus 292 ~~~~~-~~~----------~~~c~~~~~~~~~g~~l~~~l~~v~f~G~tg~i~Fd~~Gd~~~~~~~I~~~~~~~~~~VG~ 360 (377)
T cd06379 292 EKENI-TEP----------PRECVGNTVIWETGPLFKRALMSSKYPGETGRVEFNDDGDRKFANYDIMNIQNRKLVQVGL 360 (377)
T ss_pred cCCCC-CCC----------CccccCCCCCCcchHHHHHHHHhCCcCCccCceEECCCCCccCccEEEEEecCCCceEeeE
Confidence 63221 100 1245433 25888999999999999999999999999999877899999999999999999
Q ss_pred ecCC
Q 003958 417 WSNY 420 (784)
Q Consensus 417 w~~~ 420 (784)
|++.
T Consensus 361 w~~~ 364 (377)
T cd06379 361 YNGD 364 (377)
T ss_pred EcCc
Confidence 9874
No 15
>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=9.3e-44 Score=375.86 Aligned_cols=366 Identities=18% Similarity=0.285 Sum_probs=286.3
Q ss_pred EEEEEeecCCcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEE-ecCCCCHHHHHHHHHHHHhcCceEEEccCchhhHHH
Q 003958 33 NIGALLSFSTNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQM-QDCNHSGFLALAEALHLMEGQTVAIIGPQDAVTSHV 111 (784)
Q Consensus 33 ~IG~i~~~~~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~-~D~~~~~~~a~~~~~~li~~~v~aiiGp~~s~~~~~ 111 (784)
.||+||+..+ ...+.|+++|++++|.+..++++.+|.+.+ +++.+|+..+..++|+++++||.||+||.++.++..
T Consensus 1 ~iG~if~~~~---~~~~~af~~Av~~~N~~~~~l~~~~L~~~~~~~~~~d~F~~~~~ac~l~~~gV~AI~Gp~s~~~a~~ 77 (400)
T cd06392 1 HIGAIFEENA---AKDDRVFQLAVSDLSLNDDILQSEKITYSIKSIEANNPFQAVQEACDLMTQGILALVTSTGCASANA 77 (400)
T ss_pred CeeeccCCCc---hHHHHHHHHHHHHhccCccccCCceEEEEEEecCCCChhHHHHHHHHHHhcCeEEEECCCchhHHHH
Confidence 3899999765 246899999999999999999999999998 899999999999999999999999999999999999
Q ss_pred HHHhhhcCCccEEeccc-----------CCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcCCCcchh
Q 003958 112 VSHVANELQVPLLSFSA-----------TDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDDDHGRNG 180 (784)
Q Consensus 112 va~~~~~~~ip~Is~~a-----------~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~~~g~~~ 180 (784)
++.+|+..+||+|++++ +++.++..+||++.| |+ ..+.+|+++++++|+|++|++|| |++||...
T Consensus 78 v~sic~~l~VP~is~~~~~~~~~~~~~~~~p~~~~~~~~~~lr--p~-~~~~~Ai~dlV~~~~W~~v~~iY-D~d~gl~~ 153 (400)
T cd06392 78 LQSLTDAMHIPHLFVQRNSGGSPRTACHLNPSPEGEEYTLAAR--PP-VRLNDVMLKLVTELRWQKFIVFY-DSEYDIRG 153 (400)
T ss_pred HHHHhccCcCCcEeecccccccccccccCCCCcCcCceeEEec--Cc-hHHHHHHHHHHHhCCCcEEEEEE-ECcccHHH
Confidence 99999999999999866 234444445555554 55 46788999999999999999999 78999999
Q ss_pred HHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHH--------HhhcCCceEEEEeccCCcHHHHHHHHHHcCCCCCCeE
Q 003958 181 IAALGDTLAAKRCRISFKAPLSVEATEDEITDLLV--------KVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYV 252 (784)
Q Consensus 181 ~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~--------~l~~~~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~ 252 (784)
.+.+.+.+.+.+..|.... +... ...++.+.++ +++... ++||+.|+++.+..++++|.++||+..+|+
T Consensus 154 lq~L~~~~~~~~~~I~~~~-v~~~-~~~~~~~~l~~~~~~~L~~~~~~~-r~iVv~~s~~~~~~il~qA~~lgM~~~~y~ 230 (400)
T cd06392 154 LQSFLDQASRLGLDVSLQK-VDRN-ISRVFTNLFTTMKTEELNRYRDTL-RRAILLLSPRGAQTFINEAVETNLASKDSH 230 (400)
T ss_pred HHHHHHHHhhcCceEEEEE-cccC-cchhhhhHHHHHHHhhhhhccccc-eEEEEEcCcHHHHHHHHHHHHhCcccCCeE
Confidence 9999999999998888655 2211 1112333333 344334 888999999999999999999999999999
Q ss_pred EEecCccccccccCCCCCCCccccce-eeEEEeeecCCchhHHHHH----HHHHhhccCCCCCCCCCCChhHHHHhhHHH
Q 003958 253 WIATSWLSTALDTNSPFPSDVMDDIQ-GVLTLRTYTPDSVLKRKFI----SRWRNLTDAKTPNGYIGLNAYGFYAYDTVW 327 (784)
Q Consensus 253 wi~~~~~~~~~~~~~~~~~~~~~~~~-g~~~~~~~~~~~~~~~~f~----~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~ 327 (784)
||++++.....+. .+...... ++.+++.+.+......+|. .+|++...+........+..+++++||||+
T Consensus 231 wI~t~~~~~~~dl-----~~~~~g~~~niT~~r~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~l~~~aalayDaV~ 305 (400)
T cd06392 231 WVFVNEEISDTEI-----LELVHSALGRMTVIRQIFPLSKDNNQRCIRNNHRISSLLCDPQEGYLQMLQVSNLYLYDSVL 305 (400)
T ss_pred EEEecCCcccccH-----HHHhcccccceeeEEEecCCcHHHHHHHHHHHHHHHhhhcccccccccccchhHHHHHHHHH
Confidence 9999987664433 12222332 4556888877666555553 566544321111111135678999999999
Q ss_pred HHHHHHHHHhhcCCccccccCCccccccCCccc--ccccccCCchHHHHHHHhccccceeeeEEEecCCCCcCCcEEEEE
Q 003958 328 LLARAINSFFKQGGNLSFSKDSRLSDIQGHLRL--DSLRIFNGGNLLRDSILQANMTGTAGPARFNSHGDLINPAYEIIN 405 (784)
Q Consensus 328 ~~a~Al~~~~~~~~~~~~~~~~~~~~~~g~~~~--~~~~~~~~~~~l~~~l~~~~f~g~tG~v~Fd~~g~~~~~~~~I~~ 405 (784)
++|+|++++++........ ...| .+...|..|..|+++|++++|+|+||+|+||++|+|.++.|+|++
T Consensus 306 ~~A~Al~~ll~~~~~~~~~----------~l~C~~~~~~~w~~G~~ll~~ik~v~f~GLTG~I~F~~~G~r~~~~ldIi~ 375 (400)
T cd06392 306 MLANAFHRKLEDRKWHSMA----------SLNCIRKSTKPWNGGRSMLETIKKGHITGLTGVMEFKEDGANPHVQFEILG 375 (400)
T ss_pred HHHHHHHHHhhccccCCCC----------CCccCCCCCCCCCChHHHHHHHHhCCCccCccceeECCCCCCcCCceEEEe
Confidence 9999999876432221110 3456 457789999999999999999999999999999999999999999
Q ss_pred ee-----ccceEEEEEecCCCCC
Q 003958 406 VI-----GTGYRRIGYWSNYSGL 423 (784)
Q Consensus 406 ~~-----~~~~~~VG~w~~~~~l 423 (784)
++ +.++++||+|++..||
T Consensus 376 l~~~~~~g~g~~~iG~W~~~~gl 398 (400)
T cd06392 376 TSYSETFGKDVRRLATWDSEKGL 398 (400)
T ss_pred ccccccCCCCceEeEEecCCCCC
Confidence 66 4559999999998774
No 16
>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=6.5e-44 Score=385.00 Aligned_cols=359 Identities=14% Similarity=0.222 Sum_probs=290.9
Q ss_pred EEEeecC---CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEccCchhhHHH
Q 003958 35 GALLSFS---TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIGPQDAVTSHV 111 (784)
Q Consensus 35 G~i~~~~---~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiGp~~s~~~~~ 111 (784)
-+++|.+ ...+.....|+++|+|+||+++++++|++|+++++|++|++..+...+..+++++|.+||||.||..+.+
T Consensus 3 ~~l~p~~~~~~~~~~~~~~a~~lAie~IN~~~~ll~g~~l~~~~~d~~~~~~~~~~~~~~l~~~~v~aiiGp~~s~~~~~ 82 (387)
T cd06386 3 LVLLPQNNSYLFSSARVAPAIEYAQRRLEANRLLFPGFRFNVHYEDSDCGNEALFSLVDRSCARKPDLILGPVCEYAAAP 82 (387)
T ss_pred EEECCCCCCcceehhhhHHHHHHHHHHHhcCCCCCCCcEEEEEEeCCcCCchHHHHHHHHHHhhCCCEEECCCCccHHHH
Confidence 3566654 3345678899999999999999998999999999999999877777777777779999999999999999
Q ss_pred HHHhhhcCCccEEecccCCCCCCc-C-CCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcCCCcchh---HHHHHH
Q 003958 112 VSHVANELQVPLLSFSATDPTLSS-L-QFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDDDHGRNG---IAALGD 186 (784)
Q Consensus 112 va~~~~~~~ip~Is~~a~~~~l~~-~-~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~~~g~~~---~~~l~~ 186 (784)
++++++.++||+|+++++++.+++ + .||++||+.|++..++.++++++++|+|++|++||++++|++.. .+.+.+
T Consensus 83 va~ia~~~~iP~Is~~a~~~~~s~~~~~yp~~~R~~p~~~~~~~a~~~ll~~~~W~~vaiiy~~~~~~~~~~~~~~~l~~ 162 (387)
T cd06386 83 VARLASHWNIPMISAGALAAGFSHKKSEYSHLTRVAPSYVKMGETFSALFERFHWRSALLVYEDDKQERNCYFTLEGVHH 162 (387)
T ss_pred HHHHHHhCCCcEEccccCchhhccCcccCCeeEEecCchHHHHHHHHHHHHhCCCeEEEEEEEcCCCCccceehHHHHHH
Confidence 999999999999999999998886 3 69999999999999999999999999999999999999999876 889999
Q ss_pred HHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHcCCCCCCeEEEecCccccc-ccc
Q 003958 187 TLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIATSWLSTA-LDT 265 (784)
Q Consensus 187 ~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~-~~~ 265 (784)
.+++.|++|+..+..+ ....++..+++++++.. |+||+++..+.++.++++|+++||+..+|+||..+..... ...
T Consensus 163 ~~~~~gi~v~~~~~~~--~~~~d~~~~l~~ik~~~-rvii~~~~~~~~~~ll~~A~~~gm~~~~yv~i~~d~~~~~~~~~ 239 (387)
T cd06386 163 VFQEEGYHMSIYPFDE--TKDLDLDEIIRAIQASE-RVVIMCAGADTIRSIMLAAHRRGLTSGDYIFFNIELFNSSSYGD 239 (387)
T ss_pred HHHhcCceEEEEecCC--CCcccHHHHHHHHHhcC-cEEEEecCHHHHHHHHHHHHHcCCCCCCEEEEEEecccccccCC
Confidence 9999999998766554 34568999999999887 9999999999999999999999999999999999765311 100
Q ss_pred C-----CCCCCCccccceeeEEEeeecCCchhHHHHHHHHHhhccCCCCCC-CCCCChhHHHHhhHHHHHHHHHHHHhhc
Q 003958 266 N-----SPFPSDVMDDIQGVLTLRTYTPDSVLKRKFISRWRNLTDAKTPNG-YIGLNAYGFYAYDTVWLLARAINSFFKQ 339 (784)
Q Consensus 266 ~-----~~~~~~~~~~~~g~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~-~~~~~~~~~~~YDAv~~~a~Al~~~~~~ 339 (784)
. +..+.+...+...+.++....+..+++++|.+++++++....... ...++.+++.+|||++++|+||+++++.
T Consensus 240 ~~w~~~~~~~~~~~~a~~~~~~v~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~aa~~yDav~l~A~Al~~~~~~ 319 (387)
T cd06386 240 GSWKRGDKHDFEAKQAYSSLNTVTLLRTVKPEFEKFSMEVKSSVEKAGDLNDCDYVNMFVEGFHDAILLYALALHEVLKN 319 (387)
T ss_pred CCCccCCCcCHHHHHHHHhheEEeccCCCChHHHHHHHHHHHHHHhCCCCcccccchHHHHHHHHHHHHHHHHHHHHhhC
Confidence 0 000101011222233333334445788999999886554321111 1235578999999999999999998754
Q ss_pred CCccccccCCccccccCCcccccccccCCchHHHHHHHhccccceeeeEEEecCCCCcCCcEEEEEeec---cceEEEEE
Q 003958 340 GGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANMTGTAGPARFNSHGDLINPAYEIINVIG---TGYRRIGY 416 (784)
Q Consensus 340 ~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~l~~~l~~~~f~g~tG~v~Fd~~g~~~~~~~~I~~~~~---~~~~~VG~ 416 (784)
+.+ +.+|..|.++|++++|+|++|.+.||++|+| ...|.|+.+++ ++++.||.
T Consensus 320 g~~-----------------------~~~g~~l~~~l~~~~f~G~tG~v~~d~~g~r-~~~~~v~~~~~~~~~~~~~~~~ 375 (387)
T cd06386 320 GYS-----------------------KKDGTKITQRMWNRTFEGIAGQVSIDANGDR-YGDFSVIAMTDVEAGTYEVVGN 375 (387)
T ss_pred CCC-----------------------CCCHHHHHHHHhCCceeeccccEEECCCCCc-cccEEEEEccCCCCccEEEEeE
Confidence 321 3369999999999999999999999999998 66999999974 66899999
Q ss_pred ecCC
Q 003958 417 WSNY 420 (784)
Q Consensus 417 w~~~ 420 (784)
|...
T Consensus 376 ~~~~ 379 (387)
T cd06386 376 YFGK 379 (387)
T ss_pred Eccc
Confidence 9754
No 17
>cd06390 PBP1_iGluR_AMPA_GluR1 N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the GluR1 subunit of the AMPA receptor. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the GluR1 subunit of the AMPA (alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid) receptor. The AMPA receptor is a member of the glutamate-receptor ion channels (iGluRs) which are the major mediators of excitatory synaptic transmission in the central nervous system. AMPA receptors are composed of four types of subunits (GluR1, GluR2, GluR3, and GluR4) which combine to form a tetramer and play an important role in mediating the rapid excitatory synaptic current. Furthermore, this N-terminal domain of the iGluRs has homology with LIVBP, a bacterial periplasmic binding protein, as well as with the structurally related glutamate-binding domain of the G-protein-coupled metabotropic receptors (mGluRs).
Probab=100.00 E-value=1.1e-43 Score=376.09 Aligned_cols=360 Identities=20% Similarity=0.296 Sum_probs=297.2
Q ss_pred EEEEEeecCCcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEccCchhhHHHH
Q 003958 33 NIGALLSFSTNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIGPQDAVTSHVV 112 (784)
Q Consensus 33 ~IG~i~~~~~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiGp~~s~~~~~v 112 (784)
+||+||+..+ ...+.|+++|++++|.+..++|. +.+ -+..|+..+.+++|+++++||.||+||.++.++..+
T Consensus 1 ~iG~if~~~~---~~~~~af~~av~~~N~~~~l~~~--~~~---~~~~dsf~~~~~~C~~~~~gV~AI~Gp~s~~~a~~v 72 (364)
T cd06390 1 QIGGLFPNQQ---SQEHAAFRFALSQLTEPPKLLPQ--IDI---VNISDSFEMTYTFCSQFSKGVYAIFGFYDRKTVNML 72 (364)
T ss_pred CCceeeCCCC---hHHHHHHHHHHHHhccCcccccc--eEE---eccccHHHHHHHHHHHhhcCceEEEccCChhHHHHH
Confidence 4899998764 35689999999999998755542 222 234588999999999999999999999999999999
Q ss_pred HHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcCCCcchhHHHHHHHHhccC
Q 003958 113 SHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKR 192 (784)
Q Consensus 113 a~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~~l~~~g 192 (784)
+.+|+..+||+|++.+ +..+. ..+++++.|+ +++|+++++++|+|++|++||+++ ||....+.+.+.+++.|
T Consensus 73 ~sic~~~~vP~i~~~~--~~~~~--~~~~i~~~P~---~~~Ai~diI~~~~W~~v~iIYd~d-~g~~~lq~l~~~~~~~~ 144 (364)
T cd06390 73 TSFCGALHVCFITPSF--PVDTS--NQFVLQLRPE---LQDALISVIEHYKWQKFVYIYDAD-RGLSVLQKVLDTAAEKN 144 (364)
T ss_pred HHhhcCCCCCceecCC--CCCCC--CceEEEeChh---HHHHHHHHHHHcCCcEEEEEEeCC-ccHHHHHHHHHhhhccC
Confidence 9999999999999754 22222 3568999997 789999999999999999999655 99999999999999999
Q ss_pred cEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHcCCCCCCeEEEecCccccccccCCCCCCC
Q 003958 193 CRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIATSWLSTALDTNSPFPSD 272 (784)
Q Consensus 193 i~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~~~~~~~~ 272 (784)
+||.....++ .+..+++.+|+++++.++++||++|+++.+..+++++.+.+++..+|+||+++......+. ++
T Consensus 145 ~~I~~~~~~~--~~~~d~~~~L~~ik~~~~rvIVl~~~~~~~~~~L~~a~~~~~~~~gy~wI~t~l~~~~~~~-----~~ 217 (364)
T cd06390 145 WQVTAVNILT--TTEEGYRKLFQDLDKKKERLIVVDCESERLNAILNQIIKLEKNGIGYHYILANLGFMDIDL-----TK 217 (364)
T ss_pred ceeeEEEeec--CChHHHHHHHHhccccCCeEEEEECCHHHHHHHHHHHHHhhccCCceEEEecCCCcccccH-----HH
Confidence 9998776665 3466899999999999999999999999999999999888888999999999843332222 33
Q ss_pred ccccceeeEEEeeecCCchhHHHHHHHHHhhccCC-CCCCCCCCChhHHHHhhHHHHHHHHHHHHhhcCCccccccCCcc
Q 003958 273 VMDDIQGVLTLRTYTPDSVLKRKFISRWRNLTDAK-TPNGYIGLNAYGFYAYDTVWLLARAINSFFKQGGNLSFSKDSRL 351 (784)
Q Consensus 273 ~~~~~~g~~~~~~~~~~~~~~~~f~~~~~~~~~~~-~~~~~~~~~~~~~~~YDAv~~~a~Al~~~~~~~~~~~~~~~~~~ 351 (784)
......|+++++.+.++.+.+++|.++|++....+ ++.....+..+++.+||||+++|+|++++...+...+....
T Consensus 218 ~~~~~~nitg~r~~~~~~~~~~~~~~~w~~~~~~~~~~~~~~~~~~~~~l~yDaV~~~A~A~~~l~~~~~~~~~~~~--- 294 (364)
T cd06390 218 FRESGANVTGFQLVNYTDTTVSRIMQQWKNFDARDLPRVDWKRPKYTSALTYDGVRVMAEAFQNLRKQRIDISRRGN--- 294 (364)
T ss_pred HhcCCcCceEEEEecCCCHHHHHHHHHHHhhccccCCCCCcCCcchHHHHHHHHHHHHHHHHHHHHHcCCCcccCCC---
Confidence 45678899999999999999999999998866432 22233346778999999999999999998654433221111
Q ss_pred ccccCCccccc--ccccCCchHHHHHHHhccccceeeeEEEecCCCCcCCcEEEEEeeccceEEEEEecCCCCC
Q 003958 352 SDIQGHLRLDS--LRIFNGGNLLRDSILQANMTGTAGPARFNSHGDLINPAYEIINVIGTGYRRIGYWSNYSGL 423 (784)
Q Consensus 352 ~~~~g~~~~~~--~~~~~~~~~l~~~l~~~~f~g~tG~v~Fd~~g~~~~~~~~I~~~~~~~~~~VG~w~~~~~l 423 (784)
+..|.. ...|..|..|.++|++++|+|+||++.||++|+|.++.|+|+++.+.++++||.|++..||
T Consensus 295 -----~~~C~~~~~~~w~~G~~l~~~i~~~~f~GlTG~i~F~~~G~r~~~~~~I~~~~~~g~~~vG~W~~~~g~ 363 (364)
T cd06390 295 -----AGDCLANPAVPWGQGIDIQRALQQVRFEGLTGNVQFNEKGRRTNYTLHVIEMKHDGIRKIGYWNEDEKL 363 (364)
T ss_pred -----CCCCCCCCCCCCccHHHHHHHHHhhcccccccceeeCCCCCcccceEEEEEecCCcceEEEEECCCCCc
Confidence 224532 4478899999999999999999999999999999999999999999999999999988764
No 18
>cd06363 PBP1_Taste_receptor Ligand-binding domain of the T1R taste receptor. Ligand-binding domain of the T1R taste receptor. The T1R is a member of the family C receptors within the G-protein coupled receptor superfamily, which also includes the metabotropic glutamate receptors, GABAb receptors, the calcium-sensing receptor (CaSR), the V2R pheromone receptors, and a small group of uncharacterized orphan receptors.
Probab=100.00 E-value=2.3e-43 Score=384.60 Aligned_cols=352 Identities=23% Similarity=0.368 Sum_probs=295.3
Q ss_pred CCCceEEEEEEeecCC---------------------cchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHH
Q 003958 27 GRPSVVNIGALLSFST---------------------NVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLA 85 (784)
Q Consensus 27 ~~~~~i~IG~i~~~~~---------------------~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a 85 (784)
..++++.||++||.|. ..|.....|+++|+|+||+++|+|+|++|+++++|+|+ +..+
T Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~g~~~~~a~~lAv~~IN~~ggil~g~~l~~~~~D~~~-~~~a 80 (410)
T cd06363 2 RLPGDYLLGGLFPLHYATSALPHRRPEPLDCSSYRFNLSGYRLFQAMRFAVEEINNSTSLLPGVTLGYEIFDHCS-DSAN 80 (410)
T ss_pred CCCCCEEEEEEeECcccccccccCCCCCccCccCccCHHHHHHHHHHHHHHHHHhCCCccCCCCeeceEEEecCC-cHHH
Confidence 4688999999999983 12556789999999999999999999999999999977 6679
Q ss_pred HHHHHHHHh----------------cCceEEEccCchhhHHHHHHhhhcCCccEEecccCCCCCCc-CCCCceEeecCCh
Q 003958 86 LAEALHLME----------------GQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSS-LQFPYFVRTTQSD 148 (784)
Q Consensus 86 ~~~~~~li~----------------~~v~aiiGp~~s~~~~~va~~~~~~~ip~Is~~a~~~~l~~-~~~p~~~r~~ps~ 148 (784)
++.+.+|++ ++|.+||||.+|..+.+++++++.+++|+|+++++++.+++ ..||++||+.|++
T Consensus 81 ~~~~~~li~~~~~~~~~~c~~~~~~~~V~aIiGp~~S~~~~av~~i~~~~~vp~is~~~~~~~lt~~~~~~~~fr~~~~~ 160 (410)
T cd06363 81 FPPTLSLLSVNGSRIEPQCNYTNYQPRVVAVIGPDSSTLALTVAPLFSFFLIPQISYGASSEVLSNKELYPSFLRTVPSD 160 (410)
T ss_pred HHHHHHHHhccCcccCcccccccCCCCeEEEECCCccHHHHHHHHHhcccccccccccccCccccccccCCCeeEecCCc
Confidence 999999874 48999999999999999999999999999999999998887 5789999999999
Q ss_pred HHHHHHHHHHHHHcCCcEEEEEEEcCCCcchhHHHHHHHHhccCcEEEEeeccCCC-CChhHHHHHHHHhhcCCceEEEE
Q 003958 149 QYQMAAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVE-ATEDEITDLLVKVALTESRIIVV 227 (784)
Q Consensus 149 ~~~~~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~-~~~~d~~~~l~~l~~~~~~vIvl 227 (784)
..++.++++++++++|++|++|+.+++||....+.+++.+++.|++++..+.++.. ....|+..++++|+++++|+|++
T Consensus 161 ~~~~~al~~~l~~~~~k~vaii~~~~~~g~~~~~~~~~~l~~~gi~i~~~~~~~~~~~~~~d~~~~l~~i~~~~~dvIil 240 (410)
T cd06363 161 KDQIEAMVQLLQEFGWNWVAFLGSDDEYGRDGLQLFSELIANTGICIAYQGLIPLDTDPETDYQQILKQINQTKVNVIVV 240 (410)
T ss_pred HHHHHHHHHHHHHCCCcEEEEEEeCChhHHHHHHHHHHHHHHCCeEEEEEEEecCCCchHHHHHHHHHHHhcCCCeEEEE
Confidence 99999999999999999999999999999999999999999999999988877642 24689999999999999999999
Q ss_pred eccCCcHHHHHHHHHHcCCCCCCeEEEecCccccccccCCCCCCCccccceeeEEEeeecCCchhHHHHHHHHHhhccCC
Q 003958 228 HTHYNRGPVVFHVAQYLGMLGTGYVWIATSWLSTALDTNSPFPSDVMDDIQGVLTLRTYTPDSVLKRKFISRWRNLTDAK 307 (784)
Q Consensus 228 ~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~f~~~~~~~~~~~ 307 (784)
.+..+++..++++++++|+.. ..||++..+........ ....+...+++++....+..+++++|.+.
T Consensus 241 ~~~~~~~~~il~qa~~~g~~~--~~~i~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~f~~~-------- 307 (410)
T cd06363 241 FASRQPAEAFFNSVIQQNLTG--KVWIASEAWSLNDELPS---LPGIRNIGTVLGVAQQTVTIPGFSDFIYS-------- 307 (410)
T ss_pred EcChHHHHHHHHHHHhcCCCC--CEEEEeCcccccccccC---CccceeeccEEEEEeCCCCCccHHHHHHH--------
Confidence 999999999999999999854 37888876543211111 11123344577777777777777777765
Q ss_pred CCCCCCCCChhHHHHhhHHHHHHHHHHHHhhcCCccccccCCccccccCCcccccccccCCchHHHHHHHhccccceeee
Q 003958 308 TPNGYIGLNAYGFYAYDTVWLLARAINSFFKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANMTGTAGP 387 (784)
Q Consensus 308 ~~~~~~~~~~~~~~~YDAv~~~a~Al~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~l~~~l~~~~f~g~tG~ 387 (784)
+++.+||||+++|+|++++++++.. .|... ...+++.|.++|++++|+|++|+
T Consensus 308 ----------~~~~~YDaV~~~a~Al~~a~~~~~~----------------~~~~~-~~~~~~~l~~~L~~~~~~g~~g~ 360 (410)
T cd06363 308 ----------FAFSVYAAVYAVAHALHNVLQCGSG----------------GCPKR-VPVYPWQLLEELKKVNFTLLGQT 360 (410)
T ss_pred ----------HHHHHHHHHHHHHHHHHHHhCCCCC----------------CCCCC-CCCCHHHHHHHHhccEEecCCcE
Confidence 3567999999999999999776432 23211 12258889999999999999999
Q ss_pred EEEecCCCCcCCcEEEEEeecc----ceEEEEEecCC
Q 003958 388 ARFNSHGDLINPAYEIINVIGT----GYRRIGYWSNY 420 (784)
Q Consensus 388 v~Fd~~g~~~~~~~~I~~~~~~----~~~~VG~w~~~ 420 (784)
+.||++|++ ...++|++++.+ ++++||.|++.
T Consensus 361 i~fd~~G~~-~~~~~i~~~~~~~~~~~~~~vG~~~~~ 396 (410)
T cd06363 361 VRFDENGDP-NFGYDIVVWWWDNSSGTFEEVGSYSFY 396 (410)
T ss_pred EEeCCCCCC-ccceEEEEEEEcCCceeEEEEEEEECC
Confidence 999999995 667999999643 48999999873
No 19
>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=1.4e-43 Score=386.48 Aligned_cols=362 Identities=19% Similarity=0.249 Sum_probs=288.9
Q ss_pred EEEEEeecCCc---ch-hhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHH-----HHHHHHH-HhcCceEEEc
Q 003958 33 NIGALLSFSTN---VG-KVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLA-----LAEALHL-MEGQTVAIIG 102 (784)
Q Consensus 33 ~IG~i~~~~~~---~g-~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a-----~~~~~~l-i~~~v~aiiG 102 (784)
+||+++|++.. .| .....|+++|+|+||+++++|+|++|++++.|+++++..+ ...+.++ ..++|.+|||
T Consensus 1 ~~g~l~~~~~~~~~~~~~~~~~a~~lAve~IN~~~gil~g~~l~~~~~D~~~~~~~c~~~~~~~~~~~~~~~~~v~aiiG 80 (405)
T cd06385 1 TLAVILPLTNTSYPWAWPRVGPALERAIDRVNADPDLLPGLHLQYVLGSSENKEGVCSDSAAPLVAVDLKFTHNPWAFIG 80 (405)
T ss_pred CeeEECCCCCCcCccchhhhHHHHHHHHHHHhcCCCCCCCceEEEEEccccccCCCCccccchHHHHHHHHhcCCcEEEC
Confidence 48999999843 33 6778999999999999999999999999999986655432 2233332 3469999999
Q ss_pred cCchhhHHHHHHhhhcCCccEEecccCCCCCCc-CCCCceEeecCChHHHHHHHHHHHHHcCCcEEEE-EEEcCC-Ccch
Q 003958 103 PQDAVTSHVVSHVANELQVPLLSFSATDPTLSS-LQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIA-IYVDDD-HGRN 179 (784)
Q Consensus 103 p~~s~~~~~va~~~~~~~ip~Is~~a~~~~l~~-~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~i-i~~d~~-~g~~ 179 (784)
|.||..+.+++++++.++||+|+++++++.+++ ..||++||+.|++..++.++++++++|+|+++++ +|.++. +++.
T Consensus 81 p~~S~~~~~va~~a~~~~iP~Is~~a~~~~l~~~~~~~~~~R~~p~~~~~~~a~~~~~~~~~w~~va~ii~~~~~~~~~~ 160 (405)
T cd06385 81 PGCDYTASPVARFTTHWDVPLVTAGAPALGFGVKDEYATITRTGPTHKKLGEFVLHIHQHFGWRSHAMLIYSDNKVDDRP 160 (405)
T ss_pred CCccchHHHHHHHHhccCCcEEccccChhhcCCcccCcceEEecCchHHHHHHHHHHHHhCCCeEEEEEEEecCcccccc
Confidence 999999999999999999999999999999988 5799999999999999999999999999999984 565443 3333
Q ss_pred ---hHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHcCCCCCCeEEEec
Q 003958 180 ---GIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIAT 256 (784)
Q Consensus 180 ---~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~wi~~ 256 (784)
..+.+.+.+++.|++|+..+..+ .+..|+..+++++++. .|+|++++....++.++++|.++||++++|+||++
T Consensus 161 ~~~~~~~l~~~~~~~gi~v~~~~~~~--~~~~d~~~~l~~ik~~-~~iii~~~~~~~~~~i~~~a~~~g~~~~~y~~i~~ 237 (405)
T cd06385 161 CYFAMEGLYMELKKNNITVVDLVFEE--DDLINYTTLLQDIKQK-GRVIYVCCSPDIFRRLMLQFWREGLPSEDYVFFYI 237 (405)
T ss_pred hHHHHHHHHHHHHhCCeEEEEeeccC--CchhhHHHHHHHHhhc-ceEEEEeCCHHHHHHHHHHHHHcCCCCCcEEEEEe
Confidence 46889999999999998876332 2467899999999875 49999999999999999999999999999999998
Q ss_pred Ccccccccc---------CCCCCCCccccceeeEEEeeecCCchhHHHHHHHHHhhccCCCCCC--CCCCChhHHHHhhH
Q 003958 257 SWLSTALDT---------NSPFPSDVMDDIQGVLTLRTYTPDSVLKRKFISRWRNLTDAKTPNG--YIGLNAYGFYAYDT 325 (784)
Q Consensus 257 ~~~~~~~~~---------~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~--~~~~~~~~~~~YDA 325 (784)
+++...... .+..+....+++++++......+.++.+++|.++|+++.....+.+ ...++.+++.+|||
T Consensus 238 ~~~~~~~~~~~~~~~w~~~~~~~~~~~~a~~~v~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~aa~~YDa 317 (405)
T cd06385 238 DLFGASLQGPDPKRPWYRGDADDAAAREAFQSVKILTYKEPQNPEYKEFLSDLKTDAKEMFNFTVEDSLMNIIAGGFYDG 317 (405)
T ss_pred ecchhhccCCCCCCCCCCCCcccHHHHHhhheeEEEeCCCCCChhHHHHHHHHHHHhhccCCCccchhhHHHHHHHHHHH
Confidence 764322211 0100112235568888777777778889999999988632111111 11256789999999
Q ss_pred HHHHHHHHHHHhhcCCccccccCCccccccCCcccccccccCCchHHHHHHHhccccceeeeEEEecCCCCcCCcEEEEE
Q 003958 326 VWLLARAINSFFKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANMTGTAGPARFNSHGDLINPAYEIIN 405 (784)
Q Consensus 326 v~~~a~Al~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~l~~~l~~~~f~g~tG~v~Fd~~g~~~~~~~~I~~ 405 (784)
|+++|.||+++++..++ +.++..|.++|++++|+|++|.+.||++|+| ...|.+++
T Consensus 318 v~l~a~Al~~~~~~~~~-----------------------~~~g~~i~~~l~~~~f~G~tG~v~fd~~G~r-~~~~~~~~ 373 (405)
T cd06385 318 VMLYAHALNETMAKGGT-----------------------RPPGTAITQRMWNRTFYGVTGFVKIDDNGDR-ETDFALWD 373 (405)
T ss_pred HHHHHHHHHHHHhcCCC-----------------------CCCHHHHHHHhhCceEeeceeEEEEcCCCCE-eceeEEEE
Confidence 99999999998665321 2368999999999999999999999999997 57788875
Q ss_pred e---eccceEEEEEecCCC
Q 003958 406 V---IGTGYRRIGYWSNYS 421 (784)
Q Consensus 406 ~---~~~~~~~VG~w~~~~ 421 (784)
+ ++++++.||.|+..+
T Consensus 374 ~~~~~~g~~~~v~~~~~~~ 392 (405)
T cd06385 374 MTDTESGDFQVVSVYNGTQ 392 (405)
T ss_pred ccCCCCCcEEEEEEEcccC
Confidence 5 567899999998654
No 20
>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=3.3e-43 Score=378.04 Aligned_cols=339 Identities=22% Similarity=0.306 Sum_probs=289.6
Q ss_pred eEEEEEEeecCCcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhc-CceEEEccCchhh-
Q 003958 31 VVNIGALLSFSTNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEG-QTVAIIGPQDAVT- 108 (784)
Q Consensus 31 ~i~IG~i~~~~~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~-~v~aiiGp~~s~~- 108 (784)
.|+||++++.++ ...+++.|+..+|.+..+..+++++++..|+.+||.+++.++|+++.+ +|.+|+||.+|..
T Consensus 2 ~~~ig~~~~~~~-----~~~~~~~a~~~~~~~~~~~~~~~~~l~~~d~~~d~~~~~~~~~~~l~~~~v~~iig~~~s~~~ 76 (362)
T cd06367 2 TVNIGVVLSGSS-----SEPAFRDAVTAANFRHNLPYNLSLEAVAVSNDTDPISLLLSVCDLLVVQVVAGVVFSDPTDEE 76 (362)
T ss_pred ceEEEEEecCCc-----chhhHHHHhhhccccccCCcccceEEEEEecCCCHHHHHHHHHHHhcccceEEEEecCCCCcc
Confidence 589999999873 358888888888877655568999999999999999999999998765 8999999999998
Q ss_pred --HHHHHHhhhcCCccEEecccCCCCC-Cc-CCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcCCCcchhHHHH
Q 003958 109 --SHVVSHVANELQVPLLSFSATDPTL-SS-LQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDDDHGRNGIAAL 184 (784)
Q Consensus 109 --~~~va~~~~~~~ip~Is~~a~~~~l-~~-~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l 184 (784)
+.+++.+++.++||+|+++++++.+ ++ ..||++||+.|++..+++++++++++|+|++|++||++++||++..+.+
T Consensus 77 ~~~~~~~~v~~~~~iP~Is~~~~~~~~~s~~~~~~~~~R~~p~~~~~~~ai~~ll~~~~w~~vaii~~~~~~g~~~~~~l 156 (362)
T cd06367 77 AVAQILDFTSAQTRIPVVGISGRESIFMSDKNIHSLFLQTGPSLEQQADVMLEILEEYDWHQFSVVTSRDPGYRDFLDRV 156 (362)
T ss_pred chhhhhhhhhhhhcCcEEEeeccccccccCCCcccceEeecCcHHHHHHHHHHHHHHcCCeEEEEEEEcCcccHHHHHHH
Confidence 8999999999999999999999888 77 6899999999999999999999999999999999999999999999999
Q ss_pred HHHHhccCcE--EEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHcCCCCCCeEEEecCccccc
Q 003958 185 GDTLAAKRCR--ISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIATSWLSTA 262 (784)
Q Consensus 185 ~~~l~~~gi~--v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~ 262 (784)
++.+++.|+| ++....++.. ...++..++.++++.++|+|++++..+++..++++|.++|+++++|+||+++.+...
T Consensus 157 ~~~l~~~g~~~~i~~~~~~~~~-~~~~~~~~l~~l~~~~~~vivl~~~~~~~~~il~~a~~~g~~~~~~~wI~~~~~~~~ 235 (362)
T cd06367 157 ETTLEESFVGWEFQLVLTLDLS-DDDGDARLLRQLKKLESRVILLYCSKEEAERIFEAAASLGLTGPGYVWIVGELALGS 235 (362)
T ss_pred HHHHHhcccceeeeeeEEeccC-CCcchHHHHHHHHhcCCcEEEEeCCHHHHHHHHHHHHHcCCCCCCcEEEECcccccc
Confidence 9999999999 7666656532 222788999999999999999999999999999999999999999999999987642
Q ss_pred cccCCCCCCCccccceeeEEEeeecCCchhHHHHHHHHHhhccCCCCCCCCCCChhHHHHhhHHHHHHHHHHHHhhcCCc
Q 003958 263 LDTNSPFPSDVMDDIQGVLTLRTYTPDSVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTVWLLARAINSFFKQGGN 342 (784)
Q Consensus 263 ~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~~~a~Al~~~~~~~~~ 342 (784)
. ....+...|++++++... ..+.+++||||+++|+|+++++++...
T Consensus 236 ~-------~~~~~~~~G~~g~~~~~~---------------------------~~~~~~~~Dav~~~a~Al~~~~~~~~~ 281 (362)
T cd06367 236 G-------LAPEGLPVGLLGVGLDTW---------------------------YSLEARVRDAVAIVARAAESLLRDKGA 281 (362)
T ss_pred c-------CCccCCCCeeEEEEeccc---------------------------ccHHHHHHHHHHHHHHHHHHHHHhcCC
Confidence 1 123356679999976532 235778999999999999999876432
Q ss_pred cccccCCccccccCCccccccc--ccCCchHHHHHHHhccccceeeeEEEecCCCCcCCcEEEEEee-ccceEEEEEecC
Q 003958 343 LSFSKDSRLSDIQGHLRLDSLR--IFNGGNLLRDSILQANMTGTAGPARFNSHGDLINPAYEIINVI-GTGYRRIGYWSN 419 (784)
Q Consensus 343 ~~~~~~~~~~~~~g~~~~~~~~--~~~~~~~l~~~l~~~~f~g~tG~v~Fd~~g~~~~~~~~I~~~~-~~~~~~VG~w~~ 419 (784)
.... ...|.... .|.+|..|.++|++++|.|.+|+|.||+||+|.++.|+|++++ +.+|++||.|++
T Consensus 282 ~~~~----------~~~C~~~~~~~~~~g~~l~~~l~~~~f~G~tg~v~F~~~G~~~~~~~~I~~l~~~~~~~~VG~W~~ 351 (362)
T cd06367 282 LPEP----------PVNCYDTANKRESSGQYLARFLMNVTFDGETGDVSFNEDGYLSNPKLVIINLRRNRKWERVGSWEN 351 (362)
T ss_pred CCCC----------CCCcCCCCCCCCCchHHHHHHHhcccccCCCCceeECCCcccccceEEEEEecCCCcceEEEEEcC
Confidence 2111 23565543 2778999999999999999999999999999888899999999 788999999975
No 21
>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=1.4e-42 Score=376.03 Aligned_cols=375 Identities=20% Similarity=0.329 Sum_probs=297.1
Q ss_pred EEEEEeecCCcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCC-CCHHHHHHHHHHHHhcCceEEEccCchhhHHH
Q 003958 33 NIGALLSFSTNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCN-HSGFLALAEALHLMEGQTVAIIGPQDAVTSHV 111 (784)
Q Consensus 33 ~IG~i~~~~~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~-~~~~~a~~~~~~li~~~v~aiiGp~~s~~~~~ 111 (784)
+||++|+.+ +.....|+++|+++||++..++++.+|.+.+.++. +|+..+.+++|++++++|.+||||.+|.++.+
T Consensus 1 ~iG~if~~~---~~~~~~a~~~Av~~iN~~~~~~~~~~l~~~~~~~~~~d~~~~~~~~c~ll~~~V~aiiGp~~s~~~~~ 77 (382)
T cd06380 1 PIGGLFDVD---EDQEYSAFRFAISQHNTNPNSTAPFKLLPHVDNLDTSDSFALTNAICSQLSRGVFAIFGSYDKSSVNT 77 (382)
T ss_pred CceeEECCC---ChHHHHHHHHHHHHhcccccccCCeeeeeeeeEecccchHHHHHHHHHHHhcCcEEEEecCcHHHHHH
Confidence 489999998 36788999999999999876777888887777665 79999999999999999999999999999999
Q ss_pred HHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcCCCcchhHHHHHHHHhcc
Q 003958 112 VSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAK 191 (784)
Q Consensus 112 va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~~l~~~ 191 (784)
++++++.++||+|+++++++.++ ..++|+||+.|+. ..++++++++++|++|++||++++ |....+.+.+.+++.
T Consensus 78 ~~~~~~~~~iP~i~~~~~~~~l~-~~~~~~fr~~p~~---~~a~~~~~~~~~wk~vaii~~~~~-~~~~~~~~~~~~~~~ 152 (382)
T cd06380 78 LTSYSDALHVPFITPSFPTNDLD-DGNQFVLQMRPSL---IQALVDLIEHYGWRKVVYLYDSDR-GLLRLQQLLDYLREK 152 (382)
T ss_pred HHHHHhcCCCCeEecCCCcccCC-CCCcEEEEeccch---hHHHHHHHHhcCCeEEEEEECCCc-chHHHHHHHHHHhcc
Confidence 99999999999999998888774 3679999998863 458899999999999999997665 666777888888888
Q ss_pred C--cEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHcCCCCCCeEEEecCccccccccCCCC
Q 003958 192 R--CRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIATSWLSTALDTNSPF 269 (784)
Q Consensus 192 g--i~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~~~~~ 269 (784)
| +.|.... +....+..|++.+|++||+.++|+||+.+..+++..++++|+++||..++|+||++++.....+..
T Consensus 153 g~~i~v~~~~-~~~~~~~~d~~~~L~~ik~~~~~~iil~~~~~~~~~i~~qa~~~gm~~~~y~~i~~~~~~~~~~~~--- 228 (382)
T cd06380 153 DNKWQVTARR-VDNVTDEEEFLRLLEDLDRRKEKRIVLDCESERLNKILEQIVDVGKNRKGYHYILANLGFDDIDLS--- 228 (382)
T ss_pred CCceEEEEEE-ecCCCcHHHHHHHHHHhhcccceEEEEECCHHHHHHHHHHHHHhhhcccceEEEEccCCcccccHH---
Confidence 8 6665433 332124579999999999999999999999999999999999999999999999987644333221
Q ss_pred CCCccccceeeEEEeeecCCchhHHHHHHHHHhhccCC-CCCCCCCCChhHHHHhhHHHHHHHHHHHHhhcCCccccccC
Q 003958 270 PSDVMDDIQGVLTLRTYTPDSVLKRKFISRWRNLTDAK-TPNGYIGLNAYGFYAYDTVWLLARAINSFFKQGGNLSFSKD 348 (784)
Q Consensus 270 ~~~~~~~~~g~~~~~~~~~~~~~~~~f~~~~~~~~~~~-~~~~~~~~~~~~~~~YDAv~~~a~Al~~~~~~~~~~~~~~~ 348 (784)
.......++.++....+..+..++|.++|++.++.. +......+..+++++||||+++++|++++.+.+++......
T Consensus 229 --~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~aa~aYDav~~~a~Al~~~~~~~~~~~~~~~ 306 (382)
T cd06380 229 --KFLFGGVNITGFQLVDNTNPTVQKFLQRWKKLDPREWPGAGTSPIKYTAALAHDAVLVMAEAFRSLRRQRGSGRHRID 306 (382)
T ss_pred --HhccCceeeEEEeccCCCCHHHHHHHHHHHhcCccccCcCCcCCcchHHHHHHHHHHHHHHHHHHHHHhccccccccc
Confidence 111222345666666667788999999999987521 11122235678999999999999999998654321100000
Q ss_pred CccccccCCcccc--cccccCCchHHHHHHHhccccceeeeEEEecCCCCcCCcEEEEEeeccceEEEEEecCCCCC
Q 003958 349 SRLSDIQGHLRLD--SLRIFNGGNLLRDSILQANMTGTAGPARFNSHGDLINPAYEIINVIGTGYRRIGYWSNYSGL 423 (784)
Q Consensus 349 ~~~~~~~g~~~~~--~~~~~~~~~~l~~~l~~~~f~g~tG~v~Fd~~g~~~~~~~~I~~~~~~~~~~VG~w~~~~~l 423 (784)
.+....+..|. ....|.+|..|.++|++++|+|++|+++||++|+|....++|++++++++++||.|++..||
T Consensus 307 --~~~~~~~~~C~~~~~~~~~~g~~i~~~l~~~~~~G~tG~i~Fd~~G~~~~~~~~i~~~~~~~~~~vg~w~~~~g~ 381 (382)
T cd06380 307 --ISRRGNGGDCLANPAVPWEHGIDIERALKKVQFEGLTGNVQFDEFGQRTNYTLDVVELKTRGLRKVGYWNEDDGL 381 (382)
T ss_pred --cccCCCCCcCCCCCCCCccchHHHHHHHHhcccCCcccceEECCCCCcccccEEEEEecCCCceEEEEECCCcCc
Confidence 00000123454 34568889999999999999999999999999999889999999999899999999988764
No 22
>cd06370 PBP1_Speract_GC_like Ligand-binding domain of membrane bound guanylyl cyclases. Ligand-binding domain of membrane bound guanylyl cyclases (GCs), which are known to be activated by sperm-activating peptides (SAPs), such as speract or resact. These ligand peptides are released by a range of invertebrates to stimulate the metabolism and motility of spermatozoa and are also potent chemoattractants. These GCs contain a single transmembrane segment, an extracellular ligand binding domain, and intracellular protein kinase-like and cyclase catalytic domains. GCs of insect and nematodes, which exhibit high sequence similarity to the speract receptor are also included in this model.
Probab=100.00 E-value=4.2e-43 Score=381.66 Aligned_cols=356 Identities=20% Similarity=0.314 Sum_probs=292.4
Q ss_pred EEEEEEeecCC----cchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEccCchh
Q 003958 32 VNIGALLSFST----NVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIGPQDAV 107 (784)
Q Consensus 32 i~IG~i~~~~~----~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiGp~~s~ 107 (784)
|+||++.|++. ..|.....|+++|+|+||+++++++|++|++++.|++|++..|+.++++|++++|.+||||.+|.
T Consensus 1 i~iG~~~pltG~~~a~~G~~~~~a~~lAv~~IN~~ggil~g~~l~l~~~D~~~~~~~a~~~~~~li~~~v~aiiGp~~S~ 80 (404)
T cd06370 1 IKVGYLAEWTTDRTDRLGLPISGALTLAVEDVNADPNLLPGYKLQFEWVDTHGDEVLSIRAVSDWWKRGVVAFIGPECTC 80 (404)
T ss_pred CeeEecccccCCccccccccHHHHHHHHHHHHhCCCCCCCCCEEEEEEEecCCChHHHHHHHHHHHhcCceEEECCCchh
Confidence 68999999985 34888899999999999999999889999999999999999999999999999999999999985
Q ss_pred hHHHHHHhhhcCCccEEecccCCCCCCc-CCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcCCCcchhHHHHHH
Q 003958 108 TSHVVSHVANELQVPLLSFSATDPTLSS-LQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGD 186 (784)
Q Consensus 108 ~~~~va~~~~~~~ip~Is~~a~~~~l~~-~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~ 186 (784)
. +++.+++.++||+|+++++++.+++ ..||+|||+.|++..++.++++++++++|++|++|+.+++||+...+.+++
T Consensus 81 ~--~~a~i~~~~~iP~Is~~a~~~~l~~~~~~~~f~r~~~~~~~~~~a~~~~~~~~~w~~vaii~~~~~~g~~~~~~~~~ 158 (404)
T cd06370 81 T--TEARLAAAWNLPMISYKCDEEPVSDKSKYPTFARTVPPSIQVVKSVIALLKHFNWNKFSVVYENDSKYSSVFETLKE 158 (404)
T ss_pred H--HHHHHHhhcCCcEEecccCCccccccccCCCeEEcCCCHHHHHHHHHHHHHHCCCcEEEEEEecCcccHHHHHHHHH
Confidence 4 4567999999999999999999987 579999999999999999999999999999999999999999999999999
Q ss_pred HHhccCcEEEEeeccCCCC-----ChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHcCCC-CCCeEEEecCccc
Q 003958 187 TLAAKRCRISFKAPLSVEA-----TEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGML-GTGYVWIATSWLS 260 (784)
Q Consensus 187 ~l~~~gi~v~~~~~~~~~~-----~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~g~~-~~~~~wi~~~~~~ 260 (784)
.+++.|++|+..+.++... ...++..++++++.. ++++|+++...+++.++++|+++||+ ..+|+||+.+...
T Consensus 159 ~~~~~g~~iv~~~~~~~~~~~~~~~~~~~~~~l~~~~~~-~~~~v~~~~~~~~~~~l~qa~~~g~~~~~~y~~i~~~~~~ 237 (404)
T cd06370 159 EAELRNITISHVEYYADFYPPDPIMDNPFEDIIQRTKET-TRIYVFIGEANELRQFLMSMLDEGLLESGDYMVLGVDIEY 237 (404)
T ss_pred HHHHcCCEEEEEEEECCCCCchhhhHHHHHHHHHhccCC-CEEEEEEcCHHHHHHHHHHHHHcCCCCCCcEEEEEEchhh
Confidence 9999999999888887431 147888999888764 77888877777899999999999998 5789999865311
Q ss_pred ccc---------------ccCCCCCCCccccceeeEEEeeecCCchhHHHHHHHHHhhccCCCCC-------CCCCCChh
Q 003958 261 TAL---------------DTNSPFPSDVMDDIQGVLTLRTYTPDSVLKRKFISRWRNLTDAKTPN-------GYIGLNAY 318 (784)
Q Consensus 261 ~~~---------------~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~-------~~~~~~~~ 318 (784)
... ...........++++|++.+.+..+ .+.+++|.++|+++.+..+.. ....++.+
T Consensus 238 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 316 (404)
T cd06370 238 YDRDSQDYYSLHRGFQSREYNRSDDEKALEAMKSVLIIVPTPV-SPDYDSFSIFVRKYNLEPPFNGDLGESELVLEIDIE 316 (404)
T ss_pred ccccchhhhhhhhhhccccccccccHHHHHHhHheEEEecCCC-CchHHHHHHHHHHhccCCCCccccccccccccccee
Confidence 100 0000001123356788887765554 677889999998875421100 12235678
Q ss_pred HHHHhhHHHHHHHHHHHHhhcCCccccccCCccccccCCcccccccccCCchHHHHHHHhccccceee-eEEEecCCCCc
Q 003958 319 GFYAYDTVWLLARAINSFFKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANMTGTAG-PARFNSHGDLI 397 (784)
Q Consensus 319 ~~~~YDAv~~~a~Al~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~l~~~l~~~~f~g~tG-~v~Fd~~g~~~ 397 (784)
++++|||++++|+||+++++++... .++..|.++|++++|+|++| +|.||++|+|
T Consensus 317 aa~~yDAv~~~a~Al~~~~~~~~~~-----------------------~~g~~i~~~l~~~~f~GvtG~~v~fd~~G~~- 372 (404)
T cd06370 317 AAYLYDAVMLYAKALDETLLEGGDI-----------------------YNGTAIVSHILNRTYRSITGFDMYIDENGDA- 372 (404)
T ss_pred eehhHHHHHHHHHHHHHHHHhcCCC-----------------------CCHHHHHHHHhCcccccccCceEEEcCCCCc-
Confidence 8999999999999999987654321 25889999999999999999 8999999997
Q ss_pred CCcEEEEEeeccceEEEE
Q 003958 398 NPAYEIINVIGTGYRRIG 415 (784)
Q Consensus 398 ~~~~~I~~~~~~~~~~VG 415 (784)
...|.++++++++|-.-|
T Consensus 373 ~~~y~v~~~~~~~~~~~~ 390 (404)
T cd06370 373 EGNYSVLALQPIPPGDNG 390 (404)
T ss_pred ccceEEEEeccccccCCC
Confidence 688999999887654333
No 23
>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=1.1e-42 Score=372.92 Aligned_cols=342 Identities=45% Similarity=0.767 Sum_probs=299.0
Q ss_pred EEEEEeecC-CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhc-CceEEEccCchhhHH
Q 003958 33 NIGALLSFS-TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEG-QTVAIIGPQDAVTSH 110 (784)
Q Consensus 33 ~IG~i~~~~-~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~-~v~aiiGp~~s~~~~ 110 (784)
+||+++|++ +..|.....|+++|+|+||+++++++|++|+++++|++|++..+++.+++|+.+ +|.+||||.+|..+.
T Consensus 1 ~IG~~~p~sGa~~G~~~~~~~~lAv~~iN~~gg~~~g~~i~~~~~D~~~~~~~a~~~a~~l~~~~~v~~viG~~~s~~~~ 80 (350)
T cd06366 1 RIGAIFDLSGSWIGKAALPAIEMALEDVNADNSILPGYRLVLHVRDSKCDPVQAASAALDLLENKPVVAIIGPQCSSVAE 80 (350)
T ss_pred CEEEEEecCCCcccHHHHHHHHHHHHHHhcCCCcCCCcEEEEEecCCCCCHHHHHHHHHHHhccCCceEEECCCcHHHHH
Confidence 599999999 778999999999999999999977789999999999999999999999999987 999999999999999
Q ss_pred HHHHhhhcCCccEEecccCCCCCCc-CCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcCCCcchhHHHHHHHHh
Q 003958 111 VVSHVANELQVPLLSFSATDPTLSS-LQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLA 189 (784)
Q Consensus 111 ~va~~~~~~~ip~Is~~a~~~~l~~-~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~~l~ 189 (784)
+++++++.+++|+|+++++++.+++ ..+|++||+.|++..++.++++++++++|+++++|+.+++||+...+.+++.++
T Consensus 81 a~~~~~~~~~ip~i~~~~~~~~l~~~~~~~~~~r~~p~~~~~~~a~~~~~~~~~~~~v~ii~~~~~~g~~~~~~~~~~~~ 160 (350)
T cd06366 81 FVAEVANEWNVPVLSFAATSPSLSSRLQYPYFFRTTPSDSSQNPAIAALLKKFGWRRVATIYEDDDYGSGGLPDLVDALQ 160 (350)
T ss_pred HHHHHhhcCCeeEEeccCCCccccccccCCceEEcccchHhHHHHHHHHHHHCCCcEEEEEEEcCcccchhHHHHHHHHH
Confidence 9999999999999999999988866 578999999999999999999999999999999999999999999999999999
Q ss_pred ccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHcCCCCCCeEEEecCcccccccc-CCC
Q 003958 190 AKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIATSWLSTALDT-NSP 268 (784)
Q Consensus 190 ~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~-~~~ 268 (784)
+.|++|+....++......|+..++++|+++++|+|++++...++..++++++++|+..++++||+++.+....+. ...
T Consensus 161 ~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~dvvi~~~~~~~~~~~~~~a~~~g~~~~~~~~i~~~~~~~~~~~~~~~ 240 (350)
T cd06366 161 EAGIEISYRAAFPPSANDDDITDALKKLKEKDSRVIVVHFSPDLARRVFCEAYKLGMMGKGYVWILTDWLSSNWWSSSDC 240 (350)
T ss_pred HcCCEEEEEeccCCCCChhHHHHHHHHHhcCCCeEEEEECChHHHHHHHHHHHHcCCcCCCEEEEECcchhhhhccCCCC
Confidence 9999999988887432368999999999999999999999999999999999999998888999998765543210 000
Q ss_pred CCCCccccceeeEEEeeecCC-chhHHHHHHHHHhhccCCCCCCCCCCChhHHHHhhHHHHHHHHHHHHhhcCCcccccc
Q 003958 269 FPSDVMDDIQGVLTLRTYTPD-SVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTVWLLARAINSFFKQGGNLSFSK 347 (784)
Q Consensus 269 ~~~~~~~~~~g~~~~~~~~~~-~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~~~a~Al~~~~~~~~~~~~~~ 347 (784)
..+...+..+|++++.++.++ .+.+++|.++|+++++..... ...++.+++.+|||+++ .
T Consensus 241 ~~~~~~~~~~gv~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~-~~~p~~~a~~~YDav~~------~------------ 301 (350)
T cd06366 241 TDEEMLEAMQGVIGVRSYVPNSSMTLQEFTSRWRKRFGNENPE-LTEPSIYALYAYDAVWA------S------------ 301 (350)
T ss_pred ChHHHHHhhceEEEEeecccccCccHHHHHHHHHHHhcccCcC-cCCCCcccchhhhheee------e------------
Confidence 112234577899999988887 888999999999998631111 12467789999999988 1
Q ss_pred CCccccccCCcccccccccCCchHHHHHHHhccccceeeeEEEecCCCCcCCcEEEEEeeccceEEEEEecCCCCCc
Q 003958 348 DSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANMTGTAGPARFNSHGDLINPAYEIINVIGTGYRRIGYWSNYSGLS 424 (784)
Q Consensus 348 ~~~~~~~~g~~~~~~~~~~~~~~~l~~~l~~~~f~g~tG~v~Fd~~g~~~~~~~~I~~~~~~~~~~VG~w~~~~~l~ 424 (784)
.+|+|++|+++||++|++....|+++++.++++++||.|++..|++
T Consensus 302 -------------------------------~~~~G~~G~v~fd~~~~~~~~~~~~~~~~~~~~~~vg~~~~~~~~~ 347 (350)
T cd06366 302 -------------------------------TNFNGLSGPVQFDGGRRLASPAFEIINIIGKGYRKIGFWSSESGLS 347 (350)
T ss_pred -------------------------------ceEEeeeeeEEEcCCCccCCcceEEEEecCCceEEEEEEeCCCCcc
Confidence 2588999999999999988899999999999999999999877654
No 24
>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=3.9e-42 Score=362.80 Aligned_cols=365 Identities=16% Similarity=0.273 Sum_probs=299.4
Q ss_pred EEEEeecCCcchhhHHHHHHHHHHHHhcCCCCCCC-CEEEEEEecC-CCCHHHHHHHHHHHHhcCceEEEccCchhhHHH
Q 003958 34 IGALLSFSTNVGKVAKLAIKAAVDDVNSDPTTLGG-TKLKLQMQDC-NHSGFLALAEALHLMEGQTVAIIGPQDAVTSHV 111 (784)
Q Consensus 34 IG~i~~~~~~~g~~~~~a~~~Ave~IN~~~~il~g-~~l~~~~~D~-~~~~~~a~~~~~~li~~~v~aiiGp~~s~~~~~ 111 (784)
||+||+.++ ...+.|+++|++++|.+..+++. .+|...+... ..|+..+.+++|+++++||.||+||.++.++.+
T Consensus 2 iG~iF~~~~---~~~~~aF~~Av~~~N~~~~~~~~~~~l~~~i~~~~~~dsf~~~~~~C~l~~~GV~AIfGp~~~~s~~~ 78 (372)
T cd06387 2 IGGLFMRNT---VQEHSAFRFAVQLYNTNQNTTEKPFHLNYHVDHLDSSNSFSVTNAFCSQFSRGVYAIFGFYDQMSMNT 78 (372)
T ss_pred cceeecCCc---HHHHHHHHHHHHHhcccccccccCeEEEEeeEEecCCChHHHHHHHHHHhhcccEEEEecCCHhHHHH
Confidence 899998654 35689999999999999877765 4777755433 469999999999999999999999999999999
Q ss_pred HHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcCCCcchhHHHHHHHHhcc
Q 003958 112 VSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAK 191 (784)
Q Consensus 112 va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~~l~~~ 191 (784)
+..+|+..+||+|.+.... +...++.+++.|+ +..|+++++++|+|++|.+|| |+++|...++.+.+.+...
T Consensus 79 v~s~c~~~~iP~i~~~~~~----~~~~~~~l~l~P~---l~~Ai~diI~~~~Wr~~~~iY-d~d~gl~~Lq~L~~~~~~~ 150 (372)
T cd06387 79 LTSFCGALHTSFITPSFPT----DADVQFVIQMRPA---LKGAILSLLAHYKWEKFVYLY-DTERGFSILQAIMEAAVQN 150 (372)
T ss_pred HHHhhccccCCeeeeCCCC----CCCCceEEEEChh---HHHHHHHHHHhcCCCEEEEEe-cCchhHHHHHHHHHhhccC
Confidence 9999999999999873321 2334677899998 689999999999999999999 7788988999999999998
Q ss_pred CcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHcCCCCCCeEEEecCccccccccCCCCCC
Q 003958 192 RCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIATSWLSTALDTNSPFPS 271 (784)
Q Consensus 192 gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~~~~~~~ 271 (784)
+..|......+. ....+++.+++++++.+.++||+.|+++.+..++++|.+.||+..+|+||+++......+. .
T Consensus 151 ~~~V~~~~v~~~-~~~~~~~~~l~el~~~~~r~iIld~s~~~~~~il~~a~e~gM~~~~y~~ilt~ld~~~~dl-----~ 224 (372)
T cd06387 151 NWQVTARSVGNI-KDVQEFRRIIEEMDRRQEKRYLIDCEVERINTILEQVVILGKHSRGYHYMLANLGFTDISL-----E 224 (372)
T ss_pred CceEEEEEeccC-CchHHHHHHHHHhccccceEEEEECCHHHHHHHHHHHHHcCccccceEEEEecCCcccccH-----H
Confidence 988876543332 2456889999999999999999999999999999999999999999999999855444333 2
Q ss_pred CccccceeeEEEeeecCCchhHHHHHHHHHhhccC-CCCCCCCCCChhHHHHhhHHHHHHHHHHHHhhcCCccccccCCc
Q 003958 272 DVMDDIQGVLTLRTYTPDSVLKRKFISRWRNLTDA-KTPNGYIGLNAYGFYAYDTVWLLARAINSFFKQGGNLSFSKDSR 350 (784)
Q Consensus 272 ~~~~~~~g~~~~~~~~~~~~~~~~f~~~~~~~~~~-~~~~~~~~~~~~~~~~YDAv~~~a~Al~~~~~~~~~~~~~~~~~ 350 (784)
+......+++++++..+..+..++|.++|++.... .++.....+..+++.+||||+++|+|++++...+...+...
T Consensus 225 ~~~~g~~NItg~rl~~~~~~~~~~f~~~w~~~~~~~~~~~~~~~l~~~~al~yDaV~~~A~A~~~l~~~~~~~~~~~--- 301 (372)
T cd06387 225 RVMHGGANITGFQIVNNENPMVQQFLQRWVRLDEREFPEAKNSPLKYTSALTHDAILVIAEAFRYLRRQRVDVSRRG--- 301 (372)
T ss_pred HhccCCcceeEEEEecCCCchHHHHHHHHHhCCcccCCCCCCCCcchHHHHHHHHHHHHHHHHHHHHhcCCCcccCC---
Confidence 23333445999999999999999999999876542 22222234567899999999999999999855433221110
Q ss_pred cccccCCccccc--ccccCCchHHHHHHHhccccceeeeEEEecCCCCcCCcEEEEEeeccceEEEEEecCCCCC
Q 003958 351 LSDIQGHLRLDS--LRIFNGGNLLRDSILQANMTGTAGPARFNSHGDLINPAYEIINVIGTGYRRIGYWSNYSGL 423 (784)
Q Consensus 351 ~~~~~g~~~~~~--~~~~~~~~~l~~~l~~~~f~g~tG~v~Fd~~g~~~~~~~~I~~~~~~~~~~VG~w~~~~~l 423 (784)
.+..|.. ...|.+|..|.++|++++|+|+||++.|+++|+|.++.|+|+++.++++++||.|++..|+
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 0224532 4578899999999999999999999999999999999999999999999999999988764
No 25
>cd06373 PBP1_NPR_like Ligand binding domain of natriuretic peptide receptor (NPR) family. Ligand binding domain of natriuretic peptide receptor (NPR) family which consists of three different subtypes: type A natriuretic peptide receptor (NPR-A, or GC-A), type B natriuretic peptide receptors (NPR-B, or GC-B), and type C natriuretic peptide receptor (NPR-C). There are three types of natriuretic peptide (NP) ligands specific to the receptors: atrial NP (ANP), brain or B-type NP (BNP), and C-type NP (CNP). The NP family is thought to have arisen through gene duplication during evolution and plays an essential role in cardiovascular and body fluid homeostasis. ANP and BNP bind mainly to NPR-A, while CNP binds specifically to NPR-B. Both NPR-A and NPR-B have guanylyl cyclase catalytic activity and produces intracellular secondary messenger cGMP in response to peptide-ligand binding. Consequently, the NPR-A activation results in vasodilation and inhibition of vascular smooth muscle cell proli
Probab=100.00 E-value=7.8e-43 Score=379.75 Aligned_cols=363 Identities=19% Similarity=0.299 Sum_probs=296.2
Q ss_pred EEEEEeecCC----cchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCC----CHHHHHHHHHHHH-hcCceEEEcc
Q 003958 33 NIGALLSFST----NVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNH----SGFLALAEALHLM-EGQTVAIIGP 103 (784)
Q Consensus 33 ~IG~i~~~~~----~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~----~~~~a~~~~~~li-~~~v~aiiGp 103 (784)
+||+++|.+. ..|.....|+++|+|+||+++++++|++|++++.|+++ ++..++..+.+++ .++|.+||||
T Consensus 1 ~~g~l~p~~~~~~~~~~~~~~~a~~lAve~IN~~gg~l~G~~l~~~~~D~~~~~~~~~~~a~~~a~~~~~~~~v~aiiGp 80 (396)
T cd06373 1 TLAVLLPKNNTSYPWSLPRVGPAIDIAVERVNADPGLLPGHNITLVFEDSECKCGCSESEAPLVAVDLYFQHKPDAFLGP 80 (396)
T ss_pred CeEEEcCCCCCCcccchhhhhhHHHHHHHHHhcCCCcCCCeEEEEEEecCccccccchhhhHHHHHHHHhccCCeEEECC
Confidence 4899999983 34667889999999999999998899999999999999 8899998888877 4599999999
Q ss_pred CchhhHHHHHHhhhcCCccEEecccCCCCCCc-CCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcCCCc----c
Q 003958 104 QDAVTSHVVSHVANELQVPLLSFSATDPTLSS-LQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDDDHG----R 178 (784)
Q Consensus 104 ~~s~~~~~va~~~~~~~ip~Is~~a~~~~l~~-~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~~~g----~ 178 (784)
.||..+.+++++++.++||+|+++++++.+++ ..||++||+.|++..++.++++++++++|+++++|+.+++++ .
T Consensus 81 ~~S~~~~av~~~~~~~~ip~Is~~as~~~lt~~~~~~~~fr~~p~~~~~~~a~~~~~~~~~w~~vaii~~~~~~~~~~~~ 160 (396)
T cd06373 81 GCEYAAAPVARFAAHWNVPVLTAGAPAAGFSDKSEYSTLTRTGPSYTKLGEFVLALHEHFNWSRAALLYHDDKNDDRPCY 160 (396)
T ss_pred CccchhHHHHHHHhcCCCceECccCCccccccchhcCceeeccccHHHHHHHHHHHHHHcCCeEEEEEEECCCCCcchHH
Confidence 99999999999999999999999999999987 679999999999999999999999999999999999987764 5
Q ss_pred hhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHcCCCCCCeEEEecCc
Q 003958 179 NGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIATSW 258 (784)
Q Consensus 179 ~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~ 258 (784)
...+.+.+.+++.|++|+... +.......|+..+++++++.. |+|++++...++..++++++++|++..+|+||..+.
T Consensus 161 ~~~~~~~~~~~~~g~~v~~~~-~~~~~~~~d~~~~l~~ik~~~-~vii~~~~~~~~~~~~~qa~~~g~~~~~yv~i~~~~ 238 (396)
T cd06373 161 FTLEGVYTVLKEENITVSDFP-FDEDKELDDYKELLRDISKKG-RVVIMCASPDTVREIMLAAHRLGLTSGEYVFFNIDL 238 (396)
T ss_pred HHHHHHHHHHhhcCceeeEEe-ecCCccccCHHHHHHHHHhcC-cEEEEecCHHHHHHHHHHHHHcCCCCCcEEEEEEcc
Confidence 567889999999999987543 442111478999999999865 999999999999999999999999999999998765
Q ss_pred cccccccCCCC--------CCCccccceeeEEEeeecCCchhHHHHHHHHHhhccCCC--CCCCCCCChhHHHHhhHHHH
Q 003958 259 LSTALDTNSPF--------PSDVMDDIQGVLTLRTYTPDSVLKRKFISRWRNLTDAKT--PNGYIGLNAYGFYAYDTVWL 328 (784)
Q Consensus 259 ~~~~~~~~~~~--------~~~~~~~~~g~~~~~~~~~~~~~~~~f~~~~~~~~~~~~--~~~~~~~~~~~~~~YDAv~~ 328 (784)
........+.. .....+..+|++++....++.+.+++|.++|+++..... ..+...++.+++.+|||+++
T Consensus 239 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~~a~~~YDav~~ 318 (396)
T cd06373 239 FGSSLYGGGPWWWERGDEDDEKAKEAYQALMTITLREPDNPEYKEFSLEVKERAKKKFNTTSDDSLVNFFAGAFYDAVLL 318 (396)
T ss_pred chhhhccCCCCcCCCCCcccHHHHHHHHHheEEecCCCCChHHHHHHHHHHHHhhhcCCCCcchhHHHHHHHHHHHHHHH
Confidence 43211100000 011223456788888777788889999999987532100 01112356788999999999
Q ss_pred HHHHHHHHhhcCCccccccCCccccccCCcccccccccCCchHHHHHHHhccccceeeeEEEecCCCCcCCcEEEEEe--
Q 003958 329 LARAINSFFKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANMTGTAGPARFNSHGDLINPAYEIINV-- 406 (784)
Q Consensus 329 ~a~Al~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~l~~~l~~~~f~g~tG~v~Fd~~g~~~~~~~~I~~~-- 406 (784)
+++||+++.+++++ +.++..|.++|++++|+|++|+++||++|++ ...|.|+++
T Consensus 319 ~a~Al~~~~~~~~~-----------------------~~~~~~i~~~l~~~~f~G~tG~v~fd~~G~~-~~~~~v~~~~~ 374 (396)
T cd06373 319 YALALNETLAEGGD-----------------------PRDGTNITRRMWNRTFEGITGNVSIDENGDR-ESDFSLWDMTD 374 (396)
T ss_pred HHHHHHHHHhccCC-----------------------CCChHHHHHHhcCCceecccCceEeecCCcc-cceeeeeeccC
Confidence 99999998654321 1258999999999999999999999999997 677888665
Q ss_pred -eccceEEEEEecCCC
Q 003958 407 -IGTGYRRIGYWSNYS 421 (784)
Q Consensus 407 -~~~~~~~VG~w~~~~ 421 (784)
++++++.+|.|+...
T Consensus 375 ~~~g~~~~~~~~~~~~ 390 (396)
T cd06373 375 TETGTFEVVANYNGSN 390 (396)
T ss_pred CCCceEEEEeeccccc
Confidence 567899999998764
No 26
>cd06372 PBP1_GC_G_like Ligand-binding domain of membrane guanylyl cyclase G. This group includes the ligand-binding domain of membrane guanylyl cyclase G (GC-G) which is a sperm surface receptor and might function, similar to its sea urchin counterpart, in the early signaling event that regulates the Ca2+ influx/efflux and subsequent motility response in sperm. GC-G appears to be a pseudogene in human. Furthermore, in contrast to the other orphan receptor GCs, GC-G has a broad tissue distribution in rat, including lung, intestine, kidney, and skeletal muscle.
Probab=100.00 E-value=2.2e-42 Score=375.55 Aligned_cols=360 Identities=16% Similarity=0.255 Sum_probs=286.8
Q ss_pred EEEEEeecC---CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhc-CceEEEccCchhh
Q 003958 33 NIGALLSFS---TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEG-QTVAIIGPQDAVT 108 (784)
Q Consensus 33 ~IG~i~~~~---~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~-~v~aiiGp~~s~~ 108 (784)
+||++.|.+ +..+.....|+++|+++||+++++++|++|++++.|++|++..++.++++++.+ +|.+||||.||..
T Consensus 1 ~vg~~~p~~~~~~~~~~~~~~a~~lAi~~IN~~~~~l~~~~l~~~~~D~~~~~~~a~~~~~~l~~~~~v~aiiGp~~S~~ 80 (391)
T cd06372 1 TVGFQAPWNISHPFSAQRLGAALQIAMDKVNSDPVYLGNYSMEFTYTNSTCSAKESLAGFIDQVQKEHISALFGPACPEA 80 (391)
T ss_pred CceeeccccccCchhhhhHHHHHHHHHHHHhcCCCCCCCceEEEEEecCCCCccHHHHHHHHHHHhcCceEEECCCCCcH
Confidence 489999976 334666778999999999999999999999999999999999999999999875 9999999999999
Q ss_pred HHHHHHhhhcCCccEEecccCCCCCCc-CCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcC---CCc--chhHH
Q 003958 109 SHVVSHVANELQVPLLSFSATDPTLSS-LQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDD---DHG--RNGIA 182 (784)
Q Consensus 109 ~~~va~~~~~~~ip~Is~~a~~~~l~~-~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~---~~g--~~~~~ 182 (784)
+.+++++++.+++|+|+++++++.+++ ..||+++|+.|++..++.++++++++|+|++|++||.++ .++ ....+
T Consensus 81 ~~av~~va~~~~iP~is~~s~s~~ls~~~~~~~~~r~~p~~~~~~~a~~~l~~~~~w~~vaii~~~~~~~~~~~~~~~~~ 160 (391)
T cd06372 81 AEVTGLLASQWNIPMFGFVGQTAKLDNRFLYDTYVKLVPPKQKIGEVLQKSLQHFGWKHIGLFGGSSRDSSWDEVDELWK 160 (391)
T ss_pred HHHHHHHHhccCccEEEeecCCccccccccCCceEEecCchhhHHHHHHHHHHHCCCeEEEEEEeccccchhhhHHHHHH
Confidence 999999999999999999999999988 579999999999999999999999999999999998643 333 22344
Q ss_pred HHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHcCCCCCCeEEEecCc----
Q 003958 183 ALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIATSW---- 258 (784)
Q Consensus 183 ~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~---- 258 (784)
.+.+.++ .+++++..+.++ .+..++...+.+.+.+++|+||+++..++++.++++|.++||+.++|+||.+.+
T Consensus 161 ~~~~~~~-~~~~i~~~~~~~--~~~~d~~~~~l~~~~~~~~vii~~~~~~~~~~i~~~a~~~g~~~~~y~~i~~~~~~~~ 237 (391)
T cd06372 161 AVENQLK-FHFNITATVRYS--SSNPDLLQEKLRYISSVARVIILICSSEDAKAILQAAEKLGLMKGKFVFFLLQQFEDN 237 (391)
T ss_pred HHHHHHh-hCEEEEEEEecC--CCChHHHHHHHHhhhccceEEEEEcChHHHHHHHHHHHHcCCCCCCEEEEEehhhcCc
Confidence 5555554 678888877776 344666666656666899999999999999999999999999888899999542
Q ss_pred -cccccccCCCCCCCccccceeeEEEeeecCC-chhHHHHHHHHHhhccCCC----CCCCCCCChhHHHHhhHHHHHHHH
Q 003958 259 -LSTALDTNSPFPSDVMDDIQGVLTLRTYTPD-SVLKRKFISRWRNLTDAKT----PNGYIGLNAYGFYAYDTVWLLARA 332 (784)
Q Consensus 259 -~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~-~~~~~~f~~~~~~~~~~~~----~~~~~~~~~~~~~~YDAv~~~a~A 332 (784)
|...... . ......+..+|++++.+..+. .+..++|.++|+++++..+ .......+.+++++||||+++|+|
T Consensus 238 ~w~~~~~~-~-~~~~~~~~~~~~~~i~~~~~~~~~~~~~f~~~~~~~~~~~p~~~~~~~~~~~~~~a~~~yDav~~~A~A 315 (391)
T cd06372 238 FWKEVLTD-D-QVQHLPKVYESVFLIAPSSYGGYSGGYEFRKQVYQKLKRPPFQSSLSSEEQVSPYSAYLHDAVLLYALA 315 (391)
T ss_pred cccccCCC-c-chHHHHHHHhhEEEEecCCCCCCcchhHHHHHHHHHHhcCCccccccccccchHHHHHHHHHHHHHHHH
Confidence 2211100 0 001122356788877776542 3556778888877764211 111123467899999999999999
Q ss_pred HHHHhhcCCccccccCCccccccCCcccccccccCCchHHHHHHH---hccccceeeeEEEecCCCCcCCcEEEEEeec-
Q 003958 333 INSFFKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSIL---QANMTGTAGPARFNSHGDLINPAYEIINVIG- 408 (784)
Q Consensus 333 l~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~l~~~l~---~~~f~g~tG~v~Fd~~g~~~~~~~~I~~~~~- 408 (784)
++++++++. .|.++..+.++|+ +++|+|++|+|.||++|+| ...|.|+++++
T Consensus 316 l~~~~~~g~-----------------------~~~~g~~l~~~l~~~~~~~f~G~tG~v~fd~~G~r-~~~y~i~~~~~~ 371 (391)
T cd06372 316 VKEMLKAGK-----------------------DFRNGRQLVSTLRGANQVELQGITGLVLLDEQGKR-QMDYSVYALQKS 371 (391)
T ss_pred HHHHHhcCC-----------------------CCCCHHHHHHHHhhccCceEeccceeEEECCCCCc-ceeEEEEecccc
Confidence 999876532 2336889999999 6899999999999999997 88999999985
Q ss_pred -c--ceEEEEEecCCC
Q 003958 409 -T--GYRRIGYWSNYS 421 (784)
Q Consensus 409 -~--~~~~VG~w~~~~ 421 (784)
+ .+++||.|+..+
T Consensus 372 ~~~~~~~~vg~~~~~~ 387 (391)
T cd06372 372 GNSSLFLPFLHYDSHQ 387 (391)
T ss_pred CCccceeeEEEecchh
Confidence 2 389999998754
No 27
>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=9.9e-42 Score=364.95 Aligned_cols=368 Identities=21% Similarity=0.323 Sum_probs=290.8
Q ss_pred EEEEEeecCCcchhhHHHHHHHHHHHHhcCCCCCCCCEEEE--EEecCCCCHHHHHHHHHHHHhcCceEEEccCchhhHH
Q 003958 33 NIGALLSFSTNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKL--QMQDCNHSGFLALAEALHLMEGQTVAIIGPQDAVTSH 110 (784)
Q Consensus 33 ~IG~i~~~~~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~--~~~D~~~~~~~a~~~~~~li~~~v~aiiGp~~s~~~~ 110 (784)
+||++|+.++..+ +.|+++|+++||++..+|||.+|.+ ...|++ |+..+..++|++++++|.||+||.++..+.
T Consensus 1 ~IGaif~~~s~~~---~~Af~~Ai~~iN~~~~~l~~~~l~~~~~~~d~~-d~f~a~~~~c~l~~~gv~ai~Gp~~~~~~~ 76 (400)
T cd06391 1 HIGAIFDESAKKD---DEVFRMAVADLNQNNEILQTEKITVSVTFVDGN-NPFQAVQEACELMNQGILALVSSIGCTSAG 76 (400)
T ss_pred CcceeeccCCchH---HHHHHHHHHHhcCCccccCCCcceEEEEEeeCC-CcHHHHHHHHHHHhCCeEEEECCCcchHHH
Confidence 4899999987543 5699999999999999999995554 888985 999999999999999999999998888888
Q ss_pred HHHHhhhcCCccEEec----ccCC-----CCCCc--CCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcCCCcch
Q 003958 111 VVSHVANELQVPLLSF----SATD-----PTLSS--LQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDDDHGRN 179 (784)
Q Consensus 111 ~va~~~~~~~ip~Is~----~a~~-----~~l~~--~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~~~g~~ 179 (784)
.++.+|+.++||+|++ ++++ +.+++ ..||+++| |+ ..+++|+++++++|+|+++++++ |+++|..
T Consensus 77 ~v~~~~~~~~vP~i~~~~~~~~t~~~~~~~~~~~~~~~y~~~~r--p~-~~~~~ai~~li~~f~W~~v~i~~-d~~~~~~ 152 (400)
T cd06391 77 SLQSLADAMHIPHLFIQRSTAGTPRSSCGLTRSNRNDDYTLSVR--PP-VYLNDVILRVVTEYAWQKFIIFY-DTDYDIR 152 (400)
T ss_pred HHHHHhccCcCCeEEeecccccCccccCCCCCCCCcccceEEec--Ch-HHHHHHHHHHHHHcCCcEEEEEE-eCCccHH
Confidence 9999999999999974 4432 33443 46787888 54 67889999999999999999865 6778889
Q ss_pred hHHHHHHHHhccCcEEEEeeccCCCCC---hhHHHH-HHHHhhc--CCceEEEEeccCCcHHHHHHHHHHcCCCCCCeEE
Q 003958 180 GIAALGDTLAAKRCRISFKAPLSVEAT---EDEITD-LLVKVAL--TESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVW 253 (784)
Q Consensus 180 ~~~~l~~~l~~~gi~v~~~~~~~~~~~---~~d~~~-~l~~l~~--~~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~w 253 (784)
..+.+.+.+++.|+||.... +..... ...+.. .+++|++ +..++||+++.++.+..++++|+++||++.+|+|
T Consensus 153 ~l~~l~~~~~~~~i~I~~~~-~~~~~~~~~~~~~~~~~~~~l~~~~~~~rviVl~~~~~~~~~ll~~a~~~gm~~~~y~w 231 (400)
T cd06391 153 GIQEFLDKVSQQGMDVALQK-VENNINKMITGLFRTMRIEELNRYRDTLRRAILVMNPATAKSFITEVVETNLVAFDCHW 231 (400)
T ss_pred HHHHHHHHHHHcCCeEEEEe-cCcchhhhhHHHHHHHHHHHHHhhcccccEEEEECCcHHHHHHHHHHHHcCCCCCCeEE
Confidence 99999999999999999743 221111 012222 4556665 6679999999999999999999999999999999
Q ss_pred EecCccccccccCCCCCCCccccceeeEEEeeecCCchhHHHHHHHHHhhccC--CCCCC--CCCCChhHHHHhhHHHHH
Q 003958 254 IATSWLSTALDTNSPFPSDVMDDIQGVLTLRTYTPDSVLKRKFISRWRNLTDA--KTPNG--YIGLNAYGFYAYDTVWLL 329 (784)
Q Consensus 254 i~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~f~~~~~~~~~~--~~~~~--~~~~~~~~~~~YDAv~~~ 329 (784)
|++++.....+..+ .......|+.++.++.|.....++|..+|+.+++. +...+ ...+..+++.+||||+++
T Consensus 232 i~t~~~~~~~dl~~----~~~~~~~~v~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~alayDaV~~~ 307 (400)
T cd06391 232 IIINEEISDMDVQE----LVRRSIGRLTIIRQTFPLPQNISQRCFRGNHRISSSLCDPKDPFAQMMEISNLYIYDTVLLL 307 (400)
T ss_pred EEeCccccccccch----HHhcccceEEEeccCCchHHHHHHHHHHHhhhccccccCccccccccccchhhHHHHHHHHH
Confidence 99998887766532 12334567777888887777888888888876632 11111 113467899999999999
Q ss_pred HHHHHHHhhcCCccccccCCccccccCCcccc--cccccCCchHHHHHHHhccccceeeeEEEecCCCCcCCcEEEEEee
Q 003958 330 ARAINSFFKQGGNLSFSKDSRLSDIQGHLRLD--SLRIFNGGNLLRDSILQANMTGTAGPARFNSHGDLINPAYEIINVI 407 (784)
Q Consensus 330 a~Al~~~~~~~~~~~~~~~~~~~~~~g~~~~~--~~~~~~~~~~l~~~l~~~~f~g~tG~v~Fd~~g~~~~~~~~I~~~~ 407 (784)
|+|++++.......... ...|. +...|..|..|+++|++++|+|+||++.|+++|+|.++.|+|+++.
T Consensus 308 A~A~~~l~~~~~~~~~~----------~~~c~~~~~~~w~~G~~ll~~i~~~~f~GlTG~i~f~~~g~r~~~~~dIin~~ 377 (400)
T cd06391 308 ANAFHKKLEDRKWHSMA----------SLSCIRKNSKPWQGGRSMLETIKKGGVSGLTGELEFNENGGNPNVHFEILGTN 377 (400)
T ss_pred HHHHHHHHhhccccCCC----------CcccccCCCCCCCChHHHHHHHHhcCcccceeceEECCCCCccCCceEEEEee
Confidence 99999875332211100 23454 3458999999999999999999999999999999999999999996
Q ss_pred -----ccceEEEEEecCCCCC
Q 003958 408 -----GTGYRRIGYWSNYSGL 423 (784)
Q Consensus 408 -----~~~~~~VG~w~~~~~l 423 (784)
+.++++||.|++..||
T Consensus 378 ~~~~~~~g~rkiG~Ws~~~gl 398 (400)
T cd06391 378 YGEDLGRGVRKLGCWNPITGL 398 (400)
T ss_pred ccccCCCcceEEEEEcCCcCC
Confidence 7789999999998764
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=100.00 E-value=1.7e-41 Score=365.16 Aligned_cols=353 Identities=20% Similarity=0.255 Sum_probs=281.7
Q ss_pred EEEEEeecC---CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEccCchhhH
Q 003958 33 NIGALLSFS---TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIGPQDAVTS 109 (784)
Q Consensus 33 ~IG~i~~~~---~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiGp~~s~~~ 109 (784)
+||++.|++ +..|.....|+++|+|+||+++++++|++|++++.|++|++..++..+.++ .++|.+||||.||..+
T Consensus 1 ~ig~~~p~sg~~~~~g~~~~~a~~lAie~iN~~g~il~g~~l~~~~~d~~~~~~~a~~~~~~~-~~~V~aviGp~~S~~~ 79 (382)
T cd06371 1 KVGVLGPWSCDPIFSKALPDVAARLAVSRINRDPSLSLGYWFDYVLLPEPCETSRALAAFLGY-EGYASAFVGPVNPGYC 79 (382)
T ss_pred CceEecCcccCchhhhhhHHHHHHHHHHHHhCCCCCCCCceEEEEEecCCCChhHHHHHHHcc-cCCceEEECCCCchHH
Confidence 589999997 455777889999999999999999889999999999999988776554433 4699999999999999
Q ss_pred HHHHHhhhcCCccEEecccCCCCCCc-CCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcCCCcchhHHHHHHHH
Q 003958 110 HVVSHVANELQVPLLSFSATDPTLSS-LQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTL 188 (784)
Q Consensus 110 ~~va~~~~~~~ip~Is~~a~~~~l~~-~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~~l 188 (784)
.+++++++.++||+|+++++++.+++ ..||+|+|+.|++ +.++++++++|+|++|++|++++++|....+.+.+.+
T Consensus 80 ~a~a~va~~~~iP~Is~~a~~~~lt~~~~y~~f~r~~~~~---~~~~~~~~~~~~w~~vaii~~~~~~~~~~~~~l~~~l 156 (382)
T cd06371 80 EAAALLAKEWDKALFSWGCVNYELDDVRSYPTFARTLPSP---SRVLFTVLRYFRWAHVAIVSSPQDIWVETAQKLASAL 156 (382)
T ss_pred HHHHHHHHhcCceEEecccCchhhcCcccCCCceecCCCc---HHHHHHHHHHCCCeEEEEEEecccchHHHHHHHHHHH
Confidence 99999999999999999999999997 6799999999986 4678899999999999999999999999999999999
Q ss_pred hccCcEEEEeeccCCCCChhHHHHHHHHhhcCC-ceEEEEeccC-----CcHHHHHHHHHHcCCCCCCeEEEecCccccc
Q 003958 189 AAKRCRISFKAPLSVEATEDEITDLLVKVALTE-SRIIVVHTHY-----NRGPVVFHVAQYLGMLGTGYVWIATSWLSTA 262 (784)
Q Consensus 189 ~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~-~~vIvl~~~~-----~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~ 262 (784)
++.|++|+..+.++ .+..|+..+|++||..+ +|+||+++.. .++..++++|+++||+..+|+||+++.....
T Consensus 157 ~~~gi~v~~~~~~~--~~~~d~~~~L~~lk~~~~~~viv~~~~~~~~~~~~~~~i~~qa~~~Gm~~~~y~~i~~d~~~~~ 234 (382)
T cd06371 157 RAHGLPVGLVTSMG--PDEKGAREALKKVRSADRVRVVIMCMHSVLIGGEEQRLLLETALEMGMTDGRYVFIPYDTLLYS 234 (382)
T ss_pred HHCCCcEEEEEEec--CCHHHHHHHHHHHhcCCCcEEEEEEeeccccCcHHHHHHHHHHHHcCCcCCcEEEEEecccccc
Confidence 99999999887776 46689999999999987 6999998765 6778999999999999999999998743211
Q ss_pred cc----cCCC--CCCCccccceeeEEEeeecCCchhHHHHHHHHHhhccCCCCCCCCCCChhHHHHhhHHHHHHHHHHHH
Q 003958 263 LD----TNSP--FPSDVMDDIQGVLTLRTYTPDSVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTVWLLARAINSF 336 (784)
Q Consensus 263 ~~----~~~~--~~~~~~~~~~g~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~~~a~Al~~~ 336 (784)
.+ .... .+.+...+.++++.+....+..+..+.|.+.|+.... ....+....+.+++.+|||++++|+|++++
T Consensus 235 ~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~f~~~~~~~~~-~~~~~~~~~~~~~~~~YDav~~~a~Al~~a 313 (382)
T cd06371 235 LPYRNVSYPALRNNSKLRRAYDAVLTITMDSGEQSFYEAFRAAQERGEI-PSDLEPEQVSPLFGTIYNSIYLLAHAVENA 313 (382)
T ss_pred CCCCCccccCCCCCHHHHHHhHhhEEEEecCCCCcHHHHHHHHHhcCCC-CCCCCccccchhHHHHHHHHHHHHHHHHHH
Confidence 10 0000 0112224677777776655444455555555432110 000111223456668999999999999998
Q ss_pred hhcCCccccccCCccccccCCcccccccccCCchHHHHHHHhccccceeeeEEEecCCCCcCCcEEEEEeeccceEEEEE
Q 003958 337 FKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANMTGTAGPARFNSHGDLINPAYEIINVIGTGYRRIGY 416 (784)
Q Consensus 337 ~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~l~~~l~~~~f~g~tG~v~Fd~~g~~~~~~~~I~~~~~~~~~~VG~ 416 (784)
++.+++ .++.++.++|++++|+|++|+++||++|++ ...|.|+++.+.+++-+-.
T Consensus 314 ~~~g~~------------------------~d~~~l~~~l~~~~f~GvtG~v~fd~~g~~-~~~~~v~~~~~~~~~~~~~ 368 (382)
T cd06371 314 RAAGGG------------------------VSGANLAQHTRNLEFQGFNQRLRTDSGGGG-QAPYVVLDTDGKGDQLYPT 368 (382)
T ss_pred HHhCCC------------------------ccHHHHHHHHhCccccccceEEEecCCCCc-ccceEEEecCCCCCeeeee
Confidence 764332 158899999999999999999999999996 7899999999866654433
Q ss_pred e
Q 003958 417 W 417 (784)
Q Consensus 417 w 417 (784)
+
T Consensus 369 ~ 369 (382)
T cd06371 369 Y 369 (382)
T ss_pred E
Confidence 3
No 29
>cd06352 PBP1_NPR_GC_like Ligand-binding domain of membrane guanylyl-cyclase receptors. Ligand-binding domain of membrane guanylyl-cyclase receptors. Membrane guanylyl cyclases (GC) have a single membrane-spanning region and are activated by endogenous and exogenous peptides. This family can be divided into three major subfamilies: the natriuretic peptide receptors (NPRs), sensory organ-specific membrane GCs, and the enterotoxin/guanylin receptors. The binding of peptide ligands to the receptor results in the activation of the cytosolic catalytic domain. Three types of NPRs have been cloned from mammalian tissues: NPR-A/GC-A, NPR-B/ GC-B, and NPR-C. In addition, two of the GCs, GC-D and GC-G, appear to be pseudogenes in humans. Atrial natriuretic peptide (ANP) and brain natriuretic peptide (BNP) are produced in the heart, and both bind to the NPR-A. NPR-C, also termed the clearance receptor, binds each of the natriuretic peptides and can alter circulating levels of these peptides. The l
Probab=100.00 E-value=1.2e-41 Score=370.45 Aligned_cols=364 Identities=22% Similarity=0.355 Sum_probs=309.6
Q ss_pred EEEEEeecC---CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhc-CceEEEccCchhh
Q 003958 33 NIGALLSFS---TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEG-QTVAIIGPQDAVT 108 (784)
Q Consensus 33 ~IG~i~~~~---~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~-~v~aiiGp~~s~~ 108 (784)
+||+++|++ +..|.....|+++|+|+||+++++++|++|++++.|+++++..+++.+.+++.+ +|.+||||.+|..
T Consensus 1 kvG~~~~~sG~~~~~g~~~~~a~~lAve~iN~~g~~i~g~~l~~~~~D~~~~~~~a~~~a~~l~~~~~v~aiiG~~~s~~ 80 (389)
T cd06352 1 TVGVLLPWNTDYPFSLARVGPAIQLAVERVNADPNLLPGYDFTFVYLDTECSESVALLAAVDLYWEHNVDAFIGPGCPYA 80 (389)
T ss_pred CeEEEcCCCCCCCchhhcchHHHHHHHHHHhcCCCCCCCceEEEEEecCCCchhhhHHHHHHHHhhcCCcEEECCCChhH
Confidence 599999998 456888899999999999999976689999999999999999999999999875 9999999999999
Q ss_pred HHHHHHhhhcCCccEEecccCCCCCCc-CCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcCC-CcchhHHHHHH
Q 003958 109 SHVVSHVANELQVPLLSFSATDPTLSS-LQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDDD-HGRNGIAALGD 186 (784)
Q Consensus 109 ~~~va~~~~~~~ip~Is~~a~~~~l~~-~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~~-~g~~~~~~l~~ 186 (784)
+.++++++..+++|+|+++++++.+++ ..+||+||+.|++..++.++++++++++|++++++++++. ||....+.+++
T Consensus 81 ~~a~~~~~~~~~ip~Is~~~~~~~~~~~~~~~~~fr~~~~~~~~~~a~~~~l~~~~~~~v~ii~~~~~~~g~~~~~~~~~ 160 (389)
T cd06352 81 CAPVARLAAHWNIPMISWGCVALSLSDKSEYPTLTRTLPPARKLGEAVLALLRWFNWHVAVVVYSDDSENCFFTLEALEA 160 (389)
T ss_pred HHHHHHHHhcCCCCEecccccccccCccccCCceeecCCcHHHHHHHHHHHHHHcCceEEEEEEecCCccHHHHHHHHHH
Confidence 999999999999999999999888887 5789999999999999999999999999999999998887 99999999999
Q ss_pred HHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHcCCCCCCeEEEecCcccccccc-
Q 003958 187 TLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIATSWLSTALDT- 265 (784)
Q Consensus 187 ~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~- 265 (784)
.+++.|++|+....++......|+..+++++++.. |+|++++...++..++++++++|+...+++||+.+.+......
T Consensus 161 ~~~~~G~~v~~~~~~~~~~~~~d~~~~l~~i~~~~-~vii~~~~~~~~~~~l~q~~~~g~~~~~~~~i~~~~~~~~~~~~ 239 (389)
T cd06352 161 ALREFNLTVSHVVFMEDNSGAEDLLEILQDIKRRS-RIIIMCGSSEDVRELLLAAHDLGLTSGDYVFILIDLFNYSLPYQ 239 (389)
T ss_pred HHHhcCCeEEEEEEecCCccchhHHHHHHHhhhcc-eEEEEECCHHHHHHHHHHHHHcCCCCCcEEEEEEehhccccccC
Confidence 99999999999888873212688999999999887 9999998889999999999999998888999998765443211
Q ss_pred -------CCCCCCCccccceeeEEEeeecCCchhHHHHHHHHHhhccCCCCC---CCCCCChhHHHHhhHHHHHHHHHHH
Q 003958 266 -------NSPFPSDVMDDIQGVLTLRTYTPDSVLKRKFISRWRNLTDAKTPN---GYIGLNAYGFYAYDTVWLLARAINS 335 (784)
Q Consensus 266 -------~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~---~~~~~~~~~~~~YDAv~~~a~Al~~ 335 (784)
.....+...+..+|++++.+..+..+.+++|.++|+++++..+.. ....++.++..+|||++++++|+++
T Consensus 240 ~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~a~~~YDav~~~a~Al~~ 319 (389)
T cd06352 240 NSYPWERGDGDDEKAKEAYDAVLTITLRPPDNPEYEEFSEEVKEAAKRPPFNTDAEPEQVSPYAGYLYDAVLLYAHALNE 319 (389)
T ss_pred CCCCcccCCcccHHHHHHHHhheEEEecCCCCchHHHHHHHHHHHHhcccCccCCCccccchhhhhHHHHHHHHHHHHHH
Confidence 011112234567888888887777889999999999988631111 1224567899999999999999999
Q ss_pred HhhcCCccccccCCccccccCCcccccccccCCchHHHHHHHhccccceeeeEEEecCCCCcCCcEEEEEeec--cceEE
Q 003958 336 FFKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANMTGTAGPARFNSHGDLINPAYEIINVIG--TGYRR 413 (784)
Q Consensus 336 ~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~l~~~l~~~~f~g~tG~v~Fd~~g~~~~~~~~I~~~~~--~~~~~ 413 (784)
+..++.+ +.++..+.+.|++++|.|++|++.||++|+| ...|.|+++++ +.+..
T Consensus 320 ~~~~~~~-----------------------~~~~~~v~~~l~~~~f~g~~G~v~fd~~G~~-~~~~~v~~~~~~~~~~~~ 375 (389)
T cd06352 320 TLAEGGD-----------------------YNGGLIITRRMWNRTFSGITGPVTIDENGDR-EGDYSLLDLDSTGGQLEV 375 (389)
T ss_pred HHHhCCC-----------------------CCchHHHHHHhcCcEEEeeeeeEEEcCCCCe-eeeEEEEEecCCCceEEE
Confidence 8665321 2258889999999999999999999999997 67899999986 56788
Q ss_pred EEEecCCC
Q 003958 414 IGYWSNYS 421 (784)
Q Consensus 414 VG~w~~~~ 421 (784)
++.++...
T Consensus 376 ~~~~~~~~ 383 (389)
T cd06352 376 VYLYDTSS 383 (389)
T ss_pred EEeccccc
Confidence 88887654
No 30
>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=2.5e-41 Score=359.92 Aligned_cols=364 Identities=18% Similarity=0.266 Sum_probs=287.4
Q ss_pred EEEEEeecCCcchhhHHHHHHHHHHHHhcCCCCCC-CCEEEEEEecC-CCCHHHHHHHHHHHHhcCceEEEccCchhhHH
Q 003958 33 NIGALLSFSTNVGKVAKLAIKAAVDDVNSDPTTLG-GTKLKLQMQDC-NHSGFLALAEALHLMEGQTVAIIGPQDAVTSH 110 (784)
Q Consensus 33 ~IG~i~~~~~~~g~~~~~a~~~Ave~IN~~~~il~-g~~l~~~~~D~-~~~~~~a~~~~~~li~~~v~aiiGp~~s~~~~ 110 (784)
+||+||+..+ .....|+++|++.+|.+..+++ +.+|...+... ..|+..+.+++|+++++||.||+||.+|..+.
T Consensus 1 ~iG~if~~~~---~~~~~af~~a~~~~n~~~~~~~~~~~l~~~~~~~~~~dsf~~~~~~C~~~~~gV~AI~Gp~ss~~~~ 77 (371)
T cd06388 1 QIGGLFIRNT---DQEYTAFRLAIFLHNTSPNASEAPFNLVPHVDNIETANSFAVTNAFCSQYSRGVFAIFGLYDKRSVH 77 (371)
T ss_pred CCceeecCCc---hHHHHHHHHHHHHhhccccccccceEEeeeeeecCCCChhHHHHHHHHHHhCCceEEEecCCHHHHH
Confidence 4899998654 3467999999999998865533 25677665543 35999999999999999999999999999999
Q ss_pred HHHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcCCCcchhHHHHHHHHhc
Q 003958 111 VVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAA 190 (784)
Q Consensus 111 ~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~~l~~ 190 (784)
+++++|+..+||+|+++++ ++..+.+.+++.|+ +..++++++++++|++|++||+ .++|...++.+.+.+++
T Consensus 78 ~v~~i~~~~~IP~I~~~~~----~~~~~~f~i~~~p~---~~~a~~~~i~~~~wk~vaiiYd-~~~~~~~lq~l~~~~~~ 149 (371)
T cd06388 78 TLTSFCSALHISLITPSFP----TEGESQFVLQLRPS---LRGALLSLLDHYEWNRFVFLYD-TDRGYSILQAIMEKAGQ 149 (371)
T ss_pred HHHHHhhCCCCCeeecCcc----ccCCCceEEEeChh---hhhHHHHHHHhcCceEEEEEec-CCccHHHHHHHHHhhHh
Confidence 9999999999999997654 12334555566666 4578888999999999999995 34555778999999999
Q ss_pred cCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHcCCCCCCeEEEecCccccccccCCCCC
Q 003958 191 KRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIATSWLSTALDTNSPFP 270 (784)
Q Consensus 191 ~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~~~~~~ 270 (784)
.|++|+...... .+..|++.+|++|+++++++||+.|.++.+..+++||+++||+.++|+||+++......+.
T Consensus 150 ~g~~v~~~~~~~--~~~~d~~~~L~~ik~~~~~~iil~~~~~~~~~il~qa~~~gm~~~~y~~il~~~~~~~~~l----- 222 (371)
T cd06388 150 NGWQVSAICVEN--FNDASYRRLLEDLDRRQEKKFVIDCEIERLQNILEQIVSVGKHVKGYHYIIANLGFKDISL----- 222 (371)
T ss_pred cCCeeeeEEecc--CCcHHHHHHHHHhcccccEEEEEECCHHHHHHHHHHHHhcCccccceEEEEccCccccccH-----
Confidence 999988755443 2356999999999999999999999999999999999999999999999998753222221
Q ss_pred CCccccceeeEEEeeecCCchhHHHHHHHHHhhccCCC-CCCCCCCChhHHHHhhHHHHHHHHHHHHhhcCCccccccCC
Q 003958 271 SDVMDDIQGVLTLRTYTPDSVLKRKFISRWRNLTDAKT-PNGYIGLNAYGFYAYDTVWLLARAINSFFKQGGNLSFSKDS 349 (784)
Q Consensus 271 ~~~~~~~~g~~~~~~~~~~~~~~~~f~~~~~~~~~~~~-~~~~~~~~~~~~~~YDAv~~~a~Al~~~~~~~~~~~~~~~~ 349 (784)
.+....-.++.++....+..+.+++|.++|++.+.... +.. ..+...++.+||||++++.|++++.......+..
T Consensus 223 ~~~~~g~~nitg~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~-~~~~~~aAl~YDaV~l~a~A~~~l~~~~~~~~~~--- 298 (371)
T cd06388 223 ERFMHGGANVTGFQLVDFNTPMVTKLMQRWKKLDQREYPGSE-SPPKYTSALTYDGVLVMAEAFRNLRRQKIDISRR--- 298 (371)
T ss_pred HHHhccCCceEEEEeecCCChhHHHHHHHHHhcCccccCCCC-CCccchHHHHHHHHHHHHHHHHHHHhcCCCcccC---
Confidence 11112223377787778788899999999988765322 211 2466789999999999999999974432221100
Q ss_pred ccccccCCcccc--cccccCCchHHHHHHHhccccceeeeEEEecCCCCcCCcEEEEEeeccceEEEEEecCCCCC
Q 003958 350 RLSDIQGHLRLD--SLRIFNGGNLLRDSILQANMTGTAGPARFNSHGDLINPAYEIINVIGTGYRRIGYWSNYSGL 423 (784)
Q Consensus 350 ~~~~~~g~~~~~--~~~~~~~~~~l~~~l~~~~f~g~tG~v~Fd~~g~~~~~~~~I~~~~~~~~~~VG~w~~~~~l 423 (784)
..+..|. +...|.+|..|.++|++++|+|+||+++||++|+|.+..++|++++.+++++||+|++..||
T Consensus 299 -----~~~~~C~~~~~~~w~~G~~i~~~lk~~~~~GlTG~i~Fd~~G~r~~~~l~Ii~l~~~g~~kvG~W~~~~g~ 369 (371)
T cd06388 299 -----GNAGDCLANPAAPWGQGIDMERTLKQVRIQGLTGNIQFDHYGRRVNYTMDVFELKSNGPRKIGYWNDMDKL 369 (371)
T ss_pred -----CCCCCcCCCCCCCCcccHHHHHHHHhcCcCCCccceeECCCCCcccceEEEEEccCCCceEEEEEcCCCCc
Confidence 0023553 35579999999999999999999999999999999888999999999999999999998875
No 31
>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=4.4e-41 Score=359.20 Aligned_cols=362 Identities=17% Similarity=0.278 Sum_probs=290.1
Q ss_pred EEEEEeecCCcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEec-CCCCHHHHHHHHHHHHhcCceEEEccCchhhHHH
Q 003958 33 NIGALLSFSTNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQD-CNHSGFLALAEALHLMEGQTVAIIGPQDAVTSHV 111 (784)
Q Consensus 33 ~IG~i~~~~~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D-~~~~~~~a~~~~~~li~~~v~aiiGp~~s~~~~~ 111 (784)
+||+||+... ...+.|+++|++.+|... .+|...+.. ...|+..+.+++|+++++||.||+||.+|..+.+
T Consensus 1 ~ig~if~~~~---~~~~~af~~a~~~~n~~~-----~~l~~~~~~~~~~dsf~~~~~~C~~~~~GV~AI~Gp~ss~~~~~ 72 (370)
T cd06389 1 QIGGLFPRGA---DQEYSAFRVGMVQFSTSE-----FRLTPHIDNLEVANSFAVTNAFCSQFSRGVYAIFGFYDKKSVNT 72 (370)
T ss_pred CCceeecCCc---hHHHHHHHHHHHHhcccC-----ceeeeeeEEecccchHHHHHHHHHHhhcCcEEEEecCCHHHHHH
Confidence 4899998754 356799999999999862 566664433 3458999999999999999999999999999999
Q ss_pred HHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcCCCcchhHHHHHHHHhcc
Q 003958 112 VSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAK 191 (784)
Q Consensus 112 va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~~l~~~ 191 (784)
++++|+..+||+|++.++. +..+++.+++.|+ ...++++++++|+|++|++||+ ++||...++.+.+.+++.
T Consensus 73 v~~i~~~~~IP~I~~~~~~----~~~~~f~~~~~p~---~~~ai~d~i~~~~wk~vailYd-sd~gl~~lq~l~~~~~~~ 144 (370)
T cd06389 73 ITSFCGTLHVSFITPSFPT----DGTHPFVIQMRPD---LKGALLSLIEYYQWDKFAYLYD-SDRGLSTLQAVLDSAAEK 144 (370)
T ss_pred HHHhhccCCCCeeeecCCC----CCCCceEEEecch---hhhHHHHHHHhcCCcEEEEEec-CchHHHHHHHHHHhhccC
Confidence 9999999999999986542 3357888899988 4789999999999999999997 569999999999999999
Q ss_pred CcEEEEee--ccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHcCCCCCCeEEEecCccccccccCCCC
Q 003958 192 RCRISFKA--PLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIATSWLSTALDTNSPF 269 (784)
Q Consensus 192 gi~v~~~~--~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~~~~~ 269 (784)
|+.|+... .+.......|++.+|++|++.++++||+.|+.+.+..++++|.++||+.+.|+||+++......+..
T Consensus 145 g~~V~~~~~~~i~~~~~~~d~~~~L~~ik~~~~~~Iil~~~~~~~~~il~qa~~~gm~~~~y~~il~~~~~~~~~l~--- 221 (370)
T cd06389 145 KWQVTAINVGNINNDRKDEAYRSLFQDLENKKERRVILDCERDKVNDIVDQVITIGKHVKGYHYIIANLGFTDGDLS--- 221 (370)
T ss_pred CceEEEEEeecCCCccchHHHHHHHHHhccccceEEEEECCHHHHHHHHHHHHHhCccccceEEEEccCCccccchh---
Confidence 98776443 2222234669999999999999999999999999999999999999999999999987533222221
Q ss_pred CCCccccceeeEEEeeecCCchhHHHHHHHHHhhcc-CCCCCCCCCCChhHHHHhhHHHHHHHHHHHHhhcCCccccccC
Q 003958 270 PSDVMDDIQGVLTLRTYTPDSVLKRKFISRWRNLTD-AKTPNGYIGLNAYGFYAYDTVWLLARAINSFFKQGGNLSFSKD 348 (784)
Q Consensus 270 ~~~~~~~~~g~~~~~~~~~~~~~~~~f~~~~~~~~~-~~~~~~~~~~~~~~~~~YDAv~~~a~Al~~~~~~~~~~~~~~~ 348 (784)
.....-.++.++....++.+..++|.++|++... .+++.....++..++.+||||++++.|++++..........
T Consensus 222 --~~~~~~~nitg~~~~~~~~~~v~~f~~~~~~~~~~~~~~~~~~~~~~~aAl~yDAV~v~a~A~~~l~~~~~~~~~~-- 297 (370)
T cd06389 222 --KIQFGGANVSGFQIVDYDDPLVSKFIQRWSTLEEKEYPGAHTKTIKYTSALTYDAVQVMTEAFRNLRKQRIEISRR-- 297 (370)
T ss_pred --hhccCCcceEEEEEecCCCchHHHHHHHHHhcCccccCCCCCcCcchHHHHHHHHHHHHHHHHHHHHHcCCCcccC--
Confidence 1111233567777777888899999999987322 11122223467889999999999999999985443222110
Q ss_pred CccccccCCcccc--cccccCCchHHHHHHHhccccceeeeEEEecCCCCcCCcEEEEEeeccceEEEEEecCCCCC
Q 003958 349 SRLSDIQGHLRLD--SLRIFNGGNLLRDSILQANMTGTAGPARFNSHGDLINPAYEIINVIGTGYRRIGYWSNYSGL 423 (784)
Q Consensus 349 ~~~~~~~g~~~~~--~~~~~~~~~~l~~~l~~~~f~g~tG~v~Fd~~g~~~~~~~~I~~~~~~~~~~VG~w~~~~~l 423 (784)
.++..|. +...|.+|..|.++|++++|+|+||+++||++|+|.+..++|++++.+++++||.|++..||
T Consensus 298 ------~~~~~C~~~~~~~w~~G~~i~~~l~~~~~~GlTG~i~Fd~~G~r~~~~~~ii~l~~~g~~kvG~W~~~~~~ 368 (370)
T cd06389 298 ------GNAGDCLANPAVPWGQGVEIERALKQVQVEGLTGNIKFDQNGKRINYTINVMELKSNGPRKIGYWSEVDKM 368 (370)
T ss_pred ------CCCCCcCCCCCCCCCCcHHHHHHHHhcccCccccceEeCCCCccccceEEEEEecCCcceEEEEEcCCCCc
Confidence 0023454 35578899999999999999999999999999999888999999999999999999988764
No 32
>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=7.8e-41 Score=363.56 Aligned_cols=362 Identities=16% Similarity=0.203 Sum_probs=283.3
Q ss_pred EEEEEeecCC----cchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHH----HHHHHHHHH-HhcCceEEEcc
Q 003958 33 NIGALLSFST----NVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGF----LALAEALHL-MEGQTVAIIGP 103 (784)
Q Consensus 33 ~IG~i~~~~~----~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~----~a~~~~~~l-i~~~v~aiiGp 103 (784)
+||+++|.+. ..-.....|+++|+|+||+++++++|++|++.++|+++++. .+...+... +.+++.+||||
T Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~a~~lAieeiN~~g~il~g~~l~~~~~D~~~~~~~~~~~~~~~~~~~~~~~~v~aviGp 80 (399)
T cd06384 1 TLAVVLPDNNLKYAWAWPRVGPAIRMAVERIQNKGKLLRGYTITLLNKSSELNGGCSESLAPLHAVDLKLYSDPDVFFGP 80 (399)
T ss_pred CeEEECCCCCCCCeeehhhhHHHHHHHHHHHhccCCcCCCceEEEEEeccCCccccchhhhHHHHHHHHhhcCCCEEECC
Confidence 4788888652 12235678999999999999998889999999999865533 332222221 23588999999
Q ss_pred CchhhHHHHHHhhhcCCccEEecccCCCCCCc--CCCCceEeecCChHHHHHHHHHHHHHcCCc-EEEEEEEcCCCcc--
Q 003958 104 QDAVTSHVVSHVANELQVPLLSFSATDPTLSS--LQFPYFVRTTQSDQYQMAAIAEIVDHYGWR-EVIAIYVDDDHGR-- 178 (784)
Q Consensus 104 ~~s~~~~~va~~~~~~~ip~Is~~a~~~~l~~--~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~-~v~ii~~d~~~g~-- 178 (784)
.||..+.+++++++.++||+|+++++++.+++ ..||++||+.|++..++.++..++++|+|+ ++++||.++..+.
T Consensus 81 ~~S~~~~av~~i~~~~~iP~Is~~at~~~ls~~~~~y~~~fR~~p~~~~~~~~~~~i~~~~~w~~~vaiiy~~~~~~~~~ 160 (399)
T cd06384 81 GCVYPTASVARFATHWRLPLITAGAPAFGFSNKTDEYRTTVRTGPSTTKLGEFVNHLHEHFNWTSRAALLYLDLKTDDRP 160 (399)
T ss_pred CCchHHHHHHHHHhhcCCcEEeeccchhhhccccccCCceEEecCcHHHHHHHHHHHHHhCCCcEEEEEEEecCCccCCc
Confidence 99999999999999999999999999988886 379999999999999999988889999999 6889987543221
Q ss_pred --hhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHcCCCCCCeEEEec
Q 003958 179 --NGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIAT 256 (784)
Q Consensus 179 --~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~wi~~ 256 (784)
...+.+.+.+++.|++|+....+. .+..|+..++++++. ++|+|++++...++..++++++++|+++++|+||+.
T Consensus 161 ~~~~~~~~~~~~~~~gi~v~~~~~~~--~~~~d~~~~l~~ik~-~~~vIi~~~~~~~~~~i~~qa~~~g~~~~~y~~i~~ 237 (399)
T cd06384 161 HYFISEGVFLALQEENANVSAHPYHI--EKNSDIIEIIQFIKQ-NGRIVYICGPLETFLEIMLQAQREGLTPGDYVFFYL 237 (399)
T ss_pred ceEehHHHHHHHHhcCceEEEEEEec--cchhhHHHHHHHHhh-cccEEEEeCCchHHHHHHHHHHHcCCCCCcEEEEEe
Confidence 135667788888999998765544 356899999999997 899999999999999999999999999999999987
Q ss_pred Cccccccc---cCC-------CCCCCccccceeeEEEeeecCCchhHHHHHHHHHhhccCCCCCC--CCCCChhHHHHhh
Q 003958 257 SWLSTALD---TNS-------PFPSDVMDDIQGVLTLRTYTPDSVLKRKFISRWRNLTDAKTPNG--YIGLNAYGFYAYD 324 (784)
Q Consensus 257 ~~~~~~~~---~~~-------~~~~~~~~~~~g~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~--~~~~~~~~~~~YD 324 (784)
++...... ... ...++..++.+++++++...+..+.+++|.++|++++....+.. ....+.+++.+||
T Consensus 238 d~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~v~~~~~~~~~~~~~~~F~~~~~~~~~~~~~~~~~p~~~~~~aa~~YD 317 (399)
T cd06384 238 DVFGESLRVKSPRESYKQMNHSSWTVLKEAFKSVFVITYREPENPEYKEFQRELHARAKEDFGVELEPSLMNFIAGCFYD 317 (399)
T ss_pred hhcccccccCCCCccccCCCCcccHHHHHHHhheEEeecCCCCCchHHHHHHHHHHHHhhhcCCCcCcchHhhhhhhhHH
Confidence 75432111 000 00122334678888888888888889999999988643211111 1112567899999
Q ss_pred HHHHHHHHHHHHhhcCCccccccCCccccccCCcccccccccCCchHHHHHHHhccccceeeeEEEecCCCCcCCcEEE-
Q 003958 325 TVWLLARAINSFFKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANMTGTAGPARFNSHGDLINPAYEI- 403 (784)
Q Consensus 325 Av~~~a~Al~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~l~~~l~~~~f~g~tG~v~Fd~~g~~~~~~~~I- 403 (784)
||+++|.|+++++++++ .|.++..|.++|++++|+|++|.+.||++|+| ...+.+
T Consensus 318 av~l~a~Al~~~~~~~~-----------------------~~~~g~~i~~~l~~~~f~GvtG~v~fd~~G~r-~~~~~~~ 373 (399)
T cd06384 318 GVMLYAMALNETLAEGG-----------------------SQKDGLNITRKMQDRRFWGVTGLVSIDKNNDR-DIDFDLW 373 (399)
T ss_pred HHHHHHHHHHHHHhcCC-----------------------CCCCcHhHHHHHhCceeecceeEEEECCCCCc-ccceEEE
Confidence 99999999999865432 23468999999999999999999999999997 556666
Q ss_pred --EEeeccceEEEEEecCCC
Q 003958 404 --INVIGTGYRRIGYWSNYS 421 (784)
Q Consensus 404 --~~~~~~~~~~VG~w~~~~ 421 (784)
.++++++++.||+|+...
T Consensus 374 ~~~~~~~g~~~~v~~~~~~~ 393 (399)
T cd06384 374 AMTDHETGKYEVVAHYNGIT 393 (399)
T ss_pred EeecCCCCeEEEEEEEcCCC
Confidence 466789999999998754
No 33
>cd06382 PBP1_iGluR_Kainate N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the kainate receptors. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the kainate receptors, non-NMDA ionotropic receptors which respond to the neurotransmitter glutamate. While this N-terminal domain belongs to the periplasmic-binding fold type I superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type II. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR. Kainate receptors have five subunits, GluR5, GluR6, GluR7, KA1, and KA2, which are structurally similar to AMPA and NMDA subunits of ionotropic glutamate receptors. KA1 and KA2 subunits can only form functional receptors with one of the GluR5-7 subunits. Moreover, GluR5-7 can also form functional homomeri
Probab=100.00 E-value=2.6e-40 Score=350.78 Aligned_cols=321 Identities=22% Similarity=0.325 Sum_probs=270.3
Q ss_pred EEEEEeecCCcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCC-CCHHHHHHHHHHHHhcCceEEEccCchhhHHH
Q 003958 33 NIGALLSFSTNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCN-HSGFLALAEALHLMEGQTVAIIGPQDAVTSHV 111 (784)
Q Consensus 33 ~IG~i~~~~~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~-~~~~~a~~~~~~li~~~v~aiiGp~~s~~~~~ 111 (784)
+||++|++ ..|.....|+++|+|+||+++|+++|++|++++.|++ +++..+.++++++++++|.+||||.+|..+.+
T Consensus 1 ~iG~i~~~--~~g~~~~~a~~lAv~~iN~~ggil~g~~l~~~~~d~~~~~~~~a~~~~~~li~~~V~aiiG~~~S~~~~a 78 (327)
T cd06382 1 RIGAIFDD--DDDSGEELAFRYAIDRINREKELLANTTLEYDIKRVKPDDSFETTKKVCDLLQQGVAAIFGPSSSEASSI 78 (327)
T ss_pred CeEEEecC--CCchHHHHHHHHHHHHhcccccccCCceEEEEEEEecCCCcHHHHHHhhhhhhcCcEEEECCCChhHHHH
Confidence 59999997 4578899999999999999999999999999999999 89999999999999889999999999999999
Q ss_pred HHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcCCCcchhHHHHHHHHhcc
Q 003958 112 VSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAK 191 (784)
Q Consensus 112 va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~~l~~~ 191 (784)
++++++.+++|+|+++++++.++ .++++||+.|++..++.++++++++++|++|++++++++++.. +++.+++.
T Consensus 79 v~~~~~~~~vP~Is~~~~~~~~~--~~~~~fr~~p~~~~~~~a~~~~~~~~~w~~vavl~~~~~~~~~----l~~~~~~~ 152 (327)
T cd06382 79 VQSICDAKEIPHIQTRWDPEPKS--NRQFTINLYPSNADLSRAYADIVKSFNWKSFTIIYESAEGLLR----LQELLQAF 152 (327)
T ss_pred HHHHHhccCCCceeccCCcCccc--cccceEEeCCCHHHHHHHHHHHHHhcCCcEEEEEecChHHHHH----HHHHHHhh
Confidence 99999999999999988877766 4578999999999999999999999999999999998875443 44555544
Q ss_pred Cc---EEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHcCCCCCCeEEEecCccccccccCCC
Q 003958 192 RC---RISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIATSWLSTALDTNSP 268 (784)
Q Consensus 192 gi---~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~~~~ 268 (784)
+. .+.. +.++. .. |++.++++|++.++|+|++.+...++..++++|+++|+.++.|+|+++++.....+..
T Consensus 153 ~~~g~~v~~-~~~~~--~~-d~~~~l~~i~~~~~d~vv~~~~~~~~~~~~~qa~~~g~~~~~~~~i~~~~~~~~~~l~-- 226 (327)
T cd06382 153 GISGITITV-RQLDD--DL-DYRPLLKEIKNSGDNRIIIDCSADILIELLKQAQQVGMMSEYYHYIITNLDLHTLDLE-- 226 (327)
T ss_pred ccCCCeEEE-EEccC--Cc-cHHHHHHHHHhcCceEEEEECCHHHHHHHHHHHHHhCccccceEEEEecCCccccchh--
Confidence 44 4444 44552 33 9999999999999999999999999999999999999999999999987755443321
Q ss_pred CCCCccccceeeEEEeeecCCchhHHHHHHHHHhhccC-CCCCCCCCCChhHHHHhhHHHHHHHHHHHHhhcCCcccccc
Q 003958 269 FPSDVMDDIQGVLTLRTYTPDSVLKRKFISRWRNLTDA-KTPNGYIGLNAYGFYAYDTVWLLARAINSFFKQGGNLSFSK 347 (784)
Q Consensus 269 ~~~~~~~~~~g~~~~~~~~~~~~~~~~f~~~~~~~~~~-~~~~~~~~~~~~~~~~YDAv~~~a~Al~~~~~~~~~~~~~~ 347 (784)
.......++.++.+..++++.+++|.++|+++++. +.+.....++.+++.+|||++++
T Consensus 227 ---~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~p~~~~a~~yDav~~~------------------ 285 (327)
T cd06382 227 ---DYRYSGVNITGFRLVDPDSPEVKEVIRSLELSWDEGCRILPSTGVTTESALMYDAVYLF------------------ 285 (327)
T ss_pred ---hhccCceeEEEEEEecCCchhHHHHHHHHHhhcccccccCCCCCcchhhhhhhceEEEe------------------
Confidence 12223346777878888889999999999999863 12222234667788888887554
Q ss_pred CCccccccCCcccccccccCCchHHHHHHHhccccceeeeEEEecCCCCcCCcEEEEEeeccceEEEEEecCCCCC
Q 003958 348 DSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANMTGTAGPARFNSHGDLINPAYEIINVIGTGYRRIGYWSNYSGL 423 (784)
Q Consensus 348 ~~~~~~~~g~~~~~~~~~~~~~~~l~~~l~~~~f~g~tG~v~Fd~~g~~~~~~~~I~~~~~~~~~~VG~w~~~~~l 423 (784)
|+||.++||++|+|.+..++|++++++++++||.|++..||
T Consensus 286 -----------------------------------g~tG~v~f~~~g~r~~~~~~~~~~~~~~~~~vg~w~~~~~~ 326 (327)
T cd06382 286 -----------------------------------GLTGRIEFDSSGQRSNFTLDVIELTESGLRKVGTWNSSEGL 326 (327)
T ss_pred -----------------------------------ecccceeeCCCCCEeeeEEEEEeccccCceEEEEECCCCCc
Confidence 67999999999999999999999999999999999987653
No 34
>PF01094 ANF_receptor: Receptor family ligand binding region The Prosite family is a sub-family of the Pfam family; InterPro: IPR001828 This describes a ligand binding domain and includes extracellular ligand binding domains of a wide range of receptors, as well as the bacterial amino acid binding proteins of known structure [].; PDB: 3SAJ_D 3Q41_B 3QEM_C 3QEK_A 3QEL_C 3MQ4_A 3QLV_G 3OM1_A 3QLU_A 3OM0_A ....
Probab=100.00 E-value=4e-39 Score=346.12 Aligned_cols=339 Identities=28% Similarity=0.498 Sum_probs=279.7
Q ss_pred HHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHH-HHHHHHhcCceEEEccCchhhHHHHHHhhhcCCccEEec
Q 003958 48 AKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALA-EALHLMEGQTVAIIGPQDAVTSHVVSHVANELQVPLLSF 126 (784)
Q Consensus 48 ~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~-~~~~li~~~v~aiiGp~~s~~~~~va~~~~~~~ip~Is~ 126 (784)
+..|+++|+++||+++++++|++|++.+.|+|++...+.. ..+.+..++|.+||||.|+..+.+++.+++.++||+|++
T Consensus 2 ~~~a~~~Ai~~iN~~~~~~~~~~l~~~~~d~~~~~~~~~~~~~~~~~~~~v~aviGp~~~~~~~~~~~~~~~~~ip~is~ 81 (348)
T PF01094_consen 2 VLAAVQLAIDEINNNPDLLPNITLEVQVFDTCSDDSFALQAAICSLNKQGVVAVIGPSCSSSAEAVASLASEWNIPQISP 81 (348)
T ss_dssp HHHHHHHHHHHHHHSSTSSTTSEEEEEEEEETTTTHHHHHHHHHHHHHHTECEEEETSSHHHHHHHHHHHHHTT-EEEES
T ss_pred HHHHHHHHHHHHHcCCCCCCCeEEEEEEEeeccCCcccccchhhhccCCCcEEEECCCcccccchhheeecccccceeec
Confidence 5789999999999999998999999999999955444444 444555679999999999999999999999999999999
Q ss_pred ccCCCCCCc-C-CCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcCCCcchhHHHHHHHHhccC-cEEEEeeccCC
Q 003958 127 SATDPTLSS-L-QFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKR-CRISFKAPLSV 203 (784)
Q Consensus 127 ~a~~~~l~~-~-~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~~l~~~g-i~v~~~~~~~~ 203 (784)
+++++.+++ + +||+++|+.|++..++++++++|++|+|++|++|++++++|....+.+++.+++.+ .++.......
T Consensus 82 ~~~~~~ls~~~~~~~~~~r~~p~~~~~~~a~~~~l~~~~w~~v~vv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~- 160 (348)
T PF01094_consen 82 GSTSPSLSDRKTRYPTFFRTVPSDSSQARALVDLLKHFGWTRVSVVYSDDDYGNSLADSFQDLLRERGGICVAFISVVI- 160 (348)
T ss_dssp SGGSGGGGSTTTTTTTEEESSB-HHHHHHHHHHHHHHTTSSEEEEEEESSHHHHHHHHHHHHHHHHHTTCEEEEEEEEE-
T ss_pred cccccccccchhhccccccccccHHHHHHHHHHhhhcCCCceeeeeccccccccccchhhhhhhcccccceeccccccc-
Confidence 999999988 3 79999999999999999999999999999999999999999999999999999965 5555412222
Q ss_pred CCChhHHHHHHHHhhc--CCceEEEEeccCCcHHHHHHHHHHcCCCCCCeEEEecCccccccccCCCCCCCccccceeeE
Q 003958 204 EATEDEITDLLVKVAL--TESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIATSWLSTALDTNSPFPSDVMDDIQGVL 281 (784)
Q Consensus 204 ~~~~~d~~~~l~~l~~--~~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~~~~~~~~~~~~~~g~~ 281 (784)
....+....++.+++ .++++||+++....++.++++|.++|+...+|+||+++.+....... .........|++
T Consensus 161 -~~~~~~~~~~~~l~~~~~~~rvvil~~~~~~~~~~l~~a~~~~~~~~~~~~i~~~~~~~~~~~~---~~~~~~~~~~~~ 236 (348)
T PF01094_consen 161 -SSDSDAEELLKKLKEIKSGARVVILCSSPEDARQFLEAAYELGMTSGDYVWILTDLDNSSFWQN---NEDFREAFQGVL 236 (348)
T ss_dssp -TTTSHHHHHHHHHHHHTTTTSEEEEESBHHHHHHHHHHHHHTTTSSTTSEEEEETTTTTTHTST---HCHHHCCHTTEE
T ss_pred -ccccchhhhhhhhhhccccceeeeeecccccccccccchhhhhccccceeEEeecccccccccc---ccccccccccee
Confidence 233445555555555 99999999999999999999999999999999999999876542110 134567888999
Q ss_pred EEeeecCCchhHHHHHHHHHhhccC-CCCCCCCCCChhHHHHhhHHHHHHHHHHHHhhcCCccccccCCccccccCCccc
Q 003958 282 TLRTYTPDSVLKRKFISRWRNLTDA-KTPNGYIGLNAYGFYAYDTVWLLARAINSFFKQGGNLSFSKDSRLSDIQGHLRL 360 (784)
Q Consensus 282 ~~~~~~~~~~~~~~f~~~~~~~~~~-~~~~~~~~~~~~~~~~YDAv~~~a~Al~~~~~~~~~~~~~~~~~~~~~~g~~~~ 360 (784)
++.+..+..+.+++|.++|+..... +.......+..++.++|||++++++|++++++++....
T Consensus 237 ~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~yDAv~~~a~al~~~~~~~~~~~---------------- 300 (348)
T PF01094_consen 237 GFTPPPPSSPEFEDFMKKWKESNNQSSTSGSDQEPSPYAAYAYDAVYLLAHALNRALQDGGPVT---------------- 300 (348)
T ss_dssp EEEESTTTSHHHHHHHHHHHTTTHTTTTTTTTSSGCHHHHHHHHHHHHHHHHHHHHHHHHSTTT----------------
T ss_pred eeeeecccccchhhhhcccChhhccCcccccccccceeeeeehhhhHHHHHHHHHHHHhccCCC----------------
Confidence 9999999999999999999975321 12223345678999999999999999999987643321
Q ss_pred ccccccCCchHHHHHHHhccccceeeeEEEec-CCCCcCCcEEEEEee
Q 003958 361 DSLRIFNGGNLLRDSILQANMTGTAGPARFNS-HGDLINPAYEIINVI 407 (784)
Q Consensus 361 ~~~~~~~~~~~l~~~l~~~~f~g~tG~v~Fd~-~g~~~~~~~~I~~~~ 407 (784)
.....|.+|..+.++|++++|+|++|++.||+ +|+|.+..|+|+++|
T Consensus 301 ~~~~~~~~g~~l~~~l~~~~f~G~tG~v~f~~~~G~~~~~~~~i~~~~ 348 (348)
T PF01094_consen 301 NGRNPWQNGSQLLKYLRNVSFEGLTGRVSFDSNDGDRTNYDYDILNMQ 348 (348)
T ss_dssp SSSGTSTTHHHHHHHHHTEEEEETTEEEEEETTTSBEESEEEEEEEE-
T ss_pred CCccccccHHHHHHHHhheeeeCCCCCEEEeCCCCCcCCCEEEEEECC
Confidence 11145778999999999999999999999999 999889999999985
No 35
>cd06394 PBP1_iGluR_Kainate_KA1_2 N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the KA1 and KA2 subunits of Kainate receptor. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the KA1 and KA2 subunits of Kainate receptor. While this N-terminal domain belongs to the periplasmic-binding fold type I superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type II. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR. There are five types of kainate receptors, GluR5, GluR6, GluR7, KA1, and KA2, which are structurally similar to AMPA and NMDA subunits of ionotropic glutamate receptors. KA1 and KA2 subunits can only form functional receptors with one of the GluR5-7 subunits. Moreover, GluR5-7 can also form functional homomeric receptor channels act
Probab=100.00 E-value=1.6e-39 Score=337.51 Aligned_cols=325 Identities=22% Similarity=0.367 Sum_probs=259.0
Q ss_pred EEEEEeecCCcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHH-HHHHHHHHHHhcCceEEEccCchhh-HH
Q 003958 33 NIGALLSFSTNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGF-LALAEALHLMEGQTVAIIGPQDAVT-SH 110 (784)
Q Consensus 33 ~IG~i~~~~~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~-~a~~~~~~li~~~v~aiiGp~~s~~-~~ 110 (784)
+||++|+..+..|.....|+++|++++|++++++++.+|++++.|+..++. .+..++|++++++|.|||||.+|.. +.
T Consensus 1 ~iG~i~d~~s~~G~~~~~a~~lAv~~iN~~~~~~~~~~l~~~~~d~~~d~~f~~~~~~~~~l~~gV~AIiGp~ss~~~~~ 80 (333)
T cd06394 1 RIAAILDDPMECGRGERLALALARERINRAPERLGKARVEVDIFELLRDSQYETTDTMCQILPKGVVSVLGPSSSPASSS 80 (333)
T ss_pred CceeeecCCccccHHHHHHHHHHHHHhccCccccCCceeEEEEeeccccChHHHHHHHHHHHhcCeEEEECCCCchHHHH
Confidence 489999999989999999999999999999999876799999999998764 7778899999889999999999965 67
Q ss_pred HHHHhhhcCCccEEecccCC-CCCCcCCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcCCCcchhHHHHHHHHh
Q 003958 111 VVSHVANELQVPLLSFSATD-PTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLA 189 (784)
Q Consensus 111 ~va~~~~~~~ip~Is~~a~~-~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~~l~ 189 (784)
+++++|+..+||+|++++.. +.+...+|++ .++.|++..+++|+++++++|+|++|++||+++++ ...+++.++
T Consensus 81 ~v~~i~~~~~VP~Is~~~~~~~~~~~~~~~~-i~l~P~~~~~~~Ai~dli~~~~W~~v~~iYe~d~~----l~~L~~~l~ 155 (333)
T cd06394 81 IVSHICGEKEIPHFKVGPEETPKLQYLRFAS-VNLHPSNEDISVAVAGILNSFNYPTASLICAKAEC----LLRLEELLR 155 (333)
T ss_pred HHHHHhhccCCceEEeccccCcccccccceE-EEecCCHHHHHHHHHHHHHhcCCCEEEEEEeCcHH----HHHHHHHHH
Confidence 99999999999999986443 3333334444 89999999999999999999999999999999986 445555555
Q ss_pred ccCc---EEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHcCCCCCCeEEEecCccccccccC
Q 003958 190 AKRC---RISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIATSWLSTALDTN 266 (784)
Q Consensus 190 ~~gi---~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~~ 266 (784)
..++ .+... .. .+..|++.+|++|++.++++||+.+.++.+..++++|+++||+.+.|+|++++......+..
T Consensus 156 ~~~~~~~~i~~~-~~---~~~~d~~~~L~~ik~~~~~~iVv~~~~~~a~~il~qa~~lGm~~~~y~~i~T~l~~~~~~L~ 231 (333)
T cd06394 156 QFLISKETLSVR-ML---DDSRDPTPLLKEIRDDKTATIIIDANASMSHTILLKASELGMTSAFYKYILTTMDFPLLRLD 231 (333)
T ss_pred hhcccCCceeeE-Ec---cCcccHHHHHHHHHhcCCCEEEEECChHHHHHHHHHHHHcCCCCCceEEEEecCCcccccHH
Confidence 4332 22211 11 24568999999999999999999999999999999999999999999999998766533331
Q ss_pred CCCCCCccccceeeEEEeeecCCchhHHHHHHHHHhhccC-CCCCCCCCCChhHHHHhhHHHHHHHHHHHHhhcCCcccc
Q 003958 267 SPFPSDVMDDIQGVLTLRTYTPDSVLKRKFISRWRNLTDA-KTPNGYIGLNAYGFYAYDTVWLLARAINSFFKQGGNLSF 345 (784)
Q Consensus 267 ~~~~~~~~~~~~g~~~~~~~~~~~~~~~~f~~~~~~~~~~-~~~~~~~~~~~~~~~~YDAv~~~a~Al~~~~~~~~~~~~ 345 (784)
+.......+.+++..+++.+..++|.+.|++++.+ +...........++..||||+++
T Consensus 232 -----~~~~~~~niTgF~l~d~~~~~v~~f~~~~~~~~~~~~~~~~~~~~~~~~al~~D~v~~~---------------- 290 (333)
T cd06394 232 -----SIVDDRSNILGFSMFNQSHAFYQEFIRSLNQSWRENCDHSPYTGPALSSALLFDAVYAV---------------- 290 (333)
T ss_pred -----HhhcCCcceEEEEeecCCcHHHHHHHHHHHHhhhhhcccccCCCcccceeeecceEEEE----------------
Confidence 22223445788888889999999999988876631 11111111122355555555332
Q ss_pred ccCCccccccCCcccccccccCCchHHHHHHHhccccceeeeEEEecCCCCcCCcEEEEEeeccceEEEEEecCCCCCc
Q 003958 346 SKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANMTGTAGPARFNSHGDLINPAYEIINVIGTGYRRIGYWSNYSGLS 424 (784)
Q Consensus 346 ~~~~~~~~~~g~~~~~~~~~~~~~~~l~~~l~~~~f~g~tG~v~Fd~~g~~~~~~~~I~~~~~~~~~~VG~w~~~~~l~ 424 (784)
|+||+|.||++|.|.+..++|++++.++.++||+|++..||.
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 789999999999999999999999999999999999988753
No 36
>PRK15404 leucine ABC transporter subunit substrate-binding protein LivK; Provisional
Probab=100.00 E-value=1.6e-37 Score=332.67 Aligned_cols=337 Identities=14% Similarity=0.173 Sum_probs=287.2
Q ss_pred CCceEEEEEEeecC---CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEccC
Q 003958 28 RPSVVNIGALLSFS---TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIGPQ 104 (784)
Q Consensus 28 ~~~~i~IG~i~~~~---~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiGp~ 104 (784)
.+++|+||++.|++ +..|.....++++|+++||+.+|+. |++|++++.|++++|..+++.+.+|++++|.+|+|+.
T Consensus 22 ~~~~I~IG~l~plSG~~a~~G~~~~~g~~~av~~iNa~GGi~-G~~ielv~~D~~~~p~~a~~~~~~Li~~~V~~iiG~~ 100 (369)
T PRK15404 22 LADDIKIAIVGPMSGPVAQYGDMEFTGARQAIEDINAKGGIK-GDKLEGVEYDDACDPKQAVAVANKVVNDGIKYVIGHL 100 (369)
T ss_pred cCCceEEEEeecCCCcchhcCHhHHHHHHHHHHHHHhcCCCC-CeEEEEEeecCCCCHHHHHHHHHHHHhCCceEEEcCC
Confidence 35689999999998 4568888999999999999999985 8999999999999999999999999998999999999
Q ss_pred chhhHHHHHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHH-HHcCCcEEEEEEEcCCCcchhHHH
Q 003958 105 DAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIV-DHYGWREVIAIYVDDDHGRNGIAA 183 (784)
Q Consensus 105 ~s~~~~~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l-~~~~w~~v~ii~~d~~~g~~~~~~ 183 (784)
+|..+.+++++++..++|+|++.++++.+++..++|+||+.+.+..++.++++++ ++++|+++++|++|+.||+...+.
T Consensus 101 ~s~~~~a~~~~~~~~~ip~i~~~s~~~~l~~~~~~~~fr~~~~~~~~~~~~~~~~~~~~~~k~va~i~~d~~~g~~~~~~ 180 (369)
T PRK15404 101 CSSSTQPASDIYEDEGILMITPAATAPELTARGYQLIFRTIGLDSDQGPTAAKYILEKVKPKRIAVLHDKQQYGEGLARS 180 (369)
T ss_pred CchhHHHhHHHHHHCCCeEEecCCCCHHHhcCCCceEEeCCCCcHHHHHHHHHHHHHhcCCCEEEEEeCCCchhHHHHHH
Confidence 9999999999999999999999999988887678999999999999999999976 557999999999999999999999
Q ss_pred HHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHcCCCCCCeEEEecCcccccc
Q 003958 184 LGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIATSWLSTAL 263 (784)
Q Consensus 184 l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~ 263 (784)
+++.+++.|.+++....++ .+..|+..++.++++.++|+|++.....++..++++++++|+..+ |+++.+.....
T Consensus 181 ~~~~~~~~G~~v~~~~~~~--~g~~D~~~~v~~l~~~~~d~v~~~~~~~~~~~~~k~~~~~G~~~~---~i~~~~~~~~~ 255 (369)
T PRK15404 181 VKDGLKKAGANVVFFEGIT--AGDKDFSALIAKLKKENVDFVYYGGYHPEMGQILRQAREAGLKTQ---FMGPEGVGNKS 255 (369)
T ss_pred HHHHHHHcCCEEEEEEeeC--CCCCchHHHHHHHHhcCCCEEEECCCchHHHHHHHHHHHCCCCCe---EEecCcCCCHH
Confidence 9999999999999888887 467899999999999999999988877888999999999998643 67665433211
Q ss_pred ccCCCCCCCccccceeeEEEeee-cCCchhHHHHHHHHHhhccCCCCCCCCCCChhHHHHhhHHHHHHHHHHHHhhcCCc
Q 003958 264 DTNSPFPSDVMDDIQGVLTLRTY-TPDSVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTVWLLARAINSFFKQGGN 342 (784)
Q Consensus 264 ~~~~~~~~~~~~~~~g~~~~~~~-~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~~~a~Al~~~~~~~~~ 342 (784)
.. ....+..+|+++..+. ...++..++|.+.|+++++ ..++.++..+||++++++.|++++..
T Consensus 256 ~~-----~~~~~~~~Gv~~~~~~~~~~~~~~~~f~~~~~~~~~-------~~~~~~~~~~Y~~~~~l~~Al~~aG~---- 319 (369)
T PRK15404 256 LS-----NIAGPASEGMLVTLPKRYDQDPANKAIVDAFKAKKQ-------DPSGPFVWTTYAAVQSLAAGINRAGS---- 319 (369)
T ss_pred HH-----HhhhhhhcCcEEEccCCCccChhHHHHHHHHHHhcC-------CCCccchHHHHHHHHHHHHHHHhhCC----
Confidence 00 1123456787765443 2346788999999998764 23345678999999999999998511
Q ss_pred cccccCCccccccCCcccccccccCCchHHHHHHHhccccceeeeEEEecCCCCcCCcEEEEEeeccc
Q 003958 343 LSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANMTGTAGPARFNSHGDLINPAYEIINVIGTG 410 (784)
Q Consensus 343 ~~~~~~~~~~~~~g~~~~~~~~~~~~~~~l~~~l~~~~f~g~tG~v~Fd~~g~~~~~~~~I~~~~~~~ 410 (784)
.++..|.++|++.+|+|+.|+++|+++|++....|.|.||++++
T Consensus 320 ------------------------~~~~~l~~al~~~~~~~~~G~~~~~~~g~~~~~~~~i~~~~~~~ 363 (369)
T PRK15404 320 ------------------------DDPAKVAKYLKANTFDTVIGPLSWDEKGDLKGFEFGVFEWHADG 363 (369)
T ss_pred ------------------------CCHHHHHHHHHhCCCCcceEeeEECCCCCcccCCEEEEEEEcCC
Confidence 14788999999999999999999999998778889999988654
No 37
>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=100.00 E-value=9.9e-37 Score=325.19 Aligned_cols=328 Identities=20% Similarity=0.266 Sum_probs=283.4
Q ss_pred EEEEEeecC---CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEccCchhhH
Q 003958 33 NIGALLSFS---TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIGPQDAVTS 109 (784)
Q Consensus 33 ~IG~i~~~~---~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiGp~~s~~~ 109 (784)
+||++.|++ +..|.....|+++|+++||+++++ +|++|++++.|+++++..+.+.+.++++++|.+|+||.++..+
T Consensus 1 ~iG~~~p~sG~~~~~g~~~~~g~~~a~~~iN~~ggi-~g~~i~~~~~D~~~~~~~~~~~~~~li~~~v~aiiG~~~s~~~ 79 (334)
T cd06342 1 KIGVAGPLTGPNAALGKDIKNGAQLAVEDINAKGGG-KGVKLELVVEDDQADPKQAVAVAQKLVDDGVVGVVGHLNSGVT 79 (334)
T ss_pred CeeEeccCCCcchhhcHHHHHHHHHHHHHHHhcCCC-CCeEEEEEEecCCCChHHHHHHHHHHHhCCceEEECCCccHhH
Confidence 589999998 456788999999999999999887 5999999999999999999999999999999999999999999
Q ss_pred HHHHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHH-HHcCCcEEEEEEEcCCCcchhHHHHHHHH
Q 003958 110 HVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIV-DHYGWREVIAIYVDDDHGRNGIAALGDTL 188 (784)
Q Consensus 110 ~~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l-~~~~w~~v~ii~~d~~~g~~~~~~l~~~l 188 (784)
.+++++++..+||+|+++++++.+.++.||++||+.|++..++.++++++ ++++|++|++++.+++||+...+.+++.+
T Consensus 80 ~~~~~~~~~~~ip~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~v~~~~~~g~~~~~~~~~~~ 159 (334)
T cd06342 80 IPASPIYADAGIVMISPAATNPKLTERGYKNVFRVVARDDQQGPAAAKYAVETLKAKKVAIIDDKTAYGQGLADEFKKAL 159 (334)
T ss_pred HHhHHHHHhCCCeEEecCCCCchhhcCCCceEEeccCCcHHHHHHHHHHHHHhcCCCEEEEEeCCcchhhHHHHHHHHHH
Confidence 99999999999999999887777766678999999999999999999986 57899999999999999999999999999
Q ss_pred hccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHcCCCCCCeEEEecCccccccccCCC
Q 003958 189 AAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIATSWLSTALDTNSP 268 (784)
Q Consensus 189 ~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~~~~ 268 (784)
++.|++|+....++ .+..|++..++++++.++++|++.+...++..+++++++.|+.. .|+++..+... ...
T Consensus 160 ~~~g~~v~~~~~~~--~~~~d~~~~l~~i~~~~~~~vi~~~~~~~~~~~~~~~~~~g~~~---~~~~~~~~~~~-~~~-- 231 (334)
T cd06342 160 KAAGGKVVAREGTT--DGATDFSAILTKIKAANPDAVFFGGYYPEAGPLVRQMRQLGLKA---PFMGGDGLCDP-EFI-- 231 (334)
T ss_pred HHcCCEEEEEecCC--CCCccHHHHHHHHHhcCCCEEEEcCcchhHHHHHHHHHHcCCCC---cEEecCccCCH-HHH--
Confidence 99999999988887 45688999999999999999999999999999999999999853 46766543211 110
Q ss_pred CCCCccccceeeEEEeeecC--CchhHHHHHHHHHhhccCCCCCCCCCCChhHHHHhhHHHHHHHHHHHHhhcCCccccc
Q 003958 269 FPSDVMDDIQGVLTLRTYTP--DSVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTVWLLARAINSFFKQGGNLSFS 346 (784)
Q Consensus 269 ~~~~~~~~~~g~~~~~~~~~--~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~~~a~Al~~~~~~~~~~~~~ 346 (784)
.......+|++...++.+ ..+..++|.++|+++++ ..++.++..+||+++++++|++++.
T Consensus 232 --~~~~~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~~-------~~~~~~~~~~yda~~~~~~al~~~~--------- 293 (334)
T cd06342 232 --KIAGDAAEGTYATFPGGPLEKMPAGKAFVARYKAKFG-------DPPGAYAPYAYDAANVLAEAIKKAG--------- 293 (334)
T ss_pred --HHhhHhhCCcEEEecCCCCCCChHHHHHHHHHHHHhC-------CCCchhHHHHHHHHHHHHHHHHHhC---------
Confidence 112245677777766555 46788999999998886 2346788999999999999999851
Q ss_pred cCCccccccCCcccccccccCCchHHHHHHHhccccceeeeEEEecCCCCcCCcEEEEEe
Q 003958 347 KDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANMTGTAGPARFNSHGDLINPAYEIINV 406 (784)
Q Consensus 347 ~~~~~~~~~g~~~~~~~~~~~~~~~l~~~l~~~~f~g~tG~v~Fd~~g~~~~~~~~I~~~ 406 (784)
..++..+.++|++.+|+|++|++.|+++|++.+..|+|+||
T Consensus 294 -------------------~~~~~~v~~~l~~~~~~g~~g~i~f~~~g~~~~~~~~~~~~ 334 (334)
T cd06342 294 -------------------STDPAKVADALRKVDFDGVTGKISFDAKGDLKGAAVTVYQV 334 (334)
T ss_pred -------------------CCCHHHHHHHHHhCCCCCcceeeEECCCCCcccCcEEEEeC
Confidence 11478999999999999999999999999999999999886
No 38
>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=100.00 E-value=1.7e-36 Score=321.47 Aligned_cols=320 Identities=22% Similarity=0.362 Sum_probs=265.1
Q ss_pred EEEEEeecCCcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecC-CCCHHHHHHHHHHHHhcCceEEEccCchhhHHH
Q 003958 33 NIGALLSFSTNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDC-NHSGFLALAEALHLMEGQTVAIIGPQDAVTSHV 111 (784)
Q Consensus 33 ~IG~i~~~~~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~-~~~~~~a~~~~~~li~~~v~aiiGp~~s~~~~~ 111 (784)
+||++++.+. .....|+++|+|+||+++|++++.++++.+.|+ .+++..++.++++|++++|.+||||.+|..+.+
T Consensus 1 ~iG~i~~~~~---~~~~~a~~lAv~~iN~~ggil~~~~l~~~~~d~~~~~~~~a~~~a~~li~~~V~aiiG~~~S~~~~a 77 (324)
T cd06368 1 RIGAIFDEDA---RQEELAFRFAIDRINTNEEILAKFTLVPDIDELNTNDSFELTNKACDLLSQGVAAIFGPSSSSSANT 77 (324)
T ss_pred CEEEEeCCCC---hHHHHHHHHHHHHhcccccccCCceeeeEEEEecCCChHHHHHHHHHHHhcCcEEEECCCCHHHHHH
Confidence 5899999986 678899999999999999999777999999998 589999999999999999999999999999999
Q ss_pred HHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcCCCcchhHHHHHHHHhcc
Q 003958 112 VSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAK 191 (784)
Q Consensus 112 va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~~l~~~ 191 (784)
++++++.++||+|+++++++.++. ++.+++.|+...++.++++++++++|++|++||+++++ ....+.+.+.++++
T Consensus 78 v~~i~~~~~ip~is~~~~~~~~~~---~~~~~~~~~~~~~~~a~~~~~~~~~w~~vaii~~~~~~-~~~l~~~~~~~~~~ 153 (324)
T cd06368 78 VQSICDALEIPHITTSWSPNPKPR---QFTINLYPSMRDLSDALLDLIKYFGWRKFVYIYDSDEG-LLRLQELLDALSPK 153 (324)
T ss_pred HHHHHhccCCCcEEecCCcCCCCC---cceEEecCCHHHHHHHHHHHHHhcCCCEEEEEECCcHh-HHHHHHHHHhhccC
Confidence 999999999999999988887762 33455567777899999999999999999999977664 44556677778888
Q ss_pred CcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHcCCCCCCeEEEecCccccccccCCCCCC
Q 003958 192 RCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIATSWLSTALDTNSPFPS 271 (784)
Q Consensus 192 gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~~~~~~~ 271 (784)
|++|+.....+ ...|++.+++++++.++|+|++.+...++..++++++++|+..+.|+||+++......+. .
T Consensus 154 g~~v~~~~~~~---~~~d~~~~l~~i~~~~~d~Vi~~~~~~~~~~i~~qa~~~g~~~~~~~~i~~~~~~~~~~~-----~ 225 (324)
T cd06368 154 GIQVTVRRLDD---DTDMYRPLLKEIKREKERRIILDCSPERLKEFLEQAVEVGMMSEYYHYILTNLDFHTLDL-----E 225 (324)
T ss_pred CceEEEEEecC---CchHHHHHHHHHhhccCceEEEECCHHHHHHHHHHHHHhccccCCcEEEEccCCccccch-----h
Confidence 99988765443 223899999999999999999999999999999999999999889999998754332211 1
Q ss_pred CccccceeeEEEeeecCCchhHHHHHHHHHhhccC-CCCCCCCCCChhHHHHhhHHHHHHHHHHHHhhcCCccccccCCc
Q 003958 272 DVMDDIQGVLTLRTYTPDSVLKRKFISRWRNLTDA-KTPNGYIGLNAYGFYAYDTVWLLARAINSFFKQGGNLSFSKDSR 350 (784)
Q Consensus 272 ~~~~~~~g~~~~~~~~~~~~~~~~f~~~~~~~~~~-~~~~~~~~~~~~~~~~YDAv~~~a~Al~~~~~~~~~~~~~~~~~ 350 (784)
.......++.++....++++..++|.++|+++++. +.......+..+++.+|||++++
T Consensus 226 ~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~p~~~aa~~yDav~~~--------------------- 284 (324)
T cd06368 226 LFRYGGVNITGFRLVDPDNPEVQKFIQRWERSDHRICPGSGLKPIKTESALTYDAVLLF--------------------- 284 (324)
T ss_pred hhhcCCceEEEEEEecCCChHHHHHHHHHHhccccccCCCCCCCcchhhHhhhcEEEEe---------------------
Confidence 11223345666666777888999999999998863 11112225677899999988654
Q ss_pred cccccCCcccccccccCCchHHHHHHHhccccceeeeEEEecCCCCcCCcEEEEEeeccceEEEEEecCCCC
Q 003958 351 LSDIQGHLRLDSLRIFNGGNLLRDSILQANMTGTAGPARFNSHGDLINPAYEIINVIGTGYRRIGYWSNYSG 422 (784)
Q Consensus 351 ~~~~~g~~~~~~~~~~~~~~~l~~~l~~~~f~g~tG~v~Fd~~g~~~~~~~~I~~~~~~~~~~VG~w~~~~~ 422 (784)
+|+++||++|+|.+..++|+++..+++..||.|++..+
T Consensus 285 ----------------------------------tg~~~f~~~g~~~~~~~~i~~~~~~~~~~~g~W~~~~~ 322 (324)
T cd06368 285 ----------------------------------TGRIQFDENGQRSNFTLDILELKEGGLRKVGTWNPEDG 322 (324)
T ss_pred ----------------------------------eeeeEeCCCCcCcceEEEEEEEcCCCceEEEEECCCCC
Confidence 56799999999999999999999999999999998765
No 39
>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=100.00 E-value=1.9e-36 Score=324.69 Aligned_cols=308 Identities=33% Similarity=0.527 Sum_probs=262.8
Q ss_pred EEEEEeecCCc-------------chhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhc----
Q 003958 33 NIGALLSFSTN-------------VGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEG---- 95 (784)
Q Consensus 33 ~IG~i~~~~~~-------------~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~---- 95 (784)
+||++||+|.. .|.....++.+|+++||+++++++|++|++++.|+|+++.++++.+.+++.+
T Consensus 1 ~ig~lf~~~~~~~~~~~~c~~~~~~~~~~~~~~~~Av~~iN~~~~~l~g~~l~l~~~D~~~~~~~a~~~a~~li~~~~~~ 80 (348)
T cd06350 1 IIGGLFPLHSGSESVSLKCGRFGKKGLQAAEAMLFAVEEINNDPDLLPNITLGYHIYDSCCSPAVALRAALDLLLSGEGT 80 (348)
T ss_pred CeEEEEeCcccccCCCcccceechHHHHHHHHHHHHHHHHcCCCccCCCCceeEEEEecCCcchHHHHHHHHHHhcCCCC
Confidence 48999999852 2456678999999999999999999999999999999999999999999975
Q ss_pred ----------CceEEEccCchhhHHHHHHhhhcCCccEEecccCCCCCCc-CCCCceEeecCChHHHHHHHHHHHHHcCC
Q 003958 96 ----------QTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSS-LQFPYFVRTTQSDQYQMAAIAEIVDHYGW 164 (784)
Q Consensus 96 ----------~v~aiiGp~~s~~~~~va~~~~~~~ip~Is~~a~~~~l~~-~~~p~~~r~~ps~~~~~~ai~~~l~~~~w 164 (784)
+|.+|+||.+|..+.+++++++.+++|+|+++++++.+++ ..||++||+.|++..++.++++++++++|
T Consensus 81 ~~~~~~~~~~~v~aiiG~~~S~~~~a~~~~~~~~~vp~is~~~~~~~ls~~~~~~~~fr~~p~~~~~~~a~~~~~~~~~~ 160 (348)
T cd06350 81 TPPYSCRKQPKVVAVIGPGSSSVSMAVAELLGLFKIPQISYGATSPLLSDKLQFPSFFRTVPSDTSQALAIVALLKHFGW 160 (348)
T ss_pred CCCCcCCCCCceEEEECCCccHHHHHHHHHHhcCcCceecccCCChhhccccccCCeeEecCCcHHHHHHHHHHHHHCCC
Confidence 8999999999999999999999999999999999999977 57999999999999999999999999999
Q ss_pred cEEEEEEEcCCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHc
Q 003958 165 REVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYL 244 (784)
Q Consensus 165 ~~v~ii~~d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~ 244 (784)
+++++++.+++||....+.+++.+++.|+||+..+.++......|+..++++|+++++|+|++++...++..++++++++
T Consensus 161 ~~v~~l~~~~~~g~~~~~~~~~~~~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vvv~~~~~~~~~~~~~~a~~~ 240 (348)
T cd06350 161 TWVGLVYSDDDYGRSGLSDLEEELEKNGICIAFVEAIPPSSTEEDIKRILKKLKSSTARVIVVFGDEDDALRLFCEAYKL 240 (348)
T ss_pred eEEEEEEecchhHHHHHHHHHHHHHHCCCcEEEEEEccCCCcHHHHHHHHHHHHhCCCcEEEEEeCcHHHHHHHHHHHHh
Confidence 99999999999999999999999999999999988887433368999999999999999999999999999999999999
Q ss_pred CCCCCCeEEEecCccccccccCCCCCCCccccceeeEEEeeecCCchhHHHHHHHHHhhccCCCCCCCCCCChhHHHHhh
Q 003958 245 GMLGTGYVWIATSWLSTALDTNSPFPSDVMDDIQGVLTLRTYTPDSVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYD 324 (784)
Q Consensus 245 g~~~~~~~wi~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YD 324 (784)
|+ ...+ |++++.+....... ....+..+|++++..+.+.....+.|.+.+++ +++.+||
T Consensus 241 g~-~~~~-~i~~~~~~~~~~~~----~~~~~~~~g~~~~~~~~~~~~~~~~f~~~~~~---------------~~~~~YD 299 (348)
T cd06350 241 GM-TGKY-WIISTDWDTSTCLL----LFTLDAFQGVLGFSGHAPRSGEIPGFKDFLRK---------------YAYNVYD 299 (348)
T ss_pred CC-CCeE-EEEEccccCccccc----cCCcceeeeEEEEEEEeecCCcCCChHHHHHH---------------HHHHHHh
Confidence 99 4444 44544443321111 23346788998888887765555566666664 5778899
Q ss_pred HHHHHHHHHHHHhhcCCccccccCCccccccCCcccccccccCCchHHHHHHHhccccceeeeEEEecCCCCcCCcEEEE
Q 003958 325 TVWLLARAINSFFKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANMTGTAGPARFNSHGDLINPAYEII 404 (784)
Q Consensus 325 Av~~~a~Al~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~l~~~l~~~~f~g~tG~v~Fd~~g~~~~~~~~I~ 404 (784)
|+++ .+.|+++|++ ...+.|.
T Consensus 300 av~~----------------------------------------------------------~v~f~~~gd~-~~~~~i~ 320 (348)
T cd06350 300 AVYA----------------------------------------------------------EVKFDENGDR-LASYDII 320 (348)
T ss_pred heeE----------------------------------------------------------EEEecCCCCc-ccceeEE
Confidence 8876 3789999996 7778999
Q ss_pred Eeec----cceEEEEEecCC
Q 003958 405 NVIG----TGYRRIGYWSNY 420 (784)
Q Consensus 405 ~~~~----~~~~~VG~w~~~ 420 (784)
+++. ..+++||.|++.
T Consensus 321 ~~~~~~~~~~~~~vg~~~~~ 340 (348)
T cd06350 321 NWQIFPGGGGFVKVGFWDPQ 340 (348)
T ss_pred EEEEcCCcEEEEEEEEEcCC
Confidence 9976 678999999874
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=100.00 E-value=7.6e-36 Score=319.55 Aligned_cols=329 Identities=17% Similarity=0.225 Sum_probs=276.4
Q ss_pred EEEEEeecC---CcchhhHHHHHHHHHHHHhcCCCCC---CCCEEEEEEecCCCCHHHHHHHHHHHHhc-CceEEEccCc
Q 003958 33 NIGALLSFS---TNVGKVAKLAIKAAVDDVNSDPTTL---GGTKLKLQMQDCNHSGFLALAEALHLMEG-QTVAIIGPQD 105 (784)
Q Consensus 33 ~IG~i~~~~---~~~g~~~~~a~~~Ave~IN~~~~il---~g~~l~~~~~D~~~~~~~a~~~~~~li~~-~v~aiiGp~~ 105 (784)
+||+++|++ +..|.....|+++|+++||+++|+. .|++|+++++|+++++..+++.+.+|+++ +|.+||||.+
T Consensus 1 ~IG~~~p~sG~~a~~g~~~~~g~~la~~~iN~~ggi~~g~~g~~i~l~~~D~~~~~~~a~~~~~~li~~~~v~aviG~~~ 80 (345)
T cd06338 1 RIGASLSLTGPLAGGGQLTQRGYELWVEDVNAAGGIKGGGKGYPVELIYYDDQSNPARAARAYERLITQDKVDFLLGPYS 80 (345)
T ss_pred CeeEEEeCCCccccccHHHHHHHHHHHHHHHhcCCcccCCCCceEEEEEecCCCCHHHHHHHHHHHHhhcCccEEecCCc
Confidence 599999998 4568888999999999999988763 47999999999999999999999999986 9999999999
Q ss_pred hhhHHHHHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcC--CcEEEEEEEcCCCcchhHHH
Q 003958 106 AVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYG--WREVIAIYVDDDHGRNGIAA 183 (784)
Q Consensus 106 s~~~~~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~--w~~v~ii~~d~~~g~~~~~~ 183 (784)
|..+.+++++++.+++|+|+++++++.+....+|++||+.|++..++.++++++++++ |+++++++.+++||+...+.
T Consensus 81 s~~~~a~~~~~~~~~vp~i~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~v~~v~~~~~~g~~~~~~ 160 (345)
T cd06338 81 SGLTLAAAPVAEKYGVPMVAGSGASDSIFAQGFKYVFGTLPPASQYAKSLLEMLVALDPRPKKVAILYADDPFSQDVAEG 160 (345)
T ss_pred chhHHHHHHHHHHhCCcEEecCCCCchHhhcCCceEEEecCchHHHHHHHHHHHHhcCCCCceEEEEecCCcccHHHHHH
Confidence 9999999999999999999998888877756789999999999999999999999987 99999999999999999999
Q ss_pred HHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHcCCCCCCeEEEecCcccccc
Q 003958 184 LGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIATSWLSTAL 263 (784)
Q Consensus 184 l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~ 263 (784)
+++.+++.|++|+....++ ....|++.++++|++.++|+|++.+...++..+++++++.|+..+ ..+..........
T Consensus 161 ~~~~~~~~g~~v~~~~~~~--~~~~d~~~~v~~l~~~~~d~i~~~~~~~~~~~~~~~~~~~g~~~~-~~~~~~~~~~~~~ 237 (345)
T cd06338 161 AREKAEAAGLEVVYDETYP--PGTADLSPLISKAKAAGPDAVVVAGHFPDAVLLVRQMKELGYNPK-ALYMTVGPAFPAF 237 (345)
T ss_pred HHHHHHHcCCEEEEEeccC--CCccchHHHHHHHHhcCCCEEEECCcchhHHHHHHHHHHcCCCCC-EEEEecCCCcHHH
Confidence 9999999999999877776 455789999999999999999999999999999999999998754 2222221111101
Q ss_pred ccCCCCCCCccccceeeEEEeeecCC-------chhHHHHHHHHHhhccCCCCCCCCCCChhHHHHhhHHHHHHHHHHHH
Q 003958 264 DTNSPFPSDVMDDIQGVLTLRTYTPD-------SVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTVWLLARAINSF 336 (784)
Q Consensus 264 ~~~~~~~~~~~~~~~g~~~~~~~~~~-------~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~~~a~Al~~~ 336 (784)
. .......+|+++...+.+. .+..++|.++|+++|+. .++.++..+||+++++++|++++
T Consensus 238 ~------~~~g~~~~g~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~-------~p~~~~~~~y~a~~~~~~a~~~a 304 (345)
T cd06338 238 V------KALGADAEGVFGPTQWTPALDYKDDLFPSAAEFAAAYKEKYGK-------APDYHAAGAYAAGQVLQEAVERA 304 (345)
T ss_pred H------HHHhhhhCceeecceeccCcccccccCccHHHHHHHHHHHhCC-------CCCcccHHHHHHHHHHHHHHHHh
Confidence 0 1122345777777655543 36789999999999872 35667889999999999999985
Q ss_pred hhcCCccccccCCccccccCCcccccccccCCchHHHHHHHhccccceeeeEEEecCCCCcCCcEEEEEe
Q 003958 337 FKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANMTGTAGPARFNSHGDLINPAYEIINV 406 (784)
Q Consensus 337 ~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~l~~~l~~~~f~g~tG~v~Fd~~g~~~~~~~~I~~~ 406 (784)
.. .++..+.++|++++|+|+.|++.|+++|++. ..+.+++|
T Consensus 305 g~----------------------------~~~~~v~~al~~~~~~~~~G~~~f~~~~~~~-~~~~~~~~ 345 (345)
T cd06338 305 GS----------------------------LDPAAVRDALASNDFDTFYGPIKFDETGQNN-HPMTVVQW 345 (345)
T ss_pred CC----------------------------CCHHHHHHHHHhCCCcccccCeeECCCCCcC-CCceeeeC
Confidence 11 1478899999999999999999999999864 45566554
No 41
>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=100.00 E-value=1.8e-35 Score=316.04 Aligned_cols=321 Identities=18% Similarity=0.220 Sum_probs=271.3
Q ss_pred EEEEEeecC---CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhc-CceEEEccCchhh
Q 003958 33 NIGALLSFS---TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEG-QTVAIIGPQDAVT 108 (784)
Q Consensus 33 ~IG~i~~~~---~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~-~v~aiiGp~~s~~ 108 (784)
+||++.|++ +..|.....|+++|++++|+++|+ +|++++++++|+++++..+++.+++|+++ +|.+|+||.+|..
T Consensus 1 ~IG~~~~lsG~~a~~G~~~~~g~~~A~~~iN~~ggi-~g~~v~l~~~D~~~~~~~a~~~~~~li~~~~v~aiiG~~~s~~ 79 (344)
T cd06345 1 KIGVLAPLSGGASTTGEAMWNGAELAAEEINAAGGI-LGRKVELVFEDTEGSPEDAVRAFERLVSQDKVDAVVGGYSSEV 79 (344)
T ss_pred CeeEEEecCCcccccCHHHHHHHHHHHHHHHHcCCC-CCceEEEEEecCCCCHHHHHHHHHHHhccCCceEEECCcchHH
Confidence 589999998 567889999999999999999988 59999999999999999999999999987 9999999999999
Q ss_pred HHHHHHhhhcCCccEEecccCCCCCCc----CCCCceEeecCChHHHHHHHHHHHHH-----cCCcEEEEEEEcCCCcch
Q 003958 109 SHVVSHVANELQVPLLSFSATDPTLSS----LQFPYFVRTTQSDQYQMAAIAEIVDH-----YGWREVIAIYVDDDHGRN 179 (784)
Q Consensus 109 ~~~va~~~~~~~ip~Is~~a~~~~l~~----~~~p~~~r~~ps~~~~~~ai~~~l~~-----~~w~~v~ii~~d~~~g~~ 179 (784)
+.+++++++.+++|+|+++++++.+++ ..+|++||+.|++..++.++++++++ ++|++|++++.+++||+.
T Consensus 80 ~~a~~~~~~~~~vp~i~~~~~~~~~t~~~~~~~~~~~fr~~~~~~~~~~~~~~~~~~~~~~~~~~~~va~l~~~~~~g~~ 159 (344)
T cd06345 80 VLALQDVAAENKVPFIVTGAASPEITTADDYETYKYVFRAGPTNSSYAQSVADALKETLVDKHGFKTAAIVAEDAAWGKG 159 (344)
T ss_pred HHHHHHHHHHcCCcEEeccCCCCcccccccccCCceEEecCCCcHHHHHHHHHHHHHhhcccCCCceEEEEecCchhhhH
Confidence 999999999999999999888887763 46899999999999999999998876 899999999999999999
Q ss_pred hHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHcCCCCCCeEEEecCcc
Q 003958 180 GIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIATSWL 259 (784)
Q Consensus 180 ~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~ 259 (784)
..+.+++.+++.|++|+....++ .+..|++.++.+|++.++++|++.+...+...+++++.+.|+..+ ++....+
T Consensus 160 ~~~~~~~~~~~~G~~vv~~~~~~--~~~~d~~~~v~~l~~~~~d~v~~~~~~~~~~~~~~~~~~~g~~~~---~~~~~~~ 234 (344)
T cd06345 160 IDAGIKALLPEAGLEVVSVERFS--PDTTDFTPILQQIKAADPDVIIAGFSGNVGVLFTQQWAEQKVPIP---TIGISVE 234 (344)
T ss_pred HHHHHHHHHHHcCCeEEEEEecC--CCCCchHHHHHHHHhcCCCEEEEeecCchHHHHHHHHHHcCCCCc---eEEecCC
Confidence 99999999999999999888777 356789999999999999999999999999999999999998543 3333222
Q ss_pred ccccccCCCCCCCccccceeeEEEeeecC----CchhHHHHHHHHHhhccCCCCCCCCCCChhHHHHhhHHHHHHHHHHH
Q 003958 260 STALDTNSPFPSDVMDDIQGVLTLRTYTP----DSVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTVWLLARAINS 335 (784)
Q Consensus 260 ~~~~~~~~~~~~~~~~~~~g~~~~~~~~~----~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~~~a~Al~~ 335 (784)
....... .......+|.+....+.+ .++..++|.++|+++++ ..++.++..+||+++++++|+++
T Consensus 235 ~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~y~~~~g-------~~p~~~~~~~yda~~~l~~A~~~ 303 (344)
T cd06345 235 GNSPAFW----KATNGAGNYVITAESGAPGVEAITDKTVPFTEAYEAKFG-------GPPNYMGASTYDSIYILAEAIER 303 (344)
T ss_pred cCCHHHH----HhhchhcceEEeecccccCccCCCHHHHHHHHHHHHHhC-------CCCcccchHHHHHHHHHHHHHHH
Confidence 1110000 111234556555443333 46778999999999887 34677889999999999999998
Q ss_pred HhhcCCccccccCCccccccCCcccccccccCCchHHHHHHHhccccceeeeEEEecCCCCcC
Q 003958 336 FFKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANMTGTAGPARFNSHGDLIN 398 (784)
Q Consensus 336 ~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~l~~~l~~~~f~g~tG~v~Fd~~g~~~~ 398 (784)
+.. .+++.+.++|++.+|+|++|+++||++|++..
T Consensus 304 ag~----------------------------~~~~~i~~al~~~~~~g~~G~i~f~~~g~~~~ 338 (344)
T cd06345 304 AGS----------------------------TDGDALVEALEKTDFVGTAGRIQFYGDDSAFA 338 (344)
T ss_pred hcC----------------------------CCHHHHHHHHHhCCCcCCceeEEECCCCCcCc
Confidence 511 14788999999999999999999999999643
No 42
>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=100.00 E-value=1.6e-35 Score=311.59 Aligned_cols=282 Identities=21% Similarity=0.214 Sum_probs=244.5
Q ss_pred EEEEEeecC---CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhc-CceEEEccCchhh
Q 003958 33 NIGALLSFS---TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEG-QTVAIIGPQDAVT 108 (784)
Q Consensus 33 ~IG~i~~~~---~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~-~v~aiiGp~~s~~ 108 (784)
+||++.|++ +..|.....++++|+++||+++|+ +|++|+++++|+++++..+++.+.+|+.+ +|.+|+||.+|..
T Consensus 1 kIG~~~plsG~~a~~g~~~~~g~~lA~~~iN~~ggi-~G~~iel~~~D~~~~p~~a~~~a~~li~~~~v~~viG~~~s~~ 79 (312)
T cd06346 1 KIGILLPLTGDLASYGPPMADAAELAVKEVNAAGGV-LGEPVTLVTADTQTDPAAGVAAATKLVNVDGVPGIVGAACSGV 79 (312)
T ss_pred CceeeccCCCchhhcChhHHHHHHHHHHHHHHhCCC-CCceEEEEECCCCCCHHHHHHHHHHHHhhcCCCEEEccccchh
Confidence 589999999 456788899999999999999999 59999999999999999999999999986 9999999999999
Q ss_pred HHHH-HHhhhcCCccEEecccCCCCCCc-CCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcCCCcchhHHHHHH
Q 003958 109 SHVV-SHVANELQVPLLSFSATDPTLSS-LQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGD 186 (784)
Q Consensus 109 ~~~v-a~~~~~~~ip~Is~~a~~~~l~~-~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~ 186 (784)
+.++ +++++..++|+|+++++++.+++ ..++++||+.|++..++.++++++++++|+++++|+.|++||+...+.+++
T Consensus 80 ~~a~~~~~~~~~~vp~i~~~~~~~~l~~~~~~~~~fr~~~~~~~~~~~l~~~~~~~~~~~vail~~~~~~g~~~~~~~~~ 159 (312)
T cd06346 80 TIAALTSVAVPNGVVMISPSSTSPTLTTLDDNGLFFRTAPSDALQGQALAQLAAERGYKSVATTYINNDYGVGLADAFTK 159 (312)
T ss_pred hHhhhhhhhccCCcEEEecCCCCccceecCCCceEEEecCCcHHHHHHHHHHHHHcCCCeEEEEEccCchhhHHHHHHHH
Confidence 9999 89999999999999999988887 457999999999999999999999999999999999999999999999999
Q ss_pred HHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHcCCCCCCeEEEecCccccccccC
Q 003958 187 TLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIATSWLSTALDTN 266 (784)
Q Consensus 187 ~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~~ 266 (784)
.+++.|++|+....++ ....|+..+++++++.++|+|++.+.+.++..++++++++|+..+ |++++......-..
T Consensus 160 ~~~~~G~~vv~~~~~~--~~~~d~~~~v~~l~~~~pd~v~~~~~~~~~~~~~~~~~~~G~~~~---~~~~~~~~~~~~~~ 234 (312)
T cd06346 160 AFEALGGTVTNVVAHE--EGKSSYSSEVAAAAAGGPDALVVIGYPETGSGILRSAYEQGLFDK---FLLTDGMKSDSFLP 234 (312)
T ss_pred HHHHcCCEEEEEEeeC--CCCCCHHHHHHHHHhcCCCEEEEecccchHHHHHHHHHHcCCCCc---eEeeccccChHHHH
Confidence 9999999999888887 467899999999999999999999999999999999999998544 66655432211010
Q ss_pred CCCCCCccccceeeEEEeeecCCchhHHHHHHHHHhhccCCCCCCCCCCChhHHHHhhHHHHHHHH
Q 003958 267 SPFPSDVMDDIQGVLTLRTYTPDSVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTVWLLARA 332 (784)
Q Consensus 267 ~~~~~~~~~~~~g~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~~~a~A 332 (784)
.......+|+++..+..+ .+..++|.++|+++|+ ..++.++..+||+++++++|
T Consensus 235 ----~~~~~~~~g~~~~~~~~~-~~~~~~f~~~~~~~~g-------~~p~~~~~~~Yd~~~~l~~A 288 (312)
T cd06346 235 ----ADGGYILAGSYGTSPGAG-GPGLEAFTSAYKAAYG-------ESPSAFADQSYDAAALLALA 288 (312)
T ss_pred ----hhhHHHhCCcEEccCCCC-chhHHHHHHHHHHHhC-------CCCCccchhhHHHHHHHHHH
Confidence 111245678777665444 3788999999999997 34677889999999998866
No 43
>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=100.00 E-value=1e-34 Score=307.52 Aligned_cols=336 Identities=17% Similarity=0.171 Sum_probs=251.6
Q ss_pred EEEEEeecCCcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEccCchhhHHHH
Q 003958 33 NIGALLSFSTNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIGPQDAVTSHVV 112 (784)
Q Consensus 33 ~IG~i~~~~~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiGp~~s~~~~~v 112 (784)
+||+||+.++.. ....-++.+|++++|+++|+ .|+.++++.+|+.+|+.+++.++|+|++++|.||+||.+|..+.++
T Consensus 1 ~IG~if~~~~~~-~~~af~~ala~~~iN~~gg~-~~~~i~~v~~dd~~d~~~a~~~~c~Li~~gV~AI~G~~~s~~~~av 78 (363)
T cd06381 1 HIGAIFSESALE-DDEVFAVAVIDLNINEQILQ-TEKITLSISFIDLNNHFDAVQEACDLMNQGILALVTSTGCASAIAL 78 (363)
T ss_pred CeeeeccCCcch-HHHHHHHHHHHhhccccccC-CccceeeeEeecCCChHHHHHHHHHHHhcCcEEEEecCChhHHHHH
Confidence 589999987432 23345555666778888775 4677888889999999999999999999999999999999999999
Q ss_pred HHhhhcCCccEEecccCC--C------CCCc-CCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcCCCcchhHHH
Q 003958 113 SHVANELQVPLLSFSATD--P------TLSS-LQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDDDHGRNGIAA 183 (784)
Q Consensus 113 a~~~~~~~ip~Is~~a~~--~------~l~~-~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~ 183 (784)
+++|+..+||+|++.+.. + .+.+ ...+|.|++.|++ .+..++++++++++|++|+++|++++ |....+.
T Consensus 79 ~~i~~~~~IP~Is~~~~~~~~~~~~~~~~~~~~~~~~~f~~rp~~-~~~~ai~~lv~~~~wkkvavly~~d~-g~~~l~~ 156 (363)
T cd06381 79 QSLTDAMHIPHLFIQRGYGGSPRTACGLNPSPRGQQYTLALRPPV-RLNDVMLRLVTEWRWQKFVYFYDNDY-DIRGLQE 156 (363)
T ss_pred HHHhhCCCCCEEEeecCcCCCcccccccCCCcccceeEEEEeccH-HHHHHHHHHHHhCCCeEEEEEEECCc-hHHHHHH
Confidence 999999999999965421 1 1111 1234555666774 67899999999999999999998776 5566677
Q ss_pred HHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhh-------cCCceEEEEeccCCcHHHHHHHHHHcCCCCCCeEEEec
Q 003958 184 LGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVA-------LTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIAT 256 (784)
Q Consensus 184 l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~-------~~~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~wi~~ 256 (784)
+.+.+++.|+.+.... ... .....+...++.++ ..+.++||+.|+++.+..++++|.++||+..+|+||++
T Consensus 157 ~~~~~~~~g~~v~~~~-~~~-~~~~~~~~l~~~~~~~~l~~~~~~~~~vIl~~~~~~~~~~l~~a~~~gm~~~~~~wi~~ 234 (363)
T cd06381 157 FLDQLSRQGIDVLLQK-VDL-NISKMATALFTTMRCEELNRYRDTLRRALLLLSPNGAYTFIDASVETNLAIKDSHWFLI 234 (363)
T ss_pred HHHHHHhcCceEEEEe-ccc-ccchhhhhhhhHHHHHHHHhhcccceEEEEEcCcHHHHHHHHHHHHcCCCcCceEEEEe
Confidence 8888888898665432 221 11122333333332 45566888999999999999999999999999999887
Q ss_pred Cccccc-cccCCCCCCCccccceeeEEEeeecCCchhHH----HHHHHHHhhccCCCCCCCCCCChhHHHHhhHHHHHHH
Q 003958 257 SWLSTA-LDTNSPFPSDVMDDIQGVLTLRTYTPDSVLKR----KFISRWRNLTDAKTPNGYIGLNAYGFYAYDTVWLLAR 331 (784)
Q Consensus 257 ~~~~~~-~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~----~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~~~a~ 331 (784)
..+... .+. +.......|+++++...+..+..+ .+.+.|+......++ ....+...++++||||+++.
T Consensus 235 ~~l~~~~~~l-----~~~~~~~~nitgfrl~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~al~yDaV~~~~- 307 (363)
T cd06381 235 NEEISDTEID-----ELVRYAHGRMTVIRQTFSKEKTNQRCLRNNHRISSLLCDPKDG-YLQMLEISNLYIYDSVLLLL- 307 (363)
T ss_pred ccccccchhh-----HHHhhcCccEEEEEEecCCcCchHHHHHHHHHHHHhhcCCCCC-CCCChhHHHHHHHHHHHHHH-
Confidence 765542 222 344567789999999988766666 455566543321111 11234567999999999991
Q ss_pred HHHHHhhcCCccccccCCccccccCCcccccccccCCchHHHHHHHhccccceeeeEEEecCCCCcCCcEEEEEeeccc-
Q 003958 332 AINSFFKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANMTGTAGPARFNSHGDLINPAYEIINVIGTG- 410 (784)
Q Consensus 332 Al~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~l~~~l~~~~f~g~tG~v~Fd~~g~~~~~~~~I~~~~~~~- 410 (784)
++|++++|+|+||+|+||++|.|.+..++|+++..++
T Consensus 308 ------------------------------------------~~~~~~~~~GLTG~i~F~~~g~r~~~~l~i~~~~~~~~ 345 (363)
T cd06381 308 ------------------------------------------ETIKKGPITGLTGKLEFNEGGDNSNVQFEILGTGYSET 345 (363)
T ss_pred ------------------------------------------HHHHhcCccCcceeEEeCCCCCccccEEEEEEeccCCc
Confidence 2567788999999999999999999999999999544
Q ss_pred ----eEEEEEecCCCCC
Q 003958 411 ----YRRIGYWSNYSGL 423 (784)
Q Consensus 411 ----~~~VG~w~~~~~l 423 (784)
.+.+|.|++..||
T Consensus 346 ~~~~~~~~~~w~~~~~~ 362 (363)
T cd06381 346 LGKDGRWLATWNPSKGL 362 (363)
T ss_pred cccceEEeeeccCCCCC
Confidence 6889999987764
No 44
>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=100.00 E-value=9.2e-35 Score=310.74 Aligned_cols=334 Identities=19% Similarity=0.285 Sum_probs=272.3
Q ss_pred EEEEEeecC---CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhc-CceEEEccCchhh
Q 003958 33 NIGALLSFS---TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEG-QTVAIIGPQDAVT 108 (784)
Q Consensus 33 ~IG~i~~~~---~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~-~v~aiiGp~~s~~ 108 (784)
+||++.|+| +..|.....++++|+++||+++|++ |++|++++.|++++|..+.+++++|+++ +|.+|+||.+|..
T Consensus 1 ~IG~~~plsG~~a~~g~~~~~g~~~a~~~iNa~ggi~-G~~v~lv~~D~~~~p~~a~~~~~~li~~~~v~~iiG~~~s~~ 79 (344)
T cd06348 1 PLGVALALTGNAALYGQEQLAGLKLAEDRFNQAGGVN-GRPIKLVIEDSGGDEAEAINAFQTLINKDRVLAIIGPTLSQQ 79 (344)
T ss_pred CeeEEEeccCchhhcCHhHHHHHHHHHHHHhhcCCcC-CcEEEEEEecCCCChHHHHHHHHHHhhhcCceEEECCCCcHH
Confidence 599999999 5568899999999999999999985 8999999999999999999999999987 8999999999999
Q ss_pred HHHHHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHH-HHHHHHHc-CCcEEEEEEEcCC-CcchhHHHHH
Q 003958 109 SHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAA-IAEIVDHY-GWREVIAIYVDDD-HGRNGIAALG 185 (784)
Q Consensus 109 ~~~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~a-i~~~l~~~-~w~~v~ii~~d~~-~g~~~~~~l~ 185 (784)
+.++.++++..+||+|+++++++.+.+ .++++||+.+++..+... +..+++++ +|+++++||.+++ ||+...+.++
T Consensus 80 ~~a~~~~~~~~~ip~i~~~~~~~~~~~-~~~~~fr~~~~~~~~~~~~~~~~~~~~~~~~~v~~l~~~~~~~g~~~~~~~~ 158 (344)
T cd06348 80 AFAADPIAERAGVPVVGPSNTAKGIPE-IGPYVFRVSAPEAVVAPAAIAAALKLNPGIKRVAVFYAQDDAFSVSETEIFQ 158 (344)
T ss_pred HHhhhHHHHhCCCCEEeccCCCCCcCC-CCCeEEEccCcHHHHHHHHHHHHHHHhcCCeEEEEEEeCCchHHHHHHHHHH
Confidence 999999999999999998877665543 468999998777655444 45567787 9999999997654 9999999999
Q ss_pred HHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHcCCCCCCeEEEecCcccccccc
Q 003958 186 DTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIATSWLSTALDT 265 (784)
Q Consensus 186 ~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~ 265 (784)
+.+++.|++++....++ .+..|+..++.+|+++++++|++.+.+.++..+++++++.|+..+ |+.+.++.... .
T Consensus 159 ~~~~~~g~~v~~~~~~~--~~~~d~~~~v~~i~~~~~d~vi~~~~~~~~~~~~~~~~~~g~~~~---~~~~~~~~~~~-~ 232 (344)
T cd06348 159 KALRDQGLNLVTVQTFQ--TGDTDFQAQITAVLNSKPDLIVISALAADGGNLVRQLRELGYNGL---IVGGNGFNTPN-V 232 (344)
T ss_pred HHHHHcCCEEEEEEeeC--CCCCCHHHHHHHHHhcCCCEEEECCcchhHHHHHHHHHHcCCCCc---eeccccccCHH-H
Confidence 99999999999888887 456899999999999999999999999999999999999998653 55544332211 1
Q ss_pred CCCCCCCccccceeeEEEeeecC--CchhHHHHHHHHHhhccCCCCCCCCCCChhHHHHhhHHHHHHHHHHHHhhcCCcc
Q 003958 266 NSPFPSDVMDDIQGVLTLRTYTP--DSVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTVWLLARAINSFFKQGGNL 343 (784)
Q Consensus 266 ~~~~~~~~~~~~~g~~~~~~~~~--~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~~~a~Al~~~~~~~~~~ 343 (784)
. ....+..+|++....+.+ +.+..++|.+.|+++++ ..++.++..+||+++++++|++++..++...
T Consensus 233 ~----~~~g~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~g-------~~p~~~~~~~yda~~~~~~A~~~a~~~~~~~ 301 (344)
T cd06348 233 F----PVCQAACDGVLVAQAYSPENDTPVNRDFVEAYKKKYG-------KAPPQFSAQAFDAVQVVAEALKRLNQKQKLA 301 (344)
T ss_pred H----HhhhHhhcCeEEEeeccCCCCCHHHHHHHHHHHHHHC-------CCccHHHHHHHHHHHHHHHHHHHhcCCCccc
Confidence 0 123356678777766554 45678999999998886 2456778899999999999999985432110
Q ss_pred ccccCCccccccCCcccccccccCCchHHHHHHHhccccceeeeEEEecCCCCcCCcEEE
Q 003958 344 SFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANMTGTAGPARFNSHGDLINPAYEI 403 (784)
Q Consensus 344 ~~~~~~~~~~~~g~~~~~~~~~~~~~~~l~~~l~~~~f~g~tG~v~Fd~~g~~~~~~~~I 403 (784)
.|.. ...+..|.++|++.+|+|++|++.||++|++....|.+
T Consensus 302 ---------------~~~~---~~~~~~l~~~l~~~~~~g~~G~v~f~~~g~~~~~~~~~ 343 (344)
T cd06348 302 ---------------ELPL---PELRTALNAALLSGQYDTPLGEISFTPDGEVLQKAFYV 343 (344)
T ss_pred ---------------cchh---hhHHHHHHHHHhccCCccceeeeEECCCCCcccCceec
Confidence 0100 01267899999999999999999999999987776654
No 45
>cd06378 PBP1_iGluR_NMDA_NR2 N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the NR2 subunit of NMDA receptor family. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the NR2 subunit of NMDA receptor family. The ionotropic N-methyl-d-asparate (NMDA) subtype of glutamate receptor serves critical functions in neuronal development, functioning, and degeneration in the mammalian central nervous system. The functional NMDA receptor is a heterotetramer composed of two NR1 and two NR2 (A, B, C, and D) or of NR3 (A and B) subunits. The receptor controls a cation channel that is highly permeable to monovalent ions and calcium and exhibits voltage-dependent inhibition by magnesium. Dual agonists, glutamate and glycine, are required for efficient activation of the NMDA receptor. Among NMDA receptor subtypes, the NR2B subunit containing receptors appear particularly important for pain perception; thus NR2B-selective antagonists may be useful in
Probab=100.00 E-value=2.2e-34 Score=304.44 Aligned_cols=303 Identities=17% Similarity=0.268 Sum_probs=239.4
Q ss_pred CCCCHHHHHHHHHHHHhc-CceEEE-ccCchh--hHHHHHHhhhcCCccEEecccCCC-CCCc-CCCCceEeecCChHHH
Q 003958 78 CNHSGFLALAEALHLMEG-QTVAII-GPQDAV--TSHVVSHVANELQVPLLSFSATDP-TLSS-LQFPYFVRTTQSDQYQ 151 (784)
Q Consensus 78 ~~~~~~~a~~~~~~li~~-~v~aii-Gp~~s~--~~~~va~~~~~~~ip~Is~~a~~~-~l~~-~~~p~~~r~~ps~~~~ 151 (784)
...||.....++|+++.+ +|.|+| ||.++. .+..++.+++.++||+|++.+.++ .+++ ..+|+|+|+.|++..|
T Consensus 43 ~~~d~~~~~~~vC~ll~~~~V~aiIfgp~~~~~~~a~~~s~~~~~~~vP~is~~~~s~~~ls~~~~~p~flr~~Psd~~q 122 (362)
T cd06378 43 NETDPKSILTQLCDLLSTTKVHGVVFEDDTDQEAVAQILDFISAQTFLPILGIHGGSSMIMAAKDSGSTFLQFGPSIEQQ 122 (362)
T ss_pred CCCCHHHHHHHHHHHhcccceEEEEecCCCCccccchhhhhhhhceeccEEEecccccccccCCCCCceEEEeCCCHHHH
Confidence 346999999999999977 699766 999987 445677888889999999976554 5666 5799999999999999
Q ss_pred HHHHHHHHHHcCCcEEEEEEEcCCCcchhHHHHHHHHhccCcEEEEeeccCCCC-ChhHHHHHHHHhhcCCceEEEEecc
Q 003958 152 MAAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEA-TEDEITDLLVKVALTESRIIVVHTH 230 (784)
Q Consensus 152 ~~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~-~~~d~~~~l~~l~~~~~~vIvl~~~ 230 (784)
++|+++++++|+|++|++||++++.+..+.+.+++.+...++|+.....++... ...+...+++++++.++++||++|+
T Consensus 123 ~~Ai~~Ii~~f~W~~v~iV~~~~~g~~~~~~~l~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~l~~lk~~~arViVl~~s 202 (362)
T cd06378 123 AAVMLKIMEEYDWHAFSVVTSRFPGYDDFVSAVRTTVDNSFVGWELQSVLTLDMSDDDGDARTQRQLKKLESQVILLYCS 202 (362)
T ss_pred HHHHHHHHHHCCCeEEEEEEEcCCCHHHHHHHHHHHHhhcccceeEEEEEeeccCCCcchHHHHHHHHhcCCCEEEEECC
Confidence 999999999999999999999998888888888888877667765443333222 2234778899999999999999999
Q ss_pred CCcHHHHHHHHHHcCCCCCCeEEEecCccccccccCCCCCCCccccceeeEEEeeecCCchhHHHHHHHHHhhccCCCCC
Q 003958 231 YNRGPVVFHVAQYLGMLGTGYVWIATSWLSTALDTNSPFPSDVMDDIQGVLTLRTYTPDSVLKRKFISRWRNLTDAKTPN 310 (784)
Q Consensus 231 ~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~ 310 (784)
.+.+..++++|.++||++++|+||++++.....+. ...+...|++++.. ++|+.
T Consensus 203 ~~~a~~if~~A~~~gm~g~~yvWI~t~~~~~~~~~------~~~~~~~G~i~v~~------------~~w~~-------- 256 (362)
T cd06378 203 KEEAEYIFRAARSAGLTGPGYVWIVPSLVLGNTDL------GPSEFPVGLISVSY------------DGWRY-------- 256 (362)
T ss_pred HHHHHHHHHHHHHcCCcCCCeEEEecccccCCCcc------ccccCCcceEeecc------------ccccc--------
Confidence 99999999999999999999999999976654221 11234566666542 22321
Q ss_pred CCCCCChhHHHHhhHHHHHHHHHHHHhhcCCccccccCCccccccCCccccc-cc-ccCCchHHHHHHHhccccceeeeE
Q 003958 311 GYIGLNAYGFYAYDTVWLLARAINSFFKQGGNLSFSKDSRLSDIQGHLRLDS-LR-IFNGGNLLRDSILQANMTGTAGPA 388 (784)
Q Consensus 311 ~~~~~~~~~~~~YDAv~~~a~Al~~~~~~~~~~~~~~~~~~~~~~g~~~~~~-~~-~~~~~~~l~~~l~~~~f~g~tG~v 388 (784)
...+..||||+++|+|++.+++.....+.. +..|.. .. .|..|..|.++|++++|+|. ++
T Consensus 257 ------~~~a~~~DaV~vva~Al~~l~~~~~~~~~~----------~~~C~~~~~~~~~~G~~l~~~l~~v~~~G~--~i 318 (362)
T cd06378 257 ------SLRARVRDGVAIIATGASAMLRQHGFIPEA----------KGSCYGQAEKRDLPPNTLHRYMMNVTWEGR--DL 318 (362)
T ss_pred ------cHHHHHHHHHHHHHHHHHHHHhccCCCCCC----------CCCcCCCCCCCCCchHHHHHHhhcceECCC--ce
Confidence 135678999999999999987644433211 234543 33 37789999999999999996 99
Q ss_pred EEecCCCCcCCcEEEEEeec-cceEEEEEecCCCCCce
Q 003958 389 RFNSHGDLINPAYEIINVIG-TGYRRIGYWSNYSGLSV 425 (784)
Q Consensus 389 ~Fd~~g~~~~~~~~I~~~~~-~~~~~VG~w~~~~~l~~ 425 (784)
+||++|+|.++.|+|++++. .+|++||.|+.+ +|.+
T Consensus 319 ~F~~~G~r~~~~ldIinl~~~~g~~kVG~W~~~-~L~~ 355 (362)
T cd06378 319 SFTEDGYLVNPKLVVISLNKERVWEEVGKWENG-SLRL 355 (362)
T ss_pred eECCCCeEccceEEEEEecCCCCceEEEEEcCC-eEEE
Confidence 99999999999999999996 589999999844 4554
No 46
>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=100.00 E-value=1.4e-33 Score=300.94 Aligned_cols=337 Identities=15% Similarity=0.128 Sum_probs=275.4
Q ss_pred EEEEEeecC---CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhc-CceEEEccCchhh
Q 003958 33 NIGALLSFS---TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEG-QTVAIIGPQDAVT 108 (784)
Q Consensus 33 ~IG~i~~~~---~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~-~v~aiiGp~~s~~ 108 (784)
+||++.|+| +..|.....|+++|+|+||++||++ |++|+++++|++++|.++++.+.+|+++ +|.+|+|+.+|..
T Consensus 1 kIG~~~plsG~~a~~G~~~~~g~~la~~~iN~~GGi~-G~~ielv~~D~~~~p~~a~~~a~~Li~~~~V~~iiG~~~S~~ 79 (348)
T cd06355 1 KVGILHSLSGTMAISETTLKDAELLAIEEINAAGGVL-GRKIEAVVEDGASDWPTFAEKARKLLTQDKVAAVFGCWTSAS 79 (348)
T ss_pred CeEEEEcCCCcccccchhHHHHHHHHHHHHHhcCCCC-CcEEEEEEeCCCCCHHHHHHHHHHHHHhCCCcEEEeccchhh
Confidence 599999998 4568889999999999999999996 9999999999999999999999999975 8999999999999
Q ss_pred HHHHHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHH-cCCcEEEEEEEcCCCcchhHHHHHHH
Q 003958 109 SHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDH-YGWREVIAIYVDDDHGRNGIAALGDT 187 (784)
Q Consensus 109 ~~~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~-~~w~~v~ii~~d~~~g~~~~~~l~~~ 187 (784)
+.++.++++..++|++++.+... ...+|++||+.+++..++..+++++.. .+++++++|+.|++||+...+.+++.
T Consensus 80 ~~a~~~~~~~~~~~~i~~~~~~~---~~~~~~~f~~~~~~~~~~~~~~~~~~~~~g~k~vaii~~d~~~g~~~~~~~~~~ 156 (348)
T cd06355 80 RKAVLPVFERHNGLLFYPVQYEG---LEQSPNVFYTGAAPNQQIIPAVDWLMSNKGGKRFYLVGSDYVYPRTANKILKAQ 156 (348)
T ss_pred HHHHHHHHhccCCceecCCCccC---CCCCCCEEEeCCChHHhHHHHHHHHHhccCCCeEEEECCcchHHHHHHHHHHHH
Confidence 99999999999999998653221 134689999999999999999998765 57999999999999999999999999
Q ss_pred HhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHcCCCCCCeEEEecCccccccccCC
Q 003958 188 LAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIATSWLSTALDTNS 267 (784)
Q Consensus 188 l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~~~ 267 (784)
+++.|++|+....++ .+..|+..+++++++.++|+|++...+.++..+++++++.|+......++..........
T Consensus 157 ~~~~G~~vv~~~~~~--~~~~D~~~~v~~l~~~~pd~v~~~~~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~~~~--- 231 (348)
T cd06355 157 LESLGGEVVGEEYLP--LGHTDFQSIINKIKAAKPDVVVSTVNGDSNVAFFKQLKAAGITASKVPVLSFSVAEEELR--- 231 (348)
T ss_pred HHHcCCeEEeeEEec--CChhhHHHHHHHHHHhCCCEEEEeccCCchHHHHHHHHHcCCCccCCeeEEccccHHHHh---
Confidence 999999999888787 567899999999999999999999899999999999999998754444555432221111
Q ss_pred CCCCCccccceeeEEEeee--cCCchhHHHHHHHHHhhccCCCCCCCCCCChhHHHHhhHHHHHHHHHHHHhhcCCcccc
Q 003958 268 PFPSDVMDDIQGVLTLRTY--TPDSVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTVWLLARAINSFFKQGGNLSF 345 (784)
Q Consensus 268 ~~~~~~~~~~~g~~~~~~~--~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~~~a~Al~~~~~~~~~~~~ 345 (784)
....+...|++....+ ..+.+..++|.++|+++|+. ...++.++..+||+++++++|++++..
T Consensus 232 ---~~g~~~~~g~~~~~~~~~~~~~~~~~~f~~~y~~~~g~-----~~~~~~~a~~~Y~a~~~~~~Al~~ag~------- 296 (348)
T cd06355 232 ---GIGPENLAGHYAAWNYFQSVDTPENKKFVAAFKARYGQ-----DRVTNDPMEAAYIGVYLWKQAVEKAGS------- 296 (348)
T ss_pred ---hcChHhhcCCEEeccchhhcCCHHHHHHHHHHHHHcCC-----CCCCCcHHHHHHHHHHHHHHHHHHhCC-------
Confidence 1111345676554332 33567889999999999862 112355688899999999999998611
Q ss_pred ccCCccccccCCcccccccccCCchHHHHHHHhccccceeeeEEEecCCCCcCCcEEEEEee-ccceEEE
Q 003958 346 SKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANMTGTAGPARFNSHGDLINPAYEIINVI-GTGYRRI 414 (784)
Q Consensus 346 ~~~~~~~~~~g~~~~~~~~~~~~~~~l~~~l~~~~f~g~tG~v~Fd~~g~~~~~~~~I~~~~-~~~~~~V 414 (784)
.+++.|.++|++++|++..|.++|+++++.....+.|.+++ +++++.|
T Consensus 297 ---------------------~~~~~i~~aL~~~~~~~~~g~~~f~~~~~~~~~~~~i~~~~~~g~~~~v 345 (348)
T cd06355 297 ---------------------FDVDKVRAALPGQSFDAPEGPVTVDPANHHLWKPVRIGRIQADGQFEIV 345 (348)
T ss_pred ---------------------CCHHHHHHHhccCcccCCCcceEeecCCCeeeeeeEEEEEcCCCcEEEE
Confidence 14889999999999999999999998544345566777885 5666655
No 47
>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=100.00 E-value=3.5e-34 Score=305.96 Aligned_cols=324 Identities=19% Similarity=0.279 Sum_probs=271.5
Q ss_pred EEEEEeecC---CcchhhHHHHHHHHHHHHhcCCCC--CCCCEEEEEEecCCCCHHHHHHHHHHHHhc-CceEEEccCch
Q 003958 33 NIGALLSFS---TNVGKVAKLAIKAAVDDVNSDPTT--LGGTKLKLQMQDCNHSGFLALAEALHLMEG-QTVAIIGPQDA 106 (784)
Q Consensus 33 ~IG~i~~~~---~~~g~~~~~a~~~Ave~IN~~~~i--l~g~~l~~~~~D~~~~~~~a~~~~~~li~~-~v~aiiGp~~s 106 (784)
+||++.|++ +..|.....|+++|+++||+.+|+ ++|++|+++++|+++++..+++.+++++++ +|.+|+||.+|
T Consensus 1 ~IG~~~p~sG~~a~~g~~~~~g~~lA~~~iN~~GGi~~i~G~~v~lv~~D~~~~~~~a~~~~~~li~~~~v~aiiG~~~s 80 (347)
T cd06340 1 KIGVLLPLSGGLAAIGQQCKAGAELAVEEINAAGGIKSLGGAKLELVFGDSQGNPDIGATEAERLITEEGVVALVGAYQS 80 (347)
T ss_pred CceeEecCCchhhhhCHHHHHHHHHHHHHHHhcCCccCCCCceEEEEEecCCCCHHHHHHHHHHHhccCCceEEecccch
Confidence 599999998 456788999999999999999973 479999999999999999999999999988 99999999999
Q ss_pred hhHHHHHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHc------CCcEEEEEEEcCCCcchh
Q 003958 107 VTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHY------GWREVIAIYVDDDHGRNG 180 (784)
Q Consensus 107 ~~~~~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~------~w~~v~ii~~d~~~g~~~ 180 (784)
..+.+++++++..++|+|++.++++.+++..+|++||+.|++..++.++++++.++ +|+++++|+.|++||+..
T Consensus 81 ~~~~a~~~~~~~~~ip~i~~~~~~~~l~~~~~~~~fr~~p~~~~~~~~~~~~l~~~~~~~~~~~~~v~~l~~~~~~g~~~ 160 (347)
T cd06340 81 AVTLAASQVAERYGVPFVVDGAVSDSITERGFKYTFRITPHDGMFTRDMFDFLKDLNEKTGKPLKTVALVHEDTEFGTSV 160 (347)
T ss_pred HhHHHHHHHHHHhCCCEEeccccchHHhhcCCceEEecCCChHHHHHHHHHHHHHhhHhcCCCCceEEEEecCchHhHHH
Confidence 99999999999999999999888888877678999999999999999999999876 469999999999999999
Q ss_pred HHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHcCCCCCCeEEEecCccc
Q 003958 181 IAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIATSWLS 260 (784)
Q Consensus 181 ~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~ 260 (784)
.+.+++.+++.|++|+..+.++ ....|++.++++|++.++|+|++.+...++..+++++++.|+..+ .++....+..
T Consensus 161 ~~~~~~~~~~~G~~vv~~~~~~--~~~~d~~~~i~~l~~~~~d~v~~~~~~~~~~~~~~~~~~~G~~~~-~~~~~~~~~~ 237 (347)
T cd06340 161 AEAIKKFAKERGFEIVEDISYP--ANARDLTSEVLKLKAANPDAILPASYTNDAILLVRTMKEQRVEPK-AVYSVGGGAE 237 (347)
T ss_pred HHHHHHHHHHcCCEEEEeeccC--CCCcchHHHHHHHHhcCCCEEEEcccchhHHHHHHHHHHcCCCCc-EEEecCCCcC
Confidence 9999999999999999888887 346799999999999999999999999999999999999998653 2222222111
Q ss_pred cccccCCCCCCCccccceeeEEEeeecCC-chhHHHHHHHHHhhccCCCCCCCCCCChhHHHHhhHHHHHHHHHHHHhhc
Q 003958 261 TALDTNSPFPSDVMDDIQGVLTLRTYTPD-SVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTVWLLARAINSFFKQ 339 (784)
Q Consensus 261 ~~~~~~~~~~~~~~~~~~g~~~~~~~~~~-~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~~~a~Al~~~~~~ 339 (784)
.. ... ....+..+|++...++.++ .+..++|.++|+++++ ..++.++..+||+++++++|++++..
T Consensus 238 ~~-~~~----~~~g~~~~g~~~~~~~~~~~~~~~~~f~~~y~~~~~-------~~~~~~~~~~Y~a~~~l~~A~~~ag~- 304 (347)
T cd06340 238 DP-SFV----KALGKDAEGILTRNEWSDPKDPMAKDLNKRFKARFG-------VDLSGNSARAYTAVLVIADALERAGS- 304 (347)
T ss_pred cH-HHH----HHhhHhhheEEeccccCCCCChHHHHHHHHHHHHhC-------CCCChHHHHHHHHHHHHHHHHHHhcC-
Confidence 11 000 1122456788887766554 6788999999999987 23677899999999999999998621
Q ss_pred CCccccccCCccccccCCcccccccccCCchHHH--HHHHhcccc---ceeeeEEEecCCCCcCC
Q 003958 340 GGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLR--DSILQANMT---GTAGPARFNSHGDLINP 399 (784)
Q Consensus 340 ~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~l~--~~l~~~~f~---g~tG~v~Fd~~g~~~~~ 399 (784)
.++..+. .+|++..+. +..|+++||++|+..++
T Consensus 305 ---------------------------~~~~~v~~~~~~~~~~~~~~~~~~g~~~f~~~g~~~~~ 342 (347)
T cd06340 305 ---------------------------ADPEKIRDLAALASTSGEDLIMPYGPIKFDAKGQNTNA 342 (347)
T ss_pred ---------------------------CCHHHHHHHHHhccCCccccccCCCCeeECCCCCcccc
Confidence 1467777 488888775 46789999999986443
No 48
>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=100.00 E-value=1.1e-33 Score=300.66 Aligned_cols=320 Identities=17% Similarity=0.169 Sum_probs=265.6
Q ss_pred EEEEEeecC--CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhc-CceEEEccCchhhH
Q 003958 33 NIGALLSFS--TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEG-QTVAIIGPQDAVTS 109 (784)
Q Consensus 33 ~IG~i~~~~--~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~-~v~aiiGp~~s~~~ 109 (784)
+||++.|++ +..|.....|+++|+++||+.+|+ +|++|++++.|++++|..+++.+.+|+.+ +|.+|+|+.+|..+
T Consensus 1 ~iG~~~p~sG~a~~G~~~~~g~~lA~~~iNa~ggi-~G~~ielv~~D~~~~p~~a~~~a~~li~~~~v~aiiG~~~s~~~ 79 (332)
T cd06344 1 TIAVVVPIGKNPNLAEEILRGVAQAQTEINLQGGI-NGKLLKVVIANDGNDPEIAKKVADELVKDPEILGVVGHYSSDAT 79 (332)
T ss_pred CeEEEEecCCChhhHHHHHHHHHHHHHHHHhcCCC-CCCeEEEEEECCCCChHHHHHHHHHHhcccCceEEEcCCCcHHH
Confidence 489999998 556888899999999999999998 59999999999999999999999999987 99999999999999
Q ss_pred HHHHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcC-CcEEEEEEEcCC-CcchhHHHHHHH
Q 003958 110 HVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYG-WREVIAIYVDDD-HGRNGIAALGDT 187 (784)
Q Consensus 110 ~~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~-w~~v~ii~~d~~-~g~~~~~~l~~~ 187 (784)
.+++++++..++|+|++.++++.++ ..+||+||+.|++..++.++++++++.+ |+++++|+.++. ||+...+.+++.
T Consensus 80 ~a~~~~~~~~~ip~i~~~a~~~~lt-~~~~~~fr~~~~~~~~~~~~~~~~~~~~~~~~v~~i~~~~~~~g~~~~~~~~~~ 158 (332)
T cd06344 80 LAALDIYQKAKLVLISPTSTSVKLS-NPGPYFFRTVPSNAVAARALAKYLKKKNKIKKVAIFYNSTSPYSQSLKQEFTSA 158 (332)
T ss_pred HHHHHHHhhcCceEEccCcCchhhc-CCCCcEEEeCCCcHHHHHHHHHHHHhhcCCCeEEEEeCCCchHhHHHHHHHHHH
Confidence 9999999999999999888777777 4579999999999999999999998886 999999998876 999999999999
Q ss_pred Hhc-cCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHcCCCCCCeEEEecCccccccccC
Q 003958 188 LAA-KRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIATSWLSTALDTN 266 (784)
Q Consensus 188 l~~-~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~~ 266 (784)
+++ .|+++.....++ ....++..++.++++.++++|++.+.......+++++++.+. ...+++++.+... +..
T Consensus 159 ~~~~~g~~v~~~~~~~--~~~~~~~~~v~~i~~~~~d~v~~~~~~~~~~~~~~~~~~~~~---~~~i~~~~~~~~~-~~~ 232 (332)
T cd06344 159 LLERGGGIVVTPCDLS--SPDFNANTAVSQAINNGATVLVLFPDTDTLDKALEVAKANKG---RLTLLGGDSLYTP-DTL 232 (332)
T ss_pred HHHhcCCeeeeeccCC--CCCCCHHHHHHHHHhcCCCEEEEeCChhHHHHHHHHHHhcCC---CceEEecccccCH-HHH
Confidence 999 588887654444 345678889999999999999999888888889999888664 2235554433221 111
Q ss_pred CCCCCCccccceeeEEEeeecCCchhHHHHHHHHHhhccCCCCCCCCCCChhHHHHhhHHHHHHHHHHHHhhcCCccccc
Q 003958 267 SPFPSDVMDDIQGVLTLRTYTPDSVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTVWLLARAINSFFKQGGNLSFS 346 (784)
Q Consensus 267 ~~~~~~~~~~~~g~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~~~a~Al~~~~~~~~~~~~~ 346 (784)
.......+|+++..++.++.+..++|.+.|+++++ ..++.++..+||+++++++|++++...
T Consensus 233 ----~~~~~~~~G~~~~~~~~~~~~~~~~f~~~~~~~~~-------~~~~~~a~~~Yda~~~l~~A~~~ag~~------- 294 (332)
T cd06344 233 ----LDGGKDLEGLVLAVPWHPLASPNSPFAKLAQQLWG-------GDVSWRTATAYDATKALIAALSQGPTR------- 294 (332)
T ss_pred ----HhchhhhcCeEEEEecccccccchHHHHHHHHHhc-------CCchHHHHhHHHHHHHHHHHHHhCCCh-------
Confidence 11224567888888877777778999999999987 346778999999999999999985211
Q ss_pred cCCccccccCCcccccccccCCchHHH-HHHHhccccceeeeEEEecCCCCcCC
Q 003958 347 KDSRLSDIQGHLRLDSLRIFNGGNLLR-DSILQANMTGTAGPARFNSHGDLINP 399 (784)
Q Consensus 347 ~~~~~~~~~g~~~~~~~~~~~~~~~l~-~~l~~~~f~g~tG~v~Fd~~g~~~~~ 399 (784)
++..+. ..+++..|+|+.|+++||++|++...
T Consensus 295 ---------------------~~~~~~~~~~~~~~~~g~~g~i~f~~~g~~~~~ 327 (332)
T cd06344 295 ---------------------EGVQQVELSLRNFSVQGATGKIKFLPSGDRNGQ 327 (332)
T ss_pred ---------------------hhhhhhhhhcccccccCCCceeEeCCCCcccCc
Confidence 234444 67778889999999999999997543
No 49
>COG0683 LivK ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]
Probab=100.00 E-value=3.5e-33 Score=298.57 Aligned_cols=338 Identities=23% Similarity=0.264 Sum_probs=277.9
Q ss_pred CceEEEEEEeecC---CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHh-cCceEEEccC
Q 003958 29 PSVVNIGALLSFS---TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLME-GQTVAIIGPQ 104 (784)
Q Consensus 29 ~~~i~IG~i~~~~---~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~-~~v~aiiGp~ 104 (784)
.++|+||++.|+| +.+|.....++++|+|+||+.+|++ |++|++++.|+.+|+..+.+.+.+|+. ++|.+|+|+.
T Consensus 8 a~~IkIGv~~plsG~~A~~G~~~~~ga~lAv~~iNa~Ggi~-G~~velv~~D~~~dp~~a~~~A~~li~~~~V~~vvG~~ 86 (366)
T COG0683 8 ADTIKIGVVLPLSGPAAAYGQQIKNGAELAVEEINAAGGIL-GRKVELVVEDDASDPATAAAVARKLITQDGVDAVVGPT 86 (366)
T ss_pred cCceEEEEEecCCchhhhhChHHHHHHHHHHHHHhhhCCcC-CceEEEEEecCCCChHHHHHHHHHHHhhcCceEEEEec
Confidence 4489999999998 6778999999999999999999986 788999999999999999999999988 5999999999
Q ss_pred chhhHHHHHHhhhcCCccEEecccCCCCCCcCCC-CceEeecCChHHHHHHHHHHHHH-cCCcEEEEEEEcCCCcchhHH
Q 003958 105 DAVTSHVVSHVANELQVPLLSFSATDPTLSSLQF-PYFVRTTQSDQYQMAAIAEIVDH-YGWREVIAIYVDDDHGRNGIA 182 (784)
Q Consensus 105 ~s~~~~~va~~~~~~~ip~Is~~a~~~~l~~~~~-p~~~r~~ps~~~~~~ai~~~l~~-~~w~~v~ii~~d~~~g~~~~~ 182 (784)
+|..+.++.++++..++|+|+++++++.+....+ +++||+.|++..++.++++++.. .+.+++++|+.|+.||+...+
T Consensus 87 ~S~~~~a~~~v~~~~~i~~i~p~st~~~~~~~~~~~~vfr~~~~~~~q~~~~~~~l~~~~~~k~v~ii~~~~~yg~~~~~ 166 (366)
T COG0683 87 TSGVALAASPVAEEAGVPLISPSATAPQLTGRGLKPNVFRTGPTDNQQAAAAADYLVKKGGKKRVAIIGDDYAYGEGLAD 166 (366)
T ss_pred cCcccccchhhHhhcCceEEeecCCCCcccccccccceEEecCChHHHHHHHHHHHHHhcCCcEEEEEeCCCCcchhHHH
Confidence 9999999999999999999999999998777544 45999999999999999999865 555699999999999999999
Q ss_pred HHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHcCCCCCCeEEEecCccccc
Q 003958 183 ALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIATSWLSTA 262 (784)
Q Consensus 183 ~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~ 262 (784)
.+++.++++|++++..+.+.+ ...++..++.++++.++++|++.+...+...++++++++|+... ..++........
T Consensus 167 ~~~~~l~~~G~~~~~~~~~~~--~~~~~~~~v~~i~~~~~d~v~~~~~~~~~~~~~r~~~~~G~~~~-~~~~~~~~~~~~ 243 (366)
T COG0683 167 AFKAALKALGGEVVVEEVYAP--GDTDFSALVAKIKAAGPDAVLVGGYGPDAALFLRQAREQGLKAK-LIGGDGAGTAEF 243 (366)
T ss_pred HHHHHHHhCCCeEEEEEeeCC--CCCChHHHHHHHHhcCCCEEEECCCCccchHHHHHHHHcCCCCc-cccccccCchhh
Confidence 999999999998665566653 44459999999999999999999999999999999999998764 222221111111
Q ss_pred cccCCCCCCCccccce--eeEEEeeecC-CchhHHHHHHHHHhhccCCCCCCCCCCChhHHHHhhHHHHHHHHHHHHhhc
Q 003958 263 LDTNSPFPSDVMDDIQ--GVLTLRTYTP-DSVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTVWLLARAINSFFKQ 339 (784)
Q Consensus 263 ~~~~~~~~~~~~~~~~--g~~~~~~~~~-~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~~~a~Al~~~~~~ 339 (784)
.. ....... +.+...+..+ ..|..+.|.++|+++++ ....++.++..+||+++++++|++++..
T Consensus 244 ~~-------~~~~~~~~~~~~~~~~~~~~~~p~~~~f~~~~~~~~g-----~~~~~~~~~~~~y~a~~~~~~ai~~a~~- 310 (366)
T COG0683 244 EE-------IAGAGGAGAGLLATAYSTPDDSPANKKFVEAYKAKYG-----DPAAPSYFAAAAYDAVKLLAKAIEKAGK- 310 (366)
T ss_pred hh-------hcccCccccEEEEecccccccCcchHHHHHHHHHHhC-----CCCCcccchHHHHHHHHHHHHHHHHHhc-
Confidence 10 1111122 3333333333 45677889999999987 2344567899999999999999999732
Q ss_pred CCccccccCCccccccCCcccccccccCCchHHHHHHHhcc-ccceeeeEEEecCCCCcCCcEEEEEeecc
Q 003958 340 GGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQAN-MTGTAGPARFNSHGDLINPAYEIINVIGT 409 (784)
Q Consensus 340 ~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~l~~~l~~~~-f~g~tG~v~Fd~~g~~~~~~~~I~~~~~~ 409 (784)
. . +++.+.++|++.. +.+.+|.+.||++|++....+.|.+++..
T Consensus 311 ~-------------------------~-d~~~v~~al~~~~~~~~~~G~v~~~~~~~~~~~~~~i~~~~~~ 355 (366)
T COG0683 311 S-------------------------S-DREAVAEALKGGKFFDTAGGPVTFDEKGDRGSKPVYVGQVQKG 355 (366)
T ss_pred C-------------------------C-CHHHHHHHHhhCCCCccCCcceeECCCCCcCCCceEEEEEEec
Confidence 0 0 3788999999887 78999999999999999999999988853
No 50
>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=100.00 E-value=6.3e-33 Score=296.18 Aligned_cols=341 Identities=10% Similarity=0.086 Sum_probs=270.7
Q ss_pred EEEEEEeecC---CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhc-CceEEEccCchh
Q 003958 32 VNIGALLSFS---TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEG-QTVAIIGPQDAV 107 (784)
Q Consensus 32 i~IG~i~~~~---~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~-~v~aiiGp~~s~ 107 (784)
|+||++.|+| +..|.....|+++|+|+||++||++ |++|++++.|++++|..++..+.+|+++ +|.+|+|+.+|.
T Consensus 1 IkIG~~~plSG~~a~~G~~~~~G~~lAv~~iNa~GGi~-Gr~ielv~~D~~~~p~~a~~~a~~li~~d~v~~viG~~~S~ 79 (374)
T TIGR03669 1 IKLGVLEDRSGNFALVGTPKWHASQLAIEEINKSGGIL-GRQIELIDPDPQSDNERYQELTRRLLNRDKVDALWAGYSSA 79 (374)
T ss_pred CEEEEEeCCCCCchhccHHHHHHHHHHHHHHHhcCCCC-CceeEEEEeCCCCCHHHHHHHHHHHHHhCCCCEEEcCCchH
Confidence 6899999998 5568889999999999999999996 8999999999999999999999999975 899999999999
Q ss_pred hHHHHHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcCCCcchhHHHHHHH
Q 003958 108 TSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDT 187 (784)
Q Consensus 108 ~~~~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~~ 187 (784)
.+.++++++...++|+|....... ....+|+||+.|++..++.++++++....-+++++|+.|++||+...+.+++.
T Consensus 80 ~~~A~~~~~~~~~~~~i~~~~~~~---~~~~~~~Fr~~~~~~~~~~~~~~~~~~~~g~~va~l~~d~~~g~~~~~~~~~~ 156 (374)
T TIGR03669 80 TREAIRPIIDRNEQLYFYTNQYEG---GVCDEYTFAVGATARQQLGTVVPYMVEEYGKKIYTIAADYNFGQLSADWVRVI 156 (374)
T ss_pred HHHHHHHHHHhcCceEEcCccccc---ccCCCCEEEcCCChHHHHHHHHHHHHHcCCCeEEEEcCCcHHHHHHHHHHHHH
Confidence 999999999999999996432111 12358999999999999999999986543368999999999999999999999
Q ss_pred HhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHcCCCCCCeEEEecCccccccccCC
Q 003958 188 LAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIATSWLSTALDTNS 267 (784)
Q Consensus 188 l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~~~ 267 (784)
+++.|++++....++ .+..|+..++.+|+.+++|+|++.....+...++++++++|+..+ ++............
T Consensus 157 ~~~~G~~vv~~~~~~--~g~~Df~~~l~~i~~~~pD~V~~~~~g~~~~~~~kq~~~~G~~~~---~~~~~~~~~~~~~~- 230 (374)
T TIGR03669 157 AKENGAEVVGEEFIP--LSVSQFSSTIQNIQKADPDFVMSMLVGANHASFYEQAASANLNLP---MGTSTAMAQGYEHK- 230 (374)
T ss_pred HHHcCCeEEeEEecC--CCcchHHHHHHHHHHcCCCEEEEcCcCCcHHHHHHHHHHcCCCCc---ccchhhhhhhhhhh-
Confidence 999999999888887 567899999999999999999999888899999999999998654 22221111110100
Q ss_pred CCCCCccccceeeEEEeeecC--CchhHHHHHHHHHhhccCCCCCCCCCCChhHHHHhhHHHHHHHHHHHHhhcCCcccc
Q 003958 268 PFPSDVMDDIQGVLTLRTYTP--DSVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTVWLLARAINSFFKQGGNLSF 345 (784)
Q Consensus 268 ~~~~~~~~~~~g~~~~~~~~~--~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~~~a~Al~~~~~~~~~~~~ 345 (784)
........|+++...+.+ +.+..+.|.++|+++|+. ...++.++..+||+++++++|++++.+
T Consensus 231 ---~~~~~~~~g~~~~~~~~~~~~~~~~~~F~~~y~~~~g~-----~p~~~~~a~~~Yda~~~l~~Ai~~AGs------- 295 (374)
T TIGR03669 231 ---RFEPPALKDVYAGVNYMEEIDTPENEAFVERFYAKFPD-----APYINQEAENNYFSVYMYKQAVEEAGT------- 295 (374)
T ss_pred ---hcCchhhCCcEEeeeccccCCCHHHHHHHHHHHHHcCC-----CCCCChHHHHHHHHHHHHHHHHHHhCC-------
Confidence 011123556665554443 467889999999999862 112356688999999999999998621
Q ss_pred ccCCccccccCCcccccccccCCchHHHHHHHh-ccccceeeeEEEecCCCCcCCcEEEEEeec-cceEEEEEec
Q 003958 346 SKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQ-ANMTGTAGPARFNSHGDLINPAYEIINVIG-TGYRRIGYWS 418 (784)
Q Consensus 346 ~~~~~~~~~~g~~~~~~~~~~~~~~~l~~~l~~-~~f~g~tG~v~Fd~~g~~~~~~~~I~~~~~-~~~~~VG~w~ 418 (784)
.+++.+.++|++ ..|+|+.|+++||++++.....+.|.+++. +.+..+..|+
T Consensus 296 ---------------------~d~~av~~aL~~~~~~~~~~G~i~fd~~~~~~~~~~~v~~~~~~~~~~~~~~~~ 349 (374)
T TIGR03669 296 ---------------------TDQDAVRDVLESGVEMDAPEGKVCIDGATHHMSHTMRLARADADHNITFVKEQE 349 (374)
T ss_pred ---------------------CCHHHHHHHHHcCCeEECCCccEEEcCCCCeeeeeeEEEEEcCCCCEEEEEecC
Confidence 158899999997 569999999999987654455556666653 3344444444
No 51
>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=100.00 E-value=4.2e-34 Score=303.46 Aligned_cols=333 Identities=17% Similarity=0.137 Sum_probs=242.7
Q ss_pred CCcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecC------C-CCHHHHHHHHHHHHhcCc--eEEEccCchhhHHH
Q 003958 41 STNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDC------N-HSGFLALAEALHLMEGQT--VAIIGPQDAVTSHV 111 (784)
Q Consensus 41 ~~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~------~-~~~~~a~~~~~~li~~~v--~aiiGp~~s~~~~~ 111 (784)
+...|...+.|+++|++++|++. |.+|.....++ . .|...+.+++|+++++++ .|||||.++..+..
T Consensus 7 ~~~~~~~~~~A~~~Av~~~N~~~----~~~l~~~~~~~~~~~~~~~~d~~~~~~~~C~~~~~gv~~~AIiGp~ss~~a~~ 82 (368)
T cd06383 7 TEDDNDVYKQIIDDALSYINRNI----GTGLSVVHQQVETNAEVNRNDVKVALIEVCDKADSAIVPHLVLDTTTCGDASE 82 (368)
T ss_pred cccchHHHHHHHHHHHHHHhcCC----CCceEEEEecccccccccCCcHHHHHHHHHHHHHccCCcEEEECCCcchhHHH
Confidence 34467889999999999999986 56777777766 4 477777788999999988 89999999999999
Q ss_pred HHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcCCCcchhHH-HHHHHHhc
Q 003958 112 VSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDDDHGRNGIA-ALGDTLAA 190 (784)
Q Consensus 112 va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~-~l~~~l~~ 190 (784)
++.+|+.++||+|+++.. ..++.+||+++|+.|++..+++|+++++++|+|++|++||+++++.....+ .+++....
T Consensus 83 V~si~~~~~IP~Is~s~~--~~~~~~~p~~ir~~Ps~~~~~~Ai~dlI~~f~W~~v~iIYddd~gl~~~l~~~l~~~~~~ 160 (368)
T cd06383 83 IKSVTGALGIPTFSASYG--QEGDLEQPYLIQLMPPADDIVEAIRDIVSYYNITNAAILYDDDFVMDHKYKSLLQNWPTR 160 (368)
T ss_pred HHHHHhccCCCEEEccCC--CcCcccCceEEEEeCChHHHHHHHHHHHHHCCCcEEEEEEEcCchhhHHHHHHHHhHHhc
Confidence 999999999999997543 223357899999999999999999999999999999999977664432333 33333344
Q ss_pred cCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEecc-CCcHHHHHHHHHHcCCCCCCeEEEecCccccccccCCCC
Q 003958 191 KRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTH-YNRGPVVFHVAQYLGMLGTGYVWIATSWLSTALDTNSPF 269 (784)
Q Consensus 191 ~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~-~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~~~~~ 269 (784)
.+.++. + ....++..++++|++.+.+.||+.+. ++.+..++++|.++||++.+|+||++++.....+.
T Consensus 161 ~~~~v~-----~--~~~~~~~~~Lk~lk~~~~~rIIi~~s~~~~~~~il~qA~~lgm~~~~y~wilt~ld~~~~dl---- 229 (368)
T cd06383 161 HVITII-----N--SIIDEVREQIKRLRNLDIKNIFILGSTEEIIRYVLDQALAEGFMGRKYAWFLGNPDLGIYDD---- 229 (368)
T ss_pred CCEEEE-----e--ccchhHHHHHHHHHhCCCeEEEEEeCCHHHHHHHHHHHHHcCCcCCceEEEEcCCCchhhhh----
Confidence 455543 1 12356889999999988856666666 49999999999999999999999999987655433
Q ss_pred CCCccccceeeEEEeeecCCchhHHHHHHHHHhhccCCCCCCCCCCChhHHHHhhHHHHHHHHHHHHhhcCCccccccCC
Q 003958 270 PSDVMDDIQGVLTLRTYTPDSVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTVWLLARAINSFFKQGGNLSFSKDS 349 (784)
Q Consensus 270 ~~~~~~~~~g~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~~~a~Al~~~~~~~~~~~~~~~~ 349 (784)
++....-.++.++++..+.....+.+.++|.+.. ..+.........++.+||||++++.|++.+.....+..
T Consensus 230 -~~~~~~~~Nitgfrl~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~aL~~Dav~~~~~a~~~l~~~~~~~~----- 301 (368)
T cd06383 230 -LSCQLRNASIFVTRPMMDYQSSVRGALLRTDEPT--LRPVFYFEWAFRLFLAYDAVLAVGEWPRRMRKKRVEDG----- 301 (368)
T ss_pred -hhhccccCcEEEeeccccchhhhccceeeccCCc--cCchhHHHHHHHHHHHHHHHHHhccccchhheeeccCC-----
Confidence 1223334578888886665555577777663211 00111112335689999999999999998632111110
Q ss_pred ccccccCCcccccc---ccc-CCchHHHHHHHhccccceeeeEEEecCCCCcCCc
Q 003958 350 RLSDIQGHLRLDSL---RIF-NGGNLLRDSILQANMTGTAGPARFNSHGDLINPA 400 (784)
Q Consensus 350 ~~~~~~g~~~~~~~---~~~-~~~~~l~~~l~~~~f~g~tG~v~Fd~~g~~~~~~ 400 (784)
|... ....|... ..| .+|..+.++|+.++|+|+||+|+||++|.|.+..
T Consensus 302 -~~~~-~~~~~~g~~~~~~w~~~g~~~~~~~k~~~~~gltG~i~f~~~g~R~~~~ 354 (368)
T cd06383 302 -STGT-SVLPGFGISPESPLMTLQSSPFNGSSEIKFEMLAGRVAIDEGSSVSTKT 354 (368)
T ss_pred -CcCc-cccCCCCCCcccchhhcccccccCccceeEeeecCeEEEecCceeeeee
Confidence 0000 01123322 134 5666999999999999999999999999875544
No 52
>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=100.00 E-value=2.8e-33 Score=298.51 Aligned_cols=314 Identities=16% Similarity=0.204 Sum_probs=267.6
Q ss_pred EEEEEeecC---CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEccCchhhH
Q 003958 33 NIGALLSFS---TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIGPQDAVTS 109 (784)
Q Consensus 33 ~IG~i~~~~---~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiGp~~s~~~ 109 (784)
+||++.|++ +..|.....++++|+++||+.+|+. |++|+++++|+++++.++++.+.+|++++|.+||||.+|..+
T Consensus 1 ~IG~l~p~sG~~a~~G~~~~~g~~~a~~~iN~~GGi~-G~~i~l~~~D~~~~p~~a~~~a~~lv~~~v~aiiG~~~s~~~ 79 (342)
T cd06329 1 KIGVIDPLSGPFASLGELVRRGLQLAADEINAKGGVD-GRPIELVEEDNKGSPQEALRKAQKAIDDGVRLVVQGNSSSVA 79 (342)
T ss_pred CeeeeccCCCCcccccHHHHHHHHHHHHHHHhcCCcC-CeEEEEEeccCCCChHHHHHHHHHHHHhCCeEEEcccchHHH
Confidence 589999998 4568889999999999999999985 899999999999999999999999999999999999999999
Q ss_pred HHH-------HHhhhcCCccEEecccCCCCCCc-CCCCceEeecCChHHHHHHHHHHHHHcC-CcEEEEEEEcCCCcchh
Q 003958 110 HVV-------SHVANELQVPLLSFSATDPTLSS-LQFPYFVRTTQSDQYQMAAIAEIVDHYG-WREVIAIYVDDDHGRNG 180 (784)
Q Consensus 110 ~~v-------a~~~~~~~ip~Is~~a~~~~l~~-~~~p~~~r~~ps~~~~~~ai~~~l~~~~-w~~v~ii~~d~~~g~~~ 180 (784)
.++ ++++..+++|+|++.++++.+++ +.+|++||+.|++..++.++++++.+.+ |+++++++.|+.||+..
T Consensus 80 ~~~~~~~~~~~~~~~~~~ip~i~~~~~~~~~~~~~~~~~~fr~~~~~~~~~~~l~~~~~~~~~~k~v~i~~~~~~~g~~~ 159 (342)
T cd06329 80 LALTEAVRKHNQRNPGKEVLYLNYASVAPALTGEKCSFWHFRTDANTDMKMEALASYIKKQPDGKKVYLINQDYSWGQDV 159 (342)
T ss_pred HHhhhhhhhhhhhhccCCeEEEecCCCCchhhhccCcceEEEecCChHHHHHHHHHHHHhcccCceEEEEeCChHHHHHH
Confidence 988 78888999999999888888876 5679999999999999999999998876 99999999999999999
Q ss_pred HHHHHHHHhc--cCcEEEEeeccCCCCCh-hHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHcCCCCCCeEEEecC
Q 003958 181 IAALGDTLAA--KRCRISFKAPLSVEATE-DEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIATS 257 (784)
Q Consensus 181 ~~~l~~~l~~--~gi~v~~~~~~~~~~~~-~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~ 257 (784)
.+.+++.+++ .|++|+....++ .+. +|+..++.++++.++++|++.....++..++++++++|+..+ ++...
T Consensus 160 ~~~~~~~~~~~~~G~~vv~~~~~~--~~~~~d~~~~i~~l~~~~~d~v~~~~~~~~~~~~~~~~~~~g~~~~---~~~~~ 234 (342)
T cd06329 160 AAAFKAMLAAKRPDIQIVGEDLHP--LGKVKDFSPYVAKIKASGADTVITGNWGNDLLLLVKQAADAGLKLP---FYTPY 234 (342)
T ss_pred HHHHHHHHHhhcCCcEEeceeccC--CCCCCchHHHHHHHHHcCCCEEEEcccCchHHHHHHHHHHcCCCce---EEecc
Confidence 9999999999 999999877776 355 789999999999999999999888899999999999998643 45444
Q ss_pred ccccccccCCCCCCCccccceeeEEEeeecC--CchhHHHHHHHHHhhccCCCCCCCCCCChhHHHHhhHHHHHHHHHHH
Q 003958 258 WLSTALDTNSPFPSDVMDDIQGVLTLRTYTP--DSVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTVWLLARAINS 335 (784)
Q Consensus 258 ~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~--~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~~~a~Al~~ 335 (784)
+...... ....+..+|.+....+.+ +++..++|.++|+++++ ..++.++..+||+++++++|+++
T Consensus 235 ~~~~~~~------~~~g~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~~-------~~~~~~~~~~y~~~~~~~~a~~~ 301 (342)
T cd06329 235 LDQPGNP------AALGEAGLGLVVAVAYWHPNDTPANRAFVEAFKAKYG-------RVPDYYEGQAYNGIQMLADAIEK 301 (342)
T ss_pred ccchhHH------HhhcccccceEEeeeccCCCCCHHHHHHHHHHHHHhC-------CCCCchHHHHHHHHHHHHHHHHH
Confidence 3322111 122345567666655443 36788999999999886 24567789999999999999998
Q ss_pred HhhcCCccccccCCccccccCCcccccccccCCchHHHHHHHhccccceeeeEEEecC
Q 003958 336 FFKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANMTGTAGPARFNSH 393 (784)
Q Consensus 336 ~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~l~~~l~~~~f~g~tG~v~Fd~~ 393 (784)
+.. .++..+.++|++++|+|..|+++|++.
T Consensus 302 ag~----------------------------~~~~~v~~al~~~~~~~~~g~~~~~~~ 331 (342)
T cd06329 302 AGS----------------------------TDPEAVAKALEGMEVDTPVGPVTMRAS 331 (342)
T ss_pred hCC----------------------------CCHHHHHHHHhCCccccCCCCeEEccc
Confidence 411 147889999999999999999999963
No 53
>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=100.00 E-value=6.9e-33 Score=295.61 Aligned_cols=321 Identities=20% Similarity=0.309 Sum_probs=268.2
Q ss_pred EEEEEeecC---CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhc-CceEEEccCchhh
Q 003958 33 NIGALLSFS---TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEG-QTVAIIGPQDAVT 108 (784)
Q Consensus 33 ~IG~i~~~~---~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~-~v~aiiGp~~s~~ 108 (784)
+||+++|++ +..|.....|+++|+|+||+++|+ +|++|++++.|+++++.++.+.+++++++ +|.+|+||.++..
T Consensus 1 ~iG~~~~~sG~~~~~g~~~~~g~~~a~~~iN~~ggi-~g~~l~~~~~D~~~~~~~~~~~~~~li~~~~v~aiiG~~~s~~ 79 (334)
T cd06347 1 KIGVNLPLTGDVAAYGQSEKNGAKLAVKEINAAGGV-LGKKIELVVEDNKSDKEEAANAATRLIDQDKVVAIIGPVTSGA 79 (334)
T ss_pred CeeEEecCCchhhhcCHhHHHHHHHHHHHHHhcCCC-CCeeEEEEEecCCCChHHHHHHHHHHhcccCeEEEEcCCccHh
Confidence 589999998 355778899999999999999987 59999999999999999999999999987 9999999999999
Q ss_pred HHHHHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHH-HHcCCcEEEEEEEcC-CCcchhHHHHHH
Q 003958 109 SHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIV-DHYGWREVIAIYVDD-DHGRNGIAALGD 186 (784)
Q Consensus 109 ~~~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l-~~~~w~~v~ii~~d~-~~g~~~~~~l~~ 186 (784)
+.+++++++..+||+|++.++.+.+++.. +++||+.|++..++.++++++ ++++|++|++|+.++ +|+....+.+++
T Consensus 80 ~~~v~~~~~~~~ip~i~~~~~~~~~~~~~-~~~fr~~~~~~~~~~~~~~~~~~~~~~~~v~ii~~~~~~~~~~~~~~~~~ 158 (334)
T cd06347 80 TLAAGPIAEDAKVPMITPSATNPKVTQGK-DYVFRVCFIDPFQGTVMAKFATENLKAKKAAVLYDNSSDYSKGLAKAFKE 158 (334)
T ss_pred HHHhHHHHHHCCCeEEcCCCCCCCcccCC-CeEEEeeCCcHHHHHHHHHHHHHhcCCcEEEEEEeCCCchhHHHHHHHHH
Confidence 99999999999999999988877776532 589999999988999999986 677999999999875 899999999999
Q ss_pred HHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHcCCCCCCeEEEecCccccccccC
Q 003958 187 TLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIATSWLSTALDTN 266 (784)
Q Consensus 187 ~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~~ 266 (784)
.+++.|++++....++ .+..++..+++++++.++++|++.+.......+++++++.|+.. .|++++.|......
T Consensus 159 ~~~~~g~~v~~~~~~~--~~~~d~~~~~~~~~~~~~d~i~~~~~~~~~~~~~~~~~~~g~~~---~i~~~~~~~~~~~~- 232 (334)
T cd06347 159 AFKKLGGEIVAEETFN--AGDTDFSAQLTKIKAKNPDVIFLPGYYTEVGLIAKQARELGIKV---PILGGDGWDSPKLE- 232 (334)
T ss_pred HHHHcCCEEEEEEEec--CCCCcHHHHHHHHHhcCCCEEEEcCchhhHHHHHHHHHHcCCCC---cEEecccccCHHHH-
Confidence 9999999999887776 35678999999999999999999999999999999999998743 47776655432111
Q ss_pred CCCCCCccccceeeEEEeeecC--CchhHHHHHHHHHhhccCCCCCCCCCCChhHHHHhhHHHHHHHHHHHHhhcCCccc
Q 003958 267 SPFPSDVMDDIQGVLTLRTYTP--DSVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTVWLLARAINSFFKQGGNLS 344 (784)
Q Consensus 267 ~~~~~~~~~~~~g~~~~~~~~~--~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~~~a~Al~~~~~~~~~~~ 344 (784)
.......+|++...++.+ +.+..++|.+.|+++++ ..++.++..+||+++++++|++++..
T Consensus 233 ----~~~~~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~~-------~~~~~~~~~~yda~~~~~~Al~~ag~------ 295 (334)
T cd06347 233 ----EAGGAAAEGVYFTTHFSADDPTPKAKKFVKAYKAKYG-------KEPDAFAALGYDAYYLLADAIERAGS------ 295 (334)
T ss_pred ----HHHHHHhCCcEEecccCCCCCCHHHHHHHHHHHHHHC-------CCcchhHHHHHHHHHHHHHHHHHhCC------
Confidence 112245677766665554 35778999999998875 34567889999999999999998411
Q ss_pred cccCCccccccCCcccccccccCCchHHHHHHHhc-cccceeeeEEEecCCCCcCCc
Q 003958 345 FSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQA-NMTGTAGPARFNSHGDLINPA 400 (784)
Q Consensus 345 ~~~~~~~~~~~g~~~~~~~~~~~~~~~l~~~l~~~-~f~g~tG~v~Fd~~g~~~~~~ 400 (784)
. ++..+.+.|++. +|+|++|.++|+++|+.....
T Consensus 296 ---------------------~-~~~~v~~~l~~~~~~~g~~G~v~f~~~g~~~~~~ 330 (334)
T cd06347 296 ---------------------T-DPEAIRDALAKTKDFDGVTGKITIDENGNPVKSA 330 (334)
T ss_pred ---------------------C-CHHHHHHHHHhCCCcccceeeeEECCCCCcCCCc
Confidence 0 377899998765 699999999999999864433
No 54
>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=100.00 E-value=1.3e-32 Score=296.24 Aligned_cols=342 Identities=16% Similarity=0.189 Sum_probs=282.5
Q ss_pred CCceEEEEEEeecC---CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhc-CceEEEcc
Q 003958 28 RPSVVNIGALLSFS---TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEG-QTVAIIGP 103 (784)
Q Consensus 28 ~~~~i~IG~i~~~~---~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~-~v~aiiGp 103 (784)
.+++|+||+++|++ +..|.....++++|++++|+.+|+. |++|+++++|+++++..+.+.+.+++.+ +|.+|+|+
T Consensus 3 ~~~~i~iG~~~~~sG~~a~~g~~~~~g~~~a~~~~Na~gGi~-G~~i~l~~~D~~~~~~~a~~~a~~li~~~~v~avvG~ 81 (362)
T cd06343 3 TDTEIKIGNTMPLSGPASAYGVIGRTGAAYFFMINNDQGGIN-GRKIELIVEDDGYSPPKTVEQTRKLVESDEVFAMVGG 81 (362)
T ss_pred CCceEEEeeccCCCCchhhhcHHHHHHHHHHHHHHHhcCCcC-CeEEEEEEecCCCChHHHHHHHHHHHhhcCeEEEEec
Confidence 35799999999998 4568889999999999999999985 9999999999999999999999999975 99999999
Q ss_pred CchhhHHHHHHhhhcCCccEEecccCCCCCCc-CCCCceEeecCChHHHHHHHHHHH-HHcCCcEEEEEEEcCCCcchhH
Q 003958 104 QDAVTSHVVSHVANELQVPLLSFSATDPTLSS-LQFPYFVRTTQSDQYQMAAIAEIV-DHYGWREVIAIYVDDDHGRNGI 181 (784)
Q Consensus 104 ~~s~~~~~va~~~~~~~ip~Is~~a~~~~l~~-~~~p~~~r~~ps~~~~~~ai~~~l-~~~~w~~v~ii~~d~~~g~~~~ 181 (784)
.+|..+.+++++++..+||+|++.++++.+++ +.+|++||+.|++..++.++++++ ++++|+++++|+.++.||+...
T Consensus 82 ~~s~~~~~~~~~~~~~~ip~i~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~g~~~v~ii~~~~~~g~~~~ 161 (362)
T cd06343 82 LGTPTNLAVQKYLNEKKVPQLFPASGASKWNDPKPFPWTFGWQPSYQDEARIYAKYLVEEKPNAKIAVLYQNDDFGKDYL 161 (362)
T ss_pred CCcHHHHHhHHHHHhcCCceEecccccHhhhCCCCCCceEecCCChHHHHHHHHHHHHHhCCCceEEEEEeccHHHHHHH
Confidence 99999999999999999999998777777777 478999999999999999999975 5789999999999999999999
Q ss_pred HHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHcCCCCCCeEEEecCcccc
Q 003958 182 AALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIATSWLST 261 (784)
Q Consensus 182 ~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~ 261 (784)
+.+++.+++.|++++....++ .+.+|++++++++++.++++|++.+...++..+++++++.|+... ++.+.+...
T Consensus 162 ~~~~~~~~~~G~~vv~~~~~~--~~~~d~~~~v~~i~~~~~d~v~~~~~~~~~~~~~~~~~~~g~~~~---~~~~~~~~~ 236 (362)
T cd06343 162 KGLKDGLGDAGLEIVAETSYE--VTEPDFDSQVAKLKAAGADVVVLATTPKFAAQAIRKAAELGWKPT---FLLSSVSAS 236 (362)
T ss_pred HHHHHHHHHcCCeEEEEeeec--CCCccHHHHHHHHHhcCCCEEEEEcCcHHHHHHHHHHHHcCCCce---EEEEecccc
Confidence 999999999999999888887 467899999999999999999999999999999999999998753 555443322
Q ss_pred ccc-cCCCCCCCccccceeeEEEeeec-------CCchhHHHHHHHHHhhccCCCCCCCCCCChhHHHHhhHHHHHHHHH
Q 003958 262 ALD-TNSPFPSDVMDDIQGVLTLRTYT-------PDSVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTVWLLARAI 333 (784)
Q Consensus 262 ~~~-~~~~~~~~~~~~~~g~~~~~~~~-------~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~~~a~Al 333 (784)
... .. ....+..+|++...++. ...+..++|.+.|+++++. ...++.++..+||++.++++|+
T Consensus 237 ~~~~~~----~~~~~~~~g~~~~~~~~~~~~p~~~~~~~~~~f~~~~~~~~~~-----~~~~~~~~~~~y~a~~~~~~a~ 307 (362)
T cd06343 237 VASVLK----PAGLEAAEGVIAAAYLKDPTDPAWADDPGVKEFIAFYKKYFPE-----GDPPDTYAVYGYAAAETLVKVL 307 (362)
T ss_pred cHHHHH----HhhhHhhCceEEEEEecCCCccccccCHHHHHHHHHHHHhcCC-----CCCCchhhhHHHHHHHHHHHHH
Confidence 110 10 11224567776665443 2357789999999988862 1136778899999999999999
Q ss_pred HHHhhcCCccccccCCccccccCCcccccccccCCchHHHHHHHhccc---cc-eeeeEEEecCCCCcCCcEEEEEeecc
Q 003958 334 NSFFKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANM---TG-TAGPARFNSHGDLINPAYEIINVIGT 409 (784)
Q Consensus 334 ~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~l~~~l~~~~f---~g-~tG~v~Fd~~g~~~~~~~~I~~~~~~ 409 (784)
+++. .. .+++.+.++|+++++ .+ ..|+++|++++++....+.|.+++++
T Consensus 308 ~~ag---~~------------------------~~~~~v~~aL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~g 360 (362)
T cd06343 308 KQAG---DD------------------------LTRENIMKQAESLKDVLPDLLPGIRINTSPDDHLPIEQMQLMRFEGG 360 (362)
T ss_pred HHhC---CC------------------------CCHHHHHHHHHhCCCCCccccCccceecCccccccceeEEEEEEecC
Confidence 9861 11 147889999999997 32 34589999765556667788888766
Q ss_pred ce
Q 003958 410 GY 411 (784)
Q Consensus 410 ~~ 411 (784)
+|
T Consensus 361 ~~ 362 (362)
T cd06343 361 RW 362 (362)
T ss_pred cC
Confidence 54
No 55
>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=100.00 E-value=9.1e-32 Score=278.87 Aligned_cols=342 Identities=15% Similarity=0.172 Sum_probs=247.8
Q ss_pred CCCceEEEEEEeecCCcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCC-CCHHHHHHHHHHH-HhcCceEEEcc-
Q 003958 27 GRPSVVNIGALLSFSTNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCN-HSGFLALAEALHL-MEGQTVAIIGP- 103 (784)
Q Consensus 27 ~~~~~i~IG~i~~~~~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~-~~~~~a~~~~~~l-i~~~v~aiiGp- 103 (784)
..+..|+||++|+.. ...+.|+++|++.+|++..++++.+|+..+..-. .|+..+...+|++ +++||.||+|+
T Consensus 14 ~~~~~i~iG~if~~~----~~~~~af~~Av~~~N~~~~l~~~~~L~~~~~~~~~~dsf~~~~~vC~~ll~~GV~AIfg~p 89 (382)
T cd06377 14 RIGHTVRLGALLVRA----PAPRDRVLAALARANRAPLLPYNLSLEVVAAAAPSRDPASLLRSVCQTVVVQGVSALLAFP 89 (382)
T ss_pred hcCCceeeeEEecCC----chHHHHHHHHHHHhccccccccCceeEEeEEEcCCCChHHHHHHHHHhHhhCCeEEEEecC
Confidence 345579999999965 3568999999999999988888889999887654 4999999999999 59999999995
Q ss_pred CchhhHHHHHHhhhcCCccEEecccCCCCC-CcCCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcCCCcchhHH
Q 003958 104 QDAVTSHVVSHVANELQVPLLSFSATDPTL-SSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDDDHGRNGIA 182 (784)
Q Consensus 104 ~~s~~~~~va~~~~~~~ip~Is~~a~~~~l-~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~ 182 (784)
.++.++..+..+|+.++||+|++...+... ++..+....++.|+.++++.|+++++++|+|++|++||+.++....+.+
T Consensus 90 ~s~~~~~~v~sic~~l~IP~I~~~~~~~~~~~~~~~~l~L~l~P~~~~l~~a~~~ll~~~~W~~f~~iy~~~~gl~~lq~ 169 (382)
T cd06377 90 QTRPELVQLDFVSAALEIPVVSIVRREFPRGSQNPFHLQMSWASPLSTLLDVLLSVLQRNGWEDVSLVLCRERDPTGLLL 169 (382)
T ss_pred CCHHHHHHHHHHhcCCCCCEEEecCCcccccCCCceeEEEEecCCHHHHHHHHHHHHHHCCCcEEEEEEecCcCHHHHHH
Confidence 777788999999999999999986654332 2233333346699999999999999999999999999988875444333
Q ss_pred HHHHHHhccC--cEEEEeeccCCC-CChhHH-HHHHHHhhcCC-ceEEEEeccCCcHHHHHHHHHHcCCCCCCeEEEecC
Q 003958 183 ALGDTLAAKR--CRISFKAPLSVE-ATEDEI-TDLLVKVALTE-SRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIATS 257 (784)
Q Consensus 183 ~l~~~l~~~g--i~v~~~~~~~~~-~~~~d~-~~~l~~l~~~~-~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~ 257 (784)
.++. ....+ ..+... ..+.. .+..++ +.+|+++++.. .++|+++|+.+.+..+++++.+ .|+||+++
T Consensus 170 l~~~-~~~~~~~~~i~v~-~~~~~~~d~~~~~~~~L~~i~~~~~~~~ill~cs~e~~~~il~~~~~------~y~wIv~~ 241 (382)
T cd06377 170 LWTN-HARFHLGSVLNLS-RNDPSTADLLDFLRAQLELLKDPPGPAVVLFGCDVARARRVLELTPP------GPHWILGD 241 (382)
T ss_pred HHHH-hcccccCceEEEE-eccCccCChhHHHHHHHHHhhcccCceEEEEECCHHHHHHHHHhhcc------ceEEEEcC
Confidence 3332 22222 122222 22210 134455 99999999999 9999999999999999987754 49999987
Q ss_pred ccccccccCCCCCCCccccceeeEEEeeecCCchhHHHHHHHHHhhccCCCCCCCCCCChhHHHHhhHHHHHHHHHHHHh
Q 003958 258 WLSTALDTNSPFPSDVMDDIQGVLTLRTYTPDSVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTVWLLARAINSFF 337 (784)
Q Consensus 258 ~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~~~a~Al~~~~ 337 (784)
. .+... .....+..|+++. .+ .......+.+||||+++|+|++.+.
T Consensus 242 ~----~~le~---~~~~g~nigLl~~-----------------~~----------~~~~~l~ali~DAV~lvA~a~~~l~ 287 (382)
T cd06377 242 P----LPPEA---LRTEGLPPGLLAH-----------------GE----------TTQPPLEAYVQDALELVARAVGSAT 287 (382)
T ss_pred C----cChhh---ccCCCCCceEEEE-----------------ee----------cccccHHHHHHHHHHHHHHHHHHhh
Confidence 2 11110 0011223333321 10 0011338899999999999999863
Q ss_pred hcCCccccccCCccccccCCcccccc--c-ccCCchHHHHHHHhccccceeeeEEEecCCCC--cCCcEEEEEee--ccc
Q 003958 338 KQGGNLSFSKDSRLSDIQGHLRLDSL--R-IFNGGNLLRDSILQANMTGTAGPARFNSHGDL--INPAYEIINVI--GTG 410 (784)
Q Consensus 338 ~~~~~~~~~~~~~~~~~~g~~~~~~~--~-~~~~~~~l~~~l~~~~f~g~tG~v~Fd~~g~~--~~~~~~I~~~~--~~~ 410 (784)
.........+. +..|... . .|.+|..|.++|++++|+|.||+|.| ++|.| .+..++|++++ ..+
T Consensus 288 ~~~~~~~l~~~--------~~~C~~~~~~~~W~~G~~l~~~Lknv~~eGlTG~I~F-~~g~R~~~~~~l~I~~L~~~~~G 358 (382)
T cd06377 288 LVQPELALIPA--------TVNCMDLPTKGNESSGQYLARFLANTSFDGRTGPVWV-TGSSQVHSSRHFKVWSLRRDPVG 358 (382)
T ss_pred hcccccccCCC--------CCCcccCCCCCCCCchHHHHHHHHhCcccccceeEEE-ccCeeecccceEEEEEeccccCC
Confidence 11111111110 3467644 5 89999999999999999999999999 45778 79999999998 333
Q ss_pred ---eEEEEEecCCCCC
Q 003958 411 ---YRRIGYWSNYSGL 423 (784)
Q Consensus 411 ---~~~VG~w~~~~~l 423 (784)
|++||+|++...+
T Consensus 359 ~~~W~kVG~W~~~~~~ 374 (382)
T cd06377 359 QPTWTTVGSWQGGRKI 374 (382)
T ss_pred CccceEEEEecCCCce
Confidence 5999999986433
No 56
>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=100.00 E-value=1.8e-32 Score=291.44 Aligned_cols=322 Identities=15% Similarity=0.128 Sum_probs=267.3
Q ss_pred EEEEEeecC---CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhc-CceEEEccCchhh
Q 003958 33 NIGALLSFS---TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEG-QTVAIIGPQDAVT 108 (784)
Q Consensus 33 ~IG~i~~~~---~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~-~v~aiiGp~~s~~ 108 (784)
+||+++|++ +..|.....++++|+++||+++|+ .|++|+++++|++++|..+++++++|+++ +|.+|+|+.+|..
T Consensus 1 ~IG~l~p~sG~~a~~g~~~~~g~~~a~~~iN~~gGi-~G~~i~l~~~D~~~~p~~a~~~a~~Li~~~~V~aiiG~~~s~~ 79 (333)
T cd06331 1 KIGLLFSLSGPAAISEPSLRNAALLAIEEINAAGGI-LGRPLELVVEDPASDPAFAAKAARRLIRDDKVDAVFGCYTSAS 79 (333)
T ss_pred CeEEEecCCCccccccHHHHHHHHHHHHHHHhcCCC-CCeEEEEEEECCCCCHHHHHHHHHHHHhccCCcEEEecccHHH
Confidence 599999998 456788999999999999999998 59999999999999999999999999988 9999999999999
Q ss_pred HHHHHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcCCCcchhHHHHHHHH
Q 003958 109 SHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTL 188 (784)
Q Consensus 109 ~~~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~~l 188 (784)
+.+++++++..++|+|++.+.+.. ...|++||+.|+...++.++++++...+|++|++|+.|+.||+...+.+++.+
T Consensus 80 ~~a~~~~~~~~~vp~i~~~~~~~~---~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~v~il~~d~~~g~~~~~~~~~~~ 156 (333)
T cd06331 80 RKAVLPVVERGRGLLFYPTQYEGG---ECSPNVFYTGATPNQQLLPLIPYLMEKYGKRFYLIGSDYVWPRESNRIARALL 156 (333)
T ss_pred HHHHHHHHHhcCceEEeCCCCCCC---cCCCCeEEccCChHHhHHHHHHHHHHhcCCeEEEECCCchhHHHHHHHHHHHH
Confidence 999999999999999987543221 23589999999999999999998876669999999999999999999999999
Q ss_pred hccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHcCCCCCCeEEEecCccccccccCCC
Q 003958 189 AAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIATSWLSTALDTNSP 268 (784)
Q Consensus 189 ~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~~~~ 268 (784)
++.|.+|+....++ .+..|+++++.++++.++++|++.+...+...+++++++.|+......++........ ..
T Consensus 157 ~~~G~~vv~~~~~~--~~~~d~~~~v~~~~~~~~d~v~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~--~~-- 230 (333)
T cd06331 157 EELGGEVVGEEYLP--LGTSDFGSVIEKIKAAGPDVVLSTLVGDSNVAFYRQFAAAGLDADRIPILSLTLDENE--LA-- 230 (333)
T ss_pred HHcCCEEEEEEEec--CCcccHHHHHHHHHHcCCCEEEEecCCCChHHHHHHHHHcCCCcCCCeeEEcccchhh--hh--
Confidence 99999999888887 4578999999999999999999999999999999999999986433333332221111 11
Q ss_pred CCCCccccceeeEEEeeecC--CchhHHHHHHHHHhhccCCCCCCCCCCChhHHHHhhHHHHHHHHHHHHhhcCCccccc
Q 003958 269 FPSDVMDDIQGVLTLRTYTP--DSVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTVWLLARAINSFFKQGGNLSFS 346 (784)
Q Consensus 269 ~~~~~~~~~~g~~~~~~~~~--~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~~~a~Al~~~~~~~~~~~~~ 346 (784)
.......+|++...++.+ +.+..+.|.++|+++++. ...++.++..+||+++++++|++++..
T Consensus 231 --~~~~~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~~~-----~~~~~~~~~~~yda~~~~~~A~~~ag~-------- 295 (333)
T cd06331 231 --AIGAEAAEGHYSAASYFQSLDTPENKAFVARYRARYGD-----DAVINSPAEAAYEAVYLWAAAVEKAGS-------- 295 (333)
T ss_pred --ccChhhhCCcEeechhhhhcCChhHHHHHHHHHHHcCC-----CcCCCchhHHHHHHHHHHHHHHHHcCC--------
Confidence 112234678777765543 467789999999988762 113567899999999999999998411
Q ss_pred cCCccccccCCcccccccccCCchHHHHHHHhccccceeeeEEEecCCCCcCC
Q 003958 347 KDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANMTGTAGPARFNSHGDLINP 399 (784)
Q Consensus 347 ~~~~~~~~~g~~~~~~~~~~~~~~~l~~~l~~~~f~g~tG~v~Fd~~g~~~~~ 399 (784)
.++..|.++|++++|+|++|.+.|++++++...
T Consensus 296 --------------------~~~~~l~~al~~~~~~~~~G~i~f~~~~~~~~~ 328 (333)
T cd06331 296 --------------------TDPEAVRAALEGVSFDAPQGPVRIDPDNHHTWL 328 (333)
T ss_pred --------------------CCHHHHHHHhhcCcccCCCCceEecCCCCcccc
Confidence 147889999999999999999999998876433
No 57
>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=100.00 E-value=4.3e-32 Score=290.65 Aligned_cols=331 Identities=15% Similarity=0.133 Sum_probs=265.3
Q ss_pred EEEEEEeecC---CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhc-CceEEEccCchh
Q 003958 32 VNIGALLSFS---TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEG-QTVAIIGPQDAV 107 (784)
Q Consensus 32 i~IG~i~~~~---~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~-~v~aiiGp~~s~ 107 (784)
|+||++.|++ +..|.....|+++|+++||+++|++ |++|+++++|+.++|..++..+.+|+++ +|.+|+|+.+|.
T Consensus 1 I~IG~l~plsG~~a~~g~~~~~g~~lav~~iN~~GGi~-G~~i~l~~~Dd~~~p~~a~~~a~~Lv~~~~V~~iiG~~~S~ 79 (359)
T TIGR03407 1 IKVGILHSLSGTMAISETTLKDAELMAIEEINASGGVL-GKKIEPVVEDGASDWPTFAEKARKLITQDKVAAVFGCWTSA 79 (359)
T ss_pred CeEEEEeCCCCchhhcchhHHHHHHHHHHHHHhcCCCC-CcEEEEEEeCCCCCHHHHHHHHHHHHhhCCCcEEEcCCcHH
Confidence 6899999998 4567788999999999999999996 9999999999999999999999999975 899999999999
Q ss_pred hHHHHHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHH-cCCcEEEEEEEcCCCcchhHHHHHH
Q 003958 108 TSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDH-YGWREVIAIYVDDDHGRNGIAALGD 186 (784)
Q Consensus 108 ~~~~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~-~~w~~v~ii~~d~~~g~~~~~~l~~ 186 (784)
.+.++.+++...++|++++..... +...|++||+.+++..++.++++++.. .+.+++++++.|++||+...+.+++
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 999999999999999997643211 235689999999999999999998766 5999999999999999999999999
Q ss_pred HHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHcCCCCCCeEEEecCccccccccC
Q 003958 187 TLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIATSWLSTALDTN 266 (784)
Q Consensus 187 ~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~~ 266 (784)
.+++.|++++....++ .+..|++.++++|++.++|+|++.........+++++++.|+......++.+........
T Consensus 157 ~~~~~G~~vv~~~~~~--~~~~D~s~~v~~l~~~~pDav~~~~~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~~~~-- 232 (359)
T TIGR03407 157 YLKSLGGTVVGEDYTP--LGHTDFQTIINKIKAFKPDVVFNTLNGDSNVAFFKQLKNAGITAKDVPVVSFSVAEEEIR-- 232 (359)
T ss_pred HHHHcCCEEEeeEEec--CChHhHHHHHHHHHHhCCCEEEEeccCCCHHHHHHHHHHcCCCccCCcEEEeecCHHHHh--
Confidence 9999999999887777 577899999999999999999988788888899999999998654333444332221111
Q ss_pred CCCCCCccccceeeEEEeee--cCCchhHHHHHHHHHhhccCCCCCCCCCCChhHHHHhhHHHHHHHHHHHHhhcCCccc
Q 003958 267 SPFPSDVMDDIQGVLTLRTY--TPDSVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTVWLLARAINSFFKQGGNLS 344 (784)
Q Consensus 267 ~~~~~~~~~~~~g~~~~~~~--~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~~~a~Al~~~~~~~~~~~ 344 (784)
....+..+|+++...+ ..+.+..+.|.++|+++++. ...+..++..+||++.++++|++++..
T Consensus 233 ----~~g~~~~~G~~~~~~~~~~~~~~~~~~f~~~~~~~~~~-----~~~~~~~~~~~y~a~~~~~~A~~~ag~------ 297 (359)
T TIGR03407 233 ----GIGPENLVGHLAAWNYFQSVDTPANKKFVKAFKAKYGD-----DRVTNDPMEAAYLGVYLWKAAVEKAGS------ 297 (359)
T ss_pred ----hcChHhhCCeEEeccchhcCCCHHHHHHHHHHHHHcCC-----CCCCCcHHHHHHHHHHHHHHHHHHhCC------
Confidence 1112346776544222 23567889999999998862 112234566789999999999998611
Q ss_pred cccCCccccccCCcccccccccCCchHHHHHHHhccccceeeeEEEecCCCCcCCcEEEEEee
Q 003958 345 FSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANMTGTAGPARFNSHGDLINPAYEIINVI 407 (784)
Q Consensus 345 ~~~~~~~~~~~g~~~~~~~~~~~~~~~l~~~l~~~~f~g~tG~v~Fd~~g~~~~~~~~I~~~~ 407 (784)
. ++..+.++|++++|+++.|+++|+++++.....+.+.+++
T Consensus 298 ---------------------~-~~~~i~~al~~~~~~~~~G~i~f~~~~~~~~~~~~~~~~~ 338 (359)
T TIGR03407 298 ---------------------F-DVDAVRDAAIGIEFDAPEGKVKVDGKNHHLTKTVRIGEIR 338 (359)
T ss_pred ---------------------C-CHHHHHHHhcCCcccCCCccEEEeCCCCeeeeeeEEEEEc
Confidence 1 4889999999999999999999998433234444555554
No 58
>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=100.00 E-value=2.8e-32 Score=291.07 Aligned_cols=329 Identities=19% Similarity=0.256 Sum_probs=270.8
Q ss_pred EEEEEeecC---CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhc-CceEEEccCchhh
Q 003958 33 NIGALLSFS---TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEG-QTVAIIGPQDAVT 108 (784)
Q Consensus 33 ~IG~i~~~~---~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~-~v~aiiGp~~s~~ 108 (784)
+||++.|++ +..|.....++++|++++|+++|+ +|++|+++++|+++++..+.+.+.+|+++ +|.+|+|+.+|..
T Consensus 1 ~IG~~~plsG~~a~~G~~~~~g~~~a~~~iN~~ggi-~G~~i~l~~~D~~~~~~~a~~~a~~li~~~~V~~i~G~~~s~~ 79 (340)
T cd06349 1 LIGVAGPLTGDNAQYGTQWKRAFDLALDEINAAGGV-GGRPLNIVFEDSKSDPRQAVTIAQKFVADPRIVAVLGDFSSGV 79 (340)
T ss_pred CeeEEecCCCcchhcCccHHHHHHHHHHHHHhhCCc-CCeEEEEEEeCCCCChHHHHHHHHHHhccCCeEEEECCCccHh
Confidence 599999998 456889999999999999999998 59999999999999999999999999987 7999999999999
Q ss_pred HHHHHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHH-HHcCCcEEEEEEEcCCCcchhHHHHHHH
Q 003958 109 SHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIV-DHYGWREVIAIYVDDDHGRNGIAALGDT 187 (784)
Q Consensus 109 ~~~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l-~~~~w~~v~ii~~d~~~g~~~~~~l~~~ 187 (784)
+.+++++++..++|+|++.++++.+++ ..+|+||+.|++..++.++++++ ++++|+++++++.|++||+...+.+++.
T Consensus 80 ~~a~~~~~~~~~vp~i~~~~~~~~~~~-~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~v~ii~~~~~~g~~~~~~~~~~ 158 (340)
T cd06349 80 SMAASPIYQRAGLVQLSPTNSHPDFTK-GGDFIFRNSTSQAIEAPLLADYAVKDLGFKKVAILSVNTDWGRTSADIFVKA 158 (340)
T ss_pred HHHhHHHHHhCCCeEEecCCCCCcccc-CCCeEEEccCCcHHHHHHHHHHHHHHcCCcEEEEEecCChHhHHHHHHHHHH
Confidence 999999999999999998877776654 35899999999999999999986 6789999999999999999999999999
Q ss_pred HhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHcCCCCCCeEEEecCccccccccCC
Q 003958 188 LAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIATSWLSTALDTNS 267 (784)
Q Consensus 188 l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~~~ 267 (784)
+++.|++++....++ ....|++.++.+++.+++|+|++.+...++..+++++++.|+..+ ++.+.........
T Consensus 159 ~~~~g~~v~~~~~~~--~~~~d~~~~v~~l~~~~~d~v~~~~~~~~~~~~~~~~~~~g~~~~---~~~~~~~~~~~~~-- 231 (340)
T cd06349 159 AEKLGGQVVAHEEYV--PGEKDFRPTITRLRDANPDAIILISYYNDGAPIARQARAVGLDIP---VVASSSVYSPKFI-- 231 (340)
T ss_pred HHHcCCEEEEEEEeC--CCCCcHHHHHHHHHhcCCCEEEEccccchHHHHHHHHHHcCCCCc---EEccCCcCCHHHH--
Confidence 999999999877776 356789999999999999999999999999999999999998654 4544332211110
Q ss_pred CCCCCccccceeeEEEeeecC--CchhHHHHHHHHHhhccCCCCCCCCCCChhHHHHhhHHHHHHHHHHHHhhcCCcccc
Q 003958 268 PFPSDVMDDIQGVLTLRTYTP--DSVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTVWLLARAINSFFKQGGNLSF 345 (784)
Q Consensus 268 ~~~~~~~~~~~g~~~~~~~~~--~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~~~a~Al~~~~~~~~~~~~ 345 (784)
.......+|++....+.+ +.+..++|.++|+++++ ..++.++..+||++.++++|++++.. .
T Consensus 232 ---~~~~~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~~-------~~p~~~~~~~y~~~~~~~~a~~~ag~---~--- 295 (340)
T cd06349 232 ---ELGGDAVEGVYTPTAFFPGDPRPEVQSFVSAYEAKYG-------AQPDAFAAQAYDAVGILAAAVRRAGT---D--- 295 (340)
T ss_pred ---HHhHHHhCCcEEecccCCCCCCHHHHHHHHHHHHHHC-------CCcchhhhhHHHHHHHHHHHHHHhCC---C---
Confidence 111235678777765554 35778999999988876 23567899999999999999998511 0
Q ss_pred ccCCccccccCCcccccccccCCchHHHHHH--HhccccceeeeEEEecC-CCCcCCcEEEEEeeccc
Q 003958 346 SKDSRLSDIQGHLRLDSLRIFNGGNLLRDSI--LQANMTGTAGPARFNSH-GDLINPAYEIINVIGTG 410 (784)
Q Consensus 346 ~~~~~~~~~~g~~~~~~~~~~~~~~~l~~~l--~~~~f~g~tG~v~Fd~~-g~~~~~~~~I~~~~~~~ 410 (784)
+.. ....+ .+..+.+..|.++|+++ |+. ...+.++.+++++
T Consensus 296 ----------------------~~~-~~~~~~~~~~~~~~~~g~i~~~~~~~~~-~~~~~~~~~~~g~ 339 (340)
T cd06349 296 ----------------------RRA-ARDGFAKAEDVYSGVTGSTKFDPNTRRV-IKRFVPLVVRNGK 339 (340)
T ss_pred ----------------------CHH-HHHHHHHhccCcccceEeEEECCCCCCc-cCceEEEEEeCCc
Confidence 122 23333 45568899999999987 654 4577887776654
No 59
>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=100.00 E-value=2.9e-34 Score=303.92 Aligned_cols=373 Identities=20% Similarity=0.301 Sum_probs=297.9
Q ss_pred CCCceEEEEEEeecCC-----cchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhc--CceE
Q 003958 27 GRPSVVNIGALLSFST-----NVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEG--QTVA 99 (784)
Q Consensus 27 ~~~~~i~IG~i~~~~~-----~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~--~v~a 99 (784)
....+.++++++|+.. ..|+.+.+|+++|++++|+.+.||||+.|.++..|++|++..+.++..+++.. ....
T Consensus 37 ~~~~~~~~~~~~~~~~~~~~~~~g~~~~Pav~~Al~~vn~~~~ilp~y~L~~~~~ds~C~~~~g~k~~fdll~~~p~k~m 116 (865)
T KOG1055|consen 37 PSRCPRRIVGIGPLGPGSGGWPGGQACLPAVELALEDVNSRSDILPGYRLKLIHHDSECDPGQGTKALYDLLYNGPNKLM 116 (865)
T ss_pred CCCCCceeeeeecCccccCCCcCcccccHHHHHHHHHhhccccccCCcEEEEEeccccCCccccHHHHHHHHHcCCchhe
Confidence 3445788888888862 33678999999999999999999999999999999999999999999999877 4556
Q ss_pred EEccCchhhHHHHHHhhhcCCccEEecccCCCCCCc-CCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcCCCcc
Q 003958 100 IIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSS-LQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDDDHGR 178 (784)
Q Consensus 100 iiGp~~s~~~~~va~~~~~~~ip~Is~~a~~~~l~~-~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~~~g~ 178 (784)
++|+ |++.+..++..+..|+..+++|++++|.|++ ++||+|||+.||+..+...+++++++|+|++|+.++++.+-..
T Consensus 117 ll~G-Cs~v~~~iaea~~~w~l~~lsy~~ssp~ls~r~rfp~~frt~PS~~~~np~rl~l~~~~~w~rvgt~~q~e~~f~ 195 (865)
T KOG1055|consen 117 LLGG-CSSVTTLIAEAAKMWNLIVLSYGASSPALSNRKRFPTFFRTHPSANAHNPTRIKLLKKFGWKRVATLQQTEEVFS 195 (865)
T ss_pred eccC-CCCcchHHHhhccccceeeecccCCCccccchhhcchhhhcCCccccCCcceeeechhcCcceeeeeeeehhhhc
Confidence 6776 9999999999999999999999999999999 6899999999999999999999999999999999999888777
Q ss_pred hhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHcCCCCCCeEEEecCc
Q 003958 179 NGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIATSW 258 (784)
Q Consensus 179 ~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~ 258 (784)
...+.+...+.+.+++++..+.+. .|....+++++...+|+|+-......++.+++++++.+|.+..|+|+..+|
T Consensus 196 ~~~~dl~~~~~~~~ieiv~~qsf~-----~dp~~~vk~l~~~D~RiI~g~f~~~~Arkv~C~~Y~~~myg~ky~w~~~g~ 270 (865)
T KOG1055|consen 196 STLNDLEARLKEAGIEIVFRQSFS-----SDPADSVKNLKRQDARIIVGLFYETEARKVFCEAYKERLYGRKYVWFLIGW 270 (865)
T ss_pred chHHHHHHhhhccccEEEEeeccc-----cCHHHHHhhccccchhheeccchHhhhhHHHHhhchhhcccceeEEEEEEe
Confidence 888999999999999999888775 245677899999999999999999999999999999999999999999886
Q ss_pred ccccc-----ccCCCCCCCccccceeeEEEeeecCC--------chhHHHHHHHHHhhccC-CCCCCCCCCChhHHHHhh
Q 003958 259 LSTAL-----DTNSPFPSDVMDDIQGVLTLRTYTPD--------SVLKRKFISRWRNLTDA-KTPNGYIGLNAYGFYAYD 324 (784)
Q Consensus 259 ~~~~~-----~~~~~~~~~~~~~~~g~~~~~~~~~~--------~~~~~~f~~~~~~~~~~-~~~~~~~~~~~~~~~~YD 324 (784)
....+ +...+.-.+...+.+|.+++....-+ .-...+|+..+....+. |. .......+.++||
T Consensus 271 y~d~w~ev~~~~~~ctveem~~A~eg~~s~e~~pl~~~~~~tisg~T~~~~l~~~~~~r~~~~~---~~~~~~~~~~ayd 347 (865)
T KOG1055|consen 271 YADNWWEITHPSENCTVEEMTEAAEGHITTEFVMLSPANITTISGMTAQEFLEELTKYRKRHPE---ETGGFQEAPLAYD 347 (865)
T ss_pred eccchhhccCchhhhhHHHHHHHHhhheeeeeeccccccceeeccchhHHHHHHHHhhhccccc---cccCcccCchHHH
Confidence 54332 22122234556788888887653321 11235555555444331 11 1123456789999
Q ss_pred HHHHHHHHHHHHhhcCCccccccCCccccccCCcccccccccCCchHHHHHHHhccccceeeeEEEecCCCCcCCcEEEE
Q 003958 325 TVWLLARAINSFFKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANMTGTAGPARFNSHGDLINPAYEII 404 (784)
Q Consensus 325 Av~~~a~Al~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~l~~~l~~~~f~g~tG~v~Fd~~g~~~~~~~~I~ 404 (784)
|+|++|+|+++++........ .+..-....-.-..++.++|.+++|.|++|.|.|.. |+| .....|.
T Consensus 348 ~Iwa~ala~n~t~e~l~~~~~-----------~l~~f~y~~k~i~d~i~eamn~tsF~GvsG~V~F~~-geR-~a~t~ie 414 (865)
T KOG1055|consen 348 AIWALALALNKTMEGLGRSHV-----------RLEDFNYNNKTIADQIYEAMNSTSFEGVSGHVVFSN-GER-MALTLIE 414 (865)
T ss_pred HHHHHHHHHHHHHhcCCccce-----------eccccchhhhHHHHHHHHHhhcccccccccceEecc-hhh-HHHHHHH
Confidence 999999999999765431100 000000111112567999999999999999999988 987 5666889
Q ss_pred EeeccceEEEEEecCCC
Q 003958 405 NVIGTGYRRIGYWSNYS 421 (784)
Q Consensus 405 ~~~~~~~~~VG~w~~~~ 421 (784)
|+++++++++|.|+...
T Consensus 415 Q~qdg~y~k~g~Yds~~ 431 (865)
T KOG1055|consen 415 QFQDGKYKKIGYYDSTK 431 (865)
T ss_pred HHhCCceEeeccccccc
Confidence 99999999999998764
No 60
>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=100.00 E-value=1.6e-32 Score=292.02 Aligned_cols=318 Identities=16% Similarity=0.139 Sum_probs=267.3
Q ss_pred EEEEEeecCC----cchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhc-CceEEEccCchh
Q 003958 33 NIGALLSFST----NVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEG-QTVAIIGPQDAV 107 (784)
Q Consensus 33 ~IG~i~~~~~----~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~-~v~aiiGp~~s~ 107 (784)
+||++.|++. ..|.....|+++|+++|| +|+ .|++|+++++|++++|.++.+.+.+|+++ +|.+|+|+.+|.
T Consensus 1 ~IG~l~plsG~~~a~~g~~~~~g~~la~~~iN--ggi-~G~~v~l~~~D~~~~p~~a~~~~~~l~~~~~V~aviG~~~s~ 77 (334)
T cd06327 1 KIGVLTDMSGVYADAEGKGSVEAAELAVEDFG--GGV-LGRPIELVVADHQNKADVAAAKAREWIDRDGVDMIVGGPNSA 77 (334)
T ss_pred CcccccCCCCcCccccCHHHHHHHHHHHHHhc--CCc-cCeEEEEEEecCCCCchHHHHHHHHHHhhcCceEEECCccHH
Confidence 5899999983 347788999999999999 777 59999999999999999999999999987 999999999999
Q ss_pred hHHHHHHhhhcCCccEEecccCCCCCCcC-CCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcCCCcchhHHHHHH
Q 003958 108 TSHVVSHVANELQVPLLSFSATDPTLSSL-QFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGD 186 (784)
Q Consensus 108 ~~~~va~~~~~~~ip~Is~~a~~~~l~~~-~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~ 186 (784)
.+.+++++++..++|+|+++++++.+++. .+||+||+.|++..++.++++++...+++++++++.|+.||+...+.+++
T Consensus 78 ~~~a~~~~~~~~~vp~i~~~s~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~v~~i~~~~~~g~~~~~~~~~ 157 (334)
T cd06327 78 VALAVQEVAREKKKIYIVTGAGSDDLTGKDCSPYTFHWAYDTYMLANGTAPALVKAGGKKWFFLTADYAFGHSLERDARK 157 (334)
T ss_pred HHHHHHHHHHHhCceEEecCCCccccccCCCCCceEEccCChHHHHHHHHHHHHHhcCCeEEEEecchHHhHHHHHHHHH
Confidence 99999999999999999998888888774 57999999999999999999998877899999999999999999999999
Q ss_pred HHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHcCCCCCCeEEEecCccccccccC
Q 003958 187 TLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIATSWLSTALDTN 266 (784)
Q Consensus 187 ~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~~ 266 (784)
.+++.|++++....++ ....|+..+++++++.++|+|++.+...++..+++++++.|+.. +..++....+.....
T Consensus 158 ~~~~~G~~vv~~~~~~--~~~~d~~~~v~~l~~~~~d~v~~~~~~~~~~~~~~~~~~~g~~~-~~~~~~~~~~~~~~~-- 232 (334)
T cd06327 158 VVKANGGKVVGSVRHP--LGTSDFSSYLLQAQASGADVLVLANAGADTVNAIKQAAEFGLTK-GQKLAGLLLFLTDVH-- 232 (334)
T ss_pred HHHhcCCEEcCcccCC--CCCccHHHHHHHHHhCCCCEEEEeccchhHHHHHHHHHHhCCcc-CCcEEEecccHHHHH--
Confidence 9999999999888787 45779999999999999999999999999999999999999863 222333222221110
Q ss_pred CCCCCCccccceeeEEEeeecC--CchhHHHHHHHHHhhccCCCCCCCCCCChhHHHHhhHHHHHHHHHHHHhhcCCccc
Q 003958 267 SPFPSDVMDDIQGVLTLRTYTP--DSVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTVWLLARAINSFFKQGGNLS 344 (784)
Q Consensus 267 ~~~~~~~~~~~~g~~~~~~~~~--~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~~~a~Al~~~~~~~~~~~ 344 (784)
....+..+|++...++.+ +.+..++|.++|+++++ ..++.++..+||+++++++|++++...
T Consensus 233 ----~~~~~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~g-------~~p~~~~~~~Y~~~~~~~~A~~~ag~~----- 296 (334)
T cd06327 233 ----SLGLDAAQGLYLTTAWYWDLPNDETRAFVKRFQAKYG-------KMPSMVQAGAYSAVLHYLKAVEAAGTD----- 296 (334)
T ss_pred ----hhchhhhcCeEEeeeccccCCCHHHHHHHHHHHHHHC-------cCCCcHHHHHHHHHHHHHHHHHHHCCC-----
Confidence 112245678777766543 36788999999999986 236778899999999999999996211
Q ss_pred cccCCccccccCCcccccccccCCchHHHHHHHhcc-ccceeeeEEEec-CCCCc
Q 003958 345 FSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQAN-MTGTAGPARFNS-HGDLI 397 (784)
Q Consensus 345 ~~~~~~~~~~~g~~~~~~~~~~~~~~~l~~~l~~~~-f~g~tG~v~Fd~-~g~~~ 397 (784)
++..+.++|+++. +++..|.++|++ +|+..
T Consensus 297 -----------------------~~~~v~~al~~~~~~~~~~g~~~~~~~~~~~~ 328 (334)
T cd06327 297 -----------------------DADKVVAKMKETPIYDLFAGNGYIRACDHQMV 328 (334)
T ss_pred -----------------------ChHHHHHhccccceeccCCCCceeeccccchh
Confidence 4677999999986 688899999987 66643
No 61
>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=100.00 E-value=3.2e-32 Score=291.49 Aligned_cols=326 Identities=19% Similarity=0.167 Sum_probs=266.4
Q ss_pred EEEEEeecCC---cchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhc-CceEEEccCchhh
Q 003958 33 NIGALLSFST---NVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEG-QTVAIIGPQDAVT 108 (784)
Q Consensus 33 ~IG~i~~~~~---~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~-~v~aiiGp~~s~~ 108 (784)
+||++.|+++ ..|.....++++|+++||+++|+ +|++|++++.|+++++..+++.+++++.+ +|.+|+||.++..
T Consensus 1 ~iG~l~p~sG~~a~~g~~~~~g~~~a~~~iN~~ggi-~G~~v~~~~~D~~~~~~~a~~~a~~li~~~~v~aiig~~~s~~ 79 (346)
T cd06330 1 KIGVITFLSGRAAIFGEPARNGAELAVEEINAAGGI-GGRKIELVVRDEAGKPDEAIREARELVENEGVDMLIGLISSGV 79 (346)
T ss_pred CeeEEeecCCchhhhcHHHHHHHHHHHHHHhhcCCc-CCeEEEEEEecCCCCHHHHHHHHHHHHhccCCcEEEcccchHH
Confidence 5899999983 45778899999999999999988 58999999999999999999999999997 9999999999999
Q ss_pred HHHHHHhhhcCCccEEecccCCCCCCc-CCCCceEeecCChHHHHHHHHHHHHHcC--CcEEEEEEEcCCCcchhHHHHH
Q 003958 109 SHVVSHVANELQVPLLSFSATDPTLSS-LQFPYFVRTTQSDQYQMAAIAEIVDHYG--WREVIAIYVDDDHGRNGIAALG 185 (784)
Q Consensus 109 ~~~va~~~~~~~ip~Is~~a~~~~l~~-~~~p~~~r~~ps~~~~~~ai~~~l~~~~--w~~v~ii~~d~~~g~~~~~~l~ 185 (784)
+.+++++++..++|+|++.++++.+.+ ..++++||+.|++..+..++++++++++ |+++++|+.|+++|....+.++
T Consensus 80 ~~~~~~~~~~~~ip~i~~~s~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~v~~l~~~~~~g~~~~~~~~ 159 (346)
T cd06330 80 ALAVAPVAEELKVFFIATDPGTPRLTEEPDNPYVFRTRNSTIMDAVAGALYAAKLDKKAKTWATINPDYAYGQDAWADFK 159 (346)
T ss_pred HHHHHHHHHHcCCeEEEcCCCCcccccCCCCCceEEecCChHHHHHHHHHHHHHhCcCccEEEEECCchHHHHHHHHHHH
Confidence 999999999999999999888887776 5789999999999999999999998874 9999999999999999999999
Q ss_pred HHHhccC--cEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHcCCCCCCeEEEecCcccccc
Q 003958 186 DTLAAKR--CRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIATSWLSTAL 263 (784)
Q Consensus 186 ~~l~~~g--i~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~ 263 (784)
+.+++.| +.++....++ ....|+..++.+|++.++++|++.+...+...+++++++.|+.. +..|+.+.+.....
T Consensus 160 ~~~~~~g~~~~~v~~~~~~--~~~~d~~~~v~~i~~~~~d~ii~~~~~~~~~~~~~~~~~~g~~~-~~~~~~~~~~~~~~ 236 (346)
T cd06330 160 AALKRLRPDVEVVSEQWPK--LGAPDYGSEITALLAAKPDAIFSSLWGGDLVTFVRQANARGLFD-GTTVVLTLTGAPEL 236 (346)
T ss_pred HHHHHhCCCCeecccccCC--CCCcccHHHHHHHHhcCCCEEEEecccccHHHHHHHHHhcCccc-CceEEeeccchhhh
Confidence 9999985 4454433333 35678999999999999999999988999999999999999864 55677665433221
Q ss_pred ccCCCCCCCccccceeeEEEeee--c--CCchhHHHHHHHHHhhccCCCCCCCCCCChhHHHHhhHHHHHHHHHHHHhhc
Q 003958 264 DTNSPFPSDVMDDIQGVLTLRTY--T--PDSVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTVWLLARAINSFFKQ 339 (784)
Q Consensus 264 ~~~~~~~~~~~~~~~g~~~~~~~--~--~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~~~a~Al~~~~~~ 339 (784)
. ....+..+|++..... . +..+..++|.++|+++++ ..++.++..+||++.++++|++++...
T Consensus 237 ~------~~~~~~~~g~~~~~~~~~~~~~~~~~~~~f~~~~~~~~g-------~~p~~~~~~~y~a~~~l~~a~~~a~~~ 303 (346)
T cd06330 237 A------PLGDEMPEGVIIGGRGPYFIPPDTPENKAFVDAYQEKYG-------DYPTYGAYGAYQAVMALAAAVEKAGAT 303 (346)
T ss_pred h------hhhcccCCceEEeccccCCCCCCChHHHHHHHHHHHHHC-------CCCChHHHHHHHHHHHHHHHHHHhcCC
Confidence 1 1122445665544321 1 146789999999999886 345667889999999999999986332
Q ss_pred CCccccccCCccccccCCcccccccccCCchHHHHHHHhccccceeeeEEEecCCCCcCC
Q 003958 340 GGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANMTGTAGPARFNSHGDLINP 399 (784)
Q Consensus 340 ~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~l~~~l~~~~f~g~tG~v~Fd~~g~~~~~ 399 (784)
.. ..+ ...+.++|++++|.|+.|++.|+++.++...
T Consensus 304 ~~-----------------------~~~-~~~v~~al~~~~~~~~~G~~~f~~~~~~~~~ 339 (346)
T cd06330 304 DG-----------------------GAP-PEQIAAALEGLSFETPGGPITMRAADHQATQ 339 (346)
T ss_pred CC-----------------------CCc-HHHHHHHHcCCCccCCCCceeeecCCCcccc
Confidence 11 011 2579999999999999999999984433333
No 62
>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=100.00 E-value=7.5e-32 Score=286.57 Aligned_cols=325 Identities=17% Similarity=0.205 Sum_probs=266.0
Q ss_pred EEEEEeecC---CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhc-CceEEEccCchhh
Q 003958 33 NIGALLSFS---TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEG-QTVAIIGPQDAVT 108 (784)
Q Consensus 33 ~IG~i~~~~---~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~-~v~aiiGp~~s~~ 108 (784)
+||+++|++ +..|.....|+++|+++|| +++ .|++|+++++|+++++..+++.+.+|+.+ +|.+|+||.+|..
T Consensus 1 ~IG~~~plsG~~a~~g~~~~~g~~lAv~~in--ggi-~G~~i~l~~~D~~~~p~~a~~~~~~lv~~~~v~~viG~~~s~~ 77 (333)
T cd06359 1 KIGFITTLSGPAAALGQDMRDGFQLALKQLG--GKL-GGLPVEVVVEDDGLKPDVAKQAAERLIKRDKVDFVTGVVFSNV 77 (333)
T ss_pred CeEEEEecccchhhhhHHHHHHHHHHHHHhC--Ccc-CCEEEEEEecCCCCChHHHHHHHHHHHhhcCCcEEEccCCcHH
Confidence 589999998 4457788999999999998 566 59999999999999999999999999977 9999999999999
Q ss_pred HHHHHHhhhcCCccEEecccCCCCCCc-CCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcCCCcchhHHHHHHH
Q 003958 109 SHVVSHVANELQVPLLSFSATDPTLSS-LQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDT 187 (784)
Q Consensus 109 ~~~va~~~~~~~ip~Is~~a~~~~l~~-~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~~ 187 (784)
+.++++++...++|+|+++++.+.+.+ ..+||+||+.|++..++.+++++++..+|+++++++.|++||+...+.+++.
T Consensus 78 ~~a~~~~~~~~~ip~i~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~g~~~vail~~~~~~g~~~~~~~~~~ 157 (333)
T cd06359 78 LLAVVPPVLESGTFYISTNAGPSQLAGKQCSPYFFSTSWQNDQVHEAMGKYAQDKGYKRVFLIAPNYQAGKDALAGFKRT 157 (333)
T ss_pred HHHHHHHHHHcCCeEEecCCCccccccccCCCcEEEeeCChHhhHHHHHHHHHHhCCCeEEEEecCchhhHHHHHHHHHH
Confidence 999999999999999998776666665 3589999999999999999999999999999999999999999999988887
Q ss_pred HhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHcCCCCCCeEEEecCccccccccCC
Q 003958 188 LAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIATSWLSTALDTNS 267 (784)
Q Consensus 188 l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~~~ 267 (784)
++ .+++....++ .+.+|+..++.++++.++|+|++......+..+++++++.|+.. +..++++...... +..
T Consensus 158 ~~---~~v~~~~~~~--~~~~d~~~~i~~l~~~~pd~v~~~~~~~~~~~~~~~~~~~G~~~-~~~~~~~~~~~~~-~~~- 229 (333)
T cd06359 158 FK---GEVVGEVYTK--LGQLDFSAELAQIRAAKPDAVFVFLPGGMGVNFVKQYRQAGLKK-DIPLYSPGFSDEE-DTL- 229 (333)
T ss_pred hC---ceeeeeecCC--CCCcchHHHHHHHHhCCCCEEEEEccCccHHHHHHHHHHcCccc-CCeeeccCcccCH-HHH-
Confidence 74 3455555554 45679999999999999999999888888999999999999853 2335554433221 110
Q ss_pred CCCCCccccceeeEEEeeecC--CchhHHHHHHHHHhhccCCCCCCCCCCChhHHHHhhHHHHHHHHHHHHhhcCCcccc
Q 003958 268 PFPSDVMDDIQGVLTLRTYTP--DSVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTVWLLARAINSFFKQGGNLSF 345 (784)
Q Consensus 268 ~~~~~~~~~~~g~~~~~~~~~--~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~~~a~Al~~~~~~~~~~~~ 345 (784)
....+..+|++....+.+ +++..++|.++|+++++ ..++.++..+||+++++++|++++...
T Consensus 230 ---~~~g~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~~-------~~~~~~~~~~yda~~~~~~A~~~ag~~------ 293 (333)
T cd06359 230 ---PAVGDAALGLYNTAQWAPDLDNPANKKFVADFEKKYG-------RLPTLYAAQAYDAAQLLDSAVRKVGGN------ 293 (333)
T ss_pred ---HhcchhhcCeeeccccCCCCCCHHHHHHHHHHHHHhC-------CCCcHHHHHHHHHHHHHHHHHHHhcCC------
Confidence 122345678777766655 46889999999999886 346788999999999999999986210
Q ss_pred ccCCccccccCCcccccccccCCchHHHHHHHhccccceeeeEEEecCCCCcCCcEEEEE
Q 003958 346 SKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANMTGTAGPARFNSHGDLINPAYEIIN 405 (784)
Q Consensus 346 ~~~~~~~~~~g~~~~~~~~~~~~~~~l~~~l~~~~f~g~tG~v~Fd~~g~~~~~~~~I~~ 405 (784)
..++..+.++|++..|+|++|++.|+++|+. ...+.+++
T Consensus 294 --------------------~~~~~~v~~al~~~~~~~~~G~~~~~~~~~~-~~~~~~~~ 332 (333)
T cd06359 294 --------------------LSDKDALRAALRAADFKSVRGAFRFGTNHFP-IQDFYLRE 332 (333)
T ss_pred --------------------CCCHHHHHHHHhcCccccCccceEECCCCCc-ceeEEEEe
Confidence 0147889999999999999999999999874 44445543
No 63
>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=100.00 E-value=2.6e-32 Score=291.55 Aligned_cols=322 Identities=17% Similarity=0.192 Sum_probs=266.4
Q ss_pred EEEEEeecC---CcchhhHHHHHHHHHHHHhcCCCCC-CC--CEEEEEEecCCCCHHHHHHHHHHHHhc-CceEEEccCc
Q 003958 33 NIGALLSFS---TNVGKVAKLAIKAAVDDVNSDPTTL-GG--TKLKLQMQDCNHSGFLALAEALHLMEG-QTVAIIGPQD 105 (784)
Q Consensus 33 ~IG~i~~~~---~~~g~~~~~a~~~Ave~IN~~~~il-~g--~~l~~~~~D~~~~~~~a~~~~~~li~~-~v~aiiGp~~ 105 (784)
+||++.|++ +..|.....++++|++++|+++|++ +| ++|+++++|++++|..+.+.+.+|+++ +|.+|+|+.+
T Consensus 1 ~IG~l~plsG~~a~~g~~~~~g~~lA~~~iN~~GGi~~~G~~~~iel~~~D~~~~p~~a~~~~~~li~~~~v~~iiG~~~ 80 (347)
T cd06336 1 KIGFSGPLSGPAAAWGLPGLRGVQLAAEEINAAGGIKVGGKKYKVEIVSYDDKYDPAEAAANARRLVQQDGVKFILGPIG 80 (347)
T ss_pred CcceeccCcCcccccChhhHHHHHHHHHHHHhcCCcccCCceeeEEEEEecCCCCHHHHHHHHHHHHhhcCceEEEeCCC
Confidence 589999998 4567889999999999999999986 45 489999999999999999999999987 9999999999
Q ss_pred hhhHHHHHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcCCCcchhHHHHH
Q 003958 106 AVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDDDHGRNGIAALG 185 (784)
Q Consensus 106 s~~~~~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~ 185 (784)
+..+.. +++++..++|+|++.++++.++...++++||+.|++..++.++++++++.+|++|++|+.|++||+...+.++
T Consensus 81 s~~~~~-~~~~~~~~ip~i~~~~~~~~~~~~~~~~~fr~~~~~~~~~~~~~~~~~~~~~~~v~il~~d~~~g~~~~~~~~ 159 (347)
T cd06336 81 GGITAA-QQITERNKVLLLTAYSSDLSIDTAGNPLTFRVPPIYNVYGVPFLAYAKKPGGKKVALLGPNDAYGQPWVAAYK 159 (347)
T ss_pred Cchhhh-hhhhhhcCceEEeccCCcccccccCCceEEEecCCchhHHHHHHHHHhhcCCceEEEEccCCchhHHHHHHHH
Confidence 998888 9999999999999998888877556799999999999999999999988999999999999999999999999
Q ss_pred HHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCC-cHHHHHHHHHHcCCCCCCeEEEecCccccccc
Q 003958 186 DTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYN-RGPVVFHVAQYLGMLGTGYVWIATSWLSTALD 264 (784)
Q Consensus 186 ~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~-~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~ 264 (784)
+.+++.|++++....++ .+..|++.++++++++++++|++.+... ++..+++++++.|+..+ ..++..........
T Consensus 160 ~~l~~~G~~vv~~~~~~--~~~~D~s~~i~~i~~~~~d~v~~~~~~~~~~~~~~~~~~~~g~~~~-~~~~~~~~~~~~~~ 236 (347)
T cd06336 160 AAWEAAGGKVVSEEPYD--PGTTDFSPIVTKLLAEKPDVIFLGGPSPAPAALVIKQARELGFKGG-FLSCTGDKYDELLV 236 (347)
T ss_pred HHHHHcCCEEeeecccC--CCCcchHHHHHHHHhcCCCEEEEcCCCchHHHHHHHHHHHcCCCcc-EEeccCCCchHHHH
Confidence 99999999999888887 4678999999999999999999998888 99999999999998754 22221111111010
Q ss_pred cCCCCCCCccccceeeEEEeeecC----CchhHHHHHHHHHhhccCCCCCCCCCCChhHHHHhhHHHHHHHHHHHHhhcC
Q 003958 265 TNSPFPSDVMDDIQGVLTLRTYTP----DSVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTVWLLARAINSFFKQG 340 (784)
Q Consensus 265 ~~~~~~~~~~~~~~g~~~~~~~~~----~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~~~a~Al~~~~~~~ 340 (784)
....+..+|++...+..+ ..+..++|.++|+++++. .++.++..+||++.++++|++++...
T Consensus 237 ------~~~~~~~~g~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~-------~p~~~~~~~y~~~~~~~~Al~~ag~~- 302 (347)
T cd06336 237 ------ATGADFMEGVYFQFPDVDDPALAFPRAKAFVEEYKKRYGE-------PPNSEAAVSYDAVYILKAAMEAAGSV- 302 (347)
T ss_pred ------HhcHHhhCceEEEeecccccccCCHHHHHHHHHHHHHHCC-------CCcHHHHHHHHHHHHHHHHHHhcCCC-
Confidence 112245678777766544 467789999999999862 36778899999999999999985211
Q ss_pred CccccccCCccccccCCcccccccccCCchHHHHHH-H-------hccccceeeeEEEecCCCCcCC
Q 003958 341 GNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSI-L-------QANMTGTAGPARFNSHGDLINP 399 (784)
Q Consensus 341 ~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~l~~~l-~-------~~~f~g~tG~v~Fd~~g~~~~~ 399 (784)
++..+.+.+ + ...|.+..|.+.||++|+...+
T Consensus 303 ---------------------------~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~ 342 (347)
T cd06336 303 ---------------------------DDTAAVAALAAMLGVGKPAFGYARWWGKELFGVNGALVGP 342 (347)
T ss_pred ---------------------------CcHHHHHHHhhccCCCcCccccccccccccccCCCccccC
Confidence 133344443 3 2568899999999999997544
No 64
>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=100.00 E-value=3.1e-31 Score=284.14 Aligned_cols=340 Identities=16% Similarity=0.137 Sum_probs=272.9
Q ss_pred EEEEEeecC---CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhc-CceEEEccCchhh
Q 003958 33 NIGALLSFS---TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEG-QTVAIIGPQDAVT 108 (784)
Q Consensus 33 ~IG~i~~~~---~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~-~v~aiiGp~~s~~ 108 (784)
+||++.|+| +..|.....|+++|+++||+++|++ |++|+++++|++++|..++..+.+|+++ +|.+|+|+.+|..
T Consensus 1 kIG~~~plSG~~a~~g~~~~~g~~la~~~iN~~GGi~-G~~ielv~~D~~~~p~~a~~~a~~li~~~~V~aiiG~~~s~~ 79 (360)
T cd06357 1 RVGVLFSRTGVTAAIERSQRNGALLAIEEINAAGGVL-GRELEPVEYDPGGDPDAYRALAERLLREDGVRVIFGCYTSSS 79 (360)
T ss_pred CeEEEEcCCCCchhccHHHHHHHHHHHHHHhhcCCCC-CeEEEEEEECCCCCHHHHHHHHHHHHhhCCCcEEEeCccHHH
Confidence 599999998 5678899999999999999999985 8999999999999999999999999975 9999999999999
Q ss_pred HHHHHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcCCCcchhHHHHHHHH
Q 003958 109 SHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTL 188 (784)
Q Consensus 109 ~~~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~~l 188 (784)
+.+++++++..++|++++++... + ...|++|++.++...+..++++++.+.+-+++++|+.|++||+...+.+++.+
T Consensus 80 ~~a~~~~~~~~~~~~~~~~~~~~-~--~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~v~~i~~d~~~g~~~~~~~~~~~ 156 (360)
T cd06357 80 RKAVLPVVERHDALLWYPTLYEG-F--EYSPNVIYTGAAPNQNSVPLADYLLRHYGKRVFLVGSNYIYPYESNRIMRDLL 156 (360)
T ss_pred HHHHHHHHHhcCceEEeCCCccC-C--cccCCEEEeCCCcHHHHHHHHHHHHhcCCcEEEEECCCCcchHHHHHHHHHHH
Confidence 99999999999999998754321 1 22367888888877778889998876656899999999999999999999999
Q ss_pred hccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHcCCCCCCeEEEecCccccccccCCC
Q 003958 189 AAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIATSWLSTALDTNSP 268 (784)
Q Consensus 189 ~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~~~~ 268 (784)
++.|++++....++......|+..++.++++.++|+|++.+....+..++++++++|+.... ..+.+...... ...
T Consensus 157 ~~~G~~vv~~~~~~~~~~~~d~s~~v~~l~~~~pd~V~~~~~~~~~~~~~~~~~~~G~~~~~-~~~~~~~~~~~-~~~-- 232 (360)
T cd06357 157 EQRGGEVLGERYLPLGASDEDFARIVEEIREAQPDFIFSTLVGQSSYAFYRAYAAAGFDPAR-MPIASLTTSEA-EVA-- 232 (360)
T ss_pred HHcCCEEEEEEEecCCCchhhHHHHHHHHHHcCCCEEEEeCCCCChHHHHHHHHHcCCCccC-ceeEEeeccHH-HHh--
Confidence 99999998766566434589999999999999999999999999999999999999987542 22333221111 110
Q ss_pred CCCCccccceeeEEEeeecC--CchhHHHHHHHHHhhccCCCCCCCCCCChhHHHHhhHHHHHHHHHHHHhhcCCccccc
Q 003958 269 FPSDVMDDIQGVLTLRTYTP--DSVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTVWLLARAINSFFKQGGNLSFS 346 (784)
Q Consensus 269 ~~~~~~~~~~g~~~~~~~~~--~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~~~a~Al~~~~~~~~~~~~~ 346 (784)
....+..+|+++...+.+ +.+..+.|.+.|+++|+. ...++.++..+||+++++++|++++..
T Consensus 233 --~~~g~~~~g~~~~~~~~~~~~~p~~~~f~~~~~~~~g~-----~~~~~~~~~~~yda~~~l~~Al~~ag~-------- 297 (360)
T cd06357 233 --AMGAEAAAGHITAAPYFSSIDTPANRAFVARYRARFGE-----DAPVSACAEAAYFQVHLFARALQRAGS-------- 297 (360)
T ss_pred --hcchHhhCCcEEecccccccCChhHHHHHHHHHHHcCC-----CCCCCcHHHHHHHHHHHHHHHHHHcCC--------
Confidence 112355778877765433 567889999999999863 112466788999999999999998511
Q ss_pred cCCccccccCCcccccccccCCchHHHHHHHhccccceeeeEEEecCCCCcCCcEEEEEe-eccceEEEE
Q 003958 347 KDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANMTGTAGPARFNSHGDLINPAYEIINV-IGTGYRRIG 415 (784)
Q Consensus 347 ~~~~~~~~~g~~~~~~~~~~~~~~~l~~~l~~~~f~g~tG~v~Fd~~g~~~~~~~~I~~~-~~~~~~~VG 415 (784)
.++..+.++|++++|+|..|.+.|+++++.......+.++ +++++..+.
T Consensus 298 --------------------~~~~~v~~aL~~~~~~~~~g~~~f~~~~~~~~~~~~~~~~~~~G~~~~~~ 347 (360)
T cd06357 298 --------------------DDPEDVLAALLGFSFDAPQGPVRIDPDNNHTYLWPRIARVNADGQFDIVR 347 (360)
T ss_pred --------------------CCHHHHHHHhccCcccCCCcceEEeCCCCeeeeeeEEEEEcCCCCEEEEE
Confidence 1478899999999999999999999865434445566676 566666554
No 65
>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=100.00 E-value=2.9e-31 Score=281.58 Aligned_cols=316 Identities=13% Similarity=0.115 Sum_probs=259.1
Q ss_pred EEEEEeecC---CcchhhHHHHHHHHHHHHhc-CCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhc-CceEEEccCchh
Q 003958 33 NIGALLSFS---TNVGKVAKLAIKAAVDDVNS-DPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEG-QTVAIIGPQDAV 107 (784)
Q Consensus 33 ~IG~i~~~~---~~~g~~~~~a~~~Ave~IN~-~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~-~v~aiiGp~~s~ 107 (784)
+||++.|++ +..|.....|+++|+++||+ .+|+ +|++|++++.|++++|..++..+.+|+++ +|.+|+|+.+|.
T Consensus 1 ~IG~~~~lsG~~a~~G~~~~~g~~lav~~inn~~ggi-~G~~i~lv~~D~~~~p~~a~~~~~~li~~~~V~avvG~~~S~ 79 (333)
T cd06328 1 KIGLITDLSGPLAAYGKQTLTGFMLGLEYATGGTMQV-DGRPIEVIVKDDAGNPEVAVSLARELIGDDGVDILVGSTSSG 79 (333)
T ss_pred CeEEEEecCCchhhhhHHHHHHHHHHHHHHHhcCCCc-CCEEEEEEEecCCCChHHHHHHHHHHHHhcCCeEEEccCCcH
Confidence 599999998 45688899999999999955 5666 69999999999999999999999999998 999999999999
Q ss_pred hHHHHHHhhhcCCccEEecccCCCCCCcC-CCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcCCCcchhHHHHHH
Q 003958 108 TSHVVSHVANELQVPLLSFSATDPTLSSL-QFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGD 186 (784)
Q Consensus 108 ~~~~va~~~~~~~ip~Is~~a~~~~l~~~-~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~ 186 (784)
.+.+++++++..++|+|++.++++.++.. .++|+||+.+++..++.++++++... +++|++|+.|++||+...+.+++
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 99999999999999999988888888764 46999999998888888888887666 89999999999999999999999
Q ss_pred HHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCC-cHHHHHHHHHHcCCCCCCeEEEecCcccccccc
Q 003958 187 TLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYN-RGPVVFHVAQYLGMLGTGYVWIATSWLSTALDT 265 (784)
Q Consensus 187 ~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~-~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~ 265 (784)
.+++.|++++....++ .+..|+.+++.+|+++++|+|++..... .+..+++++...|+... .............
T Consensus 159 ~~~~~G~~vv~~~~~~--~~~~d~~~~v~~l~~~~pd~V~~~~~~~~~~~~~~~~~~~~g~~~~---~~~~~~~~~~~~~ 233 (333)
T cd06328 159 ALEKLGAAIVTEEYAP--TDTTDFTPYAQRLLDALKKVLFVIWAGAGGPWPKLQQMGVLGYGIE---ITLAGDILANLTM 233 (333)
T ss_pred HHHhCCCEEeeeeeCC--CCCcchHHHHHHHHhcCCCEEEEEecCchhHHHHHHHhhhhcCCCe---EEecccccCcccc
Confidence 9999999999888887 4678999999999999999998876555 56677778777766532 2222211111110
Q ss_pred CCCCCCCccccceeeEEEeeec-CCchhHHHHHHHHHhhccCCCCCCCCCCChhHHHHhhHHHHHHHHHHHHhhcCCccc
Q 003958 266 NSPFPSDVMDDIQGVLTLRTYT-PDSVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTVWLLARAINSFFKQGGNLS 344 (784)
Q Consensus 266 ~~~~~~~~~~~~~g~~~~~~~~-~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~~~a~Al~~~~~~~~~~~ 344 (784)
.......+|......+. +.++..+.|.++|+++++ ..++.++..+||++.++++|++++. +
T Consensus 234 -----~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~y~~~~g-------~~p~~~~~~~y~a~~~l~~Ai~~ag----~-- 295 (333)
T cd06328 234 -----YKAGPGMSGASYYYHYFLPKNPVNDWLVEEHKARFG-------SPPDLFTAGGMSAAIAVVEALEETG----D-- 295 (333)
T ss_pred -----ccccccccceeeeecCCCCCCHHHHHHHHHHHHHhC-------CCcchhhHHHHHHHHHHHHHHHHhC----C--
Confidence 11223355655554444 667888999999999986 3467789999999999999999862 0
Q ss_pred cccCCccccccCCcccccccccCCchHHHHHHHhccccceeeeEEEec-CCC
Q 003958 345 FSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANMTGTAGPARFNS-HGD 395 (784)
Q Consensus 345 ~~~~~~~~~~~g~~~~~~~~~~~~~~~l~~~l~~~~f~g~tG~v~Fd~-~g~ 395 (784)
.++..+.++|++.+|+++.|+++|++ +|+
T Consensus 296 ----------------------~~~~~v~~aL~~~~~~~~~g~~~f~~~~~~ 325 (333)
T cd06328 296 ----------------------TDTEALIAAMEGMSFETPKGTMTFRKEDHQ 325 (333)
T ss_pred ----------------------CCHHHHHHHHhCCeeecCCCceEECcccch
Confidence 14888999999999999999999995 444
No 66
>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=100.00 E-value=3.5e-31 Score=281.78 Aligned_cols=317 Identities=25% Similarity=0.398 Sum_probs=251.5
Q ss_pred EEEEEeecCCcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCC-CCHHHHHHHHHHHH-hcCceEEEccCchhhHH
Q 003958 33 NIGALLSFSTNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCN-HSGFLALAEALHLM-EGQTVAIIGPQDAVTSH 110 (784)
Q Consensus 33 ~IG~i~~~~~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~-~~~~~a~~~~~~li-~~~v~aiiGp~~s~~~~ 110 (784)
+||++++... .....|+++|++++|.+++++++..+.+.+.+.+ +++..++..+|+++ .++|.+|+||.++..+.
T Consensus 1 ~iG~i~~~~~---~~~~~a~~~Ai~~iN~~~~~~~~~~l~~~~~~~~~~d~~~~~~~~c~l~~~~~v~ai~G~~~s~~~~ 77 (328)
T cd06351 1 NIGAIFDRDA---RKEELAFRAAIDALNTENLNALPTKLSVEVVEVNTNDPFSLLRAVCDLLVSQGVAAIFGPTSSESAS 77 (328)
T ss_pred CeeeecCCCc---HHHHHHHHHHHHHhccCccccCCeeEEEEEEEeCCCChHHHHHHHHHHHhccCcEEEECCCCHHHHH
Confidence 4888888764 5678999999999999999887777777666555 79999999999999 77999999999999999
Q ss_pred HHHHhhhcCCccEEecccCCCCCCc-CCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcCCCcchhHHHHHHHHh
Q 003958 111 VVSHVANELQVPLLSFSATDPTLSS-LQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLA 189 (784)
Q Consensus 111 ~va~~~~~~~ip~Is~~a~~~~l~~-~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~~l~ 189 (784)
+++++++.++||+|+++++++.+++ ..+++++|+.|++..+++++++++++++|+++++||+++++.... +.+.+...
T Consensus 78 ~v~~~~~~~~iP~is~~~~~~~~~~~~~~~~~~~~~p~~~~~~~a~~~~l~~~~w~~v~iiy~~~~~~~~l-~~~~~~~~ 156 (328)
T cd06351 78 AVQSICDALEIPHISISGGSEGLSDKEESSTTLQLYPSLEDLADALLDLLEYYNWTKFAIIYDSDEGLSRL-QELLDESG 156 (328)
T ss_pred HHHHHhccCCCCeEEeecCcccccccccccceEEecCCHHHHHHHHHHHHHHcCCcEEEEEEeCchHHHHH-HHHHHhhc
Confidence 9999999999999999888887776 578999999999999999999999999999999999988854333 33333333
Q ss_pred ccCcEEEEeeccCCCCChhHHHHHHHHhhcCCc-eEEEEeccCCcHHHHHHHHHHcCCCCCCeEEEecCccccccccCCC
Q 003958 190 AKRCRISFKAPLSVEATEDEITDLLVKVALTES-RIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIATSWLSTALDTNSP 268 (784)
Q Consensus 190 ~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~-~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~~~~ 268 (784)
..+..+... .+.. ...+++.+++++++.++ ++|+.++..+.+..++++|.++||++++|+||+++......+.
T Consensus 157 ~~~~~v~~~-~~~~--~~~~~~~~l~~l~~~~~~~vil~~~~~~~~~~~l~~a~~~gm~~~~~~~i~~~~~~~~~d~--- 230 (328)
T cd06351 157 IKGIQVTVR-RLDL--DDDNYRQLLKELKRSESRRIILDCSSEEEAKEILEQAVELGMMGYGYHWILTNLDLSDIDL--- 230 (328)
T ss_pred ccCceEEEE-EecC--CchhHHHHHHHHhhcccceEEEECCcHHHHHHHHHHHHHhccccCCcEEEEecCCccccch---
Confidence 334455443 3442 33379999999999988 6655555558999999999999999999999999976654332
Q ss_pred CCCCccccceeeEEEeeecCCchhHHHHHHHHHhhccCCCCCCCCCCChhHHHHhhHHHHHHHHHHHHhhcCCccccccC
Q 003958 269 FPSDVMDDIQGVLTLRTYTPDSVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTVWLLARAINSFFKQGGNLSFSKD 348 (784)
Q Consensus 269 ~~~~~~~~~~g~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~~~a~Al~~~~~~~~~~~~~~~ 348 (784)
........|++++....+..+..++|..+|..... ......+...++.+||+++++
T Consensus 231 --~~~~~~~~~i~g~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~d~~~~~------------------- 286 (328)
T cd06351 231 --EPFQYGPANITGFRLVDPDSPDVSQFLQRWLEESP---GVNLRAPIYDAALLYDAVLLL------------------- 286 (328)
T ss_pred --hhhccCCcceEEEEEeCCCchHHHHHHHhhhhccC---CCCcCccchhhHhhhcEEEEE-------------------
Confidence 23445678999999999999999999999933221 112222333455555543111
Q ss_pred CccccccCCcccccccccCCchHHHHHHHhccccceeeeEEEecCCCCcCCcEEEEEee-ccceEEEEEecC
Q 003958 349 SRLSDIQGHLRLDSLRIFNGGNLLRDSILQANMTGTAGPARFNSHGDLINPAYEIINVI-GTGYRRIGYWSN 419 (784)
Q Consensus 349 ~~~~~~~g~~~~~~~~~~~~~~~l~~~l~~~~f~g~tG~v~Fd~~g~~~~~~~~I~~~~-~~~~~~VG~w~~ 419 (784)
+|.+.||++|.|.++.++|++++ +.++++||.|+.
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 88999999999999999999999 889999999984
No 67
>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=100.00 E-value=5e-31 Score=281.36 Aligned_cols=324 Identities=17% Similarity=0.255 Sum_probs=272.1
Q ss_pred EEEEEeecCC---cchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhc-CceEEEccCchhh
Q 003958 33 NIGALLSFST---NVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEG-QTVAIIGPQDAVT 108 (784)
Q Consensus 33 ~IG~i~~~~~---~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~-~v~aiiGp~~s~~ 108 (784)
+||++.|++. ..|.....++++|++++| +++ .|++|+++++|+++++..+.+.+.+|+.+ +|.+|||+.++..
T Consensus 1 ~IG~l~p~sG~~a~~g~~~~~g~~~a~~~~~--~~i-~G~~i~l~~~D~~~~~~~~~~~~~~lv~~~~v~~iig~~~s~~ 77 (336)
T cd06360 1 KVGLLLPYSGTYAALGEDITRGFELALQEAG--GKL-GGREVEFVVEDDEAKPDVAVEKARKLIEQDKVDVVVGPVHSGE 77 (336)
T ss_pred CeEEEEecccchHhhcHhHHHHHHHHHHHhC--CCc-CCEEEEEEEcCCCCChHHHHHHHHHHHHHhCCcEEEccCccHh
Confidence 5899999984 446788999999999986 344 69999999999999999999999999975 9999999999988
Q ss_pred HHHHHHhhhcCCccEEecccCCCCCCcC-CCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcCCCcchhHHHHHHH
Q 003958 109 SHVVSHVANELQVPLLSFSATDPTLSSL-QFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDT 187 (784)
Q Consensus 109 ~~~va~~~~~~~ip~Is~~a~~~~l~~~-~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~~ 187 (784)
+.++++.++..++|+|+++++++.+++. .+|++||+.|++..++..+++++.+.+|+++++++.++.||+...+.+++.
T Consensus 78 ~~~~~~~~~~~~ip~v~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~l~~~~~~~v~~l~~~~~~g~~~~~~~~~~ 157 (336)
T cd06360 78 ALAMVKVLREPGTPLINPNAGADDLTGRLCAPNFFRTSFSNAQWAAPMGKYAADDGYKKVVTVAWDYAFGYEVVEGFKEA 157 (336)
T ss_pred HHHHHHHHHhcCceEEecCCCCccccccCCCCcEEEEeCchHHHHHHHHHHHHHcCCCeEEEEeccchhhHHHHHHHHHH
Confidence 8888999999999999998888888763 589999999999999999999999999999999999999999999999999
Q ss_pred HhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHcCCCCCCeEEEecCccccccccCC
Q 003958 188 LAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIATSWLSTALDTNS 267 (784)
Q Consensus 188 l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~~~ 267 (784)
+++.|++++....++ ....|++.+++++++.++++|++.....++..+++++++.|+.+ +..|+++++.......
T Consensus 158 ~~~~G~~v~~~~~~~--~~~~d~~~~v~~~~~~~pd~v~~~~~~~~~~~~~~~~~~~g~~~-~~~~~~~~~~~~~~~~-- 232 (336)
T cd06360 158 FTEAGGKIVKELWVP--FGTSDFASYLAQIPDDVPDAVFVFFAGGDAIKFVKQYDAAGLKA-KIPLIGSGFLTDGTTL-- 232 (336)
T ss_pred HHHcCCEEEEEEecC--CCCcchHHHHHHHHhcCCCEEEEecccccHHHHHHHHHHcCCcc-CCeEEecccccCHHHH--
Confidence 999999998777676 45789999999999999999999988999999999999999853 2346665543322111
Q ss_pred CCCCCccccceeeEEEeeecC--CchhHHHHHHHHHhhccCCCCCCCCCCChhHHHHhhHHHHHHHHHHHHhhcCCcccc
Q 003958 268 PFPSDVMDDIQGVLTLRTYTP--DSVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTVWLLARAINSFFKQGGNLSF 345 (784)
Q Consensus 268 ~~~~~~~~~~~g~~~~~~~~~--~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~~~a~Al~~~~~~~~~~~~ 345 (784)
....+..+|++...++.+ +.+..+.|.+.|+++++ ..++.++..+||+++++++|++++...
T Consensus 233 ---~~~g~~~~g~~~~~~~~~~~~~~~~~~f~~~y~~~~~-------~~~~~~~~~~yda~~~~~~A~~~a~~~------ 296 (336)
T cd06360 233 ---GAAGEAAEGVITALHYADTLDNPANQAFVKAYRAAYP-------DTPSVYAVQGYDAGQALILALEAVGGD------ 296 (336)
T ss_pred ---HhhHhhhcCceeccccCCCCCCHHHHHHHHHHHHHhC-------CCccHHHHHHHHHHHHHHHHHHHhCCC------
Confidence 122355678777666544 46789999999999986 356788999999999999999996211
Q ss_pred ccCCccccccCCcccccccccCCchHHHHHHHhccccceeeeEEEecCCCCcCCc
Q 003958 346 SKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANMTGTAGPARFNSHGDLINPA 400 (784)
Q Consensus 346 ~~~~~~~~~~g~~~~~~~~~~~~~~~l~~~l~~~~f~g~tG~v~Fd~~g~~~~~~ 400 (784)
-.++..+.++|++.+|.|..|+++|+++|++..+.
T Consensus 297 --------------------~~~~~~v~~al~~~~~~~~~g~~~f~~~~~~~~~~ 331 (336)
T cd06360 297 --------------------LSDGQALIAAMAAAKIDSPRGPFTLDKAHNPIQDN 331 (336)
T ss_pred --------------------CCCHHHHHHHHhcCCccCCCcceEECCCCCcccce
Confidence 01367899999999999999999999999875543
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=100.00 E-value=1.7e-31 Score=286.04 Aligned_cols=332 Identities=23% Similarity=0.320 Sum_probs=274.3
Q ss_pred eEEEEEEeecC---CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHh-cCceEEEccCch
Q 003958 31 VVNIGALLSFS---TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLME-GQTVAIIGPQDA 106 (784)
Q Consensus 31 ~i~IG~i~~~~---~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~-~~v~aiiGp~~s 106 (784)
+|+||++.|++ +..|.....++++|++++|+++|+. |++|+++++|+.+++..+.+.+.++++ ++|.+|+|+.++
T Consensus 1 ~i~IG~~~~~sG~~a~~g~~~~~g~~~a~~~~N~~ggi~-G~~i~l~~~D~~~~~~~a~~~~~~l~~~~~v~~vvg~~~s 79 (343)
T PF13458_consen 1 PIKIGVLVPLSGPFAPYGQDFLRGAELAVDEINAAGGIN-GRKIELVVYDDGGDPAQAVQAARKLIDDDGVDAVVGPLSS 79 (343)
T ss_dssp SEEEEEEE-SSSTTHHHHHHHHHHHHHHHHHHHHTTEET-TEEEEEEEEE-TT-HHHHHHHHHHHHHTSTESEEEESSSH
T ss_pred CEEEEEEECCCChhhhhhHHHHHHHHHHHHHHHHhCCcC-CccceeeeccCCCChHHHHHHHHHhhhhcCcEEEEecCCc
Confidence 68999999998 3457788999999999999999985 999999999999999999999999998 699999999999
Q ss_pred hhHHHHHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHH-HHcCCcEEEEEEEcCCCcchhHHHHH
Q 003958 107 VTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIV-DHYGWREVIAIYVDDDHGRNGIAALG 185 (784)
Q Consensus 107 ~~~~~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l-~~~~w~~v~ii~~d~~~g~~~~~~l~ 185 (784)
..+.++++.+...++|+|++.+.++ ...++++||+.|++..++.++++++ ++++.+++++|+.++++|+...+.++
T Consensus 80 ~~~~~~~~~~~~~~ip~i~~~~~~~---~~~~~~~f~~~~~~~~~~~~~~~~~~~~~g~~~v~iv~~~~~~g~~~~~~~~ 156 (343)
T PF13458_consen 80 AQAEAVAPIAEEAGIPYISPSASSP---SPDSPNVFRLSPSDSQQAAALAEYLAKKLGAKKVAIVYPDDPYGRSLAEAFR 156 (343)
T ss_dssp HHHHHHHHHHHHHT-EEEESSGGGG---TTTHTTEEESS--HHHHHHHHHHHHHHTTTTSEEEEEEESSHHHHHHHHHHH
T ss_pred HHHHHHHHHHHhcCcEEEEeeccCC---CCCCCcEEEEeccccHHHHHHHHHHHHHcCCcEEEEEecCchhhhHHHHHHH
Confidence 9999999999999999999654442 2457999999999999999999986 55899999999999999999999999
Q ss_pred HHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHcCCCCCCeEEEecCcccccccc
Q 003958 186 DTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIATSWLSTALDT 265 (784)
Q Consensus 186 ~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~ 265 (784)
+.+++.|++++....++ .+..|+..+++++++.++++|++.+.+.++..+++++.+.|+..+.+....+..+......
T Consensus 157 ~~~~~~G~~vv~~~~~~--~~~~d~~~~~~~l~~~~~d~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ 234 (343)
T PF13458_consen 157 KALEAAGGKVVGEIRYP--PGDTDFSALVQQLKSAGPDVVVLAGDPADAAAFLRQLRQLGLKPPRIPLFGTSLDDASLQQ 234 (343)
T ss_dssp HHHHHTTCEEEEEEEE---TTSSHHHHHHHHHHHTTTSEEEEESTHHHHHHHHHHHHHTTGCSCTEEEEEGGGSSHHHHH
T ss_pred HHHhhcCceeccceecc--cccccchHHHHHHhhcCCCEEEEeccchhHHHHHHHHHhhccccccceeeccccCcHHHHH
Confidence 99999999988777787 4568999999999999999999999999999999999999987544444443332222111
Q ss_pred CCCCCCCccccceeeEEEeeecC--CchhHHHHHHHHHhhccCCCCCCCCCCChhHHHHhhHHHHHHHHHHHHhhcCCcc
Q 003958 266 NSPFPSDVMDDIQGVLTLRTYTP--DSVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTVWLLARAINSFFKQGGNL 343 (784)
Q Consensus 266 ~~~~~~~~~~~~~g~~~~~~~~~--~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~~~a~Al~~~~~~~~~~ 343 (784)
......+|++....+.+ +.+..++|.++|++.++. ...++.++..+||++.+++.|++++. +
T Consensus 235 ------~~~~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~~~-----~~~~~~~~~~~yda~~~~~~al~~~g----~- 298 (343)
T PF13458_consen 235 ------LGGDALEGVYIVSPWFPDPDSPAVKQFQERYRAAYGE-----EPPPSLYAAQGYDAARLLAQALERAG----S- 298 (343)
T ss_dssp ------HHGGGGTTEEEEESGGGTGGSHHHHHHHHHHHHHHSS-----TGGTCHHHHHHHHHHHHHHHHHHHHT----S-
T ss_pred ------hhhhhccCceeecccCCCCCCHHHHHHHHHHHHHcCC-----CCCCchhHHHHHHHHHHHHHHHHHhC----C-
Confidence 11245778888777655 467889999999999973 11368899999999999999999961 1
Q ss_pred ccccCCccccccCCcccccccccCCchHHHHHHHhccccceeeeEEEecCCCCcCCcEEEEEee
Q 003958 344 SFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANMTGTAGPARFNSHGDLINPAYEIINVI 407 (784)
Q Consensus 344 ~~~~~~~~~~~~g~~~~~~~~~~~~~~~l~~~l~~~~f~g~tG~v~Fd~~g~~~~~~~~I~~~~ 407 (784)
.++..+.++|++++|+|+.|++.|++.++.....+.|.+++
T Consensus 299 -----------------------~~~~~v~~al~~~~~~g~~g~~~~~~~~~~~~~~~~i~~v~ 339 (343)
T PF13458_consen 299 -----------------------LDREAVREALESLKYDGLFGPISFDPPDHQANKPVYIVQVK 339 (343)
T ss_dssp -----------------------HHHHHHHHHHHTSEEEETTEEEEEETTTSBEEEEEEEEEEE
T ss_pred -----------------------CCHHHHHHHHHhCCCcccccceEEeCCCCccccCeEEEEEe
Confidence 14889999999999999999999986555568888888888
No 69
>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=100.00 E-value=1e-30 Score=277.85 Aligned_cols=316 Identities=18% Similarity=0.175 Sum_probs=260.2
Q ss_pred EEEEEeecC---CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhc-CceEEEccCchhh
Q 003958 33 NIGALLSFS---TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEG-QTVAIIGPQDAVT 108 (784)
Q Consensus 33 ~IG~i~~~~---~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~-~v~aiiGp~~s~~ 108 (784)
+||++.|+| +..|.....|+++|+++||+.+|+. |++++++++|+++++..++..+.+|+++ +|.+|||+.+|..
T Consensus 1 kIG~~~plsG~~a~~g~~~~~g~~la~~~iN~~gGi~-G~~i~l~~~D~~~~p~~a~~~a~~Li~~~~v~aviG~~~s~~ 79 (333)
T cd06358 1 RIGLLVPLSGPAGIFGPSCEAAAELAVEEINAAGGIL-GREVELVIVDDGSPPAEAAAAAARLVDEGGVDAIIGWHTSAV 79 (333)
T ss_pred CeEEEecCcCchhhcchhHHHHHHHHHHHHHhcCCcC-CcEEEEEEECCCCChHHHHHHHHHHHHhCCCcEEEecCcHHH
Confidence 599999998 4468889999999999999999984 8999999999999999999999999987 8999999999999
Q ss_pred HHHHHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHH-HHcCCcEEEEEEEcCCCcchhHHHHHHH
Q 003958 109 SHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIV-DHYGWREVIAIYVDDDHGRNGIAALGDT 187 (784)
Q Consensus 109 ~~~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l-~~~~w~~v~ii~~d~~~g~~~~~~l~~~ 187 (784)
+.++.++++ .++|+|++.+.+.. ...|++||+.+++..++.++++++ +..+|++|++++.|+.||+...+.+++.
T Consensus 80 a~a~~~~~~-~~vp~i~~~~~~~~---~~~~~~f~~~~~~~~~~~~~~~~~~~~~g~~~v~i~~~~~~~g~~~~~~~~~~ 155 (333)
T cd06358 80 RNAVAPVVA-GRVPYVYTSLYEGG---ECNPGVFLTGETPEQQLAPAIPWLAEEKGARRWYLIGNDYVWPRGSLAAAKRY 155 (333)
T ss_pred HHHHHHHHh-cCceEEeCCCcCCC---CCCCCEEEcCCCcHHHHHHHHHHHHHhcCCCeEEEEeccchhhHHHHHHHHHH
Confidence 999999999 99999997543321 236899999999998888788776 5579999999999999999999999999
Q ss_pred HhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHcCCCCCCeEEEecC-ccccccccC
Q 003958 188 LAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIATS-WLSTALDTN 266 (784)
Q Consensus 188 l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~-~~~~~~~~~ 266 (784)
+++.|++|+....++ .+..|++.+++++++.++|+|++.....+...+++++++.|+..+ ++... .+......
T Consensus 156 ~~~~G~~v~~~~~~~--~~~~d~~~~v~~l~~~~pd~v~~~~~~~~~~~~~~~~~~~G~~~~---~~~~~~~~~~~~~~- 229 (333)
T cd06358 156 IAELGGEVVGEEYVP--LGTTDFTSVLERIAASGADAVLSTLVGQDAVAFNRQFAAAGLRDR---ILRLSPLMDENMLL- 229 (333)
T ss_pred HHHcCCEEeeeeeec--CChHHHHHHHHHHHHcCCCEEEEeCCCCchHHHHHHHHHcCCCcc---CceeecccCHHHHH-
Confidence 999999999887787 568899999999999999999998888888999999999998764 33222 12111100
Q ss_pred CCCCCCccccceeeEEEeeecC--CchhHHHHHHHHHhhccCCCCCCCCCCChhHHHHhhHHHHHHHHHHHHhhcCCccc
Q 003958 267 SPFPSDVMDDIQGVLTLRTYTP--DSVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTVWLLARAINSFFKQGGNLS 344 (784)
Q Consensus 267 ~~~~~~~~~~~~g~~~~~~~~~--~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~~~a~Al~~~~~~~~~~~ 344 (784)
.......+|++....+.+ ..+..++|.+.|+++|+. +...++.++..+||+++++++|+++.. +
T Consensus 230 ----~~~~~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~g~----~~~~~~~~~~~~yda~~~~~~A~~~ag----~-- 295 (333)
T cd06358 230 ----ASGAEAAEGLYSSSGYFASLQTPANAAFLARYRARFGD----DAPPLNSLSESCYEAVHALAAAAERAG----S-- 295 (333)
T ss_pred ----hcChHhhCCcEEeccchhhcCCHHHHHHHHHHHHHcCC----CCCCCChHHHHHHHHHHHHHHHHHHhC----C--
Confidence 111234567666554433 567899999999998863 112356788899999999999999741 0
Q ss_pred cccCCccccccCCcccccccccCCchHHHHHHHhccccceeeeEEEecCCC
Q 003958 345 FSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANMTGTAGPARFNSHGD 395 (784)
Q Consensus 345 ~~~~~~~~~~~g~~~~~~~~~~~~~~~l~~~l~~~~f~g~tG~v~Fd~~g~ 395 (784)
.++..|.++|++++|+|.+|.+.|++++.
T Consensus 296 ----------------------~~~~~v~~al~~~~~~~~~G~~~~~~~~~ 324 (333)
T cd06358 296 ----------------------LDPEALIAALEDVSYDGPRGTVTMRGRHA 324 (333)
T ss_pred ----------------------CCHHHHHHHhccCeeeCCCcceEEccccc
Confidence 14788999999999999999999998864
No 70
>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=100.00 E-value=1.8e-30 Score=275.64 Aligned_cols=317 Identities=11% Similarity=0.100 Sum_probs=258.5
Q ss_pred EEEEEeecC---CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhc-CceEEEccCchhh
Q 003958 33 NIGALLSFS---TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEG-QTVAIIGPQDAVT 108 (784)
Q Consensus 33 ~IG~i~~~~---~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~-~v~aiiGp~~s~~ 108 (784)
+||++.|+| +..|.....++++|+++||+.+|+. |++|+++.+|++++|..+...+.+|+.+ +|.+|+|+.+|..
T Consensus 1 ~IG~~~~lSG~~a~~G~~~~~g~~la~~~iNa~gGi~-Gr~v~lv~~D~~~~p~~a~~~~~~Li~~~~V~aiiG~~~s~~ 79 (334)
T cd06356 1 KVGSLEDRSGNFALYGTPKVHATQLAVDEINASGGIL-GREVELVDYDTQSDNERYQQYAQRLALQDKVDVVWGGISSAS 79 (334)
T ss_pred CeEEEecCCCchhhccHHHHHHHHHHHHHHHhcCCCC-CceEEEEEECCCCCHHHHHHHHHHHHHhCCCCEEEeCcchHH
Confidence 599999999 5668899999999999999999985 9999999999999999999999999975 8999999999999
Q ss_pred HHHHHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcCCCcchhHHHHHHHH
Q 003958 109 SHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTL 188 (784)
Q Consensus 109 ~~~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~~l 188 (784)
+.++.++++..++|+|....... +...|++||+.+++..++.++++++...+-+++++|+.|++||+...+.+++.+
T Consensus 80 ~~a~~~~~~~~~vp~i~~~~~~~---~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~~vail~~d~~~g~~~~~~~~~~~ 156 (334)
T cd06356 80 REAIRPIMDRTKQLYFYTTQYEG---GVCDRNTFCTGATPAQQFSTLVPYMMEKYGKKVYTIAADYNFGQISAEWVRKIV 156 (334)
T ss_pred HHHHHHHHHhcCceEEeCCCccC---CcccCCEEEeCCCcHHHHHHHHHHHHHccCCeEEEECCCchhhHHHHHHHHHHH
Confidence 99999999999999998633322 123489999999999999999999877655889999999999999999999999
Q ss_pred hccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHcCC-CCCCeEEEecCccccccccCC
Q 003958 189 AAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGM-LGTGYVWIATSWLSTALDTNS 267 (784)
Q Consensus 189 ~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~g~-~~~~~~wi~~~~~~~~~~~~~ 267 (784)
++.|++++....++ .+..|++.+++++++.++|+|++.....+...+++++++.|+ ..+ .+............
T Consensus 157 ~~~G~~vv~~~~~~--~~~~d~~~~v~~l~~~~pd~v~~~~~~~~~~~~~~~~~~~G~~~~~---~~~~~~~~~~~~~~- 230 (334)
T cd06356 157 EENGGEVVGEEFIP--LDVSDFGSTIQKIQAAKPDFVMSILVGANHLSFYRQWAAAGLGNIP---MASSTLGAQGYEHK- 230 (334)
T ss_pred HHcCCEEEeeeecC--CCchhHHHHHHHHHhcCCCEEEEeccCCcHHHHHHHHHHcCCccCc---eeeeecccchhHHh-
Confidence 99999999888887 467899999999999999999998888889999999999998 322 22221111110000
Q ss_pred CCCCCccccceeeEEEeeecC--CchhHHHHHHHHHhhccCCCCCCCCCCChhHHHHhhHHHHHHHHHHHHhhcCCcccc
Q 003958 268 PFPSDVMDDIQGVLTLRTYTP--DSVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTVWLLARAINSFFKQGGNLSF 345 (784)
Q Consensus 268 ~~~~~~~~~~~g~~~~~~~~~--~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~~~a~Al~~~~~~~~~~~~ 345 (784)
.......+|++....+.+ +.+..++|.+.|+++++. ...++.++..+||+++++++|++++.+
T Consensus 231 ---~~~~~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~~~-----~p~~~~~~~~~y~a~~~~~~A~~~ag~------- 295 (334)
T cd06356 231 ---RLKPPALKDMYATANYIEELDTPANKAFVERFRAKFPD-----APYINEEAENNYEAIYLYKEAVEKAGT------- 295 (334)
T ss_pred ---ccCchhcCCeEEecchhhhcCCHHHHHHHHHHHHHcCC-----CCCCCchhHHHHHHHHHHHHHHHHHCC-------
Confidence 011245677766655433 367789999999999862 111256789999999999999998621
Q ss_pred ccCCccccccCCcccccccccCCchHHHHHHHh-ccccceeeeEEEecCCC
Q 003958 346 SKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQ-ANMTGTAGPARFNSHGD 395 (784)
Q Consensus 346 ~~~~~~~~~~g~~~~~~~~~~~~~~~l~~~l~~-~~f~g~tG~v~Fd~~g~ 395 (784)
.++..|.++|++ ..|+|+.|+++|+++++
T Consensus 296 ---------------------~~~~~v~~aL~~~~~~~~~~g~~~~~~~~h 325 (334)
T cd06356 296 ---------------------TDRDAVIEALESGLVCDGPEGKVCIDGKTH 325 (334)
T ss_pred ---------------------CCHHHHHHHHHhCCceeCCCceEEEecCCC
Confidence 147889999997 56899999999997544
No 71
>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=100.00 E-value=8e-31 Score=278.94 Aligned_cols=333 Identities=14% Similarity=0.133 Sum_probs=263.6
Q ss_pred EEEEEeecC---CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhc-CceEEEccCchhh
Q 003958 33 NIGALLSFS---TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEG-QTVAIIGPQDAVT 108 (784)
Q Consensus 33 ~IG~i~~~~---~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~-~v~aiiGp~~s~~ 108 (784)
|||++.|++ +..|.....|+++|+++||+.+||+ |++|+++++|++++|..++..+.+|+.+ +|.+|+ +.+|..
T Consensus 1 kIG~~~plsG~~a~~G~~~~~g~~la~~~iNa~GGI~-Gr~ielv~~D~~~~p~~a~~~a~~Li~~~~V~~i~-~~~S~~ 78 (351)
T cd06334 1 KVGLLADRTGPTAFVGIPYAAGFADYFKYINEDGGIN-GVKLEWEECDTGYEVPRGVECYERLKGEDGAVAFQ-GWSTGI 78 (351)
T ss_pred CCCccccCCCcccccChhHHHHHHHHHHHHHHcCCcC-CeEEEEEEecCCCCcHHHHHHHHHHhccCCcEEEe-cCcHHH
Confidence 589999998 5668889999999999999999984 9999999999999999999999999988 777765 578888
Q ss_pred HHHHHHhhhcCCccEEecccCCCCCCc-CCCCceEeecCChHHHHHHHHHHHHHcC-----CcEEEEEEEcCCCcchhHH
Q 003958 109 SHVVSHVANELQVPLLSFSATDPTLSS-LQFPYFVRTTQSDQYQMAAIAEIVDHYG-----WREVIAIYVDDDHGRNGIA 182 (784)
Q Consensus 109 ~~~va~~~~~~~ip~Is~~a~~~~l~~-~~~p~~~r~~ps~~~~~~ai~~~l~~~~-----w~~v~ii~~d~~~g~~~~~ 182 (784)
+.++++++...++|+|+++++++.+++ ..+||+||+.|++..++.++++++.+.+ .++|++|+.|++||+...+
T Consensus 79 ~~a~~~~~~~~~vp~i~~~~~~~~~~~~~~~~~~Fr~~~~~~~~~~~l~~~~~~~~~~~~~~~kvaiv~~~~~~g~~~~~ 158 (351)
T cd06334 79 TEALIPKIAADKIPLMSGSYGATLADDGAVFPYNFPVGPTYSDQARALVQYIAEQEGGKLKGKKIALVYHDSPFGKEPIE 158 (351)
T ss_pred HHHhhHHHhhcCCcEEecccchhhccCCCCCCeeeeCCCCHHHHHHHHHHHHHHhcccCCCCCeEEEEeCCCccchhhHH
Confidence 899999999999999998777776764 5689999999999999999999987655 7999999999999999999
Q ss_pred HHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHcCCCCCCeEEEecCccccc
Q 003958 183 ALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIATSWLSTA 262 (784)
Q Consensus 183 ~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~ 262 (784)
.+++.+++.|++|+....++ .+.+|++.++.+++..++|+|++.....++..+++++++.|+..+ |+.+.+....
T Consensus 159 ~~~~~~~~~G~~vv~~~~~~--~~~~D~~~~v~~i~~~~pd~V~~~~~~~~~~~~~~~~~~~G~~~~---~~~~~~~~~~ 233 (351)
T cd06334 159 ALKALAEKLGFEVVLEPVPP--PGPNDQKAQWLQIRRSGPDYVILWGWGVMNPVAIKEAKRVGLDDK---FIGNWWSGDE 233 (351)
T ss_pred HHHHHHHHcCCeeeeeccCC--CCcccHHHHHHHHHHcCCCEEEEecccchHHHHHHHHHHcCCCce---EEEeeccCcH
Confidence 99999999999999888877 567899999999999999999999999999999999999998533 5544332211
Q ss_pred cccCCCCCCCccccceeeEEEeeecC--CchhHHHHHHHHHhhccCCCCCCCCCCChhHHHHhhHHHHHHHHHHHHhhcC
Q 003958 263 LDTNSPFPSDVMDDIQGVLTLRTYTP--DSVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTVWLLARAINSFFKQG 340 (784)
Q Consensus 263 ~~~~~~~~~~~~~~~~g~~~~~~~~~--~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~~~a~Al~~~~~~~ 340 (784)
. .. .......+|+++..++.+ +++..++|.+.|+++++..+. ....++.++..+||+++++++|++++.+..
T Consensus 234 ~-~~----~~~g~~~~g~~~~~~~~~~~~~p~~~~f~~~~~~~~~~~~~-~~~~~~~~~~~gy~a~~~l~~Al~~ag~~~ 307 (351)
T cd06334 234 E-DV----KPAGDAAKGYKGVTPFAGGADDPVGKEIVKEVYDKGKGSGN-DKEIGSVYYNRGVVNAMIMVEAIRRAQEKG 307 (351)
T ss_pred H-HH----HHhhhhhcCcEEeecccCCCCchHHHHHHHHHHHccCCCCC-cccccccHHHHHHHHHHHHHHHHHHHHHhc
Confidence 1 10 122245677777665543 678899999999998862110 012335788999999999999999986654
Q ss_pred CccccccCCccccccCCcccccccccCCchHHHHHHHhccccceeeeEEEecC
Q 003958 341 GNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANMTGTAGPARFNSH 393 (784)
Q Consensus 341 ~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~l~~~l~~~~f~g~tG~v~Fd~~ 393 (784)
...... ..+...+-+.-.+.+++....|+.|+++|...
T Consensus 308 ~~~~~~---------------~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~ 345 (351)
T cd06334 308 GETTIA---------------GEEQLENLKLDAARLEELGAEGLGPPVSVSCD 345 (351)
T ss_pred CCCCCc---------------HHHHHHhhhhhhhhhhhcCcccccCCceeccc
Confidence 321100 00000011233456666778889999999864
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=100.00 E-value=1.9e-30 Score=277.08 Aligned_cols=323 Identities=19% Similarity=0.257 Sum_probs=259.7
Q ss_pred EEEEEeecC---CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhc-CceEEEccCchhh
Q 003958 33 NIGALLSFS---TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEG-QTVAIIGPQDAVT 108 (784)
Q Consensus 33 ~IG~i~~~~---~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~-~v~aiiGp~~s~~ 108 (784)
+||.+.|++ +..|.....|+++|++++|+++|+. |++|+++++|+++++..+.+.+.+|+++ +|.+|+|+.+|..
T Consensus 1 ~IG~~~plsG~~a~~g~~~~~g~~la~~~iN~~gGi~-G~~i~lv~~D~~~~p~~a~~~a~~Li~~~~V~aiiG~~~s~~ 79 (347)
T cd06335 1 KIGVDADFSGGSAPSGVSIRRGARLAIDEINAAGGVL-GRKLELVERDDRGNPARGLQNAQELAADEKVVAVLGGLHTPV 79 (347)
T ss_pred CeeeecCccCccccccHHHHHHHHHHHHHHHhcCCcC-CeEEEEEeccCCCCcHHHHHHHHHHhccCCeEEEEcCCCCHH
Confidence 599999998 4668889999999999999999984 8999999999999999999999999987 8999999999999
Q ss_pred HHHHHHhhhcCCccEEecccCCCCCCc--CCCCceEeecCChHHHHHHHHHHH-HHcCCcEEEEEEEcCCCcchhHHHHH
Q 003958 109 SHVVSHVANELQVPLLSFSATDPTLSS--LQFPYFVRTTQSDQYQMAAIAEIV-DHYGWREVIAIYVDDDHGRNGIAALG 185 (784)
Q Consensus 109 ~~~va~~~~~~~ip~Is~~a~~~~l~~--~~~p~~~r~~ps~~~~~~ai~~~l-~~~~w~~v~ii~~d~~~g~~~~~~l~ 185 (784)
+.+++++++..+||+|++.++.+.+++ ..++++||+.|++..++.++++++ ++.+|++|+++|.+++||+...+.++
T Consensus 80 ~~a~~~~~~~~~vp~i~~~~~~~~l~~~~~~~~~~Fr~~~~~~~~~~~~a~~~~~~~~~~~v~ii~~~~~~g~~~~~~~~ 159 (347)
T cd06335 80 ALANLEFIQQNKIPLIGPWAAGTPITRNGAPPNYIFRVSADDSIQAPFLVDEAVKRGGFKKVALLLDNTGWGRSNRKDLT 159 (347)
T ss_pred HHhhhHHHHhcCCcEEecCCCCcccccCCCCCCCEEEeccChHHHHHHHHHHHHHhcCCCeEEEEeccCchhhhHHHHHH
Confidence 999999999999999998877766665 346899999999999999999986 55679999999999999999999999
Q ss_pred HHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHcCCCCCCeEEEecCcccccccc
Q 003958 186 DTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIATSWLSTALDT 265 (784)
Q Consensus 186 ~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~ 265 (784)
+.+++.|++++....++ ....|+++++++|++.++++|++.+...+...+++++++.|+..+ ++ ..+.....+.
T Consensus 160 ~~~~~~G~~v~~~~~~~--~~~~d~s~~i~~i~~~~~d~v~~~~~~~~~~~~~~~~~~~g~~~~---~~-~~~~~~~~~~ 233 (347)
T cd06335 160 AALAARGLKPVAVEWFN--WGDKDMTAQLLRAKAAGADAIIIVGNGPEGAQIANGMAKLGWKVP---II-SHWGLSGGNF 233 (347)
T ss_pred HHHHHcCCeeEEEeeec--CCCccHHHHHHHHHhCCCCEEEEEecChHHHHHHHHHHHcCCCCc---Ee-cccCCcCchh
Confidence 99999999999888887 456799999999999999999999999999999999999998643 23 2221111111
Q ss_pred CCCCCCCccccceeeEEEeeec---CCchhHHHHHHHHHhhccCCCCCCCCCCChhHHHHhhHHHHHHHHHHHHhhcCCc
Q 003958 266 NSPFPSDVMDDIQGVLTLRTYT---PDSVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTVWLLARAINSFFKQGGN 342 (784)
Q Consensus 266 ~~~~~~~~~~~~~g~~~~~~~~---~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~~~a~Al~~~~~~~~~ 342 (784)
. ....+...|++....+. +..+..++|.++|+++++..... ...++.++..+||+++++++|++++...
T Consensus 234 ~----~~~g~~~~g~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~-~~~~~~~~~~aYd~~~~l~~A~~~ag~~--- 305 (347)
T cd06335 234 I----EGAGPAANDALMIQTFIFEPPSNPKAKAFLAAYHKKYPEKKPA-DIPAPVGAAHAYDAVHLLAAAIKQAGST--- 305 (347)
T ss_pred h----hccchhhcCcEEEEeeccccCCCHHHHHHHHHHHHHhCCCccc-ccCcchhHHHHHHHHHHHHHHHHHhcCC---
Confidence 0 11223456765554322 25678899999999998631110 1124456778999999999999985110
Q ss_pred cccccCCccccccCCcccccccccCCchHHHHHHHhcc--ccceeee--EEEecCCC
Q 003958 343 LSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQAN--MTGTAGP--ARFNSHGD 395 (784)
Q Consensus 343 ~~~~~~~~~~~~~g~~~~~~~~~~~~~~~l~~~l~~~~--f~g~tG~--v~Fd~~g~ 395 (784)
.+..+.+.|+++. +.|+.|. +.|++..+
T Consensus 306 -------------------------~~~~v~~al~~~~~~~~G~~~~~~~~~~~~~h 337 (347)
T cd06335 306 -------------------------DGRAIKRALENLKKPVEGLVKTYDKPFSKEDH 337 (347)
T ss_pred -------------------------CHHHHHHHHHhccCCceeeecccCCCCChhhc
Confidence 2467889998764 6777774 45765433
No 73
>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=99.97 E-value=9.5e-30 Score=271.31 Aligned_cols=323 Identities=18% Similarity=0.250 Sum_probs=264.4
Q ss_pred EEEEEeecCC---cchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhc-CceEEEccCchhh
Q 003958 33 NIGALLSFST---NVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEG-QTVAIIGPQDAVT 108 (784)
Q Consensus 33 ~IG~i~~~~~---~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~-~v~aiiGp~~s~~ 108 (784)
+||++.|++. ..|.....++++|++++| +++ .|+++++.++|+.+++..+.+.+.+|+.+ +|.+|||+.++..
T Consensus 1 ~IG~~~~~sg~~~~~g~~~~~g~~~a~~~~~--~~i-~G~~i~l~~~d~~~~~~~~~~~~~~l~~~~~v~~iig~~~s~~ 77 (333)
T cd06332 1 KIGLLTTLSGPYAALGQDIRDGFELALKQLG--GKL-GGRPVEVVVEDDELKPDVAVQAARKLIEQDKVDVVVGPVFSNV 77 (333)
T ss_pred CeEEEeeccCchHhhhHHHHHHHHHHHHHhC--CCc-CCeEEEEEEecCCCCHHHHHHHHHHHHHHcCCcEEEcCCccHH
Confidence 5999999984 456788999999999997 455 69999999999999999999999999987 9999999999988
Q ss_pred HHHHHHhhhcCCccEEecccCCCCCCcC-CCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcCCCcchhHHHHHHH
Q 003958 109 SHVVSHVANELQVPLLSFSATDPTLSSL-QFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDT 187 (784)
Q Consensus 109 ~~~va~~~~~~~ip~Is~~a~~~~l~~~-~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~~ 187 (784)
+.++.+.+...++|+|+++++.+.+++. .+|++||+.|++..++..+++++...+|+++++++.++.+|+...+.+++.
T Consensus 78 ~~~~~~~~~~~~ip~v~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~l~~~g~~~v~il~~~~~~~~~~~~~~~~~ 157 (333)
T cd06332 78 ALAVVPSLTESGTFLISPNAGPSDLAGKLCSPNFFRTSWQNDQVHEAMGKYAADKGYKKVVIIAPDYAAGKDAVAGFKRT 157 (333)
T ss_pred HHHHHHHHhhcCCeEEecCCCCccccccCCCCcEEEeeCChHHhHHHHHHHHHHhCCceEEEEecCcchhHHHHHHHHHh
Confidence 8888899999999999998877777764 479999999999999999999999999999999999999999999999998
Q ss_pred HhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHcCCCCCCeEEEecCccccccccCC
Q 003958 188 LAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIATSWLSTALDTNS 267 (784)
Q Consensus 188 l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~~~ 267 (784)
++ ..+.....++ ....|+..+++++++.++++|++......+..+++++++.|+.. +..++++..+......
T Consensus 158 ~~---~~~~~~~~~~--~~~~d~~~~i~~l~~~~~d~i~~~~~~~~~~~~~~~~~~~g~~~-~~~~~~~~~~~~~~~~-- 229 (333)
T cd06332 158 FK---GEVVEEVYTP--LGQLDFSAELAQIRAAKPDAVFVFLPGGMAVNFVKQYDQAGLKK-KIPLYGPGFLTDQDTL-- 229 (333)
T ss_pred hc---EEEeeEEecC--CCCcchHHHHHHHHhcCCCEEEEecccchHHHHHHHHHHcCccc-CCceeccCCCCCHHHH--
Confidence 87 3555455555 34567989999999999999999888889999999999999843 3346665544322111
Q ss_pred CCCCCccccceeeEEEeeecC--CchhHHHHHHHHHhhccCCCCCCCCCCChhHHHHhhHHHHHHHHHHHHhhcCCcccc
Q 003958 268 PFPSDVMDDIQGVLTLRTYTP--DSVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTVWLLARAINSFFKQGGNLSF 345 (784)
Q Consensus 268 ~~~~~~~~~~~g~~~~~~~~~--~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~~~a~Al~~~~~~~~~~~~ 345 (784)
.......+|++...++.+ +.+..++|.++|+++++ ..++.++..+||++++++.|++++...
T Consensus 230 ---~~~~~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~~-------~~~~~~~~~~yda~~~~~~a~~~ag~~------ 293 (333)
T cd06332 230 ---PAQGDAAVGVLTALHWAPDLDNPANKRFVAAYKAAYG-------RVPSVYAAQGYDAAQLLDAALRAVGGD------ 293 (333)
T ss_pred ---HhhchhhcCeeeeeccCCCCCCHHHHHHHHHHHHHhC-------CCCcHHHHHHHHHHHHHHHHHHHhcCC------
Confidence 122355678877766655 35788999999999886 236778899999999999999996210
Q ss_pred ccCCccccccCCcccccccccCCchHHHHHHHhccccceeeeEEEecCCCCcCCcEEE
Q 003958 346 SKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANMTGTAGPARFNSHGDLINPAYEI 403 (784)
Q Consensus 346 ~~~~~~~~~~g~~~~~~~~~~~~~~~l~~~l~~~~f~g~tG~v~Fd~~g~~~~~~~~I 403 (784)
..++..+.++|++.+|+|+.|.+.|+++|+. ...+.+
T Consensus 294 --------------------~~~~~~v~~al~~~~~~~~~g~i~f~~~~~~-~~~~~~ 330 (333)
T cd06332 294 --------------------LSDKDALRAALRAADFDSPRGPFKFNPNHNP-IQDFYL 330 (333)
T ss_pred --------------------CCCHHHHHHHHhcCceecCccceeECCCCCc-ccceeE
Confidence 1136789999999999999999999999985 333444
No 74
>PF13433 Peripla_BP_5: Periplasmic binding protein domain; PDB: 1QNL_A 1QO0_A 1PEA_A.
Probab=99.97 E-value=2.3e-29 Score=254.38 Aligned_cols=318 Identities=15% Similarity=0.151 Sum_probs=229.4
Q ss_pred EEEEEEeecCC---cchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHh-cCceEEEccCchh
Q 003958 32 VNIGALLSFST---NVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLME-GQTVAIIGPQDAV 107 (784)
Q Consensus 32 i~IG~i~~~~~---~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~-~~v~aiiGp~~s~ 107 (784)
|+||+++++++ ..+.....|..+|++|||++||++ |++|+.+++|.++|+..-.+.+.+|+. ++|.+|+|.+.|.
T Consensus 1 ikVGiL~S~tG~~a~~e~~~~~~~~lAI~eINa~GGvl-G~~le~v~~Dp~Sd~~~ya~~A~~Li~~d~V~~ifGc~TSa 79 (363)
T PF13433_consen 1 IKVGILHSLTGTMAISERSLLDGALLAIEEINAAGGVL-GRQLEPVIYDPASDPSTYAEKAEKLIREDGVRAIFGCYTSA 79 (363)
T ss_dssp --EEEE--SSSTTHHHHHHHHHHHHHHHHHHHCTTTBT-TB--EEEEE--TT-HHHHHHHHHHHHHHS---EEEE--SHH
T ss_pred CeEEEEEeCCCchHhhhHHHHHHHHHHHHHHHhcCCcC-CeEEEEEEECCCCCHHHHHHHHHHHHHhCCccEEEecchhh
Confidence 68999999984 345678899999999999999997 899999999999999999999999986 5999999999999
Q ss_pred hHHHHHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHH-HHHcCCcEEEEEEEcCCCcchhHHHHHH
Q 003958 108 TSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEI-VDHYGWREVIAIYVDDDHGRNGIAALGD 186 (784)
Q Consensus 108 ~~~~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~-l~~~~w~~v~ii~~d~~~g~~~~~~l~~ 186 (784)
+-++|.++.+..+-+++.+..-. .+ ..-|++|-+.....++...++++ ++++|-+++.+|.+|+.|++..-+.+++
T Consensus 80 sRKaVlPvvE~~~~LL~Yp~~YE-G~--E~S~nviYtGa~PNQ~~~pl~~~~~~~~G~~r~~lvGSdYv~pre~Nri~r~ 156 (363)
T PF13433_consen 80 SRKAVLPVVERHNALLFYPTQYE-GF--ECSPNVIYTGAAPNQQLLPLIDYLLENFGAKRFYLVGSDYVYPRESNRIIRD 156 (363)
T ss_dssp HHHHHHHHHHHCT-EEEE-S-----------TTEEE-S--GGGTHHHHHHHHHHHS--SEEEEEEESSHHHHHHHHHHHH
T ss_pred hHHHHHHHHHhcCceEEeccccc-cc--cCCCceEEcCCCchhhHHHHHHHHHhccCCceEEEecCCccchHHHHHHHHH
Confidence 99999999999999998643211 11 23489999999888888888888 5778999999999999999999999999
Q ss_pred HHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHcCCCCCCeEEEecCccc-ccccc
Q 003958 187 TLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIATSWLS-TALDT 265 (784)
Q Consensus 187 ~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~-~~~~~ 265 (784)
.+++.|++|+.+..+| .+.+|+..++.+|++.++|+|+-...++....|+++..+.|+... .+=|.+.... ....
T Consensus 157 ~l~~~GgevvgE~Y~p--lg~td~~~ii~~I~~~~Pd~V~stlvG~s~~aF~r~~~~aG~~~~-~~Pi~S~~~~E~E~~- 232 (363)
T PF13433_consen 157 LLEARGGEVVGERYLP--LGATDFDPIIAEIKAAKPDFVFSTLVGDSNVAFYRAYAAAGLDPE-RIPIASLSTSEAELA- 232 (363)
T ss_dssp HHHHTT-EEEEEEEE---S-HHHHHHHHHHHHHHT-SEEEEE--TTCHHHHHHHHHHHH-SSS----EEESS--HHHHT-
T ss_pred HHHHcCCEEEEEEEec--CCchhHHHHHHHHHhhCCCEEEEeCcCCcHHHHHHHHHHcCCCcc-cCeEEEEecCHHHHh-
Confidence 9999999999999998 578999999999999999999998889999999999999998754 3334443222 1111
Q ss_pred CCCCCCCccccceeeEEEeeec--CCchhHHHHHHHHHhhccCCCCCCCCCCChhHHHHhhHHHHHHHHHHHHhhcCCcc
Q 003958 266 NSPFPSDVMDDIQGVLTLRTYT--PDSVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTVWLLARAINSFFKQGGNL 343 (784)
Q Consensus 266 ~~~~~~~~~~~~~g~~~~~~~~--~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~~~a~Al~~~~~~~~~~ 343 (784)
....+...|.++...+. -++|+.++|+++|+++++. ...++.....+|.+|+++|+|++++..
T Consensus 233 -----~~g~~~~~Gh~~~~~YFqsidtp~N~~Fv~~~~~~~g~-----~~v~s~~~eaaY~~v~l~a~Av~~ags----- 297 (363)
T PF13433_consen 233 -----AMGAEAAAGHYTSAPYFQSIDTPENQAFVARFRARYGD-----DRVTSDPMEAAYFQVHLWAQAVEKAGS----- 297 (363)
T ss_dssp -----TS-HHHHTT-EEEES--TT-SSHHHHHHHHHHHTTS-T-----T----HHHHHHHHHHHHHHHHHHHHTS-----
T ss_pred -----hcChhhcCCcEEeehhhhhCCcHHHHHHHHHHHHHhCC-----CCCCCcHHHHHHHHHHHHHHHHHHhCC-----
Confidence 12234678888876544 4689999999999999973 234566677899999999999999721
Q ss_pred ccccCCccccccCCcccccccccCCchHHHHHHHhccccceeeeEEEec-CCC
Q 003958 344 SFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANMTGTAGPARFNS-HGD 395 (784)
Q Consensus 344 ~~~~~~~~~~~~g~~~~~~~~~~~~~~~l~~~l~~~~f~g~tG~v~Fd~-~g~ 395 (784)
.+...+.++|.+.+|+.+.|.+++|+ |++
T Consensus 298 -----------------------~d~~~vr~al~g~~~~aP~G~v~id~~n~H 327 (363)
T PF13433_consen 298 -----------------------DDPEAVREALAGQSFDAPQGRVRIDPDNHH 327 (363)
T ss_dssp -------------------------HHHHHHHHTT--EEETTEEEEE-TTTSB
T ss_pred -----------------------CCHHHHHHHhcCCeecCCCcceEEcCCCCe
Confidence 15889999999999999999999997 443
No 75
>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=99.97 E-value=3.7e-29 Score=267.96 Aligned_cols=331 Identities=13% Similarity=0.093 Sum_probs=256.1
Q ss_pred EEEEEeecC---CcchhhHHHHHHHHHHHHhcCCCCCCC--CEEEEEEecCCCCHHHHHHHHHHHHhc-CceEEEccCch
Q 003958 33 NIGALLSFS---TNVGKVAKLAIKAAVDDVNSDPTTLGG--TKLKLQMQDCNHSGFLALAEALHLMEG-QTVAIIGPQDA 106 (784)
Q Consensus 33 ~IG~i~~~~---~~~g~~~~~a~~~Ave~IN~~~~il~g--~~l~~~~~D~~~~~~~a~~~~~~li~~-~v~aiiGp~~s 106 (784)
+||++.|+| +..|.....++++++++||..+++ .| ++|+++++|++++|.+++..+.+|+++ +|.+|+|+.+|
T Consensus 1 kIG~~~~lSG~~a~~G~~~~~~~~~~~~~in~g~~i-~G~~~~i~lv~~D~~~~p~~a~~~a~~li~~d~v~~iiG~~~s 79 (357)
T cd06337 1 KIGYVSPRTGPLAAFGEADPWVLETMRSALADGLVV-GGSTYEVEIIVRDSQSNPNRAGLVAQELILTDKVDLLLAGGTP 79 (357)
T ss_pred CcceeccCcCcccccccchHHHHHHHHHHhcCCeeE-CCceeEEEEEEecCCCCHHHHHHHHHHHHhccCccEEEecCCc
Confidence 589999998 556888889999999999955444 45 589999999999999999999999987 99999999999
Q ss_pred hhHHHHHHhhhcCCccEEecccCCCCC------C-cCCCCceEeecCChHHHHHHHHHHHHHcC-CcEEEEEEEcCCCcc
Q 003958 107 VTSHVVSHVANELQVPLLSFSATDPTL------S-SLQFPYFVRTTQSDQYQMAAIAEIVDHYG-WREVIAIYVDDDHGR 178 (784)
Q Consensus 107 ~~~~~va~~~~~~~ip~Is~~a~~~~l------~-~~~~p~~~r~~ps~~~~~~ai~~~l~~~~-w~~v~ii~~d~~~g~ 178 (784)
..+.+++++++..+||+|++.+..+.+ . ...++|+||+.+++..+..++++++++.+ ++++++++.|+.||+
T Consensus 80 ~~~~a~~~~~~~~~ip~i~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~k~v~ii~~~~~~g~ 159 (357)
T cd06337 80 DTTNPVSDQCEANGVPCISTMAPWQAWFFGRGGNPATGFKWTYHFFWGAEDVVATYVGMWKQLETNKKVGILYPNDPDGN 159 (357)
T ss_pred chhhHHHHHHHHhCCCeEEeccchhhhhccCCCCcccCCceeEEecCCHHHHHHHHHHHHHhCCCCceEEEEeecCchhH
Confidence 999999999999999999875432211 1 23478999999999888889999888877 999999999999999
Q ss_pred hhHHHHH---HHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHcCCCCCCeEEEe
Q 003958 179 NGIAALG---DTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIA 255 (784)
Q Consensus 179 ~~~~~l~---~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~wi~ 255 (784)
...+.+. +.+++.|++++..+.++ .+.+|++.++++|+++++|+|++.+.+.++..++++++++|+..+ ++.
T Consensus 160 ~~~~~~~~~~~~~~~~G~~vv~~~~~~--~~~~D~~~~v~~ik~a~pD~v~~~~~~~~~~~~~~~~~~~G~~~~---~~~ 234 (357)
T cd06337 160 AFADPVIGLPAALADAGYKLVDPGRFE--PGTDDFSSQINAFKREGVDIVTGFAIPPDFATFWRQAAQAGFKPK---IVT 234 (357)
T ss_pred HHHHhhhcccHHHHhCCcEEecccccC--CCCCcHHHHHHHHHhcCCCEEEeCCCccHHHHHHHHHHHCCCCCC---eEE
Confidence 7766554 56677899999888887 467899999999999999999999999999999999999998665 333
Q ss_pred cCccccccccCCCCCCCccccceeeEEEeeecCC--------chhHHHHHHHHHhhccCCCCCCCCCCChhHHHHhhHHH
Q 003958 256 TSWLSTALDTNSPFPSDVMDDIQGVLTLRTYTPD--------SVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTVW 327 (784)
Q Consensus 256 ~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~--------~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~ 327 (784)
........... ....+..+|++....+.+. ++..++|.++|+++++. .+.....++||+++
T Consensus 235 ~~~~~~~~~~~----~~~g~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~~~~g~-------~~~~~~~~~~~~~~ 303 (357)
T cd06337 235 IAKALLFPEDV----EALGDRGDGMSTEVWWSPSHPFRSSLTGQSAAELADAYEAATGR-------QWTQPLGYAHALFE 303 (357)
T ss_pred EeccccCHHHH----HHhhhhhcCccccceeccCCCcccccCCccHHHHHHHHHHHhCC-------CccCcchHHHHHHH
Confidence 22111000000 0111234565554333332 24578999999998862 23445677999999
Q ss_pred HHHHHHHHHhhcCCccccccCCccccccCCcccccccccCCchHHHHHHHhccccceeeeEEEecCCCCcCCcEEEEEee
Q 003958 328 LLARAINSFFKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANMTGTAGPARFNSHGDLINPAYEIINVI 407 (784)
Q Consensus 328 ~~a~Al~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~l~~~l~~~~f~g~tG~v~Fd~~g~~~~~~~~I~~~~ 407 (784)
++++|++++... .++..|.++|++++|+++.|++.|+++ . ..+..|..++
T Consensus 304 ~l~~Ai~~Ags~---------------------------~d~~~v~~aL~~~~~~~~~G~~~f~~~--~-~~~~~~~~~~ 353 (357)
T cd06337 304 VGVKALVRADDP---------------------------DDPAAVADAIATLKLDTVVGPVDFGNS--P-IKNVAKTPLV 353 (357)
T ss_pred HHHHHHHHcCCC---------------------------CCHHHHHHHHHcCCcccceeeeecCCC--C-Cccccccccc
Confidence 999999985110 147789999999999999999999876 2 3345666666
Q ss_pred ccc
Q 003958 408 GTG 410 (784)
Q Consensus 408 ~~~ 410 (784)
+++
T Consensus 354 ~~~ 356 (357)
T cd06337 354 GGQ 356 (357)
T ss_pred cCC
Confidence 544
No 76
>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=99.96 E-value=2e-27 Score=253.62 Aligned_cols=317 Identities=15% Similarity=0.190 Sum_probs=254.3
Q ss_pred EEEEEEeecC---CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhc-CceEEEccCchh
Q 003958 32 VNIGALLSFS---TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEG-QTVAIIGPQDAV 107 (784)
Q Consensus 32 i~IG~i~~~~---~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~-~v~aiiGp~~s~ 107 (784)
|+||++.|+| +..|.....++++|+++||+.+|+ .|+++++...|+++++..+.+.+.+++.+ +|.+|||+.++.
T Consensus 1 i~IG~~~~lsG~~a~~g~~~~~~~~~a~~~iN~~ggi-~G~~v~l~~~D~~~d~~~~~~~~~~l~~~~~v~avig~~~s~ 79 (336)
T cd06326 1 IVLGQSAPLSGPAAALGRAYRAGAQAYFDAVNAAGGV-NGRKIELVTLDDGYEPERTVANTRKLIEDDKVFALFGYVGTP 79 (336)
T ss_pred CEEEEeccCCCcchhhHHHHHHHHHHHHHHHHhcCCc-CCceEEEEEeCCCCChHHHHHHHHHHHhhcCcEEEEeCCCch
Confidence 6899999999 455788899999999999999988 59999999999999999999999999986 999999998887
Q ss_pred hHHHHHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcCCCcchhHHHHHHH
Q 003958 108 TSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDT 187 (784)
Q Consensus 108 ~~~~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~~ 187 (784)
.+.++.+++...++|+|++++.++.+++...+++||+.++....+..+++++.+.+|+++++++.++.+++...+.+++.
T Consensus 80 ~~~~~~~~~~~~~iP~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~g~~~v~~l~~~~~~~~~~~~~~~~~ 159 (336)
T cd06326 80 TTAAALPLLEEAGVPLVGPFTGASSLRDPPDRNVFNVRASYADEIAAIVRHLVTLGLKRIAVFYQDDAFGKDGLAGVEKA 159 (336)
T ss_pred hHHHHHHHHHHcCCeEEEecCCcHHhcCCCCCceEEeCCChHHHHHHHHHHHHHhCCceEEEEEecCcchHHHHHHHHHH
Confidence 77788899999999999987665555443468999999999999999999999999999999999989999999999999
Q ss_pred HhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHcCCCCCCeEEEecCccccccccCC
Q 003958 188 LAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIATSWLSTALDTNS 267 (784)
Q Consensus 188 l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~~~ 267 (784)
+++.|+++.....++ .+..|+..++.++++.++++|++......+..++++++++|+..+ ++...........
T Consensus 160 ~~~~G~~~~~~~~~~--~~~~d~~~~~~~l~~~~~dav~~~~~~~~a~~~i~~~~~~G~~~~---~~~~~~~~~~~~~-- 232 (336)
T cd06326 160 LAARGLKPVATASYE--RNTADVAAAVAQLAAARPQAVIMVGAYKAAAAFIRALRKAGGGAQ---FYNLSFVGADALA-- 232 (336)
T ss_pred HHHcCCCeEEEEeec--CCcccHHHHHHHHHhcCCCEEEEEcCcHHHHHHHHHHHhcCCCCc---EEEEeccCHHHHH--
Confidence 999999887766666 345789999999999899999998887889999999999998643 2222222111000
Q ss_pred CCCCCccccceeeEEEee----ecCCchhHHHHHHHHHhhccCCCCCCCCCCChhHHHHhhHHHHHHHHHHHHhhcCCcc
Q 003958 268 PFPSDVMDDIQGVLTLRT----YTPDSVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTVWLLARAINSFFKQGGNL 343 (784)
Q Consensus 268 ~~~~~~~~~~~g~~~~~~----~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~~~a~Al~~~~~~~~~~ 343 (784)
.......+|++.... .....+..+.|.+.|+++++. ..++.++..+||+++++++|++++. .+
T Consensus 233 ---~~~g~~~~g~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~------~~~~~~~~~~y~~~~~~~~a~~~~g---~~- 299 (336)
T cd06326 233 ---RLLGEYARGVIVTQVVPNPWSRTLPIVREYQAAMKAYGPG------APPSYVSLEGYIAAKVLVEALRRAG---PD- 299 (336)
T ss_pred ---HHhhhhhcceEEEEEecCccccCCHHHHHHHHHHHhhCCC------CCCCeeeehhHHHHHHHHHHHHHcC---CC-
Confidence 111234566654322 223467789999999988752 2456678889999999999999851 11
Q ss_pred ccccCCccccccCCcccccccccCCchHHHHHHHhcccc-ceeeeEEEec
Q 003958 344 SFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANMT-GTAGPARFNS 392 (784)
Q Consensus 344 ~~~~~~~~~~~~g~~~~~~~~~~~~~~~l~~~l~~~~f~-g~tG~v~Fd~ 392 (784)
.+++.+.++|++++.. +..+.++|++
T Consensus 300 -----------------------~~~~~v~~al~~~~~~~~~g~~~~~~~ 326 (336)
T cd06326 300 -----------------------PTRESLLAALEAMGKFDLGGFRLDFSP 326 (336)
T ss_pred -----------------------CCHHHHHHHHHhcCCCCCCCeEEecCc
Confidence 1488999999998864 4444899976
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=99.96 E-value=4.8e-28 Score=256.68 Aligned_cols=302 Identities=18% Similarity=0.173 Sum_probs=241.7
Q ss_pred EEEEEeecCC---cchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEccCchhhH
Q 003958 33 NIGALLSFST---NVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIGPQDAVTS 109 (784)
Q Consensus 33 ~IG~i~~~~~---~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiGp~~s~~~ 109 (784)
+||++.|+++ ..|.....|+++|+++|| |++++++++|+.+ +..+...+.+|++++|.+||||.+|..+
T Consensus 1 kIG~l~plsG~~a~~g~~~~~g~~lA~~~in-------G~~i~l~~~D~~~-~~~a~~~~~~li~~~V~~iiG~~~s~~~ 72 (336)
T cd06339 1 RIALLLPLSGPLASVGQAIRNGFLAALYDLN-------GASIELRVYDTAG-AAGAAAAARQAVAEGADIIVGPLLKENV 72 (336)
T ss_pred CeEEEEcCCCcchHHHHHHHHHHHHHHHhcc-------CCCceEEEEeCCC-cccHHHHHHHHHHcCCCEEEccCCHHHH
Confidence 5899999984 468888999999999999 6889999999999 9999999999998899999999999999
Q ss_pred HHHHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcCCCcchhHHHHHHHHh
Q 003958 110 HVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLA 189 (784)
Q Consensus 110 ~~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~~l~ 189 (784)
.++++++...++|+|++++++. +.. .|++||+.+++..++.++++++.+.++++|++|+.+++||+...+.+++.++
T Consensus 73 ~a~~~~~~~~~ip~i~~~~~~~-~~~--~~~~f~~~~~~~~~~~~~~~~~~~~g~k~vaii~~~~~~g~~~~~~f~~~~~ 149 (336)
T cd06339 73 AALAAAAAELGVPVLALNNDES-VAA--GPNLFYFGLSPEDEARRAAEYARSQGKRRPLVLAPDGAYGQRVADAFRQAWQ 149 (336)
T ss_pred HHHHhhhccCCCCEEEccCCcc-ccC--CCCEEEecCChHHHHHHHHHHHHhcCccceEEEecCChHHHHHHHHHHHHHH
Confidence 9999999999999999765443 222 5899999999999999999999888999999999999999999999999999
Q ss_pred ccCcEEEEeeccCCCCChhHHHHHHHHhhcC---------------------CceEEEEeccCC-cHHHHHHHHHHcCCC
Q 003958 190 AKRCRISFKAPLSVEATEDEITDLLVKVALT---------------------ESRIIVVHTHYN-RGPVVFHVAQYLGML 247 (784)
Q Consensus 190 ~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~---------------------~~~vIvl~~~~~-~~~~~~~~a~~~g~~ 247 (784)
+.|++|+..+.++ .+..|++.++++|++. ++|+|++.+.+. ++..+.++++..+..
T Consensus 150 ~~G~~vv~~~~~~--~~~~d~~~~i~~i~~~~~~~~~~~~~~~~~~~~~~~~~~d~v~~~~~~~~~~~~~~~~~~~~~~~ 227 (336)
T cd06339 150 QLGGTVVAIESYD--PSPTDLSDAIRRLLGVDDSEQRIAQLKSLESEPRRRQDIDAIDAVALPDGEARLIKPQLLFYYGV 227 (336)
T ss_pred HcCCceeeeEecC--CCHHHHHHHHHHHhccccchhhhhhhhhcccCccccCCCCcEEEEecChhhhhhhcchhhhhccC
Confidence 9999999888887 5788999999999988 999999988876 676777777665531
Q ss_pred CCCeEEEecCccccccccCCCCCCCccccceeeEEEeeecCCchhHHHHHHHHHhhccCCCCCCCCCC-ChhHHHHhhHH
Q 003958 248 GTGYVWIATSWLSTALDTNSPFPSDVMDDIQGVLTLRTYTPDSVLKRKFISRWRNLTDAKTPNGYIGL-NAYGFYAYDTV 326 (784)
Q Consensus 248 ~~~~~wi~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~-~~~~~~~YDAv 326 (784)
..+..+++++.+...... .......+|++...+.. ....+|.+.|+++++ ..| +.+++.+|||+
T Consensus 228 ~~~~~~~g~~~~~~~~~~-----~~~g~~~~g~~~~~~~~---~~~~~f~~~y~~~~~-------~~p~~~~~a~~YDa~ 292 (336)
T cd06339 228 PGDVPLYGTSRWYSGTPA-----PLRDPDLNGAWFADPPW---LLDANFELRYRAAYG-------WPPLSRLAALGYDAY 292 (336)
T ss_pred cCCCCEEEeccccCCCCC-----cccCcccCCcEEeCCCc---ccCcchhhhHHHHhc-------CCCCchHHHHHHhHH
Confidence 112347777665543111 12234567776554421 122378899998886 345 78899999999
Q ss_pred HHHHHHHHHHhhcCCccccccCCccccccCCcccccccccCCchHHHHHH-HhccccceeeeEEEecCCCC
Q 003958 327 WLLARAINSFFKQGGNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSI-LQANMTGTAGPARFNSHGDL 396 (784)
Q Consensus 327 ~~~a~Al~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~l~~~l-~~~~f~g~tG~v~Fd~~g~~ 396 (784)
.+++.++++... +. +| +...|+|++|.++|+++|+.
T Consensus 293 ~l~~~~~~~~~~-----------------------------~~-----al~~~~~~~g~~G~~~f~~~g~~ 329 (336)
T cd06339 293 ALAAALAQLGQG-----------------------------DA-----ALTPGAGFSGVTGVLRLDPDGVI 329 (336)
T ss_pred HHHHHHHHcccc-----------------------------cc-----ccCCCCccccCcceEEECCCCeE
Confidence 999887776300 11 23 33469999999999999974
No 78
>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=99.96 E-value=9.2e-27 Score=244.11 Aligned_cols=224 Identities=33% Similarity=0.524 Sum_probs=204.7
Q ss_pred EEEEEeecCC-----cchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhc-----CceEEEc
Q 003958 33 NIGALLSFST-----NVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEG-----QTVAIIG 102 (784)
Q Consensus 33 ~IG~i~~~~~-----~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~-----~v~aiiG 102 (784)
+||++++.+. ..+.....++..|++++|+. ++|+++++.+.|+++++..+...+.+++++ ++.+|+|
T Consensus 1 ~iG~~f~~~~~~~~~~~~~~~~~~~~~~~~~~n~~---~~~~~l~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~v~aiiG 77 (298)
T cd06269 1 RIGGLFPLHSGGRFGEEGAFRAAAALFAVEEINND---LPNTTLGYEIYDSCCSPSDAFSAALDLCSLLEKSRGVVAVIG 77 (298)
T ss_pred CEEEEeecccccccCHHHHHHHHHHHHHHHHHhcc---CCCCeeeeEEEecCCChHHHHHHHHHHHhcCCCCCceEEEEC
Confidence 4899999874 34556788999999999998 579999999999999999999999999874 8999999
Q ss_pred cCchhhHHHHHHhhhcCCccEEecccCCCCCCc-CCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcCCCcchhH
Q 003958 103 PQDAVTSHVVSHVANELQVPLLSFSATDPTLSS-LQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDDDHGRNGI 181 (784)
Q Consensus 103 p~~s~~~~~va~~~~~~~ip~Is~~a~~~~l~~-~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~~~g~~~~ 181 (784)
|.++..+.+++++++.+++|+|+++++++.+++ ..+|+++|+.|++..++.++++++++++|++++++|++++++....
T Consensus 78 ~~~s~~~~~v~~~~~~~~iP~is~~~~~~~~~~~~~~~~~~~~~p~~~~~~~a~~~~l~~~~w~~v~~v~~~~~~~~~~~ 157 (298)
T cd06269 78 PSSSSSAEAVASLLGALHIPQISYSATSPLLSDKEQFPSFLRTVPSDSSQAQAIVDLLKHFGWTWVGLVYSDDDYGRRLL 157 (298)
T ss_pred CCCchHHHHHHHHhccCCCcEEecccCchhhcChhhCCCeEecCCCcHHHHHHHHHHHHHCCCeEEEEEEecchhhHHHH
Confidence 999999999999999999999999999888887 5789999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHcCCCCCCeEEEecCcccc
Q 003958 182 AALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIATSWLST 261 (784)
Q Consensus 182 ~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~ 261 (784)
+.+++.+++.|+|+.....++ ....++..++++++..++++||+++.++.+..+++++.+.|+. .+++||+++.+..
T Consensus 158 ~~~~~~~~~~~~~v~~~~~~~--~~~~~~~~~l~~l~~~~~~viv~~~~~~~~~~~l~~a~~~g~~-~~~~~i~~~~~~~ 234 (298)
T cd06269 158 ELLEEELEKNGICVAFVESIP--DGSEDIRRLLKELKSSTARVIVVFSSEEDALRLLEEAVELGMM-TGYHWIITDLWLT 234 (298)
T ss_pred HHHHHHHHHCCeeEEEEEEcC--CCHHHHHHHHHHHHhcCCcEEEEEechHHHHHHHHHHHHcCCC-CCeEEEEEChhhc
Confidence 999999999999999888877 3457899999999999999999999989999999999999998 8899999987654
Q ss_pred c
Q 003958 262 A 262 (784)
Q Consensus 262 ~ 262 (784)
.
T Consensus 235 ~ 235 (298)
T cd06269 235 S 235 (298)
T ss_pred c
Confidence 3
No 79
>TIGR03863 PQQ_ABC_bind ABC transporter, substrate binding protein, PQQ-dependent alcohol dehydrogenase system. Members of this protein family are putative substrate-binding proteins of an ABC transporter family that associates, in gene neighborhood and phylogenomic profile, with pyrroloquinoline-quinone (PQQ)-dependent degradation of certain alcohols, such as 2-phenylethanol in Pseudomonas putida U.
Probab=99.95 E-value=6.4e-27 Score=246.14 Aligned_cols=298 Identities=15% Similarity=0.165 Sum_probs=229.4
Q ss_pred hhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEccCchhhHHHHHHhhhcCCccEE
Q 003958 45 GKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIGPQDAVTSHVVSHVANELQVPLL 124 (784)
Q Consensus 45 g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiGp~~s~~~~~va~~~~~~~ip~I 124 (784)
+.....|+++|+|+||+.||++ |++++++..|. ++|..++..+.+|++++|.+|+|+.+|..+.++.+++...++|+|
T Consensus 10 ~~~~~~ga~lAveeiNaaGGv~-G~~ielv~~D~-~~p~~a~~~a~~Li~~~V~~vvG~~~S~~~~Av~~~a~~~~vp~i 87 (347)
T TIGR03863 10 EDRGLDGARLAIEDNNTTGRFL-GQTFTLDEVAV-RTPEDLVAALKALLAQGVRFFVLDLPAAALLALADAAKAKGALLF 87 (347)
T ss_pred cchHHHHHHHHHHHHHhhCCcC-CceEEEEEccC-CCHHHHHHHHHHHHHCCCCEEEecCChHHHHHHHHHHHhCCcEEE
Confidence 4567899999999999999997 89999999985 689999999999998899999999999999999999999999999
Q ss_pred ecccCCCCCCc-CCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcCCCcchhHHHHHHHHhccCcEEEEeeccCC
Q 003958 125 SFSATDPTLSS-LQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSV 203 (784)
Q Consensus 125 s~~a~~~~l~~-~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~ 203 (784)
+++++++.++. ..+||+||+.|++..++.++++++...+.+++++|+.|++||+...+.+++.+++.|++|+..+.++.
T Consensus 88 ~~~a~~~~lt~~~c~~~~Fr~~~~~~~~~~ala~~~~~~g~kkvaii~~~~~~g~~~~~~~~~~~~~~G~~vv~~~~~~~ 167 (347)
T TIGR03863 88 NAGAPDDALRGADCRANLLHTLPSRAMLADALAQYLAAKRWRRILLIQGPLPADALYADAFRRSAKRFGAKIVAERPFTF 167 (347)
T ss_pred eCCCCChHHhCCCCCCCEEEecCChHhHHHHHHHHHHHcCCCEEEEEeCCCcccHHHHHHHHHHHHHCCCEEEEeEEecc
Confidence 99999998887 46799999999999999999999987899999999999999999999999999999999998888774
Q ss_pred CC--ChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHcCCCCCCeEEEecCccccccccCCCCCCCccccceeeE
Q 003958 204 EA--TEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIATSWLSTALDTNSPFPSDVMDDIQGVL 281 (784)
Q Consensus 204 ~~--~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~~~~~~~~~~~~~~g~~ 281 (784)
.. ..+|+.......+.+++|+|++.....+....+... .++. .. .....|+.
T Consensus 168 ~~~~~~~d~s~~~~~~~~s~pDvv~~~~~~~~~~~~~~~~----------~~~~-----~~-----------~~g~~G~~ 221 (347)
T TIGR03863 168 SGDPRRTDQSEVPLFTQGADYDVVVVADEAGEFARYLPYA----------TWLP-----RP-----------VAGSAGLV 221 (347)
T ss_pred CCchhhhhcccCceeecCCCCCEEEEecchhhHhhhcccc----------cccc-----cc-----------cccccCcc
Confidence 31 123444322333448999999865443321111000 0000 00 01112222
Q ss_pred EEee-ecCCchhHHHHHHHHHhhccCCCCCCCCCCChhHHHHhhHHHHHHHHHHHHhhcCCccccccCCccccccCCccc
Q 003958 282 TLRT-YTPDSVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTVWLLARAINSFFKQGGNLSFSKDSRLSDIQGHLRL 360 (784)
Q Consensus 282 ~~~~-~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~~~a~Al~~~~~~~~~~~~~~~~~~~~~~g~~~~ 360 (784)
.... +..+.+..++|.++|+++|+ ..|+.+++.+||++++++.|++++.+
T Consensus 222 ~~~~~~~~~~~~~~~f~~~f~~~~g-------~~p~~~~a~aY~av~~~a~Ai~~AGs---------------------- 272 (347)
T TIGR03863 222 PTAWHRAWERWGATQLQSRFEKLAG-------RPMTELDYAAWLAVRAVGEAVTRTRS---------------------- 272 (347)
T ss_pred ccccCCcccchhHHHHHHHHHHHhC-------CCCChHHHHHHHHHHHHHHHHHHhcC----------------------
Confidence 1111 12234677899999999986 34567789999999999999999721
Q ss_pred ccccccCCchHHHHHHHhccc--cceee-eEEEec-CCCCcCCcEEEEEe
Q 003958 361 DSLRIFNGGNLLRDSILQANM--TGTAG-PARFNS-HGDLINPAYEIINV 406 (784)
Q Consensus 361 ~~~~~~~~~~~l~~~l~~~~f--~g~tG-~v~Fd~-~g~~~~~~~~I~~~ 406 (784)
.++..|.++|++.++ .+..| +++|++ +|+. .....+.+.
T Consensus 273 ------~d~~aV~~aL~~~~~~~~~~~g~~~~~R~~Dhq~-~~~~~~~~~ 315 (347)
T TIGR03863 273 ------ADPATLRDYLLSDEFELAGFKGRPLSFRPWDGQL-RQPVLLVHP 315 (347)
T ss_pred ------CCHHHHHHHHcCCCceecccCCCcceeeCCCccc-ccceEeccc
Confidence 158999999999887 46777 699996 7764 444445444
No 80
>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=99.95 E-value=6.3e-26 Score=237.85 Aligned_cols=280 Identities=26% Similarity=0.376 Sum_probs=232.8
Q ss_pred EEEEEeecC---CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhc-CceEEEccCchhh
Q 003958 33 NIGALLSFS---TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEG-QTVAIIGPQDAVT 108 (784)
Q Consensus 33 ~IG~i~~~~---~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~-~v~aiiGp~~s~~ 108 (784)
+||+++|++ +..|.....|+++|++++|+++|+ +|+++++++.|+++++..+.+.+.+++.+ +|.+|||+.++..
T Consensus 1 ~IG~i~p~~g~~~~~~~~~~~~~~~a~~~~n~~~g~-~g~~~~~~~~d~~~~~~~~~~~~~~l~~~~~v~~iig~~~~~~ 79 (299)
T cd04509 1 KIGVLFPLSGPYAEYGAFRLAGAQLAVEEINAKGGI-PGRKLELVIYDDQSDPARALAAARRLCQQEGVDALVGPVSSGV 79 (299)
T ss_pred CeeEEEcCCCcchhcCHHHHHHHHHHHHHHHhcCCC-CCcEEEEEEecCCCCHHHHHHHHHHHhcccCceEEEcCCCcHH
Confidence 599999998 456778899999999999999976 69999999999999999999999999998 9999999999988
Q ss_pred HHHHHHhhhcCCccEEecccCCCCCCc-CCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcCCCcchhHHHHHHH
Q 003958 109 SHVVSHVANELQVPLLSFSATDPTLSS-LQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDT 187 (784)
Q Consensus 109 ~~~va~~~~~~~ip~Is~~a~~~~l~~-~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~~ 187 (784)
+.+++.++...+||+|++.+.++.+.+ ..+|++|++.|+...++.++++++++++|+++++++.++.++....+.+++.
T Consensus 80 ~~~~~~~~~~~~iP~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~v~iv~~~~~~~~~~~~~~~~~ 159 (299)
T cd04509 80 ALAVAPVAEALKIPLISPGATAPGLTDKKGYPYLFRTGPSDEQQAEALADYIKEYNWKKVAILYDDDSYGRGLLEAFKAA 159 (299)
T ss_pred HHHHHHHHhhCCceEEeccCCCcccccccCCCCEEEecCCcHHHHHHHHHHHHHcCCcEEEEEecCchHHHHHHHHHHHH
Confidence 888999999999999999887776665 4689999999999999999999999999999999999988999999999999
Q ss_pred HhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHcCCCCCCeEEEecCccccccccCC
Q 003958 188 LAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIATSWLSTALDTNS 267 (784)
Q Consensus 188 l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~~~ 267 (784)
+++.|+++.....++ .+..++...++++++.++++|++++....+..+++++++.|+. .++.|++.+.+......
T Consensus 160 ~~~~g~~i~~~~~~~--~~~~~~~~~~~~l~~~~~~~v~~~~~~~~~~~~~~~~~~~g~~-~~~~~i~~~~~~~~~~~-- 234 (299)
T cd04509 160 FKKKGGTVVGEEYYP--LGTTDFTSLLQKLKAAKPDVIVLCGSGEDAATILKQAAEAGLT-GGYPILGITLGLSDVLL-- 234 (299)
T ss_pred HHHcCCEEEEEecCC--CCCccHHHHHHHHHhcCCCEEEEcccchHHHHHHHHHHHcCCC-CCCcEEecccccCHHHH--
Confidence 999999988766665 3346788999999888899999988889999999999999987 67889998765443221
Q ss_pred CCCCCccccceeeEEEeeecCCc--hhHHHHH---HHHHhhccCCCCCCCCCCChhHHHHhhHHHH
Q 003958 268 PFPSDVMDDIQGVLTLRTYTPDS--VLKRKFI---SRWRNLTDAKTPNGYIGLNAYGFYAYDTVWL 328 (784)
Q Consensus 268 ~~~~~~~~~~~g~~~~~~~~~~~--~~~~~f~---~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~~ 328 (784)
....+...|+++..+..+.. +..+.|. ..++..++ ..++.++..+||++++
T Consensus 235 ---~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~yda~~~ 290 (299)
T cd04509 235 ---EAGGEAAEGVLTGTPYFPGDPPPESFFFVRAAAREKKKYE-------DQPDYFAALAYDAVLL 290 (299)
T ss_pred ---HHhHHhhcCcEEeeccCCCCCChHHHHHHhHHHHHHHHhC-------CCCChhhhhhcceeee
Confidence 12235567888777665433 3333333 33343332 3567889999999988
No 81
>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=99.95 E-value=1.5e-25 Score=236.11 Aligned_cols=279 Identities=22% Similarity=0.289 Sum_probs=226.0
Q ss_pred EEEEEeecC---CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhc-CceEEEccCchhh
Q 003958 33 NIGALLSFS---TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEG-QTVAIIGPQDAVT 108 (784)
Q Consensus 33 ~IG~i~~~~---~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~-~v~aiiGp~~s~~ 108 (784)
+||+++|++ +..|.....|+++|+++||+ +|+ +|+++++.+.|+++++..+.+.+.+++++ +|.+|||+.++..
T Consensus 1 ~IG~~~~lsG~~~~~g~~~~~g~~~a~~~iN~-ggi-~g~~i~l~~~d~~~~~~~a~~~~~~li~~~~v~~vig~~~s~~ 78 (312)
T cd06333 1 KIGAILSLTGPAASLGIPEKKTLELLPDEINA-GGI-GGEKVELIVLDDGSDPTKAVTNARKLIEEDKVDAIIGPSTTPA 78 (312)
T ss_pred CeeEEeecCCcchhhCHHHHHHHHHHHHHHhc-CCc-CCeEEEEEEecCCCCHHHHHHHHHHHHhhCCeEEEECCCCCHH
Confidence 599999998 45678889999999999999 887 59999999999999999999999999986 9999999988887
Q ss_pred HHHHHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcCCCcchhHHHHHHHH
Q 003958 109 SHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTL 188 (784)
Q Consensus 109 ~~~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~~l 188 (784)
+.++.+.+...++|+|+++++++.+. ..++++||+.+++...+..+++++.+.||++|++++.++.+++...+.+++.+
T Consensus 79 ~~~~~~~~~~~~vP~v~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~l~~~g~~~vail~~~~~~~~~~~~~~~~~~ 157 (312)
T cd06333 79 TMAVAPVAEEAKTPMISLAPAAAIVE-PKRKWVFKTPQNDRLMAEAILADMKKRGVKTVAFIGFSDAYGESGLKELKALA 157 (312)
T ss_pred HHHHHHHHHhcCCCEEEccCCccccC-CCCCcEEEcCCCcHHHHHHHHHHHHHcCCCEEEEEecCcHHHHHHHHHHHHHH
Confidence 77888999999999999876554333 34689999999999999999999999999999999998889999999999999
Q ss_pred hccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHcCCCCCCeEEEecCccccccccCCC
Q 003958 189 AAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIATSWLSTALDTNSP 268 (784)
Q Consensus 189 ~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~~~~ 268 (784)
++.|+++.....++. ...++...+.+++..++++|++......+..+++++++.|+..+ +++++..... +..
T Consensus 158 ~~~G~~v~~~~~~~~--~~~d~~~~~~~l~~~~pdaIi~~~~~~~~~~~~~~l~~~g~~~p---~~~~~~~~~~-~~~-- 229 (312)
T cd06333 158 PKYGIEVVADERYGR--TDTSVTAQLLKIRAARPDAVLIWGSGTPAALPAKNLRERGYKGP---IYQTHGVASP-DFL-- 229 (312)
T ss_pred HHcCCEEEEEEeeCC--CCcCHHHHHHHHHhCCCCEEEEecCCcHHHHHHHHHHHcCCCCC---EEeecCcCcH-HHH--
Confidence 999999987666753 44578889999988889999998877778889999999998765 3433322211 110
Q ss_pred CCCCccccceeeEEEeee------cC----CchhHHHHHHHHHhhccCCCCCCCCCCChhHHHHhhHHHHHH
Q 003958 269 FPSDVMDDIQGVLTLRTY------TP----DSVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTVWLLA 330 (784)
Q Consensus 269 ~~~~~~~~~~g~~~~~~~------~~----~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~~~a 330 (784)
....+..+|++.+..+ .| ..+..++|.++|+++++. ..+..++..+|||+++++
T Consensus 230 --~~~g~~~~g~~~~~~~~~~~~~~p~~~~~~~~~~~f~~~~~~~~g~------~~~~~~~~~~Yda~~~~~ 293 (312)
T cd06333 230 --RLAGKAAEGAILPAGPVLVADQLPDSDPQKKVALDFVKAYEAKYGA------GSVSTFGGHAYDALLLLA 293 (312)
T ss_pred --HHhhHhhcCcEeecccceeeeeCCCCCcchHHHHHHHHHHHHHhCC------CCCCchhHHHHHHHHHHH
Confidence 1122455676554321 12 245789999999999862 126778999999999999
No 82
>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=99.95 E-value=1.9e-25 Score=238.63 Aligned_cols=308 Identities=14% Similarity=0.097 Sum_probs=246.8
Q ss_pred EEEEEeecC---CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhc-CceEEEccCchhh
Q 003958 33 NIGALLSFS---TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEG-QTVAIIGPQDAVT 108 (784)
Q Consensus 33 ~IG~i~~~~---~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~-~v~aiiGp~~s~~ 108 (784)
+||+++|++ +..|.....++++|++++|+.+|+ .|+++++++.|+++++..+.+.+.+++++ +|.+|||+.++..
T Consensus 1 ~IGv~~p~sG~~a~~g~~~~~g~~~a~~~~N~~Ggi-~G~~i~lv~~D~~~~~~~~~~~~~~li~~~~V~~iig~~~s~~ 79 (341)
T cd06341 1 KIGLLYPDTGVAAVSFPGARAGADAAAGYANAAGGI-AGRPIEYVWCDDQGDPASAAACARDLVEDDKVVAVVGGSSGAG 79 (341)
T ss_pred CeEEEecCCCchhhccHHHHHHHHHHHHHHHhcCCc-CCceEEEEEecCCCChhHHHHHHHHHHHhcCceEEEecccccc
Confidence 599999998 456889999999999999999998 58999999999999999999999999988 9999999998877
Q ss_pred HHHHHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcCC-CcchhHHHHHHH
Q 003958 109 SHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDDD-HGRNGIAALGDT 187 (784)
Q Consensus 109 ~~~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~~-~g~~~~~~l~~~ 187 (784)
..++ +.+...++|+|++.++++.+.. .|+.|++.+++..++.++++++.+.+.+++++++.++. ||+...+.+++.
T Consensus 80 ~~~~-~~~~~~~ip~v~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~l~~~g~~~~~~i~~~~~~~g~~~~~~~~~~ 156 (341)
T cd06341 80 GSAL-PYLAGAGIPVIGGAGTSAWELT--SPNSFPFSGGTPASLTTWGDFAKDQGGTRAVALVTALSAAVSAAAALLARS 156 (341)
T ss_pred hhHH-HHHhhcCCceecCCCCCchhhc--CCCeEEecCCCcchhHHHHHHHHHcCCcEEEEEEeCCcHHHHHHHHHHHHH
Confidence 6666 8889999999998776655543 57889999998889999999999989999999987765 999999999999
Q ss_pred HhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHcCCCCCCeEEEecC-ccccccccC
Q 003958 188 LAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIATS-WLSTALDTN 266 (784)
Q Consensus 188 l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~-~~~~~~~~~ 266 (784)
+++.|++++....++ .+..|+..+++++++.++|+|++......+..++++++++|+..+. +... .......
T Consensus 157 ~~~~G~~v~~~~~~~--~~~~d~~~~~~~i~~~~pdaV~~~~~~~~a~~~~~~~~~~G~~~~~---~~~~~~~~~~~~-- 229 (341)
T cd06341 157 LAAAGVSVAGIVVIT--ATAPDPTPQAQQAAAAGADAIITVLDAAVCASVLKAVRAAGLTPKV---VLSGTCYDPALL-- 229 (341)
T ss_pred HHHcCCccccccccC--CCCCCHHHHHHHHHhcCCCEEEEecChHHHHHHHHHHHHcCCCCCE---EEecCCCCHHHH--
Confidence 999999988766665 3457899999999999999999988888999999999999987652 2222 1111110
Q ss_pred CCCCCCccccceeeEEEeeecC---CchhHHHHHHHHHhhccCCCCCCCCCCChhHHHHhhHHHHHHHHHHHHhhcCCcc
Q 003958 267 SPFPSDVMDDIQGVLTLRTYTP---DSVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTVWLLARAINSFFKQGGNL 343 (784)
Q Consensus 267 ~~~~~~~~~~~~g~~~~~~~~~---~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~~~a~Al~~~~~~~~~~ 343 (784)
....+..+|++....+.| +.+..+.|.+.+++.... ....++.++..+||+++++++|++++.. .
T Consensus 230 ----~~~g~~~~g~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~----~~~~~~~~~~~~yda~~~~~~a~~~ag~---~- 297 (341)
T cd06341 230 ----AAPGPALAGVYIAVFYRPFESGTPAVALYLAAMARYAPQ----LDPPEQGFALIGYIAADLFLRGLSGAGG---C- 297 (341)
T ss_pred ----HhcCcccCceEEEeeeccccCCCHHHHHHHHHHHHhCCC----CCCCcchHHHHHHHHHHHHHHHHHhcCC---C-
Confidence 123356788877766554 467788888766654321 1124678899999999999999999621 0
Q ss_pred ccccCCccccccCCcccccccccCCchH-HHHHHHhccccceee
Q 003958 344 SFSKDSRLSDIQGHLRLDSLRIFNGGNL-LRDSILQANMTGTAG 386 (784)
Q Consensus 344 ~~~~~~~~~~~~g~~~~~~~~~~~~~~~-l~~~l~~~~f~g~tG 386 (784)
.+++. +.++|++++.....|
T Consensus 298 -----------------------~~~~~~v~~al~~~~~~~~~g 318 (341)
T cd06341 298 -----------------------PTRASQFLRALRAVTDYDAGG 318 (341)
T ss_pred -----------------------CChHHHHHHHhhcCCCCCCCC
Confidence 03566 999999998655545
No 83
>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=99.94 E-value=3.7e-24 Score=215.55 Aligned_cols=325 Identities=15% Similarity=0.182 Sum_probs=241.2
Q ss_pred hhhHHHHHHHHHHHHhcCCCCCCCCEEEE----------EEecCCC--CHHHHHHHHHHHHhc--CceEEEccCchhhHH
Q 003958 45 GKVAKLAIKAAVDDVNSDPTTLGGTKLKL----------QMQDCNH--SGFLALAEALHLMEG--QTVAIIGPQDAVTSH 110 (784)
Q Consensus 45 g~~~~~a~~~Ave~IN~~~~il~g~~l~~----------~~~D~~~--~~~~a~~~~~~li~~--~v~aiiGp~~s~~~~ 110 (784)
-+....|++.|++.+++.. ..+|.++.+ +..+..| +.=+++++..+|..+ .-.+++||.|..++.
T Consensus 17 ~~~v~~av~~a~~~~~~~~-~~~g~~f~~~a~~~~~~~~~y~~~~C~sstceg~~~l~~l~~~~~~gcv~lGP~CtYat~ 95 (380)
T cd06369 17 LKFVKEAVEEAIEIVAERL-AEAGLNVTVNANFEGFNTSLYRSRGCRSSTCEGVELLKKLSVTGRLGCVLLGPSCTYATF 95 (380)
T ss_pred HHHHHHHHHHHHHHHHhhh-hccCceEEEEEeeeccccceeccCCCCcccchHHHHHHHHHhcCccCcEEEcCccceehh
Confidence 4567889999999887754 335666666 5555544 344666677777765 688999999999999
Q ss_pred HHHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHH------HHcCCcEEEEEEEcCCCcchh---H
Q 003958 111 VVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIV------DHYGWREVIAIYVDDDHGRNG---I 181 (784)
Q Consensus 111 ~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l------~~~~w~~v~ii~~d~~~g~~~---~ 181 (784)
+++.....+++|+||.|+..... ...+++.|+.|+....+..++++. ++++|++.. ||.+++-.+.. +
T Consensus 96 ~~~~~~~~~~~P~ISaGsfglsc--d~k~~LTR~~pparK~~~~~~~f~~~~~~~~~~~W~~ay-vyk~~~~~edCf~~i 172 (380)
T cd06369 96 QMVDDEFNLSLPIISAGSFGLSC--DYKENLTRLLPPARKISDFFVDFWKEKNFPKKPKWETAY-VYKKQENTEDCFWYI 172 (380)
T ss_pred hhhhhhhcCCCceEeccccccCC--CchhhhhhcCchHHHHHHHHHHHHhcccccCCCCCceeE-EEcCCCCccceeeEh
Confidence 99999999999999976643322 234589999999999999999999 589998655 88776433322 4
Q ss_pred HHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHcCCCCCCeEEEecCcccc
Q 003958 182 AALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIATSWLST 261 (784)
Q Consensus 182 ~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~ 261 (784)
+++....+..+..+.+.+.. ...+++..+++.++ ..+||||+|+++++.+.++.+ ++...+|++|..+....
T Consensus 173 ~al~a~~~~f~~~~~~~~~l---~~~~~~~~il~~~~-~~sRIiImCG~p~~ir~lm~~----~~~~gDYVf~~IDlF~~ 244 (380)
T cd06369 173 NALEAGVAYFSSALKFKELL---RTEEELQKLLTDKN-RKSNVIIMCGTPEDIVNLKGD----RAVAEDIVIILIDLFND 244 (380)
T ss_pred Hhhhhhhhhhhhcccceeee---cCchhHHHHHHHhc-cCccEEEEeCCHHHHHHHHhc----CccCCCEEEEEEecccc
Confidence 55655555555445443433 24567888888876 679999999999999999986 33346899999986643
Q ss_pred ccccCCCCCCCccccceeeEEEeeecCCchhHHHHHHHHHhhccCCCCCCCCCCChhHHHHhhHHHHHHHHHHHHhhcCC
Q 003958 262 ALDTNSPFPSDVMDDIQGVLTLRTYTPDSVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTVWLLARAINSFFKQGG 341 (784)
Q Consensus 262 ~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~~~a~Al~~~~~~~~ 341 (784)
.... +....++++.++.+++..|+.+.+++. ..+. .... +.+++..||||.++|+||+++++.++
T Consensus 245 sy~~----d~~a~~amqsVLvIT~~~p~~~~~~~~-----~~fn-----~~l~-~~~aa~fyDaVLLYa~AL~EtL~~G~ 309 (380)
T cd06369 245 VYYE----NTTSPPYMRNVLVLTLPPRNSTNNSSF-----TTDN-----SLLK-DDYVAAYHDGVLLFGHVLKKFLESQE 309 (380)
T ss_pred hhcc----CcchHHHHhceEEEecCCCCCcccccC-----CCCC-----cchH-HHHHHHHHHHHHHHHHHHHHHHHhCC
Confidence 3211 123456788999998888766554331 1111 1111 27899999999999999999988765
Q ss_pred ccccccCCccccccCCcccccccccCCchHHHHHHHhccccceeeeEEEecCCCCcCCcEEEEEeec--cceEEEEEecC
Q 003958 342 NLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANMTGTAGPARFNSHGDLINPAYEIINVIG--TGYRRIGYWSN 419 (784)
Q Consensus 342 ~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~l~~~l~~~~f~g~tG~v~Fd~~g~~~~~~~~I~~~~~--~~~~~VG~w~~ 419 (784)
+. ++..+.++|+|.+|+|++|.|++|+|||| ...|.++.+.. +++.+||.|+.
T Consensus 310 ~~------------------------~~~~I~~~m~NrTF~GitG~V~IDeNGDR-d~dfsLl~ms~~tg~y~vV~~y~t 364 (380)
T cd06369 310 GV------------------------QTFSFINEFRNISFEGAGGPYTLDEYGDR-DVNFTLLYTSTDTSKYKVLFEFDT 364 (380)
T ss_pred CC------------------------CcHHHHHHHhCcceecCCCceEeCCCCCc-cCceEEEEeeCCCCCeEEEEEEEC
Confidence 32 24789999999999999999999999997 88899998863 77999999987
Q ss_pred CC
Q 003958 420 YS 421 (784)
Q Consensus 420 ~~ 421 (784)
.+
T Consensus 365 ~~ 366 (380)
T cd06369 365 ST 366 (380)
T ss_pred CC
Confidence 65
No 84
>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=99.93 E-value=1.1e-23 Score=220.73 Aligned_cols=280 Identities=26% Similarity=0.330 Sum_probs=232.5
Q ss_pred EEEEEeecC---CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEccCchhhH
Q 003958 33 NIGALLSFS---TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIGPQDAVTS 109 (784)
Q Consensus 33 ~IG~i~~~~---~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiGp~~s~~~ 109 (784)
+||+++|++ +..|.....|++.|++++|+.+|+ +|+++++.++|+++++..+.+.+.+++++++.+||||.++..+
T Consensus 1 ~ig~~~p~sg~~~~~~~~~~~g~~~a~~~~n~~gg~-~g~~v~~~~~d~~~~~~~~~~~~~~l~~~~v~~iig~~~~~~~ 79 (298)
T cd06268 1 KIGVLLPLSGPLAALGEPVRNGAELAVEEINAAGGI-LGRKIELVVEDTQGDPEAAAAAARELVDDGVDAVIGPLSSGVA 79 (298)
T ss_pred CeeeeecCcCchhhcChhHHHHHHHHHHHHHhcCCC-CCeEEEEEEecCCCCHHHHHHHHHHHHhCCceEEEcCCcchhH
Confidence 589999998 456788899999999999999987 5999999999999999999999999999999999999998888
Q ss_pred HHHHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcC-CcEEEEEEEcCCCcchhHHHHHHHH
Q 003958 110 HVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYG-WREVIAIYVDDDHGRNGIAALGDTL 188 (784)
Q Consensus 110 ~~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~-w~~v~ii~~d~~~g~~~~~~l~~~l 188 (784)
..+++.+...+||+|++.+.++.+.+..+|++|++.|++..++.++++++++.+ |++|++++.+++++....+.+++.+
T Consensus 80 ~~~~~~~~~~~ip~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~v~~~~~~~~~~~~~~~~~~ 159 (298)
T cd06268 80 LAAAPVAEEAGVPLISPGATSPALTGKGNPYVFRTAPSDAQQAAALADYLAEKGKVKKVAIIYDDYAYGRGLAAAFREAL 159 (298)
T ss_pred HhhHHHHHhCCCcEEccCCCCcccccCCCceEEEcccCcHHHHHHHHHHHHHhcCCCEEEEEEcCCchhHHHHHHHHHHH
Confidence 888999999999999988877665544579999999999999999999999888 9999999999889999999999999
Q ss_pred hccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHcCCCCCCeEEEecCccccccccCCC
Q 003958 189 AAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIATSWLSTALDTNSP 268 (784)
Q Consensus 189 ~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~~~~ 268 (784)
++.|+++.....++ ....++...+++++..++++|++.+.+..+..+++++++.|+. ..|++.+.+......
T Consensus 160 ~~~g~~i~~~~~~~--~~~~~~~~~~~~l~~~~~~~vi~~~~~~~~~~~~~~~~~~g~~---~~~~~~~~~~~~~~~--- 231 (298)
T cd06268 160 KKLGGEVVAEETYP--PGATDFSPLIAKLKAAGPDAVFLAGYGGDAALFLKQAREAGLK---VPIVGGDGAAAPALL--- 231 (298)
T ss_pred HHcCCEEEEEeccC--CCCccHHHHHHHHHhcCCCEEEEccccchHHHHHHHHHHcCCC---CcEEecCccCCHHHH---
Confidence 99999988776665 2346788999999988899999988888999999999999873 347777655432211
Q ss_pred CCCCccccceeeEEEeeecCC--chhHHHHH-HHHHhhccCCCCCCCCCCChhHHHHhhHHHHHH
Q 003958 269 FPSDVMDDIQGVLTLRTYTPD--SVLKRKFI-SRWRNLTDAKTPNGYIGLNAYGFYAYDTVWLLA 330 (784)
Q Consensus 269 ~~~~~~~~~~g~~~~~~~~~~--~~~~~~f~-~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~~~a 330 (784)
....+..+|+++..++.+. .+....|. +.|++.++ ..++.++..+||++.+++
T Consensus 232 --~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~y~~~~~~~ 287 (298)
T cd06268 232 --ELAGDAAEGVLGTTPYAPDDDDPAAAAFFQKAFKAKYG-------RPPDSYAAAAYDAVRLLA 287 (298)
T ss_pred --HhhhHhhCCcEEeccCCCCCCChhhhHHHHHHHHHHhC-------CCcccchHHHHHHHHHHc
Confidence 1123456777777665543 33445555 77777765 456788999999999998
No 85
>PRK10797 glutamate and aspartate transporter subunit; Provisional
Probab=99.73 E-value=9.6e-17 Score=166.36 Aligned_cols=195 Identities=17% Similarity=0.222 Sum_probs=157.6
Q ss_pred CccEEEEecCCCccceeEeeCCCcceeeeeHHHHHHHHH----HCCC-ccceEEeeCCCCCCCCChhHHHHHHHcCcccE
Q 003958 467 GRHLRIGVPNRVSFREFVSVKGSEMTSGFCIDVFTAAIN----LLPY-AVPYKLIPFGDGHNNPSCTELVRLITAGVYDA 541 (784)
Q Consensus 467 ~~~l~v~~~~~~~~~~~~~~~~~~~~~G~~~dl~~~l~~----~l~f-~~~~~~~~~~~~~~~~~~~g~i~~l~~~~~D~ 541 (784)
.+.|+|++.. .++||.+.+.++...||++||++.+++ ++|. .++++++++ +|..++..|.+|++|+
T Consensus 39 ~g~L~Vg~~~--~~pP~~f~~~~g~~~G~didl~~~ia~~l~~~lg~~~~~~~~v~~-------~~~~~i~~L~~G~~Di 109 (302)
T PRK10797 39 NGVIVVGHRE--SSVPFSYYDNQQKVVGYSQDYSNAIVEAVKKKLNKPDLQVKLIPI-------TSQNRIPLLQNGTFDF 109 (302)
T ss_pred CCeEEEEEcC--CCCCcceECCCCCEeeecHHHHHHHHHHHHHhhCCCCceEEEEEc-------ChHhHHHHHHCCCccE
Confidence 3568888775 377777766677899999998777765 6653 345777775 4788999999999999
Q ss_pred EEeeEEeecCccccceeccccccccEEEEEeccCCccccccccccccHHHHHHHHHHHHHHHHHhhheecccCCCCCCCc
Q 003958 542 AVGDIAIITNRTKMADFTQPYIESGLVVVAPVRKLDSNAWAFLSPFTPMMWGVTAIFFLAVGAVVWILEHRLNDEFRGPP 621 (784)
Q Consensus 542 ~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~~~~~~~~~~~~~pf~~~~W~~i~~~~~~~~~~~~~~~~~~~~~~~~~~ 621 (784)
+++++++|++|.+.++||.||+..+..+++++.+
T Consensus 110 ~~~~~~~t~eR~~~~~fS~Py~~~~~~lv~r~~~---------------------------------------------- 143 (302)
T PRK10797 110 ECGSTTNNLERQKQAAFSDTIFVVGTRLLTKKGG---------------------------------------------- 143 (302)
T ss_pred EecCCccCcchhhcceecccEeeccEEEEEECCC----------------------------------------------
Confidence 9999999999999999999999999999997653
Q ss_pred cCCceeehhhhhhhhhcccccccccchhhHHHHHHHHHHHHHHhhccccceeeEeeccccCCCCChHhhhhCCCceEEee
Q 003958 622 KRQVVTIFWFSFSTMFFAHKEKTVSALGRLVLIIWLFVVLIINSSYTASLTSILTVQKLSSPIKGIDSLRSSNYPIGYQV 701 (784)
Q Consensus 622 ~~~~~~~~~~~~~~~~~~~~~~p~~~~~R~~~~~w~~~~lvl~~~Yta~L~s~l~~~~~~~~i~~~~dl~~~~~~i~~~~ 701 (784)
.|.+++||. |++||+..
T Consensus 144 -------------------------------------------------------------~i~sl~dL~--Gk~V~v~~ 160 (302)
T PRK10797 144 -------------------------------------------------------------DIKDFADLK--GKAVVVTS 160 (302)
T ss_pred -------------------------------------------------------------CCCChHHcC--CCEEEEeC
Confidence 478999998 88999999
Q ss_pred CchHHHHHHhhcc--cCccCceeCCCHHHHHHHHhcCCcCCCeeEEEechhhhHHHHcC--CC-CeEEeCCccccceEEE
Q 003958 702 NSFARNYLVDELN--IDESRLVPLNSPEEYAKALKDGPHKGGVAAVVDDRAYAELFLST--RC-EFSIVGQVFTKNGWGF 776 (784)
Q Consensus 702 ~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~l~~~~~~~~~~a~~~~~~~~~~~~~~--~c-~l~~~~~~~~~~~~~~ 776 (784)
|+..+.++++... .+..++..+.+.+++++.|.+ |++||++.|...+.+.+.+ .- .+.++++.+...+|++
T Consensus 161 gs~~~~~l~~~~~~~~~~~~i~~~~~~~~~l~~L~~----GrvDa~i~d~~~~~~~~~~~~~~~~l~i~~~~~~~~~~~~ 236 (302)
T PRK10797 161 GTTSEVLLNKLNEEQKMNMRIISAKDHGDSFRTLES----GRAVAFMMDDALLAGERAKAKKPDNWEIVGKPQSQEAYGC 236 (302)
T ss_pred CCcHHHHHHHHhhhcCCceEEEEeCCHHHHHHHHHc----CCceEEEccHHHHHHHHHcCCCCcceEECCccCCcCceeE
Confidence 9988888854322 123467788999999999999 8999999998887664433 22 4778888888889999
Q ss_pred EeeCCCC
Q 003958 777 VSIVSSF 783 (784)
Q Consensus 777 ~~~k~s~ 783 (784)
+++|+++
T Consensus 237 a~~k~~~ 243 (302)
T PRK10797 237 MLRKDDP 243 (302)
T ss_pred EEeCCCH
Confidence 9999864
No 86
>PRK11917 bifunctional adhesin/ABC transporter aspartate/glutamate-binding protein; Reviewed
Probab=99.73 E-value=1.6e-16 Score=161.44 Aligned_cols=194 Identities=17% Similarity=0.270 Sum_probs=156.5
Q ss_pred CCccEEEEecCCCccceeEee-CCCcceeeeeHHHHHHHHHHC-CCccceEEeeCCCCCCCCChhHHHHHHHcCcccEEE
Q 003958 466 NGRHLRIGVPNRVSFREFVSV-KGSEMTSGFCIDVFTAAINLL-PYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAV 543 (784)
Q Consensus 466 ~~~~l~v~~~~~~~~~~~~~~-~~~~~~~G~~~dl~~~l~~~l-~f~~~~~~~~~~~~~~~~~~~g~i~~l~~~~~D~~~ 543 (784)
..+.|+|++.. +++||.+. +.++.+.||++||++++++++ |..+++++... +|...+..|.+|++|+++
T Consensus 36 ~~g~l~vg~~~--~~pP~~~~~~~~g~~~G~~vdl~~~ia~~llg~~~~~~~~~~-------~~~~~~~~l~~g~~D~~~ 106 (259)
T PRK11917 36 SKGQLIVGVKN--DVPHYALLDQATGEIKGFEIDVAKLLAKSILGDDKKIKLVAV-------NAKTRGPLLDNGSVDAVI 106 (259)
T ss_pred hCCEEEEEECC--CCCCceeeeCCCCceeEeeHHHHHHHHHHhcCCCccEEEEEc-------ChhhHHHHHHCCCccEEE
Confidence 34678988875 47777774 346899999999999999995 86655666654 366677899999999999
Q ss_pred eeEEeecCccccceeccccccccEEEEEeccCCccccccccccccHHHHHHHHHHHHHHHHHhhheecccCCCCCCCccC
Q 003958 544 GDIAIITNRTKMADFTQPYIESGLVVVAPVRKLDSNAWAFLSPFTPMMWGVTAIFFLAVGAVVWILEHRLNDEFRGPPKR 623 (784)
Q Consensus 544 ~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~~~~~~~~~~~~~pf~~~~W~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 623 (784)
+++++|++|.+.++||.||+.++..+++++..
T Consensus 107 ~~~~~t~eR~~~~~fs~py~~~~~~lvv~~~~------------------------------------------------ 138 (259)
T PRK11917 107 ATFTITPERKRIYNFSEPYYQDAIGLLVLKEK------------------------------------------------ 138 (259)
T ss_pred ecccCChhhhheeeeccCceeeceEEEEECCC------------------------------------------------
Confidence 99999999999999999999999999998763
Q ss_pred CceeehhhhhhhhhcccccccccchhhHHHHHHHHHHHHHHhhccccceeeEeeccccCCCCChHhhhhCCCceEEeeCc
Q 003958 624 QVVTIFWFSFSTMFFAHKEKTVSALGRLVLIIWLFVVLIINSSYTASLTSILTVQKLSSPIKGIDSLRSSNYPIGYQVNS 703 (784)
Q Consensus 624 ~~~~~~~~~~~~~~~~~~~~p~~~~~R~~~~~w~~~~lvl~~~Yta~L~s~l~~~~~~~~i~~~~dl~~~~~~i~~~~~~ 703 (784)
++++++||. +++||+..|+
T Consensus 139 -----------------------------------------------------------~~~s~~dL~--g~~V~v~~gs 157 (259)
T PRK11917 139 -----------------------------------------------------------NYKSLADMK--GANIGVAQAA 157 (259)
T ss_pred -----------------------------------------------------------CCCCHHHhC--CCeEEEecCC
Confidence 578999998 8899999999
Q ss_pred hHHHHHHhhccc--CccCceeCCCHHHHHHHHhcCCcCCCeeEEEechhhhHHHHcCCCCeEEeCCccccceEEEEeeCC
Q 003958 704 FARNYLVDELNI--DESRLVPLNSPEEYAKALKDGPHKGGVAAVVDDRAYAELFLSTRCEFSIVGQVFTKNGWGFVSIVS 781 (784)
Q Consensus 704 ~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~l~~~~~~~~~~a~~~~~~~~~~~~~~~c~l~~~~~~~~~~~~~~~~~k~ 781 (784)
..+..+.+.... ...++..+++..+.+++|.+ |++||++.+...+.++.++. ..++++.+...+|+++++|+
T Consensus 158 ~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~l~~----GrvDa~~~d~~~~~~~~~~~--~~~~~~~~~~~~~~~a~~k~ 231 (259)
T PRK11917 158 TTKKAIGEAAKKIGIDVKFSEFPDYPSIKAALDA----KRVDAFSVDKSILLGYVDDK--SEILPDSFEPQSYGIVTKKD 231 (259)
T ss_pred cHHHHHHHhhHhcCCceeEEecCCHHHHHHHHHc----CCCcEEEecHHHHHHhhhcC--CeecCCcCCCCceEEEEeCC
Confidence 877766443221 12345668889999999999 89999999988776655543 45667778888999999998
Q ss_pred CC
Q 003958 782 SF 783 (784)
Q Consensus 782 s~ 783 (784)
++
T Consensus 232 ~~ 233 (259)
T PRK11917 232 DP 233 (259)
T ss_pred CH
Confidence 75
No 87
>PRK09495 glnH glutamine ABC transporter periplasmic protein; Reviewed
Probab=99.70 E-value=7.4e-16 Score=156.18 Aligned_cols=190 Identities=23% Similarity=0.358 Sum_probs=157.1
Q ss_pred CccEEEEecCCCccceeEeeCCCcceeeeeHHHHHHHHHHCCCccceEEeeCCCCCCCCChhHHHHHHHcCcccEEEeeE
Q 003958 467 GRHLRIGVPNRVSFREFVSVKGSEMTSGFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDI 546 (784)
Q Consensus 467 ~~~l~v~~~~~~~~~~~~~~~~~~~~~G~~~dl~~~l~~~l~f~~~~~~~~~~~~~~~~~~~g~i~~l~~~~~D~~~~~~ 546 (784)
.+.|+|++.. .++||.+. .++.+.|+.+|+++.+++++|.+ ++++.. .|.+++..+.+|++|++++++
T Consensus 24 ~~~l~v~~~~--~~~P~~~~-~~g~~~G~~vdl~~~ia~~lg~~--~~~~~~-------~~~~~~~~l~~G~vDi~~~~~ 91 (247)
T PRK09495 24 DKKLVVATDT--AFVPFEFK-QGDKYVGFDIDLWAAIAKELKLD--YTLKPM-------DFSGIIPALQTKNVDLALAGI 91 (247)
T ss_pred CCeEEEEeCC--CCCCeeec-CCCceEEEeHHHHHHHHHHhCCc--eEEEeC-------CHHHHHHHHhCCCcCEEEecC
Confidence 4678888653 36777664 35779999999999999999988 444433 499999999999999998889
Q ss_pred EeecCccccceeccccccccEEEEEeccCCccccccccccccHHHHHHHHHHHHHHHHHhhheecccCCCCCCCccCCce
Q 003958 547 AIITNRTKMADFTQPYIESGLVVVAPVRKLDSNAWAFLSPFTPMMWGVTAIFFLAVGAVVWILEHRLNDEFRGPPKRQVV 626 (784)
Q Consensus 547 ~~t~~r~~~~~fs~p~~~~~~~~~~~~~~~~~~~~~~~~pf~~~~W~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 626 (784)
+.|++|.+.++||.||+..++.+++++..
T Consensus 92 ~~t~~R~~~~~fs~p~~~~~~~~~~~~~~--------------------------------------------------- 120 (247)
T PRK09495 92 TITDERKKAIDFSDGYYKSGLLVMVKANN--------------------------------------------------- 120 (247)
T ss_pred ccCHHHHhhccccchheecceEEEEECCC---------------------------------------------------
Confidence 99999999999999999999999987652
Q ss_pred eehhhhhhhhhcccccccccchhhHHHHHHHHHHHHHHhhccccceeeEeeccccCCCCChHhhhhCCCceEEeeCchHH
Q 003958 627 TIFWFSFSTMFFAHKEKTVSALGRLVLIIWLFVVLIINSSYTASLTSILTVQKLSSPIKGIDSLRSSNYPIGYQVNSFAR 706 (784)
Q Consensus 627 ~~~~~~~~~~~~~~~~~p~~~~~R~~~~~w~~~~lvl~~~Yta~L~s~l~~~~~~~~i~~~~dl~~~~~~i~~~~~~~~~ 706 (784)
.++++++||. +++||+..|++..
T Consensus 121 -------------------------------------------------------~~~~~~~dL~--g~~I~v~~g~~~~ 143 (247)
T PRK09495 121 -------------------------------------------------------NDIKSVKDLD--GKVVAVKSGTGSV 143 (247)
T ss_pred -------------------------------------------------------CCCCChHHhC--CCEEEEecCchHH
Confidence 2579999998 8889999999888
Q ss_pred HHHHhhcccCccCceeCCCHHHHHHHHhcCCcCCCeeEEEechhhhHHHHcCCC--CeEEeCCccccceEEEEeeCCC
Q 003958 707 NYLVDELNIDESRLVPLNSPEEYAKALKDGPHKGGVAAVVDDRAYAELFLSTRC--EFSIVGQVFTKNGWGFVSIVSS 782 (784)
Q Consensus 707 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~a~~~~~~~~~~~~~~~c--~l~~~~~~~~~~~~~~~~~k~s 782 (784)
.++++ ..+...+..+.+.++++++|.+ |++|+++.+...+.|++++.. ++..++..+....++++++|++
T Consensus 144 ~~l~~--~~~~~~i~~~~~~~~~~~~L~~----grvDa~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~ 215 (247)
T PRK09495 144 DYAKA--NIKTKDLRQFPNIDNAYLELGT----GRADAVLHDTPNILYFIKTAGNGQFKAVGDSLEAQQYGIAFPKGS 215 (247)
T ss_pred HHHHh--cCCCCceEEcCCHHHHHHHHHc----CceeEEEeChHHHHHHHHhCCCCceEEecCcccccceEEEEcCcH
Confidence 88854 2344567778899999999999 899999999998888877642 4777777677778999999875
No 88
>PRK11260 cystine transporter subunit; Provisional
Probab=99.67 E-value=1.8e-15 Score=155.06 Aligned_cols=194 Identities=17% Similarity=0.280 Sum_probs=160.2
Q ss_pred CCccEEEEecCCCccceeEeeCCCcceeeeeHHHHHHHHHHCCCccceEEeeCCCCCCCCChhHHHHHHHcCcccEEEee
Q 003958 466 NGRHLRIGVPNRVSFREFVSVKGSEMTSGFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGD 545 (784)
Q Consensus 466 ~~~~l~v~~~~~~~~~~~~~~~~~~~~~G~~~dl~~~l~~~l~f~~~~~~~~~~~~~~~~~~~g~i~~l~~~~~D~~~~~ 545 (784)
..+.|+|++.. .++|+.+.+.++...|+.+|+++.+++++|.++++ +.. .|..++..+.+|++|+++++
T Consensus 39 ~~~~l~v~~~~--~~~P~~~~~~~g~~~G~~~dl~~~i~~~lg~~~e~--~~~-------~~~~~~~~l~~G~~D~~~~~ 107 (266)
T PRK11260 39 ERGTLLVGLEG--TYPPFSFQGEDGKLTGFEVEFAEALAKHLGVKASL--KPT-------KWDGMLASLDSKRIDVVINQ 107 (266)
T ss_pred cCCeEEEEeCC--CcCCceEECCCCCEEEehHHHHHHHHHHHCCeEEE--EeC-------CHHHHHHHHhcCCCCEEEec
Confidence 34678888754 36777776677889999999999999999988444 433 49999999999999999988
Q ss_pred EEeecCccccceeccccccccEEEEEeccCCccccccccccccHHHHHHHHHHHHHHHHHhhheecccCCCCCCCccCCc
Q 003958 546 IAIITNRTKMADFTQPYIESGLVVVAPVRKLDSNAWAFLSPFTPMMWGVTAIFFLAVGAVVWILEHRLNDEFRGPPKRQV 625 (784)
Q Consensus 546 ~~~t~~r~~~~~fs~p~~~~~~~~~~~~~~~~~~~~~~~~pf~~~~W~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 625 (784)
++.+++|.+.+.||.||+..+..+++++..
T Consensus 108 ~~~~~~r~~~~~fs~p~~~~~~~~~~~~~~-------------------------------------------------- 137 (266)
T PRK11260 108 VTISDERKKKYDFSTPYTVSGIQALVKKGN-------------------------------------------------- 137 (266)
T ss_pred cccCHHHHhccccCCceeecceEEEEEcCC--------------------------------------------------
Confidence 899999999999999999999999987653
Q ss_pred eeehhhhhhhhhcccccccccchhhHHHHHHHHHHHHHHhhccccceeeEeeccccCCCCChHhhhhCCCceEEeeCchH
Q 003958 626 VTIFWFSFSTMFFAHKEKTVSALGRLVLIIWLFVVLIINSSYTASLTSILTVQKLSSPIKGIDSLRSSNYPIGYQVNSFA 705 (784)
Q Consensus 626 ~~~~~~~~~~~~~~~~~~p~~~~~R~~~~~w~~~~lvl~~~Yta~L~s~l~~~~~~~~i~~~~dl~~~~~~i~~~~~~~~ 705 (784)
...+++++||. +.+||+..|+..
T Consensus 138 -------------------------------------------------------~~~~~~~~dL~--g~~Igv~~G~~~ 160 (266)
T PRK11260 138 -------------------------------------------------------EGTIKTAADLK--GKKVGVGLGTNY 160 (266)
T ss_pred -------------------------------------------------------cCCCCCHHHcC--CCEEEEecCCcH
Confidence 33678999997 888999999988
Q ss_pred HHHHHhhcccCccCceeCCCHHHHHHHHhcCCcCCCeeEEEechhhhHHHHcCCCC-eEEeCCccccceEEEEeeCCCC
Q 003958 706 RNYLVDELNIDESRLVPLNSPEEYAKALKDGPHKGGVAAVVDDRAYAELFLSTRCE-FSIVGQVFTKNGWGFVSIVSSF 783 (784)
Q Consensus 706 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~a~~~~~~~~~~~~~~~c~-l~~~~~~~~~~~~~~~~~k~s~ 783 (784)
..++++ ..+...+..+++..++++.|.+ |++|+++.+...+.+++++..+ +.+....+...+++++++|++|
T Consensus 161 ~~~l~~--~~~~~~i~~~~~~~~~l~~L~~----GrvD~~i~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~ 233 (266)
T PRK11260 161 EQWLRQ--NVQGVDVRTYDDDPTKYQDLRV----GRIDAILVDRLAALDLVKKTNDTLAVAGEAFSRQESGVALRKGNP 233 (266)
T ss_pred HHHHHH--hCCCCceEecCCHHHHHHHHHc----CCCCEEEechHHHHHHHHhCCCcceecCCccccCceEEEEeCCCH
Confidence 888843 3444567788999999999999 8999999999988888877554 5555666777889999999874
No 89
>PRK15007 putative ABC transporter arginine-biding protein; Provisional
Probab=99.65 E-value=4.1e-15 Score=150.58 Aligned_cols=190 Identities=20% Similarity=0.325 Sum_probs=152.1
Q ss_pred CccEEEEecCCCccceeEeeCCCcceeeeeHHHHHHHHHHCCCccceEEeeCCCCCCCCChhHHHHHHHcCcccEEEeeE
Q 003958 467 GRHLRIGVPNRVSFREFVSVKGSEMTSGFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDI 546 (784)
Q Consensus 467 ~~~l~v~~~~~~~~~~~~~~~~~~~~~G~~~dl~~~l~~~l~f~~~~~~~~~~~~~~~~~~~g~i~~l~~~~~D~~~~~~ 546 (784)
...|+|++.. .++||.+.+.++.+.|+++|+++.+++++|.+++| +. ..|..++..+.+|++|++++++
T Consensus 20 ~~~l~v~~~~--~~~P~~~~~~~g~~~G~~~dl~~~i~~~lg~~~~~--~~-------~~~~~~~~~l~~g~~D~~~~~~ 88 (243)
T PRK15007 20 AETIRFATEA--SYPPFESIDANNQIVGFDVDLAQALCKEIDATCTF--SN-------QAFDSLIPSLKFRRVEAVMAGM 88 (243)
T ss_pred CCcEEEEeCC--CCCCceeeCCCCCEEeeeHHHHHHHHHHhCCcEEE--Ee-------CCHHHHhHHHhCCCcCEEEEcC
Confidence 4678888763 36777765667889999999999999999998554 33 2599999999999999998888
Q ss_pred EeecCccccceeccccccccEEEEEeccCCccccccccccccHHHHHHHHHHHHHHHHHhhheecccCCCCCCCccCCce
Q 003958 547 AIITNRTKMADFTQPYIESGLVVVAPVRKLDSNAWAFLSPFTPMMWGVTAIFFLAVGAVVWILEHRLNDEFRGPPKRQVV 626 (784)
Q Consensus 547 ~~t~~r~~~~~fs~p~~~~~~~~~~~~~~~~~~~~~~~~pf~~~~W~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 626 (784)
+.+++|.+.++||.||+..+..++.+..
T Consensus 89 ~~~~~r~~~~~fs~p~~~~~~~~v~~~~---------------------------------------------------- 116 (243)
T PRK15007 89 DITPEREKQVLFTTPYYDNSALFVGQQG---------------------------------------------------- 116 (243)
T ss_pred ccCHHHhcccceecCccccceEEEEeCC----------------------------------------------------
Confidence 9999999999999999998877665432
Q ss_pred eehhhhhhhhhcccccccccchhhHHHHHHHHHHHHHHhhccccceeeEeeccccCCCCChHhhhhCCCceEEeeCchHH
Q 003958 627 TIFWFSFSTMFFAHKEKTVSALGRLVLIIWLFVVLIINSSYTASLTSILTVQKLSSPIKGIDSLRSSNYPIGYQVNSFAR 706 (784)
Q Consensus 627 ~~~~~~~~~~~~~~~~~p~~~~~R~~~~~w~~~~lvl~~~Yta~L~s~l~~~~~~~~i~~~~dl~~~~~~i~~~~~~~~~ 706 (784)
.+++++||. +.+||+..|+...
T Consensus 117 --------------------------------------------------------~~~~~~dL~--g~~Igv~~g~~~~ 138 (243)
T PRK15007 117 --------------------------------------------------------KYTSVDQLK--GKKVGVQNGTTHQ 138 (243)
T ss_pred --------------------------------------------------------CCCCHHHhC--CCeEEEecCcHHH
Confidence 367889997 8889999999888
Q ss_pred HHHHhhcccCccCceeCCCHHHHHHHHhcCCcCCCeeEEEechhhhHHHHcCCCCeEEeCCcc-----ccceEEEEeeCC
Q 003958 707 NYLVDELNIDESRLVPLNSPEEYAKALKDGPHKGGVAAVVDDRAYAELFLSTRCEFSIVGQVF-----TKNGWGFVSIVS 781 (784)
Q Consensus 707 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~a~~~~~~~~~~~~~~~c~l~~~~~~~-----~~~~~~~~~~k~ 781 (784)
+++++. .+...++.+.+.+++++.|.+ |++|+++.+...+.++++++.++..++..+ ...+.+++++++
T Consensus 139 ~~l~~~--~~~~~~~~~~~~~~~~~~L~~----grvDa~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 212 (243)
T PRK15007 139 KFIMDK--HPEITTVPYDSYQNAKLDLQN----GRIDAVFGDTAVVTEWLKDNPKLAAVGDKVTDKDYFGTGLGIAVRQG 212 (243)
T ss_pred HHHHHh--CCCCeEEEcCCHHHHHHHHHc----CCCCEEEeCHHHHHHHHhcCCCceeecCcccccccCCcceEEEEeCC
Confidence 888542 334456778899999999999 899999999999988887776665554322 233578999887
Q ss_pred CC
Q 003958 782 SF 783 (784)
Q Consensus 782 s~ 783 (784)
+|
T Consensus 213 ~~ 214 (243)
T PRK15007 213 NT 214 (243)
T ss_pred CH
Confidence 53
No 90
>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=99.62 E-value=4e-17 Score=151.20 Aligned_cols=107 Identities=32% Similarity=0.563 Sum_probs=83.8
Q ss_pred cHHHHHHHHHHHHHHHHHhhheecccCCCCCC-------CccCCceeehhhhhhhhhccccc-ccccchhhHHHHHHHHH
Q 003958 588 TPMMWGVTAIFFLAVGAVVWILEHRLNDEFRG-------PPKRQVVTIFWFSFSTMFFAHKE-KTVSALGRLVLIIWLFV 659 (784)
Q Consensus 588 ~~~~W~~i~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~~~~~~~~~~~~~~-~p~~~~~R~~~~~w~~~ 659 (784)
+++||++++++++++++++|++++..+.+++. +...++.+++|++++.+++|+.. .|++.++|++.++|++|
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 58999999999999999999999988776665 22345889999999999988755 89999999999999999
Q ss_pred HHHHHhhccccceeeEeeccccCCCCChHhhhhCC
Q 003958 660 VLIINSSYTASLTSILTVQKLSSPIKGIDSLRSSN 694 (784)
Q Consensus 660 ~lvl~~~Yta~L~s~l~~~~~~~~i~~~~dl~~~~ 694 (784)
+++++++|||+|+|+|+.++.+.+|+|++||.+++
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 99999999999999999999999999999999877
No 91
>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=99.62 E-value=3e-15 Score=149.64 Aligned_cols=193 Identities=24% Similarity=0.370 Sum_probs=153.8
Q ss_pred EEEEecCCCccceeEeeCCCcceeeeeHHHHHHHHHHCCCccceEEeeCCCCCCCCChhHHHHHHHcCcccEEEeeEEee
Q 003958 470 LRIGVPNRVSFREFVSVKGSEMTSGFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAII 549 (784)
Q Consensus 470 l~v~~~~~~~~~~~~~~~~~~~~~G~~~dl~~~l~~~l~f~~~~~~~~~~~~~~~~~~~g~i~~l~~~~~D~~~~~~~~t 549 (784)
|+|++.. .++||.+.+.++...|+.+|+++++++++|+++++... .|..++..|.+|++|+++++++.+
T Consensus 1 l~V~~~~--~~~P~~~~~~~~~~~G~~~dl~~~i~~~~g~~~~~~~~---------~~~~~~~~l~~g~~D~~~~~~~~~ 69 (225)
T PF00497_consen 1 LRVGVDE--DYPPFSYIDEDGEPSGIDVDLLRAIAKRLGIKIEFVPM---------PWSRLLEMLENGKADIIIGGLSIT 69 (225)
T ss_dssp EEEEEES--EBTTTBEEETTSEEESHHHHHHHHHHHHHTCEEEEEEE---------EGGGHHHHHHTTSSSEEESSEB-B
T ss_pred CEEEEcC--CCCCeEEECCCCCEEEEhHHHHHHHHhhcccccceeec---------cccccccccccccccccccccccc
Confidence 5777744 36677776778999999999999999999999555442 499999999999999999999999
Q ss_pred cCccccceeccccccccEEEEEeccCCccccccccccccHHHHHHHHHHHHHHHHHhhheecccCCCCCCCccCCceeeh
Q 003958 550 TNRTKMADFTQPYIESGLVVVAPVRKLDSNAWAFLSPFTPMMWGVTAIFFLAVGAVVWILEHRLNDEFRGPPKRQVVTIF 629 (784)
Q Consensus 550 ~~r~~~~~fs~p~~~~~~~~~~~~~~~~~~~~~~~~pf~~~~W~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 629 (784)
++|.+.++||.||+....++++++..
T Consensus 70 ~~r~~~~~~s~p~~~~~~~~~~~~~~------------------------------------------------------ 95 (225)
T PF00497_consen 70 PERAKKFDFSDPYYSSPYVLVVRKGD------------------------------------------------------ 95 (225)
T ss_dssp HHHHTTEEEESESEEEEEEEEEETTS------------------------------------------------------
T ss_pred ccccccccccccccchhheeeecccc------------------------------------------------------
Confidence 99999999999999999999998642
Q ss_pred hhhhhhhhcccccccccchhhHHHHHHHHHHHHHHhhccccceeeEeeccccCCCCChHhhhhCCCceEEeeCchHHHHH
Q 003958 630 WFSFSTMFFAHKEKTVSALGRLVLIIWLFVVLIINSSYTASLTSILTVQKLSSPIKGIDSLRSSNYPIGYQVNSFARNYL 709 (784)
Q Consensus 630 ~~~~~~~~~~~~~~p~~~~~R~~~~~w~~~~lvl~~~Yta~L~s~l~~~~~~~~i~~~~dl~~~~~~i~~~~~~~~~~~~ 709 (784)
++....+++++||. +.+||+..|+....++
T Consensus 96 ------------------------------------------------~~~~~~~~~~~dl~--~~~i~~~~g~~~~~~l 125 (225)
T PF00497_consen 96 ------------------------------------------------APPIKTIKSLDDLK--GKRIGVVRGSSYADYL 125 (225)
T ss_dssp ------------------------------------------------TCSTSSHSSGGGGT--TSEEEEETTSHHHHHH
T ss_pred ------------------------------------------------ccccccccchhhhc--CcccccccchhHHHHh
Confidence 00123567788996 7789999999888888
Q ss_pred HhhcccCccCceeCCCHHHHHHHHhcCCcCCCeeEEEechhhhHHHHcCCCC--eEEeCCccccceEEEEeeCCC
Q 003958 710 VDELNIDESRLVPLNSPEEYAKALKDGPHKGGVAAVVDDRAYAELFLSTRCE--FSIVGQVFTKNGWGFVSIVSS 782 (784)
Q Consensus 710 ~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~a~~~~~~~~~~~~~~~c~--l~~~~~~~~~~~~~~~~~k~s 782 (784)
++.... ..+++.+.+.+++++.|++ |++++++.+...+.|++++... ............++++++++.
T Consensus 126 ~~~~~~-~~~~~~~~~~~~~~~~l~~----g~~d~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 195 (225)
T PF00497_consen 126 KQQYPS-NINIVEVDSPEEALEALLS----GRIDAFIVDESTAEYLLKRHPLENIVVIPPPISPSPVYFAVRKKN 195 (225)
T ss_dssp HHHTHH-TSEEEEESSHHHHHHHHHT----TSSSEEEEEHHHHHHHHHHTTTCEEEEEEEEEEEEEEEEEEETTT
T ss_pred hhhccc-hhhhcccccHHHHHHHHhc----CCeeeeeccchhhhhhhhhcccccccccccccccceeEEeecccc
Confidence 543211 3466778999999999999 8999999999999999887542 323245566667788887754
No 92
>PRK15010 ABC transporter lysine/arginine/ornithine binding periplasmic protein; Provisional
Probab=99.61 E-value=2.7e-14 Score=145.79 Aligned_cols=195 Identities=18% Similarity=0.226 Sum_probs=148.7
Q ss_pred CCccEEEEecCCCccceeEeeCCCcceeeeeHHHHHHHHHHCCCccceEEeeCCCCCCCCChhHHHHHHHcCcccEEEee
Q 003958 466 NGRHLRIGVPNRVSFREFVSVKGSEMTSGFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGD 545 (784)
Q Consensus 466 ~~~~l~v~~~~~~~~~~~~~~~~~~~~~G~~~dl~~~l~~~l~f~~~~~~~~~~~~~~~~~~~g~i~~l~~~~~D~~~~~ 545 (784)
..++|+|++.. .++||.+.+.++.+.|+.+|+++++++++|.+++ ++.. .|..++..+..|++|+++++
T Consensus 24 ~~~~l~v~~~~--~~pPf~~~~~~g~~~G~~vdl~~~ia~~lg~~~~--~~~~-------~~~~~~~~l~~g~~Di~~~~ 92 (260)
T PRK15010 24 LPETVRIGTDT--TYAPFSSKDAKGDFVGFDIDLGNEMCKRMQVKCT--WVAS-------DFDALIPSLKAKKIDAIISS 92 (260)
T ss_pred cCCeEEEEecC--CcCCceeECCCCCEEeeeHHHHHHHHHHhCCceE--EEeC-------CHHHHHHHHHCCCCCEEEec
Confidence 34678887753 3677777656789999999999999999998844 4433 59999999999999999999
Q ss_pred EEeecCccccceeccccccccEEEEEeccCCccccccccccccHHHHHHHHHHHHHHHHHhhheecccCCCCCCCccCCc
Q 003958 546 IAIITNRTKMADFTQPYIESGLVVVAPVRKLDSNAWAFLSPFTPMMWGVTAIFFLAVGAVVWILEHRLNDEFRGPPKRQV 625 (784)
Q Consensus 546 ~~~t~~r~~~~~fs~p~~~~~~~~~~~~~~~~~~~~~~~~pf~~~~W~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 625 (784)
+..|++|.+.++||.||+....++++++..
T Consensus 93 ~~~t~eR~~~~~fs~p~~~~~~~~~~~~~~-------------------------------------------------- 122 (260)
T PRK15010 93 LSITDKRQQEIAFSDKLYAADSRLIAAKGS-------------------------------------------------- 122 (260)
T ss_pred CcCCHHHHhhcccccceEeccEEEEEECCC--------------------------------------------------
Confidence 999999999999999999999999987763
Q ss_pred eeehhhhhhhhhcccccccccchhhHHHHHHHHHHHHHHhhccccceeeEeeccccCCCCChHhhhhCCCceEEeeCchH
Q 003958 626 VTIFWFSFSTMFFAHKEKTVSALGRLVLIIWLFVVLIINSSYTASLTSILTVQKLSSPIKGIDSLRSSNYPIGYQVNSFA 705 (784)
Q Consensus 626 ~~~~~~~~~~~~~~~~~~p~~~~~R~~~~~w~~~~lvl~~~Yta~L~s~l~~~~~~~~i~~~~dl~~~~~~i~~~~~~~~ 705 (784)
+...+++||. +.+||+.+|+..
T Consensus 123 --------------------------------------------------------~~~~~~~dl~--g~~Igv~~gs~~ 144 (260)
T PRK15010 123 --------------------------------------------------------PIQPTLDSLK--GKHVGVLQGSTQ 144 (260)
T ss_pred --------------------------------------------------------CCCCChhHcC--CCEEEEecCchH
Confidence 1123688897 888999999987
Q ss_pred HHHHHhhcccCccCceeCCCHHHHHHHHhcCCcCCCeeEEEechhhhHH-HHcC-CC-CeEEeCCcc-----ccceEEEE
Q 003958 706 RNYLVDELNIDESRLVPLNSPEEYAKALKDGPHKGGVAAVVDDRAYAEL-FLST-RC-EFSIVGQVF-----TKNGWGFV 777 (784)
Q Consensus 706 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~a~~~~~~~~~~-~~~~-~c-~l~~~~~~~-----~~~~~~~~ 777 (784)
..++.+........+..+.+.+++++.|.+ |++|+++.+...+.+ +.++ .. ++..++..+ ...+++++
T Consensus 145 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~----griDa~i~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a 220 (260)
T PRK15010 145 EAYANETWRSKGVDVVAYANQDLVYSDLAA----GRLDAALQDEVAASEGFLKQPAGKDFAFAGPSVKDKKYFGDGTGVG 220 (260)
T ss_pred HHHHHHhcccCCceEEecCCHHHHHHHHHc----CCccEEEeCcHHHHHHHHhCCCCCceEEecCccccccccCCceEEE
Confidence 777754322222355667888999999999 899999999887764 3333 22 354444322 22346799
Q ss_pred eeCCCC
Q 003958 778 SIVSSF 783 (784)
Q Consensus 778 ~~k~s~ 783 (784)
++++.+
T Consensus 221 ~~~~~~ 226 (260)
T PRK15010 221 LRKDDA 226 (260)
T ss_pred EeCCCH
Confidence 998753
No 93
>cd01391 Periplasmic_Binding_Protein_Type_1 Type 1 periplasmic binding fold superfamily. Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins con
Probab=99.60 E-value=1.9e-13 Score=140.24 Aligned_cols=216 Identities=23% Similarity=0.339 Sum_probs=174.9
Q ss_pred EEEEEeecC--CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEccCchhhHH
Q 003958 33 NIGALLSFS--TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIGPQDAVTSH 110 (784)
Q Consensus 33 ~IG~i~~~~--~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiGp~~s~~~~ 110 (784)
+||+++|.+ ..++.....+++.+++++ |..+++.+.|+++++....+.+.+++.+++.+|+|+.++....
T Consensus 1 ~Ig~i~~~~~~~~~~~~~~~~~~~~~~~~--------g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~ii~~~~~~~~~ 72 (269)
T cd01391 1 KIGVLLPLSGSAPFGAQLLAGIELAAEEI--------GRGLEVILADSQSDPERALEALRDLIQQGVDGIIGPPSSSSAL 72 (269)
T ss_pred CceEEeecCCCcHHHHHHHHHHHHHHHHh--------CCceEEEEecCCCCHHHHHHHHHHHHHcCCCEEEecCCCHHHH
Confidence 589999987 455667778888888886 4568888999999998888888899888999999998887766
Q ss_pred HHHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcC-CCcchhHHHHHHHHh
Q 003958 111 VVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDD-DHGRNGIAALGDTLA 189 (784)
Q Consensus 111 ~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~-~~g~~~~~~l~~~l~ 189 (784)
.+...+...++|+|++....+... .+++++++.++....+.++++++.+.+|+++++++.+. ..+....+.+++.++
T Consensus 73 ~~~~~~~~~~ip~v~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~i~~i~~~~~~~~~~~~~~~~~~~~ 150 (269)
T cd01391 73 AVVELAAAAGIPVVSLDATAPDLT--GYPYVFRVGPDNEQAGEAAAEYLAEKGWKRVALIYGDDGAYGRERLEGFKAALK 150 (269)
T ss_pred HHHHHHHHcCCcEEEecCCCCccC--CCceEEEEcCCcHHHHHHHHHHHHHhCCceEEEEecCCcchhhHHHHHHHHHHH
Confidence 678888999999999877655443 56889999999999999999999999999999999877 677788899999999
Q ss_pred ccCcEEEEeeccCCCCChhHHHHHHHHhhcC-CceEEEEeccCCcHHHHHHHHHHcCCCCCCeEEEecCccc
Q 003958 190 AKRCRISFKAPLSVEATEDEITDLLVKVALT-ESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIATSWLS 260 (784)
Q Consensus 190 ~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~-~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~ 260 (784)
+.|+++......+.. ...++....+.+++. ++++|++.+. ..+..+++++.+.|+.+.++.|++.+.+.
T Consensus 151 ~~~~~~~~~~~~~~~-~~~~~~~~~~~l~~~~~~~~i~~~~~-~~a~~~~~~~~~~g~~~~~~~ii~~~~~~ 220 (269)
T cd01391 151 KAGIEVVAIEYGDLD-TEKGFQALLQLLKAAPKPDAIFACND-EMAAGALKAAREAGLTPGDISIIGFDGSP 220 (269)
T ss_pred hcCcEEEeccccCCC-ccccHHHHHHHHhcCCCCCEEEEcCc-hHHHHHHHHHHHcCCCCCCCEEEeccccc
Confidence 988776654444321 225677777777776 7888888776 88899999999999874556677666543
No 94
>TIGR01096 3A0103s03R lysine-arginine-ornithine-binding periplasmic protein.
Probab=99.59 E-value=4.4e-14 Score=143.70 Aligned_cols=192 Identities=23% Similarity=0.318 Sum_probs=155.3
Q ss_pred ccEEEEecCCCccceeEeeCCCcceeeeeHHHHHHHHHHCCCccceEEeeCCCCCCCCChhHHHHHHHcCcccEEEeeEE
Q 003958 468 RHLRIGVPNRVSFREFVSVKGSEMTSGFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIA 547 (784)
Q Consensus 468 ~~l~v~~~~~~~~~~~~~~~~~~~~~G~~~dl~~~l~~~l~f~~~~~~~~~~~~~~~~~~~g~i~~l~~~~~D~~~~~~~ 547 (784)
+.|+|++.. .++||.+.+.+++..|+++|+++.+++.+|.+ +++++. .|..++..+.+|++|++++++.
T Consensus 24 ~~l~v~~~~--~~~P~~~~~~~g~~~G~~~dl~~~i~~~lg~~--~~~~~~-------~~~~~~~~l~~G~~D~~~~~~~ 92 (250)
T TIGR01096 24 GSVRIGTET--GYPPFESKDANGKLVGFDVDLAKALCKRMKAK--CKFVEQ-------NFDGLIPSLKAKKVDAIMATMS 92 (250)
T ss_pred CeEEEEECC--CCCCceEECCCCCEEeehHHHHHHHHHHhCCe--EEEEeC-------CHHHHHHHHhCCCcCEEEecCc
Confidence 678888753 46677776667899999999999999999988 555443 5999999999999999988888
Q ss_pred eecCccccceeccccccccEEEEEeccCCccccccccccccHHHHHHHHHHHHHHHHHhhheecccCCCCCCCccCCcee
Q 003958 548 IITNRTKMADFTQPYIESGLVVVAPVRKLDSNAWAFLSPFTPMMWGVTAIFFLAVGAVVWILEHRLNDEFRGPPKRQVVT 627 (784)
Q Consensus 548 ~t~~r~~~~~fs~p~~~~~~~~~~~~~~~~~~~~~~~~pf~~~~W~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 627 (784)
.+++|.+.+.||.|++..+..++++..+
T Consensus 93 ~~~~r~~~~~~s~p~~~~~~~~~~~~~~---------------------------------------------------- 120 (250)
T TIGR01096 93 ITPKRQKQIDFSDPYYATGQGFVVKKGS---------------------------------------------------- 120 (250)
T ss_pred cCHHHhhccccccchhcCCeEEEEECCC----------------------------------------------------
Confidence 9999999999999999999999987653
Q ss_pred ehhhhhhhhhcccccccccchhhHHHHHHHHHHHHHHhhccccceeeEeeccccCCCCChHhhhhCCCceEEeeCchHHH
Q 003958 628 IFWFSFSTMFFAHKEKTVSALGRLVLIIWLFVVLIINSSYTASLTSILTVQKLSSPIKGIDSLRSSNYPIGYQVNSFARN 707 (784)
Q Consensus 628 ~~~~~~~~~~~~~~~~p~~~~~R~~~~~w~~~~lvl~~~Yta~L~s~l~~~~~~~~i~~~~dl~~~~~~i~~~~~~~~~~ 707 (784)
+.+.+++||. +.+||+..|+....
T Consensus 121 ------------------------------------------------------~~~~~~~dl~--g~~i~~~~g~~~~~ 144 (250)
T TIGR01096 121 ------------------------------------------------------DLAKTLEDLD--GKTVGVQSGTTHEQ 144 (250)
T ss_pred ------------------------------------------------------CcCCChHHcC--CCEEEEecCchHHH
Confidence 1246788997 88899999998888
Q ss_pred HHHhhcccCccCceeCCCHHHHHHHHhcCCcCCCeeEEEechhhhHHHHcCCC---CeEEeCCcccc-----ceEEEEee
Q 003958 708 YLVDELNIDESRLVPLNSPEEYAKALKDGPHKGGVAAVVDDRAYAELFLSTRC---EFSIVGQVFTK-----NGWGFVSI 779 (784)
Q Consensus 708 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~a~~~~~~~~~~~~~~~c---~l~~~~~~~~~-----~~~~~~~~ 779 (784)
++.+.... ..++..+.+.++++++|.+ |++|+++.+...+.+++++.. ++..+...+.. ..++++++
T Consensus 145 ~l~~~~~~-~~~~~~~~s~~~~~~~L~~----g~vD~~v~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~ 219 (250)
T TIGR01096 145 YLKDYFKP-GVDIVEYDSYDNANMDLKA----GRIDAVFTDASVLAEGFLKPPNGKDFKFVGPSVTDEKYFGDGYGIGLR 219 (250)
T ss_pred HHHHhccC-CcEEEEcCCHHHHHHHHHc----CCCCEEEeCHHHHHHHHHhCCCCCceEEeccccccccccCCceEEEEe
Confidence 88543321 3456778999999999999 899999999999999887643 37666654433 24789999
Q ss_pred CCCC
Q 003958 780 VSSF 783 (784)
Q Consensus 780 k~s~ 783 (784)
++++
T Consensus 220 ~~~~ 223 (250)
T TIGR01096 220 KGDT 223 (250)
T ss_pred CCCH
Confidence 8764
No 95
>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=99.59 E-value=2.9e-14 Score=146.76 Aligned_cols=196 Identities=17% Similarity=0.154 Sum_probs=152.8
Q ss_pred CCccEEEEecCCCccceeEeeCCCcceeeeeHHHHHHHHHHCCCc-cceEEeeCCCCCCCCChhHHHHHHHcCcccEEEe
Q 003958 466 NGRHLRIGVPNRVSFREFVSVKGSEMTSGFCIDVFTAAINLLPYA-VPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVG 544 (784)
Q Consensus 466 ~~~~l~v~~~~~~~~~~~~~~~~~~~~~G~~~dl~~~l~~~l~f~-~~~~~~~~~~~~~~~~~~g~i~~l~~~~~D~~~~ 544 (784)
..+.|+|++.. ++||.+.+.++...|+.+|+++++++++|.+ +++.. -.|+.++..+.+|++|+.++
T Consensus 31 ~~~~l~v~~~~---~pP~~~~~~~g~~~G~~~dl~~~i~~~lg~~~~~~~~---------~~w~~~~~~l~~G~~Di~~~ 98 (275)
T TIGR02995 31 EQGFARIAIAN---EPPFTYVGADGKVSGAAPDVARAIFKRLGIADVNASI---------TEYGALIPGLQAGRFDAIAA 98 (275)
T ss_pred hCCcEEEEccC---CCCceeECCCCceecchHHHHHHHHHHhCCCceeecc---------CCHHHHHHHHHCCCcCEEee
Confidence 34678888764 5666765667889999999999999999975 33332 35999999999999999988
Q ss_pred eEEeecCccccceeccccccccEEEEEeccCCccccccccccccHHHHHHHHHHHHHHHHHhhheecccCCCCCCCccCC
Q 003958 545 DIAIITNRTKMADFTQPYIESGLVVVAPVRKLDSNAWAFLSPFTPMMWGVTAIFFLAVGAVVWILEHRLNDEFRGPPKRQ 624 (784)
Q Consensus 545 ~~~~t~~r~~~~~fs~p~~~~~~~~~~~~~~~~~~~~~~~~pf~~~~W~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 624 (784)
++++|++|.+.++||.||+.....+++++.+
T Consensus 99 ~~~~t~eR~~~~~fs~py~~~~~~~~~~~~~------------------------------------------------- 129 (275)
T TIGR02995 99 GLFIKPERCKQVAFTQPILCDAEALLVKKGN------------------------------------------------- 129 (275)
T ss_pred cccCCHHHHhccccccceeecceeEEEECCC-------------------------------------------------
Confidence 8999999999999999999999999987764
Q ss_pred ceeehhhhhhhhhcccccccccchhhHHHHHHHHHHHHHHhhccccceeeEeeccccCCCCChHhhhh-CCCceEEeeCc
Q 003958 625 VVTIFWFSFSTMFFAHKEKTVSALGRLVLIIWLFVVLIINSSYTASLTSILTVQKLSSPIKGIDSLRS-SNYPIGYQVNS 703 (784)
Q Consensus 625 ~~~~~~~~~~~~~~~~~~~p~~~~~R~~~~~w~~~~lvl~~~Yta~L~s~l~~~~~~~~i~~~~dl~~-~~~~i~~~~~~ 703 (784)
...+++++||.+ .+.+||+..|+
T Consensus 130 --------------------------------------------------------~~~i~~~~dl~~~~g~~Igv~~g~ 153 (275)
T TIGR02995 130 --------------------------------------------------------PKGLKSYKDIAKNPDAKIAAPGGG 153 (275)
T ss_pred --------------------------------------------------------CCCCCCHHHhccCCCceEEEeCCc
Confidence 235788889864 36789999999
Q ss_pred hHHHHHHhhcccCccCceeCCCHHHHHHHHhcCCcCCCeeEEEechhhhHHHHcCCC--CeEEeCCc---cccceEEEEe
Q 003958 704 FARNYLVDELNIDESRLVPLNSPEEYAKALKDGPHKGGVAAVVDDRAYAELFLSTRC--EFSIVGQV---FTKNGWGFVS 778 (784)
Q Consensus 704 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~a~~~~~~~~~~~~~~~c--~l~~~~~~---~~~~~~~~~~ 778 (784)
...+++++ .+.+..++..+++.+++++.|.+ |++|+++.+...+.+.+++.- ++..+... .....+++++
T Consensus 154 ~~~~~l~~-~~~~~~~i~~~~~~~~~i~~L~~----grvDa~i~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 228 (275)
T TIGR02995 154 TEEKLARE-AGVKREQIIVVPDGQSGLKMVQD----GRADAYSLTVLTINDLASKAGDPNVEVLAPFKDAPVRYYGGAAF 228 (275)
T ss_pred HHHHHHHH-cCCChhhEEEeCCHHHHHHHHHc----CCCCEEecChHHHHHHHHhCCCCCceeecCccCCccccceeEEE
Confidence 88888854 34444567788999999999999 899999999999999876532 44433221 1112237888
Q ss_pred eCCCC
Q 003958 779 IVSSF 783 (784)
Q Consensus 779 ~k~s~ 783 (784)
+++++
T Consensus 229 ~~~~~ 233 (275)
T TIGR02995 229 RPEDK 233 (275)
T ss_pred CCCCH
Confidence 87653
No 96
>PRK15437 histidine ABC transporter substrate-binding protein HisJ; Provisional
Probab=99.59 E-value=4.4e-14 Score=144.17 Aligned_cols=194 Identities=16% Similarity=0.226 Sum_probs=147.9
Q ss_pred CCccEEEEecCCCccceeEeeCCCcceeeeeHHHHHHHHHHCCCccceEEeeCCCCCCCCChhHHHHHHHcCcccEEEee
Q 003958 466 NGRHLRIGVPNRVSFREFVSVKGSEMTSGFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGD 545 (784)
Q Consensus 466 ~~~~l~v~~~~~~~~~~~~~~~~~~~~~G~~~dl~~~l~~~l~f~~~~~~~~~~~~~~~~~~~g~i~~l~~~~~D~~~~~ 545 (784)
....|++++.. .++||.+.+.++.+.|+++|+++++++++|.++++ ... .|..++..+.+|++|+++++
T Consensus 24 ~~~~l~v~~~~--~~~P~~~~~~~g~~~G~~vdi~~~ia~~lg~~i~~--~~~-------pw~~~~~~l~~g~~D~~~~~ 92 (259)
T PRK15437 24 IPQNIRIGTDP--TYAPFESKNSQGELVGFDIDLAKELCKRINTQCTF--VEN-------PLDALIPSLKAKKIDAIMSS 92 (259)
T ss_pred cCCeEEEEeCC--CCCCcceeCCCCCEEeeeHHHHHHHHHHcCCceEE--EeC-------CHHHHHHHHHCCCCCEEEec
Confidence 34678887653 36677665667889999999999999999988554 433 49999999999999999999
Q ss_pred EEeecCccccceeccccccccEEEEEeccCCccccccccccccHHHHHHHHHHHHHHHHHhhheecccCCCCCCCccCCc
Q 003958 546 IAIITNRTKMADFTQPYIESGLVVVAPVRKLDSNAWAFLSPFTPMMWGVTAIFFLAVGAVVWILEHRLNDEFRGPPKRQV 625 (784)
Q Consensus 546 ~~~t~~r~~~~~fs~p~~~~~~~~~~~~~~~~~~~~~~~~pf~~~~W~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 625 (784)
++.|++|.+.++||.||+..+..+++++..
T Consensus 93 ~~~t~eR~~~~~fs~p~~~~~~~~~~~~~~-------------------------------------------------- 122 (259)
T PRK15437 93 LSITEKRQQEIAFTDKLYAADSRLVVAKNS-------------------------------------------------- 122 (259)
T ss_pred CCCCHHHhhhccccchhhcCceEEEEECCC--------------------------------------------------
Confidence 999999999999999999999999987763
Q ss_pred eeehhhhhhhhhcccccccccchhhHHHHHHHHHHHHHHhhccccceeeEeeccccCCCCChHhhhhCCCceEEeeCchH
Q 003958 626 VTIFWFSFSTMFFAHKEKTVSALGRLVLIIWLFVVLIINSSYTASLTSILTVQKLSSPIKGIDSLRSSNYPIGYQVNSFA 705 (784)
Q Consensus 626 ~~~~~~~~~~~~~~~~~~p~~~~~R~~~~~w~~~~lvl~~~Yta~L~s~l~~~~~~~~i~~~~dl~~~~~~i~~~~~~~~ 705 (784)
+...+++||. +.+||+..|+..
T Consensus 123 --------------------------------------------------------~~~~~~~dl~--g~~Igv~~g~~~ 144 (259)
T PRK15437 123 --------------------------------------------------------DIQPTVESLK--GKRVGVLQGTTQ 144 (259)
T ss_pred --------------------------------------------------------CCCCChHHhC--CCEEEEecCcHH
Confidence 1123688997 888999999988
Q ss_pred HHHHHhhcccCccCceeCCCHHHHHHHHhcCCcCCCeeEEEechhhhHH-HHcCC--CCeEEeC-----CccccceEEEE
Q 003958 706 RNYLVDELNIDESRLVPLNSPEEYAKALKDGPHKGGVAAVVDDRAYAEL-FLSTR--CEFSIVG-----QVFTKNGWGFV 777 (784)
Q Consensus 706 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~a~~~~~~~~~~-~~~~~--c~l~~~~-----~~~~~~~~~~~ 777 (784)
+.++.+.......++..+.+.+++++.|.+ +++|+++.+...+.+ +.++. -++...+ +.+....++++
T Consensus 145 ~~~~~~~~~~~~~~~~~~~~~~~~i~~L~~----grvD~~v~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~ia 220 (259)
T PRK15437 145 ETFGNEHWAPKGIEIVSYQGQDNIYSDLTA----GRIDAAFQDEVAASEGFLKQPVGKDYKFGGPSVKDEKLFGVGTGMG 220 (259)
T ss_pred HHHHHhhccccCceEEecCCHHHHHHHHHc----CCccEEEechHHHHHHHHhCCCCCceEEecCccccccccCcceEEE
Confidence 888854322223456778889999999999 899999999877654 33321 2343332 22233456888
Q ss_pred eeCCC
Q 003958 778 SIVSS 782 (784)
Q Consensus 778 ~~k~s 782 (784)
++++.
T Consensus 221 ~~~~~ 225 (259)
T PRK15437 221 LRKED 225 (259)
T ss_pred EeCCC
Confidence 88764
No 97
>PRK10859 membrane-bound lytic transglycosylase F; Provisional
Probab=99.54 E-value=9.1e-14 Score=153.65 Aligned_cols=192 Identities=15% Similarity=0.166 Sum_probs=149.6
Q ss_pred CCccEEEEecCCCccceeEeeCCCcceeeeeHHHHHHHHHHCCCccceEEeeCCCCCCCCChhHHHHHHHcCcccEEEee
Q 003958 466 NGRHLRIGVPNRVSFREFVSVKGSEMTSGFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGD 545 (784)
Q Consensus 466 ~~~~l~v~~~~~~~~~~~~~~~~~~~~~G~~~dl~~~l~~~l~f~~~~~~~~~~~~~~~~~~~g~i~~l~~~~~D~~~~~ 545 (784)
..+.|+|++... |+..+ .+ ++...||++||++++++++|.+++ ++.. .+|+.++..|.+|++|+++++
T Consensus 41 ~~g~LrVg~~~~-P~~~~--~~-~~~~~G~~~DLl~~ia~~LGv~~e--~v~~------~~~~~ll~aL~~G~iDi~~~~ 108 (482)
T PRK10859 41 ERGELRVGTINS-PLTYY--IG-NDGPTGFEYELAKRFADYLGVKLE--IKVR------DNISQLFDALDKGKADLAAAG 108 (482)
T ss_pred hCCEEEEEEecC-CCeeE--ec-CCCcccHHHHHHHHHHHHhCCcEE--EEec------CCHHHHHHHHhCCCCCEEecc
Confidence 346789998753 33222 22 233599999999999999998854 4433 469999999999999999999
Q ss_pred EEeecCccccceeccccccccEEEEEeccCCccccccccccccHHHHHHHHHHHHHHHHHhhheecccCCCCCCCccCCc
Q 003958 546 IAIITNRTKMADFTQPYIESGLVVVAPVRKLDSNAWAFLSPFTPMMWGVTAIFFLAVGAVVWILEHRLNDEFRGPPKRQV 625 (784)
Q Consensus 546 ~~~t~~r~~~~~fs~p~~~~~~~~~~~~~~~~~~~~~~~~pf~~~~W~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 625 (784)
+++|++|.+.++||.||+.....+++++..
T Consensus 109 lt~T~eR~~~~~FS~Py~~~~~~lv~r~~~-------------------------------------------------- 138 (482)
T PRK10859 109 LTYTPERLKQFRFGPPYYSVSQQLVYRKGQ-------------------------------------------------- 138 (482)
T ss_pred CcCChhhhccCcccCCceeeeEEEEEeCCC--------------------------------------------------
Confidence 999999999999999999999999987652
Q ss_pred eeehhhhhhhhhcccccccccchhhHHHHHHHHHHHHHHhhccccceeeEeeccccCCCCChHhhhhCCCceEEeeCchH
Q 003958 626 VTIFWFSFSTMFFAHKEKTVSALGRLVLIIWLFVVLIINSSYTASLTSILTVQKLSSPIKGIDSLRSSNYPIGYQVNSFA 705 (784)
Q Consensus 626 ~~~~~~~~~~~~~~~~~~p~~~~~R~~~~~w~~~~lvl~~~Yta~L~s~l~~~~~~~~i~~~~dl~~~~~~i~~~~~~~~ 705 (784)
..+++++||. |++||+..|+..
T Consensus 139 --------------------------------------------------------~~i~~l~dL~--Gk~I~V~~gS~~ 160 (482)
T PRK10859 139 --------------------------------------------------------PRPRSLGDLK--GGTLTVAAGSSH 160 (482)
T ss_pred --------------------------------------------------------CCCCCHHHhC--CCeEEEECCCcH
Confidence 3578999998 889999999988
Q ss_pred HHHHHhhcc-cCccCc--eeCCCHHHHHHHHhcCCcCCCeeEEEechhhhHHHHcCCCCeEEeCCccccceEEEEeeCC
Q 003958 706 RNYLVDELN-IDESRL--VPLNSPEEYAKALKDGPHKGGVAAVVDDRAYAELFLSTRCEFSIVGQVFTKNGWGFVSIVS 781 (784)
Q Consensus 706 ~~~~~~~~~-~~~~~~--~~~~~~~~~~~~l~~~~~~~~~~a~~~~~~~~~~~~~~~c~l~~~~~~~~~~~~~~~~~k~ 781 (784)
+..+++... .+...+ ..+.+.++++++|.+ |++|+++.|...+.+....+.++.+........+++|+++|+
T Consensus 161 ~~~L~~l~~~~p~i~~~~~~~~s~~e~l~aL~~----G~iDa~v~d~~~~~~~~~~~p~l~v~~~l~~~~~~~~av~k~ 235 (482)
T PRK10859 161 VETLQELKKKYPELSWEESDDKDSEELLEQVAE----GKIDYTIADSVEISLNQRYHPELAVAFDLTDEQPVAWALPPS 235 (482)
T ss_pred HHHHHHHHHhCCCceEEecCCCCHHHHHHHHHC----CCCCEEEECcHHHHHHHHhCCCceeeeecCCCceeEEEEeCC
Confidence 888754222 122222 345789999999999 899999999888876655566776655444566789999994
No 98
>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=99.54 E-value=1e-13 Score=139.86 Aligned_cols=184 Identities=15% Similarity=0.159 Sum_probs=132.2
Q ss_pred EEEEecCCCccceeEeeCCCcceeeeeHHHHHHHHHHCCCccceEEeeCCCCCCCCChhHHH---HHHHcCcccEEEeeE
Q 003958 470 LRIGVPNRVSFREFVSVKGSEMTSGFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELV---RLITAGVYDAAVGDI 546 (784)
Q Consensus 470 l~v~~~~~~~~~~~~~~~~~~~~~G~~~dl~~~l~~~l~f~~~~~~~~~~~~~~~~~~~g~i---~~l~~~~~D~~~~~~ 546 (784)
|+|++.. .|+||.+.++ .||++||+++|++++|.+++ +++. .|.+++ ..|.+|++|+++ ++
T Consensus 2 l~vg~~~--~~pPf~~~~~----~Gfdvdl~~~ia~~lg~~~~--~~~~-------~~~~~~~~~~~L~~g~~Dii~-~~ 65 (246)
T TIGR03870 2 LRVCAAT--KEAPYSTKDG----SGFENKIAAALAAAMGRKVV--FVWL-------AKPAIYLVRDGLDKKLCDVVL-GL 65 (246)
T ss_pred eEEEeCC--CCCCCccCCC----CcchHHHHHHHHHHhCCCeE--EEEe-------ccchhhHHHHHHhcCCccEEE-eC
Confidence 5666654 4788888542 79999999999999999844 4443 477766 699999999988 58
Q ss_pred EeecCccccceeccccccccEEEEEeccCCccccccccccccHHHHHHHHHHHHHHHHHhhheecccCCCCCCCccCCce
Q 003958 547 AIITNRTKMADFTQPYIESGLVVVAPVRKLDSNAWAFLSPFTPMMWGVTAIFFLAVGAVVWILEHRLNDEFRGPPKRQVV 626 (784)
Q Consensus 547 ~~t~~r~~~~~fs~p~~~~~~~~~~~~~~~~~~~~~~~~pf~~~~W~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 626 (784)
+++++| +.||.||+.++.++++++.+
T Consensus 66 ~~t~~r---~~fS~PY~~~~~~~v~~k~~--------------------------------------------------- 91 (246)
T TIGR03870 66 DTGDPR---VLTTKPYYRSSYVFLTRKDR--------------------------------------------------- 91 (246)
T ss_pred CCChHH---HhcccCcEEeeeEEEEeCCC---------------------------------------------------
Confidence 888777 67999999999999998764
Q ss_pred eehhhhhhhhhcccccccccchhhHHHHHHHHHHHHHHhhccccceeeEeeccccCCCCChHh--hhhCCC-ceEEeeCc
Q 003958 627 TIFWFSFSTMFFAHKEKTVSALGRLVLIIWLFVVLIINSSYTASLTSILTVQKLSSPIKGIDS--LRSSNY-PIGYQVNS 703 (784)
Q Consensus 627 ~~~~~~~~~~~~~~~~~p~~~~~R~~~~~w~~~~lvl~~~Yta~L~s~l~~~~~~~~i~~~~d--l~~~~~-~i~~~~~~ 703 (784)
...+.+++| |. ++ +||+..|+
T Consensus 92 ------------------------------------------------------~~~~~~~~d~~L~--g~~~vgv~~gs 115 (246)
T TIGR03870 92 ------------------------------------------------------NLDIKSWNDPRLK--KVSKIGVIFGS 115 (246)
T ss_pred ------------------------------------------------------CCCCCCccchhhc--cCceEEEecCC
Confidence 224677765 66 87 89999999
Q ss_pred hHHHHHHhhcccC-----ccCceeCC---------CHHHHHHHHhcCCcCCCeeEEEechhhhHHHHcCCC-CeE--EeC
Q 003958 704 FARNYLVDELNID-----ESRLVPLN---------SPEEYAKALKDGPHKGGVAAVVDDRAYAELFLSTRC-EFS--IVG 766 (784)
Q Consensus 704 ~~~~~~~~~~~~~-----~~~~~~~~---------~~~~~~~~l~~~~~~~~~~a~~~~~~~~~~~~~~~c-~l~--~~~ 766 (784)
..+.++++..... ...+..+. +.++++++|++ |++||.+.+.+.+.+++.++- ++. .++
T Consensus 116 ~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~aL~~----GrvDa~i~~~~~~~~~~~~~~~~~~~~~~~ 191 (246)
T TIGR03870 116 PAETMLKQIGRYEDNFAYLYSLVNFKSPRNQYTQIDPRKLVSEVAT----GKADLAVAFAPEVARYVKASPEPLRMTVIP 191 (246)
T ss_pred hHHHHHHhcCccccccccccccccccCcccccccCCHHHHHHHHHc----CCCCEEEeeHHhHHHHHHhCCCCceEEecc
Confidence 9999886422110 01112221 35789999999 899999998887777776532 232 333
Q ss_pred Ccc-------c--cceEEEEeeCCCC
Q 003958 767 QVF-------T--KNGWGFVSIVSSF 783 (784)
Q Consensus 767 ~~~-------~--~~~~~~~~~k~s~ 783 (784)
+.. . ...+|++++|+++
T Consensus 192 ~~~~~~~~~~~~~~~~~~iav~k~~~ 217 (246)
T TIGR03870 192 DDATRSDGAKIPMQYDQSMGVRKDDT 217 (246)
T ss_pred ccccccCCCCcceeeEEEEEEccCCH
Confidence 321 1 1136999999875
No 99
>COG0834 HisJ ABC-type amino acid transport/signal transduction systems, periplasmic component/domain [Amino acid transport and metabolism / Signal transduction mechanisms]
Probab=99.42 E-value=4.6e-12 Score=130.92 Aligned_cols=194 Identities=23% Similarity=0.278 Sum_probs=150.9
Q ss_pred CccEEEEecCCCccceeEeeCCC-cceeeeeHHHHHHHHHHCCCccceEEeeCCCCCCCCChhHHHHHHHcCcccEEEee
Q 003958 467 GRHLRIGVPNRVSFREFVSVKGS-EMTSGFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGD 545 (784)
Q Consensus 467 ~~~l~v~~~~~~~~~~~~~~~~~-~~~~G~~~dl~~~l~~~l~f~~~~~~~~~~~~~~~~~~~g~i~~l~~~~~D~~~~~ 545 (784)
...+++++... ..+|+.+.+.. +.+.||++|+++.+++.++......+.. ..|.+++..+..|++|+.++.
T Consensus 33 ~~~~~v~~~~~-~~~p~~~~~~~~~~~~G~dvdl~~~ia~~l~~~~~~~~~~-------~~~~~~~~~l~~g~~D~~~~~ 104 (275)
T COG0834 33 RGKLRVGTEAT-YAPPFEFLDAKGGKLVGFDVDLAKAIAKRLGGDKKVEFVP-------VAWDGLIPALKAGKVDIIIAG 104 (275)
T ss_pred cCeEEEEecCC-CCCCcccccCCCCeEEeeeHHHHHHHHHHhCCcceeEEec-------cchhhhhHHHhcCCcCEEEec
Confidence 45677777643 34577775555 5999999999999999988753233332 369999999999999999999
Q ss_pred EEeecCccccceeccccccccEEEEEeccCCccccccccccccHHHHHHHHHHHHHHHHHhhheecccCCCCCCCccCCc
Q 003958 546 IAIITNRTKMADFTQPYIESGLVVVAPVRKLDSNAWAFLSPFTPMMWGVTAIFFLAVGAVVWILEHRLNDEFRGPPKRQV 625 (784)
Q Consensus 546 ~~~t~~r~~~~~fs~p~~~~~~~~~~~~~~~~~~~~~~~~pf~~~~W~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 625 (784)
+++|++|.+.++||.||+..+..+++++.+
T Consensus 105 ~~~t~er~~~~~fs~py~~~~~~~~~~~~~-------------------------------------------------- 134 (275)
T COG0834 105 MTITPERKKKVDFSDPYYYSGQVLLVKKDS-------------------------------------------------- 134 (275)
T ss_pred cccCHHHhccccccccccccCeEEEEECCC--------------------------------------------------
Confidence 999999999999999999999999998775
Q ss_pred eeehhhhhhhhhcccccccccchhhHHHHHHHHHHHHHHhhccccceeeEeeccccCCCCChHhhhhCCCceEEeeCch-
Q 003958 626 VTIFWFSFSTMFFAHKEKTVSALGRLVLIIWLFVVLIINSSYTASLTSILTVQKLSSPIKGIDSLRSSNYPIGYQVNSF- 704 (784)
Q Consensus 626 ~~~~~~~~~~~~~~~~~~p~~~~~R~~~~~w~~~~lvl~~~Yta~L~s~l~~~~~~~~i~~~~dl~~~~~~i~~~~~~~- 704 (784)
...+.+++||. ++++|+..|+.
T Consensus 135 -------------------------------------------------------~~~~~~~~DL~--gk~v~v~~gt~~ 157 (275)
T COG0834 135 -------------------------------------------------------DIGIKSLEDLK--GKKVGVQLGTTD 157 (275)
T ss_pred -------------------------------------------------------CcCcCCHHHhC--CCEEEEEcCcch
Confidence 22378999999 88999999997
Q ss_pred -HHHHHHhhcccCccCceeCCCHHHHHHHHhcCCcCCCeeEEEechhhhHH--HHcCCCCe-EEeCCcccc-ceEEEEee
Q 003958 705 -ARNYLVDELNIDESRLVPLNSPEEYAKALKDGPHKGGVAAVVDDRAYAEL--FLSTRCEF-SIVGQVFTK-NGWGFVSI 779 (784)
Q Consensus 705 -~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~a~~~~~~~~~~--~~~~~c~l-~~~~~~~~~-~~~~~~~~ 779 (784)
...+. ....+...++.+++..+.+++|++ |+.+|++.|.+.+.+ ...+.-++ ......... ..|+++++
T Consensus 158 ~~~~~~--~~~~~~~~~~~~~~~~~~~~al~~----Gr~Da~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 231 (275)
T COG0834 158 EAEEKA--KKPGPNAKIVAYDSNAEALLALKN----GRADAVVSDSAVLAGLKLLKKNPGLYVLLVFPGLSVEYLGIALR 231 (275)
T ss_pred hHHHHH--hhccCCceEEeeCCHHHHHHHHHc----CCccEEEcchHhhhhhhhhhcCCCCceeeeccCCCcceeEEEec
Confidence 34443 222333577888999999999999 899999999999999 34444332 222333333 68999999
Q ss_pred CC
Q 003958 780 VS 781 (784)
Q Consensus 780 k~ 781 (784)
|+
T Consensus 232 ~~ 233 (275)
T COG0834 232 KG 233 (275)
T ss_pred cC
Confidence 97
No 100
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=99.40 E-value=2.9e-12 Score=159.88 Aligned_cols=194 Identities=11% Similarity=0.126 Sum_probs=156.5
Q ss_pred CCccEEEEecCCCccceeEeeCCCcceeeeeHHHHHHHHHHCCCccceEEeeCCCCCCCCChhHHHHHHHcCcccEEEee
Q 003958 466 NGRHLRIGVPNRVSFREFVSVKGSEMTSGFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGD 545 (784)
Q Consensus 466 ~~~~l~v~~~~~~~~~~~~~~~~~~~~~G~~~dl~~~l~~~l~f~~~~~~~~~~~~~~~~~~~g~i~~l~~~~~D~~~~~ 545 (784)
+.++|+|++..+. ++|+...+.++++.||.+|+++.+++++|.+ +++++. .+|.+++..|.+|++|+..+.
T Consensus 54 ~~~~l~vgv~~~~-~p~~~~~~~~g~~~G~~~D~l~~ia~~lG~~--~e~v~~------~~~~~~l~~l~~g~iDl~~~~ 124 (1197)
T PRK09959 54 SKKNLVIAVHKSQ-TATLLHTDSQQRVRGINADYLNLLKRALNIK--LTLREY------ADHQKAMDALEEGEVDIVLSH 124 (1197)
T ss_pred hCCeEEEEecCCC-CCCceeecCCCccceecHHHHHHHHHhcCCc--eEEEeC------CCHHHHHHHHHcCCCcEecCc
Confidence 3457888887531 2233334568899999999999999999988 666664 579999999999999999888
Q ss_pred EEeecCccccceeccccccccEEEEEeccCCccccccccccccHHHHHHHHHHHHHHHHHhhheecccCCCCCCCccCCc
Q 003958 546 IAIITNRTKMADFTQPYIESGLVVVAPVRKLDSNAWAFLSPFTPMMWGVTAIFFLAVGAVVWILEHRLNDEFRGPPKRQV 625 (784)
Q Consensus 546 ~~~t~~r~~~~~fs~p~~~~~~~~~~~~~~~~~~~~~~~~pf~~~~W~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 625 (784)
++.+++|.+.++||.||+.....+++++..
T Consensus 125 ~~~~~~r~~~~~fs~py~~~~~~~v~~~~~-------------------------------------------------- 154 (1197)
T PRK09959 125 LVASPPLNDDIAATKPLIITFPALVTTLHD-------------------------------------------------- 154 (1197)
T ss_pred cccccccccchhcCCCccCCCceEEEeCCC--------------------------------------------------
Confidence 999999999999999999999999987753
Q ss_pred eeehhhhhhhhhcccccccccchhhHHHHHHHHHHHHHHhhccccceeeEeeccccCCCCChHhhhhCCCceEEeeCchH
Q 003958 626 VTIFWFSFSTMFFAHKEKTVSALGRLVLIIWLFVVLIINSSYTASLTSILTVQKLSSPIKGIDSLRSSNYPIGYQVNSFA 705 (784)
Q Consensus 626 ~~~~~~~~~~~~~~~~~~p~~~~~R~~~~~w~~~~lvl~~~Yta~L~s~l~~~~~~~~i~~~~dl~~~~~~i~~~~~~~~ 705 (784)
.+.+++|+. +++++++.|+..
T Consensus 155 ---------------------------------------------------------~~~~~~~l~--~~~i~~~~g~~~ 175 (1197)
T PRK09959 155 ---------------------------------------------------------SMRPLTSSK--PVNIARVANYPP 175 (1197)
T ss_pred ---------------------------------------------------------CCCCccccc--CeEEEEeCCCCC
Confidence 456777776 788999999988
Q ss_pred HHHHHhhcccCccCceeCCCHHHHHHHHhcCCcCCCeeEEEechhhhHHHHcCCC--CeEEeCCc-cccceEEEEeeCCC
Q 003958 706 RNYLVDELNIDESRLVPLNSPEEYAKALKDGPHKGGVAAVVDDRAYAELFLSTRC--EFSIVGQV-FTKNGWGFVSIVSS 782 (784)
Q Consensus 706 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~a~~~~~~~~~~~~~~~c--~l~~~~~~-~~~~~~~~~~~k~s 782 (784)
.+++++ ..+..+++.|++.++++++|.+ |+.||++.+..++.|+++++. ++.+++.. .....+.++++|+.
T Consensus 176 ~~~~~~--~~p~~~i~~~~s~~~al~av~~----G~~Da~i~~~~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~~~~~~ 249 (1197)
T PRK09959 176 DEVIHQ--SFPKATIISFTNLYQALASVSA----GQNDYFIGSNIITSSMISRYFTHSLNVVKYYNSPRQYNFFLTRKES 249 (1197)
T ss_pred HHHHHH--hCCCCEEEeCCCHHHHHHHHHc----CCCCEEEccHHHHHHHHhcccccceEEEeeccCCCCceeEEEcCCc
Confidence 888853 4566788999999999999999 899999999999999998743 45555432 22334668888886
Q ss_pred C
Q 003958 783 F 783 (784)
Q Consensus 783 ~ 783 (784)
|
T Consensus 250 ~ 250 (1197)
T PRK09959 250 V 250 (1197)
T ss_pred H
Confidence 5
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=99.38 E-value=1.2e-11 Score=124.21 Aligned_cols=186 Identities=18% Similarity=0.197 Sum_probs=133.0
Q ss_pred EEEEecCCCccceeEeeCCCcceeeeeHHHHHHHHHHCCCccceEEeeCCCCCCCCChhHHHHHHHcCcccEEEeeEEee
Q 003958 470 LRIGVPNRVSFREFVSVKGSEMTSGFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAII 549 (784)
Q Consensus 470 l~v~~~~~~~~~~~~~~~~~~~~~G~~~dl~~~l~~~l~f~~~~~~~~~~~~~~~~~~~g~i~~l~~~~~D~~~~~~~~t 549 (784)
|+|++.. .++||.+. +..||++||++.+++++|.++++...++ .|.-++..+.+|++|++++ +
T Consensus 2 l~v~~~~--~~~P~~~~----~~~G~~~el~~~i~~~~g~~i~~~~~~~-------~~~~~~~~l~~g~~Di~~~----~ 64 (232)
T TIGR03871 2 LRVCADP--NNLPFSNE----KGEGFENKIAQLLADDLGLPLEYTWFPQ-------RRGFVRNTLNAGRCDVVIG----V 64 (232)
T ss_pred eEEEeCC--CCCCccCC----CCCchHHHHHHHHHHHcCCceEEEecCc-------chhhHHHHHhcCCccEEEe----c
Confidence 5666554 36666652 2479999999999999999965554322 2333577899999999875 5
Q ss_pred cCccccceeccccccccEEEEEeccCCccccccccccccHHHHHHHHHHHHHHHHHhhheecccCCCCCCCccCCceeeh
Q 003958 550 TNRTKMADFTQPYIESGLVVVAPVRKLDSNAWAFLSPFTPMMWGVTAIFFLAVGAVVWILEHRLNDEFRGPPKRQVVTIF 629 (784)
Q Consensus 550 ~~r~~~~~fs~p~~~~~~~~~~~~~~~~~~~~~~~~pf~~~~W~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 629 (784)
++|.+.++||.||+..++.++++...
T Consensus 65 ~~r~~~~~fs~py~~~~~~lv~~~~~------------------------------------------------------ 90 (232)
T TIGR03871 65 PAGYEMVLTTRPYYRSTYVFVTRKDS------------------------------------------------------ 90 (232)
T ss_pred cCccccccccCCcEeeeEEEEEeCCC------------------------------------------------------
Confidence 77889999999999999999997763
Q ss_pred hhhhhhhhcccccccccchhhHHHHHHHHHHHHHHhhccccceeeEeeccccCCCCChHhhhhCCCceEEeeCchHHHHH
Q 003958 630 WFSFSTMFFAHKEKTVSALGRLVLIIWLFVVLIINSSYTASLTSILTVQKLSSPIKGIDSLRSSNYPIGYQVNSFARNYL 709 (784)
Q Consensus 630 ~~~~~~~~~~~~~~p~~~~~R~~~~~w~~~~lvl~~~Yta~L~s~l~~~~~~~~i~~~~dl~~~~~~i~~~~~~~~~~~~ 709 (784)
...+++++|+.-.+.+||+..|+..++++
T Consensus 91 ---------------------------------------------------~~~~~~~~d~~l~g~~V~v~~g~~~~~~l 119 (232)
T TIGR03871 91 ---------------------------------------------------LLDVKSLDDPRLKKLRIGVFAGTPPAHWL 119 (232)
T ss_pred ---------------------------------------------------cccccchhhhhhcCCeEEEEcCChHHHHH
Confidence 23578888832227889999999998988
Q ss_pred HhhcccCccCce---------eCCCHHHHHHHHhcCCcCCCeeEEEechhhhHHHHcCC-CCeEEeCCcc------ccce
Q 003958 710 VDELNIDESRLV---------PLNSPEEYAKALKDGPHKGGVAAVVDDRAYAELFLSTR-CEFSIVGQVF------TKNG 773 (784)
Q Consensus 710 ~~~~~~~~~~~~---------~~~~~~~~~~~l~~~~~~~~~~a~~~~~~~~~~~~~~~-c~l~~~~~~~------~~~~ 773 (784)
++. ... .++. ...+.+++++.|.+ |++||++.+...+.|++++. -++.+..... ...+
T Consensus 120 ~~~-~~~-~~~~~~~~~~~~~~~~~~~~~~~~l~~----G~~Da~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 193 (232)
T TIGR03871 120 ARH-GLV-ENVVGYSLFGDYRPESPPGRMVEDLAA----GEIDVAIVWGPIAGYFAKQAGPPLVVVPLLPEDGGIPFDYR 193 (232)
T ss_pred Hhc-Ccc-cccccccccccccccCCHHHHHHHHHc----CCcCEEEeccHHHHHHHHhCCCCceeeccccCCCCCCccce
Confidence 542 211 1211 13467899999999 89999999988888887653 2444433221 2235
Q ss_pred EEEEeeCCCC
Q 003958 774 WGFVSIVSSF 783 (784)
Q Consensus 774 ~~~~~~k~s~ 783 (784)
++++++++++
T Consensus 194 ~~~~~~~~~~ 203 (232)
T TIGR03871 194 IAMGVRKGDK 203 (232)
T ss_pred EEEEEecCCH
Confidence 6888898753
No 102
>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=99.37 E-value=8.8e-12 Score=127.84 Aligned_cols=201 Identities=11% Similarity=0.092 Sum_probs=136.7
Q ss_pred CCccEEEEecCCCccceeEeeCCCcceeeeeHHHHHHHHHHC-CCccceEEeeCCCCCCCCChhHHHHHHHcCcccEEEe
Q 003958 466 NGRHLRIGVPNRVSFREFVSVKGSEMTSGFCIDVFTAAINLL-PYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVG 544 (784)
Q Consensus 466 ~~~~l~v~~~~~~~~~~~~~~~~~~~~~G~~~dl~~~l~~~l-~f~~~~~~~~~~~~~~~~~~~g~i~~l~~~~~D~~~~ 544 (784)
...+|+++... |+||.+.++++...|+..++++++++++ ++++++.. -.|..++..+ .|+.|.++.
T Consensus 16 ~~~~l~~~~~~---~pPf~~~~~~~~~~G~~~~i~~~i~~~~~~~~~~~~~---------~pw~r~l~~l-~~~~d~~~~ 82 (268)
T TIGR02285 16 AKEAITWIVND---FPPFFIFSGPSKGRGVFDVILQEIRRALPQYEHRFVR---------VSFARSLKEL-QGKGGVCTV 82 (268)
T ss_pred ccceeEEEecc---cCCeeEeCCCCCCCChHHHHHHHHHHHcCCCceeEEE---------CCHHHHHHHH-hcCCCeEEe
Confidence 34678777654 6677765566788999999999999998 87755443 2599999999 788888888
Q ss_pred eEEeecCccccceecccccc-ccEEEEEeccCCccccccccccccHHHHHHHHHHHHHHHHHhhheecccCCCCCCCccC
Q 003958 545 DIAIITNRTKMADFTQPYIE-SGLVVVAPVRKLDSNAWAFLSPFTPMMWGVTAIFFLAVGAVVWILEHRLNDEFRGPPKR 623 (784)
Q Consensus 545 ~~~~t~~r~~~~~fs~p~~~-~~~~~~~~~~~~~~~~~~~~~pf~~~~W~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 623 (784)
++++|++|.+.++||.||+. ....+++++.+... +
T Consensus 83 ~~~~t~eR~~~~~Fs~P~~~~~~~~~~~~~~~~~~-~------------------------------------------- 118 (268)
T TIGR02285 83 NLLRTPEREKFLIFSDPTLRALPVGLVLRKELTAG-V------------------------------------------- 118 (268)
T ss_pred eccCCcchhhceeecCCccccCCceEEEccchhhh-c-------------------------------------------
Confidence 89999999999999999975 57888887653000 0
Q ss_pred CceeehhhhhhhhhcccccccccchhhHHHHHHHHHHHHHHhhccccceeeEeeccccC-CCCChHhhhh-CCCceEEee
Q 003958 624 QVVTIFWFSFSTMFFAHKEKTVSALGRLVLIIWLFVVLIINSSYTASLTSILTVQKLSS-PIKGIDSLRS-SNYPIGYQV 701 (784)
Q Consensus 624 ~~~~~~~~~~~~~~~~~~~~p~~~~~R~~~~~w~~~~lvl~~~Yta~L~s~l~~~~~~~-~i~~~~dl~~-~~~~i~~~~ 701 (784)
..... ++ ++.+|.+ ++.++|+..
T Consensus 119 ------------------------------------------------------~~~~d~~~-~~~~l~~l~g~~vgv~~ 143 (268)
T TIGR02285 119 ------------------------------------------------------RDEQDGDV-DLKKLLASKKKRLGVIA 143 (268)
T ss_pred ------------------------------------------------------cccCCCCc-cHHHHhcCCCeEEEEec
Confidence 00011 11 2333322 267899998
Q ss_pred CchHH----HHHHhhcccCccCceeCCCHHHHHHHHhcCCcCCCeeEEEechhhhHHHHcCC----CCeEEeCCc--ccc
Q 003958 702 NSFAR----NYLVDELNIDESRLVPLNSPEEYAKALKDGPHKGGVAAVVDDRAYAELFLSTR----CEFSIVGQV--FTK 771 (784)
Q Consensus 702 ~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~a~~~~~~~~~~~~~~~----c~l~~~~~~--~~~ 771 (784)
|+... +++++.......++..+.+.++.++.|.+ |++|+++.+..++.|++++. .++..+... ...
T Consensus 144 g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~----GrvD~~v~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 219 (268)
T TIGR02285 144 SRSYGQQIDDILSDSGYQHNTRIIGNAAMGNLFKMLEK----GRVNYTLAYPPEKTYYEELNNGALPPLKFLPVAGMPAH 219 (268)
T ss_pred ceeccHHHHHHHHhCCcccceeeeccchHHHHHHHHHc----CCccEEEeCcHHHHHHHHhccCCcCCeeEeecCCCccc
Confidence 76543 33322111111245556778889999999 89999999999999988642 234444321 122
Q ss_pred ceEEEEeeCCC
Q 003958 772 NGWGFVSIVSS 782 (784)
Q Consensus 772 ~~~~~~~~k~s 782 (784)
..++++++|++
T Consensus 220 ~~~~i~~~k~~ 230 (268)
T TIGR02285 220 ISVWVACPKTE 230 (268)
T ss_pred eEEEEEeCCCH
Confidence 35789998864
No 103
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=99.37 E-value=6.7e-12 Score=156.66 Aligned_cols=188 Identities=11% Similarity=0.106 Sum_probs=149.4
Q ss_pred cEEEEecCCCccceeEeeCCCcceeeeeHHHHHHHHHHCCCccceEEeeCCCCCCCCChhHHHHHHHcCcccEEEeeEEe
Q 003958 469 HLRIGVPNRVSFREFVSVKGSEMTSGFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAI 548 (784)
Q Consensus 469 ~l~v~~~~~~~~~~~~~~~~~~~~~G~~~dl~~~l~~~l~f~~~~~~~~~~~~~~~~~~~g~i~~l~~~~~D~~~~~~~~ 548 (784)
.++|++. +.|+||.+.+.++++.||.+|+++.|++++|.+ +++++. ..|..+...|.+|++|++. ++..
T Consensus 303 ~l~v~~~--~~~pP~~~~d~~g~~~G~~~Dll~~i~~~~g~~--~~~v~~------~~~~~~~~~l~~g~~D~i~-~~~~ 371 (1197)
T PRK09959 303 DLKVLEN--PYSPPYSMTDENGSVRGVMGDILNIITLQTGLN--FSPITV------SHNIHAGTQLNPGGWDIIP-GAIY 371 (1197)
T ss_pred ceEEEcC--CCCCCeeEECCCCcEeeehHHHHHHHHHHHCCe--EEEEec------CCHHHHHHHHHCCCceEee-cccC
Confidence 4666544 458899987778999999999999999999987 666655 4688888999999999865 4568
Q ss_pred ecCccccceeccccccccEEEEEeccCCccccccccccccHHHHHHHHHHHHHHHHHhhheecccCCCCCCCccCCceee
Q 003958 549 ITNRTKMADFTQPYIESGLVVVAPVRKLDSNAWAFLSPFTPMMWGVTAIFFLAVGAVVWILEHRLNDEFRGPPKRQVVTI 628 (784)
Q Consensus 549 t~~r~~~~~fs~p~~~~~~~~~~~~~~~~~~~~~~~~pf~~~~W~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 628 (784)
|++|.+.++||.||+.+++++++++..
T Consensus 372 t~~r~~~~~fs~py~~~~~~~v~~~~~----------------------------------------------------- 398 (1197)
T PRK09959 372 SEDRENNVLFAEAFITTPYVFVMQKAP----------------------------------------------------- 398 (1197)
T ss_pred CccccccceeccccccCCEEEEEecCC-----------------------------------------------------
Confidence 999999999999999999999986542
Q ss_pred hhhhhhhhhcccccccccchhhHHHHHHHHHHHHHHhhccccceeeEeeccccCCCCChHhhhhCCCceEEeeCchHHHH
Q 003958 629 FWFSFSTMFFAHKEKTVSALGRLVLIIWLFVVLIINSSYTASLTSILTVQKLSSPIKGIDSLRSSNYPIGYQVNSFARNY 708 (784)
Q Consensus 629 ~~~~~~~~~~~~~~~p~~~~~R~~~~~w~~~~lvl~~~Yta~L~s~l~~~~~~~~i~~~~dl~~~~~~i~~~~~~~~~~~ 708 (784)
..+. ++. .|.+||+..|+...++
T Consensus 399 -----------------------------------------------------~~~~---~~~-~g~~vav~~g~~~~~~ 421 (1197)
T PRK09959 399 -----------------------------------------------------DSEQ---TLK-KGMKVAIPYYYELHSQ 421 (1197)
T ss_pred -----------------------------------------------------CCcc---ccc-cCCEEEEeCCcchHHH
Confidence 0112 222 4788999999988888
Q ss_pred HHhhcccCccCceeCCCHHHHHHHHhcCCcCCCeeEEEechhhhHHHHcCCC--Ce-EEeCCccccceEEEEeeCCCC
Q 003958 709 LVDELNIDESRLVPLNSPEEYAKALKDGPHKGGVAAVVDDRAYAELFLSTRC--EF-SIVGQVFTKNGWGFVSIVSSF 783 (784)
Q Consensus 709 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~a~~~~~~~~~~~~~~~c--~l-~~~~~~~~~~~~~~~~~k~s~ 783 (784)
+++ ..+..+++.+++.++++++|.+ |+.||++.+...+.|+++++. ++ ......+....++|+++|+.|
T Consensus 422 ~~~--~~p~~~~~~~~~~~~~l~av~~----G~~Da~i~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~av~k~~~ 493 (1197)
T PRK09959 422 LKE--MYPEVEWIKVDNASAAFHKVKE----GELDALVATQLNSRYMIDHYYPNELYHFLIPGVPNASLSFAFPRGEP 493 (1197)
T ss_pred HHH--HCCCcEEEEcCCHHHHHHHHHc----CCCCEEehhhHHHHHHHHhcccccceeeecCCCCchheEEeeCCCCH
Confidence 843 3445678889999999999999 899999999999999988742 23 233344556678999999875
No 104
>smart00062 PBPb Bacterial periplasmic substrate-binding proteins. bacterial proteins, eukaryotic ones are in PBPe
Probab=99.32 E-value=5.2e-11 Score=117.67 Aligned_cols=188 Identities=24% Similarity=0.390 Sum_probs=151.8
Q ss_pred EEEEecCCCccceeEeeCCCcceeeeeHHHHHHHHHHCCCccceEEeeCCCCCCCCChhHHHHHHHcCcccEEEeeEEee
Q 003958 470 LRIGVPNRVSFREFVSVKGSEMTSGFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAII 549 (784)
Q Consensus 470 l~v~~~~~~~~~~~~~~~~~~~~~G~~~dl~~~l~~~l~f~~~~~~~~~~~~~~~~~~~g~i~~l~~~~~D~~~~~~~~t 549 (784)
|++++. ..++|+...+.++...|+.+|+++.+.+.+|++ +++... .|..++..+.+|++|++++....+
T Consensus 2 l~v~~~--~~~~p~~~~~~~g~~~G~~~~~~~~~~~~~g~~--~~~~~~-------~~~~~~~~l~~g~~D~~~~~~~~~ 70 (219)
T smart00062 2 LRVGTN--GDYPPFSFADEDGELTGFDVDLAKAIAKELGLK--VEFVEV-------SFDNLLTALKSGKIDVVAAGMTIT 70 (219)
T ss_pred EEEEec--CCCCCcEEECCCCCcccchHHHHHHHHHHhCCe--EEEEec-------cHHHHHHHHHCCcccEEeccccCC
Confidence 567775 346777766677889999999999999999977 444432 589999999999999999887778
Q ss_pred cCccccceeccccccccEEEEEeccCCccccccccccccHHHHHHHHHHHHHHHHHhhheecccCCCCCCCccCCceeeh
Q 003958 550 TNRTKMADFTQPYIESGLVVVAPVRKLDSNAWAFLSPFTPMMWGVTAIFFLAVGAVVWILEHRLNDEFRGPPKRQVVTIF 629 (784)
Q Consensus 550 ~~r~~~~~fs~p~~~~~~~~~~~~~~~~~~~~~~~~pf~~~~W~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 629 (784)
.+|...+.|+.|+...+..+++++..
T Consensus 71 ~~~~~~~~~~~~~~~~~~~~~~~~~~------------------------------------------------------ 96 (219)
T smart00062 71 PERAKQVDFSDPYYKSGQVILVRKDS------------------------------------------------------ 96 (219)
T ss_pred HHHHhheeeccceeeceeEEEEecCC------------------------------------------------------
Confidence 88888899999999999888887654
Q ss_pred hhhhhhhhcccccccccchhhHHHHHHHHHHHHHHhhccccceeeEeeccccCCCCChHhhhhCCCceEEeeCchHHHHH
Q 003958 630 WFSFSTMFFAHKEKTVSALGRLVLIIWLFVVLIINSSYTASLTSILTVQKLSSPIKGIDSLRSSNYPIGYQVNSFARNYL 709 (784)
Q Consensus 630 ~~~~~~~~~~~~~~p~~~~~R~~~~~w~~~~lvl~~~Yta~L~s~l~~~~~~~~i~~~~dl~~~~~~i~~~~~~~~~~~~ 709 (784)
++.+++||. +.+|++..|+....++
T Consensus 97 -----------------------------------------------------~~~~~~dL~--g~~i~~~~g~~~~~~~ 121 (219)
T smart00062 97 -----------------------------------------------------PIKSLEDLK--GKKVAVVAGTTGEELL 121 (219)
T ss_pred -----------------------------------------------------CCCChHHhC--CCEEEEecCccHHHHH
Confidence 589999997 8889999888888887
Q ss_pred HhhcccCccCceeCCCHHHHHHHHhcCCcCCCeeEEEechhhhHHHHcCC--CCeEEeCCcccc-ceEEEEeeCCCC
Q 003958 710 VDELNIDESRLVPLNSPEEYAKALKDGPHKGGVAAVVDDRAYAELFLSTR--CEFSIVGQVFTK-NGWGFVSIVSSF 783 (784)
Q Consensus 710 ~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~a~~~~~~~~~~~~~~~--c~l~~~~~~~~~-~~~~~~~~k~s~ 783 (784)
... .+...+..+.+..+.+..|.+ +++++.+.+.+.+.+..++. +++.++...... ..++++++++++
T Consensus 122 ~~~--~~~~~~~~~~~~~~~~~~l~~----g~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 192 (219)
T smart00062 122 KKL--YPEAKIVSYDSQAEALAALKA----GRADAAVADAPALAALVKQHGLPELKIVGDPLDTPEGYAFAVRKGDP 192 (219)
T ss_pred HHh--CCCceEEEcCCHHHHHHHhhc----CcccEEEeccHHHHHHHHhcCCCceeeccCCCCCCcceEEEEECCCH
Confidence 543 222356667888999999999 89999999999888887664 677777665555 778999988864
No 105
>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=99.30 E-value=9.9e-11 Score=115.75 Aligned_cols=186 Identities=25% Similarity=0.403 Sum_probs=148.3
Q ss_pred EEEecCCCccceeEeeCCCcceeeeeHHHHHHHHHHCCCccceEEeeCCCCCCCCChhHHHHHHHcCcccEEEeeEEeec
Q 003958 471 RIGVPNRVSFREFVSVKGSEMTSGFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIIT 550 (784)
Q Consensus 471 ~v~~~~~~~~~~~~~~~~~~~~~G~~~dl~~~l~~~l~f~~~~~~~~~~~~~~~~~~~g~i~~l~~~~~D~~~~~~~~t~ 550 (784)
+|++.. .++|+.+.++++...|+..|+++.+.++++.+ +++... .|..++..+.+|++|++++....+.
T Consensus 2 ~i~~~~--~~~p~~~~~~~g~~~G~~~~~~~~~~~~~g~~--~~~~~~-------~~~~~~~~l~~g~~D~~~~~~~~~~ 70 (218)
T cd00134 2 TVGTAG--TYPPFSFRDANGELTGFDVDLAKAIAKELGVK--VKFVEV-------DWDGLITALKSGKVDLIAAGMTITP 70 (218)
T ss_pred EEecCC--CCCCeeEECCCCCEEeeeHHHHHHHHHHhCCe--EEEEeC-------CHHHHHHHHhcCCcCEEeecCcCCH
Confidence 455544 46777777788999999999999999999977 666554 3899999999999999998877889
Q ss_pred CccccceeccccccccEEEEEeccCCccccccccccccHHHHHHHHHHHHHHHHHhhheecccCCCCCCCccCCceeehh
Q 003958 551 NRTKMADFTQPYIESGLVVVAPVRKLDSNAWAFLSPFTPMMWGVTAIFFLAVGAVVWILEHRLNDEFRGPPKRQVVTIFW 630 (784)
Q Consensus 551 ~r~~~~~fs~p~~~~~~~~~~~~~~~~~~~~~~~~pf~~~~W~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 630 (784)
+|.+.+.|+.|+......+++++..
T Consensus 71 ~~~~~~~~~~~~~~~~~~~~~~~~~------------------------------------------------------- 95 (218)
T cd00134 71 ERAKQVDFSDPYYKSGQVILVKKGS------------------------------------------------------- 95 (218)
T ss_pred HHHhhccCcccceeccEEEEEECCC-------------------------------------------------------
Confidence 9999999999999999999997764
Q ss_pred hhhhhhhcccccccccchhhHHHHHHHHHHHHHHhhccccceeeEeeccccCCCCChHhhhhCCCceEEeeCchHHHHHH
Q 003958 631 FSFSTMFFAHKEKTVSALGRLVLIIWLFVVLIINSSYTASLTSILTVQKLSSPIKGIDSLRSSNYPIGYQVNSFARNYLV 710 (784)
Q Consensus 631 ~~~~~~~~~~~~~p~~~~~R~~~~~w~~~~lvl~~~Yta~L~s~l~~~~~~~~i~~~~dl~~~~~~i~~~~~~~~~~~~~ 710 (784)
++.+++||. +.++++..++....++.
T Consensus 96 ----------------------------------------------------~~~~~~dl~--g~~i~~~~~~~~~~~~~ 121 (218)
T cd00134 96 ----------------------------------------------------PIKSVKDLK--GKKVAVQKGSTAEKYLK 121 (218)
T ss_pred ----------------------------------------------------CCCChHHhC--CCEEEEEcCchHHHHHH
Confidence 456899997 88899998887777775
Q ss_pred hhcccCccCceeCCCHHHHHHHHhcCCcCCCeeEEEechhhhHHHHcCC-CCeEEeCCccc--cceEEEEeeCCC
Q 003958 711 DELNIDESRLVPLNSPEEYAKALKDGPHKGGVAAVVDDRAYAELFLSTR-CEFSIVGQVFT--KNGWGFVSIVSS 782 (784)
Q Consensus 711 ~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~a~~~~~~~~~~~~~~~-c~l~~~~~~~~--~~~~~~~~~k~s 782 (784)
+... ...+..+.+.++.++.|.+ |+.++++.+...+.+..++. +++..+..... ...++++.++++
T Consensus 122 ~~~~--~~~~~~~~~~~~~~~~l~~----g~~d~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~ 190 (218)
T cd00134 122 KALP--EAKVVSYDDNAEALAALEN----GRADAVIVDEIALAALLKKHPPELKIVGPSIDLEPLGFGVAVGKDN 190 (218)
T ss_pred HhCC--cccEEEeCCHHHHHHHHHc----CCccEEEeccHHHHHHHHhcCCCcEEeccccCCCccceEEEEcCCC
Confidence 4322 3456678889999999999 89999999999988887665 77877765423 334455555543
No 106
>PF04348 LppC: LppC putative lipoprotein; InterPro: IPR007443 This entry includes several bacterial outer membrane antigens, whose molecular function is unknown.; PDB: 3CKM_A.
Probab=99.25 E-value=1.8e-10 Score=127.44 Aligned_cols=307 Identities=16% Similarity=0.181 Sum_probs=164.7
Q ss_pred ceEEEEEEeecCCc---chhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEccCch
Q 003958 30 SVVNIGALLSFSTN---VGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIGPQDA 106 (784)
Q Consensus 30 ~~i~IG~i~~~~~~---~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiGp~~s 106 (784)
.+=+|++++|+++. .|.....|+..|. +... +.+.++.++|+..+... ....+.+.+|+..||||..-
T Consensus 218 ~~~~IavLLPlsG~~a~~~~aI~~G~~aA~---~~~~----~~~~~l~~~Dt~~~~~~--~~~~~a~~~ga~~ViGPL~k 288 (536)
T PF04348_consen 218 PPQRIAVLLPLSGRLARAGQAIRDGFLAAY---YADA----DSRPELRFYDTNADSAD--ALYQQAVADGADFVIGPLLK 288 (536)
T ss_dssp ----EEEEE--SSTTHHHHHHHHHHHHHHH------T----T--S-EEEEETTTS-HH--HHHHHHHHTT--EEE---SH
T ss_pred CccCEEEEeCCCCchhHHHHHHHHHHHHhh---cccc----cCCCceEEecCCCCCHH--HHHHHHHHcCCCEEEcCCCH
Confidence 35689999999954 3667788888888 1221 23457788898776332 34556667799999999999
Q ss_pred hhHHHHHHhhhc--CCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcCCCcchhHHHH
Q 003958 107 VTSHVVSHVANE--LQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDDDHGRNGIAAL 184 (784)
Q Consensus 107 ~~~~~va~~~~~--~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l 184 (784)
+....++..-.. -.||++.....+..- .-+.++...-+.+.++..+++.+..-|+++..||+.++++|+...+.|
T Consensus 289 ~~V~~l~~~~~~~~~~vp~LaLN~~~~~~---~~~~l~~f~LspEdEA~q~A~~a~~~g~~~alvl~p~~~~g~R~~~aF 365 (536)
T PF04348_consen 289 SNVEALAQLPQLQAQPVPVLALNQPDNSQ---APPNLYQFGLSPEDEARQAAQKAFQDGYRRALVLAPQNAWGQRMAEAF 365 (536)
T ss_dssp HHHHHHHH-GG-GGTT-EEEES---TT-------TTEEE----HHHHHHHHHHHHHHTT--S-EEEEESSHHHHHHHHHH
T ss_pred HHHHHHHhcCcccccCCceeeccCCCccc---CccceEEEeCCcHHHHHHHHHHHHhcCCCCEEEEcCCChHHHHHHHHH
Confidence 888877665442 489999986655431 124566666677888999999999999999999999999999999999
Q ss_pred HHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHcCCCCCCeEEEecCcc-cccc
Q 003958 185 GDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIATSWL-STAL 263 (784)
Q Consensus 185 ~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~-~~~~ 263 (784)
.+.....|..+.....+. ...++...++.-.+.+.|.|++.+.+.+++.+--...-. . ..+.-.+.++-. ....
T Consensus 366 ~~~W~~~gg~~~~~~~~~---~~~~~~~~i~~r~r~d~D~ifl~a~~~~ar~ikP~l~~~-~-a~~lPvyatS~~~~g~~ 440 (536)
T PF04348_consen 366 NQQWQALGGQVAEVSYYG---SPADLQAAIQPRRRQDIDAIFLVANPEQARLIKPQLDFH-F-AGDLPVYATSRSYSGSP 440 (536)
T ss_dssp HHHHHHHHSS--EEEEES---STTHHHHHHHHS--TT--EEEE---HHHHHHHHHHHTT--T--TT-EEEE-GGG--HHT
T ss_pred HHHHHHcCCCceeeEecC---CHHHHHHHHhhcCCCCCCEEEEeCCHHHHHHHhhhcccc-c-CCCCCEEEeccccCCCC
Confidence 999999988776666665 446788888866667899999999988887776555432 1 112223333322 2111
Q ss_pred ccCCCCCCCccccceeeEEEeeec---CCchhHHHHHHHHHhhccCCCCCCCCCCChhHHHHhhHHHHHHHHHHHHhhcC
Q 003958 264 DTNSPFPSDVMDDIQGVLTLRTYT---PDSVLKRKFISRWRNLTDAKTPNGYIGLNAYGFYAYDTVWLLARAINSFFKQG 340 (784)
Q Consensus 264 ~~~~~~~~~~~~~~~g~~~~~~~~---~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~YDAv~~~a~Al~~~~~~~ 340 (784)
+ ......++|+....... +..+..+.+.+.|.... .......+.+|||..++.+ +.+
T Consensus 441 ~------~~~~~dL~gv~f~d~Pwll~~~~~~~~~~~~~~~~~~--------~~~~RL~AlG~DA~~L~~~-l~~----- 500 (536)
T PF04348_consen 441 N------PSQDRDLNGVRFSDMPWLLDPNSPLRQQLAALWPNAS--------NSLQRLYALGIDAYRLAPR-LPQ----- 500 (536)
T ss_dssp -------HHHHHHTTT-EEEE-GGGG---SHHHHHHH-HHTTT---------HHHHHHHHHHHHHHHHHHT-HHH-----
T ss_pred C------cchhhhhcCCEEeccccccCCCchHHHHHHhhccCCc--------cHHHHHHHHHHHHHHHHHH-HHH-----
Confidence 1 12235678877765432 22333333433333211 1122345666776554432 111
Q ss_pred CccccccCCccccccCCcccccccccCCchHHHHHHHhccccceeeeEEEecCCCCcCCcEEEEEe
Q 003958 341 GNLSFSKDSRLSDIQGHLRLDSLRIFNGGNLLRDSILQANMTGTAGPARFNSHGDLINPAYEIINV 406 (784)
Q Consensus 341 ~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~l~~~l~~~~f~g~tG~v~Fd~~g~~~~~~~~I~~~ 406 (784)
++.+....+.|.||.+++|++|. +...+.-.++
T Consensus 501 --------------------------------l~~~~~~~~~G~TG~L~~~~~g~-i~R~l~wa~f 533 (536)
T PF04348_consen 501 --------------------------------LRQFPGYRLDGLTGQLSLDEDGR-IERQLSWAQF 533 (536)
T ss_dssp --------------------------------HHHSTT--EEETTEEEEE-TT-B-EEEE-EEEEE
T ss_pred --------------------------------HhhCCCCcccCCceeEEECCCCe-EEEeecceee
Confidence 11223346899999999999985 4444443333
No 107
>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=99.00 E-value=2.3e-10 Score=85.54 Aligned_cols=50 Identities=22% Similarity=0.443 Sum_probs=38.6
Q ss_pred CCCcceeeeeHHHHHHHHHHCCCccceEEeeCC---CCCCCCChhHHHHHHHc
Q 003958 487 KGSEMTSGFCIDVFTAAINLLPYAVPYKLIPFG---DGHNNPSCTELVRLITA 536 (784)
Q Consensus 487 ~~~~~~~G~~~dl~~~l~~~l~f~~~~~~~~~~---~~~~~~~~~g~i~~l~~ 536 (784)
.++.++.|||+||+++|++.|||++++..++.+ ..++||+|+|||++|++
T Consensus 13 ~g~~~~eGyciDll~~la~~l~F~y~i~~~~Dg~yG~~~~~g~W~GmiGeli~ 65 (65)
T PF10613_consen 13 TGNDRYEGYCIDLLEELAEELNFTYEIYLVPDGKYGSKNPNGSWNGMIGELIR 65 (65)
T ss_dssp BGGGGEESHHHHHHHHHHHHHT-EEEEEE-TTS--EEBETTSEBEHHHHHHHT
T ss_pred CCCccEEEEHHHHHHHHHHHcCCeEEEEECCCCCCcCcCCCCcCcCHHHHhcC
Confidence 578999999999999999999999444444321 22368999999999975
No 108
>smart00079 PBPe Eukaryotic homologues of bacterial periplasmic substrate binding proteins. Prokaryotic homologues are represented by a separate alignment: PBPb
Probab=98.81 E-value=1.7e-08 Score=91.47 Aligned_cols=97 Identities=22% Similarity=0.285 Sum_probs=81.5
Q ss_pred CCCChHhhhhC-CCceEEeeCchHHHHHHhhcccC------c---cCceeCCCHHHHHHHHhcCCcCCCeeEEEechhhh
Q 003958 683 PIKGIDSLRSS-NYPIGYQVNSFARNYLVDELNID------E---SRLVPLNSPEEYAKALKDGPHKGGVAAVVDDRAYA 752 (784)
Q Consensus 683 ~i~~~~dl~~~-~~~i~~~~~~~~~~~~~~~~~~~------~---~~~~~~~~~~~~~~~l~~~~~~~~~~a~~~~~~~~ 752 (784)
||++++||..+ +.+||++.|++.+.++++..... . .++..+++.++++.+|++ ++ +|++.|.+.+
T Consensus 1 ~i~~~~dl~~~~~~~vgv~~gs~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~----g~-da~v~d~~~~ 75 (134)
T smart00079 1 PITSVEDLAKQTKIEYGTIRGSSTLAFFKRSGNPEYSRMWNYMSASPSVFVKSYAEGVQRVRV----SN-YAFLMESTYL 75 (134)
T ss_pred CCCChHHHhhCCCccceEecCchHHHHHHhCCChHHHHHHHHHHhCCCCCCCCHHHHHHHHHc----CC-CEEEeehHhH
Confidence 58899999954 36899999999999996532210 0 256678999999999999 88 9999999999
Q ss_pred HHHHcCCCCeEEeCCccccceEEEEeeCCCCC
Q 003958 753 ELFLSTRCEFSIVGQVFTKNGWGFVSIVSSFY 784 (784)
Q Consensus 753 ~~~~~~~c~l~~~~~~~~~~~~~~~~~k~s~~ 784 (784)
.|++++.|++.+++..+...+||+++|||+++
T Consensus 76 ~~~~~~~~~~~~~~~~~~~~~~~ia~~k~~~l 107 (134)
T smart00079 76 DYELSQNCDLMTVGENFGRKGYGIAFPKGSPL 107 (134)
T ss_pred HHHHhCCCCeEEcCcccCCCceEEEecCCCHH
Confidence 99988899999999888889999999999874
No 109
>COG4623 Predicted soluble lytic transglycosylase fused to an ABC-type amino acid-binding protein [Cell envelope biogenesis, outer membrane]
Probab=98.80 E-value=3.5e-08 Score=98.06 Aligned_cols=192 Identities=14% Similarity=0.108 Sum_probs=151.9
Q ss_pred CccEEEEecCCCccceeEeeCCCcceeeeeHHHHHHHHHHCCCccceEEeeCCCCCCCCChhHHHHHHHcCcccEEEeeE
Q 003958 467 GRHLRIGVPNRVSFREFVSVKGSEMTSGFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDI 546 (784)
Q Consensus 467 ~~~l~v~~~~~~~~~~~~~~~~~~~~~G~~~dl~~~l~~~l~f~~~~~~~~~~~~~~~~~~~g~i~~l~~~~~D~~~~~~ 546 (784)
.+.|+|.+.++ |.+. ...++...|++++|.+.+++.||.+ .++.+. .+-+.+..+|.+|++|++++++
T Consensus 22 rGvLrV~tins-p~sy---~~~~~~p~G~eYelak~Fa~yLgV~--Lki~~~------~n~dqLf~aL~ng~~DL~Aagl 89 (473)
T COG4623 22 RGVLRVSTINS-PLSY---FEDKGGPTGLEYELAKAFADYLGVK--LKIIPA------DNIDQLFDALDNGNADLAAAGL 89 (473)
T ss_pred cCeEEEEeecC-ccce---eccCCCccchhHHHHHHHHHHhCCe--EEEEec------CCHHHHHHHHhCCCcceecccc
Confidence 46799999876 3333 2345667899999999999999987 666554 4568999999999999999999
Q ss_pred EeecCccccceeccccccccEEEEEeccCCccccccccccccHHHHHHHHHHHHHHHHHhhheecccCCCCCCCccCCce
Q 003958 547 AIITNRTKMADFTQPYIESGLVVVAPVRKLDSNAWAFLSPFTPMMWGVTAIFFLAVGAVVWILEHRLNDEFRGPPKRQVV 626 (784)
Q Consensus 547 ~~t~~r~~~~~fs~p~~~~~~~~~~~~~~~~~~~~~~~~pf~~~~W~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 626 (784)
...++|.+.+....-|+.....++.++..
T Consensus 90 ~~~~~~l~~~~~gP~y~svs~qlVyRkG~--------------------------------------------------- 118 (473)
T COG4623 90 LYNSERLKNFQPGPTYYSVSQQLVYRKGQ--------------------------------------------------- 118 (473)
T ss_pred cCChhHhcccCCCCceecccHHHHhhcCC---------------------------------------------------
Confidence 99999999999998899999999988774
Q ss_pred eehhhhhhhhhcccccccccchhhHHHHHHHHHHHHHHhhccccceeeEeeccccCCCCChHhhhhCCCceEEeeCchHH
Q 003958 627 TIFWFSFSTMFFAHKEKTVSALGRLVLIIWLFVVLIINSSYTASLTSILTVQKLSSPIKGIDSLRSSNYPIGYQVNSFAR 706 (784)
Q Consensus 627 ~~~~~~~~~~~~~~~~~p~~~~~R~~~~~w~~~~lvl~~~Yta~L~s~l~~~~~~~~i~~~~dl~~~~~~i~~~~~~~~~ 706 (784)
....++++|. +..|-+..|+...
T Consensus 119 -------------------------------------------------------~Rp~~l~~L~--g~~i~v~~gs~~~ 141 (473)
T COG4623 119 -------------------------------------------------------YRPRSLGQLK--GRQITVAKGSAHV 141 (473)
T ss_pred -------------------------------------------------------CCCCCHHHcc--CceeeccCCcHHH
Confidence 2347899999 7778899999766
Q ss_pred HHHHhhcc-cCccCceeC---CCHHHHHHHHhcCCcCCCeeEEEechhhhHHHHcCCCCeEEeCCccccceEEEEeeCCC
Q 003958 707 NYLVDELN-IDESRLVPL---NSPEEYAKALKDGPHKGGVAAVVDDRAYAELFLSTRCEFSIVGQVFTKNGWGFVSIVSS 782 (784)
Q Consensus 707 ~~~~~~~~-~~~~~~~~~---~~~~~~~~~l~~~~~~~~~~a~~~~~~~~~~~~~~~c~l~~~~~~~~~~~~~~~~~k~s 782 (784)
+-++.... .-+..+++. ...+|.++.|.. |.++-.+.|.+.+..+.+-+++|.+.-..-...+.+|.+|.++
T Consensus 142 ~~l~~lk~~kyP~l~~k~d~~~~~~dLle~v~~----Gkldytiads~~is~~q~i~P~laVafd~tde~~v~Wy~~~~d 217 (473)
T COG4623 142 EDLKLLKETKYPELIWKVDDKLGVEDLLEMVAE----GKLDYTIADSVEISLFQRVHPELAVAFDLTDEQPVAWYLPRDD 217 (473)
T ss_pred HHHHHHHHhhcchhhhhhcccccHHHHHHHHhc----CCcceeeeccHHHHHHHHhCccceeeeecccccCceeeccCCc
Confidence 66544322 122333333 367899999999 8999999999999888888999877766666788899998864
No 110
>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=98.80 E-value=3.6e-07 Score=93.41 Aligned_cols=202 Identities=12% Similarity=0.086 Sum_probs=141.0
Q ss_pred EEEEEeecC-CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEccCchhhHHH
Q 003958 33 NIGALLSFS-TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIGPQDAVTSHV 111 (784)
Q Consensus 33 ~IG~i~~~~-~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiGp~~s~~~~~ 111 (784)
+||+++|.+ ..+......+++.+.++ . |+ ++.+.|+..++....+.+.+++.+++.++|+...+.....
T Consensus 1 ~ig~v~~~~~~~~~~~~~~g~~~~~~~----~----g~--~l~~~~~~~~~~~~~~~~~~~~~~~~d~ii~~~~~~~~~~ 70 (264)
T cd01537 1 TIGVLVPDLDNPFFAQVLKGIEEAAKA----A----GY--QVLLANSQNDAEKQLSALENLIARGVDGIIIAPSDLTAPT 70 (264)
T ss_pred CeEEEEcCCCChHHHHHHHHHHHHHHH----c----CC--eEEEEeCCCCHHHHHHHHHHHHHcCCCEEEEecCCCcchh
Confidence 489999885 44445666777777766 1 34 5566677778877788888888889999988666554444
Q ss_pred HHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcCC--CcchhHHHHHHHHh
Q 003958 112 VSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDDD--HGRNGIAALGDTLA 189 (784)
Q Consensus 112 va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~~--~g~~~~~~l~~~l~ 189 (784)
....+...++|+|......+. .+++++..+.+...+..+++++...+-++|++|..+.. ++....+.+++.++
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 567788899999998665432 24566777788888999999998889999999987544 56667889999988
Q ss_pred ccC-cEEEEeeccCCCCChhHHHHHHHHhhcCC--ceEEEEeccCCcHHHHHHHHHHcCCCCCCeE
Q 003958 190 AKR-CRISFKAPLSVEATEDEITDLLVKVALTE--SRIIVVHTHYNRGPVVFHVAQYLGMLGTGYV 252 (784)
Q Consensus 190 ~~g-i~v~~~~~~~~~~~~~d~~~~l~~l~~~~--~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~ 252 (784)
+.| ..+....... .+..+....+.++.+.+ +++|+.. ....+..+++++.+.|+..++.+
T Consensus 146 ~~~~~~~~~~~~~~--~~~~~~~~~~~~~l~~~~~~~~i~~~-~~~~a~~~~~~~~~~g~~i~~~i 208 (264)
T cd01537 146 EAGPIEIVLVQEGD--WDAEKGYQAAEELLTAHPDPTAIFAA-NDDMALGALRALREAGLRVPDDI 208 (264)
T ss_pred HcCCcChhhhccCC--CCHHHHHHHHHHHHhcCCCCCEEEEc-CcHHHHHHHHHHHHhCCCCCCCe
Confidence 877 3333222222 24455666777766655 4555443 33566678899999887644333
No 111
>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=98.76 E-value=2e-06 Score=88.20 Aligned_cols=198 Identities=11% Similarity=0.060 Sum_probs=134.0
Q ss_pred EEEEEeecC-CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEccCch-hhHH
Q 003958 33 NIGALLSFS-TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIGPQDA-VTSH 110 (784)
Q Consensus 33 ~IG~i~~~~-~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiGp~~s-~~~~ 110 (784)
+||++.|.. ..+......+++.+.++. |+ .+.+.++..++......+.+++.+++.+||+...+ ....
T Consensus 1 ~ig~i~p~~~~~~~~~~~~~~~~~a~~~--------g~--~~~~~~~~~~~~~~~~~~~~l~~~~vdgvi~~~~~~~~~~ 70 (267)
T cd01536 1 KIGLVVPSLNNPFWQAMNKGAEAAAKEL--------GV--ELIVLDAQNDVSKQIQQIEDLIAQGVDGIIISPVDSAALT 70 (267)
T ss_pred CEEEEeccccCHHHHHHHHHHHHHHHhc--------Cc--eEEEECCCCCHHHHHHHHHHHHHcCCCEEEEeCCCchhHH
Confidence 589999874 444456677777777761 34 45556777788887888888888899988864433 3223
Q ss_pred HHHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHc--CCcEEEEEEEcC--CCcchhHHHHHH
Q 003958 111 VVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHY--GWREVIAIYVDD--DHGRNGIAALGD 186 (784)
Q Consensus 111 ~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~--~w~~v~ii~~d~--~~g~~~~~~l~~ 186 (784)
.....+...++|+|......+. .+.+..+.+++...+..+++++.+. +-+++++|+.+. .++....+.+++
T Consensus 71 ~~~~~l~~~~ip~V~~~~~~~~-----~~~~~~v~~d~~~~~~~~~~~l~~~~~g~~~i~~i~~~~~~~~~~~r~~gf~~ 145 (267)
T cd01536 71 PALKKANAAGIPVVTVDSDIDG-----GNRLAYVGTDNYEAGRLAGEYLAKLLGGKGKVAIIEGPPGSSNAQERVKGFRD 145 (267)
T ss_pred HHHHHHHHCCCcEEEecCCCCc-----cceeEEEecCHHHHHHHHHHHHHHHhCCCceEEEEEcccccchHHHHHHHHHH
Confidence 3456667789999997654332 1334556677777788888888776 899999998654 367778899999
Q ss_pred HHhcc-CcEEEEeeccCCCCChhHHHHHHHHhhcCCceE-EEEeccCCcHHHHHHHHHHcCCC
Q 003958 187 TLAAK-RCRISFKAPLSVEATEDEITDLLVKVALTESRI-IVVHTHYNRGPVVFHVAQYLGML 247 (784)
Q Consensus 187 ~l~~~-gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~v-Ivl~~~~~~~~~~~~~a~~~g~~ 247 (784)
.+++. |+++....... ....+....+.++.+..++. +++++....+..+++++++.|+.
T Consensus 146 ~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~i~~~~d~~a~~~~~~l~~~g~~ 206 (267)
T cd01536 146 ALKEYPDIEIVAVQDGN--WDREKALQAMEDLLQANPDIDAIFAANDSMALGAVAALKAAGRK 206 (267)
T ss_pred HHHhCCCcEEEEEecCC--CcHHHHHHHHHHHHHhCCCccEEEEecCCchHHHHHHHHhcCCC
Confidence 99888 46654332222 23345566777765544433 23334456778899999998875
No 112
>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=98.69 E-value=1.3e-06 Score=89.40 Aligned_cols=204 Identities=11% Similarity=0.040 Sum_probs=136.6
Q ss_pred EEEEEeecC-CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEccCchhhHHH
Q 003958 33 NIGALLSFS-TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIGPQDAVTSHV 111 (784)
Q Consensus 33 ~IG~i~~~~-~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiGp~~s~~~~~ 111 (784)
+||++.|.. ..+......+++.+.++. |+++ .+.|...++.+..+....++++++.+|+....+.....
T Consensus 1 ~i~~v~~~~~~~~~~~~~~g~~~~~~~~--------g~~~--~~~~~~~~~~~~~~~~~~~~~~~~d~iii~~~~~~~~~ 70 (264)
T cd06267 1 TIGVIVPDISNPFFAELLRGIEEAAREA--------GYSV--LLCNSDEDPEKEREALELLLSRRVDGIILAPSRLDDEL 70 (264)
T ss_pred CEEEEECCCCCHHHHHHHHHHHHHHHHc--------CCEE--EEEcCCCCHHHHHHHHHHHHHcCcCEEEEecCCcchHH
Confidence 378888875 334445556666666551 4444 45576778888888888999989998887665555544
Q ss_pred HHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcCC--CcchhHHHHHHHHh
Q 003958 112 VSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDDD--HGRNGIAALGDTLA 189 (784)
Q Consensus 112 va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~~--~g~~~~~~l~~~l~ 189 (784)
...+...++|+|......+. +.+..+.++....+..+++.+...|.+++++++.+.. ++....+.+++.++
T Consensus 71 -~~~~~~~~ipvv~~~~~~~~------~~~~~v~~d~~~~g~~~~~~l~~~g~~~i~~i~~~~~~~~~~~r~~g~~~~~~ 143 (264)
T cd06267 71 -LEELAALGIPVVLVDRPLDG------LGVDSVGIDNRAGAYLAVEHLIELGHRRIAFIGGPPDLSTARERLEGYREALE 143 (264)
T ss_pred -HHHHHHcCCCEEEecccccC------CCCCEEeeccHHHHHHHHHHHHHCCCceEEEecCCCccchHHHHHHHHHHHHH
Confidence 66678899999998655332 3445566677777888889888889999999986543 66777888999998
Q ss_pred ccCcEEEEeeccCCCCChhHHHHHHHHhhcCC--ceEEEEeccCCcHHHHHHHHHHcCCCCCCeEEE
Q 003958 190 AKRCRISFKAPLSVEATEDEITDLLVKVALTE--SRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWI 254 (784)
Q Consensus 190 ~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~--~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~wi 254 (784)
+.+..+..........+..+....++++.+.. .++|+. .....+..+++++++.|+..++.+.+
T Consensus 144 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~i~~-~~~~~a~~~~~al~~~g~~~~~~i~i 209 (264)
T cd06267 144 EAGIPLDEELIVEGDFSEESGYEAARELLASGERPTAIFA-ANDLMAIGALRALRELGLRVPEDVSV 209 (264)
T ss_pred HcCCCCCcceEEecccchhhHHHHHHHHHhcCCCCcEEEE-cCcHHHHHHHHHHHHhCCCCCCceEE
Confidence 88753322222221123345566777766554 565554 34456678888899988764444433
No 113
>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=98.69 E-value=3e-06 Score=87.26 Aligned_cols=202 Identities=14% Similarity=0.045 Sum_probs=135.6
Q ss_pred EEEEEeecCCc-chhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEccCch-hhHH
Q 003958 33 NIGALLSFSTN-VGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIGPQDA-VTSH 110 (784)
Q Consensus 33 ~IG~i~~~~~~-~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiGp~~s-~~~~ 110 (784)
|||+++|.... +-.....+++.+.++ .+. .|+.+++.+.|+..++....+....++.+++.+||....+ ....
T Consensus 1 ~Ig~i~~~~~~~~~~~~~~~i~~~~~~----~~~-~g~~~~l~i~~~~~~~~~~~~~~~~~~~~~vdgiIi~~~~~~~~~ 75 (272)
T cd06300 1 KIGLSNSYAGNTWRAQMLDEFKAQAKE----LKK-AGLISEFIVTSADGDVAQQIADIRNLIAQGVDAIIINPASPTALN 75 (272)
T ss_pred CeEEeccccCChHHHHHHHHHHHHHHh----hhc-cCCeeEEEEecCCCCHHHHHHHHHHHHHcCCCEEEEeCCChhhhH
Confidence 58899876422 222344555555544 111 2677888899999898888888888988999999875443 3233
Q ss_pred HHHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHc--CCcEEEEEEEc--CCCcchhHHHHHH
Q 003958 111 VVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHY--GWREVIAIYVD--DDHGRNGIAALGD 186 (784)
Q Consensus 111 ~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~--~w~~v~ii~~d--~~~g~~~~~~l~~ 186 (784)
.....+...++|+|......+ . +.+.++.+++...+..++++|.+. +-+++++|..+ ...+....+.+++
T Consensus 76 ~~l~~~~~~~iPvv~~~~~~~---~---~~~~~v~~d~~~~g~~~~~~l~~~~~g~~~i~~i~~~~~~~~~~~R~~g~~~ 149 (272)
T cd06300 76 PVIEEACEAGIPVVSFDGTVT---T---PCAYNVNEDQAEFGKQGAEWLVKELGGKGNVLVVRGLAGHPVDEDRYAGAKE 149 (272)
T ss_pred HHHHHHHHCCCeEEEEecCCC---C---CceeEecCCHHHHHHHHHHHHHHHcCCCceEEEEECCCCCcchHHHHHHHHH
Confidence 344566778999999764321 1 346677888888889999988766 88999999743 3345667788999
Q ss_pred HHhccC-cEEEEeeccCCCCChhHHHHHHHHhhcCCc--eEEEEeccCCcHHHHHHHHHHcCCCCC
Q 003958 187 TLAAKR-CRISFKAPLSVEATEDEITDLLVKVALTES--RIIVVHTHYNRGPVVFHVAQYLGMLGT 249 (784)
Q Consensus 187 ~l~~~g-i~v~~~~~~~~~~~~~d~~~~l~~l~~~~~--~vIvl~~~~~~~~~~~~~a~~~g~~~~ 249 (784)
.+++.+ +.+......+ .+..+....+.++.++++ ++|+.. ... +..+++++++.|+..+
T Consensus 150 a~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~l~~~~~~~~i~~~-~d~-A~g~~~al~~~g~~~p 211 (272)
T cd06300 150 VLKEYPGIKIVGEVYGD--WDQAVAQKAVADFLASNPDVDGIWTQ-GGD-AVGAVQAFEQAGRDIP 211 (272)
T ss_pred HHHHCCCcEEEeecCCC--CCHHHHHHHHHHHHHhCCCcCEEEec-CCC-cHHHHHHHHHcCCCCc
Confidence 998887 7765322222 233455667777665544 443333 333 8899999999997443
No 114
>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=98.63 E-value=5.8e-07 Score=91.49 Aligned_cols=184 Identities=15% Similarity=0.101 Sum_probs=128.1
Q ss_pred ccEEEEecCCCccceeEeeCCCcceeeeeHHHHHHHHHHCCCccceEEeeCCCCCCCCChhHHHHHHHcCcccEEEeeEE
Q 003958 468 RHLRIGVPNRVSFREFVSVKGSEMTSGFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIA 547 (784)
Q Consensus 468 ~~l~v~~~~~~~~~~~~~~~~~~~~~G~~~dl~~~l~~~l~f~~~~~~~~~~~~~~~~~~~g~i~~l~~~~~D~~~~~~~ 547 (784)
++|+|++... +.+ ..+.+...++.+.+++++|.+ ++++.. ++|+.++..+.+|++|+++.+..
T Consensus 32 ~~l~vg~~~~--~~~-------~~~~~~~~~l~~~l~~~~g~~--v~~~~~------~~~~~~~~~l~~g~~Di~~~~~~ 94 (254)
T TIGR01098 32 KELNFGILPG--ENA-------SNLTRRWEPLADYLEKKLGIK--VQLFVA------TDYSAVIEAMRFGRVDIAWFGPS 94 (254)
T ss_pred CceEEEECCC--CCH-------HHHHHHHHHHHHHHHHHhCCc--EEEEeC------CCHHHHHHHHHcCCccEEEECcH
Confidence 4688887642 222 223455679999999999988 554443 46999999999999999986654
Q ss_pred eec---Cccccceeccccccc------cEEEEEeccCCccccccccccccHHHHHHHHHHHHHHHHHhhheecccCCCCC
Q 003958 548 IIT---NRTKMADFTQPYIES------GLVVVAPVRKLDSNAWAFLSPFTPMMWGVTAIFFLAVGAVVWILEHRLNDEFR 618 (784)
Q Consensus 548 ~t~---~r~~~~~fs~p~~~~------~~~~~~~~~~~~~~~~~~~~pf~~~~W~~i~~~~~~~~~~~~~~~~~~~~~~~ 618 (784)
... +|.+..+|+.|+... ...+++++.
T Consensus 95 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lvv~~d-------------------------------------------- 130 (254)
T TIGR01098 95 SYVLAHYRANAEVFALTAVSTDGSPGYYSVIIVKAD-------------------------------------------- 130 (254)
T ss_pred HHHHHHHhcCCceEEeeccccCCCCceEEEEEEECC--------------------------------------------
Confidence 333 566778888886543 235555443
Q ss_pred CCccCCceeehhhhhhhhhcccccccccchhhHHHHHHHHHHHHHHhhccccceeeEeeccccCCCCChHhhhhCCCceE
Q 003958 619 GPPKRQVVTIFWFSFSTMFFAHKEKTVSALGRLVLIIWLFVVLIINSSYTASLTSILTVQKLSSPIKGIDSLRSSNYPIG 698 (784)
Q Consensus 619 ~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~R~~~~~w~~~~lvl~~~Yta~L~s~l~~~~~~~~i~~~~dl~~~~~~i~ 698 (784)
.+|++++||. +++|+
T Consensus 131 ---------------------------------------------------------------~~i~~~~dL~--gk~I~ 145 (254)
T TIGR01098 131 ---------------------------------------------------------------SPIKSLKDLK--GKTFA 145 (254)
T ss_pred ---------------------------------------------------------------CCCCChHHhc--CCEEE
Confidence 2689999997 88899
Q ss_pred Eee-CchH-----HHHHHhhcccCc----cCceeCCCHHHHHHHHhcCCcCCCeeEEEechhhhHHHHcCCC----CeEE
Q 003958 699 YQV-NSFA-----RNYLVDELNIDE----SRLVPLNSPEEYAKALKDGPHKGGVAAVVDDRAYAELFLSTRC----EFSI 764 (784)
Q Consensus 699 ~~~-~~~~-----~~~~~~~~~~~~----~~~~~~~~~~~~~~~l~~~~~~~~~~a~~~~~~~~~~~~~~~c----~l~~ 764 (784)
+.. ++.. ..++.+....+. ..+....+..+.+++|.+ |+.||.+.+.+.+.++.++.. ++.+
T Consensus 146 ~~~~~s~~~~~~~~~~l~~~~~~~~~~~~~~i~~~~~~~~~~~al~~----G~~Da~~~~~~~~~~~~~~~~~~~~~~~~ 221 (254)
T TIGR01098 146 FGDPASTSGYLVPRYQLKKEGGLDADGFFSEVVFSGSHDASALAVAN----GKVDAATNNSSAIGRLKKRGPSDMKKVRV 221 (254)
T ss_pred eeCCCCccchHhHHHHHHHhcCCChHHhhhheeecCchHHHHHHHHc----CCCCeEEecHHHHHHHHHhCccchhheEE
Confidence 874 3321 233433332221 234445567889999999 899999999998887766542 5788
Q ss_pred eCCccccceEEEEeeCC
Q 003958 765 VGQVFTKNGWGFVSIVS 781 (784)
Q Consensus 765 ~~~~~~~~~~~~~~~k~ 781 (784)
+++.....+++++++|+
T Consensus 222 ~~~~~~~~~~~~~~~~~ 238 (254)
T TIGR01098 222 IWKSPLIPNDPIAVRKD 238 (254)
T ss_pred EEecCCCCCCCEEEECC
Confidence 88766667789999998
No 115
>COG2984 ABC-type uncharacterized transport system, periplasmic component [General function prediction only]
Probab=98.52 E-value=5.3e-05 Score=75.40 Aligned_cols=204 Identities=14% Similarity=0.154 Sum_probs=139.5
Q ss_pred CCCceEEEEEEeecCCcchhhHHHHHHHHHHHHhcCCCCCCCC-EEEEEEecCCCCHHHHHHHHHHHHhcCceEEEccCc
Q 003958 27 GRPSVVNIGALLSFSTNVGKVAKLAIKAAVDDVNSDPTTLGGT-KLKLQMQDCNHSGFLALAEALHLMEGQTVAIIGPQD 105 (784)
Q Consensus 27 ~~~~~i~IG~i~~~~~~~g~~~~~a~~~Ave~IN~~~~il~g~-~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiGp~~ 105 (784)
...+.++||+....+...-.....+++-|+.+. |. .+++......+|+..+...++.+..++.++|++-..
T Consensus 26 ~~~~~~~VaI~~~veHpaLd~~~~G~~~aLk~~--------G~~n~~i~~~na~~~~~~a~~iarql~~~~~dviv~i~t 97 (322)
T COG2984 26 AAADQITVAITQFVEHPALDAAREGVKEALKDA--------GYKNVKIDYQNAQGDLGTAAQIARQLVGDKPDVIVAIAT 97 (322)
T ss_pred ccccceeEEEEEeecchhHHHHHHHHHHHHHhc--------CccCeEEEeecCCCChHHHHHHHHHhhcCCCcEEEecCC
Confidence 345577788888776444456677777777763 33 678888888999999999999999988888877444
Q ss_pred hhhHHHHHHhhhcCCccEEecccCCCC---CCcC-CCCceEeecCChHHHHHHHHHHHHHc--CCcEEEEEEEcC-CCcc
Q 003958 106 AVTSHVVSHVANELQVPLLSFSATDPT---LSSL-QFPYFVRTTQSDQYQMAAIAEIVDHY--GWREVIAIYVDD-DHGR 178 (784)
Q Consensus 106 s~~~~~va~~~~~~~ip~Is~~a~~~~---l~~~-~~p~~~r~~ps~~~~~~ai~~~l~~~--~w~~v~ii~~d~-~~g~ 178 (784)
. .+.++. .+..++|+|-.+.+++. |.+. .-|----|.-+|..-...-.+++++. +-++|+++|..+ +...
T Consensus 98 p-~Aq~~~--s~~~~iPVV~aavtd~v~a~Lv~~~~~pg~NvTGvsD~~~v~q~i~lik~~~Pnak~Igv~Y~p~E~ns~ 174 (322)
T COG2984 98 P-AAQALV--SATKTIPVVFAAVTDPVGAKLVKSLEQPGGNVTGVSDLLPVAQQIELIKALLPNAKSIGVLYNPGEANSV 174 (322)
T ss_pred H-HHHHHH--HhcCCCCEEEEccCchhhccCCccccCCCCceeecCCcchHHHHHHHHHHhCCCCeeEEEEeCCCCcccH
Confidence 3 344333 23344999987776553 3321 12333445556666566667777664 789999999654 4777
Q ss_pred hhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccC---CcHHHHHHHHHHcCC
Q 003958 179 NGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY---NRGPVVFHVAQYLGM 246 (784)
Q Consensus 179 ~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~---~~~~~~~~~a~~~g~ 246 (784)
...+.+++.++++|++|... ..+ ...|.....+.+. .++|+|++.++. .....+++.+.+.+.
T Consensus 175 ~l~eelk~~A~~~Gl~vve~-~v~---~~ndi~~a~~~l~-g~~d~i~~p~dn~i~s~~~~l~~~a~~~ki 240 (322)
T COG2984 175 SLVEELKKEARKAGLEVVEA-AVT---SVNDIPRAVQALL-GKVDVIYIPTDNLIVSAIESLLQVANKAKI 240 (322)
T ss_pred HHHHHHHHHHHHCCCEEEEE-ecC---cccccHHHHHHhc-CCCcEEEEecchHHHHHHHHHHHHHHHhCC
Confidence 88999999999999998743 333 3445666666665 678898887664 345566777777553
No 116
>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=98.50 E-value=1.1e-05 Score=83.48 Aligned_cols=201 Identities=14% Similarity=0.132 Sum_probs=133.0
Q ss_pred EEEEEeecCCcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEccCchhhHHHH
Q 003958 33 NIGALLSFSTNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIGPQDAVTSHVV 112 (784)
Q Consensus 33 ~IG~i~~~~~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiGp~~s~~~~~v 112 (784)
+||++.+.+..+-.....+++ +++++.+..+ |.++.+.+.|+..++........+++++++.+||+...+. ....
T Consensus 1 ~igv~~~~~~~~~~~~~~gi~---~~~~~~g~~~-g~~v~l~~~~~~~~~~~~~~~~~~l~~~~vd~iI~~~~~~-~~~~ 75 (281)
T cd06325 1 KVGILQLVEHPALDAARKGFK---DGLKEAGYKE-GKNVKIDYQNAQGDQSNLPTIARKFVADKPDLIVAIATPA-AQAA 75 (281)
T ss_pred CeEEecCCCCcchHHHHHHHH---HHHHHhCccC-CceEEEEEecCCCCHHHHHHHHHHHHhcCCCEEEEcCcHH-HHHH
Confidence 588888865332223333433 5566666654 7899999999999999888888889888999999865432 2222
Q ss_pred HHhhhcCCccEEecccCCCCCC---c-CCCCceEeecCChHHHHHHHHHHHHHc--CCcEEEEEEEcC-CCcchhHHHHH
Q 003958 113 SHVANELQVPLLSFSATDPTLS---S-LQFPYFVRTTQSDQYQMAAIAEIVDHY--GWREVIAIYVDD-DHGRNGIAALG 185 (784)
Q Consensus 113 a~~~~~~~ip~Is~~a~~~~l~---~-~~~p~~~r~~ps~~~~~~ai~~~l~~~--~w~~v~ii~~d~-~~g~~~~~~l~ 185 (784)
.....++|+|..+..++... + ...+....+...+...+..+++++.+. |.+++++++.+. .++....+.++
T Consensus 76 --~~~~~~iPvV~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~g~~~i~~l~~~~~~~~~~r~~g~~ 153 (281)
T cd06325 76 --ANATKDIPIVFTAVTDPVGAGLVKSLEKPGGNVTGVSDLVPVETQLELLKKLLPDAKTVGVLYNPSEANSVVQVKELK 153 (281)
T ss_pred --HHcCCCCCEEEEecCCccccccccccccCCCceeCeecccchHHHHHHHHHHCCCCcEEEEEeCCCCccHHHHHHHHH
Confidence 25567999998765433211 1 111222223334555567788888775 999999998654 36677789999
Q ss_pred HHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHcCC
Q 003958 186 DTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGM 246 (784)
Q Consensus 186 ~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~g~ 246 (784)
+.+++.|+.+.... . ....++...++++.+. +++|+... ...+..+++++.+.++
T Consensus 154 ~~~~~~g~~~~~~~-~---~~~~~~~~~~~~~~~~-~dai~~~~-d~~a~~~~~~~~~~~~ 208 (281)
T cd06325 154 KAAAKLGIEVVEAT-V---SSSNDVQQAAQSLAGK-VDAIYVPT-DNTVASAMEAVVKVAN 208 (281)
T ss_pred HHHHhCCCEEEEEe-c---CCHHHHHHHHHHhccc-CCEEEEcC-chhHHhHHHHHHHHHH
Confidence 99999998876532 2 2345666777777643 57766544 4466678888887764
No 117
>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=98.46 E-value=4.8e-05 Score=78.42 Aligned_cols=199 Identities=10% Similarity=0.040 Sum_probs=125.6
Q ss_pred EEEEEeecC-CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEE-EccCchhhHH
Q 003958 33 NIGALLSFS-TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAI-IGPQDAVTSH 110 (784)
Q Consensus 33 ~IG~i~~~~-~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~ai-iGp~~s~~~~ 110 (784)
+||++.|.. ..+-.....+++.+.++ .|+++.+...|+..++....+....++.+++.+| +.|..+....
T Consensus 1 ~igvi~~~~~~~~~~~~~~gi~~~~~~--------~g~~~~~~~~~~~~~~~~~~~~i~~l~~~~vdgiIi~~~~~~~~~ 72 (275)
T cd06320 1 KYGVVLKTLSNEFWRSLKEGYENEAKK--------LGVSVDIQAAPSEGDQQGQLSIAENMINKGYKGLLFSPISDVNLV 72 (275)
T ss_pred CeeEEEecCCCHHHHHHHHHHHHHHHH--------hCCeEEEEccCCCCCHHHHHHHHHHHHHhCCCEEEECCCChHHhH
Confidence 589999853 32223444566666655 2677777666767777776777778888888875 5555444434
Q ss_pred HHHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHc--CCcEEEEEEEcC--CCcchhHHHHHH
Q 003958 111 VVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHY--GWREVIAIYVDD--DHGRNGIAALGD 186 (784)
Q Consensus 111 ~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~--~w~~v~ii~~d~--~~g~~~~~~l~~ 186 (784)
+....+...++|+|..+.... +...+ .+.+++...+..+++++... |.++++++.... .......+.+++
T Consensus 73 ~~~~~~~~~~iPvV~~~~~~~---~~~~~---~V~~d~~~~g~~~~~~l~~~~~g~~~i~~l~~~~~~~~~~~r~~g~~~ 146 (275)
T cd06320 73 PAVERAKKKGIPVVNVNDKLI---PNATA---FVGTDNKANGVRGAEWIIDKLAEGGKVAIIEGKAGAFAAEQRTEGFTE 146 (275)
T ss_pred HHHHHHHHCCCeEEEECCCCC---Cccce---EEecCcHHHHHHHHHHHHHHhCCCceEEEEeCCCCCccHHHHHHHHHH
Confidence 455667789999998754321 11112 24566667788888888665 899999998533 233455688999
Q ss_pred HHhcc-CcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEec-cCCcHHHHHHHHHHcCCC
Q 003958 187 TLAAK-RCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHT-HYNRGPVVFHVAQYLGML 247 (784)
Q Consensus 187 ~l~~~-gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~-~~~~~~~~~~~a~~~g~~ 247 (784)
.+++. |+.+....... ....+....++++.+..+++-.+++ ....+..+++++++.|+.
T Consensus 147 ~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~l~~~~~~~ai~~~~d~~a~~~~~al~~~g~~ 207 (275)
T cd06320 147 AIKKASGIEVVASQPAD--WDREKAYDVATTILQRNPDLKAIYCNNDTMALGVVEAVKNAGKQ 207 (275)
T ss_pred HHhhCCCcEEEEecCCC--ccHHHHHHHHHHHHHhCCCccEEEECCchhHHHHHHHHHhcCCC
Confidence 99998 88765432111 2333444566665544444433444 445566788888998874
No 118
>COG3107 LppC Putative lipoprotein [General function prediction only]
Probab=98.41 E-value=2.2e-05 Score=82.24 Aligned_cols=254 Identities=12% Similarity=0.113 Sum_probs=154.7
Q ss_pred ceEEEEEEeecCC---cchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEccCch
Q 003958 30 SVVNIGALLSFST---NVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIGPQDA 106 (784)
Q Consensus 30 ~~i~IG~i~~~~~---~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiGp~~s 106 (784)
.+=+|++++|+++ ..|.....||..|-.. +.. .++-..++.++|+...+..++- .....+|+..|+||.--
T Consensus 256 ~~skiALLLPLtG~~a~~a~~IqdGF~aA~~~-~~~---~~~~~~~~~i~dT~~~~l~~i~--aqaqq~G~~~VVGPLlK 329 (604)
T COG3107 256 SPSKIALLLPLTGQAAVFARTIQDGFLAAKNA-PAT---QTAQVAELKIYDTSAQPLDAIL--AQAQQDGADFVVGPLLK 329 (604)
T ss_pred CchheeEEeccCChhHHHHHHHHHHHHHhccC-ccc---CCccccceeeccCCcccHHHHH--HHHHhcCCcEEeccccc
Confidence 4678999999993 4466677788777651 111 1333377888999887765432 22334599999999998
Q ss_pred hhHHHHHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcCCCcchhHHHHHH
Q 003958 107 VTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGD 186 (784)
Q Consensus 107 ~~~~~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~ 186 (784)
.....+..--. ..||++....++.. +..+......-+.+++++..++.|-.-|.+...++...+++|+...+.|.+
T Consensus 330 ~nVe~L~~~~q-~~i~vLALN~~~n~---r~~~~~cyfaLSPEDEa~~AA~~l~~qG~R~plvlvPr~~lG~Rv~~AF~~ 405 (604)
T COG3107 330 PNVEALLASNQ-QPIPVLALNQPENS---RNPAQLCYFALSPEDEARDAANHLWDQGKRNPLVLVPRNDLGDRVANAFNQ 405 (604)
T ss_pred hhHHHHHhCcC-CCCceeeecCCccc---cCcccceeeecChhHHHHHHHHHHHHccccCceEEecchHHHHHHHHHHHH
Confidence 88777644322 77888876554321 223455555555566789999999999999999999999999999999999
Q ss_pred HHhccCcEEEEeeccCCCCChhHHHHHHHH-----------------------hhcCC-ceEEEEeccCCcHHHHHHHHH
Q 003958 187 TLAAKRCRISFKAPLSVEATEDEITDLLVK-----------------------VALTE-SRIIVVHTHYNRGPVVFHVAQ 242 (784)
Q Consensus 187 ~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~-----------------------l~~~~-~~vIvl~~~~~~~~~~~~~a~ 242 (784)
..++.|...+..+.|. ...++...++. +.+.. .|.|++...+.+++.+--...
T Consensus 406 ~Wq~~gg~~v~~~~fg---~~~~l~~~i~~~a~ir~~~~p~~~~~~~g~~~~p~~~~d~iDaVyivAtp~el~~IKP~ia 482 (604)
T COG3107 406 EWQKLGGGTVLQQKFG---STSELRQGINDGAGIRLTGLPADLTTTNGLQTPPLDDQDTIDAVYIVATPSELALIKPMIA 482 (604)
T ss_pred HHHHhcCCchhHhhcC---cHHHHHhhcccccceeecCCccchhcccCCCCCCcccccccceEEEEecchhHhHHhhHHH
Confidence 9999887554444443 22222222211 12222 788888888888776544433
Q ss_pred HcCCCCCCeEEEecCccccccccCCCCCCCccccceeeEEEee---ecCCchhHHHHHHHHHh
Q 003958 243 YLGMLGTGYVWIATSWLSTALDTNSPFPSDVMDDIQGVLTLRT---YTPDSVLKRKFISRWRN 302 (784)
Q Consensus 243 ~~g~~~~~~~wi~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~---~~~~~~~~~~f~~~~~~ 302 (784)
-.+.... -..+.++-... .. ..++....++|+..... ..+..|.+++....|..
T Consensus 483 ~~~~~~~-~p~yaSSr~~~--gT---~~P~~~~~m~GiqysdiP~l~~~~~p~~qq~a~~~p~ 539 (604)
T COG3107 483 MANGSDS-PPLYASSRSSQ--GT---NGPDFRLEMEGIQYSDIPWLAQPNPPLMQQAAAAWPN 539 (604)
T ss_pred hhcCCCC-cceeeeccccc--cC---CCccHHHhccCccccCCchhcCCCchHHHHHHHhcCC
Confidence 2222111 11222221110 00 01344456677544322 23455666666655554
No 119
>cd06282 PBP1_GntR_like_2 Ligand-binding domain of putative DNA transcription repressors highly similar to that of the repressor specific for gluconate (GntR) which is a member of the LacI-GalR family of bacterial transcription regulators. This group includes the ligand-binding domain of putative DNA transcription repressors highly similar to that of the repressor specific for gluconate (GntR) which is a member of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding
Probab=98.33 E-value=5.3e-05 Score=77.56 Aligned_cols=199 Identities=12% Similarity=0.099 Sum_probs=123.7
Q ss_pred EEEEeecCC-cchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEccCchhhHHHH
Q 003958 34 IGALLSFST-NVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIGPQDAVTSHVV 112 (784)
Q Consensus 34 IG~i~~~~~-~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiGp~~s~~~~~v 112 (784)
||++.|... .+-.....++..+.++ .|+.+.+ .++..++....+...+++.+++.+||....+......
T Consensus 2 igvv~~~~~~~~~~~~~~~i~~~~~~--------~g~~~~~--~~~~~~~~~~~~~~~~l~~~~vdgiii~~~~~~~~~~ 71 (266)
T cd06282 2 VGVVLPSLANPVFAECVQGIQEEARA--------AGYSLLL--ATTDYDAEREADAVETLLRQRVDGLILTVADAATSPA 71 (266)
T ss_pred eEEEeCCCCcchHHHHHHHHHHHHHH--------CCCEEEE--eeCCCCHHHHHHHHHHHHhcCCCEEEEecCCCCchHH
Confidence 788887542 2222344455555444 1454444 4556677776777778888889988864333322335
Q ss_pred HHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEc---CCCcchhHHHHHHHHh
Q 003958 113 SHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVD---DDHGRNGIAALGDTLA 189 (784)
Q Consensus 113 a~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d---~~~g~~~~~~l~~~l~ 189 (784)
...+...++|+|....... ..++++ ..+....+..++++|.+.|.++++++..+ .+++....+.+++.++
T Consensus 72 ~~~~~~~~ipvV~~~~~~~----~~~~~v---~~d~~~~g~~~~~~l~~~g~~~i~~i~~~~~~~~~~~~r~~gf~~~l~ 144 (266)
T cd06282 72 LDLLDAERVPYVLAYNDPQ----PGRPSV---SVDNRAAARDVAQALAALGHRRIAMLAGRLAASDRARQRYAGYRAAMR 144 (266)
T ss_pred HHHHhhCCCCEEEEeccCC----CCCCEE---eeCcHHHHHHHHHHHHHcCcccEEEeccccccCchHHHHHHHHHHHHH
Confidence 5667888999998754322 123433 35666788888999888899999999743 2356677889999999
Q ss_pred ccCcEEEEeeccCCCCChhHHHHHHHHh-hcC-CceEEEEeccCCcHHHHHHHHHHcCCCCCCeE
Q 003958 190 AKRCRISFKAPLSVEATEDEITDLLVKV-ALT-ESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYV 252 (784)
Q Consensus 190 ~~gi~v~~~~~~~~~~~~~d~~~~l~~l-~~~-~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~ 252 (784)
+.|+.+......+ .+..+....+.++ ++. .+++|+. ++...+..+++++++.|+..++.+
T Consensus 145 ~~~~~~~~~~~~~--~~~~~~~~~~~~~l~~~~~~~ai~~-~~d~~a~g~~~al~~~g~~~p~di 206 (266)
T cd06282 145 AAGLAPLPPVEIP--FNTAALPSALLALLTAHPAPTAIFC-SNDLLALAVIRALRRLGLRVPDDL 206 (266)
T ss_pred HcCCCCCccccCC--CcHHHHHHHHHHHhcCCCCCCEEEE-CCcHHHHHHHHHHHHcCCCCCCce
Confidence 8887543322222 2223333444443 333 4566555 455567789999999997654333
No 120
>PRK10653 D-ribose transporter subunit RbsB; Provisional
Probab=98.32 E-value=0.00034 Score=72.89 Aligned_cols=200 Identities=14% Similarity=0.119 Sum_probs=119.2
Q ss_pred ceEEEEEEeecC-CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEE-EccCchh
Q 003958 30 SVVNIGALLSFS-TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAI-IGPQDAV 107 (784)
Q Consensus 30 ~~i~IG~i~~~~-~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~ai-iGp~~s~ 107 (784)
..-.||+++|.. ..+-.....+++.++++. |+++ .+.++..++....+....++++++.++ +++..+.
T Consensus 25 ~~~~I~vi~~~~~~~f~~~~~~~i~~~~~~~--------G~~~--~~~~~~~d~~~~~~~~~~l~~~~~dgiii~~~~~~ 94 (295)
T PRK10653 25 AKDTIALVVSTLNNPFFVSLKDGAQKEADKL--------GYNL--VVLDSQNNPAKELANVQDLTVRGTKILLINPTDSD 94 (295)
T ss_pred cCCeEEEEecCCCChHHHHHHHHHHHHHHHc--------CCeE--EEecCCCCHHHHHHHHHHHHHcCCCEEEEcCCChH
Confidence 345799998753 333345556666666662 4444 445666677777777777777788744 5555544
Q ss_pred hHHHHHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHc-CCc-EEEEEEEcC--CCcchhHHH
Q 003958 108 TSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHY-GWR-EVIAIYVDD--DHGRNGIAA 183 (784)
Q Consensus 108 ~~~~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~-~w~-~v~ii~~d~--~~g~~~~~~ 183 (784)
........+...++|+|....... + .+.+....+....-+..+++++... +.+ +++++..+. ...+...+.
T Consensus 95 ~~~~~l~~~~~~~ipvV~~~~~~~---~--~~~~~~V~~D~~~~g~~~~~~l~~~~~~~~~i~~~~~~~~~~~~~~R~~g 169 (295)
T PRK10653 95 AVGNAVKMANQANIPVITLDRGAT---K--GEVVSHIASDNVAGGKMAGDFIAKKLGEGAKVIQLEGIAGTSAARERGEG 169 (295)
T ss_pred HHHHHHHHHHHCCCCEEEEccCCC---C--CceeeEEccChHHHHHHHHHHHHHHhCCCceEEEEEccCCCccHHHHHHH
Confidence 444455677778999999854321 1 1223445555555567788876554 543 666665432 234566789
Q ss_pred HHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEe-ccCCcHHHHHHHHHHcCC
Q 003958 184 LGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVH-THYNRGPVVFHVAQYLGM 246 (784)
Q Consensus 184 l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~-~~~~~~~~~~~~a~~~g~ 246 (784)
+++.+++.|+.+....... .+..+....+.++.+..++.-.++ .....+..+++++++.|+
T Consensus 170 f~~al~~~g~~~~~~~~~~--~~~~~~~~~~~~~l~~~~~~~ai~~~~d~~A~g~l~al~~~G~ 231 (295)
T PRK10653 170 FKQAVAAHKFNVLASQPAD--FDRTKGLNVMQNLLTAHPDVQAVFAQNDEMALGALRALQTAGK 231 (295)
T ss_pred HHHHHhhCCCEEEEecCCC--CCHHHHHHHHHHHHHhCCCcCEEEECCChhHHHHHHHHHHcCC
Confidence 9999999998764321111 222333445556554444333333 444556578999999886
No 121
>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=98.23 E-value=0.00027 Score=72.39 Aligned_cols=203 Identities=13% Similarity=0.096 Sum_probs=123.4
Q ss_pred EEEEeecC-CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEE-EccCchhhHHH
Q 003958 34 IGALLSFS-TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAI-IGPQDAVTSHV 111 (784)
Q Consensus 34 IG~i~~~~-~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~ai-iGp~~s~~~~~ 111 (784)
||++.|.. ..+......+++.+.++. |+++ .+.++..++....+...+++.+++.+| +++..+.....
T Consensus 2 I~vv~~~~~~~~~~~~~~~i~~~~~~~--------g~~v--~~~~~~~~~~~~~~~~~~~~~~~~dgii~~~~~~~~~~~ 71 (268)
T cd06323 2 IGLSVSTLNNPFFVTLKDGAQKEAKEL--------GYEL--TVLDAQNDAAKQLNDIEDLITRGVDAIIINPTDSDAVVP 71 (268)
T ss_pred eeEecccccCHHHHHHHHHHHHHHHHc--------CceE--EecCCCCCHHHHHHHHHHHHHcCCCEEEEcCCChHHHHH
Confidence 78888753 333445566676666661 4444 456666788777777777888888884 55554443334
Q ss_pred HHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHc--CCcEEEEEEEc--CCCcchhHHHHHHH
Q 003958 112 VSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHY--GWREVIAIYVD--DDHGRNGIAALGDT 187 (784)
Q Consensus 112 va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~--~w~~v~ii~~d--~~~g~~~~~~l~~~ 187 (784)
....+...++|+|......+. .+.+-.+..+....+..+++.|.+. +-++++++..+ ........+.+++.
T Consensus 72 ~l~~l~~~~ipvv~~~~~~~~-----~~~~~~v~~d~~~~~~~~~~~l~~~~~g~~~i~~l~~~~~~~~~~~r~~g~~~~ 146 (268)
T cd06323 72 AVKAANEAGIPVFTIDREANG-----GEVVSQIASDNVAGGKMAAEYLVKLLGGKGKVVELQGIPGASAARERGKGFHEV 146 (268)
T ss_pred HHHHHHHCCCcEEEEccCCCC-----CceEEEEccCcHHHHHHHHHHHHHHhCCCceEEEEeCCCCCccHHHHHHHHHHH
Confidence 445566789999998553221 1223335555556678888888776 78999999863 33566677889999
Q ss_pred Hhcc-CcEEEEeeccCCCCChhHHHHHHHHhhcCC--ceEEEEeccCCcHHHHHHHHHHcCCCCCCeEEEec
Q 003958 188 LAAK-RCRISFKAPLSVEATEDEITDLLVKVALTE--SRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIAT 256 (784)
Q Consensus 188 l~~~-gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~--~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~wi~~ 256 (784)
+++. |+.+....... .+..+....+.++.+.. +++ +++.....+..+++++++.|+ .+...++.
T Consensus 147 l~~~~~~~~~~~~~~~--~~~~~~~~~~~~~l~~~~~~~a-i~~~~d~~a~~~~~~l~~~g~--~di~iig~ 213 (268)
T cd06323 147 VDKYPGLKVVASQPAD--FDRAKGLNVMENILQAHPDIKG-VFAQNDEMALGAIEALKAAGK--DDVKVVGF 213 (268)
T ss_pred HHhCCCcEEEecccCC--CCHHHHHHHHHHHHHHCCCcCE-EEEcCCchHHHHHHHHHHcCC--CCcEEEEe
Confidence 9884 77654322111 22233334454544333 444 333444556678899999887 33344443
No 122
>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=98.18 E-value=0.00026 Score=72.88 Aligned_cols=200 Identities=15% Similarity=0.103 Sum_probs=120.1
Q ss_pred EEEEeecC--CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEc-cCchhhHH
Q 003958 34 IGALLSFS--TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIG-PQDAVTSH 110 (784)
Q Consensus 34 IG~i~~~~--~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiG-p~~s~~~~ 110 (784)
||+++|.. ..+......+++.+.++. |+.+ .+.++..++....+....++.+++.+||- +..+....
T Consensus 2 i~vi~p~~~~~~~~~~~~~g~~~~~~~~--------g~~~--~~~~~~~~~~~~~~~~~~l~~~~vdgiii~~~~~~~~~ 71 (275)
T cd06317 2 IGYTQNNVGSHSYQTTYNKAFQAAAEED--------GVEV--IVLDANGDVARQAAQVEDLIAQKVDGIILWPTDGQAYI 71 (275)
T ss_pred eEEEecccCCCHHHHHHHHHHHHHHHhc--------CCEE--EEEcCCcCHHHHHHHHHHHHHcCCCEEEEecCCccccH
Confidence 78888863 444455667777777661 4444 45677778887777777888888998854 43343334
Q ss_pred HHHHhhhcCCccEEecccCCCCCCcCCCCceEeec-CChHHHHHHHHHHHHHc--CCcEEEEEEEcCCC--cchhHHHHH
Q 003958 111 VVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTT-QSDQYQMAAIAEIVDHY--GWREVIAIYVDDDH--GRNGIAALG 185 (784)
Q Consensus 111 ~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~-ps~~~~~~ai~~~l~~~--~w~~v~ii~~d~~~--g~~~~~~l~ 185 (784)
.....+...++|+|......+ +...++++..+ +.+...+..+++.+.+. +-++|+++..+.++ .....+.++
T Consensus 72 ~~l~~~~~~~iPvV~~~~~~~---~~~~~~v~~~v~~d~~~~g~~~~~~l~~~~~g~~~i~~l~~~~~~~~~~~r~~g~~ 148 (275)
T cd06317 72 PGLRKAKQAGIPVVITNSNIS---EKGFEFIKSFTGPDDISQGERSAEAMCKALGGKGQIVVIAGQPGNGTAIERQKGFE 148 (275)
T ss_pred HHHHHHHHCCCcEEEeCCCCC---CCccchhhhhccccHHHHHHHHHHHHHHHcCCCceEEEEecCCCCchHHHHHHHHH
Confidence 444666789999998754321 22234443333 34445666677776554 77899999864333 345568888
Q ss_pred HHHhccCcEEEEeeccCCCCChhHHHHHHHHh-hc--CCceEEEEeccCCcHHHHHHHHHHcCCC
Q 003958 186 DTLAAKRCRISFKAPLSVEATEDEITDLLVKV-AL--TESRIIVVHTHYNRGPVVFHVAQYLGML 247 (784)
Q Consensus 186 ~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l-~~--~~~~vIvl~~~~~~~~~~~~~a~~~g~~ 247 (784)
+.+++.|..+..........+..+....++++ .+ ..+++|+. +....+..+++++++.|+.
T Consensus 149 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~ai~~-~~d~~a~g~~~~l~~~g~~ 212 (275)
T cd06317 149 DELAEVCPGVEVLDTQPADWDREKAQVAMEALITKFGDDIDGVYA-GDDNMARGALNAAKEAGLA 212 (275)
T ss_pred HHHHhhCCCCEEEeccCCCCCHHHHHHHHHHHHHhCCCCccEEEE-CCCcHHHHHHHHHHhcCCc
Confidence 99988864332222121111222222334443 22 23566664 4455577899999999875
No 123
>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=98.15 E-value=0.00021 Score=73.27 Aligned_cols=201 Identities=13% Similarity=0.065 Sum_probs=124.0
Q ss_pred EEEEEeecC-CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEccCchhhHHH
Q 003958 33 NIGALLSFS-TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIGPQDAVTSHV 111 (784)
Q Consensus 33 ~IG~i~~~~-~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiGp~~s~~~~~ 111 (784)
.||++.|.. ..+-.....++..++++. |+.+. +.|+..++.........++++++.++|--..... ..
T Consensus 1 ~i~vv~p~~~~~~~~~~~~~i~~~~~~~--------g~~~~--~~~~~~~~~~~~~~~~~l~~~~vdgiii~~~~~~-~~ 69 (268)
T cd06273 1 TIGAIVPTLDNAIFARVIQAFQETLAAH--------GYTLL--VASSGYDLDREYAQARKLLERGVDGLALIGLDHS-PA 69 (268)
T ss_pred CeEEEeCCCCCchHHHHHHHHHHHHHHC--------CCEEE--EecCCCCHHHHHHHHHHHHhcCCCEEEEeCCCCC-HH
Confidence 378898853 322334455565555551 44444 4677788888777788888888877653222111 23
Q ss_pred HHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcC---CCcchhHHHHHHHH
Q 003958 112 VSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDD---DHGRNGIAALGDTL 188 (784)
Q Consensus 112 va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~---~~g~~~~~~l~~~l 188 (784)
....+...++|+|......+ +...++ ........+..+++.|...|.+++++|.... ..+....+.+++.+
T Consensus 70 ~~~~l~~~~iPvv~~~~~~~---~~~~~~---v~~d~~~~~~~~~~~l~~~g~~~i~~i~~~~~~~~~~~~r~~gf~~~l 143 (268)
T cd06273 70 LLDLLARRGVPYVATWNYSP---DSPYPC---VGFDNREAGRLAARHLIALGHRRIAMIFGPTQGNDRARARRAGVRAAL 143 (268)
T ss_pred HHHHHHhCCCCEEEEcCCCC---CCCCCE---EEeChHHHHHHHHHHHHHCCCCeEEEEeccccCCccHHHHHHHHHHHH
Confidence 34456778999998754322 112333 3456677788888888778999999998432 34567788999999
Q ss_pred hccCcEEEEeeccCCCCChhHHHHHHHHhhc--CCceEEEEeccCCcHHHHHHHHHHcCCCCCCe
Q 003958 189 AAKRCRISFKAPLSVEATEDEITDLLVKVAL--TESRIIVVHTHYNRGPVVFHVAQYLGMLGTGY 251 (784)
Q Consensus 189 ~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~--~~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~ 251 (784)
++.++.+.....+....+..+....+.++.+ ..+++|+. +....+..+++++++.|+..++.
T Consensus 144 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~-~~~~~a~~~~~~l~~~g~~~p~~ 207 (268)
T cd06273 144 AEAGLELPELWQVEAPYSIADGRAALRQLLEQPPRPTAVIC-GNDVLALGALYEARRLGLSVPED 207 (268)
T ss_pred HHcCCCCCHHHeeeCCCcHHHHHHHHHHHHcCCCCCCEEEE-cChHHHHHHHHHHHHcCCCCCCc
Confidence 9888654322222211122333455556543 34666554 45556778899999988865543
No 124
>PRK00489 hisG ATP phosphoribosyltransferase; Reviewed
Probab=98.14 E-value=1.6e-05 Score=81.72 Aligned_cols=135 Identities=18% Similarity=0.254 Sum_probs=106.0
Q ss_pred ChhHHHHHHHcCcccEEEeeEEeecCccccceeccc--cccccEEEEEeccCCccccccccccccHHHHHHHHHHHHHHH
Q 003958 526 SCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQP--YIESGLVVVAPVRKLDSNAWAFLSPFTPMMWGVTAIFFLAVG 603 (784)
Q Consensus 526 ~~~g~i~~l~~~~~D~~~~~~~~t~~r~~~~~fs~p--~~~~~~~~~~~~~~~~~~~~~~~~pf~~~~W~~i~~~~~~~~ 603 (784)
.|.+++..|.+|++|+++++..++.+|.+.++|+.| |....+.+++|...
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 589999999999999999999999999999999998 67777888876653
Q ss_pred HHhhheecccCCCCCCCccCCceeehhhhhhhhhcccccccccchhhHHHHHHHHHHHHHHhhccccceeeEeeccccCC
Q 003958 604 AVVWILEHRLNDEFRGPPKRQVVTIFWFSFSTMFFAHKEKTVSALGRLVLIIWLFVVLIINSSYTASLTSILTVQKLSSP 683 (784)
Q Consensus 604 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~R~~~~~w~~~~lvl~~~Yta~L~s~l~~~~~~~~ 683 (784)
+
T Consensus 104 -------------------------------------------------------------------------------~ 104 (287)
T PRK00489 104 -------------------------------------------------------------------------------D 104 (287)
T ss_pred -------------------------------------------------------------------------------C
Confidence 6
Q ss_pred CCChHhhhhCCCceEEeeCchHHHHHHhhcccCccCceeCCCHHHHHHHHhcCCcCCCeeEEEechhhhHHHHcCCCCeE
Q 003958 684 IKGIDSLRSSNYPIGYQVNSFARNYLVDELNIDESRLVPLNSPEEYAKALKDGPHKGGVAAVVDDRAYAELFLSTRCEFS 763 (784)
Q Consensus 684 i~~~~dl~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~a~~~~~~~~~~~~~~~c~l~ 763 (784)
|.+++||. |+++++..+.....||.+ .+. ..+++.+.+..|. .+.. |..+|++....+...+.++ ++.
T Consensus 105 i~sl~DL~--Gk~ia~~~~~~~~~~l~~-~gi-~~~iv~~~gs~ea--a~~~----G~aDaivd~~~~~~~l~~~--~L~ 172 (287)
T PRK00489 105 WQGVEDLA--GKRIATSYPNLTRRYLAE-KGI-DAEVVELSGAVEV--APRL----GLADAIVDVVSTGTTLRAN--GLK 172 (287)
T ss_pred CCChHHhC--CCEEEEcCcHHHHHHHHH-cCC-ceEEEECCCchhh--hhcC----CcccEEEeeHHHHHHHHHC--CCE
Confidence 88999998 889999888888999954 333 2345556555454 5555 7899999887777776654 577
Q ss_pred EeCCccccceEEEEeeC
Q 003958 764 IVGQVFTKNGWGFVSIV 780 (784)
Q Consensus 764 ~~~~~~~~~~~~~~~~k 780 (784)
++ +.+.....+++.+|
T Consensus 173 ~v-~~~~~~~~~li~~k 188 (287)
T PRK00489 173 IV-EVILRSEAVLIARK 188 (287)
T ss_pred EE-EeeeeeeEEEEEcc
Confidence 77 56666678899888
No 125
>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=98.10 E-value=0.00067 Score=69.89 Aligned_cols=199 Identities=10% Similarity=0.092 Sum_probs=118.0
Q ss_pred EEEEEeecC-CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEE-EccCchhhHH
Q 003958 33 NIGALLSFS-TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAI-IGPQDAVTSH 110 (784)
Q Consensus 33 ~IG~i~~~~-~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~ai-iGp~~s~~~~ 110 (784)
+||++.|.. ..+-.....++..+.++ . |+++ .+.++..++....+....++.+++.+| +++..+....
T Consensus 1 ~i~vi~~~~~~~~~~~~~~~i~~~~~~---~-----g~~~--~~~~~~~~~~~~~~~i~~~~~~~~dgiii~~~~~~~~~ 70 (277)
T cd06319 1 QIAYIVSDLRIPFWQIMGRGVKSKAKA---L-----GYDA--VELSAENSAKKELENLRTAIDKGVSGIIISPTNSSAAV 70 (277)
T ss_pred CeEEEeCCCCchHHHHHHHHHHHHHHh---c-----CCeE--EEecCCCCHHHHHHHHHHHHhcCCCEEEEcCCchhhhH
Confidence 478888754 22222333444444443 1 4444 456777788777777778888888877 4555554444
Q ss_pred HHHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHc------CCcEEEEEEEc--CCCcchhHH
Q 003958 111 VVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHY------GWREVIAIYVD--DDHGRNGIA 182 (784)
Q Consensus 111 ~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~------~w~~v~ii~~d--~~~g~~~~~ 182 (784)
.....+...++|+|......+ + ..++..+.++...-+..++++|.+. |-++++++... ...+....+
T Consensus 71 ~~l~~~~~~~ipvV~~~~~~~---~--~~~~~~v~~d~~~~g~~~~~~l~~~~~~~~~g~~~i~~i~~~~~~~~~~~r~~ 145 (277)
T cd06319 71 TLLKLAAQAKIPVVIADIGAE---G--GDYVSYIKSDNYEGAYDLGKFLAAAMKAQGWADGKVGMVAIPQKRKNGQKRTK 145 (277)
T ss_pred HHHHHHHHCCCCEEEEecCCC---C--CceEEEEeeccHHHHHHHHHHHHHHHHhhCCCCCcEEEEeccCCCccHHHHHH
Confidence 556777788999998643211 1 1123344455555566677765443 67899999853 234567788
Q ss_pred HHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEE-eccCCcHHHHHHHHHHcCCC
Q 003958 183 ALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVV-HTHYNRGPVVFHVAQYLGML 247 (784)
Q Consensus 183 ~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl-~~~~~~~~~~~~~a~~~g~~ 247 (784)
.+++.+++.|+.+.... ........+....++++.++.++...+ +.....+..+++++++.|+.
T Consensus 146 gf~~~l~~~~~~~~~~~-~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~~d~~a~g~~~al~~~g~~ 210 (277)
T cd06319 146 GFKEAMKEAGCDLAGIR-QQKDFSYQETFDYTNDLLTANPDIRAIWLQGSDRYQGALDAIATAGKT 210 (277)
T ss_pred HHHHHHHhcCCceEeec-cCCCCCHHHHHHHHHHHHHhCCCCCEEEECCCccchHHHHHHHHcCCC
Confidence 99999999987654221 111122233344555554444443233 34444567899999999875
No 126
>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=98.07 E-value=0.00096 Score=68.52 Aligned_cols=199 Identities=13% Similarity=0.095 Sum_probs=125.8
Q ss_pred EEEEEeecC--CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCC-CHHHHHHHHHHHHhcCceEEEccCch-hh
Q 003958 33 NIGALLSFS--TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNH-SGFLALAEALHLMEGQTVAIIGPQDA-VT 108 (784)
Q Consensus 33 ~IG~i~~~~--~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~-~~~~a~~~~~~li~~~v~aiiGp~~s-~~ 108 (784)
|||++.|.. ..+-.....++..+.++. |+.+.+. ++.. ++....+....++.+++.++|..... ..
T Consensus 1 ~i~~i~~~~~~~~~~~~~~~g~~~~~~~~--------g~~v~~~--~~~~~~~~~~~~~i~~l~~~~vdgiii~~~~~~~ 70 (271)
T cd06312 1 KIAFVTHGPAGDPFWTVVKNGAEDAAKDL--------GVDVEYR--GPETFDVADMARLIEAAIAAKPDGIVVTIPDPDA 70 (271)
T ss_pred CEEEecCCCCCCcHHHHHHHHHHHHHHHh--------CCEEEEE--CCCCCCHHHHHHHHHHHHHhCCCEEEEeCCChHH
Confidence 588888864 333345667777777762 5555544 4444 77777777777888888888764333 22
Q ss_pred HHHHHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHH-cCCcEEEEEEEc--CCCcchhHHHHH
Q 003958 109 SHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDH-YGWREVIAIYVD--DDHGRNGIAALG 185 (784)
Q Consensus 109 ~~~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~-~~w~~v~ii~~d--~~~g~~~~~~l~ 185 (784)
.......+...++|+|......+... ..+.+..+..+....+..++++|.+ .|-++++++..+ ...+....+.++
T Consensus 71 ~~~~l~~~~~~~ipvV~~~~~~~~~~--~~~~~~~V~~d~~~~g~~~~~~l~~~~g~~~i~~i~g~~~~~~~~~r~~g~~ 148 (271)
T cd06312 71 LDPAIKRAVAAGIPVISFNAGDPKYK--ELGALAYVGQDEYAAGEAAGERLAELKGGKNVLCVIHEPGNVTLEDRCAGFA 148 (271)
T ss_pred hHHHHHHHHHCCCeEEEeCCCCCccc--cccceEEeccChHHHHHHHHHHHHHhcCCCeEEEEecCCCCccHHHHHHHHH
Confidence 33444556778999999764322211 1234556777888889999999888 899999999753 334556788899
Q ss_pred HHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcC--CceEEEEeccCCcHHHHHHHHHHcCCC
Q 003958 186 DTLAAKRCRISFKAPLSVEATEDEITDLLVKVALT--ESRIIVVHTHYNRGPVVFHVAQYLGML 247 (784)
Q Consensus 186 ~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~--~~~vIvl~~~~~~~~~~~~~a~~~g~~ 247 (784)
+.+++.++.+.... . ..+..+....++++.+. ++++|+. .....+..+++++++.|+.
T Consensus 149 ~~~~~~~~~~~~~~--~-~~~~~~~~~~~~~~l~~~~~~~aI~~-~~d~~a~g~~~al~~~g~~ 208 (271)
T cd06312 149 DGLGGAGITEEVIE--T-GADPTEVASRIAAYLRANPDVDAVLT-LGAPSAAPAAKALKQAGLK 208 (271)
T ss_pred HHHHhcCceeeEee--c-CCCHHHHHHHHHHHHHhCCCccEEEE-eCCccchHHHHHHHhcCCC
Confidence 99988876543211 1 11223334445554333 3454433 4455677888889998875
No 127
>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=98.06 E-value=0.00074 Score=69.40 Aligned_cols=207 Identities=13% Similarity=0.001 Sum_probs=123.4
Q ss_pred EEEEEeecC-CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEcc-CchhhHH
Q 003958 33 NIGALLSFS-TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIGP-QDAVTSH 110 (784)
Q Consensus 33 ~IG~i~~~~-~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiGp-~~s~~~~ 110 (784)
+||++.|.. ..+-.....+++-+.++. |+++. +.++..++....+....++.+++.+||.. ..+....
T Consensus 1 ~Ig~i~~~~~~~~~~~~~~gi~~~~~~~--------g~~~~--~~~~~~~~~~~~~~l~~~~~~~vdgii~~~~~~~~~~ 70 (273)
T cd06305 1 RIAVVRYGGSGDFDQAYLAGTKAEAEAL--------GGDLR--VYDAGGDDAKQADQIDQAIAQKVDAIIIQHGRAEVLK 70 (273)
T ss_pred CeEEEeecCCCcHHHHHHHHHHHHHHHc--------CCEEE--EECCCCCHHHHHHHHHHHHHcCCCEEEEecCChhhhH
Confidence 478888753 333334556666666652 45444 45777788877777778888899988774 3333334
Q ss_pred HHHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHH--cCCcEEEEEEEc-CCCcchhHHHHHHH
Q 003958 111 VVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDH--YGWREVIAIYVD-DDHGRNGIAALGDT 187 (784)
Q Consensus 111 ~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~--~~w~~v~ii~~d-~~~g~~~~~~l~~~ 187 (784)
.+...+...++|+|......+. +.+..+.++....++.++++|.. .|.++|+++... ........+.+++.
T Consensus 71 ~~i~~~~~~~ipvV~~~~~~~~------~~~~~V~~d~~~~g~~~~~~l~~~~~g~~~i~~i~~~~~~~~~~R~~g~~~~ 144 (273)
T cd06305 71 PWVKRALDAGIPVVAFDVDSDN------PKVNNTTQDDYSLARLSLDQLVKDLGGKGNVGYVNVAGFPPLDRRYDVWQAV 144 (273)
T ss_pred HHHHHHHHcCCCEEEecCCCCC------CccceeeechHHHHHHHHHHHHHHhCCCCCEEEEEccCCchHHHHHHHHHHH
Confidence 4445567889999987543221 22334556667778888888765 589999999754 22234456678888
Q ss_pred HhccC-cEEEEeeccCCCCChhHHHHHHHHhhcCCceE---EEEeccCCcHHHHHHHHHHcCCCCCCeEEEec
Q 003958 188 LAAKR-CRISFKAPLSVEATEDEITDLLVKVALTESRI---IVVHTHYNRGPVVFHVAQYLGMLGTGYVWIAT 256 (784)
Q Consensus 188 l~~~g-i~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~v---Ivl~~~~~~~~~~~~~a~~~g~~~~~~~wi~~ 256 (784)
+++.+ +.+..........+..+....++++.+..++. .+++.....+..++.++++.|+.. +...++.
T Consensus 145 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~ai~~~~d~~a~g~~~~l~~~g~~~-di~iig~ 216 (273)
T cd06305 145 LKAYPGIKEVAELGDVSNNTAQDAAAQVEAVLKKYPKGGIDAIWAAWDEFAKGAKQALDEAGRTD-EIKIYGV 216 (273)
T ss_pred HHHCCCcEEecccccccccchhHHHHHHHHHHHHCCCcccCeEEEcChhhhHHHHHHHHHcCCCC-CceEEEe
Confidence 87777 55433211111112233344555554333333 233344556777888999988753 3333443
No 128
>cd06301 PBP1_rhizopine_binding_like Periplasmic binding proteins specific to rhizopines. Periplasmic binding proteins specific to rhizopines, which are simple sugar-like compounds produced in the nodules induced by the symbiotic root nodule bacteria, such as Rhizobium and Sinorhizobium. Rhizopine-binding-like proteins from other bacteria are also included. Two inositol based rhizopine compounds are known to date: L-3-O-methly-scyllo-inosamine (3-O-MSI) and scyllo-inosamine. Bacterial strains that can metabolize rhizopine have a greater competitive advantage in nodulation and rhizopine synthesis is regulated by NifA/NtrA regulatory transcription activators which are maximally expressed at the onset of nitrogen fixation in bacteroids. The members of this group belong to the pentose/hexose sugar-binding protein family of the type I periplasmic binding protein superfamily.
Probab=98.06 E-value=0.00096 Score=68.52 Aligned_cols=208 Identities=15% Similarity=0.092 Sum_probs=123.6
Q ss_pred EEEEEeecC-CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEE-ccCchhhHH
Q 003958 33 NIGALLSFS-TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAII-GPQDAVTSH 110 (784)
Q Consensus 33 ~IG~i~~~~-~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aii-Gp~~s~~~~ 110 (784)
+||++.|.. ..+-.....++..+.++ .. |+ .+.+.++..++..-.+....+++.++.++| .+..+....
T Consensus 1 ~igvi~~~~~~~~~~~~~~gi~~~~~~---~~----~~--~~~~~~~~~~~~~~~~~i~~l~~~~vdgiii~~~~~~~~~ 71 (272)
T cd06301 1 KIGVSMANFDDNFLTLLRNAMKEHAKV---LG----GV--ELQFEDAKNDVATQLSQVENFIAQGVDAIIVVPVDTAATA 71 (272)
T ss_pred CeeEeecccCCHHHHHHHHHHHHHHHH---cC----Cc--EEEEeCCCCCHHHHHHHHHHHHHcCCCEEEEecCchhhhH
Confidence 588888753 22223334444444444 11 44 444567777887777777788888888885 455444344
Q ss_pred HHHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHc--CCcEEEEEEEcC--CCcchhHHHHHH
Q 003958 111 VVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHY--GWREVIAIYVDD--DHGRNGIAALGD 186 (784)
Q Consensus 111 ~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~--~w~~v~ii~~d~--~~g~~~~~~l~~ 186 (784)
.+...+...++|+|......+.. .+.+..+..++...+..+++.|.+. +-+++++|.... .......+.+++
T Consensus 72 ~~~~~l~~~~iPvv~~~~~~~~~----~~~~~~V~~d~~~~g~~~~~~l~~~~~~~~~i~~i~~~~~~~~~~~R~~gf~~ 147 (272)
T cd06301 72 PIVKAANAAGIPLVYVNRRPENA----PKGVAYVGSDEVVAGRLQAEYVADKLGGKGNVAILMGPLGQSAQIDRTKGVEE 147 (272)
T ss_pred HHHHHHHHCCCeEEEecCCCCCC----CCeeEEEecChHHHHHHHHHHHHHHhCCCccEEEEECCCCCccHHHHHHHHHH
Confidence 55566788999999875432211 1234456667677778888887654 457999997543 234556788999
Q ss_pred HHhccC-cEEEEeeccCCCCChhHHHHHHHHhhc--CCceEEEEeccCCcHHHHHHHHHHcCCCCCCeEEEec
Q 003958 187 TLAAKR-CRISFKAPLSVEATEDEITDLLVKVAL--TESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIAT 256 (784)
Q Consensus 187 ~l~~~g-i~v~~~~~~~~~~~~~d~~~~l~~l~~--~~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~wi~~ 256 (784)
.+++.| +.+... .....+.......++++.+ ..+++| ++.....+..+++.+++.|..+.+...++.
T Consensus 148 ~l~~~~~~~~~~~--~~~~~~~~~~~~~~~~~l~~~~~~~ai-~~~~d~~a~~~~~~l~~~g~~~~di~ivg~ 217 (272)
T cd06301 148 VLAKYPDIKVVEE--QTANWSRAEAMDLMENWLSSGGKIDAV-VANNDEMALGAIMALKAAGKSDKDVPVAGI 217 (272)
T ss_pred HHHHCCCcEEEec--CCCCccHHHHHHHHHHHHHhCCCCCEE-EECCCchHHHHHHHHHHcCCCCCCcEEEee
Confidence 998887 443321 1111122222344444432 235553 445556677899999999986334444443
No 129
>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=98.01 E-value=0.002 Score=66.14 Aligned_cols=208 Identities=9% Similarity=-0.006 Sum_probs=119.2
Q ss_pred EEEEEeecC-CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEccCchhh-HH
Q 003958 33 NIGALLSFS-TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIGPQDAVT-SH 110 (784)
Q Consensus 33 ~IG~i~~~~-~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiGp~~s~~-~~ 110 (784)
|||++.|.- ..+-.....+++.+.++ .|+++.+...++..++....+....++.+++.+||-...... ..
T Consensus 1 ~Igvi~~~~~~~~~~~~~~g~~~~~~~--------~g~~~~~~~~~~~~~~~~~~~~i~~l~~~~vdgvii~~~~~~~~~ 72 (273)
T cd06310 1 KIALVPKGTTSDFWQAVKAGAEAAAKE--------LGVKVTFQGPASETDVAGQVNLLENAIARGPDAILLAPTDAKALV 72 (273)
T ss_pred CeEEEecCCCcHHHHHHHHHHHHHHHH--------cCCEEEEecCccCCCHHHHHHHHHHHHHhCCCEEEEcCCChhhhH
Confidence 589888753 22112333444444433 256666554444557777677777788888888875333322 23
Q ss_pred HHHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHc--CCcEEEEEEEcCCC--cchhHHHHHH
Q 003958 111 VVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHY--GWREVIAIYVDDDH--GRNGIAALGD 186 (784)
Q Consensus 111 ~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~--~w~~v~ii~~d~~~--g~~~~~~l~~ 186 (784)
.....+...++|+|......+. +. + +-.+.......+..+++++.+. |.++++++....++ .....+.+++
T Consensus 73 ~~l~~~~~~~ipvV~~~~~~~~--~~--~-~~~v~~d~~~~~~~~~~~l~~~~~g~~~i~~i~~~~~~~~~~~r~~gf~~ 147 (273)
T cd06310 73 PPLKEAKDAGIPVVLIDSGLNS--DI--A-VSFVATDNVAAGKLAAEALAELLGKKGKVAVISFVPGSSTTDQREEGFLE 147 (273)
T ss_pred HHHHHHHHCCCCEEEecCCCCC--Cc--c-eEEEeeChHHHHHHHHHHHHHHcCCCceEEEEeCCCCCccHHHHHHHHHH
Confidence 3445556789999987532211 11 1 2223444445667788887666 89999999754333 3446788889
Q ss_pred HHhcc-CcEEEEeeccCCCCChhHHHHHHHHhhcCCceEE-EEeccCCcHHHHHHHHHHcCCCCCCeEEEec
Q 003958 187 TLAAK-RCRISFKAPLSVEATEDEITDLLVKVALTESRII-VVHTHYNRGPVVFHVAQYLGMLGTGYVWIAT 256 (784)
Q Consensus 187 ~l~~~-gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vI-vl~~~~~~~~~~~~~a~~~g~~~~~~~wi~~ 256 (784)
.+++. |+.+....... .+..+-...+.++.+...++- |++.+...+..+++++++.|+. .+...++.
T Consensus 148 a~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~l~~~~~~~~i~~~~d~~a~g~~~~l~~~g~~-~di~vig~ 216 (273)
T cd06310 148 GLKEYPGIEIVATQYSD--SDYAKALDITEDLLTANPDLKGIFGANEGSAVGAARAVRQAGKA-GKVKVVGF 216 (273)
T ss_pred HHHhCCCcEEEecccCC--cCHHHHHHHHHHHHHhCCCceEEEecCchhHHHHHHHHHhcCCC-CCeEEEEe
Confidence 99888 77654321111 122233345555543333333 3344556688899999999874 34444443
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=97.99 E-value=0.00067 Score=69.58 Aligned_cols=200 Identities=16% Similarity=0.128 Sum_probs=120.0
Q ss_pred EEEEeecC-CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHH-hcCceEEEccCchhhHHH
Q 003958 34 IGALLSFS-TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLM-EGQTVAIIGPQDAVTSHV 111 (784)
Q Consensus 34 IG~i~~~~-~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li-~~~v~aiiGp~~s~~~~~ 111 (784)
||++.|.. ..+......+++.++++ .|+.+.+...|... ......+.+.+ .+++.+||..........
T Consensus 2 I~vi~~~~~~~~~~~~~~gi~~~~~~--------~g~~~~~~~~~~~~--~~~~~~~~~~l~~~~vdgiii~~~~~~~~~ 71 (270)
T cd01545 2 IGLLYDNPSPGYVSEIQLGALDACRD--------TGYQLVIEPCDSGS--PDLAERVRALLQRSRVDGVILTPPLSDNPE 71 (270)
T ss_pred EEEEEcCCCcccHHHHHHHHHHHHHh--------CCCeEEEEeCCCCc--hHHHHHHHHHHHHCCCCEEEEeCCCCCccH
Confidence 78888864 44555667777777764 25667666554332 22344455544 568998887544332344
Q ss_pred HHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcCCC--cchhHHHHHHHHh
Q 003958 112 VSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDDDH--GRNGIAALGDTLA 189 (784)
Q Consensus 112 va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~~~--g~~~~~~l~~~l~ 189 (784)
..+.+...++|+|......+. ...++ ...+....+..+++.+...|.++++++..+..+ .....+.+++.++
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 456677789999987654321 12232 234556667888888888899999999865543 2345678888888
Q ss_pred ccCcEEEEeeccCCCCChhHHHHHHHHhhc--CCceEEEEeccCCcHHHHHHHHHHcCCCCCC
Q 003958 190 AKRCRISFKAPLSVEATEDEITDLLVKVAL--TESRIIVVHTHYNRGPVVFHVAQYLGMLGTG 250 (784)
Q Consensus 190 ~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~--~~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~ 250 (784)
+.|+.+.............+-...+.++.+ ..+++|+ +.+...+..+++++++.|...++
T Consensus 146 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~i~-~~~d~~a~~~~~~~~~~g~~~p~ 207 (270)
T cd01545 146 EAGLPLDPELVAQGDFTFESGLEAAEALLALPDRPTAIF-ASNDDMAAGVLAVAHRRGLRVPD 207 (270)
T ss_pred HcCCCCChhhEEeCCCChhhHHHHHHHHHhCCCCCCEEE-EcCcHHHHHHHHHHHHcCCCCCC
Confidence 887654211111111111222234444432 3466655 44556677999999999876443
No 131
>PRK10936 TMAO reductase system periplasmic protein TorT; Provisional
Probab=97.98 E-value=0.0044 Score=66.00 Aligned_cols=202 Identities=9% Similarity=-0.028 Sum_probs=117.0
Q ss_pred CCCceEEEEEEeecCC-cchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEc-cC
Q 003958 27 GRPSVVNIGALLSFST-NVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIG-PQ 104 (784)
Q Consensus 27 ~~~~~i~IG~i~~~~~-~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiG-p~ 104 (784)
.....-+||++.|... .+-.....+++-+.++. |+++.+...+...+...-.+....++++++.+||= |.
T Consensus 42 ~Ar~t~~Igvv~p~~~~~f~~~~~~gi~~aa~~~--------G~~l~i~~~~~~~~~~~q~~~i~~l~~~~vdgIIl~~~ 113 (343)
T PRK10936 42 KAKKAWKLCALYPHLKDSYWLSVNYGMVEEAKRL--------GVDLKVLEAGGYYNLAKQQQQLEQCVAWGADAILLGAV 113 (343)
T ss_pred ccCCCeEEEEEecCCCchHHHHHHHHHHHHHHHh--------CCEEEEEcCCCCCCHHHHHHHHHHHHHhCCCEEEEeCC
Confidence 3345789999998742 22223445666555541 55555543322335555555666777888887763 43
Q ss_pred chhhHHHHHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHc-----CCcEEEEEEEcC--CCc
Q 003958 105 DAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHY-----GWREVIAIYVDD--DHG 177 (784)
Q Consensus 105 ~s~~~~~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~-----~w~~v~ii~~d~--~~g 177 (784)
......... .+...++|+|.+..... .+. ....+.......+...++.|... |-.+++++..+. ...
T Consensus 114 ~~~~~~~~l-~~~~~giPvV~~~~~~~--~~~---~~~~V~~D~~~~g~~aa~~L~~~~~~~~g~~~i~~i~g~~~~~~~ 187 (343)
T PRK10936 114 TPDGLNPDL-ELQAANIPVIALVNGID--SPQ---VTTRVGVSWYQMGYQAGRYLAQWHPKGSKPLNVALLPGPEGAGGS 187 (343)
T ss_pred ChHHhHHHH-HHHHCCCCEEEecCCCC--Ccc---ceEEEecChHHHHHHHHHHHHHHHHhcCCCceEEEEECCCCCchH
Confidence 333322222 45678999997643211 111 12335566667777778876554 478999997543 233
Q ss_pred chhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhc--CCceEEEEeccCCcHHHHHHHHHHcCC
Q 003958 178 RNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVAL--TESRIIVVHTHYNRGPVVFHVAQYLGM 246 (784)
Q Consensus 178 ~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~--~~~~vIvl~~~~~~~~~~~~~a~~~g~ 246 (784)
....+.+++.+++.|+++.... .. ..+...-...++++.+ .++++|+ +....+..+++++++.|+
T Consensus 188 ~~R~~Gf~~~l~~~~i~~~~~~-~~-~~~~~~~~~~~~~~l~~~~~~~ai~--~~d~~A~ga~~al~~~g~ 254 (343)
T PRK10936 188 KAVEQGFRAAIAGSDVRIVDIA-YG-DNDKELQRNLLQELLERHPDIDYIA--GSAVAAEAAIGELRGRNL 254 (343)
T ss_pred HHHHHHHHHHHhcCCCEEEEee-cC-CCcHHHHHHHHHHHHHhCCCccEEE--eCCHHHHHHHHHHHhcCC
Confidence 4557888999988888765421 11 1122223344445432 2467765 344567778888888886
No 132
>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=97.93 E-value=0.0023 Score=65.75 Aligned_cols=208 Identities=10% Similarity=0.023 Sum_probs=122.7
Q ss_pred EEEEEeecC-CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEc-cCchhhHH
Q 003958 33 NIGALLSFS-TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIG-PQDAVTSH 110 (784)
Q Consensus 33 ~IG~i~~~~-~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiG-p~~s~~~~ 110 (784)
.||++.|.- ..+-.....++..+.++ . |+++. +.++..+...-.+....++.+++.+||- +.......
T Consensus 1 ~~g~~~~~~~~~~~~~~~~~~~~~a~~----~----g~~~~--~~~~~~~~~~~~~~i~~l~~~~vdgiIi~~~~~~~~~ 70 (273)
T cd06309 1 TVGFSQVGAESPWRTAETKSIKDAAEK----R----GFDLK--FADAQQKQENQISAIRSFIAQGVDVIILAPVVETGWD 70 (273)
T ss_pred CeeeccCCCCCHHHHHHHHHHHHHHHh----c----CCEEE--EeCCCCCHHHHHHHHHHHHHcCCCEEEEcCCccccch
Confidence 378888853 22222333444444444 2 45444 4565567666666777788888887754 43333333
Q ss_pred HHHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHc--CCcEEEEEEEcCC--CcchhHHHHHH
Q 003958 111 VVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHY--GWREVIAIYVDDD--HGRNGIAALGD 186 (784)
Q Consensus 111 ~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~--~w~~v~ii~~d~~--~g~~~~~~l~~ 186 (784)
.....+...++|+|......+.. ...+++.++.+.....+..++++|... +-++++++..+.. ......+.+++
T Consensus 71 ~~i~~~~~~~iPvV~~~~~~~~~--~~~~~~~~v~~d~~~~g~~~~~~l~~~~~g~~~i~~i~~~~~~~~~~~R~~Gf~~ 148 (273)
T cd06309 71 PVLKEAKAAGIPVILVDRGVDVK--DDSLYVTFIGSDFVEEGRRAADWLAKATGGKGNIVELQGTVGSSVAIDRKKGFAE 148 (273)
T ss_pred HHHHHHHHCCCCEEEEecCcCCc--cCcceeeEecCChHHHHHHHHHHHHHHcCCCceEEEEeCCCCCchHHHHHHHHHH
Confidence 44456778899999986532211 112456677888888888888888776 8899999985432 23455788888
Q ss_pred HHhcc-CcEEEEeeccCCCCChhHHHHHHHHhhcC---CceEEEEeccCCcHHHHHHHHHHcCCCCCCeEEEe
Q 003958 187 TLAAK-RCRISFKAPLSVEATEDEITDLLVKVALT---ESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIA 255 (784)
Q Consensus 187 ~l~~~-gi~v~~~~~~~~~~~~~d~~~~l~~l~~~---~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~wi~ 255 (784)
.+++. ++.+....... .+..+....++++.+. .+++| ++.....+..+++++++.|+..++-+-|.
T Consensus 149 ~l~~~~~~~~~~~~~~~--~~~~~~~~~~~~~l~~~~~~~~aI-~~~~d~~a~g~~~a~~~~g~~ip~di~ii 218 (273)
T cd06309 149 VIKKYPNMKIVASQTGD--FTRAKGKEVMEALLKAHGDDIDAV-YAHNDEMALGAIQAIKAAGKKPGKDIKIV 218 (273)
T ss_pred HHHHCCCCEEeeccCCc--ccHHHHHHHHHHHHHhCCCCccEE-EECCcHHHHHHHHHHHHcCCCCCCCeEEE
Confidence 88876 45543211111 1223333445554433 34544 33344555678899999998755444333
No 133
>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=97.90 E-value=0.0016 Score=66.27 Aligned_cols=201 Identities=12% Similarity=0.108 Sum_probs=133.9
Q ss_pred EEEEeecCC-cchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEE-ccCchhhHHH
Q 003958 34 IGALLSFST-NVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAII-GPQDAVTSHV 111 (784)
Q Consensus 34 IG~i~~~~~-~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aii-Gp~~s~~~~~ 111 (784)
||++.+... .+......+++-+.++. |..+.+. .|...++..-.+.+..++.+++.+|| .|..+.....
T Consensus 1 I~vi~~~~~~~~~~~~~~g~~~~a~~~--------g~~~~~~-~~~~~d~~~q~~~i~~~i~~~~d~Iiv~~~~~~~~~~ 71 (257)
T PF13407_consen 1 IGVIVPSMDNPFWQQVIKGAKAAAKEL--------GYEVEIV-FDAQNDPEEQIEQIEQAISQGVDGIIVSPVDPDSLAP 71 (257)
T ss_dssp EEEEESSSSSHHHHHHHHHHHHHHHHH--------TCEEEEE-EESTTTHHHHHHHHHHHHHTTESEEEEESSSTTTTHH
T ss_pred cEEEeCCCCCHHHHHHHHHHHHHHHHc--------CCEEEEe-CCCCCCHHHHHHHHHHHHHhcCCEEEecCCCHHHHHH
Confidence 688888763 34556788888888885 4555555 78889999888999999999999876 5666666666
Q ss_pred HHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHc-C-CcEEEEEEEcCCC--cchhHHHHHHH
Q 003958 112 VSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHY-G-WREVIAIYVDDDH--GRNGIAALGDT 187 (784)
Q Consensus 112 va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~-~-w~~v~ii~~d~~~--g~~~~~~l~~~ 187 (784)
...-+...+||+|++... .....+......++....+..+++++.+. + -.+++++.....+ .....+.+++.
T Consensus 72 ~l~~~~~~gIpvv~~d~~----~~~~~~~~~~v~~d~~~~G~~~a~~l~~~~~~~~~v~~~~~~~~~~~~~~r~~g~~~~ 147 (257)
T PF13407_consen 72 FLEKAKAAGIPVVTVDSD----EAPDSPRAAYVGTDNYEAGKLAAEYLAEKLGAKGKVLILSGSPGNPNTQERLEGFRDA 147 (257)
T ss_dssp HHHHHHHTTSEEEEESST----HHTTSTSSEEEEE-HHHHHHHHHHHHHHHHTTTEEEEEEESSTTSHHHHHHHHHHHHH
T ss_pred HHHHHhhcCceEEEEecc----ccccccceeeeeccHHHHHHHHHHHHHHHhccCceEEeccCCCCchHHHHHHHHHHHH
Confidence 677788899999997554 01123455666777888889999987554 3 2688888654433 23567888888
Q ss_pred Hhcc-CcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHcCCCC
Q 003958 188 LAAK-RCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLG 248 (784)
Q Consensus 188 l~~~-gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~g~~~ 248 (784)
+++. ++++...... ...+.++....+.++.+.++-..|+++....+..+++++++.|+.+
T Consensus 148 l~~~~~~~~~~~~~~-~~~~~~~a~~~~~~~l~~~~~~~i~~~~~~~~~g~~~al~~~g~~~ 208 (257)
T PF13407_consen 148 LKEYPGVEIVDEYEY-TDWDPEDARQAIENLLQANPVDAIIACNDGMALGAAQALQQAGRAG 208 (257)
T ss_dssp HHHCTTEEEEEEEEE-CTTSHHHHHHHHHHHHHHTTEEEEEESSHHHHHHHHHHHHHTTCTT
T ss_pred Hhhcceeeeeeeeec-cCCCHHHHHHHHHHhhhcCCceEEEeCCChHHHHHHHHHHHcCCcc
Confidence 8884 5666542222 1234455555555554443322234455566677889999988743
No 134
>COG1879 RbsB ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]
Probab=97.83 E-value=0.01 Score=62.70 Aligned_cols=205 Identities=12% Similarity=0.111 Sum_probs=127.5
Q ss_pred eEEEEEEeecCCcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEE-EccCchhhH
Q 003958 31 VVNIGALLSFSTNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAI-IGPQDAVTS 109 (784)
Q Consensus 31 ~i~IG~i~~~~~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~ai-iGp~~s~~~ 109 (784)
..+||++.+... ..+..++.-++++--..- |....+...|...++...++...+++.+++.+| +.|.++...
T Consensus 33 ~~~i~~~~~~~~---~~f~~~~~~g~~~~a~~~----g~~~~~~~~~~~~d~~~Q~~~i~~~ia~~~daIiv~~~d~~~~ 105 (322)
T COG1879 33 GKTIGVVVPTLG---NPFFQAVRKGAEAAAKKL----GVVVAVVIADAQNDVAKQIAQIEDLIAQGVDAIIINPVDPDAL 105 (322)
T ss_pred CceEEEEeccCC---ChHHHHHHHHHHHHHHHc----CCcEEEEecccccChHHHHHHHHHHHHcCCCEEEEcCCChhhh
Confidence 488999888653 233344444444433332 224667777888899988889999999999877 568888888
Q ss_pred HHHHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHH-cC-CcEEEEEEEc--CCCcchhHHHHH
Q 003958 110 HVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDH-YG-WREVIAIYVD--DDHGRNGIAALG 185 (784)
Q Consensus 110 ~~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~-~~-w~~v~ii~~d--~~~g~~~~~~l~ 185 (784)
.....-+...+||+|.+....+.- ..............+...++++.+ ++ ..++.++... ........+.++
T Consensus 106 ~~~v~~a~~aGIpVv~~d~~~~~~----~~~~~~vg~dn~~~G~~~a~~l~~~~~~~g~v~~~~g~~~~~~~~~R~~G~~ 181 (322)
T COG1879 106 TPAVKKAKAAGIPVVTVDSDIPGP----GDRVAYVGSDNYKAGRLAAEYLAKALGGKGKVVVLVGSPGNSSAEERVKGFR 181 (322)
T ss_pred HHHHHHHHHCCCcEEEEecCCCCC----CceeEEEecCcHHHHHHHHHHHHHHhCCCCeEEEEecCCCCchHHHHHhhHH
Confidence 888899999999999986543321 112223333445556666666543 43 2446666643 334456788899
Q ss_pred HHHhccCc--EEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCC-cHHHHHHHHHHcCCCC
Q 003958 186 DTLAAKRC--RISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYN-RGPVVFHVAQYLGMLG 248 (784)
Q Consensus 186 ~~l~~~gi--~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~-~~~~~~~~a~~~g~~~ 248 (784)
+.+++.+- .+... ...+.+...-......+....+++-.+++..+ .+....+++++.|..+
T Consensus 182 ~~l~~~~~~~~v~~~--~~~~~~~~~a~~~~~~~L~~~pdi~~i~~~~d~~a~ga~~A~~~~g~~~ 245 (322)
T COG1879 182 DALKEHPPDIEVVDV--QTGDWDRDKALEVMEDLLAANPDIDGIYAANDGMALGAIQALKAAGRKG 245 (322)
T ss_pred HHHHhCCCcEEEeec--cCCcccHHHHHHHHHHHHHhCCCceEEEECCchhHHHHHHHHHHcCCCC
Confidence 99988774 43332 22122333344555666666667766665544 4445666777777654
No 135
>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=97.79 E-value=0.002 Score=65.94 Aligned_cols=201 Identities=11% Similarity=0.029 Sum_probs=118.7
Q ss_pred EEEEEeecC-CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEccCchhhHHH
Q 003958 33 NIGALLSFS-TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIGPQDAVTSHV 111 (784)
Q Consensus 33 ~IG~i~~~~-~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiGp~~s~~~~~ 111 (784)
.||++.|.. ..+-.....+++.+.++. |+++ .+.++..++..-.+....++.+++.++|...+......
T Consensus 1 ~I~vi~~~~~~~~~~~~~~g~~~~a~~~--------g~~~--~~~~~~~~~~~~~~~i~~~~~~~vdgiii~~~~~~~~~ 70 (268)
T cd06289 1 TIGLVINDLTNPFFAELAAGLEEVLEEA--------GYTV--FLANSGEDVERQEQLLSTMLEHGVAGIILCPAAGTSPD 70 (268)
T ss_pred CEEEEecCCCcchHHHHHHHHHHHHHHc--------CCeE--EEecCCCChHHHHHHHHHHHHcCCCEEEEeCCCCccHH
Confidence 378888753 223344556666666652 4554 34455556666666677777888998877554333333
Q ss_pred HHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcC--CCcchhHHHHHHHHh
Q 003958 112 VSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDD--DHGRNGIAALGDTLA 189 (784)
Q Consensus 112 va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~--~~g~~~~~~l~~~l~ 189 (784)
....+...++|+|......+ +...+ ...++....+..+++.+...|-++|+++..+. .......+.+.+.++
T Consensus 71 ~~~~~~~~~ipvV~~~~~~~---~~~~~---~v~~d~~~~~~~~~~~l~~~g~~~i~~l~~~~~~~~~~~r~~gf~~~l~ 144 (268)
T cd06289 71 LLKRLAESGIPVVLVAREVA---GAPFD---YVGPDNAAGARLATEHLISLGHRRIAFIGGLEDSSTRRERLAGYRAALA 144 (268)
T ss_pred HHHHHHhcCCCEEEEeccCC---CCCCC---EEeecchHHHHHHHHHHHHCCCCCEEEecCCccccchHHHHHHHHHHHH
Confidence 44567788999998754322 11222 24455666777888888778999999987543 344566788999998
Q ss_pred ccCcEEEEeeccCCCCChhHHHHHHHHhhcC--CceEEEEeccCCcHHHHHHHHHHcCCCCCC
Q 003958 190 AKRCRISFKAPLSVEATEDEITDLLVKVALT--ESRIIVVHTHYNRGPVVFHVAQYLGMLGTG 250 (784)
Q Consensus 190 ~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~--~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~ 250 (784)
+.|..+.....+....+.......++++... ..++|+ +.+...+..+++++++.|+..++
T Consensus 145 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~i~-~~~~~~a~~~~~al~~~g~~~p~ 206 (268)
T cd06289 145 EAGLPFDSELVVEGPPSRQGGAEAVAQLLDLPPRPTAIV-CFNDLVAFGAMSGLRRAGLTPGR 206 (268)
T ss_pred HcCCCCCchhEEecCcchhhHHHHHHHHHcCCCCCCEEE-EcCcHHHHHHHHHHHHcCCCCCc
Confidence 8774322111111111222223444444333 355544 33444567789999998876543
No 136
>PRK15395 methyl-galactoside ABC transporter galactose-binding periplasmic protein MglB; Provisional
Probab=97.76 E-value=0.013 Score=62.13 Aligned_cols=208 Identities=11% Similarity=0.034 Sum_probs=110.2
Q ss_pred CceEEEEEEeecC-CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEc-cCch
Q 003958 29 PSVVNIGALLSFS-TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIG-PQDA 106 (784)
Q Consensus 29 ~~~i~IG~i~~~~-~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiG-p~~s 106 (784)
.++..||++.+.. ..+-.....+++-+.++ .+ +. .+...++..+.....+....++.+++.+||= +..+
T Consensus 22 ~~~~~Igvv~~~~~~~f~~~~~~gi~~~a~~---~g----~~--~~~~~~~~~~~~~~~~~i~~l~~~~vdgiIi~~~~~ 92 (330)
T PRK15395 22 AADTRIGVTIYKYDDNFMSVVRKAIEKDAKA---AP----DV--QLLMNDSQNDQSKQNDQIDVLLAKGVKALAINLVDP 92 (330)
T ss_pred cCCceEEEEEecCcchHHHHHHHHHHHHHHh---cC----Ce--EEEEecCCCCHHHHHHHHHHHHHcCCCEEEEeccCH
Confidence 4578899998743 22222334444444444 22 23 3344566556665555666677778887764 2233
Q ss_pred hhHHHHHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHc------------CCcEEEEEEEcC
Q 003958 107 VTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHY------------GWREVIAIYVDD 174 (784)
Q Consensus 107 ~~~~~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~------------~w~~v~ii~~d~ 174 (784)
.........+...++|+|.+....+.-.-...+....+..+...-+..+++++.+. |-.++++|....
T Consensus 93 ~~~~~~l~~l~~~giPvV~vd~~~~~~~~~~~~~~~~V~~D~~~ag~~a~~~l~~~~~~~~~~~~~~~g~~~i~~i~g~~ 172 (330)
T PRK15395 93 AAAPTVIEKARGQDVPVVFFNKEPSRKALDSYDKAYYVGTDSKESGIIQGDLIAKHWKANPAWDLNKDGKIQYVLLKGEP 172 (330)
T ss_pred HHHHHHHHHHHHCCCcEEEEcCCccccccccccceeEEccChHHHHHHHHHHHHHHHhhccccccCCCCceEEEEEecCC
Confidence 32344445567789999998653211000111222334555555566555554332 333345554432
Q ss_pred --CCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcC----CceEEEEeccCCcHHHHHHHHHHcCC
Q 003958 175 --DHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALT----ESRIIVVHTHYNRGPVVFHVAQYLGM 246 (784)
Q Consensus 175 --~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~----~~~vIvl~~~~~~~~~~~~~a~~~g~ 246 (784)
.......+.+++.+++.|+.+..........+..+-...++++.+. .+++|+ +++...+..+++++++.|+
T Consensus 173 ~~~~~~~R~~G~~~al~~~g~~~~~~~~~~~~~~~~~a~~~~~~~l~~~~~~~~~ai~-~~~d~~A~gvl~al~~~Gl 249 (330)
T PRK15395 173 GHPDAEARTTYVIKELNDKGIKTEQLQLDTAMWDTAQAKDKMDAWLSGPNANKIEVVI-ANNDAMAMGAVEALKAHNK 249 (330)
T ss_pred CCchHHHHHHHHHHHHHhcCCCeeeeecccCCcCHHHHHHHHHHHHhhCcCCCeeEEE-ECCchHHHHHHHHHHhcCC
Confidence 2334567888999988887654321111111222333445554332 345444 4455667789999999887
No 137
>PRK09701 D-allose transporter subunit; Provisional
Probab=97.74 E-value=0.028 Score=59.00 Aligned_cols=204 Identities=12% Similarity=-0.010 Sum_probs=116.8
Q ss_pred EEEEEeecC-CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEc-cCchhhHH
Q 003958 33 NIGALLSFS-TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIG-PQDAVTSH 110 (784)
Q Consensus 33 ~IG~i~~~~-~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiG-p~~s~~~~ 110 (784)
+||++.|.. ..+-.....+++-+.++ .|+++.+...+...+.....+....++.+++.+||- +..+....
T Consensus 26 ~Igvi~~~~~~~f~~~~~~gi~~~a~~--------~g~~v~~~~~~~~~~~~~~~~~i~~l~~~~vDgiIi~~~~~~~~~ 97 (311)
T PRK09701 26 EYAVVLKTLSNPFWVDMKKGIEDEAKT--------LGVSVDIFASPSEGDFQSQLQLFEDLSNKNYKGIAFAPLSSVNLV 97 (311)
T ss_pred eEEEEeCCCCCHHHHHHHHHHHHHHHH--------cCCeEEEecCCCCCCHHHHHHHHHHHHHcCCCEEEEeCCChHHHH
Confidence 799999864 22223344555544443 156666554344456666666677777888887764 33332222
Q ss_pred HHHHhhhcCCccEEecccCCCC--CCcCCCCceEeecCChHHHHHHHHHHHHH-cCC--cEEEEEEEcC--CCcchhHHH
Q 003958 111 VVSHVANELQVPLLSFSATDPT--LSSLQFPYFVRTTQSDQYQMAAIAEIVDH-YGW--REVIAIYVDD--DHGRNGIAA 183 (784)
Q Consensus 111 ~va~~~~~~~ip~Is~~a~~~~--l~~~~~p~~~r~~ps~~~~~~ai~~~l~~-~~w--~~v~ii~~d~--~~g~~~~~~ 183 (784)
.....+...+||+|......+. +....-.....+..+....+..++++|.+ .|- ++++++..+. .......+.
T Consensus 98 ~~l~~~~~~giPvV~~~~~~~~~~~~~~~~~~~~~V~~d~~~~g~~aa~~L~~~~g~~~~~i~~l~g~~~~~~~~~R~~G 177 (311)
T PRK09701 98 MPVARAWKKGIYLVNLDEKIDMDNLKKAGGNVEAFVTTDNVAVGAKGASFIIDKLGAEGGEVAIIEGKAGNASGEARRNG 177 (311)
T ss_pred HHHHHHHHCCCcEEEeCCCCCcccccccCCceEEEeccchHHHHHHHHHHHHHHhCCCCCEEEEEECCCCCccHHHHHHH
Confidence 2223345689999998643221 11001112233556667778888887754 464 7999886543 234566788
Q ss_pred HHHHHhccC-cEEEEeeccCCCCChhHHHHHHHHhhcC--CceEEEEeccCCcHHHHHHHHHHcCCC
Q 003958 184 LGDTLAAKR-CRISFKAPLSVEATEDEITDLLVKVALT--ESRIIVVHTHYNRGPVVFHVAQYLGML 247 (784)
Q Consensus 184 l~~~l~~~g-i~v~~~~~~~~~~~~~d~~~~l~~l~~~--~~~vIvl~~~~~~~~~~~~~a~~~g~~ 247 (784)
+++.+++.| +.+....... ....+....++++.+. .+++ |++.....+..+++++++.|..
T Consensus 178 f~~al~~~~~~~~~~~~~~~--~~~~~~~~~~~~ll~~~~~~~~-I~~~~d~~A~g~~~al~~~G~~ 241 (311)
T PRK09701 178 ATEAFKKASQIKLVASQPAD--WDRIKALDVATNVLQRNPNIKA-IYCANDTMAMGVAQAVANAGKT 241 (311)
T ss_pred HHHHHHhCCCcEEEEecCCC--CCHHHHHHHHHHHHHhCCCCCE-EEECCcchHHHHHHHHHHcCCC
Confidence 999998877 6654322111 1222233455555333 3554 4455556777899999998874
No 138
>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=97.74 E-value=0.0035 Score=64.02 Aligned_cols=197 Identities=10% Similarity=-0.018 Sum_probs=115.1
Q ss_pred EEEEeecCC-cchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEccCchhhHHHH
Q 003958 34 IGALLSFST-NVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIGPQDAVTSHVV 112 (784)
Q Consensus 34 IG~i~~~~~-~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiGp~~s~~~~~v 112 (784)
||++.|... .+-.....+++-|.++ .|+.+ .+.|+..++.........++.+++.++|......... .
T Consensus 2 i~~v~~~~~~~~~~~~~~~i~~~~~~--------~g~~~--~~~~~~~~~~~~~~~~~~~~~~~vdgiii~~~~~~~~-~ 70 (267)
T cd06284 2 ILVLVPDIANPFFSEILKGIEDEARE--------AGYGV--LLGDTRSDPEREQEYLDLLRRKQADGIILLDGSLPPT-A 70 (267)
T ss_pred EEEEECCCCCccHHHHHHHHHHHHHH--------cCCeE--EEecCCCChHHHHHHHHHHHHcCCCEEEEecCCCCHH-H
Confidence 788887642 2223444555555555 14544 4567777776666666667777899887633222222 2
Q ss_pred HHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEc--CCCcchhHHHHHHHHhc
Q 003958 113 SHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVD--DDHGRNGIAALGDTLAA 190 (784)
Q Consensus 113 a~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d--~~~g~~~~~~l~~~l~~ 190 (784)
.... ..++|+|......+ . +.+.....+....+..+++.+...|.++++++..+ +..+....+.|++.+++
T Consensus 71 ~~~~-~~~ipvv~~~~~~~---~---~~~~~v~~d~~~~g~~~~~~l~~~g~~~i~~l~~~~~~~~~~~r~~gf~~~~~~ 143 (267)
T cd06284 71 LTAL-AKLPPIVQACEYIP---G---LAVPSVSIDNVAAARLAVDHLISLGHRRIALITGPRDNPLARDRLEGYRQALAE 143 (267)
T ss_pred HHHH-hcCCCEEEEecccC---C---CCcceEEecccHHHHHHHHHHHHcCCceEEEEcCCccchhHHHHHHHHHHHHHH
Confidence 2333 35999997643211 1 22233455566777888888888899999999864 33556678899999988
Q ss_pred cCcEEEEeeccCCCCChhHHHHHHHHhhcC--CceEEEEeccCCcHHHHHHHHHHcCCCCC
Q 003958 191 KRCRISFKAPLSVEATEDEITDLLVKVALT--ESRIIVVHTHYNRGPVVFHVAQYLGMLGT 249 (784)
Q Consensus 191 ~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~--~~~vIvl~~~~~~~~~~~~~a~~~g~~~~ 249 (784)
.|+.+..........+..+....++++.+. .+++|+. .+...+..+++++++.|+..+
T Consensus 144 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~-~~~~~a~g~~~al~~~g~~~p 203 (267)
T cd06284 144 AGLPADEELIQEGDFSLESGYAAARRLLALPDRPTAIFC-FSDEMAIGAISALKELGLRVP 203 (267)
T ss_pred cCCCCCcceEEeCCCChHHHHHHHHHHHhCCCCCcEEEE-cCcHHHHHHHHHHHHcCCCCc
Confidence 875432111111111222333444444322 3565555 344557788999999887644
No 139
>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=97.72 E-value=0.0037 Score=63.96 Aligned_cols=206 Identities=13% Similarity=0.063 Sum_probs=120.8
Q ss_pred EEEEEeecC-CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEccCchhhHHH
Q 003958 33 NIGALLSFS-TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIGPQDAVTSHV 111 (784)
Q Consensus 33 ~IG~i~~~~-~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiGp~~s~~~~~ 111 (784)
+||+++|.. ..+-.....+++-+.++ . |+.+.+. .+..++..-.+....++.+++.+||-..+.. ...
T Consensus 1 ~i~vi~~~~~~~~~~~~~~~~~~~~~~---~-----g~~~~~~--~~~~~~~~~~~~i~~l~~~~vdgiii~~~~~-~~~ 69 (268)
T cd06298 1 TVGVIIPDITNSYFAELARGIDDIATM---Y-----KYNIILS--NSDNDKEKELKVLNNLLAKQVDGIIFMGGKI-SEE 69 (268)
T ss_pred CEEEEECCCcchHHHHHHHHHHHHHHH---c-----CCeEEEE--eCCCCHHHHHHHHHHHHHhcCCEEEEeCCCC-cHH
Confidence 378888763 22222344455544444 1 4555544 3445666556666677777888887422211 123
Q ss_pred HHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcC---CCcchhHHHHHHHH
Q 003958 112 VSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDD---DHGRNGIAALGDTL 188 (784)
Q Consensus 112 va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~---~~g~~~~~~l~~~l 188 (784)
+...+...++|+|......+ ....+ ...+.....+..+++.|...|-++++++..+. ..+....+.+++.+
T Consensus 70 ~~~~l~~~~ipvV~~~~~~~---~~~~~---~v~~d~~~~~~~~~~~l~~~g~~~i~~l~~~~~~~~~~~~r~~gf~~~~ 143 (268)
T cd06298 70 HREEFKRSPTPVVLAGSVDE---DNELP---SVNIDYKKAAFEATELLIKNGHKKIAFISGPLEDSINGDERLAGYKEAL 143 (268)
T ss_pred HHHHHhcCCCCEEEEccccC---CCCCC---EEEECcHHHHHHHHHHHHHcCCceEEEEeCCcccccchhHHHHHHHHHH
Confidence 44556667999998755321 11223 24556666778888888888999999998543 35667788999999
Q ss_pred hccCcEEEEeeccCCCCChhHHHHHHHHhhcCC-ceEEEEeccCCcHHHHHHHHHHcCCCCCC-eEEEec
Q 003958 189 AAKRCRISFKAPLSVEATEDEITDLLVKVALTE-SRIIVVHTHYNRGPVVFHVAQYLGMLGTG-YVWIAT 256 (784)
Q Consensus 189 ~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~-~~vIvl~~~~~~~~~~~~~a~~~g~~~~~-~~wi~~ 256 (784)
++.|+.+..........+.......++++.+.. +++|+. .....+..+++++++.|+..++ ..+++.
T Consensus 144 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~ai~~-~~d~~a~~~~~~l~~~g~~vp~di~vvg~ 212 (268)
T cd06298 144 SEANIEFDESLIFEGDYTYESGYELAEELLEDGKPTAAFV-TDDELAIGILNAAQDAGLKVPEDFEIIGF 212 (268)
T ss_pred HHcCCCCCHHHeEeCCCChhHHHHHHHHHhcCCCCCEEEE-cCcHHHHHHHHHHHHcCCCCccceEEEee
Confidence 888865422111111112222334455554443 666654 4445577899999999986543 334443
No 140
>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=97.71 E-value=0.0096 Score=62.22 Aligned_cols=208 Identities=8% Similarity=0.034 Sum_probs=114.6
Q ss_pred EEEEEeecC-CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEE-ccCchhhHH
Q 003958 33 NIGALLSFS-TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAII-GPQDAVTSH 110 (784)
Q Consensus 33 ~IG~i~~~~-~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aii-Gp~~s~~~~ 110 (784)
+||++.|.. ..+-.....+++-+.++. + .| +.+.+.+...++..-.+....++.+++.+|| .|..+....
T Consensus 1 ~Igviv~~~~~~~~~~~~~gi~~~a~~~---~---~g--~~~~~~~~~~~~~~q~~~i~~l~~~~vdgiii~~~~~~~~~ 72 (303)
T cd01539 1 KIGVFLYKFDDTFISLVRKNLEDIQKEN---G---GK--VEFTFYDAKNNQSTQNEQIDTALAKGVDLLAVNLVDPTAAQ 72 (303)
T ss_pred CeEEEeeCCCChHHHHHHHHHHHHHHhh---C---CC--eeEEEecCCCCHHHHHHHHHHHHHcCCCEEEEecCchhhHH
Confidence 588888854 222233445555555554 1 13 4455567777777766677778888888765 344444334
Q ss_pred HHHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHc--CC---------cE--EEEEEEcCC--
Q 003958 111 VVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHY--GW---------RE--VIAIYVDDD-- 175 (784)
Q Consensus 111 ~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~--~w---------~~--v~ii~~d~~-- 175 (784)
.+...+...++|+|......+...-...+.+..+.++....+..++++|... +- .+ ++++..+..
T Consensus 73 ~~~~~~~~~giPvV~~~~~~~~~~~~~~~~~~~V~~d~~~~g~~~a~~l~~~~~~~~~~~~~~~~g~~~i~~~~g~~~~~ 152 (303)
T cd01539 73 TVINKAKQKNIPVIFFNREPEEEDIKSYDKAYYVGTDAEQSGILQGKLIADYWNANKDALDKNGDGIIQYVMLKGEPGHP 152 (303)
T ss_pred HHHHHHHHCCCCEEEeCCCCcccccccccccceeeecHHHHHHHHHHHHHHHhhccccccccCCCCceEEEEEEcCCCCc
Confidence 4555667789999987643221100111223445566666667777776543 22 12 344554322
Q ss_pred CcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhh-cC--CceEEEEeccCCcHHHHHHHHHHcCCCCC
Q 003958 176 HGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVA-LT--ESRIIVVHTHYNRGPVVFHVAQYLGMLGT 249 (784)
Q Consensus 176 ~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~-~~--~~~vIvl~~~~~~~~~~~~~a~~~g~~~~ 249 (784)
......+.+++.+++.+..+..........+.......++++. +. ..++|+. .....+..+++++++.|...+
T Consensus 153 ~~~~R~~gf~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~~~~~~ai~~-~~d~~a~g~~~al~~~g~~~p 228 (303)
T cd01539 153 DAIARTKYSIETLNDAGIKTEELASDTANWDRAQAKDKMDALLLKYGDKIEAVIA-NNDAMALGAIEALQKYGYNKG 228 (303)
T ss_pred hhhhhhhhHHHHHHhcCCCeEEEEeecCCCCHHHHHHHHHHHHHhcCCCccEEEE-CCchHHHHHHHHHHHcCCCcC
Confidence 2344567888999888765432222221122223334455543 22 2455433 445556678888888887654
No 141
>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=97.65 E-value=0.012 Score=60.63 Aligned_cols=212 Identities=8% Similarity=0.004 Sum_probs=113.7
Q ss_pred EEEEEeecC--CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCC--CCHHHHHHHHHHHHhcCceEEEccCchhh
Q 003958 33 NIGALLSFS--TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCN--HSGFLALAEALHLMEGQTVAIIGPQDAVT 108 (784)
Q Consensus 33 ~IG~i~~~~--~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~--~~~~~a~~~~~~li~~~v~aiiGp~~s~~ 108 (784)
|||+++|.. ..+-.....+++.++++ . |+.+.+...++. .++..-.+....++.+++.+||=...+..
T Consensus 1 ~Igvi~~~~~~~~~~~~~~~~i~~~~~~---~-----g~~~~~~~~~~~~~~~~~~~~~~i~~l~~~~vDgiIv~~~~~~ 72 (280)
T cd06303 1 KIAVIYPGQQISDYWVRNIASFTARLEE---L-----NIPYELTQFSSRPGIDHRLQSQQLNEALQSKPDYLIFTLDSLR 72 (280)
T ss_pred CeeEEecCccHHHHHHHHHHHHHHHHHH---c-----CCcEEEEEeccCcccCHHHHHHHHHHHHHcCCCEEEEcCCchh
Confidence 489998863 11111222333333322 2 556666544433 24555455556777788888875433322
Q ss_pred HHHHHHhhhcCCccEEeccc-CCCCCCcCCCCceEeecCChHHHHHHHHHHHHH--cCCcEEEEEEEcC-CCcchhHHHH
Q 003958 109 SHVVSHVANELQVPLLSFSA-TDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDH--YGWREVIAIYVDD-DHGRNGIAAL 184 (784)
Q Consensus 109 ~~~va~~~~~~~ip~Is~~a-~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~--~~w~~v~ii~~d~-~~g~~~~~~l 184 (784)
.......+...++|.|.... ..+.......+......+....-+..+++.|.+ .|.+++++|.... .......+.+
T Consensus 73 ~~~~~~~l~~~~~p~V~i~~~~~~~~~~~~~~~~~~V~~d~~~~g~~~~~~L~~~~~g~~~i~~l~~~~~~~~~~R~~gf 152 (280)
T cd06303 73 HRKLIERVLASGKTKIILQNITTPVKAWLKHQPLLYVGFDHAAGARLLADYFIKRYPNHARYAMLYFSPGYISTARGDTF 152 (280)
T ss_pred hHHHHHHHHhCCCCeEEEeCCCCCccccccCCCceEeCCCHHHHHHHHHHHHHHhcCCCcEEEEEECCCCcchhHHHHHH
Confidence 22222334446667665522 222100000122334556666777888888777 7999999997532 3334567888
Q ss_pred HHHHhcc-CcEEEEeeccCCCCChhHHHHHHHHhhcC--CceEEEEeccCCcHHHHHHHHHHcCCCCCCeEEEec
Q 003958 185 GDTLAAK-RCRISFKAPLSVEATEDEITDLLVKVALT--ESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIAT 256 (784)
Q Consensus 185 ~~~l~~~-gi~v~~~~~~~~~~~~~d~~~~l~~l~~~--~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~wi~~ 256 (784)
++.+++. |+.+... .....+..+....++++.+. ++++|+ +.+...+..+++++++.|+. .+...++-
T Consensus 153 ~~al~~~~~~~~~~~--~~~~~~~~~~~~~~~~~l~~~~~~~ai~-~~nd~~A~g~l~al~~~G~~-~dv~vvg~ 223 (280)
T cd06303 153 IDCVHARNNWTLTSE--FYTDATRQKAYQATSDILSNNPDVDFIY-ACSTDIALGASDALKELGRE-DDILINGW 223 (280)
T ss_pred HHHHHhCCCceEEEe--ecCCCCHHHHHHHHHHHHHhCCCCcEEE-ECCcHHHHHHHHHHHHcCCC-CCcEEEec
Confidence 9999887 6654322 12112223333445554333 345544 45556677899999999975 33444443
No 142
>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=97.64 E-value=0.018 Score=59.06 Aligned_cols=202 Identities=9% Similarity=0.015 Sum_probs=115.8
Q ss_pred EEEEeecC-CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEc-cCchhhHHH
Q 003958 34 IGALLSFS-TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIG-PQDAVTSHV 111 (784)
Q Consensus 34 IG~i~~~~-~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiG-p~~s~~~~~ 111 (784)
||++.|.. ..+-.....+++-+.++..... .| +.+.+.+...++....+....++.+++.+||- |........
T Consensus 2 Ig~i~~~~~~~f~~~~~~gi~~~a~~~~~~~---~g--~~~~~~~~~~~~~~~~~~~~~l~~~~vDgiii~~~~~~~~~~ 76 (274)
T cd06311 2 IGVSIPAADHGWTAGIVWHAQAAAKKLEAAY---PD--VEFILVTASNDTEQQNAQQDLLINRKIDALVILPFESAPLTQ 76 (274)
T ss_pred eeeeccCCCCcHHHHHHHHHHHHHHHhhhhC---CC--eEEEEEcCCCCHHHHHHHHHHHHHcCCCEEEEeCCCchhhHH
Confidence 67777643 3333345566666666654332 23 44555666666665555555677778887753 333333233
Q ss_pred HHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHc--CCcEEEEEEEcC-CCcchhHHHHHHHH
Q 003958 112 VSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHY--GWREVIAIYVDD-DHGRNGIAALGDTL 188 (784)
Q Consensus 112 va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~--~w~~v~ii~~d~-~~g~~~~~~l~~~l 188 (784)
....+...+||+|......+ +.. .......+.....+..++++|... +.++|+++.... .......+.+++.+
T Consensus 77 ~i~~~~~~gIpvV~~d~~~~---~~~-~~~~~V~~d~~~~g~~aa~~l~~~~~g~~~i~~~~g~~~~~~~~R~~gf~~~l 152 (274)
T cd06311 77 PVAKAKKAGIFVVVVDRGLS---SPG-AQDLYVAGDNYGMGRVAGEYIATKLGGNGNIVVLRGIPTPIDNERVDAFDAAI 152 (274)
T ss_pred HHHHHHHCCCeEEEEcCCCC---CCc-ccceEEcCCcHHHHHHHHHHHHHHhCCCCeEEEEECCCCcchhHHHHHHHHHH
Confidence 33445678999998754321 110 111234556666677788887665 789999997533 22345578899999
Q ss_pred hccCcEEEEeeccCCCCChhHHHHHHHHhhcC--CceEEEEeccCCcHHHHHHHHHHcCCC
Q 003958 189 AAKRCRISFKAPLSVEATEDEITDLLVKVALT--ESRIIVVHTHYNRGPVVFHVAQYLGML 247 (784)
Q Consensus 189 ~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~--~~~vIvl~~~~~~~~~~~~~a~~~g~~ 247 (784)
++.++++... .....+.......++++.+. +.++|+. .....+..+++++++.|..
T Consensus 153 ~~~~~~~~~~--~~~~~~~~~~~~~~~~~l~~~~~~~ai~~-~~d~~a~g~~~al~~~g~~ 210 (274)
T cd06311 153 AKYPIKILDR--QYANWNRDDAFSVMQDLLTKFPKIDAVWA-HDDDMAVGVLAAIKQAGRT 210 (274)
T ss_pred hhCCcEEEec--cCCCCcHHHHHHHHHHHHHhCCCcCEEEE-CCCcHHHHHHHHHHHcCCC
Confidence 8888765532 21111222233444444322 3555433 3444567888889888865
No 143
>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=97.63 E-value=0.0065 Score=62.16 Aligned_cols=204 Identities=8% Similarity=-0.024 Sum_probs=116.8
Q ss_pred EEEEeecC-CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEccCchhhHHHH
Q 003958 34 IGALLSFS-TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIGPQDAVTSHVV 112 (784)
Q Consensus 34 IG~i~~~~-~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiGp~~s~~~~~v 112 (784)
||++.|.. ..+-.....+++-+.++ .|+++. +.++..++..-.+....+..+++.+||=.........+
T Consensus 2 igvi~~~~~~~~~~~~~~gi~~~~~~--------~g~~~~--~~~~~~~~~~~~~~i~~l~~~~vdgiii~~~~~~~~~~ 71 (269)
T cd06275 2 IGMLVTTSTNPFFAEVVRGVEQYCYR--------QGYNLI--LCNTEGDPERQRSYLRMLAQKRVDGLLVMCSEYDQPLL 71 (269)
T ss_pred EEEEeCCCCcchHHHHHHHHHHHHHH--------cCCEEE--EEeCCCChHHHHHHHHHHHHcCCCEEEEecCCCChHHH
Confidence 78888764 33333445566666554 145554 34555666666666667777788777643322222222
Q ss_pred HHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcC--CCcchhHHHHHHHHhc
Q 003958 113 SHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDD--DHGRNGIAALGDTLAA 190 (784)
Q Consensus 113 a~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~--~~g~~~~~~l~~~l~~ 190 (784)
..+....++|+|......+ +..+++ ........+..+++.|...|-++++++.... .......+.+++.+++
T Consensus 72 ~~l~~~~~ipvV~i~~~~~---~~~~~~---V~~d~~~~~~~~~~~l~~~G~~~i~~i~~~~~~~~~~~r~~gf~~~~~~ 145 (269)
T cd06275 72 AMLERYRHIPMVVMDWGPE---DDFADK---IQDNSEEGGYLATRHLIELGHRRIGCITGPLEKAPAQQRLAGFRRAMAE 145 (269)
T ss_pred HHHHhcCCCCEEEEecccC---CCCCCe---EeeCcHHHHHHHHHHHHHCCCceEEEEeCCCCCccHHHHHHHHHHHHHH
Confidence 3333456999998754321 112232 3445556677778888888999999997532 2344567888999988
Q ss_pred cCcEEEEeeccCCCCChhHHHHHHHHhhcC--CceEEEEeccCCcHHHHHHHHHHcCCCCCCeEEE
Q 003958 191 KRCRISFKAPLSVEATEDEITDLLVKVALT--ESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWI 254 (784)
Q Consensus 191 ~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~--~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~wi 254 (784)
.|+.+..........+.......++++.+. ..++|+. .+...+..+++.+++.|...++.+-+
T Consensus 146 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~-~~d~~a~g~~~~l~~~g~~vp~di~v 210 (269)
T cd06275 146 AGLPVNPGWIVEGDFECEGGYEAMQRLLAQPKRPTAVFC-GNDLMAMGALCAAQEAGLRVPQDLSI 210 (269)
T ss_pred cCCCCCHHHhccCCCChHHHHHHHHHHHcCCCCCcEEEE-CChHHHHHHHHHHHHcCCCCCcceEE
Confidence 886643211111111222333455555433 3454433 44556668889999988765544333
No 144
>PRK10355 xylF D-xylose transporter subunit XylF; Provisional
Probab=97.63 E-value=0.022 Score=60.23 Aligned_cols=202 Identities=8% Similarity=-0.023 Sum_probs=119.1
Q ss_pred CceEEEEEEeecC-CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEccCch-
Q 003958 29 PSVVNIGALLSFS-TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIGPQDA- 106 (784)
Q Consensus 29 ~~~i~IG~i~~~~-~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiGp~~s- 106 (784)
.+..+||++.+.. ..+-.....+++-+.++. |+.+.+ .++..++..-.+....++++++.+||=....
T Consensus 23 ~~~~~Ig~i~~~~~~~f~~~~~~gi~~~a~~~--------g~~l~i--~~~~~~~~~~~~~i~~l~~~~vDGiIi~~~~~ 92 (330)
T PRK10355 23 AKEVKIGMAIDDLRLERWQKDRDIFVKKAESL--------GAKVFV--QSANGNEETQMSQIENMINRGVDVLVIIPYNG 92 (330)
T ss_pred CCCceEEEEecCCCchHHHHHHHHHHHHHHHc--------CCEEEE--ECCCCCHHHHHHHHHHHHHcCCCEEEEeCCCh
Confidence 3589999999854 333344555665555542 455444 5666677666666677888888888643332
Q ss_pred hhHHHHHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcC---CCcchhHHH
Q 003958 107 VTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDD---DHGRNGIAA 183 (784)
Q Consensus 107 ~~~~~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~---~~g~~~~~~ 183 (784)
.........+...++|+|......+ +. +....+.++...-+..+++.|...+-++++++.... .......+.
T Consensus 93 ~~~~~~l~~~~~~~iPvV~id~~~~---~~--~~~~~V~~D~~~~g~~a~~~L~~~g~~~i~~i~~g~~~~~~~~~R~~g 167 (330)
T PRK10355 93 QVLSNVIKEAKQEGIKVLAYDRMIN---NA--DIDFYISFDNEKVGELQAKALVDKVPQGNYFLMGGSPVDNNAKLFRAG 167 (330)
T ss_pred hhHHHHHHHHHHCCCeEEEECCCCC---CC--CccEEEecCHHHHHHHHHHHHHHhcCCCCEEEEeCCCCCccHHHHHHH
Confidence 2223444556778999998754321 11 112246677778888899998887888877665322 233455677
Q ss_pred HHHHHhcc---C-cEEEEeeccCCCCChhHHHHHHHHhh-c--CCceEEEEeccCCcHHHHHHHHHHcCCC
Q 003958 184 LGDTLAAK---R-CRISFKAPLSVEATEDEITDLLVKVA-L--TESRIIVVHTHYNRGPVVFHVAQYLGML 247 (784)
Q Consensus 184 l~~~l~~~---g-i~v~~~~~~~~~~~~~d~~~~l~~l~-~--~~~~vIvl~~~~~~~~~~~~~a~~~g~~ 247 (784)
+++.++++ | +.+....... .....+-...++++. + ..+++ |++.+...+..++++++++|+.
T Consensus 168 f~~~l~~~~~~~~i~~~~~~~~~-~~~~~~~~~~~~~lL~~~~~~~~a-I~~~nD~~A~g~l~al~~~g~~ 236 (330)
T PRK10355 168 QMKVLKPYIDSGKIKVVGDQWVD-GWLPENALKIMENALTANNNKIDA-VVASNDATAGGAIQALSAQGLS 236 (330)
T ss_pred HHHHHhhhccCCCeEEecccCCC-CCCHHHHHHHHHHHHHhCCCCccE-EEECCCchHHHHHHHHHHCCCC
Confidence 77777653 4 4432221111 112223334444433 2 23565 4445566677899999998875
No 145
>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=97.63 E-value=0.0049 Score=63.39 Aligned_cols=202 Identities=11% Similarity=0.025 Sum_probs=127.2
Q ss_pred EEEEEeecCC-cchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEccCchhhHHH
Q 003958 33 NIGALLSFST-NVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIGPQDAVTSHV 111 (784)
Q Consensus 33 ~IG~i~~~~~-~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiGp~~s~~~~~ 111 (784)
.||++.|.-. .+-.....+++-+.++ .|+.+-+ .++..++..- +....+.+++|.++|=.........
T Consensus 3 ~IGvivp~~~npff~~ii~gIe~~a~~--------~Gy~l~l--~~t~~~~~~e-~~i~~l~~~~vDGiI~~s~~~~~~~ 71 (279)
T PF00532_consen 3 TIGVIVPDISNPFFAEIIRGIEQEARE--------HGYQLLL--CNTGDDEEKE-EYIELLLQRRVDGIILASSENDDEE 71 (279)
T ss_dssp EEEEEESSSTSHHHHHHHHHHHHHHHH--------TTCEEEE--EEETTTHHHH-HHHHHHHHTTSSEEEEESSSCTCHH
T ss_pred EEEEEECCCCCcHHHHHHHHHHHHHHH--------cCCEEEE--ecCCCchHHH-HHHHHHHhcCCCEEEEecccCChHH
Confidence 5999999852 2223444555555544 2666544 4555555554 5666677778888875433333355
Q ss_pred HHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcCCcE-EEEEEEcCCC--cchhHHHHHHHH
Q 003958 112 VSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWRE-VIAIYVDDDH--GRNGIAALGDTL 188 (784)
Q Consensus 112 va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~-v~ii~~d~~~--g~~~~~~l~~~l 188 (784)
+..+.+. ++|+|......... ..+|++ ...+..-+..+++.|.+.|.++ |+++..+... .....+.+++++
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 6666666 99999865432111 123333 2345556667888899999999 9999976544 455677899999
Q ss_pred hccCcEEEEeeccCCCCChhHHHHHHHHhhcCCce--EEEEeccCCcHHHHHHHHHHcC-CCCCCeE
Q 003958 189 AAKRCRISFKAPLSVEATEDEITDLLVKVALTESR--IIVVHTHYNRGPVVFHVAQYLG-MLGTGYV 252 (784)
Q Consensus 189 ~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~--vIvl~~~~~~~~~~~~~a~~~g-~~~~~~~ 252 (784)
++.|+++..........+..+-...++++.+.+++ +|+ ++....+..+++++++.| +..++-+
T Consensus 146 ~~~Gl~~~~~~i~~~~~~~~~g~~~~~~ll~~~p~idai~-~~nd~~A~ga~~~l~~~gr~~ip~di 211 (279)
T PF00532_consen 146 KEAGLPIDEEWIFEGDFDYESGYEAARELLESHPDIDAIF-CANDMMAIGAIRALRERGRLKIPEDI 211 (279)
T ss_dssp HHTTSCEEEEEEEESSSSHHHHHHHHHHHHHTSTT-SEEE-ESSHHHHHHHHHHHHHTT-TCTTTEE
T ss_pred HHcCCCCCcccccccCCCHHHHHHHHHHHHhhCCCCEEEE-EeCHHHHHHHHHHHHHcCCcccChhh
Confidence 99998665444433223444445666666655555 544 455567788899999999 7766544
No 146
>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=97.62 E-value=0.013 Score=60.70 Aligned_cols=213 Identities=11% Similarity=0.041 Sum_probs=118.6
Q ss_pred EEEEEeecC-CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEcc-CchhhHH
Q 003958 33 NIGALLSFS-TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIGP-QDAVTSH 110 (784)
Q Consensus 33 ~IG~i~~~~-~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiGp-~~s~~~~ 110 (784)
+||++.|.. ..+-.....+++.+.++ .|+++. +.++. ++..-.+....++..++.+||=. ..+....
T Consensus 1 ~Ig~v~~~~~~~~~~~~~~gi~~~~~~--------~g~~~~--~~~~~-~~~~~~~~i~~~~~~~~dgiii~~~~~~~~~ 69 (289)
T cd01540 1 KIGFIVKQPEEPWFQTEWKFAKKAAKE--------KGFTVV--KIDVP-DGEKVLSAIDNLGAQGAKGFVICVPDVKLGP 69 (289)
T ss_pred CeeeecCCCCCcHHHHHHHHHHHHHHH--------cCCEEE--EccCC-CHHHHHHHHHHHHHcCCCEEEEccCchhhhH
Confidence 478888753 22233445666666665 255554 44555 56555556666777788877643 2333344
Q ss_pred HHHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHH----HcCC--cEEEEEE-Ec--CCCcchhH
Q 003958 111 VVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVD----HYGW--REVIAIY-VD--DDHGRNGI 181 (784)
Q Consensus 111 ~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~----~~~w--~~v~ii~-~d--~~~g~~~~ 181 (784)
.....+...++|+|...........+..+.+-....+....+..++++|. ..|+ +++++|. .. ........
T Consensus 70 ~~~~~~~~~~iPvV~~~~~~~~~~~~~~~~~~~V~~d~~~~g~~~~~~l~~~~~~~g~~~~~i~~i~~~~~~~~~~~~R~ 149 (289)
T cd01540 70 AIVAKAKAYNMKVVAVDDRLVDADGKPMEDVPHVGMSATKIGEQVGEAIADEMKKRGWDPKEVGALRITYDELDTAKPRT 149 (289)
T ss_pred HHHHHHHhCCCeEEEecCCCcccCCCccccceEecCCHHHHHHHHHHHHHHHHHhhcCCCcceEEEEecCCCCcchhhHH
Confidence 55566778999999875432211100112223344555555666666543 3577 7888875 22 23456778
Q ss_pred HHHHHHHhccCcEEEEeeccCCC-CChhHHHHHHHHhhcC--CceE-EEEeccCCcHHHHHHHHHHcCCCCCCeEEEec
Q 003958 182 AALGDTLAAKRCRISFKAPLSVE-ATEDEITDLLVKVALT--ESRI-IVVHTHYNRGPVVFHVAQYLGMLGTGYVWIAT 256 (784)
Q Consensus 182 ~~l~~~l~~~gi~v~~~~~~~~~-~~~~d~~~~l~~l~~~--~~~v-Ivl~~~~~~~~~~~~~a~~~g~~~~~~~wi~~ 256 (784)
+.+++.+++.|+........... .+.......++++... ..+. .|++.....+..+++++++.|+...+...++.
T Consensus 150 ~G~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~i~~~~d~~a~g~~~al~~~g~~~~di~vig~ 228 (289)
T cd01540 150 DGALEALKAPGFPEANIFQAPQKTTDTEGAFDAAASTLTKNPNVKNWIIYGLNDETVLGAVRATEQSGIAAADVIGVGI 228 (289)
T ss_pred HHHHHHHhcCCCCcceEecccccCcchhhHHHHHHHHHHhCCCcCeeEEEeCCcHHHHHHHHHHHHcCCCCcceEEEec
Confidence 89999998877643211111111 1112223344554333 3443 45555566688899999999987434444443
No 147
>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=97.61 E-value=0.0069 Score=61.58 Aligned_cols=200 Identities=15% Similarity=0.074 Sum_probs=122.3
Q ss_pred EEEEeecC-CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEccCchhhHHHH
Q 003958 34 IGALLSFS-TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIGPQDAVTSHVV 112 (784)
Q Consensus 34 IG~i~~~~-~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiGp~~s~~~~~v 112 (784)
||++.|.- ..+-.....+++.+.++ .|+++. +.++..++..-.+...+++.+++.++|....... ..+
T Consensus 2 igvv~~~~~~~~~~~~~~gi~~~~~~--------~g~~~~--~~~~~~~~~~~~~~i~~l~~~~~dgii~~~~~~~-~~~ 70 (259)
T cd01542 2 IGVIVPRLDSFSTSRTVKGILAALYE--------NGYQML--LMNTNFSIEKEIEALELLARQKVDGIILLATTIT-DEH 70 (259)
T ss_pred eEEEecCCccchHHHHHHHHHHHHHH--------CCCEEE--EEeCCCCHHHHHHHHHHHHhcCCCEEEEeCCCCC-HHH
Confidence 78888753 33334556666666655 255554 3455566776666777888888988886433322 234
Q ss_pred HHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEc-C--CCcchhHHHHHHHHh
Q 003958 113 SHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVD-D--DHGRNGIAALGDTLA 189 (784)
Q Consensus 113 a~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d-~--~~g~~~~~~l~~~l~ 189 (784)
...+...++|+|..+...+ ....+.++....+..+++.|.+.+-++++++... . ..++...+.+++.++
T Consensus 71 ~~~~~~~~ipvv~~~~~~~--------~~~~v~~d~~~~~~~~~~~l~~~g~~~i~~v~~~~~~~~~~~~r~~gf~~~~~ 142 (259)
T cd01542 71 REAIKKLNVPVVVVGQDYP--------GISSVVYDDYGAGYELGEYLAQQGHKNIAYLGVSESDIAVGILRKQGYLDALK 142 (259)
T ss_pred HHHHhcCCCCEEEEeccCC--------CCCEEEECcHHHHHHHHHHHHHcCCCcEEEEcCCcccchhHHHHHHHHHHHHH
Confidence 4556667999998754221 1223456667778888999888899999999643 2 233466788999998
Q ss_pred ccCc-EEEEeeccCCCCChhHHHHHHHHhhcCC-ceEEEEeccCCcHHHHHHHHHHcCCCCCCeEEEec
Q 003958 190 AKRC-RISFKAPLSVEATEDEITDLLVKVALTE-SRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIAT 256 (784)
Q Consensus 190 ~~gi-~v~~~~~~~~~~~~~d~~~~l~~l~~~~-~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~wi~~ 256 (784)
+.|. .+.... -. .+.......+.++.+.. +++|+. .+...+..+++.+++.|+..++.+.+.+
T Consensus 143 ~~~~~~~~~~~-~~--~~~~~~~~~~~~~l~~~~~~~i~~-~~d~~a~g~~~~l~~~g~~vp~di~v~g 207 (259)
T cd01542 143 EHGICPPNIVE-TD--FSYESAYEAAQELLEPQPPDAIVC-ATDTIALGAMKYLQELGRRIPEDISVAG 207 (259)
T ss_pred HcCCChHHeee-cc--CchhhHHHHHHHHhcCCCCCEEEE-cCcHHHHHHHHHHHHcCCCCCCceEEEe
Confidence 8886 211110 11 12222334444544333 565554 3455677899999999987655554443
No 148
>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=97.60 E-value=0.02 Score=58.54 Aligned_cols=194 Identities=13% Similarity=0.073 Sum_probs=114.6
Q ss_pred EEEEeecCCc-chhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEc-cCchhhHHH
Q 003958 34 IGALLSFSTN-VGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIG-PQDAVTSHV 111 (784)
Q Consensus 34 IG~i~~~~~~-~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiG-p~~s~~~~~ 111 (784)
||++.|.... +-.....+++.+.++ .|+.+ .+.++..++....+....++++++.++|- +..+.....
T Consensus 2 i~~~~~~~~~~~~~~~~~~i~~~~~~--------~g~~~--~i~~~~~~~~~~~~~~~~~~~~~vdgiii~~~~~~~~~~ 71 (267)
T cd06322 2 IGASLLTQQHPFYIELANAMKEEAKK--------QKVNL--IVSIANQDLNKQLSDVEDFITKKVDAIVLSPVDSKGIRA 71 (267)
T ss_pred eeEeecCcccHHHHHHHHHHHHHHHh--------cCCEE--EEecCCCCHHHHHHHHHHHHHcCCCEEEEcCCChhhhHH
Confidence 7888876421 122334444444443 14544 44566667777777777888888888865 433332233
Q ss_pred HHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHc--CCcEEEEEEEcC-CCcchhHHHHHHHH
Q 003958 112 VSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHY--GWREVIAIYVDD-DHGRNGIAALGDTL 188 (784)
Q Consensus 112 va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~--~w~~v~ii~~d~-~~g~~~~~~l~~~l 188 (784)
....+...++|+|......+ + .+.+....+....-+..++++|.+. |-+++++++..+ .......+.+++.+
T Consensus 72 ~~~~~~~~~ipvV~~~~~~~---~--~~~~~~v~~d~~~~g~~~~~~l~~~~~g~~~i~~i~~~~~~~~~~R~~gf~~~~ 146 (267)
T cd06322 72 AIAKAKKAGIPVITVDIAAE---G--VAVVSHVATDNYAGGVLAGELAAKVLNGKGQVAIIDYPTVQSVVDRVRGFKEAL 146 (267)
T ss_pred HHHHHHHCCCCEEEEcccCC---C--CceEEEEecChHHHHHHHHHHHHHHhCCCceEEEEecCCCccHHHHHHHHHHHH
Confidence 33556778999999754211 1 1223345566666777788887665 788999997432 23345678889999
Q ss_pred hcc-CcEEEEeeccCCCCChhHHHHHHHHhhcC--CceEEEEeccCCcHHHHHHHHHHcCC
Q 003958 189 AAK-RCRISFKAPLSVEATEDEITDLLVKVALT--ESRIIVVHTHYNRGPVVFHVAQYLGM 246 (784)
Q Consensus 189 ~~~-gi~v~~~~~~~~~~~~~d~~~~l~~l~~~--~~~vIvl~~~~~~~~~~~~~a~~~g~ 246 (784)
++. |+.+.... .. ....+....++++.+. +.++| ++.+...+..+++++.+.|.
T Consensus 147 ~~~~~~~~~~~~-~~--~~~~~~~~~~~~~l~~~~~~~ai-~~~~d~~a~~~~~al~~~g~ 203 (267)
T cd06322 147 ADYPNIKIVAVQ-PG--ITRAEALTAAQNILQANPDLDGI-FAFGDDAALGAVSAIKAAGR 203 (267)
T ss_pred HhCCCcEEEEec-CC--CChHHHHHHHHHHHHhCCCCCEE-EEcCCcHHHHHHHHHHHCCC
Confidence 888 87754221 11 1222233344444322 35543 33455567788899999887
No 149
>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=97.60 E-value=0.0054 Score=62.72 Aligned_cols=205 Identities=12% Similarity=0.037 Sum_probs=119.7
Q ss_pred EEEEEeecC--CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEccCchhhHH
Q 003958 33 NIGALLSFS--TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIGPQDAVTSH 110 (784)
Q Consensus 33 ~IG~i~~~~--~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiGp~~s~~~~ 110 (784)
.||+++|.. ..+-.....++..+.++ .|+.+.+ .++..+...-.+....+...++.+||........
T Consensus 1 ~ig~v~~~~~~~~~~~~~~~~i~~~~~~--------~g~~~~~--~~~~~~~~~~~~~~~~l~~~~~dgiii~~~~~~~- 69 (269)
T cd06288 1 TIGLISDEIATTPFAVEIILGAQDAARE--------HGYLLLV--VNTGGDDELEAEAVEALLDHRVDGIIYATMYHRE- 69 (269)
T ss_pred CeEEEeCCCCCCccHHHHHHHHHHHHHH--------CCCEEEE--EeCCCCHHHHHHHHHHHHHcCCCEEEEecCCCCh-
Confidence 388999874 33333455666665555 1455533 4444455444455566777788887764432211
Q ss_pred HHHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcCC--CcchhHHHHHHHH
Q 003958 111 VVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDDD--HGRNGIAALGDTL 188 (784)
Q Consensus 111 ~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~~--~g~~~~~~l~~~l 188 (784)
+.......++|+|......+. .. +..+.+++...+..+++.+...|-++++++..+.. ......+.+.+.+
T Consensus 70 -~~~~~~~~~ipvv~~~~~~~~---~~---~~~v~~d~~~~~~~a~~~l~~~g~~~i~~l~~~~~~~~~~~R~~gf~~~~ 142 (269)
T cd06288 70 -VTLPPELLSVPTVLLNCYDAD---GA---LPSVVPDEEQGGYDATRHLLAAGHRRIAFINGEPWMLAAKDRLKGYRQAL 142 (269)
T ss_pred -hHHHHHhcCCCEEEEecccCC---CC---CCeEEEccHHHHHHHHHHHHHcCCceEEEEeCCccchhHHHHHHHHHHHH
Confidence 112234578999987543221 12 23355677777888888887779999999985432 3345678889999
Q ss_pred hccCcEEEEeeccCCCCChhHHHHHHHHhhcC--CceEEEEeccCCcHHHHHHHHHHcCCCCCCeEEEec
Q 003958 189 AAKRCRISFKAPLSVEATEDEITDLLVKVALT--ESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIAT 256 (784)
Q Consensus 189 ~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~--~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~wi~~ 256 (784)
++.|+.+..........+..+....++++.+. .+++|+. .+...+..+++++++.|+..++-+.+.+
T Consensus 143 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~-~~d~~a~~~~~~l~~~g~~vp~di~v~g 211 (269)
T cd06288 143 AEAGIPFDPDLVVHGDWSADDGYEAAAALLDLDDRPTAIFC-GNDRMAMGAYQALLERGLRIPQDVSVVG 211 (269)
T ss_pred HHcCCCCCHHHeEeCCCChHHHHHHHHHHHhCCCCCCEEEE-eCcHHHHHHHHHHHHcCCCCcccceEEe
Confidence 88876432111111111222333445555433 3566544 5556677899999999986554444443
No 150
>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=97.59 E-value=0.0077 Score=63.81 Aligned_cols=203 Identities=9% Similarity=0.021 Sum_probs=118.6
Q ss_pred ceEEEEEEeecC-CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEccCchhh
Q 003958 30 SVVNIGALLSFS-TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIGPQDAVT 108 (784)
Q Consensus 30 ~~i~IG~i~~~~-~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiGp~~s~~ 108 (784)
..-.||+++|.. ..+-.....+++.+.++ .|+++.+. ++..++..-.+....+..+++.+||--... .
T Consensus 58 ~~~~Igvv~~~~~~~f~~~l~~~i~~~~~~--------~g~~~~i~--~~~~~~~~~~~~~~~l~~~~vdGiIi~~~~-~ 126 (329)
T TIGR01481 58 RTTTVGVIIPDISNIYYAELARGIEDIATM--------YKYNIILS--NSDEDPEKEVQVLNTLLSKQVDGIIFMGGT-I 126 (329)
T ss_pred CCCEEEEEeCCCCchhHHHHHHHHHHHHHH--------cCCEEEEE--eCCCCHHHHHHHHHHHHhCCCCEEEEeCCC-C
Confidence 456799999853 22222344455544444 25555443 444455444445556677788877631111 1
Q ss_pred HHHHHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcC--C-CcchhHHHHH
Q 003958 109 SHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDD--D-HGRNGIAALG 185 (784)
Q Consensus 109 ~~~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~--~-~g~~~~~~l~ 185 (784)
...+...+...++|+|..+...+ +..++ ........-+..+++.|...|.++|+++..+. . .+....+.++
T Consensus 127 ~~~~~~~l~~~~iPvV~~~~~~~---~~~~~---~V~~D~~~~~~~a~~~L~~~G~~~I~~i~g~~~~~~~~~~R~~Gf~ 200 (329)
T TIGR01481 127 TEKLREEFSRSPVPVVLAGTVDK---ENELP---SVNIDYKQATKEAVGELIAKGHKSIAFVGGPLSDSINGEDRLEGYK 200 (329)
T ss_pred ChHHHHHHHhcCCCEEEEecCCC---CCCCC---EEEECcHHHHHHHHHHHHHCCCCeEEEEecCcccccchHHHHHHHH
Confidence 12333455667999998654321 11223 24455556667788888888999999997432 2 2466788999
Q ss_pred HHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHcCCCCCC
Q 003958 186 DTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTG 250 (784)
Q Consensus 186 ~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~ 250 (784)
+.+++.|+.+..........+..+....++++.+..+++|+. .+...+..+++++++.|+..|+
T Consensus 201 ~~l~~~g~~~~~~~~~~~~~~~~~~~~~~~~ll~~~p~ai~~-~~d~~A~g~~~al~~~g~~vP~ 264 (329)
T TIGR01481 201 EALNKAGIQFGEDLVCEGKYSYDAGYKAFAELKGSLPTAVFV-ASDEMAAGILNAAMDAGIKVPE 264 (329)
T ss_pred HHHHHcCCCCCcceEEecCCChHHHHHHHHHHhCCCCCEEEE-cCcHHHHHHHHHHHHcCCCCCC
Confidence 999998875432111111112223334555655556776555 4445677899999999986554
No 151
>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=97.58 E-value=0.016 Score=59.31 Aligned_cols=205 Identities=8% Similarity=-0.010 Sum_probs=118.6
Q ss_pred EEEEEeecC-CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEE-ccCchhhHH
Q 003958 33 NIGALLSFS-TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAII-GPQDAVTSH 110 (784)
Q Consensus 33 ~IG~i~~~~-~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aii-Gp~~s~~~~ 110 (784)
+||+++|.. ..+-.....+++-+.++. |..+.+.+.++..++..-.+....++.+++.+|| .+.......
T Consensus 1 ~Ig~v~~~~~~~~~~~~~~gi~~~~~~~--------~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~dgiIi~~~~~~~~~ 72 (271)
T cd06321 1 KIGVSVGDLGNPFFVALAKGAEAAAKKL--------NPGVKVTVVSADYDLNKQVSQIDNFIAAKVDLILLNAVDSKGIA 72 (271)
T ss_pred CeEEEecccCCHHHHHHHHHHHHHHHHh--------CCCeEEEEccCCCCHHHHHHHHHHHHHhCCCEEEEeCCChhHhH
Confidence 488898864 222234555666666653 2234455556666766555566667777887664 343333223
Q ss_pred HHHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHc--CCcEEEEEEEcC-CCcchhHHHHHHH
Q 003958 111 VVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHY--GWREVIAIYVDD-DHGRNGIAALGDT 187 (784)
Q Consensus 111 ~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~--~w~~v~ii~~d~-~~g~~~~~~l~~~ 187 (784)
.....+...++|+|..+...+ + ....+..+....+..+++++... |.++++++..+. .......+.+++.
T Consensus 73 ~~i~~~~~~~ipvv~~~~~~~---~----~~~~V~~d~~~~g~~~~~~l~~~~~g~~~i~~i~g~~~~~~~~R~~g~~~~ 145 (271)
T cd06321 73 PAVKRAQAAGIVVVAVDVAAE---G----ADATVTTDNVQAGEISCQYLADRLGGKGNVAILNGPPVSAVLDRVAGCKAA 145 (271)
T ss_pred HHHHHHHHCCCeEEEecCCCC---C----ccceeeechHHHHHHHHHHHHHHhCCCceEEEEeCCCCchHHHHHHHHHHH
Confidence 333445668999999865322 1 11235566677778888888776 999999997543 2334556888888
Q ss_pred Hhcc-CcEEEEeeccCCCCChhHHHHHHHHhhcC--CceEEEEeccCCcHHHHHHHHHHcCCCCCCeEEEec
Q 003958 188 LAAK-RCRISFKAPLSVEATEDEITDLLVKVALT--ESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIAT 256 (784)
Q Consensus 188 l~~~-gi~v~~~~~~~~~~~~~d~~~~l~~l~~~--~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~wi~~ 256 (784)
+++. +++..... .....+...-...++++.+. .+++|+. .....+..+++++++.|+ .+..+++.
T Consensus 146 ~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~l~~~~~~~ai~~-~~d~~a~g~~~al~~~g~--~di~v~g~ 213 (271)
T cd06321 146 LAKYPGIKLLSDD-QNGKGSRDGGLRVMQGLLTRFPKLDGVFA-INDPTAIGADLAAKQAGR--NDIKITSV 213 (271)
T ss_pred HHhCCCcEEEeee-cCCCCChhhHHHHHHHHHHhCCCCCEEEE-CCchhHHHHHHHHHHcCC--CCcEEEEe
Confidence 8887 56432111 11111212222344444332 3565444 455567788899999886 24444443
No 152
>PRK15408 autoinducer 2-binding protein lsrB; Provisional
Probab=97.58 E-value=0.037 Score=58.50 Aligned_cols=199 Identities=10% Similarity=0.007 Sum_probs=108.5
Q ss_pred EEEEEeecC-CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEc-cCchhhHH
Q 003958 33 NIGALLSFS-TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIG-PQDAVTSH 110 (784)
Q Consensus 33 ~IG~i~~~~-~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiG-p~~s~~~~ 110 (784)
+|+++.... ..+-.....+++-+.++. |+++.+. ..+..+...-.+....++.+++.+|+- |..+....
T Consensus 25 ~i~~v~k~~~~pf~~~~~~Gi~~aa~~~--------G~~v~~~-~~~~~d~~~q~~~i~~li~~~vdgIiv~~~d~~al~ 95 (336)
T PRK15408 25 RIAFIPKLVGVGFFTSGGNGAKEAGKEL--------GVDVTYD-GPTEPSVSGQVQLINNFVNQGYNAIIVSAVSPDGLC 95 (336)
T ss_pred EEEEEECCCCCHHHHHHHHHHHHHHHHh--------CCEEEEE-CCCCCCHHHHHHHHHHHHHcCCCEEEEecCCHHHHH
Confidence 788887544 222234455666565542 5666542 233446666566777888899888765 44444445
Q ss_pred HHHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHc---CCcEEEEEEEcCC--CcchhHHHHH
Q 003958 111 VVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHY---GWREVIAIYVDDD--HGRNGIAALG 185 (784)
Q Consensus 111 ~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~---~w~~v~ii~~d~~--~g~~~~~~l~ 185 (784)
.....+...+||+|++.+..+. +. ..++--..++...+..+++++.+. +-.+|+++..... ......+.++
T Consensus 96 ~~l~~a~~~gIpVV~~d~~~~~--~~--~~~~V~~~~~~~~G~~~~~~l~~~l~~g~gki~il~g~~~~~~~~~r~~g~~ 171 (336)
T PRK15408 96 PALKRAMQRGVKVLTWDSDTKP--EC--RSYYINQGTPEQLGSMLVEMAAKQVGKDKAKVAFFYSSPTVTDQNQWVKEAK 171 (336)
T ss_pred HHHHHHHHCCCeEEEeCCCCCC--cc--ceEEEecCCHHHHHHHHHHHHHHhcCCCCCEEEEEECCCCCccHHHHHHHHH
Confidence 5666678889999997654221 11 111111123345666666776542 4578988875322 1223446666
Q ss_pred HHHhc--cCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCc-HHHHHHHHHHcCC
Q 003958 186 DTLAA--KRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNR-GPVVFHVAQYLGM 246 (784)
Q Consensus 186 ~~l~~--~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~-~~~~~~~a~~~g~ 246 (784)
+.+.+ .+++++... .. ..+...-....+++.++.+++=.+++.... +...++++++.|.
T Consensus 172 ~~l~~~~p~~~vv~~~-~~-~~d~~~a~~~~~~lL~~~pdi~aI~~~~~~~~~Ga~~Al~~~g~ 233 (336)
T PRK15408 172 AKIAKEHPGWEIVTTQ-FG-YNDATKSLQTAEGILKAYPDLDAIIAPDANALPAAAQAAENLKR 233 (336)
T ss_pred HHHHhhCCCCEEEeec-CC-CCcHHHHHHHHHHHHHHCCCCcEEEECCCccHHHHHHHHHhCCC
Confidence 66644 356665332 21 122233334555554444444333333333 4467888888775
No 153
>cd01575 PBP1_GntR Ligand-binding domain of DNA transcription repressor GntR specific for gluconate, a member of the LacI-GalR family of bacterial transcription regulators. This group represents the ligand-binding domain of DNA transcription repressor GntR specific for gluconate, a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of GntR is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding,
Probab=97.58 E-value=0.0086 Score=61.16 Aligned_cols=201 Identities=12% Similarity=0.066 Sum_probs=115.9
Q ss_pred EEEEeecCC-cchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEccCchhhHHHH
Q 003958 34 IGALLSFST-NVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIGPQDAVTSHVV 112 (784)
Q Consensus 34 IG~i~~~~~-~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiGp~~s~~~~~v 112 (784)
||++.|... .+-.....+++.+.++ . |+++.+ .++..++..-.+....++.+++.+||-...... ...
T Consensus 2 Ig~i~~~~~~~~~~~~~~gi~~~~~~----~----g~~~~~--~~~~~~~~~~~~~~~~l~~~~vdgiii~~~~~~-~~~ 70 (268)
T cd01575 2 VAVLVPSLSNSVFADVLQGISDVLEA----A----GYQLLL--GNTGYSPEREEELLRTLLSRRPAGLILTGLEHT-ERT 70 (268)
T ss_pred EEEEeCCCcchhHHHHHHHHHHHHHH----c----CCEEEE--ecCCCCchhHHHHHHHHHHcCCCEEEEeCCCCC-HHH
Confidence 788888642 2222344555555554 1 455544 444445555555666777778888865332222 223
Q ss_pred HHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcC--CCcchhHHHHHHHHhc
Q 003958 113 SHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDD--DHGRNGIAALGDTLAA 190 (784)
Q Consensus 113 a~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~--~~g~~~~~~l~~~l~~ 190 (784)
...+...++|+|......+ . +.......+....+..+++.+...|-+++++|..+. .......+.+++.+++
T Consensus 71 ~~~~~~~~ipvv~~~~~~~---~---~~~~~v~~d~~~~~~~~~~~l~~~g~~~i~~i~~~~~~~~~~~r~~gf~~~l~~ 144 (268)
T cd01575 71 RQLLRAAGIPVVEIMDLPP---D---PIDMAVGFSHAEAGRAMARHLLARGYRRIGFLGARMDDTRAQQRLEGFRAALRA 144 (268)
T ss_pred HHHHHhcCCCEEEEecCCC---C---CCCCeEEeCcHHHHHHHHHHHHHCCCCcEEEecCCCCcccHHHHHHHHHHHHHH
Confidence 3445667999998643211 1 112234455667788888888888999999998654 3445567889999988
Q ss_pred cCcEEEEeeccCCCCChhHHHHHHHHhhcC--CceEEEEeccCCcHHHHHHHHHHcCCCCCCeE
Q 003958 191 KRCRISFKAPLSVEATEDEITDLLVKVALT--ESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYV 252 (784)
Q Consensus 191 ~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~--~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~ 252 (784)
.|.....................+.++.+. .+++|+. ++...+..+++.+.+.|...++.+
T Consensus 145 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~-~~d~~a~~~~~~l~~~g~~~p~di 207 (268)
T cd01575 145 AGLDPPLVVTTPEPSSFALGRELLAELLARWPDLDAVFC-SNDDLALGALFECQRRGISVPEDI 207 (268)
T ss_pred cCCCCCceeEeccCCCHHHHHHHHHHHHhCCCCCCEEEE-CCcHHHHHHHHHHHHhCCCCCcce
Confidence 875322211111111223334455554333 4566554 444556788999999887654433
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=97.55 E-value=0.012 Score=60.01 Aligned_cols=202 Identities=11% Similarity=0.055 Sum_probs=118.1
Q ss_pred EEEEeecC-CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEccCchhhHHHH
Q 003958 34 IGALLSFS-TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIGPQDAVTSHVV 112 (784)
Q Consensus 34 IG~i~~~~-~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiGp~~s~~~~~v 112 (784)
||++.|.. ..+-.....+++-+.++. |+.+ .+.++..++..-......++++++.+||-.........+
T Consensus 2 igvi~~~~~~~~~~~~~~~i~~~a~~~--------g~~~--~~~~~~~~~~~~~~~~~~l~~~~~dgiii~~~~~~~~~l 71 (267)
T cd06283 2 IGVIVADITNPFSSLVLKGIEDVCRAH--------GYQV--LVCNSDNDPEKEKEYLESLLAYQVDGLIVNPTGNNKELY 71 (267)
T ss_pred EEEEecCCccccHHHHHHHHHHHHHHc--------CCEE--EEEcCCCCHHHHHHHHHHHHHcCcCEEEEeCCCCChHHH
Confidence 78888764 223334556666666542 4444 344555566655666667777788877642222222223
Q ss_pred HHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcCC--C-cchhHHHHHHHHh
Q 003958 113 SHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDDD--H-GRNGIAALGDTLA 189 (784)
Q Consensus 113 a~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~~--~-g~~~~~~l~~~l~ 189 (784)
..+...++|+|......+ ....+ .........+..+++.|...|-++++++..... . .....+.+++.++
T Consensus 72 -~~~~~~~ipvV~~~~~~~---~~~~~---~v~~d~~~~g~~~~~~l~~~g~~~i~~l~~~~~~~~~~~~r~~g~~~~~~ 144 (267)
T cd06283 72 -QRLAKNGKPVVLVDRKIP---ELGVD---TVTLDNYEAAKEAVDHLIEKGYERILFVTEPLDEISPRMERYEGFKEALA 144 (267)
T ss_pred -HHHhcCCCCEEEEcCCCC---CCCCC---EEEeccHHHHHHHHHHHHHcCCCcEEEEecCccccccHHHHHHHHHHHHH
Confidence 445678999999754322 11222 234455667888888888889999999975432 1 2356788888888
Q ss_pred ccCcEEEEeeccCCCCChhHHHHHHHHhhcCC--ceEEEEeccCCcHHHHHHHHHHcCCCCCCeEE
Q 003958 190 AKRCRISFKAPLSVEATEDEITDLLVKVALTE--SRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVW 253 (784)
Q Consensus 190 ~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~--~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~w 253 (784)
+.|+............+..+....++++.++. +++|+. .+...+..+++++++.|+..++-+-
T Consensus 145 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~-~~d~~a~g~~~~l~~~g~~vp~di~ 209 (267)
T cd06283 145 EHGIGVNEELIEIDDEDADELDERLRQLLNKPKKKTAIFA-ANGLILLEVLKALKELGIRIPEDVG 209 (267)
T ss_pred HcCCCCCcceeEecccchHHHHHHHHHHHcCCCCCCEEEE-cCcHHHHHHHHHHHHcCCCCccceE
Confidence 87743211111111112234455666654443 455444 3455667889999999986554333
No 155
>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=97.52 E-value=0.0081 Score=61.38 Aligned_cols=200 Identities=15% Similarity=0.073 Sum_probs=113.8
Q ss_pred EEEEeecC-----CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhc-CceEEEccCchh
Q 003958 34 IGALLSFS-----TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEG-QTVAIIGPQDAV 107 (784)
Q Consensus 34 IG~i~~~~-----~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~-~v~aiiGp~~s~ 107 (784)
||+++|.. ..+-.....+++.++++ .|+.+.+...+.. ....+.+.+++.+ ++.+||...+..
T Consensus 2 igvi~p~~~~~~~~~~~~~~~~~i~~~~~~--------~g~~~~~~~~~~~---~~~~~~~~~~~~~~~vdgiii~~~~~ 70 (268)
T cd06271 2 IGLVLPTGEREEGDPFFAEFLSGLSEALAE--------HGYDLVLLPVDPD---EDPLEVYRRLVESGLVDGVIISRTRP 70 (268)
T ss_pred eEEEeCCcccccCCccHHHHHHHHHHHHHH--------CCceEEEecCCCc---HHHHHHHHHHHHcCCCCEEEEecCCC
Confidence 78888752 22223344455444443 2566666544332 2233455666544 788887643322
Q ss_pred hHHHHHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcCC--CcchhHHHHH
Q 003958 108 TSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDDD--HGRNGIAALG 185 (784)
Q Consensus 108 ~~~~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~~--~g~~~~~~l~ 185 (784)
.... ...+...++|+|......+ +..+++ ..++....+..+++.+...|-++++++..... .+....+.++
T Consensus 71 ~~~~-~~~~~~~~ipvV~~~~~~~---~~~~~~---V~~d~~~~~~~a~~~l~~~g~~~i~~i~~~~~~~~~~~R~~gf~ 143 (268)
T cd06271 71 DDPR-VALLLERGFPFVTHGRTEL---GDPHPW---VDFDNEAAAYQAVRRLIALGHRRIALLNPPEDLTFAQHRRAGYR 143 (268)
T ss_pred CChH-HHHHHhcCCCEEEECCcCC---CCCCCe---EeeCcHHHHHHHHHHHHHcCCCcEEEecCccccchHHHHHHHHH
Confidence 2222 3445678999998754322 122343 33556667777888888889999999975432 3455678899
Q ss_pred HHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcC--CceEEEEeccCCcHHHHHHHHHHcCCCCCCeE
Q 003958 186 DTLAAKRCRISFKAPLSVEATEDEITDLLVKVALT--ESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYV 252 (784)
Q Consensus 186 ~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~--~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~ 252 (784)
+.+++.|+.+.....+....+.......++++.+. .+++|+. .+...+..+++++++.|+..++.+
T Consensus 144 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~-~~d~~a~g~~~al~~~g~~vp~~i 211 (268)
T cd06271 144 RALAEAGLPLDPALIVSGDMTEEGGYAAAAELLALPDRPTAIVC-SSELMALGVLAALAEAGLRPGRDV 211 (268)
T ss_pred HHHHHhCCCCCCceEEeCCCChHHHHHHHHHHHhCCCCCCEEEE-cCcHHHHHHHHHHHHhCCCCCcce
Confidence 99988876532111111111223333445554332 3565555 445566788999999998665433
No 156
>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=97.50 E-value=0.024 Score=58.05 Aligned_cols=196 Identities=11% Similarity=-0.024 Sum_probs=114.7
Q ss_pred EEEEEeecC-CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEc-cCchhhHH
Q 003958 33 NIGALLSFS-TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIG-PQDAVTSH 110 (784)
Q Consensus 33 ~IG~i~~~~-~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiG-p~~s~~~~ 110 (784)
+||+++|.. ..+-.....+++.+.++. |+++.+...+...+...-.+....++++++.+||- +.......
T Consensus 1 ~Igvi~~~~~~~f~~~~~~gi~~~a~~~--------g~~~~~~~~~~~~~~~~~~~~i~~~~~~~vdgiI~~~~~~~~~~ 72 (268)
T cd06306 1 KLCVLYPHLKDAYWLSVNYGMVEEAKRL--------GVSLKLLEAGGYPNLAKQIAQLEDCAAWGADAILLGAVSPDGLN 72 (268)
T ss_pred CeEEEcCCCCCHHHHHHHHHHHHHHHHc--------CCEEEEecCCCCCCHHHHHHHHHHHHHcCCCEEEEcCCChhhHH
Confidence 488888853 222234455666666542 45554432222234445555666777778887764 32222222
Q ss_pred HHHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcCC-----cEEEEEEEcCC--CcchhHHH
Q 003958 111 VVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGW-----REVIAIYVDDD--HGRNGIAA 183 (784)
Q Consensus 111 ~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~w-----~~v~ii~~d~~--~g~~~~~~ 183 (784)
.+ ..+...++|+|....... +. .............+..++++|.+.+- ++++++..... ......+.
T Consensus 73 ~~-~~~~~~giPvV~~~~~~~---~~--~~~~~V~~d~~~~g~~~~~~l~~~g~~~~~~~~i~~l~g~~~~~~~~~R~~g 146 (268)
T cd06306 73 EI-LQQVAASIPVIALVNDIN---SP--DITAKVGVSWYEMGYQAGEYLAQRHPKGSKPAKVAWFPGPKGAGWVKAVEKG 146 (268)
T ss_pred HH-HHHHHCCCCEEEeccCCC---Cc--ceeEEecCChHHHHHHHHHHHHHHhhcCCCCceEEEEeCCCCCchHHHHHHH
Confidence 23 445678999998743211 11 11223556666777888888877665 89999985432 34566788
Q ss_pred HHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhc--CCceEEEEeccCCcHHHHHHHHHHcCC
Q 003958 184 LGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVAL--TESRIIVVHTHYNRGPVVFHVAQYLGM 246 (784)
Q Consensus 184 l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~--~~~~vIvl~~~~~~~~~~~~~a~~~g~ 246 (784)
+++.+++.++++... .....+...-...++++.+ .++++|+. ....+..+++.+++.|+
T Consensus 147 ~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~l~~~~~~~~i~~--~d~~a~~~~~~l~~~g~ 207 (268)
T cd06306 147 FRDALAGSAIEISAI--KYGDTGKEVQRKLVEEALEAHPDIDYIVG--SAVAAEAAVGILRQRGL 207 (268)
T ss_pred HHHHHhhcCcEEeee--ccCCccHHHHHHHHHHHHHhCCCcCEEee--cchhhhHHHHHHHhcCC
Confidence 999999888876542 1111122333445555432 34677653 36667788899998886
No 157
>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=97.50 E-value=0.028 Score=57.53 Aligned_cols=207 Identities=11% Similarity=0.096 Sum_probs=118.1
Q ss_pred EEEEEeecC-CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEc-cCchhhHH
Q 003958 33 NIGALLSFS-TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIG-PQDAVTSH 110 (784)
Q Consensus 33 ~IG~i~~~~-~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiG-p~~s~~~~ 110 (784)
+||++.|.. ..+-.....+++.+.++ .. |+++. +.++..++..-.+....++.+++.+||= |.......
T Consensus 1 ~ig~~~~~~~~~~~~~~~~~i~~~~~~---~~----g~~~~--~~~~~~~~~~~~~~i~~~~~~~vdgiii~~~~~~~~~ 71 (270)
T cd06308 1 VIGFSQCNLADPWRAAMNDEIQREASN---YP----DVELI--IADAADDNSKQVADIENFIRQGVDLLIISPNEAAPLT 71 (270)
T ss_pred CEEEEeeCCCCHHHHHHHHHHHHHHHh---cC----CcEEE--EEcCCCCHHHHHHHHHHHHHhCCCEEEEecCchhhch
Confidence 478888753 22222333444333333 21 45554 4455566666666667777778877754 33322223
Q ss_pred HHHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHc--CCcEEEEEEEcCCC--cchhHHHHHH
Q 003958 111 VVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHY--GWREVIAIYVDDDH--GRNGIAALGD 186 (784)
Q Consensus 111 ~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~--~w~~v~ii~~d~~~--g~~~~~~l~~ 186 (784)
.....+...++|+|......+ +. .....+..+....+..++++|.+. |-++++++...... .....+.+++
T Consensus 72 ~~~~~~~~~~ipvV~~~~~~~---~~--~~~~~V~~d~~~~g~~~~~~l~~~~~g~~~i~~l~~~~~~~~~~~R~~g~~~ 146 (270)
T cd06308 72 PVVEEAYRAGIPVILLDRKIL---SD--KYTAYIGADNYEIGRQAGEYIANLLPGKGNILEIWGLEGSSPAIERHDGFKE 146 (270)
T ss_pred HHHHHHHHCCCCEEEeCCCCC---Cc--cceEEeecCcHHHHHHHHHHHHHHcCCCceEEEEECCCCCchHHHHHHHHHH
Confidence 333445678999998754221 11 122345567777788888887775 89999999754332 3455788899
Q ss_pred HHhcc-CcEEEEeeccCCCCChhHHHHHHHHhh-c-CCceEEEEeccCCcHHHHHHHHHHcCCCCCCeEEEecC
Q 003958 187 TLAAK-RCRISFKAPLSVEATEDEITDLLVKVA-L-TESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIATS 257 (784)
Q Consensus 187 ~l~~~-gi~v~~~~~~~~~~~~~d~~~~l~~l~-~-~~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~ 257 (784)
.+++. |+++.... .. .....+....++++. + .+.++| ++.....+..+++++++.|+. .+...++.+
T Consensus 147 ~l~~~~~~~~~~~~-~~-~~~~~~~~~~~~~~l~~~~~~~aI-~~~~d~~a~g~~~al~~~g~~-~dv~vvg~d 216 (270)
T cd06308 147 ALSKYPKIKIVAQQ-DG-DWLKEKAEEKMEELLQANPDIDLV-YAHNDPMALGAYLAAKRAGRE-KEIKFIGID 216 (270)
T ss_pred HHHHCCCCEEEEec-CC-CccHHHHHHHHHHHHHhCCCCcEE-EeCCcHHHHHHHHHHHHcCCC-CCcEEEEec
Confidence 99988 87655321 11 112222223344432 2 235654 444556677899999999976 444444443
No 158
>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=97.49 E-value=0.02 Score=59.85 Aligned_cols=209 Identities=17% Similarity=0.107 Sum_probs=120.9
Q ss_pred EEEEeecC-C-cchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhc--CceEEEccCchhhH
Q 003958 34 IGALLSFS-T-NVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEG--QTVAIIGPQDAVTS 109 (784)
Q Consensus 34 IG~i~~~~-~-~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~--~v~aiiGp~~s~~~ 109 (784)
||+++|.. . .+-.....+++.+.++ .|+++.+. ++..+..........++++ ++.+||=-..+...
T Consensus 2 Igvi~~~~~~~~~~~~~~~gi~~~~~~--------~g~~v~~~--~~~~~~~~~~~~i~~~~~~~~~vdgiIi~~~~~~~ 71 (305)
T cd06324 2 VVFLNPGKSDEPFWNSVARFMQAAADD--------LGIELEVL--YAERDRFLMLQQARTILQRPDKPDALIFTNEKSVA 71 (305)
T ss_pred eEEecCCCCCCcHHHHHHHHHHHHHHh--------cCCeEEEE--eCCCCHHHHHHHHHHHHHhccCCCEEEEcCCccch
Confidence 78888764 2 2223344555555544 15555443 5556776666777788888 89887642222223
Q ss_pred HHHHHhhhcCCccEEecccCCCCCC-----c--CCC-CceEeecCChHHHHHHHHHHHHHcCCcE--------EEEEEEc
Q 003958 110 HVVSHVANELQVPLLSFSATDPTLS-----S--LQF-PYFVRTTQSDQYQMAAIAEIVDHYGWRE--------VIAIYVD 173 (784)
Q Consensus 110 ~~va~~~~~~~ip~Is~~a~~~~l~-----~--~~~-p~~~r~~ps~~~~~~ai~~~l~~~~w~~--------v~ii~~d 173 (784)
......+...++|+|.+....+... + ..+ +++-...++...-+..+++.|.+.+.++ ++++..+
T Consensus 72 ~~~~~~~~~~giPvV~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~d~~~~g~~~~~~l~~~g~~~~~~~g~~~i~~i~~~ 151 (305)
T cd06324 72 PELLRLAEGAGVKLFLVNSGLTEAQARELGPPREKFPDWLGQLLPNDEEAGYLMAEALISQARSVQAPGGRIDLLAISGD 151 (305)
T ss_pred HHHHHHHHhCCCeEEEEecCCCcchhhcccccccccCceeeeeccCcHHHHHHHHHHHHHHhhcccCCCCceeEEEEeCC
Confidence 3344567779999998865432111 0 111 2234566777778888888887777663 7777643
Q ss_pred C--CCcchhHHHHHHHHhccC-cEEEEeeccCCCCChhHHHHHHHHhhcC--CceEEEEeccCCcHHHHHHHHHHcCCCC
Q 003958 174 D--DHGRNGIAALGDTLAAKR-CRISFKAPLSVEATEDEITDLLVKVALT--ESRIIVVHTHYNRGPVVFHVAQYLGMLG 248 (784)
Q Consensus 174 ~--~~g~~~~~~l~~~l~~~g-i~v~~~~~~~~~~~~~d~~~~l~~l~~~--~~~vIvl~~~~~~~~~~~~~a~~~g~~~ 248 (784)
. .......+.+++.++++| +.+... ........+....++++.+. +.++|+ +.....+..+++++++.|+..
T Consensus 152 ~~~~~~~~R~~Gf~~~~~~~g~~~~~~~--~~~~~~~~~~~~~~~~~l~~~~~~~ai~-~~~d~~A~g~~~al~~~g~~v 228 (305)
T cd06324 152 PTTPAAILREAGLRRALAEHPDVRLRQV--VYAGWSEDEAYEQAENLLKRYPDVRLIW-AANDQMAFGALRAAKEAGRKP 228 (305)
T ss_pred CCChHHHHHHHHHHHHHHHCCCceEeee--ecCCCCHHHHHHHHHHHHHHCCCccEEE-ECCchHHHHHHHHHHHcCCCc
Confidence 2 234456788899998887 433221 21112223334455554332 356544 445566778999999999865
Q ss_pred CC-eEEEe
Q 003958 249 TG-YVWIA 255 (784)
Q Consensus 249 ~~-~~wi~ 255 (784)
++ ...++
T Consensus 229 p~di~vig 236 (305)
T cd06324 229 GRDVLFGG 236 (305)
T ss_pred CCCEEEEe
Confidence 43 33443
No 159
>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=97.48 E-value=0.0097 Score=61.13 Aligned_cols=205 Identities=11% Similarity=0.049 Sum_probs=110.8
Q ss_pred EEEEEEeecCC----cchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHH-hcCceEEEccCch
Q 003958 32 VNIGALLSFST----NVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLM-EGQTVAIIGPQDA 106 (784)
Q Consensus 32 i~IG~i~~~~~----~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li-~~~v~aiiGp~~s 106 (784)
-.||++.|... .........+.-++++.-+.. |+++.+...+. +. .+.+.+.+ .+++.+||-..+.
T Consensus 4 ~~i~vi~p~~~~~~~~~~~~~~~~~~~gi~~~~~~~----g~~~~v~~~~~--~~---~~~~~~~l~~~~~dgiii~~~~ 74 (275)
T cd06295 4 DTIALVVPEPHERDQSFSDPFFLSLLGGIADALAER----GYDLLLSFVSS--PD---RDWLARYLASGRADGVILIGQH 74 (275)
T ss_pred eEEEEEecCccccccccCCchHHHHHHHHHHHHHHc----CCEEEEEeCCc--hh---HHHHHHHHHhCCCCEEEEeCCC
Confidence 46899998521 111222233333333332221 56666554332 21 12334444 4578877532221
Q ss_pred hhHHHHHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcCC--CcchhHHHH
Q 003958 107 VTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDDD--HGRNGIAAL 184 (784)
Q Consensus 107 ~~~~~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~~--~g~~~~~~l 184 (784)
... .....+...++|+|..+...+ +. .+..+.+.....+..++++|...|.++|+++..+.. .+....+.+
T Consensus 75 ~~~-~~~~~~~~~~ipvV~~~~~~~---~~---~~~~V~~d~~~~g~~~a~~l~~~g~~~i~~i~~~~~~~~~~~r~~gf 147 (275)
T cd06295 75 DQD-PLPERLAETGLPFVVWGRPLP---GQ---PYCYVGSDNVGGGRLATEHLLARGRRRIAFLGGPQDMPEGEERLEGY 147 (275)
T ss_pred CCh-HHHHHHHhCCCCEEEECCccC---CC---CCCEEEECcHHHHHHHHHHHHHCCCCeEEEEcCCCCcchhHHHHHHH
Confidence 111 223456778999998755322 11 223355666777888888888889999999985432 344567889
Q ss_pred HHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcC--CceEEEEeccCCcHHHHHHHHHHcCCCCCCeEE
Q 003958 185 GDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALT--ESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVW 253 (784)
Q Consensus 185 ~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~--~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~w 253 (784)
++.+++.|+.+..........+.......+.++.+. .+++|+.. ....+..+++.+++.|...++-+.
T Consensus 148 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~-~~~~a~g~~~~l~~~g~~ip~~i~ 217 (275)
T cd06295 148 REALAEAGLPLDPRLVAPGDFTEESGRAAMRALLERGPDFDAVFAA-SDLMALGALRALREAGRRVPEDVA 217 (275)
T ss_pred HHHHHHcCCCCChhhEEeccCCHHHHHHHHHHHHhCCCCCCEEEEC-CcHHHHHHHHHHHHhCCCCccceE
Confidence 999988775432111111111222333445444333 35655554 345567888899998876444333
No 160
>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=97.46 E-value=0.0014 Score=67.90 Aligned_cols=94 Identities=21% Similarity=0.265 Sum_probs=57.0
Q ss_pred CCCCChHhhhhCCCceEEee-CchHH-----HHHHhhcccCcc---CceeCC-CHHHHHHHHhcCCcCCCeeEEEechhh
Q 003958 682 SPIKGIDSLRSSNYPIGYQV-NSFAR-----NYLVDELNIDES---RLVPLN-SPEEYAKALKDGPHKGGVAAVVDDRAY 751 (784)
Q Consensus 682 ~~i~~~~dl~~~~~~i~~~~-~~~~~-----~~~~~~~~~~~~---~~~~~~-~~~~~~~~l~~~~~~~~~~a~~~~~~~ 751 (784)
.+|++++||. |.+|++.. ++... ..+.+..+.... +.+.+. +..+.++.|.+ |+++|.+.+...
T Consensus 125 s~i~sl~DL~--Gk~v~~~~~~s~~~~~~~~~~l~~~~g~~~~~~~~~v~~~~~~~~~~~al~~----G~vDa~~~~~~~ 198 (288)
T TIGR03431 125 SPIKSLEDLK--GKTFGFVDPNSTSGFLVPSYYLFKKNGIKPKEYFKKVTFSGSHEAAILAVAN----GTVDAATTNDEN 198 (288)
T ss_pred CCCCcHHHhC--CCEEEeeCCCcchhhHHHHHHHHHhcCCChHHhHHhheecCchHHHHHHHHc----CCCCeEeccHHH
Confidence 3689999997 88899863 33221 122122222211 123444 57889999999 899999998887
Q ss_pred hHHHHcC-C----CCeEEeCCccccceEEEEeeCC
Q 003958 752 AELFLST-R----CEFSIVGQVFTKNGWGFVSIVS 781 (784)
Q Consensus 752 ~~~~~~~-~----c~l~~~~~~~~~~~~~~~~~k~ 781 (784)
+..++++ . -++..+.........+++++++
T Consensus 199 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 233 (288)
T TIGR03431 199 LDRMIRKGQPDAMEDLRIIWKSPLIPNGPIVYRKD 233 (288)
T ss_pred HHHHHHcCCCCchhheEEEEEcCCCCCCcEEEeCC
Confidence 7777653 2 1244443221222456888877
No 161
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=97.44 E-value=0.013 Score=62.33 Aligned_cols=208 Identities=9% Similarity=0.013 Sum_probs=117.8
Q ss_pred ceEEEEEEeecC-CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEccCchhh
Q 003958 30 SVVNIGALLSFS-TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIGPQDAVT 108 (784)
Q Consensus 30 ~~i~IG~i~~~~-~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiGp~~s~~ 108 (784)
..-.||+++|.. ..+-.....+++-+.++. |+++. +.++..++..-.+....+..+++.+||--.....
T Consensus 58 ~~~~i~vi~~~~~~~~~~~~~~gi~~~~~~~--------g~~~~--~~~~~~~~~~~~~~i~~l~~~~vdgiii~~~~~~ 127 (341)
T PRK10703 58 HTKSIGLLATSSEAPYFAEIIEAVEKNCYQK--------GYTLI--LCNAWNNLEKQRAYLSMLAQKRVDGLLVMCSEYP 127 (341)
T ss_pred CCCeEEEEeCCCCCchHHHHHHHHHHHHHHC--------CCEEE--EEeCCCCHHHHHHHHHHHHHcCCCEEEEecCCCC
Confidence 345799999864 222233445555555441 44443 4445556666555666677778887764222111
Q ss_pred HHHHHHhhhc-CCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEc--CCCcchhHHHHH
Q 003958 109 SHVVSHVANE-LQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVD--DDHGRNGIAALG 185 (784)
Q Consensus 109 ~~~va~~~~~-~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d--~~~g~~~~~~l~ 185 (784)
. .....+.. .++|+|......+ +..+.. ...+....-+..+++.|...|-+++++|..+ ....+...+.++
T Consensus 128 ~-~~~~~l~~~~~iPvV~~d~~~~---~~~~~~--~v~~d~~~~g~~a~~~L~~~G~~~i~~i~~~~~~~~~~~R~~Gf~ 201 (341)
T PRK10703 128 E-PLLAMLEEYRHIPMVVMDWGEA---KADFTD--AIIDNAFEGGYLAGRYLIERGHRDIGVIPGPLERNTGAGRLAGFM 201 (341)
T ss_pred H-HHHHHHHhcCCCCEEEEecccC---CcCCCC--eEEECcHHHHHHHHHHHHHCCCCcEEEEeCCccccchHHHHHHHH
Confidence 2 22244445 6999998754321 111122 2344444556778888877799999999743 334456678899
Q ss_pred HHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcC--CceEEEEeccCCcHHHHHHHHHHcCCCCCCeEEE
Q 003958 186 DTLAAKRCRISFKAPLSVEATEDEITDLLVKVALT--ESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWI 254 (784)
Q Consensus 186 ~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~--~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~wi 254 (784)
+.+++.|+.+.............+....+.++.+. .+++|+. .+...+..+++++.+.|...++-+.|
T Consensus 202 ~~l~~~gi~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~-~nd~~a~g~~~al~~~g~~ip~dv~v 271 (341)
T PRK10703 202 KAMEEANIKVPEEWIVQGDFEPESGYEAMQQILSQKHRPTAVFC-GGDIMAMGAICAADEMGLRVPQDISV 271 (341)
T ss_pred HHHHHcCCCCChHHeEeCCCCHHHHHHHHHHHHhCCCCCCEEEE-CCcHHHHHHHHHHHHcCCCCCCceEE
Confidence 99998887653211111111223334455554333 4566554 44555678999999988765544433
No 162
>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=97.44 E-value=0.016 Score=59.10 Aligned_cols=198 Identities=14% Similarity=0.062 Sum_probs=115.9
Q ss_pred EEEEEeecC-CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEccCchhhHHH
Q 003958 33 NIGALLSFS-TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIGPQDAVTSHV 111 (784)
Q Consensus 33 ~IG~i~~~~-~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiGp~~s~~~~~ 111 (784)
.||+++|.. ..+-.....++.-+.++ .|+++. +.++..++..-.+....+.++++.+||=..+......
T Consensus 1 ~igvi~p~~~~~~~~~~~~gi~~~~~~--------~~~~~~--~~~~~~~~~~~~~~i~~l~~~~~dgiii~~~~~~~~~ 70 (265)
T cd06285 1 TIGVLVPRLTDTVMATMYEGIEEAAAE--------RGYSTF--VANTGDNPDAQRRAIEMLLDRRVDGLILGDARSDDHF 70 (265)
T ss_pred CEEEEeCCCCCccHHHHHHHHHHHHHH--------CCCEEE--EEeCCCCHHHHHHHHHHHHHcCCCEEEEecCCCChHH
Confidence 378999864 22223344455555444 145553 3455556665555666677778887763222222233
Q ss_pred HHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcC--CCcchhHHHHHHHHh
Q 003958 112 VSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDD--DHGRNGIAALGDTLA 189 (784)
Q Consensus 112 va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~--~~g~~~~~~l~~~l~ 189 (784)
...+...++|+|......+ .+++ +..+...-+..+++.|...|-++++++..+. .......+.+++.++
T Consensus 71 -~~~~~~~~iPvv~~~~~~~-----~~~~---V~~d~~~ag~~a~~~L~~~g~~~i~~i~~~~~~~~~~~R~~Gf~~~~~ 141 (265)
T cd06285 71 -LDELTRRGVPFVLVLRHAG-----TSPA---VTGDDVLGGRLATRHLLDLGHRRIAVLAGPDYASTARDRLAGFRAALA 141 (265)
T ss_pred -HHHHHHcCCCEEEEccCCC-----CCCE---EEeCcHHHHHHHHHHHHHCCCccEEEEeCCcccccHHHHHHHHHHHHH
Confidence 3445668999998754321 1232 3445566677788888888999999998543 234566788899998
Q ss_pred ccCcEEEEeeccCCCCChhHHHHHHHHhhcC--CceEEEEeccCCcHHHHHHHHHHcCCCCCC
Q 003958 190 AKRCRISFKAPLSVEATEDEITDLLVKVALT--ESRIIVVHTHYNRGPVVFHVAQYLGMLGTG 250 (784)
Q Consensus 190 ~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~--~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~ 250 (784)
+.|+.+.....+....+.......++++.+. .+++|+ +.+...+..+++.+++.|+..++
T Consensus 142 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~-~~~d~~a~g~~~~l~~~g~~~p~ 203 (265)
T cd06285 142 EAGIEVPPERIVYSGFDIEGGEAAAEKLLRSDSPPTAIF-AVNDFAAIGVMGAARDRGLRVPD 203 (265)
T ss_pred HcCCCCChhhEEeCCCCHHHHHHHHHHHHcCCCCCCEEE-EcCcHHHHHHHHHHHHcCCCCCc
Confidence 8886543211111111222333455555333 345543 34555667899999999976443
No 163
>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=97.43 E-value=0.021 Score=58.32 Aligned_cols=200 Identities=14% Similarity=0.048 Sum_probs=117.2
Q ss_pred EEEEEeecC-CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEccCchhhHHH
Q 003958 33 NIGALLSFS-TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIGPQDAVTSHV 111 (784)
Q Consensus 33 ~IG~i~~~~-~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiGp~~s~~~~~ 111 (784)
.||+++|.. ..+-.....++.-+.++. |+++.+. ++..++..-.+....++++++.+||--.+......
T Consensus 1 ~igvi~p~~~~~~~~~~~~g~~~~a~~~--------g~~~~~~--~~~~~~~~~~~~i~~~~~~~vdgii~~~~~~~~~~ 70 (268)
T cd06270 1 TIGLVVSDLDGPFFGPLLSGVESVARKA--------GKHLIIT--AGHHSAEKEREAIEFLLERRCDALILHSKALSDDE 70 (268)
T ss_pred CEEEEEccccCcchHHHHHHHHHHHHHC--------CCEEEEE--eCCCchHHHHHHHHHHHHcCCCEEEEecCCCCHHH
Confidence 378888864 323334556666665551 4555543 34445555555566677788888775333222222
Q ss_pred HHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcCC--CcchhHHHHHHHHh
Q 003958 112 VSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDDD--HGRNGIAALGDTLA 189 (784)
Q Consensus 112 va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~~--~g~~~~~~l~~~l~ 189 (784)
...+...++|+|......+ +..+++ ...+...-+..+++.|...|-+++++|..+.. ......+.+++.++
T Consensus 71 -~~~~~~~~ipvV~~~~~~~---~~~~~~---v~~d~~~~~~~~~~~l~~~g~~~i~~i~~~~~~~~~~~R~~gf~~~~~ 143 (268)
T cd06270 71 -LIELAAQVPPLVLINRHIP---GLADRC---IWLDNEQGGYLATEHLIELGHRKIACITGPLTKEDARLRLQGYRDALA 143 (268)
T ss_pred -HHHHhhCCCCEEEEeccCC---CCCCCe---EEECcHHHHHHHHHHHHHCCCceEEEEeCCcccccHHHHHHHHHHHHH
Confidence 3445678999998754322 111222 44666777888889988889999999985432 23455778889998
Q ss_pred ccCcEEEEeeccCCCCChhHHHHHHHHhhcC--CceEEEEeccCCcHHHHHHHHHHcCCCCCC
Q 003958 190 AKRCRISFKAPLSVEATEDEITDLLVKVALT--ESRIIVVHTHYNRGPVVFHVAQYLGMLGTG 250 (784)
Q Consensus 190 ~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~--~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~ 250 (784)
+.|+.+..........+..+....++++.+. .+++|+. +....+..+++.+++.|+..++
T Consensus 144 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~-~~d~~a~g~~~~l~~~g~~ip~ 205 (268)
T cd06270 144 EAGIALDESLIIEGDFTEEGGYAAMQELLARGAPFTAVFC-ANDEMAAGAISALREHGISVPQ 205 (268)
T ss_pred HcCCCCCcceEEECCCCHHHHHHHHHHHHhCCCCCCEEEE-cCcHHHHHHHHHHHHcCCCCCC
Confidence 8876542111111112223344555555433 3565443 4445667889999998876543
No 164
>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=97.42 E-value=0.022 Score=58.29 Aligned_cols=205 Identities=11% Similarity=0.011 Sum_probs=116.9
Q ss_pred EEEEEeecC-CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEccCchhhHHH
Q 003958 33 NIGALLSFS-TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIGPQDAVTSHV 111 (784)
Q Consensus 33 ~IG~i~~~~-~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiGp~~s~~~~~ 111 (784)
.||++.|.. ..+-.....++.-+.++ .|+++.+. ++..++..-.+....+...++.+||--.+......
T Consensus 1 ~Ig~i~~~~~~~~~~~~~~gi~~~~~~--------~gy~v~~~--~~~~~~~~~~~~i~~~~~~~~dgiii~~~~~~~~~ 70 (269)
T cd06293 1 TIGLVVPDIANPFFAELADAVEEEADA--------RGLSLVLC--ATRNRPERELTYLRWLDTNHVDGLIFVTNRPDDGA 70 (269)
T ss_pred CEEEEeCCCCCCcHHHHHHHHHHHHHH--------CCCEEEEE--eCCCCHHHHHHHHHHHHHCCCCEEEEeCCCCCHHH
Confidence 378888753 22223444555555553 25666444 33345555455555666678888875333222223
Q ss_pred HHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcCC--CcchhHHHHHHHHh
Q 003958 112 VSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDDD--HGRNGIAALGDTLA 189 (784)
Q Consensus 112 va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~~--~g~~~~~~l~~~l~ 189 (784)
+..+. ..++|+|......+. .. .....+.+...+..+++.|...|-+++++|..+.. ......+.+++.++
T Consensus 71 ~~~~~-~~~~pvV~i~~~~~~---~~---~~~V~~d~~~~~~~~~~~L~~~G~~~i~~i~~~~~~~~~~~R~~Gf~~a~~ 143 (269)
T cd06293 71 LAKLI-NSYGNIVLVDEDVPG---AK---VPKVFCDNEQGGRLATRHLARAGHRRIAFVGGPDALISARERYAGYREALA 143 (269)
T ss_pred HHHHH-hcCCCEEEECCCCCC---CC---CCEEEECCHHHHHHHHHHHHHCCCceEEEEecCcccccHHHHHHHHHHHHH
Confidence 33333 357999987643221 11 22355677778888889888889999999975433 23456788999998
Q ss_pred ccCcEEEEeeccCCCCChhHHHHHHHHhhc--CCceEEEEeccCCcHHHHHHHHHHcCCCCCCeEEEe
Q 003958 190 AKRCRISFKAPLSVEATEDEITDLLVKVAL--TESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIA 255 (784)
Q Consensus 190 ~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~--~~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~wi~ 255 (784)
+.|..+..........+..+....+.++.+ ..+++|+. +....+..+++++++.|...|+-+-|.
T Consensus 144 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~-~~d~~a~g~~~al~~~g~~vp~di~i~ 210 (269)
T cd06293 144 EAHIPEVPEYVCFGDYTREFGRAAAAQLLARGDPPTAIFA-ASDEIAIGLLEVLRERGLSIPGDMSLV 210 (269)
T ss_pred HcCCCCChheEEecCCCHHHHHHHHHHHHcCCCCCCEEEE-cCcHHHHHHHHHHHHcCCCCccceEEE
Confidence 887643211111111122233344555432 34565444 455566788999999987655444433
No 165
>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=97.42 E-value=0.041 Score=57.13 Aligned_cols=203 Identities=14% Similarity=0.074 Sum_probs=113.0
Q ss_pred EEEEEeecCCcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEc-cCchhhHHH
Q 003958 33 NIGALLSFSTNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIG-PQDAVTSHV 111 (784)
Q Consensus 33 ~IG~i~~~~~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiG-p~~s~~~~~ 111 (784)
|||++.+... ......+..++++.-++. |+++.+. .++..++..-.+....++.+++.+||= +........
T Consensus 1 ~i~~i~~~~~---~~~~~~~~~gi~~~a~~~----g~~~~~~-~~~~~~~~~~~~~l~~~~~~~~dgiii~~~~~~~~~~ 72 (294)
T cd06316 1 KAAIVMHTSG---SDWSNAQVRGAKDEFAKL----GIEVVAT-TDAQFDPAKQVADIETTISQKPDIIISIPVDPVSTAA 72 (294)
T ss_pred CeEEEecCCC---ChHHHHHHHHHHHHHHHc----CCEEEEe-cCCCCCHHHHHHHHHHHHHhCCCEEEEcCCCchhhhH
Confidence 5888887432 123333444444433332 5555433 355567766666777777878887654 333222234
Q ss_pred HHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHc--CCcEEEEEEEcCC--CcchhHHHHHHH
Q 003958 112 VSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHY--GWREVIAIYVDDD--HGRNGIAALGDT 187 (784)
Q Consensus 112 va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~--~w~~v~ii~~d~~--~g~~~~~~l~~~ 187 (784)
....+...++|+|.+....+..... -+++..+..+...-+..++++|... +-++++++..+.+ ......+.+.+.
T Consensus 73 ~i~~~~~~~iPvV~~~~~~~~~~~~-~~~~~~v~~d~~~~g~~~~~~l~~~~~g~~~i~~l~~~~~~~~~~~R~~gf~~~ 151 (294)
T cd06316 73 AYKKVAEAGIKLVFMDNVPSGLEHG-KDYAGIVTDDNYGNGQIAADALAKALPGKGKVGLIYHGADYFVTNQRDQGFKET 151 (294)
T ss_pred HHHHHHHcCCcEEEecCCCcccccC-cceEEEEccCcHHHHHHHHHHHHHHhCCCceEEEEeCCCCcccHHHHHHHHHHH
Confidence 4455677899999876543222110 1223335556666678888888765 7899999975433 334557788888
Q ss_pred HhccCcEEEEeeccCCCCChhHHHHHHHHhhc--CCceEEEEeccCCcHHHHHHHHHHcCC
Q 003958 188 LAAKRCRISFKAPLSVEATEDEITDLLVKVAL--TESRIIVVHTHYNRGPVVFHVAQYLGM 246 (784)
Q Consensus 188 l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~--~~~~vIvl~~~~~~~~~~~~~a~~~g~ 246 (784)
+++++..+........ .+.......++++.+ ..+++|+. .+...+..+++.+++.|+
T Consensus 152 l~~~~~~~~~~~~~~~-~~~~~~~~~~~~~l~~~~~~~ai~~-~~d~~a~g~~~~l~~~g~ 210 (294)
T cd06316 152 IKKNYPDITIVAEKGI-DGPSKAEDIANAMLTQNPDLKGIYA-VWDVPAEGVIAALRAAGR 210 (294)
T ss_pred HHHhCCCcEEEeecCC-cchhHHHHHHHHHHHhCCCeeEEEe-CCCchhHHHHHHHHHcCC
Confidence 8765532221111110 111222334444432 23555443 455678889999999886
No 166
>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=97.41 E-value=0.033 Score=56.72 Aligned_cols=200 Identities=14% Similarity=0.084 Sum_probs=114.0
Q ss_pred EEEEEeecCC-cchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEccCchhhHHH
Q 003958 33 NIGALLSFST-NVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIGPQDAVTSHV 111 (784)
Q Consensus 33 ~IG~i~~~~~-~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiGp~~s~~~~~ 111 (784)
.||+++|... ..-.....+++-+.++ .|+.+.+...+. .++....+....++++++.++|--........
T Consensus 1 ~i~vi~~~~~~~~~~~~~~gi~~~~~~--------~~~~~~~~~~~~-~~~~~~~~~~~~l~~~~vdgiii~~~~~~~~~ 71 (264)
T cd01574 1 TIGVVTTDLALHGPSSTLAAIESAARE--------AGYAVTLSMLAE-ADEEALRAAVRRLLAQRVDGVIVNAPLDDADA 71 (264)
T ss_pred CEEEEeCCCCcccHHHHHHHHHHHHHH--------CCCeEEEEeCCC-CchHHHHHHHHHHHhcCCCEEEEeCCCCChHH
Confidence 3788888542 2223444555555554 155555543221 23344445555677778888864222222223
Q ss_pred HHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcCCC--cchhHHHHHHHHh
Q 003958 112 VSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDDDH--GRNGIAALGDTLA 189 (784)
Q Consensus 112 va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~~~--g~~~~~~l~~~l~ 189 (784)
+.. ....++|+|......+ +.+.........-+..+++.+...|-++|+++..+... .....+.+++.++
T Consensus 72 ~~~-~~~~~ipvv~~~~~~~-------~~~~~v~~d~~~~g~~~~~~l~~~g~~~i~~i~~~~~~~~~~~r~~gf~~~l~ 143 (264)
T cd01574 72 ALA-AAPADVPVVFVDGSPS-------PRVSTVSVDQEGGARLATEHLLELGHRTIAHVAGPEEWLSARARLAGWRAALE 143 (264)
T ss_pred HHH-HHhcCCCEEEEeccCC-------CCCCEEEeCcHHHHHHHHHHHHHCCCCEEEEEecCCccchHHHHHHHHHHHHH
Confidence 333 3567899999765321 12233455666778888888888899999999754332 2345678888888
Q ss_pred ccCcEEEEeeccCCCCChhHHHHHHHHhhcC-CceEEEEeccCCcHHHHHHHHHHcCCCCCCeE
Q 003958 190 AKRCRISFKAPLSVEATEDEITDLLVKVALT-ESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYV 252 (784)
Q Consensus 190 ~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~-~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~ 252 (784)
+.|+.+... +....+..+....+.++.+. .+++|+. ++...+..+++++++.|...++.+
T Consensus 144 ~~~~~~~~~--~~~~~~~~~~~~~~~~~l~~~~~~ai~~-~~d~~a~g~~~~~~~~g~~ip~~i 204 (264)
T cd01574 144 AAGIAPPPV--LEGDWSAESGYRAGRELLREGDPTAVFA-ANDQMALGVLRALHELGLRVPDDV 204 (264)
T ss_pred HCCCCccee--eecCCCHHHHHHHHHHHHhCCCCcEEEE-cCcHHHHHHHHHHHHcCCCCccce
Confidence 877765422 11111222333444454433 3555443 455667789999999887544433
No 167
>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=97.39 E-value=0.04 Score=57.04 Aligned_cols=199 Identities=9% Similarity=0.058 Sum_probs=113.6
Q ss_pred EEEEEeecC-CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEc-cCchhhHH
Q 003958 33 NIGALLSFS-TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIG-PQDAVTSH 110 (784)
Q Consensus 33 ~IG~i~~~~-~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiG-p~~s~~~~ 110 (784)
.||+++|.. ..+-.....+++-+.++ . |+++ .+.++..++....+....++.+++.+||- +..+....
T Consensus 1 ~I~vi~~~~~~~~~~~~~~gi~~~a~~---~-----g~~~--~~~~~~~~~~~~~~~i~~~~~~~vdgiii~~~~~~~~~ 70 (288)
T cd01538 1 KIGLSLPTKTEERWIRDRPNFEAALKE---L-----GAEV--IVQNANGDPAKQISQIENMIAKGVDVLVIAPVDGEALA 70 (288)
T ss_pred CeEEEEeCCCcHHHHHHHHHHHHHHHH---c-----CCEE--EEECCCCCHHHHHHHHHHHHHcCCCEEEEecCChhhHH
Confidence 388999853 22223444555555554 1 4444 44566667776667777788888887764 33333333
Q ss_pred HHHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHc------CCcEEEEEEEcCC--CcchhHH
Q 003958 111 VVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHY------GWREVIAIYVDDD--HGRNGIA 182 (784)
Q Consensus 111 ~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~------~w~~v~ii~~d~~--~g~~~~~ 182 (784)
.....+...++|+|......+. ...++. +..+....+..+++.|... |-.+++++..+.. ......+
T Consensus 71 ~~l~~l~~~~ipvV~~~~~~~~---~~~~~~--v~~d~~~~g~~~~~~l~~~~~~~~~g~~~i~~l~g~~~~~~~~~R~~ 145 (288)
T cd01538 71 SAVEKAADAGIPVIAYDRLILN---SNVDYY--VSFDNEKVGELQGQALVDGLGAKGKPPGNIELIAGSPTDNNAKLFFN 145 (288)
T ss_pred HHHHHHHHCCCCEEEECCCCCC---CCcceE--EEeChHHHHHHHHHHHHHHHhhcCCCCceEEEEECCCCCchHHHHHH
Confidence 4445566789999987654321 112222 3345555666677776555 8899999975433 2334577
Q ss_pred HHHHHHhccC----cEEEEeeccCCCCChhHHHHHHHHhhcC---CceEEEEeccCCcHHHHHHHHHHcCCCC
Q 003958 183 ALGDTLAAKR----CRISFKAPLSVEATEDEITDLLVKVALT---ESRIIVVHTHYNRGPVVFHVAQYLGMLG 248 (784)
Q Consensus 183 ~l~~~l~~~g----i~v~~~~~~~~~~~~~d~~~~l~~l~~~---~~~vIvl~~~~~~~~~~~~~a~~~g~~~ 248 (784)
.+++.+++.+ +.+.... .....+..+-...++++.+. .+++|+. .....+..+++++++.|+..
T Consensus 146 gf~~~l~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~l~~~~~~~~~I~~-~~d~~a~g~~~al~~~g~~~ 216 (288)
T cd01538 146 GAMSVLKPLIDSGKITIVGEV-ATPDWDPETAQKRMENALTANYNKVDGVLA-ANDGTAGGAIAALKAAGLAG 216 (288)
T ss_pred HHHHHHHhccccCCeeEEecc-ccCCCCHHHHHHHHHHHHHhCCCCccEEEe-CCcHHHHHHHHHHHHcCCCC
Confidence 8888888887 4433221 11111222223444444332 3454433 34556777889999988754
No 168
>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=97.39 E-value=0.012 Score=60.31 Aligned_cols=200 Identities=12% Similarity=-0.004 Sum_probs=116.7
Q ss_pred EEEEEeecC-CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEccCchhhHHH
Q 003958 33 NIGALLSFS-TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIGPQDAVTSHV 111 (784)
Q Consensus 33 ~IG~i~~~~-~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiGp~~s~~~~~ 111 (784)
.||+++|.. ..+-.....++..+.++. |+.+ .+.++..++....+....+..+++.+||--.+......
T Consensus 1 ~Igvv~~~~~~~~~~~~~~~i~~~a~~~--------g~~~--~~~~~~~~~~~~~~~i~~l~~~~vdgii~~~~~~~~~~ 70 (269)
T cd06281 1 TIGCLVSDITNPLLAQLFSGAEDRLRAA--------GYSL--LIANSLNDPERELEILRSFEQRRMDGIIIAPGDERDPE 70 (269)
T ss_pred CEEEEecCCccccHHHHHHHHHHHHHHc--------CCEE--EEEeCCCChHHHHHHHHHHHHcCCCEEEEecCCCCcHH
Confidence 378888853 332234556666555551 4554 44566667766666666677778888875333222234
Q ss_pred HHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcC--CCcchhHHHHHHHHh
Q 003958 112 VSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDD--DHGRNGIAALGDTLA 189 (784)
Q Consensus 112 va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~--~~g~~~~~~l~~~l~ 189 (784)
+...+...++|+|......+ ...++ ...+...-+..+++.|...|-++++++.... .......+.+++.++
T Consensus 71 ~~~~~~~~~ipvV~i~~~~~----~~~~~---V~~d~~~~g~~a~~~l~~~G~~~i~~l~~~~~~~~~~~R~~Gf~~~~~ 143 (269)
T cd06281 71 LVDALASLDLPIVLLDRDMG----GGADA---VLFDHAAGMRQAVEYLISLGHRRIALVGGGSNTRPGRERLEGYKAAFA 143 (269)
T ss_pred HHHHHHhCCCCEEEEecccC----CCCCE---EEECcHHHHHHHHHHHHHCCCcEEEEecCccccccHHHHHHHHHHHHH
Confidence 45566778999998865432 11222 3344444456677777777999999997532 233455688889998
Q ss_pred ccCcEEEEeeccCCCCChhHHHHHHHHhhc--CCceEEEEeccCCcHHHHHHHHHHcCCCCCCe
Q 003958 190 AKRCRISFKAPLSVEATEDEITDLLVKVAL--TESRIIVVHTHYNRGPVVFHVAQYLGMLGTGY 251 (784)
Q Consensus 190 ~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~--~~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~ 251 (784)
++|+.+.....+.... .......+.++.+ ..+++|+ +.+...+..+++++.+.|+..++.
T Consensus 144 ~~~~~~~~~~~~~~~~-~~~~~~~~~~~l~~~~~~~ai~-~~~d~~a~g~~~~l~~~g~~ip~d 205 (269)
T cd06281 144 AAGLPPDPALVRLSTP-AASGFDATRALLALPDRPTAII-AGGTQVLVGVLRALREAGLRIPRD 205 (269)
T ss_pred HcCCCCCHHHeecCcH-HHHHHHHHHHHHcCCCCCcEEE-EcCcHHHHHHHHHHHHcCCCCCcc
Confidence 8886542111111111 2222334444432 3467765 345556668899999998865543
No 169
>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=97.38 E-value=0.017 Score=58.98 Aligned_cols=204 Identities=11% Similarity=0.047 Sum_probs=115.9
Q ss_pred EEEEEeecC-CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEccCchhhHHH
Q 003958 33 NIGALLSFS-TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIGPQDAVTSHV 111 (784)
Q Consensus 33 ~IG~i~~~~-~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiGp~~s~~~~~ 111 (784)
.||+++|.. ..+-.....++..+.++. |+.+.+ .++..++..-......++..++.+||-.........
T Consensus 1 ~igvv~~~~~~~~~~~~~~gi~~~~~~~--------g~~~~~--~~~~~~~~~~~~~~~~l~~~~vdgiIi~~~~~~~~~ 70 (265)
T cd06299 1 TIGVIVPDIRNPYFASLATAIQDAASAA--------GYSTII--GNSDENPETENRYLDNLLSQRVDGIIVVPHEQSAEQ 70 (265)
T ss_pred CEEEEecCCCCccHHHHHHHHHHHHHHc--------CCEEEE--EeCCCCHHHHHHHHHHHHhcCCCEEEEcCCCCChHH
Confidence 378888853 323334556666666552 444443 344456655555566677778888775333322233
Q ss_pred HHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcC--CCcchhHHHHHHHHh
Q 003958 112 VSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDD--DHGRNGIAALGDTLA 189 (784)
Q Consensus 112 va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~--~~g~~~~~~l~~~l~ 189 (784)
...+...++|+|..+...+ +..++++ ......-+..+++.+...|-++|+++.... .......+.+++.++
T Consensus 71 -~~~l~~~~ipvV~~~~~~~---~~~~~~v---~~d~~~~~~~~~~~l~~~g~~~I~~i~~~~~~~~~~~R~~gf~~~~~ 143 (265)
T cd06299 71 -LEDLLKRGIPVVFVDREIT---GSPIPFV---TSDPQPGMTEAVSLLVALGHKKIGYISGPQDTSTGRERLEAFRQACA 143 (265)
T ss_pred -HHHHHhCCCCEEEEecccC---CCCCCEE---EECcHHHHHHHHHHHHHcCCCcEEEEeCCCCcccHHHHHHHHHHHHH
Confidence 3555668999998765322 1223333 233344455666777777999999997543 234455678899998
Q ss_pred ccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHcCCCCCCeEEE
Q 003958 190 AKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWI 254 (784)
Q Consensus 190 ~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~wi 254 (784)
+.|+.+.............+....++++.+..+++|+. .....+..+++++++.|+..++-+-|
T Consensus 144 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~av~~-~~d~~a~gv~~al~~~g~~vp~dv~v 207 (265)
T cd06299 144 SLGLEVNEDLVVLGGYSQESGYAGATKLLDQGATAIIA-GDSMMTIGAIRAIHDAGLVIGEDISL 207 (265)
T ss_pred HCCCCCChHhEEecCcchHHHHHHHHHHHcCCCCEEEE-cCcHHHHHHHHHHHHhCCCCCcceeE
Confidence 88754321111111112223334555554444776444 45556778899999988765543333
No 170
>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=97.38 E-value=0.029 Score=57.16 Aligned_cols=205 Identities=14% Similarity=0.103 Sum_probs=115.6
Q ss_pred EEEEeecCCcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEccCchhhHHHHH
Q 003958 34 IGALLSFSTNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIGPQDAVTSHVVS 113 (784)
Q Consensus 34 IG~i~~~~~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiGp~~s~~~~~va 113 (784)
||+++|.... .....+...+++.-+.. |+.+.+ .++..++..-.+....++.+++.+|+-.........+
T Consensus 2 igvi~~~~~~---~~~~~~~~~~~~~~~~~----g~~~~~--~~~~~~~~~~~~~i~~l~~~~vdgiii~~~~~~~~~~- 71 (264)
T cd06274 2 IGLIIPDLEN---RSFARIAKRLEALARER----GYQLLI--ACSDDDPETERETVETLIARQVDALIVAGSLPPDDPY- 71 (264)
T ss_pred EEEEeccccC---chHHHHHHHHHHHHHHC----CCEEEE--EeCCCCHHHHHHHHHHHHHcCCCEEEEcCCCCchHHH-
Confidence 7888886421 22233333333332222 455544 4445566555566667778888877643332222223
Q ss_pred HhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcCC--CcchhHHHHHHHHhcc
Q 003958 114 HVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDDD--HGRNGIAALGDTLAAK 191 (784)
Q Consensus 114 ~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~~--~g~~~~~~l~~~l~~~ 191 (784)
..+...++|+|......+ +...++ +......-+..+++.+.+.|-++++++..+.. ......+.+++.+++.
T Consensus 72 ~~~~~~~ipvV~~~~~~~---~~~~~~---V~~d~~~~g~~~~~~l~~~g~~~i~~i~~~~~~~~~~~R~~gf~~~~~~~ 145 (264)
T cd06274 72 YLCQKAGLPVVALDRPGD---PSRFPS---VVSDNRDGAAELTRELLAAPPEEVLFLGGLPELSPSRERLAGFRQALADA 145 (264)
T ss_pred HHHHhcCCCEEEecCccC---CCCCCE---EEEccHHHHHHHHHHHHHCCCCcEEEEeCCCcccchHHHHHHHHHHHHHc
Confidence 345668999998755422 112233 34455555677888887889999999976432 3455678899999888
Q ss_pred CcEEEEeeccCCCCChhHHHHHHHHhhcC---CceEEEEeccCCcHHHHHHHHHHcCCCCCCeEEEe
Q 003958 192 RCRISFKAPLSVEATEDEITDLLVKVALT---ESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIA 255 (784)
Q Consensus 192 gi~v~~~~~~~~~~~~~d~~~~l~~l~~~---~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~wi~ 255 (784)
|+.+..........+.......++++.+. .+++|+. .+...+..+++++++.|+..++-+-|.
T Consensus 146 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~ai~~-~~d~~A~g~~~al~~~g~~ip~dv~v~ 211 (264)
T cd06274 146 GLPVQPDWIYAEGYSPESGYQLMAELLARLGRLPRALFT-TSYTLLEGVLRFLRERPGLAPSDLRIA 211 (264)
T ss_pred CCCCCcceeecCCCChHHHHHHHHHHHccCCCCCcEEEE-cChHHHHHHHHHHHHcCCCCCcceEEE
Confidence 75432111111111222333444454322 3566554 445567789999999987655544443
No 171
>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=97.38 E-value=0.019 Score=58.51 Aligned_cols=191 Identities=15% Similarity=0.075 Sum_probs=109.8
Q ss_pred EEEEeecC-CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEccCchhhHHHH
Q 003958 34 IGALLSFS-TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIGPQDAVTSHVV 112 (784)
Q Consensus 34 IG~i~~~~-~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiGp~~s~~~~~v 112 (784)
||++.|.. ..+-.....++.-+.++ . |+++.+...+. +. ...+....++.+++.+||--.+.... ..
T Consensus 2 I~~i~~~~~~~~~~~~~~~i~~~~~~---~-----g~~~~~~~~~~--~~-~~~~~i~~~~~~~vdgiii~~~~~~~-~~ 69 (266)
T cd06278 2 IGVVVADLDNPFYSELLEALSRALQA---R-----GYQPLLINTDD--DE-DLDAALRQLLQYRVDGVIVTSGTLSS-EL 69 (266)
T ss_pred EEEEeCCCCCchHHHHHHHHHHHHHH---C-----CCeEEEEcCCC--CH-HHHHHHHHHHHcCCCEEEEecCCCCH-HH
Confidence 78888764 22223334444433333 2 56666554443 22 23344556777788887753333222 23
Q ss_pred HHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcCC--CcchhHHHHHHHHhc
Q 003958 113 SHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDDD--HGRNGIAALGDTLAA 190 (784)
Q Consensus 113 a~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~~--~g~~~~~~l~~~l~~ 190 (784)
...+...++|+|......+ + +.+....++....+..+++.|...|-++|+++..+.. ......+.+.+.+++
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 4556778999999754322 1 1233466677778888889888889999999985433 445567889999988
Q ss_pred cCcEEEEeeccCCCCChhHHHHHHHHhhcC--CceEEEEeccCCcHHHHHHHHHHcC
Q 003958 191 KRCRISFKAPLSVEATEDEITDLLVKVALT--ESRIIVVHTHYNRGPVVFHVAQYLG 245 (784)
Q Consensus 191 ~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~--~~~vIvl~~~~~~~~~~~~~a~~~g 245 (784)
.|..+.... .. ..+..+....+.++.+. .+++|+.. +...+..+++.+++.+
T Consensus 144 ~~~~~~~~~-~~-~~~~~~~~~~~~~~l~~~~~~~~i~~~-~~~~a~~~~~~l~~~~ 197 (266)
T cd06278 144 AGVPVVVEE-AG-DYSYEGGYEAARRLLASRPRPDAIFCA-NDLLAIGVMDAARQEG 197 (266)
T ss_pred cCCChhhhc-cC-CCCHHHHHHHHHHHHhcCCCCCEEEEc-CcHHHHHHHHHHHHhc
Confidence 887643211 11 11222333444444333 35654443 3445667777777653
No 172
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=97.36 E-value=0.025 Score=60.22 Aligned_cols=203 Identities=10% Similarity=0.025 Sum_probs=117.1
Q ss_pred ceEEEEEEeecC-CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEccCchhh
Q 003958 30 SVVNIGALLSFS-TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIGPQDAVT 108 (784)
Q Consensus 30 ~~i~IG~i~~~~-~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiGp~~s~~ 108 (784)
..-.||+++|.. ..+-.....++.-+.++ . |+.+-+ .++..++.........+..+++.+||-......
T Consensus 63 ~~~~Igvv~~~~~~~~~~~i~~gi~~~a~~---~-----g~~~~~--~~~~~~~~~~~~~~~~l~~~~vdgiIi~~~~~~ 132 (342)
T PRK10014 63 QSGVIGLIVRDLSAPFYAELTAGLTEALEA---Q-----GRMVFL--LQGGKDGEQLAQRFSTLLNQGVDGVVIAGAAGS 132 (342)
T ss_pred CCCEEEEEeCCCccchHHHHHHHHHHHHHH---c-----CCEEEE--EeCCCCHHHHHHHHHHHHhCCCCEEEEeCCCCC
Confidence 456799999853 22223344455544443 2 444433 344455555555566677778887764222222
Q ss_pred HHHHHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcCC--CcchhHHHHHH
Q 003958 109 SHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDDD--HGRNGIAALGD 186 (784)
Q Consensus 109 ~~~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~~--~g~~~~~~l~~ 186 (784)
.......+...++|+|...... ....+++ +.......+..++++|.+.|.++|++|..+.. ......+.+++
T Consensus 133 ~~~~~~~l~~~~iPvV~~~~~~---~~~~~~~---V~~D~~~~~~~a~~~L~~~G~~~I~~i~g~~~~~~~~~R~~Gf~~ 206 (342)
T PRK10014 133 SDDLREMAEEKGIPVVFASRAS---YLDDVDT---VRPDNMQAAQLLTEHLIRNGHQRIAWLGGQSSSLTRAERVGGYCA 206 (342)
T ss_pred cHHHHHHHhhcCCCEEEEecCC---CCCCCCE---EEeCCHHHHHHHHHHHHHCCCCEEEEEcCCcccccHHHHHHHHHH
Confidence 2344456677899999875321 1122232 44556667788888888889999999975433 23456778999
Q ss_pred HHhccCcEEEEeeccCCCCChhHHHHHHHHhhcC--CceEEEEeccCCcHHHHHHHHHHcCCCCC
Q 003958 187 TLAAKRCRISFKAPLSVEATEDEITDLLVKVALT--ESRIIVVHTHYNRGPVVFHVAQYLGMLGT 249 (784)
Q Consensus 187 ~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~--~~~vIvl~~~~~~~~~~~~~a~~~g~~~~ 249 (784)
.+++.|+.+.....+............++++.+. .+++|+ +.+...+..+++.+.+.|+..+
T Consensus 207 al~~~g~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~-~~nd~~A~g~~~~l~~~g~~vp 270 (342)
T PRK10014 207 TLLKFGLPFHSEWVLECTSSQKQAAEAITALLRHNPTISAVV-CYNETIAMGAWFGLLRAGRQSG 270 (342)
T ss_pred HHHHcCCCCCcceEecCCCChHHHHHHHHHHHcCCCCCCEEE-ECCcHHHHHHHHHHHHcCCCCC
Confidence 9998887543211111111222233444444333 355544 4555667788899999887654
No 173
>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=97.34 E-value=0.022 Score=58.32 Aligned_cols=201 Identities=11% Similarity=0.034 Sum_probs=115.6
Q ss_pred EEEEeecC-CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEc-cCchhhHHH
Q 003958 34 IGALLSFS-TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIG-PQDAVTSHV 111 (784)
Q Consensus 34 IG~i~~~~-~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiG-p~~s~~~~~ 111 (784)
||++.|.. ..+-.....+++-+.++ .|+++.+ .++..+...-.+....++.+++.+||- +.... . .
T Consensus 2 i~vi~~~~~~~~~~~~~~gi~~~~~~--------~g~~~~~--~~~~~~~~~~~~~i~~l~~~~~dgiii~~~~~~-~-~ 69 (270)
T cd06296 2 IGLVFPDLDSPWASEVLRGVEEAAAA--------AGYDVVL--SESGRRTSPERQWVERLSARRTDGVILVTPELT-S-A 69 (270)
T ss_pred eEEEECCCCCccHHHHHHHHHHHHHH--------cCCeEEE--ecCCCchHHHHHHHHHHHHcCCCEEEEecCCCC-h-H
Confidence 78888763 33334445555555554 1455544 444455544445556677778887753 33222 2 2
Q ss_pred HHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcC--CCcchhHHHHHHHHh
Q 003958 112 VSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDD--DHGRNGIAALGDTLA 189 (784)
Q Consensus 112 va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~--~~g~~~~~~l~~~l~ 189 (784)
....+...++|+|........ ...++ ...++....+..+++.+...|.++++++..+. .......+.+.+.++
T Consensus 70 ~~~~~~~~~ipvV~i~~~~~~--~~~~~---~v~~d~~~~~~~a~~~l~~~g~~~i~~i~~~~~~~~~~~r~~gf~~~~~ 144 (270)
T cd06296 70 QRAALRRTGIPFVVVDPAGDP--DADVP---SVGATNWAGGLAATEHLLELGHRRIGFITGPPDLLCSRARLDGYRAALA 144 (270)
T ss_pred HHHHHhcCCCCEEEEecccCC--CCCCC---EEEeCcHHHHHHHHHHHHHcCCCcEEEEcCCCcchhHHHHHHHHHHHHH
Confidence 345567789999997653211 11223 24556666778888888778999999997542 234566788889988
Q ss_pred ccCcEEEEeeccCCCCChhHHHHHHHHhhcC--CceEEEEeccCCcHHHHHHHHHHcCCCCCCeE
Q 003958 190 AKRCRISFKAPLSVEATEDEITDLLVKVALT--ESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYV 252 (784)
Q Consensus 190 ~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~--~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~ 252 (784)
+.++.+.............+....+.++.+. .+++|+ +.+...+..+++.+++.|+..++.+
T Consensus 145 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~-~~~d~~a~~~~~~l~~~g~~~p~~i 208 (270)
T cd06296 145 EAGIPVDPALVREGDFSTESGFRAAAELLALPERPTAIF-AGNDLMALGVYEAARERGLRIPEDL 208 (270)
T ss_pred HcCCCCChHHheeCCCCHHHHHHHHHHHHhCCCCCcEEE-EcCcHHHHHHHHHHHHhCCCCCCce
Confidence 8776543211111111222333444444332 345444 3455567789999999998654433
No 174
>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=97.32 E-value=0.034 Score=57.00 Aligned_cols=206 Identities=15% Similarity=0.062 Sum_probs=117.9
Q ss_pred EEEEEeecC-CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEc-cCc-hh--
Q 003958 33 NIGALLSFS-TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIG-PQD-AV-- 107 (784)
Q Consensus 33 ~IG~i~~~~-~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiG-p~~-s~-- 107 (784)
.||++.|.. ..+-.....+++-+.++ . |+.+. +.++..++..-.+....++.+++.++|= +.. ..
T Consensus 1 ~Igvi~~~~~~~~~~~~~~gi~~~~~~----~----g~~~~--~~~~~~~~~~~~~~i~~l~~~~vdgiIi~~~~~~~~~ 70 (273)
T cd06292 1 LVGLLVPELSNPIFPAFAEAIEAALAQ----Y----GYTVL--LCNTYRGGVSEADYVEDLLARGVRGVVFISSLHADTH 70 (273)
T ss_pred CEEEEeCCCcCchHHHHHHHHHHHHHH----C----CCEEE--EEeCCCChHHHHHHHHHHHHcCCCEEEEeCCCCCccc
Confidence 378888864 22223344455555544 2 55554 3455556665556677788888887763 221 11
Q ss_pred hHHHHHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcC--CCcchhHHHHH
Q 003958 108 TSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDD--DHGRNGIAALG 185 (784)
Q Consensus 108 ~~~~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~--~~g~~~~~~l~ 185 (784)
........+...++|+|..+...+. ...++ ....+....+..+++.|...|-++++++.... .......+.++
T Consensus 71 ~~~~~i~~~~~~~ipvV~i~~~~~~--~~~~~---~V~~d~~~~~~~~~~~l~~~g~~~i~~i~~~~~~~~~~~R~~gf~ 145 (273)
T cd06292 71 ADHSHYERLAERGLPVVLVNGRAPP--PLKVP---HVSTDDALAMRLAVRHLVALGHRRIGFASGPGRTVPRRRKIAGFR 145 (273)
T ss_pred chhHHHHHHHhCCCCEEEEcCCCCC--CCCCC---EEEECcHHHHHHHHHHHHHCCCceEEEEeCCcccccHHHHHHHHH
Confidence 1122234456789999998654321 01223 24456677788888888888999999997543 23445678899
Q ss_pred HHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHcCCCCCCeEEE
Q 003958 186 DTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWI 254 (784)
Q Consensus 186 ~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~wi 254 (784)
+.+++.|+............+.......++++....+++|+ +.....+..+++.+.+.|+..++-+-+
T Consensus 146 ~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~l~~~~~ai~-~~~d~~a~g~~~~l~~~g~~ip~di~i 213 (273)
T cd06292 146 AALEEAGLEPPEALVARGMFSVEGGQAAAVELLGSGPTAIV-AASDLMALGAIRAARRRGLRVPEDVSV 213 (273)
T ss_pred HHHHHcCCCCChhheEeCCCCHHHHHHHHHHHhcCCCCEEE-EcCcHHHHHHHHHHHHcCCCCCcceEE
Confidence 99988875321111111111222233444444433477654 445556678899999988765543333
No 175
>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=97.29 E-value=0.079 Score=54.28 Aligned_cols=171 Identities=8% Similarity=0.008 Sum_probs=105.6
Q ss_pred CCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEc-cCchhhHHHHHHhhhcCCccEEecccCCCCCCcCCCCceEeecC
Q 003958 68 GTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIG-PQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQ 146 (784)
Q Consensus 68 g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiG-p~~s~~~~~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~p 146 (784)
|+.+. +.++..++..-.+....++.+++.+||= +..+.........+...+||+|......+ ....+.+....+
T Consensus 29 G~~~~--~~~~~~d~~~~~~~i~~~~~~~vdgiii~~~~~~~~~~~i~~~~~~~iPvV~~~~~~~---~~~~~~~~~v~~ 103 (272)
T cd06313 29 GVDVT--WYGGALDAVKQVAAIENMASQGWDFIAVDPLGIGTLTEAVQKAIARGIPVIDMGTLIA---PLQINVHSFLAP 103 (272)
T ss_pred CCEEE--EecCCCCHHHHHHHHHHHHHcCCCEEEEcCCChHHhHHHHHHHHHCCCcEEEeCCCCC---CCCCceEEEECC
Confidence 45444 4466667777777788888888887764 33333333433455667999999755332 111122334567
Q ss_pred ChHHHHHHHHHHHHHc--CCcEEEEEEEcCC--CcchhHHHHHHHHhccC-cEEEEeeccCCCCChhHHHHHHHHhhcCC
Q 003958 147 SDQYQMAAIAEIVDHY--GWREVIAIYVDDD--HGRNGIAALGDTLAAKR-CRISFKAPLSVEATEDEITDLLVKVALTE 221 (784)
Q Consensus 147 s~~~~~~ai~~~l~~~--~w~~v~ii~~d~~--~g~~~~~~l~~~l~~~g-i~v~~~~~~~~~~~~~d~~~~l~~l~~~~ 221 (784)
.....+..++++|.+. +.++++++..+.. ......+.+++.+++.+ +++... .....+.......++++.+.+
T Consensus 104 d~~~~g~~~~~~l~~~~~g~~~i~~l~g~~~~~~~~~R~~gf~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~l~~~ 181 (272)
T cd06313 104 DNYFMGASVAQALCNAMGGKGKIAMLQGALGHTGAQGRAQGFNDVIKKYPDIEVVDE--QPANWDVSKAARIWETWLTKY 181 (272)
T ss_pred CcHHHHHHHHHHHHHHcCCCceEEEEECCCCCcchhHHHHHHHHHHHhCCCCEEEec--cCCCCCHHHHHHHHHHHHHhC
Confidence 7777888888888766 8899999986433 23456788999998875 554431 111122233345555544333
Q ss_pred --ceEEEEeccCCcHHHHHHHHHHcCC
Q 003958 222 --SRIIVVHTHYNRGPVVFHVAQYLGM 246 (784)
Q Consensus 222 --~~vIvl~~~~~~~~~~~~~a~~~g~ 246 (784)
+++ |++.+...+..+++++++.|+
T Consensus 182 ~~~~a-i~~~nd~~a~g~~~al~~~g~ 207 (272)
T cd06313 182 PQLDG-AFCHNDSMALAAYQIMKAAGR 207 (272)
T ss_pred CCCCE-EEECCCcHHHHHHHHHHHcCC
Confidence 454 334555667788899999887
No 176
>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=97.29 E-value=0.074 Score=54.74 Aligned_cols=200 Identities=14% Similarity=0.048 Sum_probs=113.6
Q ss_pred EEEEEeecCC-cchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEc-cCchhhHH
Q 003958 33 NIGALLSFST-NVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIG-PQDAVTSH 110 (784)
Q Consensus 33 ~IG~i~~~~~-~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiG-p~~s~~~~ 110 (784)
+||++.|... .+-.....+++.+.++ . |+.+ .+.++..++..-.+....++++++.+||- +..+....
T Consensus 1 ~igv~~~~~~~~~~~~~~~~i~~~~~~---~-----g~~v--~~~~~~~~~~~~~~~i~~~~~~~~Dgiii~~~~~~~~~ 70 (282)
T cd06318 1 KIGFSQYTLNSPFFAALTEAAKAHAKA---L-----GYEL--ISTDAQGDLTKQIADVEDLLTRGVNVLIINPVDPEGLV 70 (282)
T ss_pred CeeEEeccccCHHHHHHHHHHHHHHHH---c-----CCEE--EEEcCCCCHHHHHHHHHHHHHcCCCEEEEecCCccchH
Confidence 4888888642 2222334455555554 1 4544 44555567666666667777888877764 33333223
Q ss_pred HHHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHH-cCCc--EEEEEEEc--CCCcchhHHHHH
Q 003958 111 VVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDH-YGWR--EVIAIYVD--DDHGRNGIAALG 185 (784)
Q Consensus 111 ~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~-~~w~--~v~ii~~d--~~~g~~~~~~l~ 185 (784)
.....+...++|+|.+....+. . .+.+..+..+....+..+++.|.+ .|-+ +++++..+ ...+....+.++
T Consensus 71 ~~i~~~~~~~iPvV~~~~~~~~---~-~~~~~~v~~d~~~~g~~~~~~l~~~~g~~~~~i~~i~~~~~~~~~~~R~~gf~ 146 (282)
T cd06318 71 PAVAAAKAAGVPVVVVDSSINL---E-AGVVTQVQSSNAKNGNLVGEWVVGELGDKPMKIILLSGDAGNLVGQARRDGFL 146 (282)
T ss_pred HHHHHHHHCCCCEEEecCCCCC---C-cCeEEEEecCcHHHHHHHHHHHHHHhCCCCceEEEEECCCCCchHhHHHHhHH
Confidence 3345566789999988653211 0 122344566667778888888755 6765 89988753 234566778899
Q ss_pred HHHhccCcE------EEEeeccCCCCChhHHHHHHHHhhc--CCceEEEEeccCCcHHHHHHHHHHcCCC
Q 003958 186 DTLAAKRCR------ISFKAPLSVEATEDEITDLLVKVAL--TESRIIVVHTHYNRGPVVFHVAQYLGML 247 (784)
Q Consensus 186 ~~l~~~gi~------v~~~~~~~~~~~~~d~~~~l~~l~~--~~~~vIvl~~~~~~~~~~~~~a~~~g~~ 247 (784)
+.+++.|+. +..........+..+....+.++.. .++++|+. .....+..+++++++.|+.
T Consensus 147 ~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~-~~d~~a~g~~~al~~~g~~ 215 (282)
T cd06318 147 LGVSEAQLRKYGKTNFTIVAQGYGDWTREGGLKAMEDLLVAHPDINVVYS-ENDDMALGAMRVLAEAGKT 215 (282)
T ss_pred HHHhhCcccccccCCeEEEecCCCCCCHHHHHHHHHHHHHhCCCcCEEEE-CCcchHHHHHHHHHHcCCC
Confidence 999887632 1111101111122222334444332 23555444 4455677889999998874
No 177
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=97.26 E-value=0.053 Score=57.35 Aligned_cols=203 Identities=12% Similarity=0.053 Sum_probs=116.2
Q ss_pred ceEEEEEEeecC-CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEccCc-hh
Q 003958 30 SVVNIGALLSFS-TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIGPQD-AV 107 (784)
Q Consensus 30 ~~i~IG~i~~~~-~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiGp~~-s~ 107 (784)
..-.||+++|.. ..+-.....+++.+.++ .|+.+.+. ++..++..-.+....+..+++.+||-... ..
T Consensus 60 ~~~~Igvv~~~~~~~~~~~l~~gi~~~~~~--------~g~~~~~~--~~~~~~~~~~~~~~~l~~~~vdgiIi~~~~~~ 129 (328)
T PRK11303 60 RTRSIGLIIPDLENTSYARIAKYLERQARQ--------RGYQLLIA--CSDDQPDNEMRCAEHLLQRQVDALIVSTSLPP 129 (328)
T ss_pred CCceEEEEeCCCCCchHHHHHHHHHHHHHH--------cCCEEEEE--eCCCCHHHHHHHHHHHHHcCCCEEEEcCCCCC
Confidence 356799999853 22222334455544443 25665543 34445554444555666778888764322 21
Q ss_pred hHHHHHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcCC--CcchhHHHHH
Q 003958 108 TSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDDD--HGRNGIAALG 185 (784)
Q Consensus 108 ~~~~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~~--~g~~~~~~l~ 185 (784)
....+ ..+...++|+|..+...+ +..+++ ....+...+..+++.|...|.++|+++..... ......+.++
T Consensus 130 ~~~~~-~~l~~~~iPvV~v~~~~~---~~~~~~---V~~d~~~~~~~a~~~L~~~G~r~I~~i~~~~~~~~~~~R~~Gf~ 202 (328)
T PRK11303 130 EHPFY-QRLQNDGLPIIALDRALD---REHFTS---VVSDDQDDAEMLAESLLKFPAESILLLGALPELSVSFEREQGFR 202 (328)
T ss_pred ChHHH-HHHHhcCCCEEEECCCCC---CCCCCE---EEeCCHHHHHHHHHHHHHCCCCeEEEEeCccccccHHHHHHHHH
Confidence 22222 334567999998754321 122332 34566666777888888889999999985432 3456678899
Q ss_pred HHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcC--CceEEEEeccCCcHHHHHHHHHHcCCCCCCeE
Q 003958 186 DTLAAKRCRISFKAPLSVEATEDEITDLLVKVALT--ESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYV 252 (784)
Q Consensus 186 ~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~--~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~ 252 (784)
+.+++.|+.+..... . ..+..+-...++++.+. .+++|+. .+...+..+++++.+.|+..|+-+
T Consensus 203 ~al~~~g~~~~~~~~-~-~~~~~~~~~~~~~~l~~~~~~~ai~~-~~d~~A~g~~~al~~~g~~vP~di 268 (328)
T PRK11303 203 QALKDDPREVHYLYA-N-SFEREAGAQLFEKWLETHPMPDALFT-TSYTLLQGVLDVLLERPGELPSDL 268 (328)
T ss_pred HHHHHcCCCceEEEe-C-CCChHHHHHHHHHHHcCCCCCCEEEE-cCcHHHHHHHHHHHHcCCCCCCce
Confidence 999988875432211 1 11222233444554332 4666554 344567788999999998655433
No 178
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=97.25 E-value=0.041 Score=58.13 Aligned_cols=205 Identities=9% Similarity=0.002 Sum_probs=114.2
Q ss_pred ceEEEEEEeecC-CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEc-cCchh
Q 003958 30 SVVNIGALLSFS-TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIG-PQDAV 107 (784)
Q Consensus 30 ~~i~IG~i~~~~-~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiG-p~~s~ 107 (784)
..-.||+++|.. ..+-.....+++-+.++ . |+++.+ .++..++..-.+....+..+++.+||= |....
T Consensus 55 ~~~~Igvi~~~~~~~~~~~~~~gi~~~~~~---~-----g~~~~~--~~~~~~~~~~~~~~~~l~~~~vdGiI~~~~~~~ 124 (327)
T PRK10423 55 QTRTIGMLITASTNPFYSELVRGVERSCFE---R-----GYSLVL--CNTEGDEQRMNRNLETLMQKRVDGLLLLCTETH 124 (327)
T ss_pred CCCeEEEEeCCCCCCcHHHHHHHHHHHHHH---c-----CCEEEE--EeCCCCHHHHHHHHHHHHHcCCCEEEEeCCCcc
Confidence 456799999863 22223444555555554 1 555544 344455555455556677777887763 22211
Q ss_pred hHHHHHHhhhc-CCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcC--CCcchhHHHH
Q 003958 108 TSHVVSHVANE-LQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDD--DHGRNGIAAL 184 (784)
Q Consensus 108 ~~~~va~~~~~-~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~--~~g~~~~~~l 184 (784)
. ........ .++|+|..+.... ...++ ....+...-+..+++.|...|-++|++|..+. .......+.+
T Consensus 125 ~--~~~~~l~~~~~iPvV~i~~~~~---~~~~~---~v~~d~~~~~~~a~~~L~~~G~~~I~~i~~~~~~~~~~~R~~Gf 196 (327)
T PRK10423 125 Q--PSREIMQRYPSVPTVMMDWAPF---DGDSD---LIQDNSLLGGDLATQYLIDKGYTRIACITGPLDKTPARLRLEGY 196 (327)
T ss_pred h--hhHHHHHhcCCCCEEEECCccC---CCCCC---EEEEChHHHHHHHHHHHHHcCCCeEEEEeCCccccchHHHHHHH
Confidence 1 11122233 4899998753211 11111 23344445577788888889999999997432 3345667899
Q ss_pred HHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcC--CceEEEEeccCCcHHHHHHHHHHcCCCCCCeEE
Q 003958 185 GDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALT--ESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVW 253 (784)
Q Consensus 185 ~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~--~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~w 253 (784)
++.+++.|+.+.....+.......+-...+.++.+. .+++|+. ++...+..+++++++.|+..|+-+-
T Consensus 197 ~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~-~~d~~A~g~~~~l~~~g~~vP~dvs 266 (327)
T PRK10423 197 RAAMKRAGLNIPDGYEVTGDFEFNGGFDAMQQLLALPLRPQAVFT-GNDAMAVGVYQALYQAGLSVPQDIA 266 (327)
T ss_pred HHHHHHcCCCCCcceEEeCCCChHHHHHHHHHHhcCCCCCCEEEE-cCcHHHHHHHHHHHHcCCCCCCceE
Confidence 999999887542211111111112223344454332 3555444 4556677899999999987654443
No 179
>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=97.22 E-value=0.037 Score=56.37 Aligned_cols=199 Identities=10% Similarity=0.020 Sum_probs=110.4
Q ss_pred EEEEEeecC-CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEccCchhhHHH
Q 003958 33 NIGALLSFS-TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIGPQDAVTSHV 111 (784)
Q Consensus 33 ~IG~i~~~~-~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiGp~~s~~~~~ 111 (784)
.||++.|.. ..+-.....+++.+.+ +. |+++.+ .++..++..-.+....+.++++.++|--.+......
T Consensus 1 ~i~vi~~~~~~~~~~~~~~gi~~~~~----~~----gy~~~~--~~~~~~~~~~~~~i~~l~~~~~dgiii~~~~~~~~~ 70 (265)
T cd06290 1 TIGVLTQDFASPFYGRILKGMERGLN----GS----GYSPII--ATGHWNQSRELEALELLKSRRVDALILLGGDLPEEE 70 (265)
T ss_pred CEEEEECCCCCchHHHHHHHHHHHHH----HC----CCEEEE--EeCCCCHHHHHHHHHHHHHCCCCEEEEeCCCCChHH
Confidence 378888753 2222233334433333 22 455544 444556655555566677778888864322211222
Q ss_pred HHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEc--CCCcchhHHHHHHHHh
Q 003958 112 VSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVD--DDHGRNGIAALGDTLA 189 (784)
Q Consensus 112 va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d--~~~g~~~~~~l~~~l~ 189 (784)
+..+ . .++|+|..+...+ +...+ ....+...-+..+++.|...|-++++++..+ ........+.+++.++
T Consensus 71 ~~~~-~-~~iPvV~i~~~~~---~~~~~---~V~~d~~~a~~~~~~~l~~~g~~~i~~i~~~~~~~~~~~r~~gf~~~~~ 142 (265)
T cd06290 71 ILAL-A-EEIPVLAVGRRVP---GPGAA---SIAVDNFQGGYLATQHLIDLGHRRIAHITGPRGHIDARDRLAGYRKALE 142 (265)
T ss_pred HHHH-h-cCCCEEEECCCcC---CCCCC---EEEECcHHHHHHHHHHHHHCCCCeEEEEeCccccchhhHHHHHHHHHHH
Confidence 2222 3 4899998865322 11222 2345666667788888877799999999754 2334456788888888
Q ss_pred ccCcEEEEeeccCCCCChhHHHHHHHHhhcC--CceEEEEeccCCcHHHHHHHHHHcCCCCCC
Q 003958 190 AKRCRISFKAPLSVEATEDEITDLLVKVALT--ESRIIVVHTHYNRGPVVFHVAQYLGMLGTG 250 (784)
Q Consensus 190 ~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~--~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~ 250 (784)
+.|+.+.....+....+.......++++.+. .+++|+ +++...+..+++.+++.|+..++
T Consensus 143 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~aii-~~~~~~a~~~~~~l~~~g~~ip~ 204 (265)
T cd06290 143 EAGLEVQPDLIVQGDFEEESGLEAVEELLQRGPDFTAIF-AANDQTAYGARLALYRRGLRVPE 204 (265)
T ss_pred HcCCCCCHHHEEecCCCHHHHHHHHHHHHcCCCCCCEEE-EcCcHHHHHHHHHHHHcCCCCCc
Confidence 8776543211111111122223445554433 356544 45556677889999998876543
No 180
>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=97.19 E-value=0.095 Score=53.72 Aligned_cols=208 Identities=12% Similarity=0.048 Sum_probs=109.9
Q ss_pred EEEEEeecCC-cchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEc-cCchhhHH
Q 003958 33 NIGALLSFST-NVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIG-PQDAVTSH 110 (784)
Q Consensus 33 ~IG~i~~~~~-~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiG-p~~s~~~~ 110 (784)
+||++.|... .+-.....++.-+.++.+-. ...+..... ...++..-.+....+.. ++.++|= +.......
T Consensus 1 ~ig~v~~~~~~~~~~~~~~~i~~~~~~~g~~-----~~~~~~~~~-~~~~~~~~~~~i~~~~~-~vdgiii~~~~~~~~~ 73 (275)
T cd06307 1 RLGFLLPKGSNAFYRELAAALEAAAAAFPDA-----RIRVRIHFV-ESFDPAALAAALLRLGA-RSDGVALVAPDHPQVR 73 (275)
T ss_pred CeEEEeCCCCChHHHHHHHHHHHHHhhhhcc-----CceEEEEEc-cCCCHHHHHHHHHHHHh-cCCEEEEeCCCcHHHH
Confidence 5888887642 22234445555555553211 122232222 23455544455555556 7887753 33323222
Q ss_pred HHHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHc-C--CcEEEEEEEcCC--CcchhHHHHH
Q 003958 111 VVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHY-G--WREVIAIYVDDD--HGRNGIAALG 185 (784)
Q Consensus 111 ~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~-~--w~~v~ii~~d~~--~g~~~~~~l~ 185 (784)
.....+...++|+|.+....+. ... +..+.......+..++++|.+. | -++++++..+.. ......+.++
T Consensus 74 ~~i~~~~~~~ipvV~~~~~~~~--~~~---~~~V~~d~~~~g~~~~~~l~~~~g~~~~~i~~i~~~~~~~~~~~R~~gf~ 148 (275)
T cd06307 74 AAVARLAAAGVPVVTLVSDLPG--SPR---AGYVGIDNRAAGRTAAWLIGRFLGRRPGKVAVLAGSHRFRGHEEREMGFR 148 (275)
T ss_pred HHHHHHHHCCCcEEEEeCCCCC--Cce---eeEEccChHHHHHHHHHHHHHHhCCCCCeEEEEecCCCCcchHHHHHHHH
Confidence 3345556689999987543211 111 2224445556666667766554 5 469999976432 3345678899
Q ss_pred HHHhccCcEEEEeeccCCCCChhHHHHHHHHhhc--CCceEEEEeccCCcHHHHHHHHHHcCCCCCCeEEEe
Q 003958 186 DTLAAKRCRISFKAPLSVEATEDEITDLLVKVAL--TESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIA 255 (784)
Q Consensus 186 ~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~--~~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~wi~ 255 (784)
+.+++++..+..........+..+....++++.+ .++++|+...+ .+..+++++++.|+. .+...++
T Consensus 149 ~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~~d--~~~g~~~al~~~g~~-~di~Ivg 217 (275)
T cd06307 149 SVLREEFPGLRVLETLEGLDDPARAYEATRKLLARHPDLVGIYNAGG--GNRGVIRALREAGRA-GKVVFVG 217 (275)
T ss_pred HHHHhhCCCcEEEeeccCCCChHHHHHHHHHHHHhCCCceEEEECCC--ChHHHHHHHHHcCCC-CCcEEEE
Confidence 9998876544332222211222333345555432 34666666544 346889999998874 2334343
No 181
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=97.18 E-value=0.057 Score=56.99 Aligned_cols=201 Identities=10% Similarity=0.038 Sum_probs=128.0
Q ss_pred ceEEEEEEeecC-CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEccCchhh
Q 003958 30 SVVNIGALLSFS-TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIGPQDAVT 108 (784)
Q Consensus 30 ~~i~IG~i~~~~-~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiGp~~s~~ 108 (784)
..-.||++.|.- ..+-.....+++.++++ .|+.+- +.++..++..-.+....+..++|.+||=-. ...
T Consensus 57 ~s~~Ig~i~p~~~~~~~~~i~~gi~~~~~~--------~gy~~~--l~~~~~~~~~e~~~~~~l~~~~vdGiIi~~-~~~ 125 (333)
T COG1609 57 RTKTIGLVVPDITNPFFAEILKGIEEAARE--------AGYSLL--LANTDDDPEKEREYLETLLQKRVDGLILLG-ERP 125 (333)
T ss_pred CCCEEEEEeCCCCCchHHHHHHHHHHHHHH--------cCCEEE--EECCCCCHHHHHHHHHHHHHcCCCEEEEec-CCC
Confidence 567799999943 21222344455544444 245444 444444666655566667777899887544 233
Q ss_pred HHHHHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEc--CCCcchhHHHHHH
Q 003958 109 SHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVD--DDHGRNGIAALGD 186 (784)
Q Consensus 109 ~~~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d--~~~g~~~~~~l~~ 186 (784)
.......+...++|+|..+...+ + +.+-....++..-+..+++.|.+.|.+++++|... ...++...+.+++
T Consensus 126 ~~~~~~~l~~~~~P~V~i~~~~~---~---~~~~~V~~Dn~~~~~~a~~~L~~~G~~~i~~i~~~~~~~~~~~R~~Gf~~ 199 (333)
T COG1609 126 NDSLLELLAAAGIPVVVIDRSPP---G---LGVPSVGIDNFAGAYLATEHLIELGHRRIAFIGGPLDSSASRERLEGYRA 199 (333)
T ss_pred CHHHHHHHHhcCCCEEEEeCCCc---c---CCCCEEEEChHHHHHHHHHHHHHCCCceEEEEeCCCccccHhHHHHHHHH
Confidence 34445666777999998766443 2 22334456677788889999999999999999975 4455778899999
Q ss_pred HHhccCcEE--EEeeccCCCCChhHHHHHHHHhhcC--C-ceEEEEeccCCcHHHHHHHHHHcCCCCCC
Q 003958 187 TLAAKRCRI--SFKAPLSVEATEDEITDLLVKVALT--E-SRIIVVHTHYNRGPVVFHVAQYLGMLGTG 250 (784)
Q Consensus 187 ~l~~~gi~v--~~~~~~~~~~~~~d~~~~l~~l~~~--~-~~vIvl~~~~~~~~~~~~~a~~~g~~~~~ 250 (784)
.+++.|+.. .....-. ....+-...+.++... . +++| ++++...+..+++++.++|+..|+
T Consensus 200 al~~~~~~~~~~~i~~~~--~~~~~g~~~~~~ll~~~~~~ptAi-f~~nD~~Alg~l~~~~~~g~~vP~ 265 (333)
T COG1609 200 ALREAGLPINPEWIVEGD--FSEESGYEAAERLLARGEPRPTAI-FCANDLMALGALRALRELGLRVPE 265 (333)
T ss_pred HHHHCCCCCCcceEEecC--CChHHHHHHHHHHHhcCCCCCcEE-EEcCcHHHHHHHHHHHHcCCCCCC
Confidence 999999874 2211111 1223333444444432 2 5664 446667788999999999987654
No 182
>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=97.17 E-value=0.039 Score=56.41 Aligned_cols=199 Identities=15% Similarity=0.095 Sum_probs=109.4
Q ss_pred EEEEeecC------CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhc-CceEEEccCch
Q 003958 34 IGALLSFS------TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEG-QTVAIIGPQDA 106 (784)
Q Consensus 34 IG~i~~~~------~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~-~v~aiiGp~~s 106 (784)
||++.|.. ..+-.....+++-+.++ .|+++.+. +... +..-.+...+++.+ ++.+||-....
T Consensus 2 igli~p~~~~~~~~~~~~~~~~~~~~~~~~~--------~g~~~~~~--~~~~-~~~~~~~~~~~~~~~~~dgiii~~~~ 70 (270)
T cd06294 2 IGVVLPPSADEAFQNPFFIEVLRGISAVANE--------NGYDISLA--TGKN-EEELLEEVKKMIQQKRVDGFILLYSR 70 (270)
T ss_pred EEEEeCCccccCcCCCCHHHHHHHHHHHHHH--------CCCEEEEe--cCCC-cHHHHHHHHHHHHHcCcCEEEEecCc
Confidence 78888852 22223444555555554 15566543 3332 33334455565544 57776543221
Q ss_pred hhHHHHHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcCCC--cchhHHHH
Q 003958 107 VTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDDDH--GRNGIAAL 184 (784)
Q Consensus 107 ~~~~~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~~~--g~~~~~~l 184 (784)
.. ......+...++|+|......+ + .+.+..+.......++.+++.|...|-++++++.....+ .....+.+
T Consensus 71 ~~-~~~~~~~~~~~ipvV~~~~~~~---~--~~~~~~v~~d~~~~g~~~~~~l~~~g~~~i~~i~~~~~~~~~~~r~~gf 144 (270)
T cd06294 71 ED-DPIIDYLKEEKFPFVVIGKPED---D--KENITYVDNDNIQAGYDATEYLIKLGHKKIAFVGGDLDLEVTQDRLQGY 144 (270)
T ss_pred CC-cHHHHHHHhcCCCEEEECCCCC---C--CCCCCeEEECcHHHHHHHHHHHHHcCCccEEEecCCcccHHHHHHHHHH
Confidence 11 2333445678999998754321 1 011222344556667778888877799999999754332 34457888
Q ss_pred HHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcC--CceEEEEeccCCcHHHHHHHHHHcCCCCCC
Q 003958 185 GDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALT--ESRIIVVHTHYNRGPVVFHVAQYLGMLGTG 250 (784)
Q Consensus 185 ~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~--~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~ 250 (784)
++.+++.|+.+..........+..+....+.++.++ .+++|+. .+...+..+++++++.|+..++
T Consensus 145 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~-~~d~~a~g~~~al~~~g~~iP~ 211 (270)
T cd06294 145 KQALEDHGIPDRNEVIISLDFSEEGGYKALKKLLEQHPRPTAIVA-TDDLLALGVLKVLNELGLKVPE 211 (270)
T ss_pred HHHHHHcCCCCCcceEEecCCchHHHHHHHHHHHhCCCCCCEEEE-CChHHHHHHHHHHHHcCCCCCc
Confidence 999988875321111111111222333445554333 3555444 4455777899999999986544
No 183
>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=97.16 E-value=0.19 Score=51.37 Aligned_cols=197 Identities=15% Similarity=0.119 Sum_probs=106.7
Q ss_pred EEEEEeecCCcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEc-cCchhhHHH
Q 003958 33 NIGALLSFSTNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIG-PQDAVTSHV 111 (784)
Q Consensus 33 ~IG~i~~~~~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiG-p~~s~~~~~ 111 (784)
+||++...+..+-.....++.-+.++ .|+.+.+.. ++..+...-.+....++.+++.++|= |........
T Consensus 1 ~i~~v~~~~~~~~~~~~~gi~~~~~~--------~g~~~~~~~-~~~~~~~~~~~~i~~l~~~~vDgiIi~~~~~~~~~~ 71 (271)
T cd06314 1 TIAVVTNGASPFWKIAEAGVKAAGKE--------LGVDVEFVV-PQQGTVNAQLRMLEDLIAEGVDGIAISPIDPKAVIP 71 (271)
T ss_pred CeEEEcCCCcHHHHHHHHHHHHHHHH--------cCCeEEEeC-CCCCCHHHHHHHHHHHHhcCCCEEEEecCChhHhHH
Confidence 37777654432222334444444444 145554442 23345555555666677778887764 433332233
Q ss_pred HHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHc--CCcEEEEEEEcC--CCcchhHHHHHHH
Q 003958 112 VSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHY--GWREVIAIYVDD--DHGRNGIAALGDT 187 (784)
Q Consensus 112 va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~--~w~~v~ii~~d~--~~g~~~~~~l~~~ 187 (784)
....+.. ++|+|......+. ... +..+......-+..++++|.+. +-.+++++.... .......+.+++.
T Consensus 72 ~l~~~~~-~ipvV~~~~~~~~--~~~---~~~V~~D~~~~g~~a~~~l~~~~~~g~~~~~~~~~~~~~~~~~R~~gf~~~ 145 (271)
T cd06314 72 ALNKAAA-GIKLITTDSDAPD--SGR---YVYIGTDNYAAGRTAGEIMKKALPGGGKVAIFVGSLGADNAKERIQGIKDA 145 (271)
T ss_pred HHHHHhc-CCCEEEecCCCCc--cce---eEEEccChHHHHHHHHHHHHHHcCCCCEEEEEecCCCCCCHHHHHHHHHHH
Confidence 3333445 9999987542211 111 1224455566677788887654 345666666432 2345667889999
Q ss_pred HhccCcEEEEeeccCCCCChhHHHHHHHHhhcC--CceEEEEeccCCcHHHHHHHHHHcCCC
Q 003958 188 LAAKRCRISFKAPLSVEATEDEITDLLVKVALT--ESRIIVVHTHYNRGPVVFHVAQYLGML 247 (784)
Q Consensus 188 l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~--~~~vIvl~~~~~~~~~~~~~a~~~g~~ 247 (784)
+++.|+++.... .. .....+....++++.+. .+++|+. .....+..+++++++.|+.
T Consensus 146 ~~~~~~~~~~~~-~~-~~~~~~~~~~~~~~l~~~~~~~~i~~-~~d~~a~~~~~al~~~g~~ 204 (271)
T cd06314 146 IKDSKIEIVDTR-GD-EEDFAKAKSNAEDALNAHPDLKCMFG-LYAYNGPAIAEAVKAAGKL 204 (271)
T ss_pred HhcCCcEEEEEe-cC-ccCHHHHHHHHHHHHHhCCCccEEEe-cCCccHHHHHHHHHHcCCC
Confidence 999888765321 11 11223334455555333 3455543 3445566688888888875
No 184
>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=97.15 E-value=0.033 Score=56.58 Aligned_cols=198 Identities=13% Similarity=0.008 Sum_probs=116.1
Q ss_pred EEEEEeecC-CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEccCchhhHHH
Q 003958 33 NIGALLSFS-TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIGPQDAVTSHV 111 (784)
Q Consensus 33 ~IG~i~~~~-~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiGp~~s~~~~~ 111 (784)
.||++.|.. ..+-.....+++.+.++. |+++.+ .++..++....+....+..+++.+||=..+......
T Consensus 1 ~i~~i~~~~~~~~~~~i~~gi~~~~~~~--------g~~~~~--~~~~~~~~~~~~~i~~l~~~~vdgiii~~~~~~~~~ 70 (260)
T cd06286 1 TIGVVLPYINHPYFSQLVDGIEKAALKH--------GYKVVL--LQTNYDKEKELEYLELLKTKQVDGLILCSRENDWEV 70 (260)
T ss_pred CEEEEeCCCCCchHHHHHHHHHHHHHHc--------CCEEEE--EeCCCChHHHHHHHHHHHHcCCCEEEEeCCCCCHHH
Confidence 378888863 333345556666666642 565544 345556665555666677778887764322222233
Q ss_pred HHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcC--CCcchhHHHHHHHHh
Q 003958 112 VSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDD--DHGRNGIAALGDTLA 189 (784)
Q Consensus 112 va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~--~~g~~~~~~l~~~l~ 189 (784)
+..+.+ .+ |+|....... ...+ ...++....+..+++.|...|-+++++|..+. .......+.+++.++
T Consensus 71 ~~~~~~-~~-pvv~~~~~~~----~~~~---~v~~d~~~~~~~~~~~l~~~g~~~i~~i~~~~~~~~~~~R~~Gf~~~l~ 141 (260)
T cd06286 71 IEPYTK-YG-PIVLCEEYDS----KNIS---SVYIDHYEAFYEALKYLIQKGYRKIAYCIGRKKSLNSQSRKKAYKDALE 141 (260)
T ss_pred HHHHhc-CC-CEEEEecccC----CCCC---EEEECChHHHHHHHHHHHHCCCceEEEEcCCcccchhHHHHHHHHHHHH
Confidence 333333 34 8887643211 1223 34556667778888888888999999997542 344556788999998
Q ss_pred ccCcEEEEeeccCCCCChhHHHHHHHHhhc--CCceEEEEeccCCcHHHHHHHHHHcCCCCCC
Q 003958 190 AKRCRISFKAPLSVEATEDEITDLLVKVAL--TESRIIVVHTHYNRGPVVFHVAQYLGMLGTG 250 (784)
Q Consensus 190 ~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~--~~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~ 250 (784)
+.|+.+.....+....+..+-...++++.+ ..+++|+ +++...+..+++.++++|+..++
T Consensus 142 ~~~~~~~~~~i~~~~~~~~~~~~~~~~~l~~~~~~~ai~-~~~d~~a~~~~~~l~~~g~~ip~ 203 (260)
T cd06286 142 EYGLTPDEEWIFEGCFTIEDGERIGHQLLKMKDRPDAIF-TGSDEVAAGIITEAKKQGIRVPE 203 (260)
T ss_pred HcCCCCChHheEeCCCCHHHHHHHHHHHHcCCCCCCEEE-EcchHHHHHHHHHHHHcCCCCCc
Confidence 888654321111111122233345555543 3456544 45556677899999999986544
No 185
>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=97.13 E-value=0.065 Score=54.69 Aligned_cols=195 Identities=12% Similarity=0.003 Sum_probs=104.4
Q ss_pred EEEEEeecC----CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEccCchhh
Q 003958 33 NIGALLSFS----TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIGPQDAVT 108 (784)
Q Consensus 33 ~IG~i~~~~----~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiGp~~s~~ 108 (784)
+||++.|.. ..+-.....+++.+.++ .|+++.+. ++. ++..-.+....+.++++.+||--... .
T Consensus 1 ~I~~i~~~~~~~~~~f~~~~~~gi~~~~~~--------~gy~~~i~--~~~-~~~~~~~~i~~l~~~~vdgiI~~~~~-~ 68 (265)
T cd06354 1 KVALVTDVGGLGDKSFNQSAWEGLERAAKE--------LGIEYKYV--ESK-SDADYEPNLEQLADAGYDLIVGVGFL-L 68 (265)
T ss_pred CEEEEeCCCCcCchhHHHHHHHHHHHHHHH--------cCCeEEEE--ecC-CHHHHHHHHHHHHhCCCCEEEEcCcc-h
Confidence 588888852 12222334455555554 25555554 332 33333445556777788888853222 1
Q ss_pred HHHHHHhhhcC-CccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHH-cCCcEEEEEEEcCCCcc-hhHHHHH
Q 003958 109 SHVVSHVANEL-QVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDH-YGWREVIAIYVDDDHGR-NGIAALG 185 (784)
Q Consensus 109 ~~~va~~~~~~-~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~-~~w~~v~ii~~d~~~g~-~~~~~l~ 185 (784)
..........+ ++|+|..+...+.. +.+-+.......-+..+++++.. .|-+++++|..+..... ...+.++
T Consensus 69 ~~~~~~~~~~~~~~PiV~i~~~~~~~-----~~~~~v~~d~~~a~~~a~~ll~~~~G~~~I~~i~~~~~~~~~~r~~gf~ 143 (265)
T cd06354 69 ADALKEVAKQYPDQKFAIIDAVVDDP-----PNVASIVFKEEEGSFLAGYLAALMTKTGKVGFIGGMDIPLIRRFEAGFE 143 (265)
T ss_pred HHHHHHHHHHCCCCEEEEEecccCCC-----CcEEEEEecchhHHHHHHHHHHhhcCCCeEEEEecccChHHHHHHHHHH
Confidence 23344555555 89999875422110 11222333444444444566654 39999999975432122 2236788
Q ss_pred HHHhccC---cEEEEeeccCCCCC-hhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHcC
Q 003958 186 DTLAAKR---CRISFKAPLSVEAT-EDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLG 245 (784)
Q Consensus 186 ~~l~~~g---i~v~~~~~~~~~~~-~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~g 245 (784)
+.+++.| ..+..........+ ..+-...++++.+.++++|+. .....+..+++++++.|
T Consensus 144 ~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~pdaI~~-~nd~~A~gv~~al~~~g 206 (265)
T cd06354 144 AGVKYVNPGVPDIEVLVQYAGSFNDPAKGKEIAQAMYDQGADVIFA-AAGGTGNGVFQAAKEAG 206 (265)
T ss_pred HHHHHHhccCCCceEEEEEcCcccCHHHHHHHHHHHHHCCCcEEEE-CCCCCchHHHHHHHhcC
Confidence 8888877 54332211111111 223334555654445776444 45667778999999987
No 186
>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=97.13 E-value=0.038 Score=57.34 Aligned_cols=184 Identities=11% Similarity=0.138 Sum_probs=107.9
Q ss_pred EEEEEeecCCcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEccCchhhHHHH
Q 003958 33 NIGALLSFSTNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIGPQDAVTSHVV 112 (784)
Q Consensus 33 ~IG~i~~~~~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiGp~~s~~~~~v 112 (784)
+||++...+...-.....|++-++++. + ... ..+++...+...|+..+...+.++..+++.+|+--. +..+..+
T Consensus 1 ~v~i~~~~~~~~~~~~~~gf~~~L~~~---g-~~~-~~~~~~~~~a~~d~~~~~~~~~~l~~~~~DlIi~~g-t~aa~~~ 74 (294)
T PF04392_consen 1 KVGILQFISHPALDDIVRGFKDGLKEL---G-YDE-KNVEIEYKNAEGDPEKLRQIARKLKAQKPDLIIAIG-TPAAQAL 74 (294)
T ss_dssp EEEEEESS--HHHHHHHHHHHHHHHHT---T---C-CCEEEEEEE-TT-HHHHHHHHHHHCCTS-SEEEEES-HHHHHHH
T ss_pred CeEEEEEeccHHHHHHHHHHHHHHHHc---C-Ccc-ccEEEEEecCCCCHHHHHHHHHHHhcCCCCEEEEeC-cHHHHHH
Confidence 578887776433345667777777664 2 222 467888889999999988888888777888877533 3444555
Q ss_pred HHhhhcCCccEEecccCCCCCCc----CCCC--ceEeecCChHHHHHHHHHHHHHc--CCcEEEEEEEcCCC-cchhHHH
Q 003958 113 SHVANELQVPLLSFSATDPTLSS----LQFP--YFVRTTQSDQYQMAAIAEIVDHY--GWREVIAIYVDDDH-GRNGIAA 183 (784)
Q Consensus 113 a~~~~~~~ip~Is~~a~~~~l~~----~~~p--~~~r~~ps~~~~~~ai~~~l~~~--~w~~v~ii~~d~~~-g~~~~~~ 183 (784)
....... +|+|-.+.++|.-.+ ...| ++.-+. +.......+++++++ +-++++++|++++- +....+.
T Consensus 75 ~~~~~~~-iPVVf~~V~dp~~~~l~~~~~~~~~nvTGv~--~~~~~~~~l~l~~~l~P~~k~igvl~~~~~~~~~~~~~~ 151 (294)
T PF04392_consen 75 AKHLKDD-IPVVFCGVSDPVGAGLVDSLDRPGKNVTGVS--ERPPIEKQLELIKKLFPDAKRIGVLYDPSEPNSVAQIEQ 151 (294)
T ss_dssp HHH-SS--S-EEEECES-TTTTTS-S-SSS--SSEEEEE--E---HHHHHHHHHHHSTT--EEEEEEETT-HHHHHHHHH
T ss_pred HHhcCCC-cEEEEEeccChhhhhccccccCCCCCEEEEE--CCcCHHHHHHHHHHhCCCCCEEEEEecCCCccHHHHHHH
Confidence 5444433 999977765654322 2233 444333 444455666777665 46999999976643 4456788
Q ss_pred HHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEecc
Q 003958 184 LGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTH 230 (784)
Q Consensus 184 l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~ 230 (784)
+++.+++.|+++... .++ +..++...+..+.+ +.+++++..+
T Consensus 152 ~~~~a~~~g~~l~~~-~v~---~~~~~~~~~~~l~~-~~da~~~~~~ 193 (294)
T PF04392_consen 152 LRKAAKKLGIELVEI-PVP---SSEDLEQALEALAE-KVDALYLLPD 193 (294)
T ss_dssp HHHHHHHTT-EEEEE-EES---SGGGHHHHHHHHCT-T-SEEEE-S-
T ss_pred HHHHHHHcCCEEEEE-ecC---cHhHHHHHHHHhhc-cCCEEEEECC
Confidence 888888899987643 233 45678888888754 5677777543
No 187
>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=97.12 E-value=0.058 Score=54.97 Aligned_cols=194 Identities=13% Similarity=0.087 Sum_probs=109.9
Q ss_pred EEEEeecC-CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEccCchhhHHHH
Q 003958 34 IGALLSFS-TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIGPQDAVTSHVV 112 (784)
Q Consensus 34 IG~i~~~~-~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiGp~~s~~~~~v 112 (784)
||++.|.. ..+-.....+++-+.++ . |+++. +.++..++..-.+....+..+++.+||--......
T Consensus 2 I~vi~~~~~~~~~~~~~~gi~~~~~~----~----g~~~~--~~~~~~~~~~~~~~i~~~~~~~~dgiii~~~~~~~--- 68 (265)
T cd06291 2 IGLIVPTISNPFFSELARAVEKELYK----K----GYKLI--LCNSDNDPEKEREYLEMLRQNQVDGIIAGTHNLGI--- 68 (265)
T ss_pred EEEEECCCCChhHHHHHHHHHHHHHH----C----CCeEE--EecCCccHHHHHHHHHHHHHcCCCEEEEecCCcCH---
Confidence 78888743 22223344455444444 1 45554 34444555554555556666778777642222221
Q ss_pred HHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcC---CCcchhHHHHHHHHh
Q 003958 113 SHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDD---DHGRNGIAALGDTLA 189 (784)
Q Consensus 113 a~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~---~~g~~~~~~l~~~l~ 189 (784)
..+...++|+|......+ ..+++ ..++....+..+++.|...|.++++++.... .......+.+++.++
T Consensus 69 -~~~~~~gipvv~~~~~~~----~~~~~---V~~d~~~~g~~~~~~l~~~g~~~i~~i~~~~~~~~~~~~r~~gf~~~l~ 140 (265)
T cd06291 69 -EEYENIDLPIVSFDRYLS----ENIPI---VSSDNYEGGRLAAEELIERGCKHIAHIGGPNNTVSPTNLRYEGFLDVLK 140 (265)
T ss_pred -HHHhcCCCCEEEEeCCCC----CCCCe---EeechHHHHHHHHHHHHHcCCcEEEEEccCcccccchHHHHHHHHHHHH
Confidence 234567999998765432 12232 3455566677888888888999999997533 234566788999998
Q ss_pred ccCcEEEEeeccCCCCChhHHHHHHHHhhcC--CceEEEEeccCCcHHHHHHHHHHcCCCCCC
Q 003958 190 AKRCRISFKAPLSVEATEDEITDLLVKVALT--ESRIIVVHTHYNRGPVVFHVAQYLGMLGTG 250 (784)
Q Consensus 190 ~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~--~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~ 250 (784)
+.|+.+.... .....+..+....++++.+. .+++|+. .....+..+++++.+.|+..++
T Consensus 141 ~~~~~~~~~~-~~~~~~~~~~~~~~~~~l~~~~~~~ai~~-~~d~~a~~~~~al~~~g~~vp~ 201 (265)
T cd06291 141 ENGLEVRIIE-IQENFDDAEKKEEIKELLEEYPDIDGIFA-SNDLTAILVLKEAQQRGIRVPE 201 (265)
T ss_pred HcCCCCChhe-eeccccchHHHHHHHHHHhCCCCCCEEEE-CChHHHHHHHHHHHHcCCCCCc
Confidence 8887543211 11111111123444444333 3455444 3445677889999998876444
No 188
>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=97.12 E-value=0.046 Score=55.58 Aligned_cols=198 Identities=10% Similarity=-0.010 Sum_probs=106.1
Q ss_pred EEEEEeecCCcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEccCchhhHHHH
Q 003958 33 NIGALLSFSTNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIGPQDAVTSHVV 112 (784)
Q Consensus 33 ~IG~i~~~~~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiGp~~s~~~~~v 112 (784)
|||+++|... ........+..++++.-++. |+.+.+ .++. ++....+....+...++.+||-.... ....+
T Consensus 1 ~Igvi~~~~~-~~~~f~~~l~~gi~~~~~~~----gy~~~~--~~~~-~~~~~~~~~~~l~~~~vdgiii~~~~-~~~~~ 71 (260)
T cd06304 1 KVALVYDGGG-GDKSFNQSAYEGLEKAEKEL----GVEVKY--VESV-EDADYEPNLRQLAAQGYDLIFGVGFG-FMDAV 71 (260)
T ss_pred CEEEEecCCC-CcchHHHHHHHHHHHHHHhc----CceEEE--EecC-CHHHHHHHHHHHHHcCCCEEEECCcc-hhHHH
Confidence 5899998511 11233334444444443332 555444 3444 55544455556666788877543322 12334
Q ss_pred HHhhhcC-CccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHc-CCcEEEEEEEcC-CCcchhHHHHHHHHh
Q 003958 113 SHVANEL-QVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHY-GWREVIAIYVDD-DHGRNGIAALGDTLA 189 (784)
Q Consensus 113 a~~~~~~-~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~-~w~~v~ii~~d~-~~g~~~~~~l~~~l~ 189 (784)
....... ++|++......+. +...+ .....+..-+..+++++... |-+++++|..+. .......+.+++.++
T Consensus 72 ~~~~~~~~~ipvv~~~~~~~~--~~~~~---~v~~d~~~~~~~a~~l~~~~~g~~~I~~i~~~~~~~~~~R~~Gf~~~~~ 146 (260)
T cd06304 72 EKVAKEYPDVKFAIIDGVVDA--PPNVA---SYVFREYEGSYLAGVLAALMTKTGKVGFVGGMPIPEVNRFINGFAAGAK 146 (260)
T ss_pred HHHHHHCCCCEEEEecCccCC--CCCee---eeecchHHHHHHHHHHHHHhccCCceEEEeccccHHHHHHHHHHHHHHH
Confidence 4445443 7898876543221 01112 22333344444455666655 899999997532 223445778888998
Q ss_pred ccCcEEEEeeccCCCC-ChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHcC
Q 003958 190 AKRCRISFKAPLSVEA-TEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLG 245 (784)
Q Consensus 190 ~~gi~v~~~~~~~~~~-~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~g 245 (784)
+.|..+.......... +..+-...++++.+.++++| ++.....+..++++++++|
T Consensus 147 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~ai-~~~~d~~A~gv~~al~~~g 202 (260)
T cd06304 147 SVNPDITVLVIYTGSFFDPAKGKEAALALIDQGADVI-FAAAGGTGPGVIQAAKEAG 202 (260)
T ss_pred HhCCCcEEEEEEecCccCcHHHHHHHHHHHhCCCCEE-EEcCCCCchHHHHHHHHcC
Confidence 8876433211111111 12233345566554557765 5566677778999999987
No 189
>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=97.11 E-value=0.066 Score=56.56 Aligned_cols=202 Identities=11% Similarity=0.046 Sum_probs=114.6
Q ss_pred ceEEEEEEeecC-CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEc-cCchh
Q 003958 30 SVVNIGALLSFS-TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIG-PQDAV 107 (784)
Q Consensus 30 ~~i~IG~i~~~~-~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiG-p~~s~ 107 (784)
..-.||+++|.. ..+-.....+++-+.++ .|+.+.+. ++..++..-.+....+..+++.+||- |....
T Consensus 59 ~~~~Igvi~~~~~~~~~~~~~~~i~~~~~~--------~gy~~~i~--~~~~~~~~~~~~~~~l~~~~vdgiIi~~~~~~ 128 (327)
T TIGR02417 59 RSRTIGLVIPDLENYSYARIAKELEQQCRE--------AGYQLLIA--CSDDNPDQEKVVIENLLARQVDALIVASCMPP 128 (327)
T ss_pred CCceEEEEeCCCCCccHHHHHHHHHHHHHH--------CCCEEEEE--eCCCCHHHHHHHHHHHHHcCCCEEEEeCCCCC
Confidence 356899999853 22222334444444433 25666544 33445554444555667778887763 33221
Q ss_pred hHHHHHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcCC--CcchhHHHHH
Q 003958 108 TSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDDD--HGRNGIAALG 185 (784)
Q Consensus 108 ~~~~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~~--~g~~~~~~l~ 185 (784)
.... ...+...++|+|......+ +..+++ +.+.+..-+..+++.|...|.++|+++..... ......+.++
T Consensus 129 ~~~~-~~~l~~~~iPvV~~~~~~~---~~~~~~---V~~dn~~~~~~~~~~L~~~G~~~I~~i~~~~~~~~~~~R~~Gf~ 201 (327)
T TIGR02417 129 EDAY-YQKLQNEGLPVVALDRSLD---DEHFCS---VISDDVDAAAELIERLLSQHADEFWYLGAQPELSVSRDRLAGFR 201 (327)
T ss_pred ChHH-HHHHHhcCCCEEEEccccC---CCCCCE---EEeCcHHHHHHHHHHHHHCCCCeEEEEeCcccchhHHHHHHHHH
Confidence 2222 3345567999998754322 112232 34455555667778888889999999985432 3455678899
Q ss_pred HHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcC---CceEEEEeccCCcHHHHHHHHHHcCCCCCCeE
Q 003958 186 DTLAAKRCRISFKAPLSVEATEDEITDLLVKVALT---ESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYV 252 (784)
Q Consensus 186 ~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~---~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~ 252 (784)
+.+++.|+..... +.......+-...+.++.+. .+++|+. .....+..+++++++.| ..|+-+
T Consensus 202 ~al~~~~~~~~~~--~~~~~~~~~~~~~~~~ll~~~~~~~~Ai~~-~~D~~A~g~~~al~~~g-~vP~dv 267 (327)
T TIGR02417 202 QALKQATLEVEWV--YGGNYSRESGYQMFAKLCARLGRLPQALFT-TSYTLLEGVLDYMLERP-LLDSQL 267 (327)
T ss_pred HHHHHcCCChHhE--EeCCCChHHHHHHHHHHHhcCCCCCcEEEE-cCcHHHHHHHHHHHHcC-CCCCcc
Confidence 9998888653211 11111222223445554332 3566554 44556778999999999 655433
No 190
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=97.06 E-value=0.066 Score=57.03 Aligned_cols=204 Identities=11% Similarity=0.079 Sum_probs=112.2
Q ss_pred ceEEEEEEeecC-CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEccCchhh
Q 003958 30 SVVNIGALLSFS-TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIGPQDAVT 108 (784)
Q Consensus 30 ~~i~IG~i~~~~-~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiGp~~s~~ 108 (784)
..-.||+++|.- ..+-.....+++.+.++ . |+.+ .+.++..++..-.+....++.+++.++|-......
T Consensus 58 ~~~~Igvi~~~~~~~f~~~~~~gi~~~~~~---~-----g~~~--~~~~~~~~~~~~~~~i~~l~~~~vdgiIi~~~~~~ 127 (343)
T PRK10727 58 STETVGLVVGDVSDPFFGAMVKAVEQVAYH---T-----GNFL--LIGNGYHNEQKERQAIEQLIRHRCAALVVHAKMIP 127 (343)
T ss_pred CCCeEEEEeCCCCcchHHHHHHHHHHHHHH---c-----CCEE--EEEeCCCCHHHHHHHHHHHHhcCCCEEEEecCCCC
Confidence 456799998742 22222334444444443 2 4444 34455556555455566677778887764222111
Q ss_pred HHHHHHhhhcCCcc-EEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcCC--CcchhHHHHH
Q 003958 109 SHVVSHVANELQVP-LLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDDD--HGRNGIAALG 185 (784)
Q Consensus 109 ~~~va~~~~~~~ip-~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~~--~g~~~~~~l~ 185 (784)
...+..+.+ ++| +|......+ +...++ ..+.+..-+..+++.|...|.++|++|..... ......+.++
T Consensus 128 ~~~~~~~~~--~~p~vV~i~~~~~---~~~~~~---V~~Dn~~~~~~a~~~L~~~G~~~I~~i~~~~~~~~~~~R~~Gf~ 199 (343)
T PRK10727 128 DAELASLMK--QIPGMVLINRILP---GFENRC---IALDDRYGAWLATRHLIQQGHTRIGYLCSNHSISDAEDRLQGYY 199 (343)
T ss_pred hHHHHHHHh--cCCCEEEEecCCC---CCCCCE---EEECcHHHHHHHHHHHHHCCCccEEEEeCCccccchHHHHHHHH
Confidence 122333333 677 676543221 111222 34455566677778888889999999975432 3456678899
Q ss_pred HHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcC--CceEEEEeccCCcHHHHHHHHHHcCCCCCCeE
Q 003958 186 DTLAAKRCRISFKAPLSVEATEDEITDLLVKVALT--ESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYV 252 (784)
Q Consensus 186 ~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~--~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~ 252 (784)
+.+++.|+.+..........+...-...++++.+. .+++|+ +.....+..++++++++|+..|+-+
T Consensus 200 ~al~~~gi~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~-~~nD~~A~g~~~al~~~G~~vP~di 267 (343)
T PRK10727 200 DALAESGIPANDRLVTFGEPDESGGEQAMTELLGRGRNFTAVA-CYNDSMAAGAMGVLNDNGIDVPGEI 267 (343)
T ss_pred HHHHHCCCCCChhhEEeCCCChhHHHHHHHHHHhCCCCCCEEE-EcCcHHHHHHHHHHHHcCCCCCcce
Confidence 99999887542211111111212222344444333 356544 4455667789999999998665443
No 191
>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=97.05 E-value=0.081 Score=53.82 Aligned_cols=200 Identities=11% Similarity=0.072 Sum_probs=114.9
Q ss_pred EEEEEeecCC-cchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEccCchhhHHH
Q 003958 33 NIGALLSFST-NVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIGPQDAVTSHV 111 (784)
Q Consensus 33 ~IG~i~~~~~-~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiGp~~s~~~~~ 111 (784)
.||+++|... .+-.....++..++++ .|+++.+ .++..++..-......+..+++.+||=....... .
T Consensus 1 ~Ig~i~p~~~~~~~~~~~~~i~~~~~~--------~g~~~~~--~~~~~~~~~~~~~i~~l~~~~~dgiii~~~~~~~-~ 69 (263)
T cd06280 1 TVGLIVADIRNPFFTAVSRAVEDAAYR--------AGLRVIL--CNTDEDPEKEAMYLELMEEERVTGVIFAPTRATL-R 69 (263)
T ss_pred CEEEEecccccccHHHHHHHHHHHHHH--------CCCEEEE--EeCCCCHHHHHHHHHHHHhCCCCEEEEeCCCCCc-h
Confidence 3788888652 2223455666666655 2566644 4444555544444555666677766542222111 1
Q ss_pred HHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcC-CCcchhHHHHHHHHhc
Q 003958 112 VSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDD-DHGRNGIAALGDTLAA 190 (784)
Q Consensus 112 va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~-~~g~~~~~~l~~~l~~ 190 (784)
... ....++|+|......+ +..++++ ..+...-+..+++.|.+.|-++++++..+. .......+.+++.+++
T Consensus 70 ~~~-~~~~~iPvV~~~~~~~---~~~~~~v---~~d~~~~g~~a~~~L~~~g~~~i~~~~~~~~~~~~~R~~gf~~~~~~ 142 (263)
T cd06280 70 RLA-ELRLSFPVVLIDRAGP---AGRVDAV---VLDNRAAARTLVEHLVAQGYRRIGGLFGNASTTGAERRAGYEDAMRR 142 (263)
T ss_pred HHH-HHhcCCCEEEECCCCC---CCCCCEE---EECcHHHHHHHHHHHHHCCCceEEEEeCCCCCCHHHHHHHHHHHHHH
Confidence 222 3456899998765432 2223432 345566677788888888999999997542 2334557888899988
Q ss_pred cCcEEEEeeccCCCCChhHHHHHHHHhhcC--CceEEEEeccCCcHHHHHHHHHHcCCCCCCeEEE
Q 003958 191 KRCRISFKAPLSVEATEDEITDLLVKVALT--ESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWI 254 (784)
Q Consensus 191 ~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~--~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~wi 254 (784)
.|+...... .. .+..+....+.++... .+++| ++.+...+..+++.+++.|+..++-+.+
T Consensus 143 ~~~~~~~~~-~~--~~~~~~~~~~~~~l~~~~~~~ai-~~~~d~~a~g~~~~l~~~g~~~p~di~i 204 (263)
T cd06280 143 HGLAPDARF-VA--PTAEAAEAALAAWLAAPERPEAL-VASNGLLLLGALRAVRAAGLRIPQDLAL 204 (263)
T ss_pred cCCCCChhh-cc--cCHHHHHHHHHHHhcCCCCCcEE-EECCcHHHHHHHHHHHHcCCCCCCcEEE
Confidence 886543211 11 1222223344444332 45554 4455666888999999999865544433
No 192
>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=97.05 E-value=0.06 Score=55.05 Aligned_cols=200 Identities=13% Similarity=0.020 Sum_probs=112.6
Q ss_pred EEEEeecC-CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHH-HHhcCceEEEccCchhhHHH
Q 003958 34 IGALLSFS-TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALH-LMEGQTVAIIGPQDAVTSHV 111 (784)
Q Consensus 34 IG~i~~~~-~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~-li~~~v~aiiGp~~s~~~~~ 111 (784)
||++.|.. ..+-.....++..+.++ .|+++.+...+ .+ ....+...+ +...++.+||=...... ..
T Consensus 2 Igvi~p~~~~~~~~~~~~~i~~~~~~--------~gy~~~~~~~~--~~-~~~~~~~~~~l~~~~vdgvi~~~~~~~-~~ 69 (269)
T cd06297 2 ISVLLPVVATEFYRRLLEGIEGALLE--------QRYDLALFPLL--SL-ARLKRYLESTTLAYLTDGLLLASYDLT-ER 69 (269)
T ss_pred EEEEeCCCcChhHHHHHHHHHHHHHH--------CCCEEEEEeCC--Cc-HHHHHHHHHHHHhcCCCEEEEecCccC-hH
Confidence 78888864 22223334455555444 25666665443 22 222233333 44557777754322222 23
Q ss_pred HHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcC--C------CcchhHHH
Q 003958 112 VSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDD--D------HGRNGIAA 183 (784)
Q Consensus 112 va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~--~------~g~~~~~~ 183 (784)
....+...++|+|......+ ..++ +.++...-+..+++.|... .++++++..+. . ......+.
T Consensus 70 ~~~~l~~~~iPvv~~~~~~~-----~~~~---v~~d~~~~g~~a~~~L~~~-~~~i~~i~~~~~~~~~~~~~~~~~R~~g 140 (269)
T cd06297 70 LAERRLPTERPVVLVDAENP-----RFDS---FYLDNRLGGRLAGAYLADF-PGRIGAITVEEEPDRAFRRTVFAERRAG 140 (269)
T ss_pred HHHHHhhcCCCEEEEccCCC-----CCCE---EEECcHHHHHHHHHHHHHh-CCceEEEeCccccccccccccHHHHHHH
Confidence 44556678999998755321 1232 3456667777788887666 89999987432 2 34566889
Q ss_pred HHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcC--CceEEEEeccCCcHHHHHHHHHHcCCCCCCeEEEe
Q 003958 184 LGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALT--ESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIA 255 (784)
Q Consensus 184 l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~--~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~wi~ 255 (784)
+++.+++.|+.+.....+....+..+....+.++.+. .+++|+. .....+..+++.+++.|...++.+-+.
T Consensus 141 f~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~-~~d~~a~g~~~~l~~~g~~vP~di~vv 213 (269)
T cd06297 141 FQQALKDAGRPFSPDLLAITDHSEEGGRLAMRHLLEKASPPLAVFA-SADQQALGALQEAVELGLTVGEDVRVV 213 (269)
T ss_pred HHHHHHHcCCCCChhhEEeCCCChhhHHHHHHHHHcCCCCCcEEEE-cCcHHHHHHHHHHHHcCCCCCCceEEE
Confidence 9999998887643211111111223334555565433 3455444 445567789999999998766544443
No 193
>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=97.04 E-value=0.048 Score=55.40 Aligned_cols=196 Identities=12% Similarity=0.071 Sum_probs=109.2
Q ss_pred EEEEEeecCC-cchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEccCchhhHHH
Q 003958 33 NIGALLSFST-NVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIGPQDAVTSHV 111 (784)
Q Consensus 33 ~IG~i~~~~~-~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiGp~~s~~~~~ 111 (784)
.||++.|... .+-.....+++-+.++ .|+.+.+...+ +... ....+..+++.+||-.........
T Consensus 1 ~igvv~~~~~~~~~~~~~~gi~~~~~~--------~g~~~~~~~~~---~~~~---~~~~l~~~~vdgii~~~~~~~~~~ 66 (261)
T cd06272 1 TIGLIWPSVSRVALTELVTGINQAISK--------NGYNMNVSITP---SLAE---AEDLFKENRFDGVIIFGESASDVE 66 (261)
T ss_pred CEEEEecCCCchhHHHHHHHHHHHHHH--------cCCEEEEEecc---cHHH---HHHHHHHcCcCEEEEeCCCCChHH
Confidence 3788888642 2222334444444443 25565555433 2222 233455667887763322222222
Q ss_pred HHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcCC--CcchhHHHHHHHHh
Q 003958 112 VSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDDD--HGRNGIAALGDTLA 189 (784)
Q Consensus 112 va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~~--~g~~~~~~l~~~l~ 189 (784)
...+...++|+|..+...+ ..+++ +...+...+..+++.+...|-++++++..... ......+.+++.++
T Consensus 67 -~~~~~~~~ipvV~~~~~~~----~~~~~---V~~d~~~~~~~~~~~l~~~g~~~i~~i~~~~~~~~~~~R~~gf~~~~~ 138 (261)
T cd06272 67 -YLYKIKLAIPVVSYGVDYD----LKYPI---VNVDNEKAMELAVLYLAEKGHKKIAYIGDLSLDRRQRKRFKGFLETCD 138 (261)
T ss_pred -HHHHHHcCCCEEEEcccCC----CCCCE---EEEChHHHHHHHHHHHHHcCchhEEEeecccccccHHHHHHHHHHHHH
Confidence 2445678899998754322 11232 44566677788888888889999999975433 33455678889998
Q ss_pred ccCcEEEEeeccCCCCChhHHHHHHHHhhcCC--ceEEEEeccCCcHHHHHHHHHHcCCCCCCe
Q 003958 190 AKRCRISFKAPLSVEATEDEITDLLVKVALTE--SRIIVVHTHYNRGPVVFHVAQYLGMLGTGY 251 (784)
Q Consensus 190 ~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~--~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~ 251 (784)
+.|+.+..........+..+....++++.+.. +++ |++++...+..+++.+++.|+..++-
T Consensus 139 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~a-i~~~~d~~a~~~~~~l~~~g~~vp~d 201 (261)
T cd06272 139 ENGISISDSHIDVDGLSAEGGDNAAKKLLKESDLPTA-IICGSYDIALGVLSALNKQGISIPED 201 (261)
T ss_pred HcCCCCCHHHeeeCCCCHHHHHHHHHHHHcCCCCCCE-EEECCcHHHHHHHHHHHHhCCCCCCc
Confidence 88853322111111112223334455544332 455 34455556778999999999865543
No 194
>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=97.00 E-value=0.25 Score=51.40 Aligned_cols=201 Identities=10% Similarity=-0.007 Sum_probs=112.7
Q ss_pred EEEEEeecC-CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEc-cCchhhHH
Q 003958 33 NIGALLSFS-TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIG-PQDAVTSH 110 (784)
Q Consensus 33 ~IG~i~~~~-~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiG-p~~s~~~~ 110 (784)
+||++.+.. ..+-.....+++-+.++ .|+++.+. .++..++....+....++.+++.+||- +..+....
T Consensus 1 ~I~vi~~~~~~~f~~~i~~gi~~~a~~--------~g~~v~~~-~~~~~d~~~~~~~i~~~~~~~~DgiIi~~~~~~~~~ 71 (298)
T cd06302 1 TIAFVPKVTGIPYFNRMEEGAKEAAKE--------LGVDAIYV-GPTTADAAGQVQIIEDLIAQGVDAIAVVPNDPDALE 71 (298)
T ss_pred CEEEEEcCCCChHHHHHHHHHHHHHHH--------hCCeEEEE-CCCCCCHHHHHHHHHHHHhcCCCEEEEecCCHHHHH
Confidence 478888743 22223444555555555 14554432 234456666666666777778887764 33333223
Q ss_pred HHHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHc-CC-cEEEEEEEcCC--CcchhHHHHHH
Q 003958 111 VVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHY-GW-REVIAIYVDDD--HGRNGIAALGD 186 (784)
Q Consensus 111 ~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~-~w-~~v~ii~~d~~--~g~~~~~~l~~ 186 (784)
.....+...++|+|......+. .+ ..+....+.....+..++++|.+. +- ++++++..+.. ......+.+++
T Consensus 72 ~~~~~~~~~~iPvV~v~~~~~~-~~---~~~~~v~~D~~~~g~~a~~~l~~~~~~~~~I~~l~g~~~~~~~~~R~~Gf~~ 147 (298)
T cd06302 72 PVLKKAREAGIKVVTHDSDVQP-DN---RDYDIEQADNKAIGETLMDSLAEQMGGKGEYAIFVGSLTATNQNAWIDAAKA 147 (298)
T ss_pred HHHHHHHHCCCeEEEEcCCCCC-Cc---ceeEEeccCHHHHHHHHHHHHHHHcCCCCEEEEEeCCCCCcchHHHHHHHHH
Confidence 4445567789999987543211 00 123334566677778888887665 44 69999975432 33455688999
Q ss_pred HHhccCc-EEEEeeccCCCCChhHHHHHHHHhhcC--CceEEEEeccCCcHHHHHHHHHHcCCC
Q 003958 187 TLAAKRC-RISFKAPLSVEATEDEITDLLVKVALT--ESRIIVVHTHYNRGPVVFHVAQYLGML 247 (784)
Q Consensus 187 ~l~~~gi-~v~~~~~~~~~~~~~d~~~~l~~l~~~--~~~vIvl~~~~~~~~~~~~~a~~~g~~ 247 (784)
.++++|. .+..........+..+-...++++.+. .+++|+. .....+..++++++++|+.
T Consensus 148 ~l~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~-~~D~~A~g~~~al~~~g~~ 210 (298)
T cd06302 148 YQKEKYYPMLELVDRQYGDDDADKSYQTAQELLKAYPDLKGIIG-PTSVGIPGAARAVEEAGLK 210 (298)
T ss_pred HHhhcCCCCeEEeCcccCCCCHHHHHHHHHHHHHhCCCceEEEE-CCCcchhHHHHHHHhcCCC
Confidence 9988862 122111111111222223344444322 3444333 4456788899999998875
No 195
>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=96.97 E-value=0.091 Score=53.60 Aligned_cols=196 Identities=14% Similarity=0.066 Sum_probs=108.1
Q ss_pred EEEEeecC----CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEccCchhhH
Q 003958 34 IGALLSFS----TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIGPQDAVTS 109 (784)
Q Consensus 34 IG~i~~~~----~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiGp~~s~~~ 109 (784)
||++.|.. ..+-.....+++-+.++ .|+++.+...|. +...-......+.+.++.+||-......
T Consensus 2 vgv~~~~~~~~~~~~~~~~~~~i~~~~~~--------~g~~~~~~~~~~--~~~~~~~~~~~l~~~~vdgiii~~~~~~- 70 (268)
T cd06277 2 IGLIASKRILNSPAFYSEIYRAIEEEAKK--------YGYNLILKFVSD--EDEEEFELPSFLEDGKVDGIILLGGIST- 70 (268)
T ss_pred eEEEEeccccccCCcHHHHHHHHHHHHHH--------cCCEEEEEeCCC--ChHHHHHHHHHHHHCCCCEEEEeCCCCh-
Confidence 78888862 22222334444444443 156676665543 2222222233455678888875333222
Q ss_pred HHHHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcCC--CcchhHHHHHHH
Q 003958 110 HVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDDD--HGRNGIAALGDT 187 (784)
Q Consensus 110 ~~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~~--~g~~~~~~l~~~ 187 (784)
.....+...++|+|......+ +...++ +..+....+..+++.+.+.|.++++++..+.. ......+.+.+.
T Consensus 71 -~~~~~l~~~~ipvV~~~~~~~---~~~~~~---V~~d~~~~~~~a~~~l~~~g~~~i~~i~~~~~~~~~~~R~~gf~~~ 143 (268)
T cd06277 71 -EYIKEIKELGIPFVLVDHYIP---NEKADC---VLTDNYSGAYAATEYLIEKGHRKIGFVGDPLYSPSFEERYEGYKKA 143 (268)
T ss_pred -HHHHHHhhcCCCEEEEccCCC---CCCCCE---EEecchHHHHHHHHHHHHCCCCcEEEECCCCCCcchHHHHHHHHHH
Confidence 224556678999998754322 112232 33455556666778887889999999976543 234567788999
Q ss_pred HhccCcEEEEeeccCC-CCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHcCCCCC
Q 003958 188 LAAKRCRISFKAPLSV-EATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGMLGT 249 (784)
Q Consensus 188 l~~~gi~v~~~~~~~~-~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~g~~~~ 249 (784)
+++.|+.+........ ......+...++.+. ..+++|+. .....+..+++++++.|+..+
T Consensus 144 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~-~~~~ai~~-~~d~~a~g~~~a~~~~g~~~p 204 (268)
T cd06277 144 LLDHGIPFNEDYDITEKEEDEEDIGKFIDELK-PLPTAFFC-SNDGVAFLLIKVLKEMGIRVP 204 (268)
T ss_pred HHHcCCCCCcceEEEcchhHHHHHHHHHhcCC-CCCCEEEE-CCcHHHHHHHHHHHHcCCCCC
Confidence 9888865432111110 011223333333322 23555443 445556778888888887644
No 196
>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=96.97 E-value=0.17 Score=52.60 Aligned_cols=194 Identities=11% Similarity=-0.000 Sum_probs=106.6
Q ss_pred EEEEEeecCC-cchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEc-cCchhh-H
Q 003958 33 NIGALLSFST-NVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIG-PQDAVT-S 109 (784)
Q Consensus 33 ~IG~i~~~~~-~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiG-p~~s~~-~ 109 (784)
+||++.|... .+-.....+++-+.++ .|+.+.+...+...+...-.+....++.+++.+||- +..... .
T Consensus 1 ~igvvvp~~~n~f~~~~~~gi~~~a~~--------~g~~v~~~~~~~~~~~~~~~~~i~~l~~~~vDgiIi~~~~~~~~~ 72 (295)
T TIGR02955 1 KLCALYPHLKDSYWLSINYGMVEQAKH--------LGVELKVLEAGGYPNLDKQLAQIEQCKSWGADAILLGTVSPEALN 72 (295)
T ss_pred CeeEEecCCCcHHHHHHHHHHHHHHHH--------hCCEEEEEcCCCCCCHHHHHHHHHHHHHcCCCEEEEecCChhhhh
Confidence 5888888532 1111223344433333 156665544333335555556667778888888764 322222 2
Q ss_pred HHHHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcCC------cEEEEEEEcC--CCcchhH
Q 003958 110 HVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGW------REVIAIYVDD--DHGRNGI 181 (784)
Q Consensus 110 ~~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~w------~~v~ii~~d~--~~g~~~~ 181 (784)
..+.. +. .++|+|....... +. ..+..+......-+..+++.|.+ +- .+|+++.... .......
T Consensus 73 ~~l~~-~~-~~iPvV~~~~~~~---~~--~~~~~V~~D~~~~g~~~~~~L~~-~~~~~~g~~~I~~i~g~~~~~~~~~R~ 144 (295)
T TIGR02955 73 HDLAQ-LT-KSIPVFALVNQID---SN--QVKGRVGVDWYQMGYQAGEYLAQ-RHPKGSGPTTLAWLPGPKNRGGTKPVT 144 (295)
T ss_pred HHHHH-Hh-cCCCEEEEecCCC---cc--ceeEEEeecHHHHHHHHHHHHHH-hcccCCCCeeEEEEeCCCcCCchhHHH
Confidence 23333 33 4899997633211 11 12233455556666777777665 33 4699998543 3345678
Q ss_pred HHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhc--CCceEEEEeccCCcHHHHHHHHHHcCC
Q 003958 182 AALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVAL--TESRIIVVHTHYNRGPVVFHVAQYLGM 246 (784)
Q Consensus 182 ~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~--~~~~vIvl~~~~~~~~~~~~~a~~~g~ 246 (784)
+.+++.+++.|+.+... .....+..+-...++++.+ ...++| ++....+..+++++++.|.
T Consensus 145 ~Gf~~al~~~g~~~~~~--~~~~~~~~~~~~~~~~~L~~~~~~d~i--~~~d~~a~g~l~al~~~g~ 207 (295)
T TIGR02955 145 QGFRAALEGSDVEISAI--LWADNDKELQRNLLQDLLKKHPDIDYL--VGSAVAAEAAISELRSLHM 207 (295)
T ss_pred HHHHHHHhcCCcEEEEE--ecCCCcHHHHHHHHHHHHHhCCCcCEE--EeccHHHHHHHHHHHhhCc
Confidence 89999999888876532 1111222333344555433 235654 4455557788888888775
No 197
>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=96.96 E-value=0.078 Score=54.29 Aligned_cols=204 Identities=13% Similarity=0.145 Sum_probs=117.4
Q ss_pred EEEEeecC-CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEc-cCchhh---
Q 003958 34 IGALLSFS-TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIG-PQDAVT--- 108 (784)
Q Consensus 34 IG~i~~~~-~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiG-p~~s~~--- 108 (784)
||++.|.. ..+-.....+++-+.++ . |+++ .+.++..++....+....++.+++.++|= +..+..
T Consensus 2 igvv~~~~~~~~~~~~~~gi~~~~~~----~----g~~~--~~~~~~~~~~~~~~~i~~l~~~~vdgii~~~~~~~~~~~ 71 (273)
T cd01541 2 IGVITTYISDYIFPSIIRGIESVLSE----K----GYSL--LLASTNNDPERERKCLENMLSQGIDGLIIEPTKSALPNP 71 (273)
T ss_pred eEEEeCCccchhHHHHHHHHHHHHHH----c----CCEE--EEEeCCCCHHHHHHHHHHHHHcCCCEEEEeccccccccc
Confidence 78888753 22222333444433333 2 4555 44566667777777777888888888863 322211
Q ss_pred HHHHHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcC-CCcchhHHHHHHH
Q 003958 109 SHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDD-DHGRNGIAALGDT 187 (784)
Q Consensus 109 ~~~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~-~~g~~~~~~l~~~ 187 (784)
.......+...++|+|..+...+. . .+..+..++..-+..+++.|...|.++++++...+ ..+....+.+++.
T Consensus 72 ~~~~~~~~~~~~ipvV~~~~~~~~---~---~~~~V~~D~~~~g~~~~~~l~~~G~~~i~~l~~~~~~~~~~r~~g~~~~ 145 (273)
T cd01541 72 NIDLYLKLEKLGIPYVFINASYEE---L---NFPSLVLDDEKGGYKATEYLIELGHRKIAGIFKADDLQGVKRMKGFIKA 145 (273)
T ss_pred cHHHHHHHHHCCCCEEEEecCCCC---C---CCCEEEECcHHHHHHHHHHHHHcCCcCEEEecCCCcccHHHHHHHHHHH
Confidence 112234456779999987643211 1 12335566667778888988888999999887432 2344556788888
Q ss_pred HhccCcEEEEee--ccCCCCChhHHHHHHHHhhcC--CceEEEEeccCCcHHHHHHHHHHcCCCCCCeEEE
Q 003958 188 LAAKRCRISFKA--PLSVEATEDEITDLLVKVALT--ESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWI 254 (784)
Q Consensus 188 l~~~gi~v~~~~--~~~~~~~~~d~~~~l~~l~~~--~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~wi 254 (784)
+++.|..+.... ..............++++.+. .+++| ++.+...+..+++++++.|+..++-+-|
T Consensus 146 l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~av-~~~~d~~a~g~~~al~~~g~~~p~dv~v 215 (273)
T cd01541 146 YREHGIPFNPSNVITYTTEEKEEKLFEKIKEILKRPERPTAI-VCYNDEIALRVIDLLKELGLKIPEDISV 215 (273)
T ss_pred HHHcCCCCChHHEEeccccchhhHHHHHHHHHHcCCCCCCEE-EEcCcHHHHHHHHHHHHcCCCCCCcEEE
Confidence 888876422111 111111112233445554332 35654 4455566778999999999865544333
No 198
>PRK09526 lacI lac repressor; Reviewed
Probab=96.89 E-value=0.18 Score=53.62 Aligned_cols=202 Identities=13% Similarity=0.065 Sum_probs=113.2
Q ss_pred ceEEEEEEeecCC-cchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEc--cCch
Q 003958 30 SVVNIGALLSFST-NVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIG--PQDA 106 (784)
Q Consensus 30 ~~i~IG~i~~~~~-~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiG--p~~s 106 (784)
..-.||+++|... ..-.....+++-+.++ .|+.+.+...+. .+...-.+....+..+++.+||- +..+
T Consensus 62 ~~~~Igvv~~~~~~~~~~~~~~gi~~~a~~--------~g~~~~i~~~~~-~~~~~~~~~l~~l~~~~vdGiii~~~~~~ 132 (342)
T PRK09526 62 QSLTIGLATTSLALHAPSQIAAAIKSRADQ--------LGYSVVISMVER-SGVEACQAAVNELLAQRVSGVIINVPLED 132 (342)
T ss_pred CCceEEEEeCCCCcccHHHHHHHHHHHHHH--------CCCEEEEEeCCC-ChHHHHHHHHHHHHhcCCCEEEEecCCCc
Confidence 3457999988532 2222344455544443 256666543332 22333334555677778888764 3333
Q ss_pred hhHHHHHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcC--CCcchhHHHH
Q 003958 107 VTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDD--DHGRNGIAAL 184 (784)
Q Consensus 107 ~~~~~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~--~~g~~~~~~l 184 (784)
.....+. ....++|+|..... + +... ..+..+...-+..++++|...|.++|+++.... .......+.+
T Consensus 133 ~~~~~~~--~~~~~iPvV~~d~~-~---~~~~---~~V~~d~~~~~~~a~~~L~~~G~~~I~~l~g~~~~~~~~~R~~Gf 203 (342)
T PRK09526 133 ADAEKIV--ADCADVPCLFLDVS-P---QSPV---NSVSFDPEDGTRLGVEHLVELGHQRIALLAGPESSVSARLRLAGW 203 (342)
T ss_pred chHHHHH--hhcCCCCEEEEecc-C---CCCC---CEEEECcHHHHHHHHHHHHHCCCCeEEEEeCCCccccHHHHHHHH
Confidence 2222221 12358999987532 1 1112 234556666667788888888999999997543 2334567889
Q ss_pred HHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcC--CceEEEEeccCCcHHHHHHHHHHcCCCCCCeE
Q 003958 185 GDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALT--ESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYV 252 (784)
Q Consensus 185 ~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~--~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~ 252 (784)
++.+++.|+.+.....-. .+..+-...+.++.+. .+++|+ +.+...+..+++++++.|+..|+-+
T Consensus 204 ~~al~~~gi~~~~~~~~~--~~~~~~~~~~~~~l~~~~~~~ai~-~~~d~~A~g~~~al~~~g~~vP~di 270 (342)
T PRK09526 204 LEYLTDYQLQPIAVREGD--WSAMSGYQQTLQMLREGPVPSAIL-VANDQMALGVLRALHESGLRVPGQI 270 (342)
T ss_pred HHHHHHcCCCcceEEeCC--CchHHHHHHHHHHhcCCCCCcEEE-EcCcHHHHHHHHHHHHcCCCCCCce
Confidence 999998887543211111 1222222334444322 356544 4455667789999999998765444
No 199
>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=96.87 E-value=0.1 Score=53.80 Aligned_cols=194 Identities=13% Similarity=0.066 Sum_probs=110.1
Q ss_pred EEEEeecC------CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEccCchh
Q 003958 34 IGALLSFS------TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIGPQDAV 107 (784)
Q Consensus 34 IG~i~~~~------~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiGp~~s~ 107 (784)
||++.|.. ..+-.....+++-+.++ .|+++.+...+. .. +....+...++.++|-.....
T Consensus 2 igvi~p~~~~~~~~~~~~~~~~~gi~~~a~~--------~g~~~~~~~~~~---~~---~~~~~~~~~~~dgiii~~~~~ 67 (283)
T cd06279 2 VGVVLTDSLSYAFSDPVASQFLAGVAEVLDA--------AGVNLLLLPASS---ED---SDSALVVSALVDGFIVYGVPR 67 (283)
T ss_pred EEEEeCCcccccccCccHHHHHHHHHHHHHH--------CCCEEEEecCcc---HH---HHHHHHHhcCCCEEEEeCCCC
Confidence 78888862 22222334444444443 156665543322 11 233445566888887533322
Q ss_pred hHHHHHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcC-------------
Q 003958 108 TSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDD------------- 174 (784)
Q Consensus 108 ~~~~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~------------- 174 (784)
.. .....+...++|+|......+ +.+-.........+..++++|...|-++++++..+.
T Consensus 68 ~~-~~~~~~~~~~ipvV~~~~~~~-------~~~~~v~~d~~~~g~~~~~~L~~~g~~~i~~i~~~~~~~~~~~~~~~~~ 139 (283)
T cd06279 68 DD-PLVAALLRRGLPVVVVDQPLP-------PGVPSVGIDDRAAAREAARHLLDLGHRRIGILGLRLGRDRNTGRVTDER 139 (283)
T ss_pred Ch-HHHHHHHHcCCCEEEEecCCC-------CCCCEEeeCcHHHHHHHHHHHHHcCCCcEEEecCccccccccccccccc
Confidence 22 334456778999998754321 112234566677788888998889999999997532
Q ss_pred ------CCcchhHHHHHHHHhccCcEEEEeeccC-CCCChhHHHHHHHHhhcC--CceEEEEeccCCcHHHHHHHHHHcC
Q 003958 175 ------DHGRNGIAALGDTLAAKRCRISFKAPLS-VEATEDEITDLLVKVALT--ESRIIVVHTHYNRGPVVFHVAQYLG 245 (784)
Q Consensus 175 ------~~g~~~~~~l~~~l~~~gi~v~~~~~~~-~~~~~~d~~~~l~~l~~~--~~~vIvl~~~~~~~~~~~~~a~~~g 245 (784)
.......+.+++.+++.|++......+. ...+..+....++++.++ ..++|+ +++...+..+++++++.|
T Consensus 140 ~~~~~~~~~~~R~~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~-~~~d~~a~gv~~al~~~g 218 (283)
T cd06279 140 LASATFSVARERLEGYLEALEEAGIDISDVPIWEIPENDRASGEEAARELLDASPRPTAIL-CMSDVLALGALQVARELG 218 (283)
T ss_pred ccccccccHHHHHHHHHHHHHHcCCCCChheEEecCCCchHHHHHHHHHHHcCCCCCcEEE-ECCcHHHHHHHHHHHHcC
Confidence 1234557888888888875432111111 111223344555555433 345443 445556778999999999
Q ss_pred CCCCC
Q 003958 246 MLGTG 250 (784)
Q Consensus 246 ~~~~~ 250 (784)
+..++
T Consensus 219 ~~ip~ 223 (283)
T cd06279 219 LRVPE 223 (283)
T ss_pred CCCCC
Confidence 86543
No 200
>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=96.74 E-value=0.094 Score=53.44 Aligned_cols=200 Identities=14% Similarity=0.079 Sum_probs=111.9
Q ss_pred EEEEEeecCCcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEccCchhhHHHH
Q 003958 33 NIGALLSFSTNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIGPQDAVTSHVV 112 (784)
Q Consensus 33 ~IG~i~~~~~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiGp~~s~~~~~v 112 (784)
+||++.|.+..+-.....+++-+.++. + |+++-+. ++ +. .+....+..+++.++|-...+. ..
T Consensus 1 ~ig~i~~~~~~~~~~~~~gi~~~~~~~---~----g~~~~~~--~~--~~---~~~~~~l~~~~vdGiI~~~~~~---~~ 63 (265)
T cd01543 1 RVALLVETSSSYGRGVLRGIARYAREH---G----PWSIYLE--PR--GL---QEPLRWLKDWQGDGIIARIDDP---EM 63 (265)
T ss_pred CeEEEecccchhhHHHHHHHHHHHHhc---C----CeEEEEe--cc--cc---hhhhhhccccccceEEEECCCH---HH
Confidence 489999855333334445555554442 2 4554432 22 11 2333445556888887533222 22
Q ss_pred HHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcCC-CcchhHHHHHHHHhcc
Q 003958 113 SHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDDD-HGRNGIAALGDTLAAK 191 (784)
Q Consensus 113 a~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~~-~g~~~~~~l~~~l~~~ 191 (784)
...+...++|+|......+. +.+-++......-+..+++.+.+.|-++++++..... ......+.+++.+++.
T Consensus 64 ~~~l~~~~~PvV~~~~~~~~------~~~~~v~~d~~~~g~~~~~~l~~~g~~~i~~i~~~~~~~~~~R~~gf~~~~~~~ 137 (265)
T cd01543 64 AEALQKLGIPVVDVSGSREK------PGIPRVTTDNAAIGRMAAEHFLERGFRHFAFYGLPGARWSDEREEAFRQLVAEA 137 (265)
T ss_pred HHHHhhCCCCEEEEeCccCC------CCCCEEeeCHHHHHHHHHHHHHHCCCcEEEEEcCCCCHHHHHHHHHHHHHHHHc
Confidence 24455679999988653221 2233466677777888888888889999999875433 2234567889999988
Q ss_pred CcEEEEeecc--CCCCChhHHHHHHHHhhcC--CceEEEEeccCCcHHHHHHHHHHcCCCCC-CeEEEec
Q 003958 192 RCRISFKAPL--SVEATEDEITDLLVKVALT--ESRIIVVHTHYNRGPVVFHVAQYLGMLGT-GYVWIAT 256 (784)
Q Consensus 192 gi~v~~~~~~--~~~~~~~d~~~~l~~l~~~--~~~vIvl~~~~~~~~~~~~~a~~~g~~~~-~~~wi~~ 256 (784)
|+.+...... ....+..+-...++++.++ .+++ |++++...+..+++.+++.|+..+ +...++-
T Consensus 138 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~a-i~~~~d~~a~g~~~~l~~~g~~vp~di~vigf 206 (265)
T cd01543 138 GYECSFFYRGLSTDAQSWEEEQEELAQWLQSLPKPVG-IFACTDARARQLLEACRRAGIAVPEEVAVLGV 206 (265)
T ss_pred CCccccccCccccccccHHHHHHHHHHHHhcCCCCcE-EEecChHHHHHHHHHHHHhCCCCCCceEEEee
Confidence 8765211111 1001112223344444322 3554 444556677788999999887544 3344443
No 201
>PRK09492 treR trehalose repressor; Provisional
Probab=96.72 E-value=0.21 Score=52.34 Aligned_cols=192 Identities=14% Similarity=0.016 Sum_probs=111.4
Q ss_pred ceEEEEEEeecC-CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEccCchhh
Q 003958 30 SVVNIGALLSFS-TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIGPQDAVT 108 (784)
Q Consensus 30 ~~i~IG~i~~~~-~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiGp~~s~~ 108 (784)
..-.||++.|.. ..+-.....++. +++++. |+++ .+.++..++....+....+..+++.++|-...+..
T Consensus 61 ~~~~Ig~i~~~~~~~~~~~~~~~i~---~~~~~~-----gy~~--~~~~~~~~~~~~~~~~~~l~~~~vdgiIi~~~~~~ 130 (315)
T PRK09492 61 SDKVVGIIVSRLDSLSENQAVRTML---PAFYEQ-----GYDP--IIMESQFSPEKVNEHLGVLKRRNVDGVILFGFTGI 130 (315)
T ss_pred CCCeEEEEecCCcCcccHHHHHHHH---HHHHHc-----CCeE--EEEecCCChHHHHHHHHHHHhcCCCEEEEeCCCcc
Confidence 345799999853 222223333443 344433 4544 44556666665555556666778888875332211
Q ss_pred HHHHHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEc-C--CCcchhHHHHH
Q 003958 109 SHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVD-D--DHGRNGIAALG 185 (784)
Q Consensus 109 ~~~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d-~--~~g~~~~~~l~ 185 (784)
. .......++|+|...... +.+-.+.++...-+..+++.|...|.++|+++... . ..+....+.++
T Consensus 131 ~---~~~l~~~~~pvv~i~~~~--------~~~~~V~~D~~~~~~~a~~~L~~~G~~~I~~i~~~~~~~~~~~~R~~Gf~ 199 (315)
T PRK09492 131 T---EEMLAPWQDKLVLLARDA--------KGFSSVCYDDEGAIKLLMQRLYDQGHRHISYLGVDHSDVTTGKRRHQAYL 199 (315)
T ss_pred c---HHHHHhcCCCEEEEeccC--------CCCcEEEECcHHHHHHHHHHHHHcCCCeEEEEcCCcccchhHHHHHHHHH
Confidence 1 122334567887754321 11223445556666778888888899999999632 2 23456788999
Q ss_pred HHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHcCC
Q 003958 186 DTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGM 246 (784)
Q Consensus 186 ~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~g~ 246 (784)
+.+++.|+.+... ... .+..+-...++++.+.++++|+. .+...+..+++++++.|+
T Consensus 200 ~al~~~g~~~~~~--~~~-~~~~~~~~~~~~~l~~~~~ai~~-~~D~~A~g~~~al~~~g~ 256 (315)
T PRK09492 200 AFCKQHKLTPVAA--LGG-LSMQSGYELVAKVLTPETTALVC-ATDTLALGASKYLQEQGR 256 (315)
T ss_pred HHHHHcCCCceee--cCC-CCchHHHHHHHHHhhcCCCEEEE-cCcHHHHHHHHHHHHcCC
Confidence 9999999765321 111 11122223444544456777654 445667789999999886
No 202
>PRK11041 DNA-binding transcriptional regulator CytR; Provisional
Probab=96.66 E-value=0.25 Score=51.58 Aligned_cols=209 Identities=9% Similarity=0.020 Sum_probs=116.1
Q ss_pred CceEEEEEEeecC-CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEccCchh
Q 003958 29 PSVVNIGALLSFS-TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIGPQDAV 107 (784)
Q Consensus 29 ~~~i~IG~i~~~~-~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiGp~~s~ 107 (784)
...-.||++.|.. ..+-.....+++-+.++. |+.+.+ .+...+...-......+..+++.+||=-....
T Consensus 33 ~~~~~ig~v~~~~~~~~~~~~~~gi~~~~~~~--------g~~~~~--~~~~~~~~~~~~~i~~l~~~~vDgiIi~~~~~ 102 (309)
T PRK11041 33 NESRTILVIVPDICDPFFSEIIRGIEVTAAEH--------GYLVLI--GDCAHQNQQEKTFVNLIITKQIDGMLLLGSRL 102 (309)
T ss_pred CCCcEEEEEeCCCcCccHHHHHHHHHHHHHHC--------CCEEEE--EeCCCChHHHHHHHHHHHHcCCCEEEEecCCC
Confidence 3456899999853 333344556666666552 444443 34444555444555566677888776422211
Q ss_pred hHHHHHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcCC--CcchhHHHHH
Q 003958 108 TSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDDD--HGRNGIAALG 185 (784)
Q Consensus 108 ~~~~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~~--~g~~~~~~l~ 185 (784)
...... .......|++..+...+. ..+++ ........+..+++.|.+.|-+++++|..... ......+.|+
T Consensus 103 ~~~~~~-~~~~~~~pvv~~~~~~~~---~~~~~---V~~Dn~~~g~~a~~~l~~~G~~~I~~l~~~~~~~~~~~R~~Gf~ 175 (309)
T PRK11041 103 PFDASK-EEQRNLPPMVMANEFAPE---LELPT---VHIDNLTAAFEAVNYLHELGHKRIACIAGPEEMPLCHYRLQGYV 175 (309)
T ss_pred ChHHHH-HHHhcCCCEEEEccccCC---CCCCE---EEECcHHHHHHHHHHHHHcCCceEEEEeCCccccchHHHHHHHH
Confidence 111111 122223467664432221 11232 34456667777888888889999999975433 2345678899
Q ss_pred HHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcC--CceEEEEeccCCcHHHHHHHHHHcCCCCCCeEEEe
Q 003958 186 DTLAAKRCRISFKAPLSVEATEDEITDLLVKVALT--ESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIA 255 (784)
Q Consensus 186 ~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~--~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~wi~ 255 (784)
+.+++.|+.+..................+.++.+. .+++|+. +....+..+++++++.|+..++-+.|.
T Consensus 176 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~-~~d~~a~gv~~al~~~g~~ip~di~vv 246 (309)
T PRK11041 176 QALRRCGITVDPQYIARGDFTFEAGAKALKQLLDLPQPPTAVFC-HSDVMALGALSQAKRMGLRVPQDLSII 246 (309)
T ss_pred HHHHHcCCCCCHHHeEeCCCCHHHHHHHHHHHHcCCCCCCEEEE-cCcHHHHHHHHHHHHcCCCCCcceEEE
Confidence 99988887643211111111222334555555433 3666554 455566688999999887655444444
No 203
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=96.65 E-value=0.28 Score=52.33 Aligned_cols=205 Identities=8% Similarity=-0.013 Sum_probs=111.8
Q ss_pred ceEEEEEEeecC-CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEccCchhh
Q 003958 30 SVVNIGALLSFS-TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIGPQDAVT 108 (784)
Q Consensus 30 ~~i~IG~i~~~~-~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiGp~~s~~ 108 (784)
..-.||+++|.. ..+-.....++.-+.++. |+.+- +.++..++..-.+....+.++++.+||-......
T Consensus 58 ~~~~Igvi~~~~~~~f~~~l~~gi~~~~~~~--------gy~~~--~~~~~~~~~~~~~~i~~l~~~~vdGiIi~~~~~~ 127 (346)
T PRK10401 58 VSDTIGVVVMDVSDAFFGALVKAVDLVAQQH--------QKYVL--IGNSYHEAEKERHAIEVLIRQRCNALIVHSKALS 127 (346)
T ss_pred CCCEEEEEeCCCCCccHHHHHHHHHHHHHHC--------CCEEE--EEcCCCChHHHHHHHHHHHhcCCCEEEEeCCCCC
Confidence 355799999853 222223444555444441 44443 3444445554444555666777887664221111
Q ss_pred HHHHHHhhhcCCcc-EEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcC--CCcchhHHHHH
Q 003958 109 SHVVSHVANELQVP-LLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDD--DHGRNGIAALG 185 (784)
Q Consensus 109 ~~~va~~~~~~~ip-~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~--~~g~~~~~~l~ 185 (784)
...+..+.. ++| +|......+ +..+++ ....+..-+..++++|...|.+++++|.... .......+.++
T Consensus 128 ~~~~~~~~~--~~p~vV~i~~~~~---~~~~~~---V~~D~~~~~~~a~~~L~~~G~~~I~~i~~~~~~~~~~~R~~Gf~ 199 (346)
T PRK10401 128 DDELAQFMD--QIPGMVLINRVVP---GYAHRC---VCLDNVSGARMATRMLLNNGHQRIGYLSSSHGIEDDAMRRAGWM 199 (346)
T ss_pred hHHHHHHHh--cCCCEEEEecccC---CCCCCE---EEECcHHHHHHHHHHHHHCCCCeEEEEeCCCcCcchHHHHHHHH
Confidence 122333333 355 666543221 111222 3345555566777888888999999997543 33456788999
Q ss_pred HHHhccCcEEEEeeccCCCCChhHHHHHHHHhhc--CCceEEEEeccCCcHHHHHHHHHHcCCCCCCeEE
Q 003958 186 DTLAAKRCRISFKAPLSVEATEDEITDLLVKVAL--TESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVW 253 (784)
Q Consensus 186 ~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~--~~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~w 253 (784)
+.+++.|+.+..............-...++++.+ ..+++|+ +.....+..+++++++.|+..|+-+-
T Consensus 200 ~al~~~gi~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~-~~nd~~A~g~~~al~~~G~~vP~dis 268 (346)
T PRK10401 200 SALKEQGIIPPESWIGTGTPDMQGGEAAMVELLGRNLQLTAVF-AYNDNMAAGALTALKDNGIAIPLHLS 268 (346)
T ss_pred HHHHHcCCCCChhheecCCCChHHHHHHHHHHHcCCCCCcEEE-ECCcHHHHHHHHHHHHcCCCCCCceE
Confidence 9999988754321111111111222234444432 2456655 45556677899999999987664443
No 204
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=96.63 E-value=0.32 Score=51.41 Aligned_cols=206 Identities=10% Similarity=0.010 Sum_probs=115.6
Q ss_pred eEEEEEEeecC-CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEccCchhhH
Q 003958 31 VVNIGALLSFS-TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIGPQDAVTS 109 (784)
Q Consensus 31 ~i~IG~i~~~~-~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiGp~~s~~~ 109 (784)
.-.||++.|.. ..+-.....+++-+.++ .|+++.+ .++..++..-.+....++.+++.+||-......
T Consensus 63 ~~~Igvi~~~~~~~~~~~~~~gi~~~~~~--------~g~~~~~--~~~~~~~~~~~~~~~~~~~~~vdgiI~~~~~~~- 131 (331)
T PRK14987 63 SRAIGVLLPSLTNQVFAEVLRGIESVTDA--------HGYQTML--AHYGYKPEMEQERLESMLSWNIDGLILTERTHT- 131 (331)
T ss_pred CCEEEEEeCCCcchhHHHHHHHHHHHHHH--------CCCEEEE--ecCCCCHHHHHHHHHHHHhcCCCEEEEcCCCCC-
Confidence 45799998852 22222344455544443 2555544 344445554444555566778888774222212
Q ss_pred HHHHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcC-CCcchhHHHHHHHH
Q 003958 110 HVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDD-DHGRNGIAALGDTL 188 (784)
Q Consensus 110 ~~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~-~~g~~~~~~l~~~l 188 (784)
......+...++|+|....... + .... ........-+..+++.|...|.++|+++.... .......+.+++.+
T Consensus 132 ~~~~~~l~~~~iPvV~~~~~~~---~-~~~~--~V~~Dn~~~~~~a~~~L~~~Gh~~I~~i~~~~~~~~~~R~~Gf~~al 205 (331)
T PRK14987 132 PRTLKMIEVAGIPVVELMDSQS---P-CLDI--AVGFDNFEAARQMTTAIIARGHRHIAYLGARLDERTIIKQKGYEQAM 205 (331)
T ss_pred HHHHHHHHhCCCCEEEEecCCC---C-CCCc--eEEeCcHHHHHHHHHHHHHCCCceEEEEcCCCcccHHHHHHHHHHHH
Confidence 2233445678999997532111 1 1111 24556666677788888889999999997432 22334578889999
Q ss_pred hccCcEEEEeeccCCCCChhHHHHHHHHhhcC--CceEEEEeccCCcHHHHHHHHHHcCCCCCCeEEEe
Q 003958 189 AAKRCRISFKAPLSVEATEDEITDLLVKVALT--ESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYVWIA 255 (784)
Q Consensus 189 ~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~--~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~wi~ 255 (784)
++.|+.... ..+.......+-...++++.+. .+++|+ +++...+..+++++++.|+..|+-+-|.
T Consensus 206 ~~~g~~~~~-~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~-~~nD~~A~g~~~al~~~g~~vP~disvi 272 (331)
T PRK14987 206 LDAGLVPYS-VMVEQSSSYSSGIELIRQARREYPQLDGVF-CTNDDLAVGAAFECQRLGLKVPDDMAIA 272 (331)
T ss_pred HHcCCCccc-eeecCCCChhhHHHHHHHHHhcCCCCCEEE-ECCcHHHHHHHHHHHHcCCCCCCccEEE
Confidence 988863110 1111111111222344554333 356544 4555677789999999998766544433
No 205
>PRK11553 alkanesulfonate transporter substrate-binding subunit; Provisional
Probab=96.40 E-value=0.032 Score=58.59 Aligned_cols=71 Identities=23% Similarity=0.295 Sum_probs=48.9
Q ss_pred CCCCChHhhhhCCCceEEeeCchHHHHHHhh---cccCccCc-eeCCCHHHHHHHHhcCCcCCCeeEEEechhhhHHHHc
Q 003958 682 SPIKGIDSLRSSNYPIGYQVNSFARNYLVDE---LNIDESRL-VPLNSPEEYAKALKDGPHKGGVAAVVDDRAYAELFLS 757 (784)
Q Consensus 682 ~~i~~~~dl~~~~~~i~~~~~~~~~~~~~~~---~~~~~~~~-~~~~~~~~~~~~l~~~~~~~~~~a~~~~~~~~~~~~~ 757 (784)
.+|.+++||. +++|++..++..+.++.+. .+.+...+ ..+.+..+...+|.+ |++||++...++......
T Consensus 119 s~i~s~~dL~--Gk~I~~~~gs~~~~~l~~~l~~~g~~~~dv~~v~~~~~~~~~al~~----G~vDa~~~~ep~~~~~~~ 192 (314)
T PRK11553 119 SPIKTVADLK--GHKVAFQKGSSSHNLLLRALRKAGLKFTDIQPTYLTPADARAAFQQ----GNVDAWAIWDPYYSAALL 192 (314)
T ss_pred CCCCCHHHhC--CCEEeecCCCcHHHHHHHHHHHcCCCHHHeEEEecChHHHHHHHHc----CCCCEEEEcCcHHHHHHh
Confidence 3688999998 8889998887666665432 22222222 234567788999999 899999887777666554
Q ss_pred C
Q 003958 758 T 758 (784)
Q Consensus 758 ~ 758 (784)
+
T Consensus 193 ~ 193 (314)
T PRK11553 193 Q 193 (314)
T ss_pred c
Confidence 3
No 206
>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=96.37 E-value=0.91 Score=47.26 Aligned_cols=171 Identities=8% Similarity=0.005 Sum_probs=99.1
Q ss_pred CCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEc-cCchhhHHHHHHhhhcCCccEEecccCCCCCCcCCCCceEeecC
Q 003958 68 GTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIG-PQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQ 146 (784)
Q Consensus 68 g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiG-p~~s~~~~~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~p 146 (784)
|+++ .+.++..++..-.+....++.+++.+||= +............+...++|+|......+ + .+....+..
T Consensus 28 g~~v--~~~~~~~~~~~q~~~i~~l~~~~vDgIIi~~~~~~~~~~~l~~~~~~~iPvV~~d~~~~---~--~~~~~~V~~ 100 (302)
T TIGR02634 28 GAKV--FVQSANGNEAKQISQIENLIARGVDVLVIIPQNGQVLSNAVQEAKDEGIKVVAYDRLIN---D--ADIDFYLSF 100 (302)
T ss_pred CCEE--EEEeCCCCHHHHHHHHHHHHHcCCCEEEEeCCChhHHHHHHHHHHHCCCeEEEecCcCC---C--CCccEEEec
Confidence 4555 44566667776667777788888887754 33333334444556778999998754321 1 112234556
Q ss_pred ChHHHHHHHHHHHHHcCCc-EEEEEEEcCC--CcchhHHHHHHHHhcc----CcEEEEeeccCCCCChhHHHHHHHHhhc
Q 003958 147 SDQYQMAAIAEIVDHYGWR-EVIAIYVDDD--HGRNGIAALGDTLAAK----RCRISFKAPLSVEATEDEITDLLVKVAL 219 (784)
Q Consensus 147 s~~~~~~ai~~~l~~~~w~-~v~ii~~d~~--~g~~~~~~l~~~l~~~----gi~v~~~~~~~~~~~~~d~~~~l~~l~~ 219 (784)
+...-+..++++|.+.+-+ +++++..+.. ......+.+++.+++. ++.+.... +.......+....++++..
T Consensus 101 d~~~~g~~~~~~L~~~g~~~~i~~i~g~~~~~~~~~R~~g~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~ll~ 179 (302)
T TIGR02634 101 DNEKVGEMQARAVLEAAPKGNYFLMGGSPTDNNAKLLRGGQMKVLQPAIDSGDIKIVGDQ-WVDGWLPENALRIMENALT 179 (302)
T ss_pred CHHHHHHHHHHHHHhhCCCCCEEEEeCCCCCcchHHHHHHHHHHHhhhccCCCeEEecCc-CCCCCCHHHHHHHHHHHHH
Confidence 6677788888888776655 7888775322 2333456777777653 35443221 1111122333455555432
Q ss_pred ---CCceEEEEeccCCcHHHHHHHHHHcCCC
Q 003958 220 ---TESRIIVVHTHYNRGPVVFHVAQYLGML 247 (784)
Q Consensus 220 ---~~~~vIvl~~~~~~~~~~~~~a~~~g~~ 247 (784)
..+++|+. .....+..+++++++.|+.
T Consensus 180 ~~~~~~~aI~~-~~D~~A~g~~~al~~~g~~ 209 (302)
T TIGR02634 180 ANDNKVDAVVA-SNDATAGGAIQALTAQGLA 209 (302)
T ss_pred hCCCCccEEEE-CCCchHHHHHHHHHHCCCC
Confidence 23565444 4555677889999998863
No 207
>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=96.12 E-value=0.34 Score=49.44 Aligned_cols=195 Identities=11% Similarity=0.010 Sum_probs=105.6
Q ss_pred EEEEEeecCCc--chhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEc-cCchhhH
Q 003958 33 NIGALLSFSTN--VGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIG-PQDAVTS 109 (784)
Q Consensus 33 ~IG~i~~~~~~--~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiG-p~~s~~~ 109 (784)
+||++.+.+.. .+......+..++++..++. |+.+.+...+ .+. ....+++.++|- +..+.
T Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~gi~~~~~~~----g~~~~~~~~~--~~~--------~~~~~~vdgii~~~~~~~-- 64 (270)
T cd01544 1 RIAIVQWYSEEEELDDPYYLSIRLGIEKRAQEL----GIELTKFFRD--DDL--------LEILEDVDGIIAIGKFSQ-- 64 (270)
T ss_pred CeEEEEeccccccccCccHHHHHHHHHHHHHHc----CCEEEEEecc--chh--------HHhccCcCEEEEecCCCH--
Confidence 58899885421 22233333444444433332 5666554332 111 123456776652 22222
Q ss_pred HHHHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcCC-------CcchhHH
Q 003958 110 HVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDDD-------HGRNGIA 182 (784)
Q Consensus 110 ~~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~~-------~g~~~~~ 182 (784)
.....+...++|+|...... .+..++ .+...+...+..+++.+.+.|-++++++..... ......+
T Consensus 65 -~~~~~~~~~~~pvV~~~~~~---~~~~~~---~v~~D~~~a~~~~~~~l~~~g~~~i~~i~~~~~~~~~~~~~~~~R~~ 137 (270)
T cd01544 65 -EQLAKLAKLNPNLVFVDSNP---APDGFD---SVVPDFEQAVEKALDYLLELGHTRIGFIGGEEKTTDGHEYIEDPRET 137 (270)
T ss_pred -HHHHHHHhhCCCEEEECCCC---CCCCCC---EEEECHHHHHHHHHHHHHHcCCCcEEEECCCcccccccchhhhHHHH
Confidence 33344566789999875432 122233 245566677777888888889999999986542 3345578
Q ss_pred HHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhh-cC---CceEEEEeccCCcHHHHHHHHHHcCCCCCCeE
Q 003958 183 ALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVA-LT---ESRIIVVHTHYNRGPVVFHVAQYLGMLGTGYV 252 (784)
Q Consensus 183 ~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~-~~---~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~~~ 252 (784)
.+++.+++.|.. .....+....+..+....++++. +. .+++ |+++....+..+++.+++.|+..++-+
T Consensus 138 gf~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~a-i~~~~d~~a~g~~~~l~~~g~~vp~di 209 (270)
T cd01544 138 AFREYMKEKGLY-DPELIYIGDFTVESGYQLMKEALKSLGDNLPTA-FFIASDPMAIGALRALQEAGIKVPEDV 209 (270)
T ss_pred HHHHHHHHcCCC-ChheEeeCCCCHHHHHHHHHHHHhccCCCCCCE-EEEcCcHHHHHHHHHHHHcCCCCCCce
Confidence 888899888731 10011111112222233444433 22 2454 444556668889999999998655433
No 208
>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=96.03 E-value=1.1 Score=46.99 Aligned_cols=191 Identities=12% Similarity=0.009 Sum_probs=107.3
Q ss_pred ceEEEEEEeecC-CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEccCch-h
Q 003958 30 SVVNIGALLSFS-TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIGPQDA-V 107 (784)
Q Consensus 30 ~~i~IG~i~~~~-~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiGp~~s-~ 107 (784)
..-.||+++|.- ..+-.....++.-+.++ . |+.+- +.++..++..-.+....+...++.++|--... .
T Consensus 58 ~~~~Ig~i~~~~~~~~~~~~~~~i~~~~~~---~-----gy~~~--i~~~~~~~~~~~~~~~~l~~~~vdGvIi~~~~~~ 127 (311)
T TIGR02405 58 SDKVVAVIVSRLDSPSENLAVSGMLPVFYT---A-----GYDPI--IMESQFSPQLTNEHLSVLQKRNVDGVILFGFTGC 127 (311)
T ss_pred CCCEEEEEeCCcccccHHHHHHHHHHHHHH---C-----CCeEE--EecCCCChHHHHHHHHHHHhcCCCEEEEeCCCCC
Confidence 345799999752 21112223333333332 2 45543 33444555544444445556678877642211 1
Q ss_pred hHHHHHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEc-C--CCcchhHHHH
Q 003958 108 TSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVD-D--DHGRNGIAAL 184 (784)
Q Consensus 108 ~~~~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d-~--~~g~~~~~~l 184 (784)
... .....++|+|..+... ..++ ...+++..-+..+++.|...|.++|++|..+ . ..+....+.+
T Consensus 128 ~~~----~l~~~~~p~V~i~~~~-----~~~~---~V~~D~~~~~~~a~~~L~~~Ghr~I~~i~~~~~~~~~~~~R~~gf 195 (311)
T TIGR02405 128 DEE----ILESWNHKAVVIARDT-----GGFS---SVCYDDYGAIELLMANLYQQGHRHISFLGVDPSDKTTGLMRHNAY 195 (311)
T ss_pred CHH----HHHhcCCCEEEEecCC-----CCcc---EEEeCcHHHHHHHHHHHHHcCCCcEEEEccCcccchhHHHHHHHH
Confidence 111 2234678888765321 1122 3445666667778888888899999999732 2 2445678889
Q ss_pred HHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHcCC
Q 003958 185 GDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGM 246 (784)
Q Consensus 185 ~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~g~ 246 (784)
++.+++.|+..... .. .....+....++++.+.++++|+ +++...+..+++.+.+.|.
T Consensus 196 ~~a~~~~gi~~~~~--~~-~~~~~~~~~~~~~~l~~~~tAi~-~~~D~~A~g~~~~l~~~g~ 253 (311)
T TIGR02405 196 LAYCESANLEPIYQ--TG-QLSHESGYVLTDKVLKPETTALV-CATDTLALGAAKYLQELDR 253 (311)
T ss_pred HHHHHHcCCCceee--eC-CCCHHHHHHHHHHHHhcCCCEEE-ECCcHHHHHHHHHHHHcCC
Confidence 99999999752211 11 11222223344444334577654 5666678888999999885
No 209
>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=96.02 E-value=0.036 Score=57.81 Aligned_cols=71 Identities=15% Similarity=0.110 Sum_probs=48.3
Q ss_pred CCCCChHhhhhCCCceEEeeCchHHHHHHh---hcccCccCcee-CCCHHHHHHHHhcCCcCCCeeEEEechhhhHHHHc
Q 003958 682 SPIKGIDSLRSSNYPIGYQVNSFARNYLVD---ELNIDESRLVP-LNSPEEYAKALKDGPHKGGVAAVVDDRAYAELFLS 757 (784)
Q Consensus 682 ~~i~~~~dl~~~~~~i~~~~~~~~~~~~~~---~~~~~~~~~~~-~~~~~~~~~~l~~~~~~~~~~a~~~~~~~~~~~~~ 757 (784)
..|++++||+ |++||+..++..+.++.. ..+.+...+.. ...+.+...++.+ |+++|.+...+......+
T Consensus 90 s~I~s~~DLk--GK~Igv~~~s~~~~~l~~~L~~~Gl~~~dv~~v~~~~~~~~~al~~----G~vDa~~~~~p~~~~~~~ 163 (300)
T TIGR01729 90 SGIEKPEDLK--GKNVAVPFVSTTHYSLLAALKHWKTDPREVNILNLKPPQIVAAWQR----GDIDAAYVWPPALSELLK 163 (300)
T ss_pred CCCCChhHcC--CCEEEeCCCCcHHHHHHHHHHHcCCChhheEEEecCcHHHHHHHHc----CCcCEEEEecHHHHHHHh
Confidence 4799999999 999999877655544322 22332222211 2356788999999 899999888887766554
Q ss_pred C
Q 003958 758 T 758 (784)
Q Consensus 758 ~ 758 (784)
+
T Consensus 164 ~ 164 (300)
T TIGR01729 164 S 164 (300)
T ss_pred c
Confidence 4
No 210
>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=95.76 E-value=3 Score=43.29 Aligned_cols=163 Identities=6% Similarity=-0.029 Sum_probs=85.9
Q ss_pred cCCCCHHHHHHHHHHHHhcCceEEEc-cCchhhHHHHHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChH-HHHHH
Q 003958 77 DCNHSGFLALAEALHLMEGQTVAIIG-PQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQ-YQMAA 154 (784)
Q Consensus 77 D~~~~~~~a~~~~~~li~~~v~aiiG-p~~s~~~~~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~-~~~~a 154 (784)
++..++....+....++++++.+||- |..+.........+...+||+|......+. + +....+...+. ..++.
T Consensus 37 ~~~~d~~~q~~~i~~l~~~~vdgiIi~~~~~~~~~~~l~~~~~~giPvV~~~~~~~~--~---~~~~~v~~~Dn~~~g~~ 111 (302)
T TIGR02637 37 PTGTTAEGQIEVVNSLIAQKVDAIAISANDPDALVPALKKAMKRGIKVVTWDSGVAP--E---GRNLFLNQASADLIGRT 111 (302)
T ss_pred CCCCCHHHHHHHHHHHHHcCCCEEEEeCCChHHHHHHHHHHHHCCCEEEEeCCCCCC--C---ceeEEEecCCHHHHHHH
Confidence 34456777677777788888887654 333333334445567789999987543211 1 11233333333 33444
Q ss_pred HHHHH-HHc-CCcEEEEEEEcCCC--cchhHHHHHHHHhccC---cEEEEeeccCCCCChhHHHHHHHHhhcCC--ceEE
Q 003958 155 IAEIV-DHY-GWREVIAIYVDDDH--GRNGIAALGDTLAAKR---CRISFKAPLSVEATEDEITDLLVKVALTE--SRII 225 (784)
Q Consensus 155 i~~~l-~~~-~w~~v~ii~~d~~~--g~~~~~~l~~~l~~~g---i~v~~~~~~~~~~~~~d~~~~l~~l~~~~--~~vI 225 (784)
.++.+ +++ +-.+|++|..+... .....+.+++.++++| +++... ........+-...++++.+.+ .++|
T Consensus 112 aa~~l~~~l~~~~~I~~i~g~~~~~~~~~r~~g~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~L~~~~~~~ai 189 (302)
T TIGR02637 112 QVQLAAEQIGNGGEIAILSAASTATNQNAWIEIMKKELKDPKYPKVKLVAT--VYGDDDAQKSYQEAQGLLKSYPNLKGI 189 (302)
T ss_pred HHHHHHHHcCCCcEEEEEECCCCCccHHHHHHHHHHHHhhccCCCCEEEee--ecCCchHHHHHHHHHHHHHhCCCccEE
Confidence 45544 332 23689999854322 2234577777776543 343221 111112233334455544333 4444
Q ss_pred EEeccCCcHHHHHHHHHHcCCC
Q 003958 226 VVHTHYNRGPVVFHVAQYLGML 247 (784)
Q Consensus 226 vl~~~~~~~~~~~~~a~~~g~~ 247 (784)
+. .....+..+++++++.|..
T Consensus 190 ~~-~~d~~a~ga~~al~~~g~~ 210 (302)
T TIGR02637 190 IA-PTTVGIKAAAQAVSDAKLI 210 (302)
T ss_pred Ee-CCCchHHHHHHHHHhcCCC
Confidence 43 3455667788888888764
No 211
>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=95.30 E-value=3.4 Score=42.33 Aligned_cols=203 Identities=11% Similarity=-0.005 Sum_probs=103.1
Q ss_pred EEEEEeecC-CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEccCch-hhHH
Q 003958 33 NIGALLSFS-TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIGPQDA-VTSH 110 (784)
Q Consensus 33 ~IG~i~~~~-~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiGp~~s-~~~~ 110 (784)
+||++.|.. ..+-.....++..+.++ . |+++ .+.++..++..-.+....++.+++.+||=-... ....
T Consensus 2 ~ig~i~~~~~~~~~~~~~~gi~~~a~~---~-----gy~~--~~~~~~~~~~~~~~~i~~l~~~~vdgiil~~~~~~~~~ 71 (280)
T cd06315 2 NIIFVASDLKNGGILGVGEGVREAAKA---I-----GWNL--RILDGRGSEAGQAAALNQAIALKPDGIVLGGVDAAELQ 71 (280)
T ss_pred eEEEEecccCCcHHHHHHHHHHHHHHH---c-----CcEE--EEECCCCCHHHHHHHHHHHHHcCCCEEEEcCCCHHHHH
Confidence 478888753 22212333444444443 2 4443 444555566665566666777788877643222 2112
Q ss_pred HHHHhhhcCCccEEecccCCCCCCcCCCC-ceEeecCChHHHHHHHHHHHHHc--CCcEEEEEEEcCC-Ccc---hhHHH
Q 003958 111 VVSHVANELQVPLLSFSATDPTLSSLQFP-YFVRTTQSDQYQMAAIAEIVDHY--GWREVIAIYVDDD-HGR---NGIAA 183 (784)
Q Consensus 111 ~va~~~~~~~ip~Is~~a~~~~l~~~~~p-~~~r~~ps~~~~~~ai~~~l~~~--~w~~v~ii~~d~~-~g~---~~~~~ 183 (784)
.....+...++|+|........ .+...+ .+-.........+..+++.|... |-++++++..... ... ...+.
T Consensus 72 ~~~~~~~~~~iPvV~~d~~~~~-~~~~~~~~~~~v~~D~~~~~~~~~~~L~~~~~G~~~i~~i~~~~~~~~~~r~~~~~~ 150 (280)
T cd06315 72 AELELAQKAGIPVVGWHAGPEP-GPIEEPGIFYNVTTDPLAVAEVAALYAIANSGGKAGVVIFTDSRFSIAKAKANAMKE 150 (280)
T ss_pred HHHHHHHHCCCCEEEecCCCCC-CcccCCceeEEecCCHHHHHHHHHHHHHHHcCCCceEEEEeCCCCccHHHHHHHHHH
Confidence 2234456689999987553211 000011 13334555666677788887665 8899999864322 111 23344
Q ss_pred HHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhc---CCceEEEEeccCCcHHHHHHHHHHcCCCCC
Q 003958 184 LGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVAL---TESRIIVVHTHYNRGPVVFHVAQYLGMLGT 249 (784)
Q Consensus 184 l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~---~~~~vIvl~~~~~~~~~~~~~a~~~g~~~~ 249 (784)
+.+.+++.+ +...................+++.+ ..+++ |++++...+..+++.+++.|+..+
T Consensus 151 ~~~a~~~~~--~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~a-i~~~~D~~A~g~~~~l~~~g~~~p 216 (280)
T cd06315 151 IIEACKGCT--VLSIEDVPISRTATRMPALTARLLQRYGDKWTH-SLAINDLYFDYMAPPLASAGRKAD 216 (280)
T ss_pred HHHhCCCCE--EEEecccCcchhhhhhHHHHHHHHHhcCcccce-ecccchhhhHHhHHHHHHhcccCC
Confidence 444333333 2111111111111111133344332 22554 445566677889999999998654
No 212
>PF13379 NMT1_2: NMT1-like family; PDB: 2G29_A 3UN6_A 2I4C_A 2I49_A 2I4B_A 2I48_A 3QSL_A.
Probab=95.30 E-value=0.11 Score=52.54 Aligned_cols=73 Identities=23% Similarity=0.182 Sum_probs=47.4
Q ss_pred CCCCChHhhhh-----CCCceEE-eeCchHHHHHHh---hcccCc---cCceeCCCHHHHHHHHhcCCcCCCeeEEEech
Q 003958 682 SPIKGIDSLRS-----SNYPIGY-QVNSFARNYLVD---ELNIDE---SRLVPLNSPEEYAKALKDGPHKGGVAAVVDDR 749 (784)
Q Consensus 682 ~~i~~~~dl~~-----~~~~i~~-~~~~~~~~~~~~---~~~~~~---~~~~~~~~~~~~~~~l~~~~~~~~~~a~~~~~ 749 (784)
+.+++++||.+ .+++|++ ..++..+-.++. ..+.+. -++..+.. .+..+++++ +++|+++.-.
T Consensus 104 ~~~~~~~dl~~~~~~~kGk~i~~~~~gs~~~~~l~~~l~~~Gl~~~~dv~~~~~~~-~~~~~al~~----g~iDa~~~~e 178 (252)
T PF13379_consen 104 SDIKSLADLIKKRKAQKGKKIAVPFPGSTHDMLLRYLLKKAGLDPKDDVTLVNVPP-PEMVAALRA----GEIDAAVLWE 178 (252)
T ss_dssp STTCCGHHHHHTCCSCSTEEEEESSTTSHHHHHHHHHHHHTT--TTTSSEEEE--G-HHHHHHHHT----TS-SEEEEET
T ss_pred CCccCHHHHHhhhcccCCcEEEEcCCCCHHHHHHHHHHHhCCCCcccceEEEecCH-HHHHHHHhC----CCcCEEEecC
Confidence 47899999933 3778999 455644333322 233333 23443444 999999999 8999999988
Q ss_pred hhhHHHHcCC
Q 003958 750 AYAELFLSTR 759 (784)
Q Consensus 750 ~~~~~~~~~~ 759 (784)
|+.....++.
T Consensus 179 P~~~~~~~~g 188 (252)
T PF13379_consen 179 PFASQAEAKG 188 (252)
T ss_dssp THHHHHHHTT
T ss_pred CHHHHHHhcc
Confidence 9888777664
No 213
>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=95.29 E-value=0.92 Score=45.92 Aligned_cols=192 Identities=14% Similarity=0.020 Sum_probs=98.5
Q ss_pred EEEEEeecCCcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEccCchhhHHHH
Q 003958 33 NIGALLSFSTNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIGPQDAVTSHVV 112 (784)
Q Consensus 33 ~IG~i~~~~~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiGp~~s~~~~~v 112 (784)
+||++++-. .....+-.+..-+++++.++. |.++ .+.+...++....+...++++++..+||++. .....++
T Consensus 1 kva~l~~g~-~~D~~~n~~~~~G~~~~~~~~----gv~~--~~~e~~~~~~~~~~~i~~~~~~g~dlIi~~g-~~~~~~~ 72 (258)
T cd06353 1 KVAFVYVGP-IGDQGWNYAHDEGRKAAEKAL----GVEV--TYVENVPEGADAERVLRELAAQGYDLIFGTS-FGFMDAA 72 (258)
T ss_pred CEEEEEeCC-CCccchhHHHHHHHHHHHHhc----CCeE--EEEecCCchHhHHHHHHHHHHcCCCEEEECc-hhhhHHH
Confidence 478888732 111223333344455544442 4444 4445444667777788888889999999843 3344455
Q ss_pred HHhhhcC-CccEEecccCCCCCCcCCCCceEeecCChH---HHHHHHHHHHHHcCCcEEEEEEEcCC-CcchhHHHHHHH
Q 003958 113 SHVANEL-QVPLLSFSATDPTLSSLQFPYFVRTTQSDQ---YQMAAIAEIVDHYGWREVIAIYVDDD-HGRNGIAALGDT 187 (784)
Q Consensus 113 a~~~~~~-~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~---~~~~ai~~~l~~~~w~~v~ii~~d~~-~g~~~~~~l~~~ 187 (784)
..++..+ ++..+...... . -|++........ .++-.++..+.+ -.+|++|...+. ........|.+.
T Consensus 73 ~~vA~~~p~~~F~~~d~~~---~---~~Nv~~~~~~~~e~~ylaG~~Aa~~t~--t~kVG~I~g~~~~~~~~~~~gF~~G 144 (258)
T cd06353 73 LKVAKEYPDVKFEHCSGYK---T---APNVGSYFARIYEGRYLAGVVAGKMTK--TNKVGYVAAFPIPEVVRGINAFALG 144 (258)
T ss_pred HHHHHHCCCCEEEECCCCC---C---CCCeeeEechhhHHHHHHHHHHHHhhc--CCcEEEEcCcccHHHHHHHHHHHHH
Confidence 5555555 33333322211 1 133332222222 233334444433 368999985432 223444566655
Q ss_pred Hhcc--CcEEEEeeccCCC-CChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHcC
Q 003958 188 LAAK--RCRISFKAPLSVE-ATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLG 245 (784)
Q Consensus 188 l~~~--gi~v~~~~~~~~~-~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~g 245 (784)
++.. ++++.. .+.-. .+...-......+.+.++|+|+-.+ ....+++++++.|
T Consensus 145 ~~~~~p~~~v~~--~~~g~~~D~~~a~~~a~~l~~~G~DvI~~~~---~~~g~~~aa~~~g 200 (258)
T cd06353 145 ARSVNPDATVKV--IWTGSWFDPAKEKEAALALIDQGADVIYQHT---DSPGVIQAAEEKG 200 (258)
T ss_pred HHHHCCCcEEEE--EEecCCCCcHHHHHHHHHHHHCCCcEEEecC---CChHHHHHHHHhC
Confidence 5433 344332 22111 1222334455556668999888777 3346888888866
No 214
>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=94.65 E-value=0.68 Score=45.86 Aligned_cols=90 Identities=10% Similarity=0.056 Sum_probs=72.5
Q ss_pred HHHHHHHHHHHcCCcEEEEEEEcCCCcchhHHHHHHHHhccCcEEEEeeccCCC-------CChhHHHHHHHHhhcCCce
Q 003958 151 QMAAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVE-------ATEDEITDLLVKVALTESR 223 (784)
Q Consensus 151 ~~~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~-------~~~~d~~~~l~~l~~~~~~ 223 (784)
-+.|+.+.|+++|-++|+++.. |-....+.+.+.+++.|++|+....+... -+...+...++++...++|
T Consensus 107 ~~~A~~~AL~alg~~RIalvTP---Y~~~v~~~~~~~l~~~G~eV~~~~~~~~~~~~~ia~i~p~~i~~~~~~~~~~~aD 183 (239)
T TIGR02990 107 PSSAAVDGLAALGVRRISLLTP---YTPETSRPMAQYFAVRGFEIVNFTCLGLTDDREMARISPDCIVEAALAAFDPDAD 183 (239)
T ss_pred HHHHHHHHHHHcCCCEEEEECC---CcHHHHHHHHHHHHhCCcEEeeeeccCCCCCceeeecCHHHHHHHHHHhcCCCCC
Confidence 3678999999999999999984 77788999999999999999876555432 1334566666666678999
Q ss_pred EEEEeccCCcHHHHHHHHHH
Q 003958 224 IIVVHTHYNRGPVVFHVAQY 243 (784)
Q Consensus 224 vIvl~~~~~~~~~~~~~a~~ 243 (784)
+|++.|..=....++.++++
T Consensus 184 AifisCTnLrt~~vi~~lE~ 203 (239)
T TIGR02990 184 ALFLSCTALRAATCAQRIEQ 203 (239)
T ss_pred EEEEeCCCchhHHHHHHHHH
Confidence 99999988888888888866
No 215
>PF12974 Phosphonate-bd: ABC transporter, phosphonate, periplasmic substrate-binding protein ; PDB: 3N5L_B 3QUJ_C 3P7I_A 3QK6_A 3S4U_A.
Probab=94.50 E-value=0.13 Score=51.71 Aligned_cols=101 Identities=18% Similarity=0.247 Sum_probs=56.2
Q ss_pred eEeeccccCCCCChHhhhhCCCceEEeeCchHH-----H-HHHhhcccCcc---CceeCCCHHHHHHHHhcCCcCCCeeE
Q 003958 674 ILTVQKLSSPIKGIDSLRSSNYPIGYQVNSFAR-----N-YLVDELNIDES---RLVPLNSPEEYAKALKDGPHKGGVAA 744 (784)
Q Consensus 674 ~l~~~~~~~~i~~~~dl~~~~~~i~~~~~~~~~-----~-~~~~~~~~~~~---~~~~~~~~~~~~~~l~~~~~~~~~~a 744 (784)
.+.+.+ ..+|++++||. |.+|++...++.- . +|.+..+.... ..+...+.++.+..|.+ |+.+|
T Consensus 88 ~ivv~~-ds~i~~l~dL~--Gk~v~~~~~~s~sg~l~~~~~L~~~~Gl~~~~~~~~~~~~~~~~~~~~l~~----G~~Da 160 (243)
T PF12974_consen 88 VIVVRA-DSPITSLADLK--GKRVAFPDPSSTSGYLIPRYELLREAGLDPGDDFKQVFVGSHDAVLEALLN----GKADA 160 (243)
T ss_dssp EEEEET-TSS--SHHHHG--GSEEEEE-TT-TTTTHHHHHHTCCCCT--HHHHSSEEEEE-HHHHHHHHHT----TSSSE
T ss_pred EEEEEC-CCCCCChhhcC--CCEEEEecCCccHHHHHHHHHHHHHcCCChhHceeEEEeCCHHHHHHHHHc----CCccE
Confidence 344444 35799999998 8889987544221 1 22012222221 22234577889999999 89999
Q ss_pred EEechhhhHHHHcCC----CCeEEeCCccccceEEEEeeCC
Q 003958 745 VVDDRAYAELFLSTR----CEFSIVGQVFTKNGWGFVSIVS 781 (784)
Q Consensus 745 ~~~~~~~~~~~~~~~----c~l~~~~~~~~~~~~~~~~~k~ 781 (784)
.+......+.+.... -++.++...-...++.++..++
T Consensus 161 ~~~~~~~~~~~~~~~~~~~~~~rvl~~s~~~p~~~~~~~~~ 201 (243)
T PF12974_consen 161 AAIPSDAFERLEAEGPDIPSQLRVLWTSPPYPNWPLVASPD 201 (243)
T ss_dssp EEEEHHHHHHHHHH-HHHHTTEEEEEEEEEEE--EEEEETT
T ss_pred EEEechhHHHHHHccCcccccEEEEEEeCCCCCcEEEEeCC
Confidence 888887777766542 3577775433334445666554
No 216
>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=94.23 E-value=0.23 Score=52.20 Aligned_cols=60 Identities=25% Similarity=0.204 Sum_probs=40.0
Q ss_pred CCCCChHhhhhCCCceEEee-CchHH----HHHHhhcccCccC--ceeCCCHHHHHHHHhcCCcCCCeeEEEec
Q 003958 682 SPIKGIDSLRSSNYPIGYQV-NSFAR----NYLVDELNIDESR--LVPLNSPEEYAKALKDGPHKGGVAAVVDD 748 (784)
Q Consensus 682 ~~i~~~~dl~~~~~~i~~~~-~~~~~----~~~~~~~~~~~~~--~~~~~~~~~~~~~l~~~~~~~~~~a~~~~ 748 (784)
.++++++||. +.++++.. ++..+ .+++ ..+..... .+.+.+..+.+.+|.+ |++|+++.+
T Consensus 131 ~~i~sl~dL~--gk~v~~~~~~s~~~~~~~~~l~-~~G~~~~~~~~v~~~~~~~~~~al~~----G~vDa~~~~ 197 (320)
T TIGR02122 131 SGIKTVADLK--GKRVAVGAPGSGTELNARAVLK-AAGLTYDDVKKVEYLGYAEAADALKD----GKIDAAFYT 197 (320)
T ss_pred CCCCcHHHcC--CCEEecCCCCcchHHHHHHHHH-HcCCCHHHccchhcCCHHHHHHHHHC----CCccEEEEe
Confidence 4789999998 66777753 33322 2332 23333222 3467788899999999 899999987
No 217
>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=93.57 E-value=0.082 Score=42.31 Aligned_cols=55 Identities=24% Similarity=0.440 Sum_probs=46.2
Q ss_pred cCCceeehhhhhhhhhccc--ccccccchhhHHHHHHHHHHHHHHhhccccceeeEe
Q 003958 622 KRQVVTIFWFSFSTMFFAH--KEKTVSALGRLVLIIWLFVVLIINSSYTASLTSILT 676 (784)
Q Consensus 622 ~~~~~~~~~~~~~~~~~~~--~~~p~~~~~R~~~~~w~~~~lvl~~~Yta~L~s~l~ 676 (784)
..++.+++|+++.++..-| +-.|++..+|++...+.+.++.+.....+.+++.++
T Consensus 22 ~~~~~da~yfs~~t~tTvGyGDi~p~t~~gr~~~~~~~~~G~~~~~~~~~~~~~~l~ 78 (79)
T PF07885_consen 22 KWSFIDALYFSFVTITTVGYGDIVPQTPAGRIFTIIYMLIGIFLFALFLSVLASVLT 78 (79)
T ss_dssp TTSHHHHHHHHHHHHTT---SSSSTSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred cCCHHHHHHHHHHHHhcccCCCccCCccchHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 4578999999999998665 558999999999999999999999999888877653
No 218
>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=93.54 E-value=0.46 Score=46.59 Aligned_cols=59 Identities=31% Similarity=0.329 Sum_probs=38.4
Q ss_pred CCCCChHhhhhCCCceEEeeCchHHHHHHhh---cccCccCceeC-CCHHHHHHHHhcCCcCCCeeEEE
Q 003958 682 SPIKGIDSLRSSNYPIGYQVNSFARNYLVDE---LNIDESRLVPL-NSPEEYAKALKDGPHKGGVAAVV 746 (784)
Q Consensus 682 ~~i~~~~dl~~~~~~i~~~~~~~~~~~~~~~---~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~a~~ 746 (784)
..|+++.||+ |++||+..++..+.++... .+.+.+.+... .+..+...+|.+ +++||.+
T Consensus 83 s~i~~~~DLk--GK~i~v~~~s~~~~~~~~~l~~~g~~~~~v~~v~~~~~~~~~al~~----g~vDa~~ 145 (216)
T PF09084_consen 83 SGIKSPADLK--GKKIGVSRGSSSEYFLRALLKKNGIDPDDVKIVNLGPPELAQALLS----GQVDAAI 145 (216)
T ss_dssp TS-SSGGGGT--TSEEEESTTSHHHHHHHHHHHHTTT-GGGSEEEES-HHHHHHHHHT----TSSSEEE
T ss_pred CCCCCHHHhC--CCEEEEecCcchhHHHHHHHHHhccccccceeeeeehhhhhhhhhc----CCCCEEE
Confidence 3599999999 9999999877555555332 23333333222 235677779999 8999888
No 219
>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=93.45 E-value=7.5 Score=39.52 Aligned_cols=151 Identities=11% Similarity=0.009 Sum_probs=87.9
Q ss_pred hcCceEEEccCchhhHHHHHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEc
Q 003958 94 EGQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVD 173 (784)
Q Consensus 94 ~~~v~aiiGp~~s~~~~~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d 173 (784)
..++.++|-.........+ ..+...++|+|..+..... +..+++ +...+..-+..+++.|...|.+++++|...
T Consensus 54 ~~~vdgiIi~~~~~~~~~~-~~l~~~~iPvV~i~~~~~~--~~~~~~---V~~d~~~~~~~a~~~L~~~G~~~I~~i~~~ 127 (269)
T cd06287 54 ALDIDGAILVEPMADDPQV-ARLRQRGIPVVSIGRPPGD--RTDVPY---VDLQSAATARMLLEHLRAQGARQIALIVGS 127 (269)
T ss_pred ccCcCeEEEecCCCCCHHH-HHHHHcCCCEEEeCCCCCC--CCCCCe---EeeCcHHHHHHHHHHHHHcCCCcEEEEeCC
Confidence 4577776532111111223 3345679999987553210 112333 334556666778888888899999999743
Q ss_pred C--CCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcC--CceEEEEeccCCcHHHHHHHHHHcCCCCC
Q 003958 174 D--DHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALT--ESRIIVVHTHYNRGPVVFHVAQYLGMLGT 249 (784)
Q Consensus 174 ~--~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~--~~~vIvl~~~~~~~~~~~~~a~~~g~~~~ 249 (784)
. .......+.+++.+++.|+...... .....+..+-...++++.+. .+++|+ +.+...+..+++++++.|+..+
T Consensus 128 ~~~~~~~~R~~gf~~a~~~~g~~~~~~~-~~~~~~~~~~~~~~~~~l~~~~~~~ai~-~~~d~~A~gvl~al~~~gl~vP 205 (269)
T cd06287 128 ARRNSYLEAEAAYRAFAAEHGMPPVVLR-VDEAGGEEAGYAACAQLLAQHPDLDALC-VPVDAFAVGAVRAATELGRAVP 205 (269)
T ss_pred cccccHHHHHHHHHHHHHHcCCCcceeE-ecCCCChHHHHHHHHHHHhCCCCCCEEE-EcCcHHHHHHHHHHHHcCCCCC
Confidence 2 3344567888999988886532111 11111222333445554332 456554 4566778899999999998766
Q ss_pred CeE
Q 003958 250 GYV 252 (784)
Q Consensus 250 ~~~ 252 (784)
+-+
T Consensus 206 ~dv 208 (269)
T cd06287 206 DQL 208 (269)
T ss_pred Cce
Confidence 544
No 220
>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=93.38 E-value=0.37 Score=49.68 Aligned_cols=71 Identities=15% Similarity=0.245 Sum_probs=48.0
Q ss_pred CCCCChHhhhhCCCceEEeeCchHHHHHHhh---cccCccCc-eeCCCHHHHHHHHhcCCcCCCeeEEEechhhhHHHHc
Q 003958 682 SPIKGIDSLRSSNYPIGYQVNSFARNYLVDE---LNIDESRL-VPLNSPEEYAKALKDGPHKGGVAAVVDDRAYAELFLS 757 (784)
Q Consensus 682 ~~i~~~~dl~~~~~~i~~~~~~~~~~~~~~~---~~~~~~~~-~~~~~~~~~~~~l~~~~~~~~~~a~~~~~~~~~~~~~ 757 (784)
.+|++++||. |++|++..++.....+... .+.+...+ ..+.+..+..+++++ |++++++...++......
T Consensus 91 ~~i~s~~dL~--Gk~i~~~~~~~~~~~~~~~l~~~G~~~~~v~~~~~~~~~~~~al~~----g~vda~~~~~p~~~~~~~ 164 (288)
T TIGR01728 91 SPIRTVADLK--GKRIAVPKGGSGHDLLLRALLKAGLSGDDVTILYLGPSDARAAFAA----GQVDAWAIWEPWGSALVE 164 (288)
T ss_pred CCCCCHHHcC--CCEEEecCCccHHHHHHHHHHHcCCCccceeEEecCcHHHHHHHHC----CCCCEEEeccchHhHHhh
Confidence 4789999999 8889988776544444321 22322222 223456788999999 889999888777766554
Q ss_pred C
Q 003958 758 T 758 (784)
Q Consensus 758 ~ 758 (784)
+
T Consensus 165 ~ 165 (288)
T TIGR01728 165 E 165 (288)
T ss_pred c
Confidence 4
No 221
>COG1744 Med Uncharacterized ABC-type transport system, periplasmic component/surface lipoprotein [General function prediction only]
Probab=92.84 E-value=15 Score=38.89 Aligned_cols=156 Identities=15% Similarity=0.041 Sum_probs=78.9
Q ss_pred HHHHHHHHHHHHhcCceEEEccCchhhHHHHHHhhhcC-CccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHH
Q 003958 82 GFLALAEALHLMEGQTVAIIGPQDAVTSHVVSHVANEL-QVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVD 160 (784)
Q Consensus 82 ~~~a~~~~~~li~~~v~aiiGp~~s~~~~~va~~~~~~-~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~ 160 (784)
.....+...++.+++...|+|....- ..++..++..+ ++..+-..+.-.. .++...+.||..-..-..+.+.+...+
T Consensus 83 ~~~~~~~~~~~a~~g~~lI~~~gf~~-~d~~~~va~~~Pd~~F~iid~~~~~-~~Nv~s~~f~~~egayL~G~~AA~~sk 160 (345)
T COG1744 83 EADYERALRALAEDGYDLIFGTGFAF-SDALEKVAAEYPDVKFVIIDGVVKK-EDNVASYVFREYEGAYLAGVAAAKMSK 160 (345)
T ss_pred hhHHHHHHHHHHhcCCCEEEEeccch-hhHHHHHHHHCCCCEEEEecCccCC-CCceEEEEeccccHHHHHHHHHHHhhc
Confidence 44555566677778888888755443 34445555555 3333322221110 112335666665433333333333334
Q ss_pred HcCCcEEEEEEE-cCCCcchhHHHHHHHHhccC----cEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHH
Q 003958 161 HYGWREVIAIYV-DDDHGRNGIAALGDTLAAKR----CRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGP 235 (784)
Q Consensus 161 ~~~w~~v~ii~~-d~~~g~~~~~~l~~~l~~~g----i~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~ 235 (784)
-.+++.|.. +-+--..+...|..-++..+ +.+.+...+. +...-....+.+..+++|||+-.+.+.-.
T Consensus 161 ---~~~vG~vgg~~~p~v~~f~~gF~~Gak~~np~i~v~v~~~gsf~---D~~k~k~~a~~li~~GaDVI~~~ag~~~~- 233 (345)
T COG1744 161 ---SGKVGFVGGMDIPEVNRFINGFLAGAKSVNPDIKVKVVYVGSFS---DPAKGKEAANALIDQGADVIYPAAGGTGV- 233 (345)
T ss_pred ---CCceeEEecccchhhHHHHHHHHHHHHhhCCCccEEEEEecCcc---ChHHHHHHHHHHHhcCCCEEEecCCCCcc-
Confidence 334555542 33333445556666555443 3333333333 22333447777888999998887655443
Q ss_pred HHHHHHHHcCC
Q 003958 236 VVFHVAQYLGM 246 (784)
Q Consensus 236 ~~~~~a~~~g~ 246 (784)
.++.+|++.+.
T Consensus 234 gv~~~A~~~~~ 244 (345)
T COG1744 234 GVFQAAKELGA 244 (345)
T ss_pred hHHHHHHHhCC
Confidence 33336777664
No 222
>COG4213 XylF ABC-type xylose transport system, periplasmic component [Carbohydrate transport and metabolism]
Probab=92.73 E-value=12 Score=37.75 Aligned_cols=207 Identities=10% Similarity=0.093 Sum_probs=114.0
Q ss_pred cCCCceEEEEEEeecC--CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEE-Ec
Q 003958 26 SGRPSVVNIGALLSFS--TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAI-IG 102 (784)
Q Consensus 26 ~~~~~~i~IG~i~~~~--~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~ai-iG 102 (784)
+...++..||+..|.- ..+ ..-..++.-+.|.. |.+. ...+-..+...-+.....++++++.++ |+
T Consensus 20 aa~~~d~~IGis~~d~~~eRW-~~D~~~~~~~~e~~--------g~k~--~~q~A~~~~~~Q~~qien~i~qg~~vlvi~ 88 (341)
T COG4213 20 AAAAKDGVIGISMPDLRSERW-IKDRDAFVKKAEAL--------GAKV--DVQSADGDEEKQLAQIENMINQGVKVLVIG 88 (341)
T ss_pred hhhccCCeEEEEcCChhHhhh-hhhhHHHHHHHHhc--------cchh--hhhhhccChhHHHHHHHHHHhcCCCEEEEE
Confidence 3456688899988863 222 12234455455543 3333 344445677777788899999977654 78
Q ss_pred cCchhhHHHHHHhhhcCCccEEecccCCCCCCcCCCCceEeecCC---hHHHHHHHHHHHHHcC---CcEEEEEE-EcCC
Q 003958 103 PQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQS---DQYQMAAIAEIVDHYG---WREVIAIY-VDDD 175 (784)
Q Consensus 103 p~~s~~~~~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps---~~~~~~ai~~~l~~~~---w~~v~ii~-~d~~ 175 (784)
+..+.+...+...+...+||+|+|.- ...+....| +-+.-+ -..|+.++++-++... -..+.++. +-++
T Consensus 89 a~d~~~l~~~i~~A~~~gikViaYDR---lI~n~dvd~-YvsFDN~~VG~lQa~~l~~~lk~k~~~~~gn~~l~~GSp~D 164 (341)
T COG4213 89 AIDGGVLSNAVEKAKSEGIKVIAYDR---LINNADVDF-YVSFDNEKVGELQAKALVKGLKLKPLTSEGNYVLLGGSPDD 164 (341)
T ss_pred eccchhHHHHHHHHHHcCCeEEEeec---ccccCCccE-EEEecchhHHHHHHHHHHHHhccCCCCCCCCEEEecCCCCC
Confidence 99999888888999999999999833 233322333 222222 2356777766665443 23344444 3222
Q ss_pred -----CcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhh-c--CCceEEEEeccCCcHHHHHHHHHHcCCC
Q 003958 176 -----HGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVA-L--TESRIIVVHTHYNRGPVVFHVAQYLGML 247 (784)
Q Consensus 176 -----~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~-~--~~~~vIvl~~~~~~~~~~~~~a~~~g~~ 247 (784)
+-....+.++..+..-.+.++.+...+ .-..+.-...+..+. . .+.+.|+-.-+ ..+...+.++...|+.
T Consensus 165 nNA~lf~~G~m~VLkp~idsGkik~~Ge~~~d-~W~ps~Aq~~men~lta~~~~vdaVvA~nD-gtagGaI~aL~a~Gl~ 242 (341)
T COG4213 165 NNAKLFFAGAMKVLKPLIDSGKIKVVGEQWTD-GWLPSNAQQIMENLLTANYNDIDAVVAPND-GTAGGAIAALKAQGLA 242 (341)
T ss_pred cchHHHHhcHHHHHHHHhhCCceEEeeecccc-ccCHHHHHHHHHHHHhcccCceeEEEcCCC-chhHHHHHHHHhcccC
Confidence 111224444444443345564444333 112222222222221 1 33455444333 5567788888888886
Q ss_pred CC
Q 003958 248 GT 249 (784)
Q Consensus 248 ~~ 249 (784)
++
T Consensus 243 g~ 244 (341)
T COG4213 243 GK 244 (341)
T ss_pred CC
Confidence 43
No 223
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=92.07 E-value=10 Score=39.89 Aligned_cols=147 Identities=9% Similarity=-0.026 Sum_probs=82.4
Q ss_pred cCceEEEccCchhhHHHHHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcC
Q 003958 95 GQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDD 174 (784)
Q Consensus 95 ~~v~aiiGp~~s~~~~~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~ 174 (784)
+++.++|--.... ......+...++|+|......+ +..++ ........-+..+++.|...|.++++++..+.
T Consensus 113 ~~vDgiI~~~~~~--~~~~~~l~~~~~pvV~~~~~~~---~~~~~---~V~~D~~~~~~~a~~~l~~~G~~~i~~i~~~~ 184 (327)
T PRK10339 113 KNVTGILIVGKPT--PALRAAASALTDNICFIDFHEP---GSGYD---AVDIDLARISKEIIDFYINQGVNRIGFIGGED 184 (327)
T ss_pred ccCCEEEEeCCCC--HHHHHHHHhcCCCEEEEeCCCC---CCCCC---EEEECHHHHHHHHHHHHHHCCCCeEEEeCCcc
Confidence 4677665422211 1233445667899998643221 11233 24555566667788888888999999996433
Q ss_pred --CCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhc--CCceEEEEeccCCcHHHHHHHHHHcCCCCCC
Q 003958 175 --DHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVAL--TESRIIVVHTHYNRGPVVFHVAQYLGMLGTG 250 (784)
Q Consensus 175 --~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~--~~~~vIvl~~~~~~~~~~~~~a~~~g~~~~~ 250 (784)
.......+.+.+.++..|+ +.....+.......+....++++.+ ..+++ +++.....+..++++++++|+..|+
T Consensus 185 ~~~~~~~R~~gf~~~~~~~g~-~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~a-i~~~~D~~A~g~~~al~~~g~~vP~ 262 (327)
T PRK10339 185 EPGKADIREVAFAEYGRLKQV-VREEDIWRGGFSSSSGYELAKQMLAREDYPKA-LFVASDSIAIGVLRAIHERGLNIPQ 262 (327)
T ss_pred ccchhhHHHHHHHHHHHHcCC-CChhheeecCcChhHHHHHHHHHHhCCCCCCE-EEECCcHHHHHHHHHHHHcCCCCCC
Confidence 2334556778888877775 1110111111112222334444433 23555 4445556677899999999986554
Q ss_pred e
Q 003958 251 Y 251 (784)
Q Consensus 251 ~ 251 (784)
-
T Consensus 263 d 263 (327)
T PRK10339 263 D 263 (327)
T ss_pred c
Confidence 3
No 224
>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=92.06 E-value=0.93 Score=47.52 Aligned_cols=68 Identities=18% Similarity=0.172 Sum_probs=47.9
Q ss_pred CCChHhhhhCCCceEEeeCchHHHHHHhh---cccCcc--CceeCCCHHHHHHHHhcCCcCCCeeEEEechhhhHHHHcC
Q 003958 684 IKGIDSLRSSNYPIGYQVNSFARNYLVDE---LNIDES--RLVPLNSPEEYAKALKDGPHKGGVAAVVDDRAYAELFLST 758 (784)
Q Consensus 684 i~~~~dl~~~~~~i~~~~~~~~~~~~~~~---~~~~~~--~~~~~~~~~~~~~~l~~~~~~~~~~a~~~~~~~~~~~~~~ 758 (784)
|+|++||+ |++||+..++..+-++.+. .+.... .++. -++.++..++.+ |++||...-.|++.....+
T Consensus 98 i~svaDLK--GKkIav~~gs~~~~ll~~aL~~aGL~~~DV~~v~-~~~~d~~aAl~~----G~VDAa~~~eP~~s~~~~~ 170 (328)
T TIGR03427 98 GKSLADLK--GQKVNLVELSVSHYLLARALESVGLSEKDVKVVN-TSDADIVAAFIT----KDVTAVVTWNPQLSEIKAQ 170 (328)
T ss_pred CCCHHHcC--CCEEeccCCChHHHHHHHHHHHcCCCHHHeEEEe-CChHHHHHHHhc----CCCcEEEEcCchHHHHHhC
Confidence 89999999 9999999998665444332 222222 2222 355788999999 8999998877877655543
No 225
>KOG1419 consensus Voltage-gated K+ channel KCNQ [Inorganic ion transport and metabolism]
Probab=90.88 E-value=0.36 Score=51.76 Aligned_cols=87 Identities=14% Similarity=0.181 Sum_probs=70.6
Q ss_pred HHHHHHHHHHHHHHHHhhheecccCCCCCCCccCCceeehhhhhhhhh--cccccccccchhhHHHHHHHHHHHHHHhhc
Q 003958 590 MMWGVTAIFFLAVGAVVWILEHRLNDEFRGPPKRQVVTIFWFSFSTMF--FAHKEKTVSALGRLVLIIWLFVVLIINSSY 667 (784)
Q Consensus 590 ~~W~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~p~~~~~R~~~~~w~~~~lvl~~~Y 667 (784)
.+|..-++.++..+.++++.|.-...|-.+.....+-+++||...++. +.|+..|+.+.+|+++.+..++++-+.+.=
T Consensus 235 Tt~YIGFL~LIfsSflVYLaEKd~~~e~~n~~F~TyADALWWG~ITltTIGYGDk~P~TWlGr~laa~fsligiSFFALP 314 (654)
T KOG1419|consen 235 TTWYIGFLVLIFSSFLVYLAEKDAQGEGTNDEFPTYADALWWGVITLTTIGYGDKTPQTWLGRLLAACFSLIGISFFALP 314 (654)
T ss_pred HHHHHHHHHHHHHHHHHHHhhcccccccccccchhHHHHHHhhheeEEeeccCCcCcccchhHHHHHHHHHHHHHHHhcc
Confidence 578888999999999999998875555444455568899999998887 456779999999999999888888777777
Q ss_pred cccceeeEe
Q 003958 668 TASLTSILT 676 (784)
Q Consensus 668 ta~L~s~l~ 676 (784)
.+.|-|-++
T Consensus 315 AGILGSGfA 323 (654)
T KOG1419|consen 315 AGILGSGFA 323 (654)
T ss_pred cccccchhh
Confidence 777776664
No 226
>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=89.34 E-value=23 Score=35.46 Aligned_cols=143 Identities=6% Similarity=0.013 Sum_probs=84.2
Q ss_pred HHHHHhcCceEEEccCchhhHHHHHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHH--cCCcE
Q 003958 89 ALHLMEGQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDH--YGWRE 166 (784)
Q Consensus 89 ~~~li~~~v~aiiGp~~s~~~~~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~--~~w~~ 166 (784)
..+.++.++.++|=-............+...++|+|..+...+. ...+++ ....+..-+..+++.+.. .|.++
T Consensus 45 ~~~~~~~~vdGvIi~~~~~~~~~~~~~~~~~~~PvV~i~~~~~~--~~~~~~---V~~D~~~~~~~a~~~L~~~~~G~~~ 119 (247)
T cd06276 45 IISNTKGKYSGYVVMPHFKNEIQYFLLKKIPKEKLLILDHSIPE--GGEYSS---VAQDFEKAIYNALQEGLEKLKKYKK 119 (247)
T ss_pred HHHHHhcCCCEEEEecCCCCcHHHHHHhccCCCCEEEEcCcCCC--CCCCCe---EEEccHHHHHHHHHHHHHHhcCCCE
Confidence 33444567776653111111121334555578999987543211 112332 444566667778888878 89999
Q ss_pred EEEEEEcC-CCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHcC
Q 003958 167 VIAIYVDD-DHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLG 245 (784)
Q Consensus 167 v~ii~~d~-~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~g 245 (784)
+++|.... ..++...+.+++.+++.|+.... .. .... . .+ ...++ |++.+...+..+++++++.|
T Consensus 120 Ia~i~~~~~~~~~~R~~gf~~~l~~~g~~~~~---~~-~~~~----~---~~--~~~~a-i~~~~d~~A~g~~~~l~~~g 185 (247)
T cd06276 120 LILVFPNKTAIPKEIKRGFERFCKDYNIETEI---IN-DYEN----R---EI--EKGDL-YIILSDTDLVFLIKKARESG 185 (247)
T ss_pred EEEEecCccHhHHHHHHHHHHHHHHcCCCccc---cc-ccch----h---hc--cCCcE-EEEeCHHHHHHHHHHHHHcC
Confidence 99997543 34556788999999999875431 11 0010 0 01 12354 55556677888999999999
Q ss_pred CCCCC
Q 003958 246 MLGTG 250 (784)
Q Consensus 246 ~~~~~ 250 (784)
+..|+
T Consensus 186 ~~iP~ 190 (247)
T cd06276 186 LLLGK 190 (247)
T ss_pred CcCCc
Confidence 86554
No 227
>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=88.72 E-value=15 Score=33.92 Aligned_cols=69 Identities=22% Similarity=0.328 Sum_probs=42.2
Q ss_pred eeeHHHHHHHHHHCCCccceEEeeCCCCCCCCChhHHHHHHHcCcccEEEeeEEeecCccccceeccccccccEEEEEec
Q 003958 494 GFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPV 573 (784)
Q Consensus 494 G~~~dl~~~l~~~l~f~~~~~~~~~~~~~~~~~~~g~i~~l~~~~~D~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~ 573 (784)
.+..++++.+.+... ++++++.. .....++..|.+|++|+++..... ....++ ..++....+++++++
T Consensus 13 ~~l~~~i~~~~~~~p-~i~i~~~~-------~~~~~~~~~l~~g~~D~~i~~~~~---~~~~~~-~~~l~~~~~~~~~~~ 80 (197)
T cd05466 13 YLLPPLLAAFRQRYP-GVELSLVE-------GGSSELLEALLEGELDLAIVALPV---DDPGLE-SEPLFEEPLVLVVPP 80 (197)
T ss_pred HHhHHHHHHHHHHCC-CCEEEEEE-------CChHHHHHHHHcCCceEEEEcCCC---CCCcce-EeeeeccceEEEecC
Confidence 345566777766642 23355543 245688999999999999865443 222232 345666677777655
Q ss_pred c
Q 003958 574 R 574 (784)
Q Consensus 574 ~ 574 (784)
.
T Consensus 81 ~ 81 (197)
T cd05466 81 D 81 (197)
T ss_pred C
Confidence 4
No 228
>PRK11480 tauA taurine transporter substrate binding subunit; Provisional
Probab=88.40 E-value=3.2 Score=43.54 Aligned_cols=68 Identities=13% Similarity=0.077 Sum_probs=44.4
Q ss_pred CCCChHhhhhCCCceEEeeCchHHHHHH---hhcccCccCceeC-CCHHHHHHHHhcCCcCCCeeEEEechhhhHHHH
Q 003958 683 PIKGIDSLRSSNYPIGYQVNSFARNYLV---DELNIDESRLVPL-NSPEEYAKALKDGPHKGGVAAVVDDRAYAELFL 756 (784)
Q Consensus 683 ~i~~~~dl~~~~~~i~~~~~~~~~~~~~---~~~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~a~~~~~~~~~~~~ 756 (784)
+|++++||+ |++||+..++..+.++. +..+.+...+... ..+.+...++.+ |++||...-.+......
T Consensus 113 ~I~s~~DLk--GK~Iav~~~s~~~~~l~~~L~~~Gl~~~dv~~v~~~~~~~~~Al~~----G~VDAa~~~~p~~~~~~ 184 (320)
T PRK11480 113 TISKPEDLI--GKRIAVPFISTTHYSLLAALKHWGIKPGQVEIVNLQPPAIIAAWQR----GDIDGAYVWAPAVNALE 184 (320)
T ss_pred CCCChHHcC--CCEEecCCCCchHHHHHHHHHHcCCCHhheEEEECCcHHHHHHHHc----CCcCEEEEcchHHHHHH
Confidence 599999999 99999987665443322 2233333332221 246788999999 89998776666654443
No 229
>COG3473 Maleate cis-trans isomerase [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=88.39 E-value=16 Score=34.51 Aligned_cols=88 Identities=13% Similarity=0.022 Sum_probs=64.8
Q ss_pred HHHHHHHHHcCCcEEEEEEEcCCCcchhHHHHHHHHhccCcEEEEeeccCCCC-------ChhHHHHHHHHhhcCCceEE
Q 003958 153 AAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEA-------TEDEITDLLVKVALTESRII 225 (784)
Q Consensus 153 ~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~-------~~~d~~~~l~~l~~~~~~vI 225 (784)
.|.++-|+.++-+++.+++. |-....+...+.++.+|++|+....+.... .....-.+.+++...++|.|
T Consensus 107 ~Avv~aL~al~a~ri~vlTP---Y~~evn~~e~ef~~~~Gfeiv~~~~Lgi~dn~eigr~~P~~~y~lAk~~~~~~~Dai 183 (238)
T COG3473 107 TAVVEALNALGAQRISVLTP---YIDEVNQREIEFLEANGFEIVDFKGLGITDNLEIGRQEPWAVYRLAKEVFTPDADAI 183 (238)
T ss_pred HHHHHHHHhhCcceEEEecc---chhhhhhHHHHHHHhCCeEEEEeeccCCcccchhcccChHHHHHHHHHhcCCCCCeE
Confidence 57888899999999999984 556677888899999999998766543221 12233455566677899999
Q ss_pred EEeccCCcHHHHHHHHHH
Q 003958 226 VVHTHYNRGPVVFHVAQY 243 (784)
Q Consensus 226 vl~~~~~~~~~~~~~a~~ 243 (784)
++.|..-....++...++
T Consensus 184 FiSCTnlRt~eii~~lE~ 201 (238)
T COG3473 184 FISCTNLRTFEIIEKLER 201 (238)
T ss_pred EEEeeccccHHHHHHHHH
Confidence 999887666667766654
No 230
>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=88.37 E-value=1.3 Score=40.85 Aligned_cols=97 Identities=10% Similarity=0.078 Sum_probs=62.4
Q ss_pred HHHHHHcCCcEEEEEEEc--CCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHH-HHhhcCCceEEEEeccCC
Q 003958 156 AEIVDHYGWREVIAIYVD--DDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLL-VKVALTESRIIVVHTHYN 232 (784)
Q Consensus 156 ~~~l~~~~w~~v~ii~~d--~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l-~~l~~~~~~vIvl~~~~~ 232 (784)
++.|.+.|.+++++|..+ ..+.....+.+++.+++.|+.......... ....+..... ..+++..+++|+. .+..
T Consensus 1 ~~~L~~~G~r~i~~i~~~~~~~~~~~r~~gf~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~l~~~~pdaii~-~~~~ 78 (160)
T PF13377_consen 1 VDYLIERGHRRIAFIGGPPNSSVSRERLEGFREALKEHGIEFEELIFFSD-DDSEDAREAQLLWLRRLRPDAIIC-SNDR 78 (160)
T ss_dssp HHHHHHTT-SSEEEEESSTTSHHHHHHHHHHHHHHHHTTSEEEGEEEEES-SSHHHHHHHHHHHHHTCSSSEEEE-SSHH
T ss_pred ChHHHHCCCCeEEEEecCCCChhHHHHHHHHHHHHHHCCCCCCeeEeecC-CcchhHHHHHHHHHhcCCCcEEEE-cCHH
Confidence 467888999999999933 334456678899999999988654443332 2222232222 2344346676554 6667
Q ss_pred cHHHHHHHHHHcCCCCCCeEEE
Q 003958 233 RGPVVFHVAQYLGMLGTGYVWI 254 (784)
Q Consensus 233 ~~~~~~~~a~~~g~~~~~~~wi 254 (784)
.+..+++++.+.|+..++-+-|
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 7889999999999866543333
No 231
>COG3221 PhnD ABC-type phosphate/phosphonate transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=88.31 E-value=4 Score=41.92 Aligned_cols=96 Identities=16% Similarity=0.156 Sum_probs=60.0
Q ss_pred cCCCCChHhhhhCCCceEEeeCchHH------HHHHhhcccCc-c--CceeCCC-HHHHHHHHhcCCcCCCeeEEEechh
Q 003958 681 SSPIKGIDSLRSSNYPIGYQVNSFAR------NYLVDELNIDE-S--RLVPLNS-PEEYAKALKDGPHKGGVAAVVDDRA 750 (784)
Q Consensus 681 ~~~i~~~~dl~~~~~~i~~~~~~~~~------~~~~~~~~~~~-~--~~~~~~~-~~~~~~~l~~~~~~~~~~a~~~~~~ 750 (784)
.++|++++||+ |+++++..-+++- .++.+.-..++ . .-+.|.. -+..+..|.+ |++|+-.....
T Consensus 133 ds~i~sl~dlk--gk~~af~d~~StSG~l~P~~~L~~~g~~d~~~~f~~v~~~G~H~~a~~aV~n----G~vDva~~~~~ 206 (299)
T COG3221 133 DSPIKSLEDLK--GKRFAFGDPDSTSGYLFPLYYLAKEGGIDPDKFFGEVIFSGGHDAAVLAVAN----GQVDVAAVNSS 206 (299)
T ss_pred CCCcchHHHhc--CCeEeccCCCcchhhHhHHHHHHHhcCCChhhhhceeeccChHHHHHHHHHc----CCceEEeccHH
Confidence 66899999999 9999987533222 22222221221 1 1122444 7889999999 88988777766
Q ss_pred hhHHHHcC--C---CCeEEeCCccccceEEEEeeCCC
Q 003958 751 YAELFLST--R---CEFSIVGQVFTKNGWGFVSIVSS 782 (784)
Q Consensus 751 ~~~~~~~~--~---c~l~~~~~~~~~~~~~~~~~k~s 782 (784)
....+... . -++.++.+.-...+..|+++++-
T Consensus 207 ~~~~~~~~~~~~~~~~l~vi~~S~~iP~~pi~vr~~L 243 (299)
T COG3221 207 ARGLLKKAAPEGVAEKLRVIWKSPLIPNDPIAVRSDL 243 (299)
T ss_pred HHhhhhhcccccchhhceEEEecCCCCCCCEEEeCCC
Confidence 65555443 2 35777776555666677777653
No 232
>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=87.50 E-value=16 Score=34.61 Aligned_cols=71 Identities=15% Similarity=0.125 Sum_probs=45.3
Q ss_pred eeeHHHHHHHHHHC-CCccceEEeeCCCCCCCCChhHHHHHHHcCcccEEEeeEEeecCccccceeccccccccEEEEEe
Q 003958 494 GFCIDVFTAAINLL-PYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAP 572 (784)
Q Consensus 494 G~~~dl~~~l~~~l-~f~~~~~~~~~~~~~~~~~~~g~i~~l~~~~~D~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~ 572 (784)
.+..+++..+.++. +.+ +++.. +....+++.|.+|++|+++............+.+ .+.....++++++
T Consensus 13 ~~l~~~l~~~~~~~P~v~--i~~~~-------~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~~~~-~~l~~~~~~~~~~ 82 (202)
T cd08468 13 AVMPRLMARLEELAPSVR--LNLVH-------AEQKLPLDALLAGEIDFALGYSHDDGAEPRLIEE-RDWWEDTYVVIAS 82 (202)
T ss_pred HHhHHHHHHHHhhCCCCE--EEEEE-------CChHhHHHHHHCCCccEEEecccccccCCCCEEE-EEEecCcEEEEEe
Confidence 45677888888776 344 55543 3577899999999999998643221000123333 4677777777775
Q ss_pred cc
Q 003958 573 VR 574 (784)
Q Consensus 573 ~~ 574 (784)
..
T Consensus 83 ~~ 84 (202)
T cd08468 83 RD 84 (202)
T ss_pred CC
Confidence 54
No 233
>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=87.26 E-value=15 Score=34.92 Aligned_cols=69 Identities=16% Similarity=0.166 Sum_probs=45.6
Q ss_pred eeeHHHHHHHHHHCCCccceEEeeCCCCCCCCChhHHHHHHHcCcccEEEeeEEeecCccccceeccccccccEEEEEec
Q 003958 494 GFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPV 573 (784)
Q Consensus 494 G~~~dl~~~l~~~l~f~~~~~~~~~~~~~~~~~~~g~i~~l~~~~~D~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~ 573 (784)
.+..+++..+.+..- .+++++.. +....++..|.+|++|+++..... ....+. ..|+....+++++++
T Consensus 19 ~~l~~~l~~~~~~~P-~i~i~~~~-------~~~~~~~~~l~~g~~Dl~i~~~~~---~~~~~~-~~~l~~~~~~~~~~~ 86 (209)
T PF03466_consen 19 SLLPPLLAEFRERHP-NIRIEIRE-------GDSDELIEALRSGELDLAITFGPP---PPPGLE-SEPLGEEPLVLVVSP 86 (209)
T ss_dssp HTHHHHHHHHHHHST-TEEEEEEE-------ESHHHHHHHHHTTSSSEEEESSSS---SSTTEE-EEEEEEEEEEEEEET
T ss_pred HHHHHHHHHHHHHCC-CcEEEEEe-------ccchhhhHHHhcccccEEEEEeec---cccccc-cccccceeeeeeeec
Confidence 345667777777653 23344443 356799999999999999865544 222222 456778888888876
Q ss_pred c
Q 003958 574 R 574 (784)
Q Consensus 574 ~ 574 (784)
.
T Consensus 87 ~ 87 (209)
T PF03466_consen 87 D 87 (209)
T ss_dssp T
T ss_pred c
Confidence 5
No 234
>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=87.22 E-value=8.7 Score=38.81 Aligned_cols=86 Identities=16% Similarity=0.093 Sum_probs=65.6
Q ss_pred EEEEEeecCCcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEccCchhhHHHH
Q 003958 33 NIGALLSFSTNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIGPQDAVTSHVV 112 (784)
Q Consensus 33 ~IG~i~~~~~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiGp~~s~~~~~v 112 (784)
+||.+.+.....-.....|+...++..| |+.++...+..+-.|+.++.+.+..++++++.+|.+.. +. ..+
T Consensus 122 kVG~I~g~~~~~~~~~~~gF~~G~~~~~------p~~~v~~~~~g~~~D~~~a~~~a~~l~~~G~DvI~~~~-~~--~g~ 192 (258)
T cd06353 122 KVGYVAAFPIPEVVRGINAFALGARSVN------PDATVKVIWTGSWFDPAKEKEAALALIDQGADVIYQHT-DS--PGV 192 (258)
T ss_pred cEEEEcCcccHHHHHHHHHHHHHHHHHC------CCcEEEEEEecCCCCcHHHHHHHHHHHHCCCcEEEecC-CC--hHH
Confidence 6898888764444456688998998887 45666666767778999999999999999999888765 22 345
Q ss_pred HHhhhcCCccEEecc
Q 003958 113 SHVANELQVPLLSFS 127 (784)
Q Consensus 113 a~~~~~~~ip~Is~~ 127 (784)
...++..++..|.+.
T Consensus 193 ~~aa~~~g~~~IG~d 207 (258)
T cd06353 193 IQAAEEKGVYAIGYV 207 (258)
T ss_pred HHHHHHhCCEEEeec
Confidence 566777899999865
No 235
>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=86.99 E-value=41 Score=34.92 Aligned_cols=197 Identities=13% Similarity=0.050 Sum_probs=99.6
Q ss_pred EEEEEEeecC---CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCC-CHHHHHHHHHHHHhcCceEEEccCchh
Q 003958 32 VNIGALLSFS---TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNH-SGFLALAEALHLMEGQTVAIIGPQDAV 107 (784)
Q Consensus 32 i~IG~i~~~~---~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~-~~~~a~~~~~~li~~~v~aiiGp~~s~ 107 (784)
.+++++.+-. ..+.+....|++.+.++. +|. ++...+... ++........++.+++...||++.. .
T Consensus 2 ~~v~~~~~g~~~D~g~n~~~~~G~~~~~~~~-------~~i--~~~~~e~~~~~~~~~~~~~~~~~~~g~dlIi~~g~-~ 71 (306)
T PF02608_consen 2 KKVALLDPGGINDKGFNQSAYEGLKRAEKEL-------DGI--EIIYVENVPETDADYEEAIRQLADQGYDLIIGHGF-E 71 (306)
T ss_dssp EEEEEESSS-CCCSSHHHHHHHHHHHHHHHC-------TTE--EEEEEES-S-TCHHHHHHHHHHHHTT-SEEEEESG-G
T ss_pred eEEEEEECCCCCCccHHHHHHHHHHHHHHHc-------CCc--eEEEEecCCccHHHHHHHHHHHHHcCCCEEEEccH-H
Confidence 3566776654 223334455555555552 233 444444443 4555666777788888888888543 3
Q ss_pred hHHHHHHhhhcC-CccEEecccCCCCCCcCCCCceEeecCChH---HHHHHHHHHHHHcCCcEEEEEE---E-cCCCcch
Q 003958 108 TSHVVSHVANEL-QVPLLSFSATDPTLSSLQFPYFVRTTQSDQ---YQMAAIAEIVDHYGWREVIAIY---V-DDDHGRN 179 (784)
Q Consensus 108 ~~~~va~~~~~~-~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~---~~~~ai~~~l~~~~w~~v~ii~---~-d~~~g~~ 179 (784)
...++..++..+ ++-.+...+..... .|++........ .++-.++.++.+- .+++++. . +...-..
T Consensus 72 ~~~~~~~vA~~yPd~~F~~~d~~~~~~----~~Nv~~~~f~~~e~~fLaG~~Aa~~tkt--~~vg~ig~i~G~~~p~~~~ 145 (306)
T PF02608_consen 72 YSDALQEVAKEYPDTKFIIIDGYIDAP----EPNVISITFREEEASFLAGYLAALMTKT--GKVGFIGDIGGMDIPPVNR 145 (306)
T ss_dssp GHHHHHHHHTC-TTSEEEEESS---ST-----TTEEEEEE-HHHHHHHHHHHHHHHHSS--TEEEEEEEEES--SCTTHH
T ss_pred HHHHHHHHHHHCCCCEEEEEecCcCCC----CCcEEEEEccccchhHHHHHHHHHHhcc--CcccccccccCCCcHhHHH
Confidence 344556666666 45444433322111 134444444333 2333344444433 5788887 3 3344445
Q ss_pred hHHHHHHHHhcc--CcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHcCC
Q 003958 180 GIAALGDTLAAK--RCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGM 246 (784)
Q Consensus 180 ~~~~l~~~l~~~--gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~g~ 246 (784)
+...|..-++.. ++++.....-.. .+...-...-+.+-..++|+|+-.+. .....+++++++.|.
T Consensus 146 ~~~gF~~Ga~~~np~i~v~~~~~gs~-~D~~~~~~~a~~li~~GaDvI~~~ag-~~~~gv~~aa~e~g~ 212 (306)
T PF02608_consen 146 FINGFIAGAKYVNPDIKVNVSYTGSF-NDPAKAKEAAEALIDQGADVIFPVAG-GSGQGVIQAAKEAGV 212 (306)
T ss_dssp HHHHHHHHHHHTTTT-EEEEEE-SSS-S-HHHHHHHHHHHHHTT-SEEEEE-C-CCHHHHHHHHHHHTH
T ss_pred HHHHHHHHHHHhCcCceEEEEEcCCc-CchHHHHHHHHHHhhcCCeEEEECCC-CCchHHHHHHHHcCC
Confidence 566676666554 344432221111 23334445555566689999888554 455678889988774
No 236
>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=86.80 E-value=27 Score=32.71 Aligned_cols=68 Identities=21% Similarity=0.260 Sum_probs=44.0
Q ss_pred eeeHHHHHHHHHHC-CCccceEEeeCCCCCCCCChhHHHHHHHcCcccEEEeeEEeecCccccceeccccccccEEEEEe
Q 003958 494 GFCIDVFTAAINLL-PYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAP 572 (784)
Q Consensus 494 G~~~dl~~~l~~~l-~f~~~~~~~~~~~~~~~~~~~g~i~~l~~~~~D~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~ 572 (784)
.+..+++..+.+.. +.+ +++.. ++...+++.+.+|++|+++..... ....+. ..+.....+.++++
T Consensus 13 ~~l~~~l~~~~~~~P~i~--i~~~~-------~~~~~~~~~l~~~~~D~~i~~~~~---~~~~~~-~~~l~~~~~~~v~~ 79 (198)
T cd08421 13 EFLPEDLASFLAAHPDVR--IDLEE-------RLSADIVRAVAEGRADLGIVAGNV---DAAGLE-TRPYRTDRLVVVVP 79 (198)
T ss_pred hhhHHHHHHHHHHCCCce--EEEEe-------cCcHHHHHHHhcCCceEEEEecCC---CCCCcE-EEEeecCcEEEEeC
Confidence 34567788888775 334 55442 346688999999999999864322 223333 35677777877775
Q ss_pred cc
Q 003958 573 VR 574 (784)
Q Consensus 573 ~~ 574 (784)
+.
T Consensus 80 ~~ 81 (198)
T cd08421 80 RD 81 (198)
T ss_pred CC
Confidence 54
No 237
>PRK09860 putative alcohol dehydrogenase; Provisional
Probab=86.24 E-value=3.3 Score=44.65 Aligned_cols=86 Identities=6% Similarity=0.013 Sum_probs=63.1
Q ss_pred HHHHHHHHHcCCcEEEEEEEcCCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccC-
Q 003958 153 AAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY- 231 (784)
Q Consensus 153 ~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~- 231 (784)
..+.+.++.+|.+++.+++...-......+.+.+.+++.|+.+.....+.+++..++....++.+++.++|+||-.+.+
T Consensus 20 ~~l~~~~~~~g~~~~livt~~~~~~~g~~~~v~~~L~~~~i~~~~f~~v~~np~~~~v~~~~~~~~~~~~D~IiaiGGGS 99 (383)
T PRK09860 20 TDAMNMMADYGFTRTLIVTDNMLTKLGMAGDVQKALEERNIFSVIYDGTQPNPTTENVAAGLKLLKENNCDSVISLGGGS 99 (383)
T ss_pred HHHHHHHHhcCCCEEEEEcCcchhhCccHHHHHHHHHHcCCeEEEeCCCCCCcCHHHHHHHHHHHHHcCCCEEEEeCCch
Confidence 4567788999999999998643333456788999999999876554455555677888888999999999999976543
Q ss_pred -CcHHHHH
Q 003958 232 -NRGPVVF 238 (784)
Q Consensus 232 -~~~~~~~ 238 (784)
-++...+
T Consensus 100 ~iD~AK~i 107 (383)
T PRK09860 100 PHDCAKGI 107 (383)
T ss_pred HHHHHHHH
Confidence 3344444
No 238
>COG1454 EutG Alcohol dehydrogenase, class IV [Energy production and conversion]
Probab=85.87 E-value=4.8 Score=42.68 Aligned_cols=91 Identities=10% Similarity=-0.020 Sum_probs=71.9
Q ss_pred HHHHHHHHHcCCcEEEEEEEcCCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccC-
Q 003958 153 AAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY- 231 (784)
Q Consensus 153 ~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~- 231 (784)
..+.+.++.+|++++.||++..-......+.+.+.|++.|+.+.....+.+++..+....-+...++.++|.||-.+.+
T Consensus 18 ~~l~~~~~~~g~~r~liVTd~~~~~~g~~~~v~~~L~~~~i~~~if~~v~p~P~~~~v~~~~~~~~~~~~D~iIalGGGS 97 (377)
T COG1454 18 KELGEEVKRLGAKRALIVTDRGLAKLGLLDKVLDSLDAAGIEYEVFDEVEPEPTIETVEAGAEVAREFGPDTIIALGGGS 97 (377)
T ss_pred HHHHHHHHhcCCCceEEEECCccccchhHHHHHHHHHhcCCeEEEecCCCCCCCHHHHHHHHHHHHhcCCCEEEEeCCcc
Confidence 4667778889999999999877666778999999999999887777777777778888888899999999999987544
Q ss_pred -CcHHHHHHHHHH
Q 003958 232 -NRGPVVFHVAQY 243 (784)
Q Consensus 232 -~~~~~~~~~a~~ 243 (784)
-++...+.-...
T Consensus 98 ~~D~AK~i~~~~~ 110 (377)
T COG1454 98 VIDAAKAIALLAE 110 (377)
T ss_pred HHHHHHHHHHHhh
Confidence 344444444433
No 239
>TIGR00035 asp_race aspartate racemase.
Probab=85.36 E-value=8.1 Score=38.21 Aligned_cols=44 Identities=18% Similarity=0.241 Sum_probs=24.3
Q ss_pred HHHHHHHHHH-HHhcCceEEEccCchhhHHHHHHhhhcCCccEEec
Q 003958 82 GFLALAEALH-LMEGQTVAIIGPQDAVTSHVVSHVANELQVPLLSF 126 (784)
Q Consensus 82 ~~~a~~~~~~-li~~~v~aiiGp~~s~~~~~va~~~~~~~ip~Is~ 126 (784)
+...+..+.+ |.+.++.+|+=+..+.... +..+-+..++|+|+.
T Consensus 60 ~~~~l~~~~~~L~~~g~d~iviaCNTah~~-~~~l~~~~~iPii~i 104 (229)
T TIGR00035 60 PRPILIDIAVKLENAGADFIIMPCNTAHKF-AEDIQKAIGIPLISM 104 (229)
T ss_pred HHHHHHHHHHHHHHcCCCEEEECCccHHHH-HHHHHHhCCCCEech
Confidence 4444433333 3344888887655444332 345555678888863
No 240
>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=84.87 E-value=15 Score=34.43 Aligned_cols=99 Identities=11% Similarity=0.051 Sum_probs=64.5
Q ss_pred HHHHHHHHHHHcCCcEEEEEEEcCCCcchhHHHHHHHHhcc--CcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEe
Q 003958 151 QMAAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAK--RCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVH 228 (784)
Q Consensus 151 ~~~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~~l~~~--gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~ 228 (784)
....+.+.+...++ ++.++..+.+. .+.+.+.+++. |+.|+....-+ .+..+...+++.|+++++|+|++.
T Consensus 36 l~~~l~~~~~~~~~-~ifllG~~~~~----~~~~~~~l~~~yP~l~ivg~~~g~--f~~~~~~~i~~~I~~~~pdiv~vg 108 (172)
T PF03808_consen 36 LFPDLLRRAEQRGK-RIFLLGGSEEV----LEKAAANLRRRYPGLRIVGYHHGY--FDEEEEEAIINRINASGPDIVFVG 108 (172)
T ss_pred HHHHHHHHHHHcCC-eEEEEeCCHHH----HHHHHHHHHHHCCCeEEEEecCCC--CChhhHHHHHHHHHHcCCCEEEEE
Confidence 34555555555554 88888876653 45555555554 66776544322 256678899999999999999998
Q ss_pred ccCCcHHHHHHHHHHcCCCCCCeEEEecCcc
Q 003958 229 THYNRGPVVFHVAQYLGMLGTGYVWIATSWL 259 (784)
Q Consensus 229 ~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~ 259 (784)
.....-..++.+.++.. . .. +|+..+..
T Consensus 109 lG~PkQE~~~~~~~~~l-~-~~-v~i~vG~~ 136 (172)
T PF03808_consen 109 LGAPKQERWIARHRQRL-P-AG-VIIGVGGA 136 (172)
T ss_pred CCCCHHHHHHHHHHHHC-C-CC-EEEEECch
Confidence 77776667776665532 2 22 67776643
No 241
>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=84.71 E-value=4.5 Score=44.08 Aligned_cols=79 Identities=15% Similarity=0.097 Sum_probs=60.4
Q ss_pred HHHHHHHHHcCCcEEEEEEEcCCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccC
Q 003958 153 AAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY 231 (784)
Q Consensus 153 ~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~ 231 (784)
..+.+++++++.+++.||++.........+.+.+.+++.|+.+.....+..+++.+.....++..++.++|+||-.+.+
T Consensus 12 ~~l~~~l~~~g~~~vlivt~~~~~~~g~~~~v~~~L~~~gi~~~~f~~v~~~p~~~~v~~~~~~~~~~~~D~IIaiGGG 90 (414)
T cd08190 12 AEVGMDLKNLGARRVCLVTDPNLAQLPPVKVVLDSLEAAGINFEVYDDVRVEPTDESFKDAIAFAKKGQFDAFVAVGGG 90 (414)
T ss_pred HHHHHHHHHcCCCeEEEEECcchhhcchHHHHHHHHHHcCCcEEEeCCCCCCcCHHHHHHHHHHHHhcCCCEEEEeCCc
Confidence 4566778899999999998766554456788999999889877654445545566778888888889999999987554
No 242
>PRK15454 ethanol dehydrogenase EutG; Provisional
Probab=84.51 E-value=3.9 Score=44.21 Aligned_cols=79 Identities=10% Similarity=0.050 Sum_probs=59.9
Q ss_pred HHHHHHHHHcCCcEEEEEEEcCCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccC
Q 003958 153 AAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY 231 (784)
Q Consensus 153 ~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~ 231 (784)
..+.+.++.+|.+++.+++...-......+.+.+.|++.|+.+.....+.+++..+.....++..++.++|+||-.+.+
T Consensus 38 ~~l~~~~~~~g~~~~lvv~~~~~~~~g~~~~v~~~L~~~gi~~~~~~~v~~~P~~~~v~~~~~~~r~~~~D~IiavGGG 116 (395)
T PRK15454 38 SSCGQQAQTRGLKHLFVMADSFLHQAGMTAGLTRSLAVKGIAMTLWPCPVGEPCITDVCAAVAQLRESGCDGVIAFGGG 116 (395)
T ss_pred HHHHHHHHhcCCCEEEEEcCcchhhCccHHHHHHHHHHcCCeEEEECCCCCCcCHHHHHHHHHHHHhcCcCEEEEeCCh
Confidence 4567788889998888887544333456788999999999887654445555666778888888999999999987654
No 243
>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=84.43 E-value=4.7 Score=43.30 Aligned_cols=88 Identities=7% Similarity=-0.050 Sum_probs=63.6
Q ss_pred HHHHHHHHHcCCcEEEEEEEcCCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccC-
Q 003958 153 AAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY- 231 (784)
Q Consensus 153 ~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~- 231 (784)
..+.++++.++.+++.++++.........+.+.+.+++.|+++.....+..+++.+.....+...++.++|.||-.+.+
T Consensus 13 ~~l~~~l~~~g~~~~liv~~~~~~~~~~~~~v~~~L~~~g~~~~~~~~v~~~p~~~~v~~~~~~~~~~~~d~IIaiGGGS 92 (370)
T cd08192 13 KELPAECAELGIKRPLIVTDPGLAALGLVARVLALLEDAGLAAALFDEVPPNPTEAAVEAGLAAYRAGGCDGVIAFGGGS 92 (370)
T ss_pred HHHHHHHHHcCCCeEEEEcCcchhhCccHHHHHHHHHHcCCeEEEeCCCCCCCCHHHHHHHHHHHHhcCCCEEEEeCCch
Confidence 4567788889999999998655443446788999999989887654445555667778888888888999999976443
Q ss_pred -CcHHHHHHH
Q 003958 232 -NRGPVVFHV 240 (784)
Q Consensus 232 -~~~~~~~~~ 240 (784)
-++..++..
T Consensus 93 viD~aK~ia~ 102 (370)
T cd08192 93 ALDLAKAVAL 102 (370)
T ss_pred HHHHHHHHHH
Confidence 444444433
No 244
>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=83.61 E-value=37 Score=31.47 Aligned_cols=69 Identities=17% Similarity=0.232 Sum_probs=43.4
Q ss_pred eeeHHHHHHHHHHCCCccceEEeeCCCCCCCCChhHHHHHHHcCcccEEEeeEEeecCccccceeccccccccEEEEEec
Q 003958 494 GFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPV 573 (784)
Q Consensus 494 G~~~dl~~~l~~~l~f~~~~~~~~~~~~~~~~~~~g~i~~l~~~~~D~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~ 573 (784)
.+..+++..+.+..- ++++++.. +....+.+.+.+|++|+++..... ....+ -+.++....+++++++
T Consensus 13 ~~l~~~l~~~~~~~p-~v~i~i~~-------~~~~~~~~~l~~g~~D~~i~~~~~---~~~~~-~~~~l~~~~~~~~~~~ 80 (197)
T cd08440 13 TLLPPVLAAFRRRHP-GIRVRLRD-------VSAEQVIEAVRSGEVDFGIGSEPE---ADPDL-EFEPLLRDPFVLVCPK 80 (197)
T ss_pred hHHHHHHHHHHHhCC-CcEEEEEe-------CChHHHHHHHHcCCccEEEEeCCC---CCCCe-eEEEeecccEEEEecC
Confidence 455677888877652 33355542 346788999999999999864322 22222 2346667777777755
Q ss_pred c
Q 003958 574 R 574 (784)
Q Consensus 574 ~ 574 (784)
.
T Consensus 81 ~ 81 (197)
T cd08440 81 D 81 (197)
T ss_pred C
Confidence 4
No 245
>PRK10624 L-1,2-propanediol oxidoreductase; Provisional
Probab=83.45 E-value=5 Score=43.26 Aligned_cols=78 Identities=10% Similarity=0.103 Sum_probs=58.8
Q ss_pred HHHHHHHHHcCCcEEEEEEEcCCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEecc
Q 003958 153 AAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTH 230 (784)
Q Consensus 153 ~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~ 230 (784)
..+.+.++.++.+++.|+++....-....+.+.+.+++.|+.+.....+..++..++....++.+++.++|+||-.+.
T Consensus 19 ~~l~~~~~~~g~~~~lvvtd~~~~~~g~~~~v~~~L~~~g~~~~~~~~v~~~p~~~~v~~~~~~~~~~~~D~IIaiGG 96 (382)
T PRK10624 19 GALTDEVKRRGFKKALIVTDKTLVKCGVVAKVTDVLDAAGLAYEIYDGVKPNPTIEVVKEGVEVFKASGADYLIAIGG 96 (382)
T ss_pred HHHHHHHHhcCCCEEEEEeCcchhhCcchHHHHHHHHHCCCeEEEeCCCCCCcCHHHHHHHHHHHHhcCCCEEEEeCC
Confidence 457778888999999999865444344678899999999987665444544456677888888889899999987644
No 246
>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=83.27 E-value=39 Score=31.38 Aligned_cols=68 Identities=16% Similarity=0.101 Sum_probs=42.4
Q ss_pred eeeHHHHHHHHHHC-CCccceEEeeCCCCCCCCChhHHHHHHHcCcccEEEeeEEeecCccccceeccccccccEEEEEe
Q 003958 494 GFCIDVFTAAINLL-PYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAP 572 (784)
Q Consensus 494 G~~~dl~~~l~~~l-~f~~~~~~~~~~~~~~~~~~~g~i~~l~~~~~D~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~ 572 (784)
.+..+++..+.+.. +.+ +++.. +....++..+.+|++|+++... +.....+ -..+.....+.++++
T Consensus 13 ~~l~~~l~~~~~~~P~i~--l~i~~-------~~~~~~~~~l~~g~~Dl~i~~~---~~~~~~~-~~~~l~~~~~~~v~~ 79 (193)
T cd08442 13 VRLPPLLAAYHARYPKVD--LSLST-------GTTGALIQAVLEGRLDGAFVAG---PVEHPRL-EQEPVFQEELVLVSP 79 (193)
T ss_pred hhhHHHHHHHHHHCCCce--EEEEe-------CCcHHHHHHHHCCCccEEEEeC---CCCCCCc-EEEEeecCcEEEEec
Confidence 44567788887775 444 44432 3466889999999999998542 2222222 234566677777765
Q ss_pred cc
Q 003958 573 VR 574 (784)
Q Consensus 573 ~~ 574 (784)
..
T Consensus 80 ~~ 81 (193)
T cd08442 80 KG 81 (193)
T ss_pred CC
Confidence 43
No 247
>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=82.58 E-value=5.8 Score=42.71 Aligned_cols=87 Identities=10% Similarity=0.051 Sum_probs=62.8
Q ss_pred HHHHHHHHHcCCcEEEEEEEcCCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccC-
Q 003958 153 AAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY- 231 (784)
Q Consensus 153 ~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~- 231 (784)
..+.++++.++.+++.+++...-......+.+.+.+++.|+.+.....+..+++.+.....++.+++.++|.||-.+.+
T Consensus 15 ~~l~~~l~~~~~~~~livt~~~~~~~~~~~~v~~~L~~~~~~~~~~~~v~~~p~~~~v~~~~~~~~~~~~D~IIaiGGGs 94 (376)
T cd08193 15 ARLGELLAALGAKRVLVVTDPGILKAGLIDPLLASLEAAGIEVTVFDDVEADPPEAVVEAAVEAARAAGADGVIGFGGGS 94 (376)
T ss_pred HHHHHHHHHcCCCeEEEEcCcchhhCccHHHHHHHHHHcCCeEEEECCCCCCcCHHHHHHHHHHHHhcCCCEEEEeCCch
Confidence 4566778888999999998654333446788999999999877644445555667788888889999999999987544
Q ss_pred -CcHHHHHH
Q 003958 232 -NRGPVVFH 239 (784)
Q Consensus 232 -~~~~~~~~ 239 (784)
-++..++.
T Consensus 95 ~iD~aK~ia 103 (376)
T cd08193 95 SMDVAKLVA 103 (376)
T ss_pred HHHHHHHHH
Confidence 34444443
No 248
>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=82.40 E-value=42 Score=31.22 Aligned_cols=69 Identities=14% Similarity=0.144 Sum_probs=43.0
Q ss_pred eeeeHHHHHHHHHHC-CCccceEEeeCCCCCCCCChhHHHHHHHcCcccEEEeeEEeecCccccceeccccccccEEEEE
Q 003958 493 SGFCIDVFTAAINLL-PYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVA 571 (784)
Q Consensus 493 ~G~~~dl~~~l~~~l-~f~~~~~~~~~~~~~~~~~~~g~i~~l~~~~~D~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~ 571 (784)
..+..+++..+.+.. +.+ +++.. +.-..++..|.+|++|+++...... ...+ .+.+.....+.+++
T Consensus 12 ~~~l~~~l~~~~~~~P~~~--l~~~~-------~~~~~~~~~l~~g~~D~~i~~~~~~---~~~~-~~~~l~~~~~~~v~ 78 (201)
T cd08420 12 EYLLPRLLARFRKRYPEVR--VSLTI-------GNTEEIAERVLDGEIDLGLVEGPVD---HPDL-IVEPFAEDELVLVV 78 (201)
T ss_pred hhhhHHHHHHHHHHCCCce--EEEEe-------CCcHHHHHHHHCCCccEEEecCCCC---Ccce-EEEeecCccEEEEe
Confidence 345567788887775 344 54443 2355788999999999988643222 2222 23566777777776
Q ss_pred ecc
Q 003958 572 PVR 574 (784)
Q Consensus 572 ~~~ 574 (784)
+..
T Consensus 79 ~~~ 81 (201)
T cd08420 79 PPD 81 (201)
T ss_pred cCC
Confidence 544
No 249
>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=81.96 E-value=23 Score=33.36 Aligned_cols=69 Identities=19% Similarity=0.222 Sum_probs=43.4
Q ss_pred eeeHHHHHHHHHHCCCccceEEeeCCCCCCCCChhHHHHHHHcCcccEEEeeEEeecCccccceeccccccccEEEEEec
Q 003958 494 GFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPV 573 (784)
Q Consensus 494 G~~~dl~~~l~~~l~f~~~~~~~~~~~~~~~~~~~g~i~~l~~~~~D~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~ 573 (784)
.+..+++..+.++.- .+++++.. +..+.+...|.+|++|+++...... ...+ .+.|.....++++++.
T Consensus 13 ~~l~~~l~~~~~~~P-~v~v~i~~-------~~~~~~~~~l~~g~~D~~i~~~~~~---~~~l-~~~~l~~~~~~~v~~~ 80 (201)
T cd08459 13 YFLPRLLAALREVAP-GVRIETVR-------LPVDELEEALESGEIDLAIGYLPDL---GAGF-FQQRLFRERYVCLVRK 80 (201)
T ss_pred HHHHHHHHHHHHHCC-CCeEEEEe-------cCccCHHHHhhCCCceEEEEcCCCC---cccc-eEEEeecCceEEEEcC
Confidence 345567777777752 23355442 3455788999999999998543221 2223 3467777888887765
Q ss_pred c
Q 003958 574 R 574 (784)
Q Consensus 574 ~ 574 (784)
.
T Consensus 81 ~ 81 (201)
T cd08459 81 D 81 (201)
T ss_pred C
Confidence 4
No 250
>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=81.89 E-value=6.9 Score=42.05 Aligned_cols=89 Identities=8% Similarity=0.010 Sum_probs=63.8
Q ss_pred HHHHHHHHHcCCcEEEEEEEcCCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccC-
Q 003958 153 AAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY- 231 (784)
Q Consensus 153 ~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~- 231 (784)
..+.+.++.++-+++.+++..........+.+.+.+++.|+.+.....+..+...+.....+..+++.++|+||-.+.+
T Consensus 15 ~~l~~~l~~~g~~~~lvvt~~~~~~~g~~~~v~~~L~~~g~~~~~~~~v~~~p~~~~v~~~~~~~~~~~~d~IIaiGGGS 94 (374)
T cd08189 15 AQLPAAISQLGVKKVLIVTDKGLVKLGLLDKVLEALEGAGIEYAVYDGVPPDPTIENVEAGLALYRENGCDAILAVGGGS 94 (374)
T ss_pred HHHHHHHHhcCCCeEEEEeCcchhhcccHHHHHHHHHhcCCeEEEeCCCCCCcCHHHHHHHHHHHHhcCCCEEEEeCCcc
Confidence 4567778888889999998655443345788999999989877655455555667778888888999999999976443
Q ss_pred -CcHHHHHHHH
Q 003958 232 -NRGPVVFHVA 241 (784)
Q Consensus 232 -~~~~~~~~~a 241 (784)
-++..++...
T Consensus 95 ~~D~aK~ia~~ 105 (374)
T cd08189 95 VIDCAKAIAAR 105 (374)
T ss_pred HHHHHHHHHHH
Confidence 4444444333
No 251
>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=81.88 E-value=6.9 Score=42.01 Aligned_cols=87 Identities=7% Similarity=0.001 Sum_probs=63.2
Q ss_pred HHHHHHHHHcCCcEEEEEEEcCCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccC-
Q 003958 153 AAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY- 231 (784)
Q Consensus 153 ~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~- 231 (784)
..+.++++.++.+++.+|+....+.....+.+.+.+++.|+++.....+..+.+.++....+..+++.++|.||-.+.+
T Consensus 12 ~~l~~~l~~~~~~~~lvv~~~~~~~~~~~~~v~~~L~~~~~~~~~~~~~~~~p~~~~v~~~~~~~~~~~~d~IiaiGGGs 91 (370)
T cd08551 12 EKLGEEIKNLGGRKALIVTDPGLVKTGVLDKVIDSLKEAGIEVVIFDGVEPNPTLSNVDAAVAAYREEGCDGVIAVGGGS 91 (370)
T ss_pred HHHHHHHHHcCCCeEEEEeCcchhhCccHHHHHHHHHHcCCeEEEECCCCCCCCHHHHHHHHHHHHhcCCCEEEEeCCch
Confidence 4667778888999999998655443466788999999888876644445545577788888989988999999876543
Q ss_pred -CcHHHHHH
Q 003958 232 -NRGPVVFH 239 (784)
Q Consensus 232 -~~~~~~~~ 239 (784)
-++..++.
T Consensus 92 ~~D~AK~va 100 (370)
T cd08551 92 VLDTAKAIA 100 (370)
T ss_pred HHHHHHHHH
Confidence 34444443
No 252
>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=81.79 E-value=6.9 Score=42.09 Aligned_cols=79 Identities=9% Similarity=0.053 Sum_probs=60.1
Q ss_pred HHHHHHHHHcCCcEEEEEEEcCCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccC
Q 003958 153 AAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY 231 (784)
Q Consensus 153 ~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~ 231 (784)
..+.++++.++.+++.+|+....+.....+.+.+.+++.|+.+.....+..++..+.....+..+++.++|.||-.+.+
T Consensus 12 ~~l~~~~~~~~~~r~livt~~~~~~~g~~~~v~~~L~~~gi~~~~~~~v~~~p~~~~v~~~~~~~~~~~~D~IIaiGGG 90 (375)
T cd08194 12 DETGAVLADLGGKRPLIVTDKVMVKLGLVDKLTDSLKKEGIESAIFDDVVSEPTDESVEEGVKLAKEGGCDVIIALGGG 90 (375)
T ss_pred HHHHHHHHHcCCCeEEEEcCcchhhcchHHHHHHHHHHCCCeEEEECCCCCCcCHHHHHHHHHHHHhcCCCEEEEeCCc
Confidence 4556677778889999999655553346788999999999887655556555667778888888999999999977543
No 253
>PRK11151 DNA-binding transcriptional regulator OxyR; Provisional
Probab=81.39 E-value=51 Score=34.10 Aligned_cols=69 Identities=9% Similarity=0.101 Sum_probs=44.2
Q ss_pred eeeHHHHHHHHHHCCCccceEEeeCCCCCCCCChhHHHHHHHcCcccEEEeeEEeecCccccceeccccccccEEEEEec
Q 003958 494 GFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPV 573 (784)
Q Consensus 494 G~~~dl~~~l~~~l~f~~~~~~~~~~~~~~~~~~~g~i~~l~~~~~D~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~ 573 (784)
.+...++..+.+.. -.+++.+.. +.-+.+++.|.+|++|+++.......+ .+ .+.|+....+++++++
T Consensus 104 ~~~~~~l~~~~~~~-P~v~i~~~~-------~~~~~~~~~l~~g~~Dl~i~~~~~~~~---~l-~~~~l~~~~~~~~~~~ 171 (305)
T PRK11151 104 YLLPHIIPMLHQTF-PKLEMYLHE-------AQTHQLLAQLDSGKLDCAILALVKESE---AF-IEVPLFDEPMLLAVYE 171 (305)
T ss_pred HHHHHHHHHHHHHC-CCcEEEEEe-------CCHHHHHHHHHcCCccEEEEecCCCCC---Ce-EEEEeccCcEEEEecC
Confidence 34455666666654 233355543 346789999999999999864322211 22 4578888888888865
Q ss_pred c
Q 003958 574 R 574 (784)
Q Consensus 574 ~ 574 (784)
.
T Consensus 172 ~ 172 (305)
T PRK11151 172 D 172 (305)
T ss_pred C
Confidence 4
No 254
>KOG3713 consensus Voltage-gated K+ channel KCNB/KCNC [Inorganic ion transport and metabolism]
Probab=81.24 E-value=2.4 Score=45.43 Aligned_cols=62 Identities=19% Similarity=0.299 Sum_probs=47.3
Q ss_pred HHHHHhhheecccCCCCCCCccCCceeehhhhhhhhh--cccccccccchhhHHHHHHHHHHHHHHhh
Q 003958 601 AVGAVVWILEHRLNDEFRGPPKRQVVTIFWFSFSTMF--FAHKEKTVSALGRLVLIIWLFVVLIINSS 666 (784)
Q Consensus 601 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~p~~~~~R~~~~~w~~~~lvl~~~ 666 (784)
+.+-+++.+|+-.+. ....++.-++||++.+|. +.|+-.|++++||++++.-.+.+.++++.
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 445566777664432 224568889999999997 45667999999999999999999877654
No 255
>COG0715 TauA ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]
Probab=80.87 E-value=6.8 Score=41.36 Aligned_cols=73 Identities=19% Similarity=0.247 Sum_probs=50.1
Q ss_pred cCCCCChHhhhhCCCceEEeeCchHHHHHHh----hcccCccCce-eCCCHHHHHHHHhcCCcCCCeeEEEechhhhHHH
Q 003958 681 SSPIKGIDSLRSSNYPIGYQVNSFARNYLVD----ELNIDESRLV-PLNSPEEYAKALKDGPHKGGVAAVVDDRAYAELF 755 (784)
Q Consensus 681 ~~~i~~~~dl~~~~~~i~~~~~~~~~~~~~~----~~~~~~~~~~-~~~~~~~~~~~l~~~~~~~~~~a~~~~~~~~~~~ 755 (784)
..+|++++||+ |+++|+..+++...++.. ..+.+.+++. ..-.+.++..+++. +.++|+..-.+.....
T Consensus 125 ~~~i~~~adlk--Gk~vg~~~~~~~~~~~l~~~L~~~Gl~~~dv~~v~~~~~~~~~al~~----g~vda~~~~ep~~~~~ 198 (335)
T COG0715 125 DSGIKSVADLK--GKKVGVPFGGSTSDFLLRYALAKAGLDPDDVELVNLPPADAVAALAA----GQVDAFVVWEPWNAAA 198 (335)
T ss_pred CCCcccccCCC--CceEEEeCCCchHHHHHHHHHHHcCCCcccceEEeeCcHHHHHHHhc----CCcceEEecCCchhhh
Confidence 45889999998 999999987753333322 2333333332 23455688999988 8999988888877776
Q ss_pred HcCC
Q 003958 756 LSTR 759 (784)
Q Consensus 756 ~~~~ 759 (784)
..+.
T Consensus 199 ~~~~ 202 (335)
T COG0715 199 EGEG 202 (335)
T ss_pred hccC
Confidence 6553
No 256
>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=80.85 E-value=6.8 Score=42.19 Aligned_cols=79 Identities=9% Similarity=0.045 Sum_probs=58.8
Q ss_pred HHHHHHHHHcCCcEEEEEEEcCCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccC
Q 003958 153 AAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY 231 (784)
Q Consensus 153 ~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~ 231 (784)
..+.+.++.++.+++.|++.....-....+.+.+.+++.|+.+.....+..++..+......+.+++.++|.||-.+.+
T Consensus 18 ~~l~~~l~~~g~~r~lvvt~~~~~~~g~~~~v~~~L~~~~i~~~~~~~v~~~p~~~~v~~~~~~~~~~~~D~IiaiGGG 96 (379)
T TIGR02638 18 EDIVDEVKRRGFKKALVVTDKDLIKFGVADKVTDLLDEAGIAYELFDEVKPNPTITVVKAGVAAFKASGADYLIAIGGG 96 (379)
T ss_pred HHHHHHHHhcCCCEEEEEcCcchhhccchHHHHHHHHHCCCeEEEECCCCCCcCHHHHHHHHHHHHhcCCCEEEEeCCh
Confidence 4566778889999999998654333346788999999989876654444444566778888888888999999977543
No 257
>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=80.03 E-value=51 Score=30.62 Aligned_cols=68 Identities=16% Similarity=0.137 Sum_probs=42.9
Q ss_pred eeeHHHHHHHHHHC-CCccceEEeeCCCCCCCCChhHHHHHHHcCcccEEEeeEEeecCccccceeccccccccEEEEEe
Q 003958 494 GFCIDVFTAAINLL-PYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAP 572 (784)
Q Consensus 494 G~~~dl~~~l~~~l-~f~~~~~~~~~~~~~~~~~~~g~i~~l~~~~~D~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~ 572 (784)
.+..+++..+.++. +.+ +++.. +....++..+.+|++|+++....... ..+ -..++....++++++
T Consensus 12 ~~l~~~l~~~~~~~P~i~--l~i~~-------~~~~~~~~~l~~g~~Dl~i~~~~~~~---~~~-~~~~l~~~~~~~~~~ 78 (197)
T cd08419 12 YFAPRLLGAFCRRHPGVE--VSLRV-------GNREQVLERLADNEDDLAIMGRPPED---LDL-VAEPFLDNPLVVIAP 78 (197)
T ss_pred hHhhHHHHHHHHHCCCce--EEEEE-------CCHHHHHHHHhcCCccEEEecCCCCC---CCe-EEEEeccCCEEEEec
Confidence 35567777887775 444 44432 34667899999999999985422211 112 245677777777775
Q ss_pred cc
Q 003958 573 VR 574 (784)
Q Consensus 573 ~~ 574 (784)
..
T Consensus 79 ~~ 80 (197)
T cd08419 79 PD 80 (197)
T ss_pred CC
Confidence 44
No 258
>KOG3857 consensus Alcohol dehydrogenase, class IV [Energy production and conversion]
Probab=79.95 E-value=13 Score=38.03 Aligned_cols=95 Identities=9% Similarity=-0.003 Sum_probs=74.5
Q ss_pred CCCceEeecCChHHHHHHHH----HHHHHcCCcEEEEEEEcCCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHH
Q 003958 137 QFPYFVRTTQSDQYQMAAIA----EIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITD 212 (784)
Q Consensus 137 ~~p~~~r~~ps~~~~~~ai~----~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~ 212 (784)
.-++-|-+.||....+.... .-++..|.+++.++++.+---....+..++.|+++||.+.......++++..++..
T Consensus 39 ~~~~af~m~~s~~rfG~gv~~Evg~dikn~gaKk~llvTDkni~~~~~~~~a~~~L~~~~I~~~vyD~v~~ePtv~s~~~ 118 (465)
T KOG3857|consen 39 MMSVAFFMIPSTSRFGKGVLAEVGDDIKNLGAKKTLLVTDKNIAKLGLVKVAQDSLEENGINVEVYDKVQPEPTVGSVTA 118 (465)
T ss_pred cceeeEEeccchhhhcchhHHHHHHHHHhcCccceEEeeCCChhhcccHHHHHHHHHHcCCceEEecCccCCCchhhHHH
Confidence 34677777787776655543 44788999999999977765566778889999999999987777766677888999
Q ss_pred HHHHhhcCCceEEEEeccC
Q 003958 213 LLVKVALTESRIIVVHTHY 231 (784)
Q Consensus 213 ~l~~l~~~~~~vIvl~~~~ 231 (784)
.+.-.|+.+.|.+|-.+.+
T Consensus 119 alefak~~~fDs~vaiGGG 137 (465)
T KOG3857|consen 119 ALEFAKKKNFDSFVAIGGG 137 (465)
T ss_pred HHHHHHhcccceEEEEcCc
Confidence 9999999999988876543
No 259
>CHL00180 rbcR LysR transcriptional regulator; Provisional
Probab=79.88 E-value=61 Score=33.50 Aligned_cols=71 Identities=18% Similarity=0.231 Sum_probs=43.7
Q ss_pred eeHHHHHHHHHHCCCccceEEeeCCCCCCCCChhHHHHHHHcCcccEEEeeEEeecCccccceeccccccccEEEEEecc
Q 003958 495 FCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPVR 574 (784)
Q Consensus 495 ~~~dl~~~l~~~l~f~~~~~~~~~~~~~~~~~~~g~i~~l~~~~~D~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~~ 574 (784)
+..+++..+.+... .+++.+.. +....++..+.+|++|+++..-....+....+ ...++....++++++..
T Consensus 109 ~~~~~l~~~~~~~P-~v~i~~~~-------~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~~-~~~~l~~~~~~~v~~~~ 179 (305)
T CHL00180 109 LMPRLIGLFRQRYP-QINVQLQV-------HSTRRIAWNVANGQIDIAIVGGEVPTELKKIL-EITPYVEDELALIIPKS 179 (305)
T ss_pred HHHHHHHHHHHHCC-CceEEEEe-------CCHHHHHHHHHcCCccEEEEcCccCcccccce-eEEEeccCcEEEEECCC
Confidence 45567777776642 23344432 35788999999999999986422221111122 34677778888888665
No 260
>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=79.85 E-value=25 Score=33.13 Aligned_cols=69 Identities=19% Similarity=0.239 Sum_probs=43.8
Q ss_pred eeeeHHHHHHHHHHCCCccceEEeeCCCCCCCCChhHHHHHHHcCcccEEEeeEEeecCccccceeccccccccEEEEEe
Q 003958 493 SGFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAP 572 (784)
Q Consensus 493 ~G~~~dl~~~l~~~l~f~~~~~~~~~~~~~~~~~~~g~i~~l~~~~~D~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~ 572 (784)
..+..+++..+.++.- .+++++.. +.. .+++.+.+|++|+++..... ....+. ..|+....++++++
T Consensus 12 ~~~l~~~l~~~~~~~P-~v~v~l~~-------~~~-~~~~~l~~g~~D~~i~~~~~---~~~~~~-~~~l~~~~~~~v~~ 78 (200)
T cd08460 12 AAFGPALLAAVAAEAP-GVRLRFVP-------ESD-KDVDALREGRIDLEIGVLGP---TGPEIR-VQTLFRDRFVGVVR 78 (200)
T ss_pred HHHHHHHHHHHHHHCC-CCEEEEec-------Cch-hHHHHHHCCCccEEEecCCC---CCcchh-eeeeeccceEEEEe
Confidence 4556677888877752 33355532 234 67899999999999863221 122233 36777788888876
Q ss_pred cc
Q 003958 573 VR 574 (784)
Q Consensus 573 ~~ 574 (784)
..
T Consensus 79 ~~ 80 (200)
T cd08460 79 AG 80 (200)
T ss_pred CC
Confidence 54
No 261
>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=79.60 E-value=20 Score=34.27 Aligned_cols=91 Identities=22% Similarity=0.201 Sum_probs=56.2
Q ss_pred cCCCCChHhhhhCCCceE-EeeCchHHHHHHhhcc---cCccCcee----CCCHHHHHHHHhcCCcCCCeeEEEechhhh
Q 003958 681 SSPIKGIDSLRSSNYPIG-YQVNSFARNYLVDELN---IDESRLVP----LNSPEEYAKALKDGPHKGGVAAVVDDRAYA 752 (784)
Q Consensus 681 ~~~i~~~~dl~~~~~~i~-~~~~~~~~~~~~~~~~---~~~~~~~~----~~~~~~~~~~l~~~~~~~~~~a~~~~~~~~ 752 (784)
...|.+++||.+.+.++. =..||.+..+|..... .....+.. ..+..+....|.. |..|+-+.-...+
T Consensus 80 p~~i~~~~dL~~~~~r~vnR~~GSGtR~l~d~~l~~~gi~~~~i~gy~~~~~th~~vA~aVa~----G~AD~G~g~~~~A 155 (193)
T PF12727_consen 80 PKGITSLEDLADPGLRFVNRQPGSGTRILFDQLLAEEGIDPEDIPGYAQEANTHLAVAAAVAS----GKADAGIGIRAAA 155 (193)
T ss_pred CccCCCHHHhccCCcEEEECCCCCHHHHHHHHHHHHcCCChhhCCCccccccChHHHHHHHHc----CCCCEEeehHHHH
Confidence 457999999987777644 3578888888865432 23333333 3566788888988 7888887765555
Q ss_pred HHHHcCCCCeEEeCCccccceEEEEeeCC
Q 003958 753 ELFLSTRCEFSIVGQVFTKNGWGFVSIVS 781 (784)
Q Consensus 753 ~~~~~~~c~l~~~~~~~~~~~~~~~~~k~ 781 (784)
+.+. .-++. ++....|-++++|.
T Consensus 156 ~~~~--gL~Fv----pl~~E~~dlv~~~~ 178 (193)
T PF12727_consen 156 EEFY--GLDFV----PLAEERYDLVIRRE 178 (193)
T ss_pred Hhhc--CCCcE----EccccceEEEEEhh
Confidence 4221 11221 22335566666664
No 262
>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=79.42 E-value=18 Score=35.29 Aligned_cols=56 Identities=5% Similarity=-0.044 Sum_probs=32.0
Q ss_pred CCCHHHHHHHHhcCCcCCCeeEEEechhhhHHHHcCCCCeEEeCC-ccccceEEEEeeCCCC
Q 003958 723 LNSPEEYAKALKDGPHKGGVAAVVDDRAYAELFLSTRCEFSIVGQ-VFTKNGWGFVSIVSSF 783 (784)
Q Consensus 723 ~~~~~~~~~~l~~~~~~~~~~a~~~~~~~~~~~~~~~c~l~~~~~-~~~~~~~~~~~~k~s~ 783 (784)
..+..+..+.+.+ |+.++-+.....+.. ....+....+.+ ......|++++.|+++
T Consensus 135 ~~~~~~~~~~~~~----Ge~~~~~~~~~~~~~-~~~~~~~~~~P~~~~~~~~~~~ai~k~a~ 191 (216)
T TIGR01256 135 GEDVRQALQFVET----GNAPAGIVALSDVIP-SKKVGSVATFPEDLYKPIRYPAVIVKGGK 191 (216)
T ss_pred cCcHHHHHHHHHc----CCCCEEeeehhhhcc-cCCccEEEEeCccccCCccccEEEEECCC
Confidence 4566788888888 788776654322211 122333333333 2233467899999876
No 263
>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=78.84 E-value=6.1 Score=39.71 Aligned_cols=78 Identities=10% Similarity=0.072 Sum_probs=59.0
Q ss_pred EEEEEE--cCCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEe-ccCCcHHHHHHHHHH
Q 003958 167 VIAIYV--DDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVH-THYNRGPVVFHVAQY 243 (784)
Q Consensus 167 v~ii~~--d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~-~~~~~~~~~~~~a~~ 243 (784)
|++|.. ++.|.....+.+++.+++.|+.+... .+...+.......++++...++|.|++. ..+.....+++++.+
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 456663 45678888999999999999988765 2222355666677888777899999987 556678899999999
Q ss_pred cCC
Q 003958 244 LGM 246 (784)
Q Consensus 244 ~g~ 246 (784)
.|.
T Consensus 79 ~gI 81 (257)
T PF13407_consen 79 AGI 81 (257)
T ss_dssp TTS
T ss_pred cCc
Confidence 875
No 264
>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=78.75 E-value=57 Score=30.44 Aligned_cols=69 Identities=17% Similarity=0.244 Sum_probs=42.2
Q ss_pred eeeHHHHHHHHHHCCCccceEEeeCCCCCCCCChhHHHHHHHcCcccEEEeeEEeecCccccceeccccccccEEEEEec
Q 003958 494 GFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPV 573 (784)
Q Consensus 494 G~~~dl~~~l~~~l~f~~~~~~~~~~~~~~~~~~~g~i~~l~~~~~D~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~ 573 (784)
.+..+++..+.+... ++++++.. ..-..+...|.+|++|+++... +.....+ -+.+.....++++++.
T Consensus 13 ~~l~~~l~~~~~~~P-~i~i~~~~-------~~~~~~~~~l~~~~~D~~i~~~---~~~~~~~-~~~~l~~~~~~~~~~~ 80 (198)
T cd08433 13 VLAVPLLRAVRRRYP-GIRLRIVE-------GLSGHLLEWLLNGRLDLALLYG---PPPIPGL-STEPLLEEDLFLVGPA 80 (198)
T ss_pred hcchHHHHHHHHHCC-CcEEEEEe-------cCcHHHHHHHhCCCCcEEEEeC---CCCCCCe-eEEEeccccEEEEecC
Confidence 345677778877752 33355542 2345788999999999998532 2222222 3456777777777755
Q ss_pred c
Q 003958 574 R 574 (784)
Q Consensus 574 ~ 574 (784)
.
T Consensus 81 ~ 81 (198)
T cd08433 81 D 81 (198)
T ss_pred C
Confidence 4
No 265
>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=78.71 E-value=11 Score=40.75 Aligned_cols=85 Identities=6% Similarity=-0.012 Sum_probs=60.8
Q ss_pred HHHHHHHHHcCCcEEEEEEEcCC-CcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccC
Q 003958 153 AAIAEIVDHYGWREVIAIYVDDD-HGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY 231 (784)
Q Consensus 153 ~ai~~~l~~~~w~~v~ii~~d~~-~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~ 231 (784)
..+.++++.++ +++.||+.... ......+.+.+.+++.|+++.....+.+++..++........++.++|.||-.+.+
T Consensus 15 ~~l~~~~~~~g-~r~livt~~~~~~~~g~~~~v~~~L~~~~~~~~~~~~v~~~p~~~~v~~~~~~~~~~~~D~IiavGGG 93 (380)
T cd08185 15 NELGEEALKPG-KKALIVTGNGSSKKTGYLDRVIELLKQAGVEVVVFDKVEPNPTTTTVMEGAALAREEGCDFVVGLGGG 93 (380)
T ss_pred HHHHHHHHhcC-CeEEEEeCCCchhhccHHHHHHHHHHHcCCeEEEeCCccCCCCHHHHHHHHHHHHHcCCCEEEEeCCc
Confidence 34666777787 89999986554 24556788999999999887654455555667778888888888999999976543
Q ss_pred --CcHHHHH
Q 003958 232 --NRGPVVF 238 (784)
Q Consensus 232 --~~~~~~~ 238 (784)
-++...+
T Consensus 94 S~iD~aK~i 102 (380)
T cd08185 94 SSMDTAKAI 102 (380)
T ss_pred cHHHHHHHH
Confidence 3344444
No 266
>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=78.62 E-value=7 Score=39.51 Aligned_cols=59 Identities=17% Similarity=0.128 Sum_probs=45.1
Q ss_pred CCCCChHhhhhCCCceEEeeCchHHHHHHhhcccCccCceeCCCHHHHHHHHhcCCcCCCeeEEEechhh
Q 003958 682 SPIKGIDSLRSSNYPIGYQVNSFARNYLVDELNIDESRLVPLNSPEEYAKALKDGPHKGGVAAVVDDRAY 751 (784)
Q Consensus 682 ~~i~~~~dl~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~a~~~~~~~ 751 (784)
.+|++++||+ |+++.+..++....+++. .+. ..+ ..+..|.+.+|++ |.+|+.+.....
T Consensus 126 ~~i~s~~Dl~--G~kir~~~~~~~~~~~~~-~Ga---~~v-~~~~~e~~~aL~~----G~vDg~~~~~~~ 184 (257)
T TIGR00787 126 KPITKPEDLK--GLKIRIPNSPMNEAQFKA-LGA---NPE-PMAFSEVYTALQT----GVVDGQENPLSN 184 (257)
T ss_pred CccCChHHhC--CCEEecCCCHHHHHHHHH-cCC---ccc-ccCHHHHHHHHHc----CCcccccCCHHH
Confidence 5799999999 999999877766777743 332 222 5677899999999 788888876443
No 267
>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=77.99 E-value=60 Score=30.27 Aligned_cols=69 Identities=10% Similarity=0.067 Sum_probs=42.8
Q ss_pred eeeHHHHHHHHHHCCCccceEEeeCCCCCCCCChhHHHHHHHcCcccEEEeeEEeecCccccceeccccccccEEEEEec
Q 003958 494 GFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPV 573 (784)
Q Consensus 494 G~~~dl~~~l~~~l~f~~~~~~~~~~~~~~~~~~~g~i~~l~~~~~D~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~ 573 (784)
.+..+++..+.+..- ++++++.. +....++..+.+|++|+++..... ....+. +.++....++++++.
T Consensus 13 ~~l~~~l~~~~~~~P-~i~l~i~~-------~~~~~~~~~l~~~~~D~~i~~~~~---~~~~~~-~~~l~~~~~~~v~~~ 80 (199)
T cd08426 13 ELLPSLIARFRQRYP-GVFFTVDV-------ASTADVLEAVLSGEADIGLAFSPP---PEPGIR-VHSRQPAPIGAVVPP 80 (199)
T ss_pred HHHHHHHHHHHHhCC-CeEEEEEe-------CCcHHHHHHHHCCCccEEEecCCC---CCCCeE-EEeeccCcEEEEecC
Confidence 345667777776642 23344432 345688999999999999853222 112232 456777788887755
Q ss_pred c
Q 003958 574 R 574 (784)
Q Consensus 574 ~ 574 (784)
.
T Consensus 81 ~ 81 (199)
T cd08426 81 G 81 (199)
T ss_pred C
Confidence 4
No 268
>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=77.94 E-value=59 Score=30.17 Aligned_cols=69 Identities=17% Similarity=0.240 Sum_probs=44.0
Q ss_pred eeeHHHHHHHHHHCCCccceEEeeCCCCCCCCChhHHHHHHHcCcccEEEeeEEeecCccccceeccccccccEEEEEec
Q 003958 494 GFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPV 573 (784)
Q Consensus 494 G~~~dl~~~l~~~l~f~~~~~~~~~~~~~~~~~~~g~i~~l~~~~~D~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~ 573 (784)
.+..++++.+.+... .+++++.. ++...++..|.+|++|+++...... ...+. ..++....+.++++.
T Consensus 13 ~~l~~~l~~~~~~~p-~v~i~i~~-------~~~~~~~~~L~~~~~Dl~i~~~~~~---~~~~~-~~~l~~~~~~~v~~~ 80 (197)
T cd08438 13 LLFAPLLAAFRQRYP-NIELELVE-------YGGKKVEQAVLNGELDVGITVLPVD---EEEFD-SQPLCNEPLVAVLPR 80 (197)
T ss_pred hhcHHHHHHHHHHCc-CeEEEEEE-------cCcHHHHHHHHcCCCCEEEEecccc---cCCce-eEEeccccEEEEecC
Confidence 456678888887753 33355443 3466889999999999998643321 22232 345667777777755
Q ss_pred c
Q 003958 574 R 574 (784)
Q Consensus 574 ~ 574 (784)
.
T Consensus 81 ~ 81 (197)
T cd08438 81 G 81 (197)
T ss_pred C
Confidence 4
No 269
>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=77.46 E-value=63 Score=30.21 Aligned_cols=68 Identities=15% Similarity=0.236 Sum_probs=41.4
Q ss_pred eeHHHHHHHHHHCCCccceEEeeCCCCCCCCChhHHHHHHHcCcccEEEeeEEeecCccccceeccccccccEEEEEecc
Q 003958 495 FCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPVR 574 (784)
Q Consensus 495 ~~~dl~~~l~~~l~f~~~~~~~~~~~~~~~~~~~g~i~~l~~~~~D~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~~ 574 (784)
+..+++..+.++.. ++++++.. ++...++..|.+|++|+++..-... ...+. ..++....++++++..
T Consensus 15 ~l~~~l~~~~~~~P-~i~i~i~~-------~~~~~~~~~l~~~~~Dl~i~~~~~~---~~~~~-~~~l~~~~~~~v~~~~ 82 (200)
T cd08411 15 LLPRLLPALRQAYP-KLRLYLRE-------DQTERLLEKLRSGELDAALLALPVD---EPGLE-EEPLFDEPFLLAVPKD 82 (200)
T ss_pred hhHHHHHHHHHHCC-CcEEEEEe-------CcHHHHHHHHHcCCccEEEEeccCC---CCCce-EEEeeccceEEEecCC
Confidence 55677777777752 23354432 3467889999999999998542211 12222 2456667777776544
No 270
>PRK12684 transcriptional regulator CysB-like protein; Reviewed
Probab=77.43 E-value=79 Score=32.87 Aligned_cols=90 Identities=8% Similarity=0.036 Sum_probs=51.4
Q ss_pred CChHhhhhCCCceEEeeCchH----HHHHHhhcccCccCceeCCCHHHHHHHHhcCCcCCCeeEEEechhhhHHHHcCCC
Q 003958 685 KGIDSLRSSNYPIGYQVNSFA----RNYLVDELNIDESRLVPLNSPEEYAKALKDGPHKGGVAAVVDDRAYAELFLSTRC 760 (784)
Q Consensus 685 ~~~~dl~~~~~~i~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~a~~~~~~~~~~~~~~~c 760 (784)
-+++||.+... |....++.. ..++. ..+..+......++.+...+.+.. |.-.+++.+. ..+.... -
T Consensus 184 i~~~dL~~~~~-i~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~v~~----g~Gv~~lp~~-~~~~~~~--~ 254 (313)
T PRK12684 184 LTLEDLAQYPL-ITYDFAFAGRSKINKAFA-LRGLKPDIVLEAIDADVIKTYVEL----GLGVGIVADM-AFDPERD--R 254 (313)
T ss_pred cCHHHHhcCCc-EecCCCCcHHHHHHHHHH-HcCCCCCeEEEeCCHHHHHHHHHh----CCceEEeehh-hcccccc--C
Confidence 46788885442 555555433 33442 234444445567888889999988 5445777653 3332222 2
Q ss_pred CeEEeC--CccccceEEEEeeCCCC
Q 003958 761 EFSIVG--QVFTKNGWGFVSIVSSF 783 (784)
Q Consensus 761 ~l~~~~--~~~~~~~~~~~~~k~s~ 783 (784)
++..+. .......+.++.+|+.+
T Consensus 255 ~l~~~~i~~~~~~~~~~l~~~~~~~ 279 (313)
T PRK12684 255 NLRAIDAGHLFGSSTTRLGLRRGAY 279 (313)
T ss_pred CeEEEECCCCCcceeEEEEEECCCc
Confidence 444442 33344578899998875
No 271
>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=77.01 E-value=20 Score=37.21 Aligned_cols=89 Identities=15% Similarity=0.064 Sum_probs=61.4
Q ss_pred EEEEEe---ecCCcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEccCchhhH
Q 003958 33 NIGALL---SFSTNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIGPQDAVTS 109 (784)
Q Consensus 33 ~IG~i~---~~~~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiGp~~s~~~ 109 (784)
++|.+. ......-.....|+...++..| |+.++...+..+-.|+.++.+.+..++++++.+|... .....
T Consensus 128 ~vg~ig~i~G~~~p~~~~~~~gF~~Ga~~~n------p~i~v~~~~~gs~~D~~~~~~~a~~li~~GaDvI~~~-ag~~~ 200 (306)
T PF02608_consen 128 KVGFIGDIGGMDIPPVNRFINGFIAGAKYVN------PDIKVNVSYTGSFNDPAKAKEAAEALIDQGADVIFPV-AGGSG 200 (306)
T ss_dssp EEEEEEEEES--SCTTHHHHHHHHHHHHHTT------TT-EEEEEE-SSSS-HHHHHHHHHHHHHTT-SEEEEE--CCCH
T ss_pred cccccccccCCCcHhHHHHHHHHHHHHHHhC------cCceEEEEEcCCcCchHHHHHHHHHHhhcCCeEEEEC-CCCCc
Confidence 456555 5553333567789999999998 6677888877888899999999999999999998872 23344
Q ss_pred HHHHHhhhcCCcc--EEeccc
Q 003958 110 HVVSHVANELQVP--LLSFSA 128 (784)
Q Consensus 110 ~~va~~~~~~~ip--~Is~~a 128 (784)
..+...++..+.. .|....
T Consensus 201 ~gv~~aa~e~g~~~~~IG~d~ 221 (306)
T PF02608_consen 201 QGVIQAAKEAGVYGYVIGVDS 221 (306)
T ss_dssp HHHHHHHHHHTHETEEEEEES
T ss_pred hHHHHHHHHcCCceEEEEecc
Confidence 5566777778877 776544
No 272
>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=76.98 E-value=12 Score=40.25 Aligned_cols=79 Identities=8% Similarity=-0.001 Sum_probs=57.5
Q ss_pred HHHHHHHHHcCCcEEEEEEEcCCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccC
Q 003958 153 AAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY 231 (784)
Q Consensus 153 ~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~ 231 (784)
..+.++++.++.+++.|+++.........+.+.+.+++.|+.+.....+..++...+....+...++.++|.||-.+.+
T Consensus 17 ~~l~~~l~~~g~~~~livt~~~~~~~~~~~~v~~~L~~~~~~~~~~~~v~~~p~~~~v~~~~~~~~~~~~d~IIaiGGG 95 (377)
T cd08188 17 KLAGRYARRLGAKKVLLVSDPGVIKAGWVDRVIESLEEAGLEYVVFSDVSPNPRDEEVMAGAELYLENGCDVIIAVGGG 95 (377)
T ss_pred HHHHHHHHHcCCCeEEEEeCcchhhCccHHHHHHHHHHcCCeEEEeCCCCCCCCHHHHHHHHHHHHhcCCCEEEEeCCc
Confidence 4567778888999999998654333345788899998888876544444444566677788888888999999977544
No 273
>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=76.67 E-value=51 Score=30.83 Aligned_cols=69 Identities=20% Similarity=0.253 Sum_probs=43.3
Q ss_pred eeeHHHHHHHHHHCCCccceEEeeCCCCCCCCChhHHHHHHHcCcccEEEeeEEeecCccccceeccccccccEEEEEec
Q 003958 494 GFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPV 573 (784)
Q Consensus 494 G~~~dl~~~l~~~l~f~~~~~~~~~~~~~~~~~~~g~i~~l~~~~~D~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~ 573 (784)
.+..+++..+.++.. ++++++.. +....+...+.+|++|+++..-. .....+ -..++....++++++.
T Consensus 13 ~~~~~~i~~~~~~~P-~i~l~~~~-------~~~~~~~~~l~~g~~D~~i~~~~---~~~~~~-~~~~l~~~~~~~v~~~ 80 (200)
T cd08417 13 LLLPPLLARLRQEAP-GVRLRFVP-------LDRDDLEEALESGEIDLAIGVFP---ELPPGL-RSQPLFEDRFVCVARK 80 (200)
T ss_pred HHHHHHHHHHHhhCC-CeEEEecc-------CCHHHHHHHHHcCCCCEEEeecc---cCCCcc-chhhhhcCceEEEecC
Confidence 445566777776652 22344432 45678999999999999986432 222223 2357777888888765
Q ss_pred c
Q 003958 574 R 574 (784)
Q Consensus 574 ~ 574 (784)
.
T Consensus 81 ~ 81 (200)
T cd08417 81 D 81 (200)
T ss_pred C
Confidence 4
No 274
>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=76.56 E-value=64 Score=29.82 Aligned_cols=68 Identities=21% Similarity=0.214 Sum_probs=42.3
Q ss_pred eeeHHHHHHHHHHC-CCccceEEeeCCCCCCCCChhHHHHHHHcCcccEEEeeEEeecCccccceeccccccccEEEEEe
Q 003958 494 GFCIDVFTAAINLL-PYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAP 572 (784)
Q Consensus 494 G~~~dl~~~l~~~l-~f~~~~~~~~~~~~~~~~~~~g~i~~l~~~~~D~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~ 572 (784)
.+...++..+.+.. +.+ +++.. +....++..+.+|++|+++..-. .....+. ..++....++++++
T Consensus 13 ~~l~~~l~~~~~~~P~i~--i~i~~-------~~~~~~~~~l~~~~~Dl~i~~~~---~~~~~l~-~~~l~~~~~~~v~~ 79 (195)
T cd08434 13 SLVPDLIRAFRKEYPNVT--FELHQ-------GSTDELLDDLKNGELDLALCSPV---PDEPDIE-WIPLFTEELVLVVP 79 (195)
T ss_pred hhhHHHHHHHHHhCCCeE--EEEec-------CcHHHHHHHHHcCCccEEEEccC---CCCCCee-EEEeecceEEEEec
Confidence 34556677777765 334 44432 34667899999999999885422 2222333 34667777777775
Q ss_pred cc
Q 003958 573 VR 574 (784)
Q Consensus 573 ~~ 574 (784)
+.
T Consensus 80 ~~ 81 (195)
T cd08434 80 KD 81 (195)
T ss_pred CC
Confidence 54
No 275
>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=75.83 E-value=14 Score=39.52 Aligned_cols=77 Identities=5% Similarity=0.038 Sum_probs=56.9
Q ss_pred HHHHHHHHcCCcEEEEEEEcCCCc-chhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccC
Q 003958 154 AIAEIVDHYGWREVIAIYVDDDHG-RNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY 231 (784)
Q Consensus 154 ai~~~l~~~~w~~v~ii~~d~~~g-~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~ 231 (784)
.+.++++.++ +++.+|++...+- ....+.+.+.+++.|+.+.....+.++++.++.....+..++.++|.||-.+.+
T Consensus 16 ~l~~~~~~~g-~r~lvVt~~~~~~~~g~~~~v~~~L~~~g~~~~~~~~v~~~p~~~~v~~~~~~~~~~~~D~IIavGGG 93 (357)
T cd08181 16 KHGEELAALG-KRALIVTGKSSAKKNGSLDDVTKALEELGIEYEIFDEVEENPSLETIMEAVEIAKKFNADFVIGIGGG 93 (357)
T ss_pred HHHHHHHHcC-CEEEEEeCCchHhhcCcHHHHHHHHHHcCCeEEEeCCCCCCcCHHHHHHHHHHHHhcCCCEEEEeCCc
Confidence 4556778888 8998888655433 234678889999989877654445555667778888888999999999987554
No 276
>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=75.69 E-value=74 Score=30.14 Aligned_cols=71 Identities=13% Similarity=0.227 Sum_probs=45.2
Q ss_pred eeeeHHHHHHHHHHCCCccceEEeeCCCCCCCCChhHHHHHHHcCcccEEEeeEEeecCccccceeccccccccEEEEEe
Q 003958 493 SGFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAP 572 (784)
Q Consensus 493 ~G~~~dl~~~l~~~l~f~~~~~~~~~~~~~~~~~~~g~i~~l~~~~~D~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~ 572 (784)
..+..+++..+.+..- .+++++... +....+++.|.+|++|+++..... ..+.+++ .++....+.++++
T Consensus 12 ~~~~~~~l~~~~~~~P-~~~v~~~~~------~~~~~l~~~L~~g~lDl~i~~~~~---~~~~l~~-~~l~~~~~~lv~~ 80 (203)
T cd08463 12 ALFLPELVARFRREAP-GARLEIHPL------GPDFDYERALASGELDLVIGNWPE---PPEHLHL-SPLFSDEIVCLMR 80 (203)
T ss_pred HHHhHHHHHHHHHHCC-CCEEEEEeC------CcchhHHHHHhcCCeeEEEecccc---CCCCcEE-eEeecCceEEEEe
Confidence 3466788888887753 233555432 235689999999999999863221 1122333 5677778887776
Q ss_pred cc
Q 003958 573 VR 574 (784)
Q Consensus 573 ~~ 574 (784)
..
T Consensus 81 ~~ 82 (203)
T cd08463 81 AD 82 (203)
T ss_pred CC
Confidence 55
No 277
>PRK11242 DNA-binding transcriptional regulator CynR; Provisional
Probab=75.63 E-value=1e+02 Score=31.61 Aligned_cols=69 Identities=13% Similarity=0.116 Sum_probs=45.1
Q ss_pred eeeHHHHHHHHHHCCCccceEEeeCCCCCCCCChhHHHHHHHcCcccEEEeeEEeecCccccceeccccccccEEEEEec
Q 003958 494 GFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPV 573 (784)
Q Consensus 494 G~~~dl~~~l~~~l~f~~~~~~~~~~~~~~~~~~~g~i~~l~~~~~D~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~ 573 (784)
.+..+++..+.++.. ++.+++.. +....++..+.+|++|+++..... ..+.+ .+.++....++++++.
T Consensus 104 ~~l~~~l~~~~~~~p-~~~i~~~~-------~~~~~~~~~l~~g~~Dl~i~~~~~---~~~~l-~~~~l~~~~~~~~~~~ 171 (296)
T PRK11242 104 YLIGPLIDAFHARYP-GITLTIRE-------MSQERIEALLADDELDVGIAFAPV---HSPEI-EAQPLFTETLALVVGR 171 (296)
T ss_pred hhhHHHHHHHHHHCC-CCEEEEEe-------CCHHHHHHHHHCCCCcEEEEecCC---CCcce-eEEEeeeccEEEEEcC
Confidence 445677888887752 33355542 346788999999999999864322 22223 3467777888888766
Q ss_pred c
Q 003958 574 R 574 (784)
Q Consensus 574 ~ 574 (784)
.
T Consensus 172 ~ 172 (296)
T PRK11242 172 H 172 (296)
T ss_pred C
Confidence 5
No 278
>COG1464 NlpA ABC-type metal ion transport system, periplasmic component/surface antigen [Inorganic ion transport and metabolism]
Probab=75.52 E-value=15 Score=36.51 Aligned_cols=75 Identities=21% Similarity=0.166 Sum_probs=43.0
Q ss_pred CchhhHHHHHHHHHHHHHHhhhccccCCCceEEEEEEeecCCcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCC
Q 003958 1 MKLSGVMLLMIFYCELFVYRITAQASGRPSVVNIGALLSFSTNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNH 80 (784)
Q Consensus 1 M~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~IG~i~~~~~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~ 80 (784)
|+++..+.+++++ ++++++|.++......+|+||..-..++ ..++..++-+.++ .|++|+++.+.+..
T Consensus 1 m~~~~~~~~~~~~-~l~~~~~~~~~~~~~~~I~vg~~~~p~a---~ile~~~k~~~~k--------~Gi~l~i~~FtDY~ 68 (268)
T COG1464 1 MKKLKKLALALVA-LLALAACGAAAAKATKTIKVGATPGPHA---EILEVVVKPALKK--------KGLDLKIVEFTDYV 68 (268)
T ss_pred CchHHHHHHHHHH-HHHHHhhhhhccccCCcEEEeecCCchH---HHHHHHHHHHHHh--------cCceEEEEEecCCc
Confidence 5555443333222 1233444443222226899998754442 2333355556555 37899999999888
Q ss_pred CHHHHHH
Q 003958 81 SGFLALA 87 (784)
Q Consensus 81 ~~~~a~~ 87 (784)
.|..|+.
T Consensus 69 ~PN~AL~ 75 (268)
T COG1464 69 QPNEALA 75 (268)
T ss_pred chhHHHh
Confidence 8887764
No 279
>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=75.13 E-value=11 Score=40.44 Aligned_cols=79 Identities=10% Similarity=0.076 Sum_probs=58.2
Q ss_pred HHHHHHHHHcCCcEEEEEEEcCCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccC
Q 003958 153 AAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY 231 (784)
Q Consensus 153 ~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~ 231 (784)
..+.+.++.++-+++.+++..........+.+.+.+++.|+.+.....+..++..+......+..++.++|.||-.+.+
T Consensus 17 ~~l~~~l~~~g~~~~lvv~~~~~~~~~~~~~v~~~L~~~~~~~~~f~~v~~~p~~~~v~~~~~~~~~~~~D~IIavGGG 95 (377)
T cd08176 17 KEIGDELKNLGFKKALIVTDKGLVKIGVVEKVTDVLDEAGIDYVIYDGVKPNPTITNVKDGLAVFKKEGCDFIISIGGG 95 (377)
T ss_pred HHHHHHHHHhCCCeEEEECCchHhhcCcHHHHHHHHHHcCCeEEEeCCCCCCCCHHHHHHHHHHHHhcCCCEEEEeCCc
Confidence 4566778888888998888544333356788999999888876554445445566778888888888999999977544
No 280
>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=74.86 E-value=37 Score=31.73 Aligned_cols=101 Identities=12% Similarity=0.008 Sum_probs=60.1
Q ss_pred HHHHHHHHHHHHcCCcEEEEEEEcCCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEec
Q 003958 150 YQMAAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHT 229 (784)
Q Consensus 150 ~~~~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~ 229 (784)
+....+.+.+...+ .++.++.+..+......+.+++.. -|+.++....-+ ....+-...++.|+++++|+|++..
T Consensus 33 dl~~~ll~~~~~~~-~~v~llG~~~~~~~~~~~~l~~~y--p~l~i~g~~~g~--~~~~~~~~i~~~I~~~~pdiv~vgl 107 (171)
T cd06533 33 DLMPALLELAAQKG-LRVFLLGAKPEVLEKAAERLRARY--PGLKIVGYHHGY--FGPEEEEEIIERINASGADILFVGL 107 (171)
T ss_pred HHHHHHHHHHHHcC-CeEEEECCCHHHHHHHHHHHHHHC--CCcEEEEecCCC--CChhhHHHHHHHHHHcCCCEEEEEC
Confidence 33455555555444 678888766654333333333322 367777643222 2334444589999999999999997
Q ss_pred cCCcHHHHHHHHHHcCCCCCCeEEEecCc
Q 003958 230 HYNRGPVVFHVAQYLGMLGTGYVWIATSW 258 (784)
Q Consensus 230 ~~~~~~~~~~~a~~~g~~~~~~~wi~~~~ 258 (784)
....-..++.+..+.. +.-++++.+.
T Consensus 108 G~PkQE~~~~~~~~~l---~~~v~~~vG~ 133 (171)
T cd06533 108 GAPKQELWIARHKDRL---PVPVAIGVGG 133 (171)
T ss_pred CCCHHHHHHHHHHHHC---CCCEEEEece
Confidence 7777777776666543 2335565543
No 281
>PRK11233 nitrogen assimilation transcriptional regulator; Provisional
Probab=74.66 E-value=57 Score=33.77 Aligned_cols=67 Identities=18% Similarity=0.106 Sum_probs=40.3
Q ss_pred eeHHHHHHHHHHC-CCccceEEeeCCCCCCCCChhHHHHHHHcCcccEEEeeEEeecCccccceeccccccccEEEEEec
Q 003958 495 FCIDVFTAAINLL-PYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPV 573 (784)
Q Consensus 495 ~~~dl~~~l~~~l-~f~~~~~~~~~~~~~~~~~~~g~i~~l~~~~~D~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~ 573 (784)
+..+++..+.++. +.. +++.. +....+...+.+|++|+++..-... ...+ ...|+....+.++++.
T Consensus 106 ~~~~~l~~~~~~~p~i~--l~~~~-------~~~~~~~~~l~~g~~Di~i~~~~~~---~~~~-~~~~l~~~~~~lv~~~ 172 (305)
T PRK11233 106 LTMPLLQAVRAEFPGIV--LYLHE-------NSGATLNEKLMNGQLDMAVIYEHSP---VAGL-SSQPLLKEDLFLVGTQ 172 (305)
T ss_pred HHHHHHHHHHHHCCCcE--EEEEE-------CCcHHHHHHHHCCCCCEEEEcCCcC---CCCc-EEEEEeeeeEEEEEcC
Confidence 3445777887765 444 44432 3456788999999999998532211 1222 2346666777766644
Q ss_pred c
Q 003958 574 R 574 (784)
Q Consensus 574 ~ 574 (784)
.
T Consensus 173 ~ 173 (305)
T PRK11233 173 D 173 (305)
T ss_pred c
Confidence 3
No 282
>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=74.41 E-value=98 Score=30.94 Aligned_cols=206 Identities=8% Similarity=0.014 Sum_probs=112.3
Q ss_pred eEEEEEEeecCCcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEe-cC-CCCHHHHHHHHHHHHhc-CceEEEc-cCch
Q 003958 31 VVNIGALLSFSTNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQ-DC-NHSGFLALAEALHLMEG-QTVAIIG-PQDA 106 (784)
Q Consensus 31 ~i~IG~i~~~~~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~-D~-~~~~~~a~~~~~~li~~-~v~aiiG-p~~s 106 (784)
+++||++.+-.+. +....+|++..+++--+. .|.-.++ |. ..+.++.+.....|.++ .+-+||- ..-+
T Consensus 2 ~~kIGivTgtvSq-~ed~~r~Ae~l~~~Yg~~-------~I~h~tyPdnf~~e~EttIskI~~lAdDp~mKaIVv~q~vp 73 (275)
T PF12683_consen 2 DYKIGIVTGTVSQ-SEDEYRGAEELIKKYGDV-------MIKHVTYPDNFMSEQETTISKIVSLADDPDMKAIVVSQAVP 73 (275)
T ss_dssp -EEEEEEE--TTT--HHHHHHHHHHHHHHHHH-------EEEEEE--TTGGGCHHHHHHHHHGGGG-TTEEEEEEE-SS-
T ss_pred ceEEEEEeCCccc-ChHHHHHHHHHHHHhCcc-------eEEEEeCCCcccchHHHHHHHHHHhccCCCccEEEEeCCCc
Confidence 6899999876432 345566777677654322 3444444 32 34667777777777766 5666553 2344
Q ss_pred hhHHHHHHhh-hcCCccEEecccCC-CCCCcCCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcCCCcc----hh
Q 003958 107 VTSHVVSHVA-NELQVPLLSFSATD-PTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDDDHGR----NG 180 (784)
Q Consensus 107 ~~~~~va~~~-~~~~ip~Is~~a~~-~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~~~g~----~~ 180 (784)
+++.++-.+= .+-+|..|+-.+.. +..-....+ +-+.+.....+..++...+++|-+.+..+.....-.. ..
T Consensus 74 Gt~~af~kIkekRpDIl~ia~~~~EDp~~i~~~aD--i~~~~D~~~~G~~i~~~Ak~mGAktFVh~sfprhms~~~l~~R 151 (275)
T PF12683_consen 74 GTAEAFRKIKEKRPDILLIAGEPHEDPEVISSAAD--IVVNPDEISRGYTIVWAAKKMGAKTFVHYSFPRHMSYELLARR 151 (275)
T ss_dssp --HHHHHHHHHH-TTSEEEESS--S-HHHHHHHSS--EEEE--HHHHHHHHHHHHHHTT-S-EEEEEETTGGGSHHHHHH
T ss_pred chHHHHHHHHhcCCCeEEEcCCCcCCHHHHhhccC--eEeccchhhccHHHHHHHHHcCCceEEEEechhhcchHHHHHH
Confidence 5555555543 34477777633222 111111122 3344677788999999999999999999975443332 33
Q ss_pred HHHHHHHHhccCcEEEEeeccCCCCCh--hH-----HHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHcCC
Q 003958 181 IAALGDTLAAKRCRISFKAPLSVEATE--DE-----ITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYLGM 246 (784)
Q Consensus 181 ~~~l~~~l~~~gi~v~~~~~~~~~~~~--~d-----~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~g~ 246 (784)
.+.+++..++.|++.+....-.+..+. .. ....-+.+++.+.++-+.++.......+++++.+.|.
T Consensus 152 r~~M~~~C~~lGi~fv~~taPDP~sd~gv~gaqqfIlE~vp~~i~kYGkdtaff~TN~a~~epllk~~~~~g~ 224 (275)
T PF12683_consen 152 RDIMEEACKDLGIKFVEVTAPDPTSDVGVAGAQQFILEDVPKWIKKYGKDTAFFCTNDAMTEPLLKQALEYGG 224 (275)
T ss_dssp HHHHHHHHHHCT--EEEEEE---SSTCHHHHHHHHHHHHHHHHHHHH-S--EEEESSHHHHHHHHHHHHHH--
T ss_pred HHHHHHHHHHcCCeEEEEeCCCCCCCCCcHHHHHHHHHHHHHHHHHhCCceeEEecCccccHHHHHHHHHcCC
Confidence 567778888899988866544333221 11 1233345666789999999888888899999998774
No 283
>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=74.28 E-value=6.8 Score=42.00 Aligned_cols=89 Identities=8% Similarity=0.037 Sum_probs=65.1
Q ss_pred HHHHHHHHHcCCcEEEEEEEcCCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccC-
Q 003958 153 AAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY- 231 (784)
Q Consensus 153 ~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~- 231 (784)
..+.+.++.+| ++.+|+...-......+.+.+.+++.|+.+.....+.......+....+..+++.++|.||-.+.+
T Consensus 12 ~~l~~~l~~~g--r~lvVt~~~~~~~~~~~~v~~~L~~~~i~~~~~~~~~~~p~~~~v~~~~~~~~~~~~D~IIaiGGGS 89 (366)
T PF00465_consen 12 EELGEELKRLG--RVLVVTDPSLSKSGLVDRVLDALEEAGIEVQVFDGVGPNPTLEDVDEAAEQARKFGADCIIAIGGGS 89 (366)
T ss_dssp GGHHHHHHCTT--EEEEEEEHHHHHHTHHHHHHHHHHHTTCEEEEEEEESSS-BHHHHHHHHHHHHHTTSSEEEEEESHH
T ss_pred HHHHHHHHhcC--CEEEEECchHHhCccHHHHHHHHhhCceEEEEEecCCCCCcHHHHHHHHHHHHhcCCCEEEEcCCCC
Confidence 45667778887 999999763333346899999999999998776667666778889999999999999999987554
Q ss_pred -CcHHHHHHHHHH
Q 003958 232 -NRGPVVFHVAQY 243 (784)
Q Consensus 232 -~~~~~~~~~a~~ 243 (784)
-++..++..+..
T Consensus 90 ~~D~aK~va~~~~ 102 (366)
T PF00465_consen 90 VMDAAKAVALLLA 102 (366)
T ss_dssp HHHHHHHHHHHHT
T ss_pred cCcHHHHHHhhcc
Confidence 344444444433
No 284
>PRK10200 putative racemase; Provisional
Probab=74.24 E-value=31 Score=34.10 Aligned_cols=86 Identities=13% Similarity=0.070 Sum_probs=47.8
Q ss_pred CHHHHHHHHHHHHh-cCceEEEccCchhhHHHHHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHH
Q 003958 81 SGFLALAEALHLME-GQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIV 159 (784)
Q Consensus 81 ~~~~a~~~~~~li~-~~v~aiiGp~~s~~~~~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l 159 (784)
++...+....+.+. .|+.+|+=|..+..+. ...+-+..++|+|+. .++..+.+
T Consensus 59 ~~~~~l~~~~~~L~~~g~~~iviaCNTah~~-~~~l~~~~~iPii~i-------------------------i~~~~~~~ 112 (230)
T PRK10200 59 KTGDILAEAALGLQRAGAEGIVLCTNTMHKV-ADAIESRCSLPFLHI-------------------------ADATGRAI 112 (230)
T ss_pred hHHHHHHHHHHHHHHcCCCEEEECCchHHHH-HHHHHHhCCCCEeeh-------------------------HHHHHHHH
Confidence 46655555555444 4888888655555444 345556678888862 12333334
Q ss_pred HHcCCcEEEEEEEcCCCcchhHHHHHHHHhcc-CcEE
Q 003958 160 DHYGWREVIAIYVDDDHGRNGIAALGDTLAAK-RCRI 195 (784)
Q Consensus 160 ~~~~w~~v~ii~~d~~~g~~~~~~l~~~l~~~-gi~v 195 (784)
++.+-++|+++.+.... ....+++.+.++ |+++
T Consensus 113 ~~~~~~~VglLaT~~Ti---~s~~Y~~~l~~~~g~~~ 146 (230)
T PRK10200 113 TGAGMTRVALLGTRYTM---EQDFYRGRLTEQFSINC 146 (230)
T ss_pred HHcCCCeEEEeccHHHH---HHhHHHHHHHHhcCCeE
Confidence 44566778887765432 233444554433 6554
No 285
>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=73.88 E-value=17 Score=39.34 Aligned_cols=86 Identities=13% Similarity=0.087 Sum_probs=57.6
Q ss_pred HHHHHHHHHcCCcEEEEEEEcCCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccC-
Q 003958 153 AAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY- 231 (784)
Q Consensus 153 ~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~- 231 (784)
..+.++++.++ +++.+|+..........+.+.+.+++.|+++.......+.....+....+...++.++|.||-.+.+
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 34667788888 8998888544333466788999999989876544333322345556677777788899999977543
Q ss_pred -CcHHHHHH
Q 003958 232 -NRGPVVFH 239 (784)
Q Consensus 232 -~~~~~~~~ 239 (784)
-++..++.
T Consensus 91 ~iD~aK~ia 99 (386)
T cd08191 91 CIDLAKIAG 99 (386)
T ss_pred HHHHHHHHH
Confidence 34444443
No 286
>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=73.82 E-value=12 Score=39.92 Aligned_cols=76 Identities=17% Similarity=0.117 Sum_probs=56.0
Q ss_pred HHHHHHHHHcCCcEEEEEEEcCCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccC
Q 003958 153 AAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY 231 (784)
Q Consensus 153 ~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~ 231 (784)
..+.++++.++ +++.||+....+. ...+.+.+.+++.|+.+.+. .+..++..++....++..++.++|.||-.+.+
T Consensus 12 ~~l~~~~~~~~-~r~livt~~~~~~-~~~~~v~~~L~~~~i~~~~~-~~~~~p~~~~v~~~~~~~~~~~~D~IIavGGG 87 (351)
T cd08170 12 DELGEYLARLG-KRALIIADEFVLD-LVGAKIEESLAAAGIDARFE-VFGGECTRAEIERLAEIARDNGADVVIGIGGG 87 (351)
T ss_pred HHHHHHHHHhC-CeEEEEECHHHHH-HHHHHHHHHHHhCCCeEEEE-EeCCcCCHHHHHHHHHHHhhcCCCEEEEecCc
Confidence 34566777776 8998888544433 67888999999999887643 35445566778888888888999999887544
No 287
>PF13685 Fe-ADH_2: Iron-containing alcohol dehydrogenase; PDB: 3CE9_C.
Probab=73.58 E-value=16 Score=36.41 Aligned_cols=99 Identities=15% Similarity=0.229 Sum_probs=57.5
Q ss_pred HHHHHHHHcCCcEEEEEEEcCCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCc
Q 003958 154 AIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNR 233 (784)
Q Consensus 154 ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~ 233 (784)
.+.+++++++.+++.+|+..+.| ....+.+++.+++.|+++..........+..+......+++..++++|+-.+.+ .
T Consensus 9 ~l~~~l~~~~~~~~lvv~d~~t~-~~~g~~v~~~l~~~g~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~d~ii~vGgG-~ 86 (250)
T PF13685_consen 9 KLPEILSELGLKKVLVVTDENTY-KAAGEKVEESLKSAGIEVAVIEEFVGDADEDEVEKLVEALRPKDADLIIGVGGG-T 86 (250)
T ss_dssp GHHHHHGGGT-SEEEEEEETTHH-HHHHHHHHHHHHTTT-EEEEEE-EE---BHHHHHHHHTTS--TT--EEEEEESH-H
T ss_pred HHHHHHHhcCCCcEEEEEcCCHH-HHHHHHHHHHHHHcCCeEEEEecCCCCCCHHHHHHHHHHhcccCCCEEEEeCCc-H
Confidence 45678888889999999977653 345678889999999888744322222355566666777777788888877654 3
Q ss_pred HHHHHHH-HHHcCCCCCCeEEEecC
Q 003958 234 GPVVFHV-AQYLGMLGTGYVWIATS 257 (784)
Q Consensus 234 ~~~~~~~-a~~~g~~~~~~~wi~~~ 257 (784)
+.++.|. |.+++ ..|+-+-|.
T Consensus 87 i~D~~K~~A~~~~---~p~isVPTa 108 (250)
T PF13685_consen 87 IIDIAKYAAFELG---IPFISVPTA 108 (250)
T ss_dssp HHHHHHHHHHHHT-----EEEEES-
T ss_pred HHHHHHHHHHhcC---CCEEEeccc
Confidence 4444444 44444 345555554
No 288
>COG1794 RacX Aspartate racemase [Cell envelope biogenesis, outer membrane]
Probab=73.45 E-value=73 Score=30.89 Aligned_cols=86 Identities=20% Similarity=0.155 Sum_probs=50.9
Q ss_pred CHHHHHHH-HHHHHhcCceEEEccCchhhHHHHHHhh-hcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHH
Q 003958 81 SGFLALAE-ALHLMEGQTVAIIGPQDAVTSHVVSHVA-NELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEI 158 (784)
Q Consensus 81 ~~~~a~~~-~~~li~~~v~aiiGp~~s~~~~~va~~~-~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~ 158 (784)
++...+.. +..|-..|+..|+=| ..++..+++-. +.-+||+|+. .++.++-
T Consensus 59 ~~~~~L~~~a~~Le~~GAd~i~l~--~NT~H~~~d~iq~~~~iPllhI-------------------------idaTa~~ 111 (230)
T COG1794 59 EAGEILIDAAKKLERAGADFIVLP--TNTMHKVADDIQKAVGIPLLHI-------------------------IDATAKA 111 (230)
T ss_pred cHHHHHHHHHHHHHhcCCCEEEEe--CCcHHHHHHHHHHhcCCCeehH-------------------------HHHHHHH
Confidence 44444433 334434488888844 45556666544 4779999963 3455666
Q ss_pred HHHcCCcEEEEEEEcCCCcchhHHHHHHHHhccCcEEE
Q 003958 159 VDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRIS 196 (784)
Q Consensus 159 l~~~~w~~v~ii~~d~~~g~~~~~~l~~~l~~~gi~v~ 196 (784)
+++-|-++++++.....-- ..-.++.+.++|++++
T Consensus 112 ik~~g~kkvgLLgT~~Tm~---~~fY~~~l~~~gievv 146 (230)
T COG1794 112 IKAAGAKKVGLLGTRFTME---QGFYRKRLEEKGIEVV 146 (230)
T ss_pred HHhcCCceeEEeeccchHH---hHHHHHHHHHCCceEe
Confidence 6666777777777643321 2334566777776654
No 289
>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=72.77 E-value=83 Score=29.36 Aligned_cols=69 Identities=17% Similarity=0.150 Sum_probs=43.5
Q ss_pred eeeHHHHHHHHHHCCCccceEEeeCCCCCCCCChhHHHHHHHcCcccEEEeeEEeecCccccceeccccccccEEEEEec
Q 003958 494 GFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPV 573 (784)
Q Consensus 494 G~~~dl~~~l~~~l~f~~~~~~~~~~~~~~~~~~~g~i~~l~~~~~D~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~ 573 (784)
.+..+++..+.+++- .+++++.. ++...++..|.+|++|+++.... .....+ -+.++....++++++.
T Consensus 13 ~~l~~~l~~f~~~~P-~v~l~~~~-------~~~~~~~~~l~~g~~Dl~i~~~~---~~~~~~-~~~~l~~~~~~lv~~~ 80 (200)
T cd08466 13 LLLPRLLARLKQLAP-NISLRESP-------SSEEDLFEDLRLQEVDLVIDYVP---FRDPSF-KSELLFEDELVCVARK 80 (200)
T ss_pred HHHHHHHHHHHHHCC-CCEEEEec-------CchHhHHHHHHcCCccEEEeccc---CCCCCc-eeeeecccceEEEEeC
Confidence 445677777777752 23355442 45678899999999999985322 112223 2356777888888765
Q ss_pred c
Q 003958 574 R 574 (784)
Q Consensus 574 ~ 574 (784)
.
T Consensus 81 ~ 81 (200)
T cd08466 81 D 81 (200)
T ss_pred C
Confidence 4
No 290
>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=72.01 E-value=85 Score=29.20 Aligned_cols=69 Identities=13% Similarity=0.048 Sum_probs=42.7
Q ss_pred eeeeHHHHHHHHHHC-CCccceEEeeCCCCCCCCChhHHHHHHHcCcccEEEeeEEeecCccccceeccccccccEEEEE
Q 003958 493 SGFCIDVFTAAINLL-PYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVA 571 (784)
Q Consensus 493 ~G~~~dl~~~l~~~l-~f~~~~~~~~~~~~~~~~~~~g~i~~l~~~~~D~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~ 571 (784)
..+..+++..+.+.+ +.+ +++.. +....+...+.+|++|+++..... ....+ -+.++....+.+++
T Consensus 12 ~~~l~~~l~~f~~~~P~v~--i~i~~-------~~~~~~~~~l~~~~~Di~i~~~~~---~~~~~-~~~~l~~~~~~lv~ 78 (198)
T cd08461 12 KAILPPLLAALRQEAPGVR--VAIRD-------LESDNLEAQLERGEVDLALTTPEY---APDGL-RSRPLFEERYVCVT 78 (198)
T ss_pred HHHhHHHHHHHHHHCCCcE--EEEee-------CCcccHHHHHhcCCCcEEEecCcc---CCccc-eeeeeecCcEEEEE
Confidence 345567778887775 344 44432 234568899999999999853221 11222 24567777777777
Q ss_pred ecc
Q 003958 572 PVR 574 (784)
Q Consensus 572 ~~~ 574 (784)
+..
T Consensus 79 ~~~ 81 (198)
T cd08461 79 RRG 81 (198)
T ss_pred cCC
Confidence 554
No 291
>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=71.77 E-value=67 Score=30.21 Aligned_cols=69 Identities=16% Similarity=0.155 Sum_probs=43.1
Q ss_pred eeeHHHHHHHHHHCCCccceEEeeCCCCCCCCChhHHHHHHHcCcccEEEeeEEeecCccccceeccccccccEEEEEec
Q 003958 494 GFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPV 573 (784)
Q Consensus 494 G~~~dl~~~l~~~l~f~~~~~~~~~~~~~~~~~~~g~i~~l~~~~~D~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~ 573 (784)
.+..+++..+.++.. ++++++.. +....+++.|.+|++|+++.... .. ...+. ..+.....++++++.
T Consensus 13 ~~l~~~l~~~~~~~P-~i~l~~~~-------~~~~~~~~~l~~g~~D~~i~~~~--~~-~~~~~-~~~l~~~~~~~v~~~ 80 (200)
T cd08467 13 ALLPRLAPRLRERAP-GLDLRLCP-------IGDDLAERGLEQGTIDLAVGRFA--VP-PDGLV-VRRLYDDGFACLVRH 80 (200)
T ss_pred HHHHHHHHHHHhhCC-CCEEEEec-------CCcccHHHHhhCCCcCEEEecCC--CC-Cccce-eEEeeeccEEEEEcC
Confidence 455677777777652 23355543 34557899999999999885321 11 22233 356777788877754
Q ss_pred c
Q 003958 574 R 574 (784)
Q Consensus 574 ~ 574 (784)
.
T Consensus 81 ~ 81 (200)
T cd08467 81 G 81 (200)
T ss_pred C
Confidence 4
No 292
>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=71.63 E-value=24 Score=34.70 Aligned_cols=97 Identities=11% Similarity=0.015 Sum_probs=53.8
Q ss_pred CCCCChHhhhhCCCceEEeeC---c---hHHHHHHhhc-----ccCccCce-eCCCHHHHHHHHhcCCcCCCeeEEEech
Q 003958 682 SPIKGIDSLRSSNYPIGYQVN---S---FARNYLVDEL-----NIDESRLV-PLNSPEEYAKALKDGPHKGGVAAVVDDR 749 (784)
Q Consensus 682 ~~i~~~~dl~~~~~~i~~~~~---~---~~~~~~~~~~-----~~~~~~~~-~~~~~~~~~~~l~~~~~~~~~~a~~~~~ 749 (784)
..+.+++||.+.+.+|++..- . .....+.+.. ..-..++. ...+..+....+.+ ++.++.+...
T Consensus 91 ~~~~~~~dL~~~~~~i~~~dP~~s~~g~~~~~~l~~~g~~~~~~~l~~~~~~~~~~~~~~~~~v~~----g~~d~~~~~~ 166 (230)
T PF13531_consen 91 KGIRSWADLAQPGLRIAIPDPSTSPSGLAALQVLAAAGGQELLDALQKNIVQYVPSTSQVLSAVAS----GEADAGIVYE 166 (230)
T ss_dssp TSTTCHHHHCSTT--EEEE-TTTTHHHHHHHHHHHHHTHCHHHHHHHHTEEEEESSHHHHHHHHHT----TSSSEEEEEH
T ss_pred cccCCHHHHhhccCEEEecCcccChhhHHHHHHHHHcccHHHHHHHHHhCcccccchHHHHHHHHc----CCCcceeeHH
Confidence 367889999987778888752 1 2333332211 00012333 34667888889988 7788877765
Q ss_pred hhhHHHHcCCCCe--EEeCCccc--cceEEEEeeCCCC
Q 003958 750 AYAELFLSTRCEF--SIVGQVFT--KNGWGFVSIVSSF 783 (784)
Q Consensus 750 ~~~~~~~~~~c~l--~~~~~~~~--~~~~~~~~~k~s~ 783 (784)
..+.+. .+.-++ ..+.+... ...|++++.++++
T Consensus 167 s~~~~~-~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~ 203 (230)
T PF13531_consen 167 SQAIFA-RQGDPLSYVYPPDGVNSPPIDYPIAILKNAP 203 (230)
T ss_dssp HHHHHC-TSHTTEEEEE-STTTSSSEEEEEEEEBTTCT
T ss_pred HHHHHh-hcCCCeEEEECCchhcCCCEEEEEEEecCCC
Confidence 555322 232333 33344444 3568888888764
No 293
>COG1880 CdhB CO dehydrogenase/acetyl-CoA synthase epsilon subunit [Energy production and conversion]
Probab=71.46 E-value=65 Score=29.06 Aligned_cols=121 Identities=14% Similarity=0.178 Sum_probs=75.9
Q ss_pred HHHHHHhc--CceEEEccCch--hhHHHHHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcC
Q 003958 88 EALHLMEG--QTVAIIGPQDA--VTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYG 163 (784)
Q Consensus 88 ~~~~li~~--~v~aiiGp~~s--~~~~~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~ 163 (784)
.+..++++ +...|+||.-- +.-..+..+.+.+++|.+..+++...+.+++-. +......++..+++.-+
T Consensus 27 v~ammIkkAkrPLlivGp~~~dee~~E~~vKi~ekfnipivaTa~~~~~~~~~~i~-------~~~~~lh~it~~l~Dp~ 99 (170)
T COG1880 27 VVAMMIKKAKRPLLIVGPLALDEELLELAVKIIEKFNIPIVATASSMGNLIGRGIG-------SEYINLHAITQYLTDPN 99 (170)
T ss_pred HHHHHHHhcCCceEEecccccCHHHHHHHHHHHHhcCCceEecchhhcchhhcccc-------cchhHHHHHHHHhcCCC
Confidence 34455554 89999998754 556678899999999999877776666664322 44455678888888866
Q ss_pred CcE---------EEEEEEcCCCcchhHHHHHHHHhccCcEEEEeeccCCCC-------ChhHHHHHHHHh
Q 003958 164 WRE---------VIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEA-------TEDEITDLLVKV 217 (784)
Q Consensus 164 w~~---------v~ii~~d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~-------~~~d~~~~l~~l 217 (784)
|.- |.++..-..|....++.++....- ..|+....+.++. ...++-..|+++
T Consensus 100 w~G~dg~g~yDlviflG~~~yy~sq~Ls~lKhFs~i--~tiaId~~Y~pnAd~SFpNl~kde~~~~L~el 167 (170)
T COG1880 100 WPGFDGNGNYDLVIFLGSIYYYLSQVLSGLKHFSNI--KTIAIDRYYQPNADYSFPNLSKDEYLAYLDEL 167 (170)
T ss_pred CCCcCCCCCcceEEEEeccHHHHHHHHHHhhhhhcc--eEEEeccccCcCccccCCCcCHHHHHHHHHHH
Confidence 643 555555566666666666654411 2344444444331 234455555554
No 294
>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=71.38 E-value=86 Score=28.99 Aligned_cols=69 Identities=19% Similarity=0.202 Sum_probs=42.5
Q ss_pred eeeHHHHHHHHHHCCCccceEEeeCCCCCCCCChhHHHHHHHcCcccEEEeeEEeecCccccceeccccccccEEEEEec
Q 003958 494 GFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPV 573 (784)
Q Consensus 494 G~~~dl~~~l~~~l~f~~~~~~~~~~~~~~~~~~~g~i~~l~~~~~D~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~ 573 (784)
.+..+++..+.+... ++++++.. +....++..+.+|++|+++...... ...+. ..++....++++++.
T Consensus 13 ~~l~~~l~~~~~~~p-~i~i~i~~-------~~~~~~~~~l~~~~~Dl~i~~~~~~---~~~~~-~~~l~~~~~~~v~~~ 80 (197)
T cd08414 13 GLLPRLLRRFRARYP-DVELELRE-------MTTAEQLEALRAGRLDVGFVRPPPD---PPGLA-SRPLLREPLVVALPA 80 (197)
T ss_pred HHHHHHHHHHHHHCC-CcEEEEec-------CChHHHHHHHHcCCccEEEEcCCCC---CCCee-EEEEeeccEEEEecC
Confidence 345567777777652 33354432 3456889999999999998643221 22222 356777777777755
Q ss_pred c
Q 003958 574 R 574 (784)
Q Consensus 574 ~ 574 (784)
.
T Consensus 81 ~ 81 (197)
T cd08414 81 D 81 (197)
T ss_pred C
Confidence 4
No 295
>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=71.31 E-value=20 Score=38.48 Aligned_cols=85 Identities=7% Similarity=0.017 Sum_probs=59.2
Q ss_pred HHHHHHHHHcCCcEEEEEEEcCCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccC-
Q 003958 153 AAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY- 231 (784)
Q Consensus 153 ~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~- 231 (784)
..+.+.++.++.+++.+|++...+ ..+.+.+.+++.|+.+.....+..+++.+.....+..+++.++|.||-.+.+
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 356677888888999999865543 4566788888888766544445544566778888888888899999876543
Q ss_pred -CcHHHHHHH
Q 003958 232 -NRGPVVFHV 240 (784)
Q Consensus 232 -~~~~~~~~~ 240 (784)
-++..++..
T Consensus 89 ~~D~aK~ia~ 98 (367)
T cd08182 89 VLDTAKALAA 98 (367)
T ss_pred HHHHHHHHHH
Confidence 444444443
No 296
>PRK07475 hypothetical protein; Provisional
Probab=71.09 E-value=29 Score=34.68 Aligned_cols=119 Identities=17% Similarity=0.068 Sum_probs=64.3
Q ss_pred CHHHHHH-HHHHHHhcCceEEEccCchhhHHHHHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHH
Q 003958 81 SGFLALA-EALHLMEGQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIV 159 (784)
Q Consensus 81 ~~~~a~~-~~~~li~~~v~aiiGp~~s~~~~~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l 159 (784)
++..... ++.+|...++.+|+.+. .........+.+..++|+++. +.+.+..+
T Consensus 62 ~~~~~l~~aa~~L~~~G~d~I~~~C-gt~~~~~~~l~~~~~VPv~~s-------------------------s~~~v~~l 115 (245)
T PRK07475 62 SLLDAFVAAARELEAEGVRAITTSC-GFLALFQRELAAALGVPVATS-------------------------SLLQVPLI 115 (245)
T ss_pred cHHHHHHHHHHHHHHcCCCEEEech-HHHHHHHHHHHHHcCCCEecc-------------------------HHHHHHHH
Confidence 3444443 34444455999998744 333333445666779998851 12333334
Q ss_pred HHc--CCcEEEEEEEcCCCcchhHHHHHHHHhccCcEE-E---EeeccCC----------C---CC----hhHHHHHHHH
Q 003958 160 DHY--GWREVIAIYVDDDHGRNGIAALGDTLAAKRCRI-S---FKAPLSV----------E---AT----EDEITDLLVK 216 (784)
Q Consensus 160 ~~~--~w~~v~ii~~d~~~g~~~~~~l~~~l~~~gi~v-~---~~~~~~~----------~---~~----~~d~~~~l~~ 216 (784)
++. +-++|+++..+... ..++.+++.|+.. . ....... . .+ ..++...+++
T Consensus 116 ~~~~~~~~kIGILtt~~t~------l~~~~l~~~Gi~~~~~~~~~~g~e~~~~~~~~I~~~~~~~d~~~~~~~l~~~~~~ 189 (245)
T PRK07475 116 QALLPAGQKVGILTADASS------LTPAHLLAVGVPPDTSSLPIAGLEEGGEFRRNILENRGELDNEAAEQEVVAAARA 189 (245)
T ss_pred HHhccCCCeEEEEeCCchh------hhHHHHHhCCCCCCCccccccCcccchHHHHHHhcccccccHHHHHHHHHHHHHH
Confidence 433 36889999876542 2346677777741 1 0000010 0 01 2355666666
Q ss_pred hh--cCCceEEEEeccC
Q 003958 217 VA--LTESRIIVVHTHY 231 (784)
Q Consensus 217 l~--~~~~~vIvl~~~~ 231 (784)
+. ..++++|++.|..
T Consensus 190 l~~~~~~~daIvL~CTe 206 (245)
T PRK07475 190 LLERHPDIGAIVLECTN 206 (245)
T ss_pred HHhhCCCCCEEEEcCcC
Confidence 65 3478999887653
No 297
>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=70.95 E-value=93 Score=29.17 Aligned_cols=67 Identities=19% Similarity=0.305 Sum_probs=40.6
Q ss_pred eeHHHHHHHHHHCCCccceEEeeCCCCCCCCChhHHHHHHHcCcccEEEeeEEeecCccccceeccccccccEEEEEecc
Q 003958 495 FCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPVR 574 (784)
Q Consensus 495 ~~~dl~~~l~~~l~f~~~~~~~~~~~~~~~~~~~g~i~~l~~~~~D~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~~ 574 (784)
+...++..+.+... ++++++.. ++. .+++.|.+|++|+++..-... ...+. ..|+....++++++..
T Consensus 14 ~l~~~i~~~~~~~P-~i~l~i~~-------~~~-~~~~~l~~g~~D~~i~~~~~~---~~~~~-~~~l~~~~~~~v~~~~ 80 (200)
T cd08462 14 LLPPVIERVAREAP-GVRFELLP-------PDD-QPHELLERGEVDLLIAPERFM---SDGHP-SEPLFEEEFVCVVWAD 80 (200)
T ss_pred HHHHHHHHHHHHCC-CCEEEEec-------CCh-hHHHHHhcCCeeEEEecCCCC---CCCce-eeeeeccceEEEEcCC
Confidence 44566777776652 22355542 234 899999999999998642221 12232 3467777777777554
No 298
>COG1910 Periplasmic molybdate-binding protein/domain [Inorganic ion transport and metabolism]
Probab=70.31 E-value=75 Score=30.55 Aligned_cols=70 Identities=23% Similarity=0.186 Sum_probs=43.6
Q ss_pred cCCCCChHhhhhCCCce-EEeeCchHHHHHHhh---cccCccCceeCC----CHHHHHHHHhcCCcCCCeeEEEechhhh
Q 003958 681 SSPIKGIDSLRSSNYPI-GYQVNSFARNYLVDE---LNIDESRLVPLN----SPEEYAKALKDGPHKGGVAAVVDDRAYA 752 (784)
Q Consensus 681 ~~~i~~~~dl~~~~~~i-~~~~~~~~~~~~~~~---~~~~~~~~~~~~----~~~~~~~~l~~~~~~~~~~a~~~~~~~~ 752 (784)
...|++++||.+.+.++ -=.+||.++..|.+. .+..+..+.-|. +-.....++.. ++.|+=+.-+..+
T Consensus 86 pk~i~~~edl~~~d~~fVNR~rGSGTR~LlD~~L~~~~~~~~~I~GY~~e~~th~avA~aVa~----G~AD~GvGlr~~A 161 (223)
T COG1910 86 PKNISSLEDLLRKDLRFVNRNRGSGTRILLDELLGELNILPDSIKGYSDEATTHDAVASAVAS----GRADAGVGLRHAA 161 (223)
T ss_pred CCccccHHHHhhcCcEEEecCCCccHHHHHHHHHHHcCcCchhcCCccccccccHHHHHHHHc----CCCCccccHHHHH
Confidence 34689999999655442 224688777777543 233334554442 34456667777 8888888865554
Q ss_pred HH
Q 003958 753 EL 754 (784)
Q Consensus 753 ~~ 754 (784)
+.
T Consensus 162 ~~ 163 (223)
T COG1910 162 EK 163 (223)
T ss_pred HH
Confidence 43
No 299
>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=70.10 E-value=93 Score=28.84 Aligned_cols=69 Identities=12% Similarity=0.033 Sum_probs=44.1
Q ss_pred eeeeHHHHHHHHHHC-CCccceEEeeCCCCCCCCChhHHHHHHHcCcccEEEeeEEeecCccccceeccccccccEEEEE
Q 003958 493 SGFCIDVFTAAINLL-PYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVA 571 (784)
Q Consensus 493 ~G~~~dl~~~l~~~l-~f~~~~~~~~~~~~~~~~~~~g~i~~l~~~~~D~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~ 571 (784)
..+..+++..+.+.. +.+ +++.. ++...++..+.+|++|+++.... .....+ ...|+....+++++
T Consensus 12 ~~~l~~~l~~~~~~~P~i~--l~i~~-------~~~~~~~~~l~~~~~D~~i~~~~---~~~~~~-~~~~l~~~~~~~~~ 78 (198)
T cd08412 12 PYYLPGLLRRFREAYPGVE--VRVVE-------GNQEELEEGLRSGELDLALTYDL---DLPEDI-AFEPLARLPPYVWL 78 (198)
T ss_pred hhhhHHHHHHHHHHCCCcE--EEEEE-------CCHHHHHHHHHcCCCcEEEEcCC---CCCccc-ceeeeeccceEEEe
Confidence 345667888887775 344 44432 34668899999999999985322 112223 23667777777777
Q ss_pred ecc
Q 003958 572 PVR 574 (784)
Q Consensus 572 ~~~ 574 (784)
+..
T Consensus 79 ~~~ 81 (198)
T cd08412 79 PAD 81 (198)
T ss_pred cCC
Confidence 554
No 300
>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=70.04 E-value=21 Score=38.45 Aligned_cols=87 Identities=9% Similarity=0.042 Sum_probs=59.9
Q ss_pred HHHHHHHHHc---CCcEEEEEEEcCCCc-chhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEe
Q 003958 153 AAIAEIVDHY---GWREVIAIYVDDDHG-RNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVH 228 (784)
Q Consensus 153 ~ai~~~l~~~---~w~~v~ii~~d~~~g-~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~ 228 (784)
..+.++++.+ +.+++.+|++..... ....+.+.+.+++.|+.+.....+.++++.++....++.+++.++|+||-.
T Consensus 12 ~~l~~~l~~~~~~g~kr~livtd~~~~~~~g~~~~v~~~L~~~gi~~~~f~~v~~~p~~~~v~~~~~~~~~~~~D~IIai 91 (383)
T cd08186 12 EKIGEILKDLKSKGISKVLLVTGKSAYKKSGAWDKVEPALDEHGIEYVLYNKVTPNPTVDQVDEAAKLGREFGAQAVIAI 91 (383)
T ss_pred HHHHHHHHHhcccCCCEEEEEcCccHHhhcChHHHHHHHHHHcCCeEEEeCCCCCCCCHHHHHHHHHHHHHcCCCEEEEe
Confidence 3456667776 779999998554333 234688889999888876554445545566778888888898999999876
Q ss_pred ccC--CcHHHHHH
Q 003958 229 THY--NRGPVVFH 239 (784)
Q Consensus 229 ~~~--~~~~~~~~ 239 (784)
+.+ -++..++.
T Consensus 92 GGGS~iD~aK~ia 104 (383)
T cd08186 92 GGGSPIDSAKSAA 104 (383)
T ss_pred CCccHHHHHHHHH
Confidence 443 34444443
No 301
>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=69.76 E-value=19 Score=38.24 Aligned_cols=84 Identities=18% Similarity=0.152 Sum_probs=57.4
Q ss_pred HHHHHHHHHcCCcEEEEEEEcCCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccC-
Q 003958 153 AAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY- 231 (784)
Q Consensus 153 ~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~- 231 (784)
..+.+.++.++ +++.+|+....+ ....+.+.+.+++.|+.+.....+..++..+......+..++.++|.||-.+.+
T Consensus 12 ~~l~~~~~~~~-~r~liv~d~~~~-~~~~~~v~~~l~~~~~~~~~~~~~~~~p~~~~v~~~~~~~~~~~~d~iiavGGGs 89 (345)
T cd08171 12 KKIPEVCEKYG-KKVVVIGGKTAL-AAAKDKIKAALEQSGIEITDFIWYGGESTYENVERLKKNPAVQEADMIFAVGGGK 89 (345)
T ss_pred HHHHHHHHhcC-CEEEEEeCHHHH-HHHHHHHHHHHHHCCCeEEEEEecCCCCCHHHHHHHHHHHhhcCCCEEEEeCCcH
Confidence 34566677777 888888865443 345778888898888876644445544566777777787888899999977543
Q ss_pred -CcHHHHH
Q 003958 232 -NRGPVVF 238 (784)
Q Consensus 232 -~~~~~~~ 238 (784)
-++..++
T Consensus 90 ~~D~aK~i 97 (345)
T cd08171 90 AIDTVKVL 97 (345)
T ss_pred HHHHHHHH
Confidence 3344444
No 302
>PRK12681 cysB transcriptional regulator CysB; Reviewed
Probab=69.74 E-value=1.2e+02 Score=31.76 Aligned_cols=70 Identities=20% Similarity=0.092 Sum_probs=42.7
Q ss_pred eeeHHHHHHHHHHCCCccceEEeeCCCCCCCCChhHHHHHHHcCcccEEEeeEEeecCccccceeccccccccEEEEEec
Q 003958 494 GFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPV 573 (784)
Q Consensus 494 G~~~dl~~~l~~~l~f~~~~~~~~~~~~~~~~~~~g~i~~l~~~~~D~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~ 573 (784)
.+..+++..+.+... ++++++.. +....++..|.+|++|+++..-. ......+. ..|+....++++++.
T Consensus 106 ~~l~~~l~~f~~~~P-~i~i~i~~-------~~~~~~~~~L~~g~iDl~i~~~~--~~~~~~l~-~~~l~~~~~~~v~~~ 174 (324)
T PRK12681 106 YALPPVIKGFIERYP-RVSLHMHQ-------GSPTQIAEAAAKGNADFAIATEA--LHLYDDLI-MLPCYHWNRSVVVPP 174 (324)
T ss_pred HhhHHHHHHHHHHCC-CcEEEEEe-------CCHHHHHHHHHcCCCCEEEecCc--ccCCCCeE-EEEeccceeEEEeCC
Confidence 345667777776652 33355432 45789999999999999986321 11122232 346666777777654
Q ss_pred c
Q 003958 574 R 574 (784)
Q Consensus 574 ~ 574 (784)
.
T Consensus 175 ~ 175 (324)
T PRK12681 175 D 175 (324)
T ss_pred C
Confidence 3
No 303
>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=69.68 E-value=23 Score=37.33 Aligned_cols=86 Identities=9% Similarity=0.068 Sum_probs=58.1
Q ss_pred HHHHHHHHcCCcEEEEEEEcCCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccC--
Q 003958 154 AIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY-- 231 (784)
Q Consensus 154 ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~-- 231 (784)
.+.+.++.++.+++.+|++..... ...+.+.+.+++. +.+........+.+.++....+..+++.++|.||-.+.+
T Consensus 13 ~l~~~~~~~g~~~~liv~~~~~~~-~~~~~v~~~l~~~-~~~~~~~~~~~~p~~~~v~~~~~~~~~~~~d~IIaiGGGs~ 90 (332)
T cd07766 13 KIGEEIKRGGFDRALVVSDEGVVK-GVGEKVADSLKKL-IAVHIFDGVGPNPTFEEVKEAVERARAAEVDAVIAVGGGST 90 (332)
T ss_pred HHHHHHHhcCCCeEEEEeCCchhh-hHHHHHHHHHHhc-CcEEEeCCcCCCcCHHHHHHHHHHHHhcCcCEEEEeCCchH
Confidence 456677888889999998554433 6677888888876 655443333333566778888888888899999876543
Q ss_pred CcHHHHHHHH
Q 003958 232 NRGPVVFHVA 241 (784)
Q Consensus 232 ~~~~~~~~~a 241 (784)
-++..++...
T Consensus 91 ~D~aK~ia~~ 100 (332)
T cd07766 91 LDTAKAVAAL 100 (332)
T ss_pred HHHHHHHHHH
Confidence 3444444333
No 304
>COG1744 Med Uncharacterized ABC-type transport system, periplasmic component/surface lipoprotein [General function prediction only]
Probab=69.49 E-value=70 Score=33.83 Aligned_cols=75 Identities=15% Similarity=0.030 Sum_probs=58.5
Q ss_pred eEEEEEEeecCCcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEccCchhhHH
Q 003958 31 VVNIGALLSFSTNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIGPQDAVTSH 110 (784)
Q Consensus 31 ~i~IG~i~~~~~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiGp~~s~~~~ 110 (784)
.-++|.+..+....-.....|+...++..|.+ .++...+..+=.|+..+.+.+..++++|+.+|.....+....
T Consensus 161 ~~~vG~vgg~~~p~v~~f~~gF~~Gak~~np~------i~v~v~~~gsf~D~~k~k~~a~~li~~GaDVI~~~ag~~~~g 234 (345)
T COG1744 161 SGKVGFVGGMDIPEVNRFINGFLAGAKSVNPD------IKVKVVYVGSFSDPAKGKEAANALIDQGADVIYPAAGGTGVG 234 (345)
T ss_pred CCceeEEecccchhhHHHHHHHHHHHHhhCCC------ccEEEEEecCccChHHHHHHHHHHHhcCCCEEEecCCCCcch
Confidence 55678877776444456778999999999955 567777777778999999999999999999999876665444
Q ss_pred H
Q 003958 111 V 111 (784)
Q Consensus 111 ~ 111 (784)
.
T Consensus 235 v 235 (345)
T COG1744 235 V 235 (345)
T ss_pred H
Confidence 3
No 305
>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=69.35 E-value=98 Score=28.81 Aligned_cols=67 Identities=10% Similarity=0.085 Sum_probs=40.7
Q ss_pred eeHHHHHHHHHHC-CCccceEEeeCCCCCCCCChhHHHHHHHcCcccEEEeeEEeecCccccceeccccccccEEEEEec
Q 003958 495 FCIDVFTAAINLL-PYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPV 573 (784)
Q Consensus 495 ~~~dl~~~l~~~l-~f~~~~~~~~~~~~~~~~~~~g~i~~l~~~~~D~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~ 573 (784)
+...++..+.++. +.+ +++.. +....+...|.+|++|+++..-.. ....+. ..++....+.++++.
T Consensus 14 ~~~~~l~~~~~~~P~i~--i~i~~-------~~~~~~~~~l~~g~~Dl~i~~~~~---~~~~~~-~~~l~~~~~~~~~~~ 80 (198)
T cd08441 14 WLMPVLDQFRERWPDVE--LDLSS-------GFHFDPLPALLRGELDLVITSDPL---PLPGIA-YEPLFDYEVVLVVAP 80 (198)
T ss_pred hhHHHHHHHHHhCCCeE--EEEEe-------CCchhHHHHHHcCCceEEEecCCc---CCCCcE-EEEccCCcEEEEEcC
Confidence 4456777777775 334 44432 345688999999999999853221 112222 345666777777654
Q ss_pred c
Q 003958 574 R 574 (784)
Q Consensus 574 ~ 574 (784)
.
T Consensus 81 ~ 81 (198)
T cd08441 81 D 81 (198)
T ss_pred C
Confidence 4
No 306
>PRK10537 voltage-gated potassium channel; Provisional
Probab=68.73 E-value=7.9 Score=41.65 Aligned_cols=56 Identities=21% Similarity=0.258 Sum_probs=43.5
Q ss_pred ccCCceeehhhhhhhhhcc--cccccccchhhHHHHHHHHHHHHHHhhccccceeeEe
Q 003958 621 PKRQVVTIFWFSFSTMFFA--HKEKTVSALGRLVLIIWLFVVLIINSSYTASLTSILT 676 (784)
Q Consensus 621 ~~~~~~~~~~~~~~~~~~~--~~~~p~~~~~R~~~~~w~~~~lvl~~~Yta~L~s~l~ 676 (784)
...++.+++|+++.++..- |...|.+..+|++.+++.++++.+..+..+.++..+.
T Consensus 165 ~~~s~~dA~y~svvt~tTvGyGdi~p~t~~grl~~i~~ii~Gi~vf~~~is~i~~p~i 222 (393)
T PRK10537 165 PIESLSTAFYFSIVTMSTVGYGDIVPVSESARLFTISVIILGITVFATSISAIFGPVI 222 (393)
T ss_pred CCCCHHHHHHhhheeeecccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3457899999999988754 4558999999999999999998877666555555443
No 307
>PRK00945 acetyl-CoA decarbonylase/synthase complex subunit epsilon; Provisional
Probab=68.73 E-value=41 Score=31.27 Aligned_cols=91 Identities=12% Similarity=0.162 Sum_probs=55.5
Q ss_pred HHHHhc--CceEEEccCchh---hHHHHHHhhhcCCccEEecccCCCCCCcCC-CCceEeecCChHHHHHHHHHHHHHcC
Q 003958 90 LHLMEG--QTVAIIGPQDAV---TSHVVSHVANELQVPLLSFSATDPTLSSLQ-FPYFVRTTQSDQYQMAAIAEIVDHYG 163 (784)
Q Consensus 90 ~~li~~--~v~aiiGp~~s~---~~~~va~~~~~~~ip~Is~~a~~~~l~~~~-~p~~~r~~ps~~~~~~ai~~~l~~~~ 163 (784)
.+++++ ++..++|..... ....+.++++.+++|+++...+...|.+++ .|. ....-.+..+++.-+
T Consensus 28 a~lI~~AKrPlIivG~ga~~~~ea~e~l~elaEkl~iPVvtT~~~~~~~~~kgv~~~--------~~~lg~lg~~~~~p~ 99 (171)
T PRK00945 28 AMMIKKAKRPLLVVGSLLLDDEELLDRAVKIAKKANIPVAATGGSYKGLIDKGVDAK--------YINLHELTNYLKDPN 99 (171)
T ss_pred HHHHHhCCCcEEEECcCccccchHHHHHHHHHHHHCCCEEEccccccccccCCccCC--------cccHHHHHhhccCch
Confidence 344443 899999987643 667788999999999998655555555532 122 122235556666555
Q ss_pred CcEE---------EEEEEcCCCcchhHHHHHHHH
Q 003958 164 WREV---------IAIYVDDDHGRNGIAALGDTL 188 (784)
Q Consensus 164 w~~v---------~ii~~d~~~g~~~~~~l~~~l 188 (784)
|.-+ .++..+..+....+..++...
T Consensus 100 ~e~~~g~~~~DlvlfvG~~~~~~~~~l~~lk~f~ 133 (171)
T PRK00945 100 WKGLDGNGNYDLVIFIGVTYYYASQGLSALKHFS 133 (171)
T ss_pred hhhhcCCCCcCEEEEecCCchhHHHHHHHHhhcC
Confidence 5444 445556666555666665533
No 308
>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=68.66 E-value=99 Score=28.59 Aligned_cols=69 Identities=13% Similarity=0.082 Sum_probs=45.2
Q ss_pred eeeeHHHHHHHHHHC-CCccceEEeeCCCCCCCCChhHHHHHHHcCcccEEEeeEEeecCccccceeccccccccEEEEE
Q 003958 493 SGFCIDVFTAAINLL-PYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVA 571 (784)
Q Consensus 493 ~G~~~dl~~~l~~~l-~f~~~~~~~~~~~~~~~~~~~g~i~~l~~~~~D~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~ 571 (784)
..+..+++..+.+.. +.+ +.+.. +....+...+.+|++|+++...... ...+ .+.|+....+.+++
T Consensus 12 ~~~l~~~l~~~~~~~P~i~--l~i~~-------~~~~~~~~~l~~~~~Dl~i~~~~~~---~~~~-~~~~l~~~~~~~v~ 78 (196)
T cd08415 12 LSLLPRAIARFRARHPDVR--ISLHT-------LSSSTVVEAVLSGQADLGLASLPLD---HPGL-ESEPLASGRAVCVL 78 (196)
T ss_pred ccccHHHHHHHHHHCCCcE--EEEEe-------cchHHHHHHHHcCCccEEEEeCCCC---CCcc-eeeeecccceEEEE
Confidence 345667888887765 344 55443 3467889999999999998643221 2222 35667777888877
Q ss_pred ecc
Q 003958 572 PVR 574 (784)
Q Consensus 572 ~~~ 574 (784)
++.
T Consensus 79 ~~~ 81 (196)
T cd08415 79 PPG 81 (196)
T ss_pred cCC
Confidence 554
No 309
>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=68.26 E-value=1.1e+02 Score=28.79 Aligned_cols=128 Identities=20% Similarity=0.223 Sum_probs=76.4
Q ss_pred CCHHHHHHHHHHH-HhcCceEEEccCchhhHHHHHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHH
Q 003958 80 HSGFLALAEALHL-MEGQTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEI 158 (784)
Q Consensus 80 ~~~~~a~~~~~~l-i~~~v~aiiGp~~s~~~~~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~ 158 (784)
.+-+.++..+.++ ..+++.+||.-+. ++.. +-+..++|+|.... +..+..+++.+.
T Consensus 17 ~~~e~~v~~a~~~~~~~g~dViIsRG~--ta~~---lr~~~~iPVV~I~~------------------s~~Dil~al~~a 73 (176)
T PF06506_consen 17 ASLEEAVEEARQLLESEGADVIISRGG--TAEL---LRKHVSIPVVEIPI------------------SGFDILRALAKA 73 (176)
T ss_dssp --HHHHHHHHHHHHTTTT-SEEEEEHH--HHHH---HHCC-SS-EEEE---------------------HHHHHHHHHHC
T ss_pred ecHHHHHHHHHHhhHhcCCeEEEECCH--HHHH---HHHhCCCCEEEECC------------------CHhHHHHHHHHH
Confidence 4667888889999 7789999996443 2232 33455899997522 233344444443
Q ss_pred HHHcCCcEEEEEEEcCCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHH
Q 003958 159 VDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVF 238 (784)
Q Consensus 159 l~~~~w~~v~ii~~d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~ 238 (784)
. .+ -++++++...+... ....+.+.+ |+.+.... + .+..++...+++++..+.++||-... ..
T Consensus 74 ~-~~-~~~Iavv~~~~~~~--~~~~~~~ll---~~~i~~~~-~---~~~~e~~~~i~~~~~~G~~viVGg~~------~~ 136 (176)
T PF06506_consen 74 K-KY-GPKIAVVGYPNIIP--GLESIEELL---GVDIKIYP-Y---DSEEEIEAAIKQAKAEGVDVIVGGGV------VC 136 (176)
T ss_dssp C-CC-TSEEEEEEESS-SC--CHHHHHHHH---T-EEEEEE-E---SSHHHHHHHHHHHHHTT--EEEESHH------HH
T ss_pred H-hc-CCcEEEEecccccH--HHHHHHHHh---CCceEEEE-E---CCHHHHHHHHHHHHHcCCcEEECCHH------HH
Confidence 3 33 38999998765542 356666666 55555332 3 25778999999999999999887532 35
Q ss_pred HHHHHcCCC
Q 003958 239 HVAQYLGML 247 (784)
Q Consensus 239 ~~a~~~g~~ 247 (784)
+.|++.|+.
T Consensus 137 ~~A~~~gl~ 145 (176)
T PF06506_consen 137 RLARKLGLP 145 (176)
T ss_dssp HHHHHTTSE
T ss_pred HHHHHcCCc
Confidence 667787763
No 310
>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=67.78 E-value=22 Score=38.37 Aligned_cols=78 Identities=8% Similarity=0.087 Sum_probs=55.8
Q ss_pred HHHHHHHHHcCCcEEEEEEEcCCCc-chhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccC
Q 003958 153 AAIAEIVDHYGWREVIAIYVDDDHG-RNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY 231 (784)
Q Consensus 153 ~ai~~~l~~~~w~~v~ii~~d~~~g-~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~ 231 (784)
..+.++++.++ +++.||+....+- ....+.+.+.+++.|+++.....+..++..++....+...++.++|.||-.+.+
T Consensus 18 ~~l~~~~~~~~-~r~livt~~~~~~~~~~~~~v~~~L~~~g~~~~~~~~v~~~p~~~~v~~~~~~~~~~~~D~IIaiGGG 96 (382)
T cd08187 18 SELGKELKKYG-KKVLLVYGGGSIKKNGLYDRVIASLKEAGIEVVELGGVEPNPRLETVREGIELCKEEKVDFILAVGGG 96 (382)
T ss_pred HHHHHHHHHhC-CEEEEEeCCcHHHhcCcHHHHHHHHHHcCCeEEEECCccCCCCHHHHHHHHHHHHHcCCCEEEEeCCh
Confidence 34566777775 8998887543332 245688999999989877654445544566778888888899999999976543
No 311
>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=67.31 E-value=1.1e+02 Score=28.43 Aligned_cols=69 Identities=13% Similarity=0.087 Sum_probs=42.6
Q ss_pred eeeHHHHHHHHHHCCCccceEEeeCCCCCCCCChhHHHHHHHcCcccEEEeeEEeecCccccceeccccccccEEEEEec
Q 003958 494 GFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPV 573 (784)
Q Consensus 494 G~~~dl~~~l~~~l~f~~~~~~~~~~~~~~~~~~~g~i~~l~~~~~D~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~ 573 (784)
.+..+++..+.+... .+++++.. +....+++.+.+|++|+++..-.. ....+ -+.+.....++++++.
T Consensus 13 ~~l~~~l~~~~~~~P-~i~~~i~~-------~~~~~~~~~l~~g~~Dl~i~~~~~---~~~~~-~~~~l~~~~~~~~~~~ 80 (196)
T cd08456 13 SFLPRAIKAFLQRHP-DVTISIHT-------RDSPTVEQWLSAQQCDLGLVSTLH---EPPGI-ERERLLRIDGVCVLPP 80 (196)
T ss_pred hhHHHHHHHHHHHCC-CcEEEEEe-------CCHHHHHHHHHcCCccEEEEecCC---CCCCe-eEEEeeccCeEEEecC
Confidence 455677888888762 23355543 346678899999999999853221 11222 2445666777776654
Q ss_pred c
Q 003958 574 R 574 (784)
Q Consensus 574 ~ 574 (784)
.
T Consensus 81 ~ 81 (196)
T cd08456 81 G 81 (196)
T ss_pred C
Confidence 3
No 312
>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=66.94 E-value=1.4e+02 Score=30.56 Aligned_cols=70 Identities=13% Similarity=0.171 Sum_probs=42.6
Q ss_pred eeHHHHHHHHHHCCCccceEEeeCCCCCCCCChhHHHHHHHcCcccEEEeeEEeecCccccceeccccccccEEEEEecc
Q 003958 495 FCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPVR 574 (784)
Q Consensus 495 ~~~dl~~~l~~~l~f~~~~~~~~~~~~~~~~~~~g~i~~l~~~~~D~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~~ 574 (784)
+..+++..+.++.- ++++.+.. +....++..+.+|++|++++..... .....+ -..|.....+++++++.
T Consensus 107 ~~~~~l~~~~~~~P-~~~i~~~~-------~~~~~~~~~l~~g~~D~~i~~~~~~-~~~~~~-~~~~l~~~~~~~~~~~~ 176 (300)
T TIGR02424 107 LMPEVVKRFLARAP-RLRVRIMT-------GPNAYLLDQLRVGALDLVVGRLGAP-ETMQGL-SFEHLYNEPVVFVVRAG 176 (300)
T ss_pred hhHHHHHHHHHhCC-CcEEEEEe-------CchHHHHHHHHCCCCCEEEEecCCc-ccccce-eeeeecCCceEEEEcCC
Confidence 34566667776653 33355443 3466889999999999998643321 112223 23467777777777544
No 313
>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=66.51 E-value=1.1e+02 Score=28.38 Aligned_cols=71 Identities=23% Similarity=0.262 Sum_probs=43.1
Q ss_pred eeeHHHHHHHHHHCCCccceEEeeCCCCCCCCChhHHHHHHHcCcccEEEeeEEeecCccccceeccccccccEEEEEec
Q 003958 494 GFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPV 573 (784)
Q Consensus 494 G~~~dl~~~l~~~l~f~~~~~~~~~~~~~~~~~~~g~i~~l~~~~~D~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~ 573 (784)
.+...++..+.+... .+++++.. +....+...|.+|++|+++....... ....+ -..+.....+.++++.
T Consensus 13 ~~l~~~l~~~~~~~P-~i~l~i~~-------~~~~~~~~~l~~g~~Dl~i~~~~~~~-~~~~~-~~~~l~~~~~~~v~~~ 82 (201)
T cd08418 13 TLMPAVINRFKEQFP-DVQISIYE-------GQLSSLLPELRDGRLDFAIGTLPDEM-YLKEL-ISEPLFESDFVVVARK 82 (201)
T ss_pred hhhHHHHHHHHHHCC-CceEEEEe-------CcHHHHHHHHHcCCCcEEEEecCCCC-CCcce-eEEeecCCceEEEeCC
Confidence 445667777777752 33355543 35678899999999999986432111 11223 2355666777777654
Q ss_pred c
Q 003958 574 R 574 (784)
Q Consensus 574 ~ 574 (784)
.
T Consensus 83 ~ 83 (201)
T cd08418 83 D 83 (201)
T ss_pred C
Confidence 4
No 314
>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=66.43 E-value=22 Score=35.93 Aligned_cols=78 Identities=9% Similarity=0.031 Sum_probs=54.5
Q ss_pred EEEEEEEc--CCCcchhHHHHHHHHhc-cCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccC-CcHHHHHHHH
Q 003958 166 EVIAIYVD--DDHGRNGIAALGDTLAA-KRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY-NRGPVVFHVA 241 (784)
Q Consensus 166 ~v~ii~~d--~~~g~~~~~~l~~~l~~-~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~-~~~~~~~~~a 241 (784)
+|++|.++ +.|.....+.+.+.+++ .|+.+...... .+.......++++.+.+.+.|++.... .....++.++
T Consensus 1 ~igvi~~~~~~~~~~~~~~gi~~~~~~~~~~~~~~~~~~---~~~~~~~~~i~~l~~~~vdgiii~~~~~~~~~~~~~~l 77 (272)
T cd06301 1 KIGVSMANFDDNFLTLLRNAMKEHAKVLGGVELQFEDAK---NDVATQLSQVENFIAQGVDAIIVVPVDTAATAPIVKAA 77 (272)
T ss_pred CeeEeecccCCHHHHHHHHHHHHHHHHcCCcEEEEeCCC---CCHHHHHHHHHHHHHcCCCEEEEecCchhhhHHHHHHH
Confidence 46777754 66777888899999999 89887764321 244556677888877889999886543 3345667777
Q ss_pred HHcCC
Q 003958 242 QYLGM 246 (784)
Q Consensus 242 ~~~g~ 246 (784)
.+.+.
T Consensus 78 ~~~~i 82 (272)
T cd06301 78 NAAGI 82 (272)
T ss_pred HHCCC
Confidence 76553
No 315
>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=66.27 E-value=1.1e+02 Score=28.30 Aligned_cols=72 Identities=18% Similarity=0.123 Sum_probs=43.2
Q ss_pred eeeHHHHHHHHHHCCCccceEEeeCCCCCCCCChhHHHHHHHcCcccEEEeeEEee--cCccccceeccccccccEEEEE
Q 003958 494 GFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAII--TNRTKMADFTQPYIESGLVVVA 571 (784)
Q Consensus 494 G~~~dl~~~l~~~l~f~~~~~~~~~~~~~~~~~~~g~i~~l~~~~~D~~~~~~~~t--~~r~~~~~fs~p~~~~~~~~~~ 571 (784)
.+..+++..+.+... .+++++.. ++...+...+.+|++|+++..-... ......+ ...+.....+.+++
T Consensus 13 ~~l~~~l~~~~~~~P-~i~i~~~~-------~~~~~~~~~l~~~~~Dl~i~~~~~~~~~~~~~~~-~~~~l~~~~~~~~~ 83 (200)
T cd08423 13 ALLPPALAALRARHP-GLEVRLRE-------AEPPESLDALRAGELDLAVVFDYPVTPPPDDPGL-TRVPLLDDPLDLVL 83 (200)
T ss_pred HhhhHHHHHHHHhCC-CCeEEEEe-------CCHHHHHHHHhcCCccEEEEeccccccCCCCCCc-EEEEeccCcEEEEe
Confidence 345667777777752 23355542 3456789999999999998542110 1122223 34567777777777
Q ss_pred ecc
Q 003958 572 PVR 574 (784)
Q Consensus 572 ~~~ 574 (784)
+..
T Consensus 84 ~~~ 86 (200)
T cd08423 84 PAD 86 (200)
T ss_pred cCC
Confidence 544
No 316
>PRK09423 gldA glycerol dehydrogenase; Provisional
Probab=65.55 E-value=23 Score=37.88 Aligned_cols=83 Identities=12% Similarity=0.093 Sum_probs=57.8
Q ss_pred HHHHHHHHHcCCcEEEEEEEcCCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccC-
Q 003958 153 AAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY- 231 (784)
Q Consensus 153 ~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~- 231 (784)
..+.+.++.++ +++.+|++...+ ....+.+.+.+++.|+.+.+. .+..++..+.....++.+++.++|+||-.+.+
T Consensus 19 ~~l~~~l~~~g-~~~livtd~~~~-~~~~~~v~~~l~~~~~~~~~~-~~~~ep~~~~v~~~~~~~~~~~~d~IIavGGGs 95 (366)
T PRK09423 19 ARLGEYLKPLG-KRALVIADEFVL-GIVGDRVEASLKEAGLTVVFE-VFNGECSDNEIDRLVAIAEENGCDVVIGIGGGK 95 (366)
T ss_pred HHHHHHHHHcC-CEEEEEEChhHH-HHHHHHHHHHHHhCCCeEEEE-EeCCCCCHHHHHHHHHHHHhcCCCEEEEecChH
Confidence 44567788888 899998854443 346788888898888876543 34444566778888888888899999987543
Q ss_pred -CcHHHHH
Q 003958 232 -NRGPVVF 238 (784)
Q Consensus 232 -~~~~~~~ 238 (784)
-++..++
T Consensus 96 v~D~aK~i 103 (366)
T PRK09423 96 TLDTAKAV 103 (366)
T ss_pred HHHHHHHH
Confidence 3444444
No 317
>PF01177 Asp_Glu_race: Asp/Glu/Hydantoin racemase; InterPro: IPR015942 This entry represents a group of related proteins that includes aspartate racemase, glutamate racemase, hydantoin racemase and arylmalonate decarboxylase. Aspartate racemase (5.1.1.13 from EC) and glutamate racemase (5.1.1.3 from EC) are two evolutionary related bacterial enzymes that do not seem to require a cofactor for their activity []. Glutamate racemase, which interconverts L-glutamate into D-glutamate, is required for the biosynthesis of peptidoglycan and some peptide-based antibiotics such as gramicidin S. In addition to characterised aspartate and glutamate racemases, this family also includes a hypothetical protein from Erwinia carotovora and one from Escherichia coli (ygeA). Two conserved cysteines are present in the sequence of these enzymes. They are expected to play a role in catalytic activity by acting as bases in proton abstraction from the substrate.; PDB: 3S7Z_A 3S81_C 3OUT_A 3EIS_B 3IXL_A 3IP8_A 2VLB_D 3DTV_A 3IXM_A 3DG9_A ....
Probab=65.50 E-value=1.3e+02 Score=28.98 Aligned_cols=123 Identities=7% Similarity=0.059 Sum_probs=69.8
Q ss_pred HHHhcCceEEEccCchhhHHHHHHhh-hcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcCCcEEEE
Q 003958 91 HLMEGQTVAIIGPQDAVTSHVVSHVA-NELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIA 169 (784)
Q Consensus 91 ~li~~~v~aiiGp~~s~~~~~va~~~-~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~i 169 (784)
++...++.+|+-+.++. ...+..+- ...++|+++.. ++.++-+.+ +-++|++
T Consensus 60 ~l~~~g~d~i~i~C~s~-~~~~~~~~~~~~~iPv~~~~-------------------------~a~~~~~~~-~~~ri~v 112 (216)
T PF01177_consen 60 KLEKAGVDAIVIACNSA-HPFVDELRKERVGIPVVGIV-------------------------EAALEAAKA-GGKRIGV 112 (216)
T ss_dssp HHHHTTESEEEESSHHH-HHHHHHHHHHHHSSEEEESH-------------------------HHHHHHHHH-TSSEEEE
T ss_pred HHHhCCCCEEEEcCCch-hhhHHHHhhhcCceEEEecc-------------------------HHHHHHHHh-cCCEEEE
Confidence 33344898887644333 23333444 56689988631 222444445 8899999
Q ss_pred EEEcCCCcchhHHHHHHHHhcc-Cc--EEEEee------ccCCCC-Ch---hHHHHHHHHh-hcCCceEEEEeccC-CcH
Q 003958 170 IYVDDDHGRNGIAALGDTLAAK-RC--RISFKA------PLSVEA-TE---DEITDLLVKV-ALTESRIIVVHTHY-NRG 234 (784)
Q Consensus 170 i~~d~~~g~~~~~~l~~~l~~~-gi--~v~~~~------~~~~~~-~~---~d~~~~l~~l-~~~~~~vIvl~~~~-~~~ 234 (784)
+.. ++......+.+.+++. |+ .+.... ...... .. ..+...++++ +..++++|++.|.. ..+
T Consensus 113 l~t---~~~~~~~~~~~~~~~~~gi~~~~~~~i~~~~~~~~e~~~~~~~~~~~~~~~~~~l~~~~~~d~iiLgCt~l~~~ 189 (216)
T PF01177_consen 113 LTT---YTTEKSPLYEEFIEEAAGIDDEVVAGIHNAIYDVIELGDIPPEQIEILAEAARELIKEDGADAIILGCTHLPLL 189 (216)
T ss_dssp EES---HHHHHHTHHHHHHHHCTTEECEEEEEEEEEHTHHHHTTCTTHHHHHHHHHHHHHHHHCTTSSEEEEESTTGGGG
T ss_pred Eec---CcccchHHHHHHHHHhcCCcHHHHHHHHhhcHHHHhhhcCCHHHHHHHHHHHHHHhccCCCCEEEECCCchHHH
Confidence 995 3344556677777777 76 444311 010111 22 2344444444 37899999998765 333
Q ss_pred HHHHHHHHH
Q 003958 235 PVVFHVAQY 243 (784)
Q Consensus 235 ~~~~~~a~~ 243 (784)
....+.+.+
T Consensus 190 ~~~~~~l~~ 198 (216)
T PF01177_consen 190 LGAIEALEE 198 (216)
T ss_dssp HHHHHHHHH
T ss_pred HHHHHhhcc
Confidence 366666655
No 318
>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=65.45 E-value=1.2e+02 Score=28.36 Aligned_cols=70 Identities=19% Similarity=0.168 Sum_probs=44.2
Q ss_pred eeeHHHHHHHHHHCCCccceEEeeCCCCCCCCChhHHHHHHHcCcccEEEeeEEeecCccccceeccccccccEEEEEec
Q 003958 494 GFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPV 573 (784)
Q Consensus 494 G~~~dl~~~l~~~l~f~~~~~~~~~~~~~~~~~~~g~i~~l~~~~~D~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~ 573 (784)
.+..+++..+.+... .+++++.. +....+.+.+.+|++|+++..... .....+. +.+.....++++++.
T Consensus 13 ~~l~~~l~~~~~~~P-~i~v~~~~-------~~~~~~~~~l~~g~~D~~i~~~~~--~~~~~~~-~~~l~~~~~~~v~~~ 81 (198)
T cd08413 13 YVLPPVIAAFRKRYP-KVKLSLHQ-------GTPSQIAEMVLKGEADIAIATEAL--DDHPDLV-TLPCYRWNHCVIVPP 81 (198)
T ss_pred hhccHHHHHHHHhCC-ceEEEEEe-------CCHHHHHHHHHcCCCCEEEEccCC--CCCCCcE-EEEeeeeeEEEEecC
Confidence 345677788877753 23354443 357788999999999999853221 1112233 366777788888765
Q ss_pred c
Q 003958 574 R 574 (784)
Q Consensus 574 ~ 574 (784)
.
T Consensus 82 ~ 82 (198)
T cd08413 82 G 82 (198)
T ss_pred C
Confidence 4
No 319
>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=65.24 E-value=27 Score=34.78 Aligned_cols=77 Identities=9% Similarity=0.113 Sum_probs=51.6
Q ss_pred EEEEEEEc--CCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHH
Q 003958 166 EVIAIYVD--DDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQY 243 (784)
Q Consensus 166 ~v~ii~~d--~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~ 243 (784)
+|+++.+. ..++....+.+++.+++.|+.+.....- .+.......++++.+.+++.||+..........++.+.+
T Consensus 1 ~ig~v~~~~~~~~~~~~~~g~~~~~~~~g~~l~~~~~~---~~~~~~~~~~~~~~~~~~d~ii~~~~~~~~~~~~~~l~~ 77 (264)
T cd01537 1 TIGVLVPDLDNPFFAQVLKGIEEAAKAAGYQVLLANSQ---NDAEKQLSALENLIARGVDGIIIAPSDLTAPTIVKLARK 77 (264)
T ss_pred CeEEEEcCCCChHHHHHHHHHHHHHHHcCCeEEEEeCC---CCHHHHHHHHHHHHHcCCCEEEEecCCCcchhHHHHhhh
Confidence 36777754 5677888899999999999877643321 233456677777777789988887544333335666665
Q ss_pred cC
Q 003958 244 LG 245 (784)
Q Consensus 244 ~g 245 (784)
.+
T Consensus 78 ~~ 79 (264)
T cd01537 78 AG 79 (264)
T ss_pred cC
Confidence 54
No 320
>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=65.17 E-value=1.2e+02 Score=28.09 Aligned_cols=70 Identities=21% Similarity=0.236 Sum_probs=43.4
Q ss_pred eeeHHHHHHHHHHC-CCccceEEeeCCCCCCCCChhHHHHHHHcCcccEEEeeEEeecCccccceeccccccccEEEEEe
Q 003958 494 GFCIDVFTAAINLL-PYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAP 572 (784)
Q Consensus 494 G~~~dl~~~l~~~l-~f~~~~~~~~~~~~~~~~~~~g~i~~l~~~~~D~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~ 572 (784)
.+..+++..+.+.. +.+ +++.. +..+.+++.+.+|++|+++..-.. ......+ .+.+.....++++++
T Consensus 13 ~~l~~~l~~~~~~~P~i~--l~~~~-------~~~~~~~~~l~~g~~Dl~i~~~~~-~~~~~~~-~~~~l~~~~~~~v~~ 81 (195)
T cd08427 13 GLLPRALARLRRRHPDLE--VHIVP-------GLSAELLARVDAGELDAAIVVEPP-FPLPKDL-VWTPLVREPLVLIAP 81 (195)
T ss_pred HHhHHHHHHHHHHCCCce--EEEEe-------CCcHHHHHHHHCCCCCEEEEcCCC-CccccCc-eEEEcccCcEEEEEC
Confidence 45567777877776 444 54432 356788999999999999863211 0101223 235567777777775
Q ss_pred cc
Q 003958 573 VR 574 (784)
Q Consensus 573 ~~ 574 (784)
..
T Consensus 82 ~~ 83 (195)
T cd08427 82 AE 83 (195)
T ss_pred CC
Confidence 54
No 321
>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=64.89 E-value=1.2e+02 Score=28.31 Aligned_cols=70 Identities=17% Similarity=0.105 Sum_probs=43.6
Q ss_pred eeeeHHHHHHHHHHC-CCccceEEeeCCCCCCCCChhHHHHHHHcCcccEEEeeEEeecCccccceeccccccccEEEEE
Q 003958 493 SGFCIDVFTAAINLL-PYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVA 571 (784)
Q Consensus 493 ~G~~~dl~~~l~~~l-~f~~~~~~~~~~~~~~~~~~~g~i~~l~~~~~D~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~ 571 (784)
..+..+++..+.+.. +.+ +++.. +....++..+.+|++|+++..-. ......+. +.++....+.+++
T Consensus 12 ~~~l~~~l~~f~~~~P~~~--i~i~~-------~~~~~~~~~l~~g~~Dl~i~~~~--~~~~~~~~-~~~l~~~~~~~v~ 79 (198)
T cd08443 12 RYVLPPVIKGFIERYPRVS--LQMHQ-------GSPTQIAEMVSKGLVDFAIATEA--LHDYDDLI-TLPCYHWNRCVVV 79 (198)
T ss_pred eeECcHHHHHHHHHCCCeE--EEEEe-------CCHHHHHHHHHCCCccEEEEecc--ccccCCce-EeeeeeceEEEEE
Confidence 345667788887765 333 44432 34668899999999999985321 11112232 4567777887777
Q ss_pred ecc
Q 003958 572 PVR 574 (784)
Q Consensus 572 ~~~ 574 (784)
+..
T Consensus 80 ~~~ 82 (198)
T cd08443 80 KRD 82 (198)
T ss_pred cCC
Confidence 554
No 322
>cd06305 PBP1_methylthioribose_binding_like Methylthioribose-binding protein-like of ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily. Methylthioribose-binding protein-like of ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding. The sugar-binding domain of the periplasmic proteins in this group is also homologous to the ligand-binding domain of eukaryotic receptors such as metabotropic glutamate receptor (mGluR), DNA-binding transcriptional repressors such as LacI and GalR.
Probab=64.56 E-value=28 Score=35.10 Aligned_cols=78 Identities=9% Similarity=0.046 Sum_probs=53.2
Q ss_pred EEEEEEE--cCCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEecc-CCcHHHHHHHHH
Q 003958 166 EVIAIYV--DDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTH-YNRGPVVFHVAQ 242 (784)
Q Consensus 166 ~v~ii~~--d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~-~~~~~~~~~~a~ 242 (784)
+|+++.. ++.|.....+.+.+.+++.|+++..... ..+.......+..+...+.+.||+... .......++++.
T Consensus 1 ~Ig~i~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~---~~~~~~~~~~l~~~~~~~vdgii~~~~~~~~~~~~i~~~~ 77 (273)
T cd06305 1 RIAVVRYGGSGDFDQAYLAGTKAEAEALGGDLRVYDA---GGDDAKQADQIDQAIAQKVDAIIIQHGRAEVLKPWVKRAL 77 (273)
T ss_pred CeEEEeecCCCcHHHHHHHHHHHHHHHcCCEEEEECC---CCCHHHHHHHHHHHHHcCCCEEEEecCChhhhHHHHHHHH
Confidence 3667765 4667778889999999999998776321 123344456677766678999998743 333456777787
Q ss_pred HcCC
Q 003958 243 YLGM 246 (784)
Q Consensus 243 ~~g~ 246 (784)
+.|.
T Consensus 78 ~~~i 81 (273)
T cd06305 78 DAGI 81 (273)
T ss_pred HcCC
Confidence 7664
No 323
>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=64.25 E-value=31 Score=37.08 Aligned_cols=80 Identities=10% Similarity=0.109 Sum_probs=56.4
Q ss_pred HHHHHHHHcCCcEEEEEEEcCCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccC--
Q 003958 154 AIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY-- 231 (784)
Q Consensus 154 ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~-- 231 (784)
.+.++++.++ +++.||+..... ..+.+.+.+++.|+.+.... +..++..++....++..++.++|.||-.+.+
T Consensus 13 ~l~~~l~~~~-~r~livtd~~~~---~~~~v~~~L~~~g~~~~~~~-~~~~p~~~~v~~~~~~~~~~~~D~IIaiGGGS~ 87 (374)
T cd08183 13 ELPALAAELG-RRVLLVTGASSL---RAAWLIEALRAAGIEVTHVV-VAGEPSVELVDAAVAEARNAGCDVVIAIGGGSV 87 (374)
T ss_pred HHHHHHHHcC-CcEEEEECCchH---HHHHHHHHHHHcCCeEEEec-CCCCcCHHHHHHHHHHHHhcCCCEEEEecCchH
Confidence 4566777775 899999855443 67788888999998765443 3334566778888888888999999987554
Q ss_pred CcHHHHH
Q 003958 232 NRGPVVF 238 (784)
Q Consensus 232 ~~~~~~~ 238 (784)
-++..++
T Consensus 88 ~D~aK~i 94 (374)
T cd08183 88 IDAGKAI 94 (374)
T ss_pred HHHHHHH
Confidence 3444444
No 324
>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=63.63 E-value=1.3e+02 Score=28.17 Aligned_cols=69 Identities=12% Similarity=0.000 Sum_probs=43.6
Q ss_pred eeeHHHHHHHHHHCCCccceEEeeCCCCCCCCChhHHHHHHHcCcccEEEeeEEeecCccccceeccccccccEEEEEec
Q 003958 494 GFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPV 573 (784)
Q Consensus 494 G~~~dl~~~l~~~l~f~~~~~~~~~~~~~~~~~~~g~i~~l~~~~~D~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~ 573 (784)
.+..+++..+.+++ -++++++.. +....++..|.+|++|+++..-. . ....++ +.+.....+.++++.
T Consensus 14 ~~l~~~l~~f~~~~-P~v~i~i~~-------~~~~~l~~~l~~g~~D~~~~~~~--~-~~~~~~-~~~l~~~~~~lv~~~ 81 (198)
T cd08486 14 RSLPLLLRAFLTST-PTATVSLTH-------MTKDEQVEGLLAGTIHVGFSRFF--P-RHPGIE-IVNIAQEDLYLAVHR 81 (198)
T ss_pred HHHHHHHHHHHHhC-CCeEEEEEE-------CCHHHHHHHHHcCCceEEEecCC--C-CCCceE-EEEEeeccEEEEecC
Confidence 44567777777775 233355443 46789999999999999985321 1 112232 345667778887765
Q ss_pred c
Q 003958 574 R 574 (784)
Q Consensus 574 ~ 574 (784)
.
T Consensus 82 ~ 82 (198)
T cd08486 82 S 82 (198)
T ss_pred C
Confidence 4
No 325
>PLN03192 Voltage-dependent potassium channel; Provisional
Probab=63.50 E-value=5.6 Score=47.83 Aligned_cols=53 Identities=13% Similarity=0.319 Sum_probs=45.9
Q ss_pred ceeehhhhhhhhhcc--cccccccchhhHHHHHHHHHHHHHHhhccccceeeEee
Q 003958 625 VVTIFWFSFSTMFFA--HKEKTVSALGRLVLIIWLFVVLIINSSYTASLTSILTV 677 (784)
Q Consensus 625 ~~~~~~~~~~~~~~~--~~~~p~~~~~R~~~~~w~~~~lvl~~~Yta~L~s~l~~ 677 (784)
+..++||++.+|..- |.-.|.+...|++.++|.++++.+.++..+++++.+..
T Consensus 251 Yi~slYwai~TmtTVGYGDi~p~t~~E~i~~i~~ml~g~~~~a~~ig~i~~li~~ 305 (823)
T PLN03192 251 YISAIYWSITTMTTVGYGDLHAVNTIEMIFIIFYMLFNLGLTAYLIGNMTNLVVE 305 (823)
T ss_pred HHHHHHHHHHHHhhccCCCcCCCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 445899999999854 55689999999999999999999999999999987754
No 326
>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=63.33 E-value=31 Score=34.37 Aligned_cols=76 Identities=8% Similarity=0.059 Sum_probs=53.5
Q ss_pred EEEEEEc--CCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHc
Q 003958 167 VIAIYVD--DDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYL 244 (784)
Q Consensus 167 v~ii~~d--~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~ 244 (784)
|+++..+ +.|.....+.+++.+++.|+.+..... ..+.......++++...+.+.|++......... ++.+.+.
T Consensus 2 i~~v~~~~~~~~~~~~~~g~~~~~~~~g~~~~~~~~---~~~~~~~~~~~~~~~~~~~d~iii~~~~~~~~~-~~~~~~~ 77 (264)
T cd06267 2 IGVIVPDISNPFFAELLRGIEEAAREAGYSVLLCNS---DEDPEKEREALELLLSRRVDGIILAPSRLDDEL-LEELAAL 77 (264)
T ss_pred EEEEECCCCCHHHHHHHHHHHHHHHHcCCEEEEEcC---CCCHHHHHHHHHHHHHcCcCEEEEecCCcchHH-HHHHHHc
Confidence 5666654 678888889999999988988764321 233445567777777789999998766555544 7777776
Q ss_pred CC
Q 003958 245 GM 246 (784)
Q Consensus 245 g~ 246 (784)
|.
T Consensus 78 ~i 79 (264)
T cd06267 78 GI 79 (264)
T ss_pred CC
Confidence 64
No 327
>COG0078 ArgF Ornithine carbamoyltransferase [Amino acid transport and metabolism]
Probab=63.16 E-value=1.8e+02 Score=29.71 Aligned_cols=162 Identities=15% Similarity=0.199 Sum_probs=95.2
Q ss_pred eEEEEEEeecCCcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEccCchhhHH
Q 003958 31 VVNIGALLSFSTNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIGPQDAVTSH 110 (784)
Q Consensus 31 ~i~IG~i~~~~~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiGp~~s~~~~ 110 (784)
.=.||.||.-++. ..+-+++.|+-+. +|..+-+..-|++-...+.++-..+.+++-+++|.--..+. .
T Consensus 44 gk~laliFeK~ST---RTR~SFeva~~ql-------Gg~~~~l~~~~~Qlgr~Esi~DTArVLsr~~D~I~~R~~~~--~ 111 (310)
T COG0078 44 GKNLALIFEKTST---RTRVSFEVAATQL-------GGHAIYLGPGDSQLGRGESIKDTARVLSRMVDAIMIRGFSH--E 111 (310)
T ss_pred CceEEEEecCCCc---hhhhhHHHHHHHc-------CCCeEEeCCCccccCCCCcHHHHHHHHHhhhheEEEecccH--H
Confidence 4468999988653 5577788888874 34444444444443333444455556676677776544444 3
Q ss_pred HHHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHH---HHcC---CcEEEEEEEcCCCcchhHHHH
Q 003958 111 VVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIV---DHYG---WREVIAIYVDDDHGRNGIAAL 184 (784)
Q Consensus 111 ~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l---~~~~---w~~v~ii~~d~~~g~~~~~~l 184 (784)
.+..+++...+|+|. .|+|...| .+++++++ +|+| -.+++.+.+. .+....+
T Consensus 112 ~ve~lA~~s~VPViN------gLtD~~HP------------~Q~LADl~Ti~E~~g~l~g~k~a~vGDg----NNv~nSl 169 (310)
T COG0078 112 TLEELAKYSGVPVIN------GLTDEFHP------------CQALADLMTIKEHFGSLKGLKLAYVGDG----NNVANSL 169 (310)
T ss_pred HHHHHHHhCCCceEc------ccccccCc------------HHHHHHHHHHHHhcCcccCcEEEEEcCc----chHHHHH
Confidence 667889999999995 24443223 34556653 5665 3556655532 5677888
Q ss_pred HHHHhccCcEEEEeeccCCCCChhHHHHHHHHh-hcCCceEEEE
Q 003958 185 GDTLAAKRCRISFKAPLSVEATEDEITDLLVKV-ALTESRIIVV 227 (784)
Q Consensus 185 ~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l-~~~~~~vIvl 227 (784)
-......|+.+.....-... ...++....+++ +++++.+.+.
T Consensus 170 ~~~~a~~G~dv~ia~Pk~~~-p~~~~~~~a~~~a~~~g~~i~~t 212 (310)
T COG0078 170 LLAAAKLGMDVRIATPKGYE-PDPEVVEKAKENAKESGGKITLT 212 (310)
T ss_pred HHHHHHhCCeEEEECCCcCC-cCHHHHHHHHHHHHhcCCeEEEe
Confidence 88888889877654322221 234455555554 4455554433
No 328
>PRK03692 putative UDP-N-acetyl-D-mannosaminuronic acid transferase; Provisional
Probab=62.99 E-value=93 Score=31.00 Aligned_cols=88 Identities=11% Similarity=0.059 Sum_probs=54.8
Q ss_pred HHHHHHHHHHHHcCCcEEEEEEEcCCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEec
Q 003958 150 YQMAAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHT 229 (784)
Q Consensus 150 ~~~~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~ 229 (784)
+....+.+.....+ .+|.++..+.+-.....+.+++. .|+.|+.... .+ .+.++...+++.|.++++|++++..
T Consensus 92 dl~~~ll~~~~~~~-~~v~llG~~~~v~~~a~~~l~~~---y~l~i~g~~~-Gy-f~~~e~~~i~~~I~~s~~dil~Vgl 165 (243)
T PRK03692 92 DLWEALMARAGKEG-TPVFLVGGKPEVLAQTEAKLRTQ---WNVNIVGSQD-GY-FTPEQRQALFERIHASGAKIVTVAM 165 (243)
T ss_pred HHHHHHHHHHHhcC-CeEEEECCCHHHHHHHHHHHHHH---hCCEEEEEeC-CC-CCHHHHHHHHHHHHhcCCCEEEEEC
Confidence 34555666665556 67888876655333344444433 2677665432 11 1344556789999999999999987
Q ss_pred cCCcHHHHHHHHHH
Q 003958 230 HYNRGPVVFHVAQY 243 (784)
Q Consensus 230 ~~~~~~~~~~~a~~ 243 (784)
....-..++.+..+
T Consensus 166 G~PkQE~~~~~~~~ 179 (243)
T PRK03692 166 GSPKQEIFMRDCRL 179 (243)
T ss_pred CCcHHHHHHHHHHH
Confidence 76666666655544
No 329
>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=62.68 E-value=23 Score=36.38 Aligned_cols=87 Identities=13% Similarity=0.129 Sum_probs=53.2
Q ss_pred cCCCCChHhhhhCCCceEEeeCchHHHHHHhhcccCccCceeCCCHHHHHHHHhcCCcCCCeeEEEechhhhHHH-HcCC
Q 003958 681 SSPIKGIDSLRSSNYPIGYQVNSFARNYLVDELNIDESRLVPLNSPEEYAKALKDGPHKGGVAAVVDDRAYAELF-LSTR 759 (784)
Q Consensus 681 ~~~i~~~~dl~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~a~~~~~~~~~~~-~~~~ 759 (784)
..||++++||+ |.++.+..+.....+++ ..+..+. .-...|.+.+|++ |-+|+.......+... ....
T Consensus 125 ~~pi~s~~Dlk--G~kiR~~~~~~~~~~~~-~lGa~pv----~ip~~evy~aLq~----G~vDg~~~~~~~~~~~~~~ev 193 (286)
T PF03480_consen 125 KKPIRSPEDLK--GLKIRVPGSPVMSDFFE-ALGASPV----PIPWSEVYQALQQ----GVVDGAENSASSIYSLGLYEV 193 (286)
T ss_dssp SS--SSGGGGT--TEEEEETSSHHHHHHHH-HCTSEEE----E-TGGGHHHHHHT----TSSSEEEEEHHHHHHTTGGGT
T ss_pred ccCCccHhhHh--hCeEEecCCHHHHHHHH-HcCCeee----cCcHHHHHHHHhc----CCcCeEecCHHHHHhcChhhh
Confidence 46899999999 98898886666677774 3443222 2345689999999 8999999876655221 1224
Q ss_pred CCeEEeCCccccceEEEEee
Q 003958 760 CEFSIVGQVFTKNGWGFVSI 779 (784)
Q Consensus 760 c~l~~~~~~~~~~~~~~~~~ 779 (784)
+++..... ....++.+++.
T Consensus 194 ~~y~~~~~-~~~~~~~~~~n 212 (286)
T PF03480_consen 194 AKYFTDTN-HGWSPYAVIMN 212 (286)
T ss_dssp SSEEEEEE-EEEEEEEEEEE
T ss_pred CCeeEeec-ccCcceEEEEc
Confidence 56444333 33344444443
No 330
>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=62.61 E-value=1.4e+02 Score=28.56 Aligned_cols=69 Identities=12% Similarity=0.117 Sum_probs=43.7
Q ss_pred eeeHHHHHHHHHHCCCccceEEeeCCCCCCCCChhHHHHHHHcCcccEEEeeEEeecCccccceeccccccccEEEEEec
Q 003958 494 GFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPV 573 (784)
Q Consensus 494 G~~~dl~~~l~~~l~f~~~~~~~~~~~~~~~~~~~g~i~~l~~~~~D~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~ 573 (784)
.+..+++..+.++.. ++++++.. .+...+.+.+.+|++|++++... .....+. ..|.....++++++.
T Consensus 13 ~~l~~~l~~f~~~~P-~v~l~i~~-------~~~~~~~~~l~~g~~Di~i~~~~---~~~~~l~-~~~l~~~~~~~v~~~ 80 (221)
T cd08469 13 VLLPALVRRLETEAP-GIDLRIRP-------VTRLDLAEQLDLGRIDLVIGIFE---QIPPRFR-RRTLFDEDEVWVMRK 80 (221)
T ss_pred HHHHHHHHHHHHHCC-CcEEEEee-------CChhhHHHHHHCCCccEEEecCC---CCCccce-eeeeeccceEEEEeC
Confidence 345667777777653 23355543 34667899999999999986432 2223343 357777888888765
Q ss_pred c
Q 003958 574 R 574 (784)
Q Consensus 574 ~ 574 (784)
.
T Consensus 81 ~ 81 (221)
T cd08469 81 D 81 (221)
T ss_pred C
Confidence 4
No 331
>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=62.60 E-value=93 Score=29.24 Aligned_cols=86 Identities=13% Similarity=0.048 Sum_probs=54.4
Q ss_pred HHHHHHHHHHHHcCCcEEEEEEEcCCCcchhHHHHHHHHhcc--CcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEE
Q 003958 150 YQMAAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAK--RCRISFKAPLSVEATEDEITDLLVKVALTESRIIVV 227 (784)
Q Consensus 150 ~~~~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~~l~~~--gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl 227 (784)
+....+.+.....+ .++.++....+ ..+.+.+.+++. |++|+....+ .+..+-..+++.|.++++|++++
T Consensus 35 dl~~~l~~~~~~~~-~~vfllG~~~~----v~~~~~~~l~~~yP~l~i~g~~g~---f~~~~~~~i~~~I~~s~~dil~V 106 (177)
T TIGR00696 35 DLMEELCQRAGKEK-LPIFLYGGKPD----VLQQLKVKLIKEYPKLKIVGAFGP---LEPEERKAALAKIARSGAGIVFV 106 (177)
T ss_pred HHHHHHHHHHHHcC-CeEEEECCCHH----HHHHHHHHHHHHCCCCEEEEECCC---CChHHHHHHHHHHHHcCCCEEEE
Confidence 44555666555556 57888876655 344444444443 6777764222 23445567899999999999999
Q ss_pred eccCCcHHHHHHHHHH
Q 003958 228 HTHYNRGPVVFHVAQY 243 (784)
Q Consensus 228 ~~~~~~~~~~~~~a~~ 243 (784)
......-..++.+.+.
T Consensus 107 glG~PkQE~~~~~~~~ 122 (177)
T TIGR00696 107 GLGCPKQEIWMRNHRH 122 (177)
T ss_pred EcCCcHhHHHHHHhHH
Confidence 8776666666655433
No 332
>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=62.32 E-value=1.4e+02 Score=27.95 Aligned_cols=70 Identities=17% Similarity=0.137 Sum_probs=44.6
Q ss_pred eeeeHHHHHHHHHHC-CCccceEEeeCCCCCCCCChhHHHHHHHcCcccEEEeeEEeecCccccceeccccccccEEEEE
Q 003958 493 SGFCIDVFTAAINLL-PYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVA 571 (784)
Q Consensus 493 ~G~~~dl~~~l~~~l-~f~~~~~~~~~~~~~~~~~~~g~i~~l~~~~~D~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~ 571 (784)
.++..+++..+.++. +.. +++.. +....+++.+.+|++|+++..-.. .....+ .+.++....+++++
T Consensus 12 ~~~l~~~l~~~~~~~P~v~--l~i~~-------~~~~~~~~~l~~g~~Dl~i~~~~~--~~~~~~-~~~~l~~~~~~~~~ 79 (198)
T cd08444 12 RYALPWVVQAFKEQFPNVH--LVLHQ-------GSPEEIASMLANGQADIGIATEAL--ENHPEL-VSFPYYDWHHHIIV 79 (198)
T ss_pred hhhhhHHHHHHHHHCCCeE--EEEEe-------CCHHHHHHHHHCCCccEEEecccc--CCCcCc-EEeeccccceeEEe
Confidence 345677788888875 344 44432 356678999999999999853211 111223 24667777788777
Q ss_pred ecc
Q 003958 572 PVR 574 (784)
Q Consensus 572 ~~~ 574 (784)
+..
T Consensus 80 ~~~ 82 (198)
T cd08444 80 PVG 82 (198)
T ss_pred cCC
Confidence 654
No 333
>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=62.32 E-value=39 Score=33.87 Aligned_cols=77 Identities=12% Similarity=0.069 Sum_probs=51.1
Q ss_pred EEEEEE--cCCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHc
Q 003958 167 VIAIYV--DDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYL 244 (784)
Q Consensus 167 v~ii~~--d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~ 244 (784)
|++|.. .+.|.....+.+++.+++.|.++.... . ..+.......++++.+.+++.|++..........++++.+.
T Consensus 2 I~vi~~~~~~~~~~~~~~g~~~~a~~~g~~~~~~~--~-~~~~~~~~~~i~~~~~~~vdgiii~~~~~~~~~~~~~~~~~ 78 (268)
T cd06289 2 IGLVINDLTNPFFAELAAGLEEVLEEAGYTVFLAN--S-GEDVERQEQLLSTMLEHGVAGIILCPAAGTSPDLLKRLAES 78 (268)
T ss_pred EEEEecCCCcchHHHHHHHHHHHHHHcCCeEEEec--C-CCChHHHHHHHHHHHHcCCCEEEEeCCCCccHHHHHHHHhc
Confidence 566665 356777788889899999998775431 1 12334455677777778899888875444434467777766
Q ss_pred CC
Q 003958 245 GM 246 (784)
Q Consensus 245 g~ 246 (784)
|.
T Consensus 79 ~i 80 (268)
T cd06289 79 GI 80 (268)
T ss_pred CC
Confidence 54
No 334
>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=60.65 E-value=1.5e+02 Score=28.00 Aligned_cols=72 Identities=11% Similarity=0.135 Sum_probs=42.8
Q ss_pred eeeHHHHHHHHHHCCCccceEEeeCCCCCCCCChhHHHHHHHcCcccEEEeeEEeecCccccceeccccccccEEEEEec
Q 003958 494 GFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPV 573 (784)
Q Consensus 494 G~~~dl~~~l~~~l~f~~~~~~~~~~~~~~~~~~~g~i~~l~~~~~D~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~ 573 (784)
.+..+++..+.+..- .+++++.. +....++..|.+|++|+++............+ ...|+....+.++.+.
T Consensus 13 ~~l~~~l~~f~~~~P-~v~l~i~~-------~~~~~~~~~L~~~~~D~~i~~~~~~~~~~~~~-~~~~l~~~~~~~~~~~ 83 (204)
T cd08429 13 SIAYRLLEPAMDLHE-PIRLVCRE-------GKLEQLLADLALHRLDMVLADRPMPSSLDVKG-YSHRLGECGVSFFAAP 83 (204)
T ss_pred HHHHHHHHHHHHhCC-CcEEEEEe-------CCHHHHHHHHHcCCccEEEecCCCccccchhe-eeccccccceEEEecC
Confidence 455677777777752 23344443 56889999999999999885332111100111 2346777777776544
Q ss_pred c
Q 003958 574 R 574 (784)
Q Consensus 574 ~ 574 (784)
+
T Consensus 84 ~ 84 (204)
T cd08429 84 P 84 (204)
T ss_pred C
Confidence 3
No 335
>KOG0025 consensus Zn2+-binding dehydrogenase (nuclear receptor binding factor-1) [Transcription; Energy production and conversion]
Probab=60.49 E-value=58 Score=32.84 Aligned_cols=97 Identities=8% Similarity=0.039 Sum_probs=68.2
Q ss_pred CCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcCCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHh
Q 003958 138 FPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKV 217 (784)
Q Consensus 138 ~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l 217 (784)
-+++++...+.. .++++.++.+++|.+.|.+|.+.++ .+.+++.|+..|.+.++++.-. ...++. -.+.
T Consensus 161 GD~vIQNganS~-VG~~ViQlaka~GiktinvVRdR~~-----ieel~~~Lk~lGA~~ViTeeel---~~~~~~--k~~~ 229 (354)
T KOG0025|consen 161 GDSVIQNGANSG-VGQAVIQLAKALGIKTINVVRDRPN-----IEELKKQLKSLGATEVITEEEL---RDRKMK--KFKG 229 (354)
T ss_pred CCeeeecCcccH-HHHHHHHHHHHhCcceEEEeecCcc-----HHHHHHHHHHcCCceEecHHHh---cchhhh--hhhc
Confidence 357888777654 5899999999999999999997664 7899999999887655443221 111111 1112
Q ss_pred hcCCceEEEEeccCCcHHHHHHHHHHcC
Q 003958 218 ALTESRIIVVHTHYNRGPVVFHVAQYLG 245 (784)
Q Consensus 218 ~~~~~~vIvl~~~~~~~~~~~~~a~~~g 245 (784)
...+++.-+-+..+..+..+.+.+.+-|
T Consensus 230 ~~~~prLalNcVGGksa~~iar~L~~Gg 257 (354)
T KOG0025|consen 230 DNPRPRLALNCVGGKSATEIARYLERGG 257 (354)
T ss_pred cCCCceEEEeccCchhHHHHHHHHhcCc
Confidence 3356777777777888888888887755
No 336
>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=60.32 E-value=41 Score=34.43 Aligned_cols=77 Identities=5% Similarity=-0.007 Sum_probs=54.4
Q ss_pred EEEEEEc--CCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEecc-CCcHHHHHHHHHH
Q 003958 167 VIAIYVD--DDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTH-YNRGPVVFHVAQY 243 (784)
Q Consensus 167 v~ii~~d--~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~-~~~~~~~~~~a~~ 243 (784)
|++|..+ +.|.....+.+++.+++.|+.+...... .+......+++++.+.+++.|++... .+.....++++.+
T Consensus 2 I~vi~~~~~~~~~~~~~~gi~~~a~~~g~~~~~~~~~---~~~~~~~~~i~~~~~~~vdgiii~~~~~~~~~~~l~~l~~ 78 (288)
T cd01538 2 IGLSLPTKTEERWIRDRPNFEAALKELGAEVIVQNAN---GDPAKQISQIENMIAKGVDVLVIAPVDGEALASAVEKAAD 78 (288)
T ss_pred eEEEEeCCCcHHHHHHHHHHHHHHHHcCCEEEEECCC---CCHHHHHHHHHHHHHcCCCEEEEecCChhhHHHHHHHHHH
Confidence 6777754 5677788899999999999887754322 23444567777777789999988753 3345677788877
Q ss_pred cCC
Q 003958 244 LGM 246 (784)
Q Consensus 244 ~g~ 246 (784)
.|.
T Consensus 79 ~~i 81 (288)
T cd01538 79 AGI 81 (288)
T ss_pred CCC
Confidence 663
No 337
>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=59.80 E-value=36 Score=36.13 Aligned_cols=76 Identities=16% Similarity=0.178 Sum_probs=51.8
Q ss_pred HHHHHHHHHcCCcEEEEEEEcCCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccC
Q 003958 153 AAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY 231 (784)
Q Consensus 153 ~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~ 231 (784)
..+.++++.++ +++.+|+....+ +...+.+.+.+++.|+.+.... +..+...+.....++.+++.++|.||-.+.+
T Consensus 12 ~~l~~~~~~~g-~~~liv~~~~~~-~~~~~~v~~~l~~~~i~~~~~~-~~~~p~~~~v~~~~~~~~~~~~d~IIavGGG 87 (349)
T cd08550 12 KEIAAILSTFG-SKVAVVGGKTVL-KKSRPRFEAALAKSIIVVDVIV-FGGECSTEEVVKALCGAEEQEADVIIGVGGG 87 (349)
T ss_pred HHHHHHHHHcC-CeEEEEEChHHH-HHHHHHHHHHHHhcCCeeEEEE-cCCCCCHHHHHHHHHHHHhcCCCEEEEecCc
Confidence 34667788888 888888754433 2456788888988887654332 4333355667777888888899998876543
No 338
>PRK09508 leuO leucine transcriptional activator; Reviewed
Probab=59.35 E-value=94 Score=32.29 Aligned_cols=68 Identities=7% Similarity=0.024 Sum_probs=44.6
Q ss_pred eeeHHHHHHHHHHC-CCccceEEeeCCCCCCCCChhHHHHHHHcCcccEEEeeEEeecCccccceeccccccccEEEEEe
Q 003958 494 GFCIDVFTAAINLL-PYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAP 572 (784)
Q Consensus 494 G~~~dl~~~l~~~l-~f~~~~~~~~~~~~~~~~~~~g~i~~l~~~~~D~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~ 572 (784)
++..+++..+.+.. +.+ +++.. +....+++.|.+|++|+++...... ...+.+ .++....++++++
T Consensus 125 ~~l~~~l~~f~~~~P~i~--l~i~~-------~~~~~~~~~l~~g~~Di~i~~~~~~---~~~l~~-~~l~~~~~~lv~~ 191 (314)
T PRK09508 125 RLTSQIYNRIEQIAPNIH--VVFKS-------SLNQNIEHQLRYQETEFVISYEEFD---RPEFTS-VPLFKDELVLVAS 191 (314)
T ss_pred HHHHHHHHHHHHhCCCcE--EEEEe-------CcchhHHHHHhcCCccEEEecCCCC---ccccce-eeeecCceEEEEc
Confidence 46678888888776 445 44432 3456889999999999998653221 222333 3567777888876
Q ss_pred cc
Q 003958 573 VR 574 (784)
Q Consensus 573 ~~ 574 (784)
..
T Consensus 192 ~~ 193 (314)
T PRK09508 192 KN 193 (314)
T ss_pred CC
Confidence 54
No 339
>TIGR00315 cdhB CO dehydrogenase/acetyl-CoA synthase complex, epsilon subunit. Nomenclature follows the description for Methanosarcina thermophila. The complex is also found in Archaeoglobus fulgidus, not considered a methanogen, but is otherwise generally associated with methanogenesis.
Probab=59.31 E-value=78 Score=29.19 Aligned_cols=86 Identities=10% Similarity=0.227 Sum_probs=50.4
Q ss_pred cCceEEEccCch--hhHHHHHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcCCcEE-----
Q 003958 95 GQTVAIIGPQDA--VTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREV----- 167 (784)
Q Consensus 95 ~~v~aiiGp~~s--~~~~~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v----- 167 (784)
+++..++|.... .....+..+++..++|+++.......+.++. +. ..|. ....+..++.+-+|+-+
T Consensus 28 KRPvIivG~ga~~~~a~e~l~~laEklgiPVvtT~~~~~~~~~kg---v~-~~~~---~lg~~g~~~~~p~~e~~~g~g~ 100 (162)
T TIGR00315 28 KRPLLIVGPENLEDEEKELIVKFIEKFDLPVVATADTYRALIEAG---IE-SEEM---NLHEITQFLADPSWEGFDGEGN 100 (162)
T ss_pred CCcEEEECCCcCcccHHHHHHHHHHHHCCCEEEcCccccccccCC---ee-cCCC---CHHHHHHhccCchhhhccCCCC
Confidence 389999998664 6778888999999999998544333344422 11 2221 11355566666555544
Q ss_pred ----EEEEEcCCCcchhHHHHHHH
Q 003958 168 ----IAIYVDDDHGRNGIAALGDT 187 (784)
Q Consensus 168 ----~ii~~d~~~g~~~~~~l~~~ 187 (784)
.++..+..++...+..++..
T Consensus 101 ~DlvlfvG~~~y~~~~~ls~lk~f 124 (162)
T TIGR00315 101 YDLVLFLGIIYYYLSQMLSSLKHF 124 (162)
T ss_pred cCEEEEeCCcchHHHHHHHHHHhh
Confidence 33444554444455555543
No 340
>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=59.23 E-value=1.5e+02 Score=27.43 Aligned_cols=69 Identities=12% Similarity=0.100 Sum_probs=43.3
Q ss_pred eeeHHHHHHHHHHCCCccceEEeeCCCCCCCCChhHHHHHHHcCcccEEEeeEEeecCccccceeccccccccEEEEEec
Q 003958 494 GFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPV 573 (784)
Q Consensus 494 G~~~dl~~~l~~~l~f~~~~~~~~~~~~~~~~~~~g~i~~l~~~~~D~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~ 573 (784)
.+...++..+.++.. ++++++.. +....+...+.+|++|+++..... ....+ ...++....++++++.
T Consensus 14 ~~l~~~l~~~~~~~P-~v~i~i~~-------~~~~~~~~~l~~g~~Dl~i~~~~~---~~~~~-~~~~l~~~~~~~v~~~ 81 (197)
T cd08425 14 YLIGPLIDRFHARYP-GIALSLRE-------MPQERIEAALADDRLDLGIAFAPV---RSPDI-DAQPLFDERLALVVGA 81 (197)
T ss_pred hhhHHHHHHHHHHCC-CcEEEEEE-------CcHHHHHHHHHcCCccEEEEecCC---CCCCc-EEEEeccccEEEEecC
Confidence 344677778777653 33355543 245678999999999999854322 22223 2356777777777755
Q ss_pred c
Q 003958 574 R 574 (784)
Q Consensus 574 ~ 574 (784)
.
T Consensus 82 ~ 82 (197)
T cd08425 82 T 82 (197)
T ss_pred C
Confidence 4
No 341
>PRK11063 metQ DL-methionine transporter substrate-binding subunit; Provisional
Probab=58.70 E-value=39 Score=34.37 Aligned_cols=78 Identities=13% Similarity=0.076 Sum_probs=39.2
Q ss_pred HHHHHHHHHHHHHHhhhccccCCCceEEEEEEeecCCcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHH
Q 003958 6 VMLLMIFYCELFVYRITAQASGRPSVVNIGALLSFSTNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLA 85 (784)
Q Consensus 6 ~~~~~~~~~~~~~~~~~~~~~~~~~~i~IG~i~~~~~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a 85 (784)
.++++++++++++.+|+.. ....++|+||..-..+ . ....++.+.+-+.. |++++++.+++...+..|
T Consensus 8 ~~~~~~~~~~l~l~gC~~~-~~~~~~I~IG~~~~~~----~---~~~~~~~~~l~~~~----G~~Vel~~f~~~~~~~~A 75 (271)
T PRK11063 8 FAAVGALIGTLALVGCGQD-EKDPNHIKVGVIVGAE----Q---QVAEVAQKVAKEKY----GLDVELVTFNDYVLPNEA 75 (271)
T ss_pred HHHHHHHHHHHHHHhcccc-cCCCCcEEEEeCCCCh----H---HHHHHHHHHHHHhc----CCeEEEEEecCcHHHHHH
Confidence 3333333333444566432 2334569999983211 1 11333444443342 678999988765444333
Q ss_pred HHHHHHHHhcCceEEE
Q 003958 86 LAEALHLMEGQTVAII 101 (784)
Q Consensus 86 ~~~~~~li~~~v~aii 101 (784)
+.+..+.+-.
T Consensus 76 ------La~GdID~~~ 85 (271)
T PRK11063 76 ------LSKGDIDANA 85 (271)
T ss_pred ------HHcCCcceec
Confidence 3344566533
No 342
>PRK12683 transcriptional regulator CysB-like protein; Reviewed
Probab=58.58 E-value=2.3e+02 Score=29.32 Aligned_cols=68 Identities=21% Similarity=0.142 Sum_probs=42.1
Q ss_pred eeHHHHHHHHHHC-CCccceEEeeCCCCCCCCChhHHHHHHHcCcccEEEeeEEeecCccccceeccccccccEEEEEec
Q 003958 495 FCIDVFTAAINLL-PYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPV 573 (784)
Q Consensus 495 ~~~dl~~~l~~~l-~f~~~~~~~~~~~~~~~~~~~g~i~~l~~~~~D~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~ 573 (784)
+...++..+.++. +.+ +++.. +.+..++..|.+|++|+++..-... ....+.+ .|+....+.++++.
T Consensus 107 ~l~~~i~~f~~~~P~i~--l~~~~-------~~~~~~~~~L~~~~~D~~i~~~~~~--~~~~l~~-~~l~~~~~~~v~~~ 174 (309)
T PRK12683 107 ALPKVVRQFKEVFPKVH--LALRQ-------GSPQEIAEMLLNGEADIGIATEALD--REPDLVS-FPYYSWHHVVVVPK 174 (309)
T ss_pred HHHHHHHHHHHHCCCce--EEEEe-------CCHHHHHHHHHcCCccEEEecCCCC--CCCCceE-EEcccCeEEEEecC
Confidence 3445677776665 333 44432 4688999999999999988532111 1222433 36777777777765
Q ss_pred c
Q 003958 574 R 574 (784)
Q Consensus 574 ~ 574 (784)
.
T Consensus 175 ~ 175 (309)
T PRK12683 175 G 175 (309)
T ss_pred C
Confidence 4
No 343
>PRK10837 putative DNA-binding transcriptional regulator; Provisional
Probab=58.47 E-value=2.1e+02 Score=28.98 Aligned_cols=68 Identities=12% Similarity=0.081 Sum_probs=41.8
Q ss_pred eeeHHHHHHHHHHC-CCccceEEeeCCCCCCCCChhHHHHHHHcCcccEEEeeEEeecCccccceeccccccccEEEEEe
Q 003958 494 GFCIDVFTAAINLL-PYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAP 572 (784)
Q Consensus 494 G~~~dl~~~l~~~l-~f~~~~~~~~~~~~~~~~~~~g~i~~l~~~~~D~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~ 572 (784)
.+..+++..+.+.. +.+ +++.. +....++..+.+|++|+++...... ...+ -..|+....+.++++
T Consensus 102 ~~~~~~l~~~~~~~P~i~--i~v~~-------~~~~~~~~~l~~g~~Di~i~~~~~~---~~~~-~~~~l~~~~~~lv~~ 168 (290)
T PRK10837 102 YILPAMIARYRRDYPQLP--LELSV-------GNSQDVINAVLDFRVDIGLIEGPCH---SPEL-ISEPWLEDELVVFAA 168 (290)
T ss_pred hhhHHHHHHHHHHCCCce--EEEEE-------CCHHHHHHHHHhCCceEEEecCCCC---CCce-eEEEeecceEEEEEc
Confidence 34456777777775 444 44432 3466889999999999998532211 1222 234566677777775
Q ss_pred cc
Q 003958 573 VR 574 (784)
Q Consensus 573 ~~ 574 (784)
+.
T Consensus 169 ~~ 170 (290)
T PRK10837 169 PD 170 (290)
T ss_pred CC
Confidence 54
No 344
>PRK15116 sulfur acceptor protein CsdL; Provisional
Probab=58.46 E-value=2e+02 Score=29.13 Aligned_cols=114 Identities=11% Similarity=0.172 Sum_probs=64.5
Q ss_pred hhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEccCch-hhHHHHHHhhhcCCccE
Q 003958 45 GKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIGPQDA-VTSHVVSHVANELQVPL 123 (784)
Q Consensus 45 g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiGp~~s-~~~~~va~~~~~~~ip~ 123 (784)
|..-..++.-.+.+|| |+.+++.+ +..-++. ...+++..+...||-...+ ..-..+...|...++|+
T Consensus 82 G~~Kve~~~~rl~~IN------P~~~V~~i--~~~i~~e----~~~~ll~~~~D~VIdaiD~~~~k~~L~~~c~~~~ip~ 149 (268)
T PRK15116 82 GLAKAEVMAERIRQIN------PECRVTVV--DDFITPD----NVAEYMSAGFSYVIDAIDSVRPKAALIAYCRRNKIPL 149 (268)
T ss_pred ChHHHHHHHHHHHhHC------CCcEEEEE--ecccChh----hHHHHhcCCCCEEEEcCCCHHHHHHHHHHHHHcCCCE
Confidence 4444456666777776 44455433 3322322 2334555567788876665 44556888999999999
Q ss_pred EecccCCCCCCcCCCCceEeecCC----hHHHHHHHHHHHHH-cCCc-------EEEEEEEcC
Q 003958 124 LSFSATDPTLSSLQFPYFVRTTQS----DQYQMAAIAEIVDH-YGWR-------EVIAIYVDD 174 (784)
Q Consensus 124 Is~~a~~~~l~~~~~p~~~r~~ps----~~~~~~ai~~~l~~-~~w~-------~v~ii~~d~ 174 (784)
|+.+.....+. |.-++..-- ....++.+-+.|++ +|.. .+-++|++.
T Consensus 150 I~~gGag~k~d----p~~~~~~di~~t~~~pla~~~R~~lr~~~~~~~~~~~~~~~~~v~S~E 208 (268)
T PRK15116 150 VTTGGAGGQID----PTQIQVVDLAKTIQDPLAAKLRERLKSDFGVVKNSKGKLGVDCVFSTE 208 (268)
T ss_pred EEECCcccCCC----CCeEEEEeeecccCChHHHHHHHHHHHhhCCCcccCccCCeEEEeCCC
Confidence 98655443332 554554422 22345555556665 5654 255666543
No 345
>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=58.37 E-value=1.3e+02 Score=28.18 Aligned_cols=70 Identities=11% Similarity=0.080 Sum_probs=43.5
Q ss_pred eeeeHHHHHHHHHHCCCccceEEeeCCCCCCCCChhHHHHHHHcCcccEEEeeEEeecCccccceeccccccccEEEEEe
Q 003958 493 SGFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAP 572 (784)
Q Consensus 493 ~G~~~dl~~~l~~~l~f~~~~~~~~~~~~~~~~~~~g~i~~l~~~~~D~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~ 572 (784)
.++..+++..+.++. -.+++++.. +....+++.|.+|++|+++...... ...+.. .+.....+.++++
T Consensus 12 ~~~l~~~l~~f~~~~-P~i~l~i~~-------~~~~~~~~~L~~g~~Dl~i~~~~~~---~~~~~~-~~l~~~~~~lv~~ 79 (200)
T cd08465 12 RLVLPALMRQLRAEA-PGIDLAVSQ-------ASREAMLAQVADGEIDLALGVFPEL---PEELHA-ETLFEERFVCLAD 79 (200)
T ss_pred HHhhhHHHHHHHHHC-CCcEEEEec-------CChHhHHHHHHCCCccEEEeccccC---CcCeeE-EEeeeccEEEEEe
Confidence 345567777776653 233355442 4578899999999999998633221 122333 3566677777776
Q ss_pred cc
Q 003958 573 VR 574 (784)
Q Consensus 573 ~~ 574 (784)
..
T Consensus 80 ~~ 81 (200)
T cd08465 80 RA 81 (200)
T ss_pred CC
Confidence 54
No 346
>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=57.87 E-value=39 Score=34.10 Aligned_cols=80 Identities=8% Similarity=-0.061 Sum_probs=52.4
Q ss_pred EEEEEEEc--CCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHH
Q 003958 166 EVIAIYVD--DDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQY 243 (784)
Q Consensus 166 ~v~ii~~d--~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~ 243 (784)
+|++|..+ +.|.......+++.+++.|..+.....-. ..+.......++.+...+++.|++..........++++.+
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 46777754 56777788899999999998876542211 1123445567777777899999987543333225677777
Q ss_pred cCC
Q 003958 244 LGM 246 (784)
Q Consensus 244 ~g~ 246 (784)
.|.
T Consensus 80 ~gi 82 (268)
T cd06306 80 ASI 82 (268)
T ss_pred CCC
Confidence 664
No 347
>PRK15408 autoinducer 2-binding protein lsrB; Provisional
Probab=57.67 E-value=42 Score=35.41 Aligned_cols=82 Identities=10% Similarity=0.009 Sum_probs=57.5
Q ss_pred CCcEEEEEEE--cCCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEecc-CCcHHHHHH
Q 003958 163 GWREVIAIYV--DDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTH-YNRGPVVFH 239 (784)
Q Consensus 163 ~w~~v~ii~~--d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~-~~~~~~~~~ 239 (784)
.-.+|+++.. ++.|.....+.+++.+++.|+++.... +...+...-..+++.+...+.+.|++... ++.....++
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 4568888885 467888888899999999998886532 21123333346777777789999998643 344467888
Q ss_pred HHHHcCC
Q 003958 240 VAQYLGM 246 (784)
Q Consensus 240 ~a~~~g~ 246 (784)
++.+.|.
T Consensus 100 ~a~~~gI 106 (336)
T PRK15408 100 RAMQRGV 106 (336)
T ss_pred HHHHCCC
Confidence 8888774
No 348
>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=57.52 E-value=46 Score=33.19 Aligned_cols=77 Identities=4% Similarity=-0.085 Sum_probs=51.6
Q ss_pred EEEEEEEc--CCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccC-CcHHHHHHHHH
Q 003958 166 EVIAIYVD--DDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY-NRGPVVFHVAQ 242 (784)
Q Consensus 166 ~v~ii~~d--~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~-~~~~~~~~~a~ 242 (784)
+|++|..+ +.|.....+.+++.+++.|+.+.....- .+.......++++...+.+.||+.... ......++.+.
T Consensus 1 ~ig~i~p~~~~~~~~~~~~~~~~~a~~~g~~~~~~~~~---~~~~~~~~~~~~l~~~~vdgvi~~~~~~~~~~~~~~~l~ 77 (267)
T cd01536 1 KIGLVVPSLNNPFWQAMNKGAEAAAKELGVELIVLDAQ---NDVSKQIQQIEDLIAQGVDGIIISPVDSAALTPALKKAN 77 (267)
T ss_pred CEEEEeccccCHHHHHHHHHHHHHHHhcCceEEEECCC---CCHHHHHHHHHHHHHcCCCEEEEeCCCchhHHHHHHHHH
Confidence 46778754 5677888899999999999887653322 233445577777777789988887543 33334666666
Q ss_pred HcC
Q 003958 243 YLG 245 (784)
Q Consensus 243 ~~g 245 (784)
+.+
T Consensus 78 ~~~ 80 (267)
T cd01536 78 AAG 80 (267)
T ss_pred HCC
Confidence 644
No 349
>COG2358 Imp TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]
Probab=57.46 E-value=93 Score=32.25 Aligned_cols=80 Identities=25% Similarity=0.184 Sum_probs=45.9
Q ss_pred cCCCCChHhhhhCCCceEEe-eCchHHHHHHh---hcccCccC--ceeCCCHHHHHHHHhcCCcCCCeeEEEechh---h
Q 003958 681 SSPIKGIDSLRSSNYPIGYQ-VNSFARNYLVD---ELNIDESR--LVPLNSPEEYAKALKDGPHKGGVAAVVDDRA---Y 751 (784)
Q Consensus 681 ~~~i~~~~dl~~~~~~i~~~-~~~~~~~~~~~---~~~~~~~~--~~~~~~~~~~~~~l~~~~~~~~~~a~~~~~~---~ 751 (784)
...|+++.||+ |++|++. .||..+.-.+. ..+..... +...-...+..+.+++ +.+||.+.-.. .
T Consensus 126 d~~Ikti~DL~--GKrV~iG~~gSgt~~~a~~il~a~Gi~~~~~~~~~~~~~a~~~~~l~~----g~iDA~~~~~G~p~~ 199 (321)
T COG2358 126 DAGIKTIADLK--GKRVAIGPPGSGTEATARQILEALGITYDDYELDLGLGDAESADALKN----GTIDAAFYVAGVPNP 199 (321)
T ss_pred CCCcceehhcC--CCEEeecCCCCccHHHHHHHHHHcCCCCcchhhhhhcCchhhHHHhhC----CcccEEEEecCCCCc
Confidence 34699999999 9998885 34433333322 23332221 1112234455778888 88998766422 2
Q ss_pred hHHHHcCCCCeEEeC
Q 003958 752 AELFLSTRCEFSIVG 766 (784)
Q Consensus 752 ~~~~~~~~c~l~~~~ 766 (784)
+-..+...|++.++.
T Consensus 200 ai~el~~~~~i~lv~ 214 (321)
T COG2358 200 AISELATTCDIVLVP 214 (321)
T ss_pred cHHHHHhhCCeEEEe
Confidence 224455577766664
No 350
>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=57.46 E-value=55 Score=32.69 Aligned_cols=77 Identities=4% Similarity=-0.007 Sum_probs=51.2
Q ss_pred EEEEEE--cCCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHc
Q 003958 167 VIAIYV--DDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYL 244 (784)
Q Consensus 167 v~ii~~--d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~ 244 (784)
|+++.. ++.|.....+.+.+.+++.|+.+..... . .+.......++++...+.+.||+..........++.+.+.
T Consensus 2 igvv~~~~~~~~~~~~~~~i~~~~~~~g~~~~~~~~-~--~~~~~~~~~~~~l~~~~vdgiii~~~~~~~~~~~~~~~~~ 78 (266)
T cd06282 2 VGVVLPSLANPVFAECVQGIQEEARAAGYSLLLATT-D--YDAEREADAVETLLRQRVDGLILTVADAATSPALDLLDAE 78 (266)
T ss_pred eEEEeCCCCcchHHHHHHHHHHHHHHCCCEEEEeeC-C--CCHHHHHHHHHHHHhcCCCEEEEecCCCCchHHHHHHhhC
Confidence 566664 3567777888999999999988775432 1 2344455677777777899998864333333467777776
Q ss_pred CC
Q 003958 245 GM 246 (784)
Q Consensus 245 g~ 246 (784)
|.
T Consensus 79 ~i 80 (266)
T cd06282 79 RV 80 (266)
T ss_pred CC
Confidence 64
No 351
>COG2247 LytB Putative cell wall-binding domain [Cell envelope biogenesis, outer membrane]
Probab=56.77 E-value=2.4e+02 Score=29.02 Aligned_cols=78 Identities=15% Similarity=0.126 Sum_probs=42.3
Q ss_pred CceEEEccCchhhHHHHHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHH-----HcCCcEEEEE
Q 003958 96 QTVAIIGPQDAVTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVD-----HYGWREVIAI 170 (784)
Q Consensus 96 ~v~aiiGp~~s~~~~~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~-----~~~w~~v~ii 170 (784)
..+.|||+.- .++......++.+|+++.-.++.+. ...+.-++..++ .|+-.+++++
T Consensus 77 d~VLIIGGp~-AVs~~yE~~Lks~GitV~RigG~nR-----------------~ETa~~v~~~~~~~yp~af~n~kvvvv 138 (337)
T COG2247 77 DLVLIIGGPI-AVSPNYENALKSLGITVKRIGGANR-----------------YETAEKVAKFFREDYPNAFKNVKVVVV 138 (337)
T ss_pred ceEEEECCCC-cCChhHHHHHHhCCcEEEEecCcch-----------------HHHHHHHHHHHHhhchhhhcCeEEEEE
Confidence 5566666432 2333444556677776665443221 123445566664 2344578887
Q ss_pred EEcCCCcchhHHHHHHHHhccCcEEEE
Q 003958 171 YVDDDHGRNGIAALGDTLAAKRCRISF 197 (784)
Q Consensus 171 ~~d~~~g~~~~~~l~~~l~~~gi~v~~ 197 (784)
|.=| ....+.+.+++ |+|-..
T Consensus 139 ~GwD-----y~~~~~e~~k~-~~~p~~ 159 (337)
T COG2247 139 YGWD-----YADALMELMKE-GIVPVI 159 (337)
T ss_pred eccc-----cHHHHHHHHhc-CcceeE
Confidence 7433 23367777777 877554
No 352
>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=56.75 E-value=63 Score=32.29 Aligned_cols=76 Identities=12% Similarity=-0.003 Sum_probs=52.4
Q ss_pred EEEEEE--cCCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHc
Q 003958 167 VIAIYV--DDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYL 244 (784)
Q Consensus 167 v~ii~~--d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~ 244 (784)
|+++.. ++.|.....+.+.+.+++.|+.+.....- .+.......++.+.+.+.|.||+....... ..++++.+.
T Consensus 2 igvv~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~~---~~~~~~~~~~~~l~~~~vdgiIi~~~~~~~-~~~~~l~~~ 77 (265)
T cd06299 2 IGVIVPDIRNPYFASLATAIQDAASAAGYSTIIGNSD---ENPETENRYLDNLLSQRVDGIIVVPHEQSA-EQLEDLLKR 77 (265)
T ss_pred EEEEecCCCCccHHHHHHHHHHHHHHcCCEEEEEeCC---CCHHHHHHHHHHHHhcCCCEEEEcCCCCCh-HHHHHHHhC
Confidence 566765 45677788889999999999887754321 234445577778888899999887544333 446777776
Q ss_pred CC
Q 003958 245 GM 246 (784)
Q Consensus 245 g~ 246 (784)
|.
T Consensus 78 ~i 79 (265)
T cd06299 78 GI 79 (265)
T ss_pred CC
Confidence 53
No 353
>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=56.32 E-value=36 Score=34.63 Aligned_cols=80 Identities=13% Similarity=0.065 Sum_probs=50.0
Q ss_pred EEEEEEEc---CCCcchhHHHHHHHHhccCcEEEEeeccCCC-CChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHH
Q 003958 166 EVIAIYVD---DDHGRNGIAALGDTLAAKRCRISFKAPLSVE-ATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVA 241 (784)
Q Consensus 166 ~v~ii~~d---~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~-~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a 241 (784)
+|++|..+ ++|.....+.+.+.+++.|..+......... .+.......++.+.+.+.|.||+..........++++
T Consensus 1 ~Igvi~~~~~~~~~~~~~~~~i~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~i~~l~~~~vDgiIv~~~~~~~~~~~~~l 80 (280)
T cd06303 1 KIAVIYPGQQISDYWVRNIASFTARLEELNIPYELTQFSSRPGIDHRLQSQQLNEALQSKPDYLIFTLDSLRHRKLIERV 80 (280)
T ss_pred CeeEEecCccHHHHHHHHHHHHHHHHHHcCCcEEEEEeccCcccCHHHHHHHHHHHHHcCCCEEEEcCCchhhHHHHHHH
Confidence 37777764 4577777888899999999776643211111 1233445667777778899998865433334555666
Q ss_pred HHcC
Q 003958 242 QYLG 245 (784)
Q Consensus 242 ~~~g 245 (784)
.+.+
T Consensus 81 ~~~~ 84 (280)
T cd06303 81 LASG 84 (280)
T ss_pred HhCC
Confidence 5544
No 354
>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=55.78 E-value=62 Score=32.44 Aligned_cols=77 Identities=8% Similarity=0.040 Sum_probs=49.7
Q ss_pred EEEEEEc--CCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHc
Q 003958 167 VIAIYVD--DDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYL 244 (784)
Q Consensus 167 v~ii~~d--~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~ 244 (784)
|+++..+ +.|.....+.+++.+++.|..+.....-. .........++.+...+.+.|++..........++.+.+.
T Consensus 2 I~vi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~~~--~~~~~~~~~~~~l~~~~vdgiii~~~~~~~~~~~~~~~~~ 79 (270)
T cd01545 2 IGLLYDNPSPGYVSEIQLGALDACRDTGYQLVIEPCDS--GSPDLAERVRALLQRSRVDGVILTPPLSDNPELLDLLDEA 79 (270)
T ss_pred EEEEEcCCCcccHHHHHHHHHHHHHhCCCeEEEEeCCC--CchHHHHHHHHHHHHCCCCEEEEeCCCCCccHHHHHHHhc
Confidence 5666643 67888889999999999998876543221 1222445566667777889888864332334556666665
Q ss_pred C
Q 003958 245 G 245 (784)
Q Consensus 245 g 245 (784)
+
T Consensus 80 ~ 80 (270)
T cd01545 80 G 80 (270)
T ss_pred C
Confidence 5
No 355
>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=55.73 E-value=34 Score=37.11 Aligned_cols=78 Identities=6% Similarity=-0.028 Sum_probs=54.9
Q ss_pred cCCcEEEEEEEcCCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccC--CcHHHHHH
Q 003958 162 YGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY--NRGPVVFH 239 (784)
Q Consensus 162 ~~w~~v~ii~~d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~--~~~~~~~~ 239 (784)
.+.+++.+|+..........+.+.+.+++.|+.+.....+.++++.+.....+..+++.++|+||-.+.+ -++..++.
T Consensus 19 ~~~~k~liVtd~~~~~~g~~~~v~~~L~~~gi~~~~f~~v~~~p~~~~v~~~~~~~~~~~~D~IIaiGGGS~iD~AK~iA 98 (398)
T cd08178 19 KGKKRAFIVTDRFMVKLGYVDKVIDVLKRRGVETEVFSDVEPDPSLETVRKGLELMNSFKPDTIIALGGGSPMDAAKIMW 98 (398)
T ss_pred cCCCeEEEEcChhHHhCccHHHHHHHHHHCCCeEEEecCCCCCcCHHHHHHHHHHHHhcCCCEEEEeCCccHHHHHHHHH
Confidence 3568998888544333346788999999999877655455555666778888888898999999976443 44444443
No 356
>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=55.58 E-value=49 Score=33.52 Aligned_cols=78 Identities=5% Similarity=-0.084 Sum_probs=51.5
Q ss_pred EEEEEEE--cCCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccC-CcHHHHHHHHH
Q 003958 166 EVIAIYV--DDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY-NRGPVVFHVAQ 242 (784)
Q Consensus 166 ~v~ii~~--d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~-~~~~~~~~~a~ 242 (784)
+|+++.. .+.|.....+.+.+.+++.|..+..... ..+.......+..+...++|.|++.... +.....++.+.
T Consensus 1 ~igv~~~~~~~~~~~~~~~~i~~~~~~~g~~v~~~~~---~~~~~~~~~~i~~~~~~~~Dgiii~~~~~~~~~~~i~~~~ 77 (282)
T cd06318 1 KIGFSQYTLNSPFFAALTEAAKAHAKALGYELISTDA---QGDLTKQIADVEDLLTRGVNVLIINPVDPEGLVPAVAAAK 77 (282)
T ss_pred CeeEEeccccCHHHHHHHHHHHHHHHHcCCEEEEEcC---CCCHHHHHHHHHHHHHcCCCEEEEecCCccchHHHHHHHH
Confidence 3566664 3567777888999999999988765322 1233444567777778899999886433 33345677777
Q ss_pred HcCC
Q 003958 243 YLGM 246 (784)
Q Consensus 243 ~~g~ 246 (784)
+.|.
T Consensus 78 ~~~i 81 (282)
T cd06318 78 AAGV 81 (282)
T ss_pred HCCC
Confidence 6553
No 357
>PRK10341 DNA-binding transcriptional activator TdcA; Provisional
Probab=55.42 E-value=2.6e+02 Score=28.94 Aligned_cols=70 Identities=20% Similarity=0.325 Sum_probs=43.9
Q ss_pred eeHHHHHHHHHHCCCccceEEeeCCCCCCCCChhHHHHHHHcCcccEEEeeEEeecCccccceeccccccccEEEEEecc
Q 003958 495 FCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPVR 574 (784)
Q Consensus 495 ~~~dl~~~l~~~l~f~~~~~~~~~~~~~~~~~~~g~i~~l~~~~~D~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~~ 574 (784)
+..+++..+.+..- ++++++.. +....++..|.+|++|+++....... ..+.+ -..|+....++++++..
T Consensus 111 ~l~~~l~~~~~~~p-~v~i~~~~-------~~~~~~~~~l~~g~~Dl~i~~~~~~~-~~~~l-~~~~l~~~~~~lv~~~~ 180 (312)
T PRK10341 111 FMSDMINKFKEVFP-KAQVSMYE-------AQLSSFLPAIRDGRLDFAIGTLSNEM-KLQDL-HVEPLFESEFVLVASKS 180 (312)
T ss_pred hHHHHHHHHHHhCC-CCEEEEEe-------CCHHHHHHHHHcCCCcEEEecCCccc-ccCCe-eEEEEecccEEEEEcCC
Confidence 44567777776542 33355543 34678999999999999985432111 11222 34677778888888654
No 358
>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=55.38 E-value=68 Score=32.19 Aligned_cols=74 Identities=12% Similarity=0.020 Sum_probs=47.9
Q ss_pred EEEEEEc-----CCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHH
Q 003958 167 VIAIYVD-----DDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVA 241 (784)
Q Consensus 167 v~ii~~d-----~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a 241 (784)
|+++.++ +.|.....+.+++.+++.|..+.... .. ........++..+...++|.|++...... ..++.+
T Consensus 2 vgv~~~~~~~~~~~~~~~~~~~i~~~~~~~g~~~~~~~-~~--~~~~~~~~~~~~l~~~~vdgiii~~~~~~--~~~~~l 76 (268)
T cd06277 2 IGLIASKRILNSPAFYSEIYRAIEEEAKKYGYNLILKF-VS--DEDEEEFELPSFLEDGKVDGIILLGGIST--EYIKEI 76 (268)
T ss_pred eEEEEeccccccCCcHHHHHHHHHHHHHHcCCEEEEEe-CC--CChHHHHHHHHHHHHCCCCEEEEeCCCCh--HHHHHH
Confidence 5666655 67778888899999999998776543 22 12233345556666778999998754333 236666
Q ss_pred HHcC
Q 003958 242 QYLG 245 (784)
Q Consensus 242 ~~~g 245 (784)
.+.+
T Consensus 77 ~~~~ 80 (268)
T cd06277 77 KELG 80 (268)
T ss_pred hhcC
Confidence 6655
No 359
>TIGR00249 sixA phosphohistidine phosphatase SixA.
Probab=55.07 E-value=84 Score=28.65 Aligned_cols=98 Identities=10% Similarity=-0.006 Sum_probs=59.2
Q ss_pred cCChHHHHHHHHHHHHHcCCcEEEEEEEcCCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceE
Q 003958 145 TQSDQYQMAAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRI 224 (784)
Q Consensus 145 ~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~v 224 (784)
.+.-..+++.+++.|+..+...-.|+.+.-.-.+..++.+.+.+.. ...+.....+.+..+..++...++.+.....+.
T Consensus 24 t~~G~~qa~~~~~~l~~~~~~~d~i~sSp~~Ra~qTa~~l~~~~~~-~~~~~~~~~l~p~~~~~~~~~~l~~~~~~~~~~ 102 (152)
T TIGR00249 24 TTNGCDESRLVAQWLKGQGVEIERILVSPFVRAEQTAEIVGDCLNL-PSSAEVLEGLTPCGDIGLVSDYLEALTNEGVAS 102 (152)
T ss_pred CHHHHHHHHHHHHHHHhCCCCCCEEEECCcHHHHHHHHHHHHHcCC-CcceEEccCcCCCCCHHHHHHHHHHHHhcCCCE
Confidence 3444578888999998866544455555544444445555444321 122332333332334556777777776555677
Q ss_pred EEEeccCCcHHHHHHHHHH
Q 003958 225 IVVHTHYNRGPVVFHVAQY 243 (784)
Q Consensus 225 Ivl~~~~~~~~~~~~~a~~ 243 (784)
+++++....+..++.++-.
T Consensus 103 vliVgH~P~i~~l~~~l~~ 121 (152)
T TIGR00249 103 VLLVSHLPLVGYLVAELCP 121 (152)
T ss_pred EEEEeCCCCHHHHHHHHhC
Confidence 8888999999988888743
No 360
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=54.89 E-value=88 Score=32.62 Aligned_cols=79 Identities=11% Similarity=0.024 Sum_probs=51.4
Q ss_pred CcEEEEEEEc--CCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHH
Q 003958 164 WREVIAIYVD--DDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVA 241 (784)
Q Consensus 164 w~~v~ii~~d--~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a 241 (784)
-+.|+++..+ +.|.....+.+.+.+++.|..+...... .+...-...++.+...+.+.||+..........++++
T Consensus 61 ~~~Igvv~~~~~~~~~~~l~~gi~~~~~~~g~~~~~~~~~---~~~~~~~~~~~~l~~~~vdgiIi~~~~~~~~~~~~~l 137 (328)
T PRK11303 61 TRSIGLIIPDLENTSYARIAKYLERQARQRGYQLLIACSD---DQPDNEMRCAEHLLQRQVDALIVSTSLPPEHPFYQRL 137 (328)
T ss_pred CceEEEEeCCCCCchHHHHHHHHHHHHHHcCCEEEEEeCC---CCHHHHHHHHHHHHHcCCCEEEEcCCCCCChHHHHHH
Confidence 4578888753 5566777888999999999887654321 1233344567777777899988865432234456666
Q ss_pred HHcC
Q 003958 242 QYLG 245 (784)
Q Consensus 242 ~~~g 245 (784)
.+.+
T Consensus 138 ~~~~ 141 (328)
T PRK11303 138 QNDG 141 (328)
T ss_pred HhcC
Confidence 6655
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=54.73 E-value=48 Score=33.44 Aligned_cols=78 Identities=12% Similarity=0.069 Sum_probs=52.2
Q ss_pred EEEEEEEc---CCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccC-CcHHHHHHHH
Q 003958 166 EVIAIYVD---DDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY-NRGPVVFHVA 241 (784)
Q Consensus 166 ~v~ii~~d---~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~-~~~~~~~~~a 241 (784)
+|++|..+ +.|.....+.+++.+++.|..+..... . ..+.......++++...+++.||+.... +.....++.+
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 46777743 567778889999999999988765322 1 1134445577777777889998887533 2345567777
Q ss_pred HHcC
Q 003958 242 QYLG 245 (784)
Q Consensus 242 ~~~g 245 (784)
.+.|
T Consensus 79 ~~~~ 82 (271)
T cd06312 79 VAAG 82 (271)
T ss_pred HHCC
Confidence 7755
No 362
>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=54.49 E-value=51 Score=34.99 Aligned_cols=77 Identities=10% Similarity=0.198 Sum_probs=51.4
Q ss_pred HHHHHHHHHcCCcEEEEEEEcCCCcchhHHHHHHHHhccCcEEEEeeccCCC--CChhHHHHHHHHhhcCCceEEEEecc
Q 003958 153 AAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVE--ATEDEITDLLVKVALTESRIIVVHTH 230 (784)
Q Consensus 153 ~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~--~~~~d~~~~l~~l~~~~~~vIvl~~~ 230 (784)
..+.++++.++.+++.+|++...+ ....+.+.+.+++.|+.+......... .+.+.....++.+++ ++|+||-.+.
T Consensus 12 ~~l~~~~~~~~~~~~livtd~~~~-~~~~~~v~~~l~~~~i~~~~~~~~~~~~~pt~~~v~~~~~~~~~-~~d~IIaIGG 89 (348)
T cd08175 12 ERLPEILKEFGYKKALIVADENTY-AAAGKKVEALLKRAGVVVLLIVLPAGDLIADEKAVGRVLKELER-DTDLIIAVGS 89 (348)
T ss_pred HHHHHHHHhcCCCcEEEEECCcHH-HHHHHHHHHHHHHCCCeeEEeecCCCcccCCHHHHHHHHHHhhc-cCCEEEEECC
Confidence 346677888888999888844333 223578888899888866443333322 455667777777776 8999887654
Q ss_pred C
Q 003958 231 Y 231 (784)
Q Consensus 231 ~ 231 (784)
+
T Consensus 90 G 90 (348)
T cd08175 90 G 90 (348)
T ss_pred c
Confidence 3
No 363
>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=53.89 E-value=51 Score=33.22 Aligned_cols=79 Identities=14% Similarity=0.118 Sum_probs=51.2
Q ss_pred EEEEEEEc--CCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCc-HHHHHHHHH
Q 003958 166 EVIAIYVD--DDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNR-GPVVFHVAQ 242 (784)
Q Consensus 166 ~v~ii~~d--~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~-~~~~~~~a~ 242 (784)
||++|..+ +.|.......+++.+++.|..+.....-. ..+......+++++...+.+.||+...... ....++.+.
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 57777754 56777788899999999998876543211 123344456677777778998888643332 245666666
Q ss_pred HcC
Q 003958 243 YLG 245 (784)
Q Consensus 243 ~~g 245 (784)
+.+
T Consensus 80 ~~~ 82 (273)
T cd06310 80 DAG 82 (273)
T ss_pred HCC
Confidence 654
No 364
>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=53.83 E-value=1.8e+02 Score=26.66 Aligned_cols=70 Identities=16% Similarity=0.126 Sum_probs=42.2
Q ss_pred eeeHHHHHHHHHHCCCccceEEeeCCCCCCCCChhHHHHHHHcCcccEEEeeEEeecCccccceeccccccccEEEEEec
Q 003958 494 GFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPV 573 (784)
Q Consensus 494 G~~~dl~~~l~~~l~f~~~~~~~~~~~~~~~~~~~g~i~~l~~~~~D~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~ 573 (784)
.+..+++..+.+... ++++++.. +....+...+.+|++|+++..... .....+ ...+.....+.++++.
T Consensus 13 ~~l~~~l~~~~~~~P-~v~i~i~~-------~~~~~~~~~l~~~~~Dl~i~~~~~--~~~~~~-~~~~l~~~~~~~~~~~ 81 (194)
T cd08436 13 VDLPELLARFHRRHP-GVDIRLRQ-------AGSDDLLAAVREGRLDLAFVGLPE--RRPPGL-ASRELAREPLVAVVAP 81 (194)
T ss_pred HHHHHHHHHHHHHCC-CcEEEEec-------CCHHHHHHHHHcCCccEEEEecCC--CCCCCc-EEEEeecceEEEEecC
Confidence 445667777777652 22344432 345688999999999999864322 122223 2355666777777654
Q ss_pred c
Q 003958 574 R 574 (784)
Q Consensus 574 ~ 574 (784)
.
T Consensus 82 ~ 82 (194)
T cd08436 82 D 82 (194)
T ss_pred C
Confidence 4
No 365
>PRK00865 glutamate racemase; Provisional
Probab=53.79 E-value=2e+02 Score=29.07 Aligned_cols=35 Identities=9% Similarity=0.254 Sum_probs=23.9
Q ss_pred HHHhcCceEEEccCchhhHHHHHHhhhcCCccEEe
Q 003958 91 HLMEGQTVAIIGPQDAVTSHVVSHVANELQVPLLS 125 (784)
Q Consensus 91 ~li~~~v~aiiGp~~s~~~~~va~~~~~~~ip~Is 125 (784)
.|.+.++.+|+=+..+.++.++..+-+..++|+|.
T Consensus 62 ~L~~~g~d~iVIaCNTa~~~~l~~lr~~~~iPvig 96 (261)
T PRK00865 62 FLLEYGVKMLVIACNTASAVALPDLRERYDIPVVG 96 (261)
T ss_pred HHHhCCCCEEEEeCchHHHHHHHHHHHhCCCCEEe
Confidence 34445888887666555555556666677999997
No 366
>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=52.92 E-value=1.9e+02 Score=28.86 Aligned_cols=129 Identities=12% Similarity=0.040 Sum_probs=71.2
Q ss_pred eEEEEEEeecCCcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEccCchhhHH
Q 003958 31 VVNIGALLSFSTNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIGPQDAVTSH 110 (784)
Q Consensus 31 ~i~IG~i~~~~~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiGp~~s~~~~ 110 (784)
.-+||.+.+........-..|+.-++++.+. +.+.......+..+...+.+.+.++++++..+|+... ...+.
T Consensus 120 ~~~I~~i~~~~~~~~~~R~~Gf~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~ai~~~~-d~~A~ 192 (260)
T cd06304 120 TGKVGFVGGMPIPEVNRFINGFAAGAKSVNP------DITVLVIYTGSFFDPAKGKEAALALIDQGADVIFAAA-GGTGP 192 (260)
T ss_pred CCceEEEeccccHHHHHHHHHHHHHHHHhCC------CcEEEEEEecCccCcHHHHHHHHHHHhCCCCEEEEcC-CCCch
Confidence 3457776542222223345677777776431 2222222222333455667777788776678887644 34444
Q ss_pred HHHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcCCcEEE
Q 003958 111 VVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVI 168 (784)
Q Consensus 111 ~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ 168 (784)
.+...+...++-++++..+ ....-..|-+.....+....+..+++.+..-.|+..-
T Consensus 193 gv~~al~~~gv~vigfD~~--~~~~~~~p~lttv~~~~~~~~~~~~~~~~~~~~~~~~ 248 (260)
T cd06304 193 GVIQAAKEAGVYAIGVDSD--QSALAPDAVLTSAVKNVDVAVYDAIKAVLDGTWKGGV 248 (260)
T ss_pred HHHHHHHHcCCEEEeecCc--hhhhcCccEEEEEEeccHHHHHHHHHHHHcCCCCCcc
Confidence 4556666667666665443 1222224666666666677777777777666664433
No 367
>TIGR00854 pts-sorbose PTS system, mannose/fructose/sorbose family, IIB component. Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains.The Man family is unique in several respects among PTS permease families.It is the only PTS family in which members possess a IID protein. It is the only PTS family in which the IIB constituent is phosphorylated on a histidyl rather than a cysteyl residue. Its permease members exhibit broad specificity for a range of sugars, rather than being specific for just one or a few sugars. The mannose permease of E. coli, for example, can transport and phosphorylate glucose, mannose, fructose, glucosamine, N-acetylglucosamine, and other sugars. Other members of this can transport sorbose, fructose and N-acetylglucosamine. This family is specific for the IIB components of this family of PTS transporters.
Probab=52.83 E-value=58 Score=29.69 Aligned_cols=82 Identities=11% Similarity=0.097 Sum_probs=57.0
Q ss_pred HHHHHHHHHHHHcCCcEEEEEEEcCCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEec
Q 003958 150 YQMAAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHT 229 (784)
Q Consensus 150 ~~~~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~ 229 (784)
.+++.+..|.++++-++|.++-+ ..-.....+.+.+...-.|+++... +.++....+++-+..+.++++++-
T Consensus 12 IHGQV~~~W~~~~~~~~IiVvdD-~~A~D~~~k~~lkma~P~gvk~~i~-------sve~a~~~l~~~~~~~~~v~vl~k 83 (151)
T TIGR00854 12 IHGQVGTTWTKVAGANRIIVVND-DVANDEVRQTLMGIVAPTGFKVRFV-------SLEKTINVIHKPAYHDQTIFLLFR 83 (151)
T ss_pred hhhHhhhhhhcccCCCEEEEEcc-cccCCHHHHHHHHhhCCCCCEEEEE-------EHHHHHHHHhCcCCCCceEEEEEC
Confidence 46888999999999999988853 3333345666666666678776542 233455555554556678999999
Q ss_pred cCCcHHHHHH
Q 003958 230 HYNRGPVVFH 239 (784)
Q Consensus 230 ~~~~~~~~~~ 239 (784)
++.++..+++
T Consensus 84 ~~~da~~l~~ 93 (151)
T TIGR00854 84 NPQDVLTLVE 93 (151)
T ss_pred CHHHHHHHHH
Confidence 8888877754
No 368
>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=52.80 E-value=73 Score=31.99 Aligned_cols=76 Identities=12% Similarity=0.104 Sum_probs=49.5
Q ss_pred EEEEEE--cCCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHc
Q 003958 167 VIAIYV--DDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYL 244 (784)
Q Consensus 167 v~ii~~--d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~ 244 (784)
|++|.. ++.|.....+.+.+.+++.|..+.....- .+.......++.+...+.+.|++.........+++.+++.
T Consensus 2 Igvv~~~~~~~~~~~~~~~i~~~a~~~g~~~~~~~~~---~~~~~~~~~i~~l~~~~vdgii~~~~~~~~~~~~~~~~~~ 78 (269)
T cd06281 2 IGCLVSDITNPLLAQLFSGAEDRLRAAGYSLLIANSL---NDPERELEILRSFEQRRMDGIIIAPGDERDPELVDALASL 78 (269)
T ss_pred EEEEecCCccccHHHHHHHHHHHHHHcCCEEEEEeCC---CChHHHHHHHHHHHHcCCCEEEEecCCCCcHHHHHHHHhC
Confidence 566765 35677777888889999988887654221 2334455667777777888888865433334566666664
Q ss_pred C
Q 003958 245 G 245 (784)
Q Consensus 245 g 245 (784)
+
T Consensus 79 ~ 79 (269)
T cd06281 79 D 79 (269)
T ss_pred C
Confidence 4
No 369
>PRK12682 transcriptional regulator CysB-like protein; Reviewed
Probab=52.69 E-value=2.8e+02 Score=28.57 Aligned_cols=71 Identities=20% Similarity=0.191 Sum_probs=44.0
Q ss_pred eeeeHHHHHHHHHHCCCccceEEeeCCCCCCCCChhHHHHHHHcCcccEEEeeEEeecCccccceeccccccccEEEEEe
Q 003958 493 SGFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAP 572 (784)
Q Consensus 493 ~G~~~dl~~~l~~~l~f~~~~~~~~~~~~~~~~~~~g~i~~l~~~~~D~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~ 572 (784)
..+..+++..+.+... ++++++.. +.-+.++..|.+|++|+++..-.. .....++ +.|+....++++++
T Consensus 105 ~~~l~~~l~~~~~~~P-~i~i~i~~-------~~~~~~~~~l~~g~~D~~i~~~~~--~~~~~l~-~~~l~~~~~~~~~~ 173 (309)
T PRK12682 105 RYVLPRVVAAFRKRYP-KVNLSLHQ-------GSPDEIARMVISGEADIGIATESL--ADDPDLA-TLPCYDWQHAVIVP 173 (309)
T ss_pred HHHHHHHHHHHHHhCC-CeEEEEec-------CCHHHHHHHHHcCCccEEEecCcc--cCCCcce-EEEeeeeeEEEEec
Confidence 3455677777777652 22244432 345688999999999999864221 1122333 35777788888876
Q ss_pred cc
Q 003958 573 VR 574 (784)
Q Consensus 573 ~~ 574 (784)
..
T Consensus 174 ~~ 175 (309)
T PRK12682 174 PD 175 (309)
T ss_pred CC
Confidence 55
No 370
>cd00755 YgdL_like Family of activating enzymes (E1) of ubiquitin-like proteins related to the E.coli hypothetical protein ygdL. The common reaction mechanism catalyzed by E1-like enzymes begins with a nucleophilic attack of the C-terminal carboxylate of the ubiquitin-like substrate, on the alpha-phosphate of an ATP molecule bound at the active site of the activating enzymes, leading to the formation of a high-energy acyladenylate intermediate and subsequently to the formation of a thiocarboxylate at the C termini of the substrate. The exact function of this family is unknown.
Probab=52.36 E-value=2.4e+02 Score=27.79 Aligned_cols=116 Identities=14% Similarity=0.186 Sum_probs=66.6
Q ss_pred cchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEccCchhh-HHHHHHhhhcCCc
Q 003958 43 NVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIGPQDAVT-SHVVSHVANELQV 121 (784)
Q Consensus 43 ~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiGp~~s~~-~~~va~~~~~~~i 121 (784)
..|..-..++.-.+.+|| |..+++.. +..-++. ...+++..+...||....+.. -..+...|...++
T Consensus 61 diG~~Kae~~~~~l~~in------P~~~V~~~--~~~i~~~----~~~~l~~~~~D~VvdaiD~~~~k~~L~~~c~~~~i 128 (231)
T cd00755 61 TVGKPKVEVMAERIRDIN------PECEVDAV--EEFLTPD----NSEDLLGGDPDFVVDAIDSIRAKVALIAYCRKRKI 128 (231)
T ss_pred hCCCcHHHHHHHHHHHHC------CCcEEEEe--eeecCHh----HHHHHhcCCCCEEEEcCCCHHHHHHHHHHHHHhCC
Confidence 345555567777778877 44455443 3222322 234555556778887655543 4557788999999
Q ss_pred cEEecccCCCCCCcCCCCceEeecCChH----HHHHHHHHHHHHcCCc-EEEEEEEcC
Q 003958 122 PLLSFSATDPTLSSLQFPYFVRTTQSDQ----YQMAAIAEIVDHYGWR-EVIAIYVDD 174 (784)
Q Consensus 122 p~Is~~a~~~~l~~~~~p~~~r~~ps~~----~~~~ai~~~l~~~~w~-~v~ii~~d~ 174 (784)
|+|+.......+ -|.-+|...-.. -.++.+-+-|++-+.. .+-++|++.
T Consensus 129 p~I~s~g~g~~~----dp~~i~i~di~~t~~~pla~~~R~~Lrk~~~~~~~~~v~S~E 182 (231)
T cd00755 129 PVISSMGAGGKL----DPTRIRVADISKTSGDPLARKVRKRLRKRGIFFGVPVVYSTE 182 (231)
T ss_pred CEEEEeCCcCCC----CCCeEEEccEeccccCcHHHHHHHHHHHcCCCCCeEEEeCCC
Confidence 999865433222 255555543322 2344444455555554 577777654
No 371
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=52.35 E-value=98 Score=32.50 Aligned_cols=79 Identities=11% Similarity=0.017 Sum_probs=53.4
Q ss_pred CcEEEEEEEc--CCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHH
Q 003958 164 WREVIAIYVD--DDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVA 241 (784)
Q Consensus 164 w~~v~ii~~d--~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a 241 (784)
-+.|+++..+ +.|.....+.+.+.+++.|..+..... . .+.......++.+...+.+.||+..........++.+
T Consensus 64 ~~~Igvv~~~~~~~~~~~i~~gi~~~a~~~g~~~~~~~~-~--~~~~~~~~~~~~l~~~~vdgiIi~~~~~~~~~~~~~l 140 (342)
T PRK10014 64 SGVIGLIVRDLSAPFYAELTAGLTEALEAQGRMVFLLQG-G--KDGEQLAQRFSTLLNQGVDGVVIAGAAGSSDDLREMA 140 (342)
T ss_pred CCEEEEEeCCCccchHHHHHHHHHHHHHHcCCEEEEEeC-C--CCHHHHHHHHHHHHhCCCCEEEEeCCCCCcHHHHHHH
Confidence 3578888864 567777888899999999977654321 1 2334456777778778899999875443344566677
Q ss_pred HHcC
Q 003958 242 QYLG 245 (784)
Q Consensus 242 ~~~g 245 (784)
.+.+
T Consensus 141 ~~~~ 144 (342)
T PRK10014 141 EEKG 144 (342)
T ss_pred hhcC
Confidence 6655
No 372
>PRK09791 putative DNA-binding transcriptional regulator; Provisional
Probab=52.18 E-value=2.8e+02 Score=28.41 Aligned_cols=84 Identities=12% Similarity=0.183 Sum_probs=51.5
Q ss_pred ccEEEEecCCCccceeEeeCCCcceeeeeHHHHHHHHHHCCCccceEEeeCCCCCCCCChhHHHHHHHcCcccEEEeeEE
Q 003958 468 RHLRIGVPNRVSFREFVSVKGSEMTSGFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIA 547 (784)
Q Consensus 468 ~~l~v~~~~~~~~~~~~~~~~~~~~~G~~~dl~~~l~~~l~f~~~~~~~~~~~~~~~~~~~g~i~~l~~~~~D~~~~~~~ 547 (784)
+.|+|++.... ...+..+++..+.+... .+++.+.. +....++..|.+|++|+++....
T Consensus 95 g~l~I~~~~~~-------------~~~~l~~~l~~~~~~~p-~i~~~~~~-------~~~~~~~~~l~~g~~Di~i~~~~ 153 (302)
T PRK09791 95 GQINIGMGASI-------------ARSLMPAVISRFHQQHP-QVKVRIME-------GQLVSMINELRQGELDFTINTYY 153 (302)
T ss_pred eEEEEEechHH-------------HHhhhHHHHHHHHHHCC-CeEEEEEe-------CChHHHHHHHHCCCccEEEEecC
Confidence 56777765421 23455677777776654 33344432 34678999999999999886321
Q ss_pred eecCccccceeccccccccEEEEEecc
Q 003958 548 IITNRTKMADFTQPYIESGLVVVAPVR 574 (784)
Q Consensus 548 ~t~~r~~~~~fs~p~~~~~~~~~~~~~ 574 (784)
... ....+.+ .|+....+++++++.
T Consensus 154 ~~~-~~~~~~~-~~l~~~~~~l~~~~~ 178 (302)
T PRK09791 154 QGP-YDHEFTF-EKLLEKQFAVFCRPG 178 (302)
T ss_pred Ccc-cccceeE-EEeccceEEEEEcCC
Confidence 111 1122433 677888888887654
No 373
>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=52.10 E-value=1.6e+02 Score=27.30 Aligned_cols=78 Identities=12% Similarity=0.054 Sum_probs=51.2
Q ss_pred CcEEEEEEEcCCCcc---hhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhh-cCCceEEEEeccC-----CcH
Q 003958 164 WREVIAIYVDDDHGR---NGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVA-LTESRIIVVHTHY-----NRG 234 (784)
Q Consensus 164 w~~v~ii~~d~~~g~---~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~-~~~~~vIvl~~~~-----~~~ 234 (784)
.-++++|...|+-+. .....+...+++.|.++.....++ .+..++...+++.. ..+.|+|+..+.. +..
T Consensus 4 ~~rv~vit~~d~~~~~~d~n~~~l~~~L~~~G~~v~~~~iv~--Dd~~~i~~~l~~~~~~~~~DlVIttGGtg~g~~D~t 81 (163)
T TIGR02667 4 PLRIAILTVSDTRTEEDDTSGQYLVERLTEAGHRLADRAIVK--DDIYQIRAQVSAWIADPDVQVILITGGTGFTGRDVT 81 (163)
T ss_pred ccEEEEEEEeCcCCccCCCcHHHHHHHHHHCCCeEEEEEEcC--CCHHHHHHHHHHHHhcCCCCEEEECCCcCCCCCCCc
Confidence 457888775543222 235577888899999988777776 45667778887764 3579999987442 345
Q ss_pred HHHHHHHHH
Q 003958 235 PVVFHVAQY 243 (784)
Q Consensus 235 ~~~~~~a~~ 243 (784)
.+.+..+.+
T Consensus 82 ~eal~~l~~ 90 (163)
T TIGR02667 82 PEALEPLFD 90 (163)
T ss_pred HHHHHHHHC
Confidence 555555533
No 374
>PRK09756 PTS system N-acetylgalactosamine-specific transporter subunit IIB; Provisional
Probab=51.98 E-value=64 Score=29.66 Aligned_cols=81 Identities=11% Similarity=0.008 Sum_probs=55.8
Q ss_pred HHHHHHHHHHHHcCCcEEEEEEEcCCCcchhHHHHHHHHh-ccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEe
Q 003958 150 YQMAAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLA-AKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVH 228 (784)
Q Consensus 150 ~~~~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~~l~-~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~ 228 (784)
.+++.+..|.++++-++|.++-+ ..-.....+.+.+.+. -.|+++... +..+....+++ +..+.++++++
T Consensus 16 IHGQV~~~W~~~~~~~~IiVvdD-~vA~D~~~k~~lkma~~P~gvk~~i~-------sv~~a~~~l~~-~~~~~~vlvl~ 86 (158)
T PRK09756 16 VHGQVGVTWTSTIGANLLVVVDD-VVANDDIQQKLMGITAETYGFGIRFF-------TIEKTINVIGK-AAPHQKIFLIC 86 (158)
T ss_pred hhHHHHHhhhcccCCCEEEEEcc-hhcCCHHHHHHHHhcCCCCCCEEEEE-------EHHHHHHHHHh-ccCCceEEEEE
Confidence 57889999999999999988853 2233345555555544 567776532 33455566666 55667899999
Q ss_pred ccCCcHHHHHH
Q 003958 229 THYNRGPVVFH 239 (784)
Q Consensus 229 ~~~~~~~~~~~ 239 (784)
.++.++..+++
T Consensus 87 ~~~~da~~l~~ 97 (158)
T PRK09756 87 RTPQTVRKLVE 97 (158)
T ss_pred CCHHHHHHHHH
Confidence 88888877654
No 375
>PF00448 SRP54: SRP54-type protein, GTPase domain; InterPro: IPR000897 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]. SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 []. This entry represents the GTPase domain of the 54 kDa SRP54 component, a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 of the signal recognition particle has a three-domain structure: an N-terminal helical bundle domain, a GTPase domain, and the M-domain that binds the 7s RNA and also binds the signal sequence. The extreme C-terminal region is glycine-rich and lower in complexity and poorly conserved between species. The GTPase domain is evolutionary related to P-loop NTPase domains found in a variety of other proteins []. These proteins include Escherichia coli and Bacillus subtilis ffh protein (P48), which seems to be the prokaryotic counterpart of SRP54; signal recognition particle receptor alpha subunit (docking protein), an integral membrane GTP-binding protein which ensures, in conjunction with SRP, the correct targeting of nascent secretory proteins to the endoplasmic reticulum membrane; bacterial FtsY protein, which is believed to play a similar role to that of the docking protein in eukaryotes; the pilA protein from Neisseria gonorrhoeae, the homologue of ftsY; and bacterial flagellar biosynthesis protein flhF.; GO: 0005525 GTP binding, 0006614 SRP-dependent cotranslational protein targeting to membrane; PDB: 2OG2_A 3B9Q_A 3DM9_B 3DMD_B 3E70_C 3DM5_B 2XXA_C 2J28_9 1ZU5_B 1ZU4_A ....
Probab=51.89 E-value=2e+02 Score=27.53 Aligned_cols=76 Identities=11% Similarity=0.041 Sum_probs=47.6
Q ss_pred CcEEEEEEEcCCCcchhHHHHHHHHhccCcEEEEeeccCCCCCh-hHHHHHHHHhhcCCceEEEEeccC--CcHHHHHHH
Q 003958 164 WREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATE-DEITDLLVKVALTESRIIVVHTHY--NRGPVVFHV 240 (784)
Q Consensus 164 w~~v~ii~~d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~-~d~~~~l~~l~~~~~~vIvl~~~~--~~~~~~~~~ 240 (784)
-++|++|..|. |-....++++...+..|+.+...... .+. ......+++.+..+.|+|++...+ ..-...+.+
T Consensus 29 ~~~v~lis~D~-~R~ga~eQL~~~a~~l~vp~~~~~~~---~~~~~~~~~~l~~~~~~~~D~vlIDT~Gr~~~d~~~~~e 104 (196)
T PF00448_consen 29 GKKVALISADT-YRIGAVEQLKTYAEILGVPFYVARTE---SDPAEIAREALEKFRKKGYDLVLIDTAGRSPRDEELLEE 104 (196)
T ss_dssp T--EEEEEEST-SSTHHHHHHHHHHHHHTEEEEESSTT---SCHHHHHHHHHHHHHHTTSSEEEEEE-SSSSTHHHHHHH
T ss_pred cccceeecCCC-CCccHHHHHHHHHHHhccccchhhcc---hhhHHHHHHHHHHHhhcCCCEEEEecCCcchhhHHHHHH
Confidence 67899998654 55677889999998888776542211 122 234556777777889999998654 333444444
Q ss_pred HHH
Q 003958 241 AQY 243 (784)
Q Consensus 241 a~~ 243 (784)
.++
T Consensus 105 l~~ 107 (196)
T PF00448_consen 105 LKK 107 (196)
T ss_dssp HHH
T ss_pred HHH
Confidence 444
No 376
>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=51.79 E-value=1.2e+02 Score=26.48 Aligned_cols=72 Identities=11% Similarity=0.112 Sum_probs=44.4
Q ss_pred EEEEcCCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccC----CcHHHHHHHHHHc
Q 003958 169 AIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY----NRGPVVFHVAQYL 244 (784)
Q Consensus 169 ii~~d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~----~~~~~~~~~a~~~ 244 (784)
+....++.-.-....+...++..|+++..-.... .....+..+++.++++|++++.. +.+..+++++++.
T Consensus 4 ~~~~~gd~H~lG~~~~~~~l~~~G~~vi~lG~~v------p~e~~~~~a~~~~~d~V~iS~~~~~~~~~~~~~~~~L~~~ 77 (122)
T cd02071 4 VAKPGLDGHDRGAKVIARALRDAGFEVIYTGLRQ------TPEEIVEAAIQEDVDVIGLSSLSGGHMTLFPEVIELLREL 77 (122)
T ss_pred EEecCCChhHHHHHHHHHHHHHCCCEEEECCCCC------CHHHHHHHHHHcCCCEEEEcccchhhHHHHHHHHHHHHhc
Confidence 3333444444456667777888898877543221 23456666777889999998654 3455566666666
Q ss_pred CC
Q 003958 245 GM 246 (784)
Q Consensus 245 g~ 246 (784)
+.
T Consensus 78 ~~ 79 (122)
T cd02071 78 GA 79 (122)
T ss_pred CC
Confidence 54
No 377
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=51.78 E-value=3.8e+02 Score=29.87 Aligned_cols=140 Identities=12% Similarity=0.129 Sum_probs=72.3
Q ss_pred EEccCchhhHHHHHHhhh-cCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEEEcCCCc-
Q 003958 100 IIGPQDAVTSHVVSHVAN-ELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIYVDDDHG- 177 (784)
Q Consensus 100 iiGp~~s~~~~~va~~~~-~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~~d~~~g- 177 (784)
|++|.+.....++..+.+ ...+=+|.++- .-++|- ......+...++.+...-+++.|+|.. .||
T Consensus 198 i~~p~~~~v~~~l~~~~~l~l~~~~i~p~H----------G~i~r~--~~~~~l~~Y~~~~~~~~~~kv~IvY~S-~~Gn 264 (479)
T PRK05452 198 ILTPFSRLVTPKITEILGFNLPVDMIATSH----------GVVWRD--NPTQIVELYLKWAADYQEDRITIFYDT-MSNN 264 (479)
T ss_pred hhhhhHHHHHHHHHHHhhcCCCCCEEECCC----------CceEeC--CHHHHHHHHHHHhhccCcCcEEEEEEC-CccH
Confidence 677777665555655554 22344443321 123452 222333344455544345789999943 344
Q ss_pred -chhHHHHHHHHhcc--CcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccC------CcHHHHHHHHHHcCCCC
Q 003958 178 -RNGIAALGDTLAAK--RCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY------NRGPVVFHVAQYLGMLG 248 (784)
Q Consensus 178 -~~~~~~l~~~l~~~--gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~------~~~~~~~~~a~~~g~~~ 248 (784)
+..++.+.+.+++. |+.+.... +. ..+...++..+. +++.|++.+.. .....++.......+.+
T Consensus 265 Te~mA~~ia~gl~~~g~gv~v~~~~-v~----~~~~~~i~~~~~--~ad~vilGspT~~~~~~p~~~~fl~~l~~~~l~g 337 (479)
T PRK05452 265 TRMMADAIAQGIAEVDPRVAVKIFN-VA----RSDKNEILTNVF--RSKGVLVGSSTMNNVMMPKIAGLLEEITGLRFRN 337 (479)
T ss_pred HHHHHHHHHHHHHhhCCCceEEEEE-CC----CCCHHHHHhHHh--hCCEEEEECCccCCcchHHHHHHHHHhhccCcCC
Confidence 46678888888876 45544322 22 223344444443 56777776543 22445565555555444
Q ss_pred CCeEEEecCcc
Q 003958 249 TGYVWIATSWL 259 (784)
Q Consensus 249 ~~~~wi~~~~~ 259 (784)
....-+++..|
T Consensus 338 K~~~vFGSygw 348 (479)
T PRK05452 338 KRASAFGSHGW 348 (479)
T ss_pred CEEEEEECCCc
Confidence 43334444433
No 378
>PRK15395 methyl-galactoside ABC transporter galactose-binding periplasmic protein MglB; Provisional
Probab=51.18 E-value=1.7e+02 Score=30.61 Aligned_cols=124 Identities=10% Similarity=0.041 Sum_probs=67.4
Q ss_pred CceEEEEEEeecC-CcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEec-CCCCHHHHHHHHHHHHhc----CceEEEc
Q 003958 29 PSVVNIGALLSFS-TNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQD-CNHSGFLALAEALHLMEG----QTVAIIG 102 (784)
Q Consensus 29 ~~~i~IG~i~~~~-~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D-~~~~~~~a~~~~~~li~~----~v~aiiG 102 (784)
.+.+.++.+.... ......-..|++-|+++.+ .++.....+ ...+...+.+.+.+++.+ .+.+|+.
T Consensus 160 ~g~~~i~~i~g~~~~~~~~~R~~G~~~al~~~g--------~~~~~~~~~~~~~~~~~a~~~~~~~l~~~~~~~~~ai~~ 231 (330)
T PRK15395 160 DGKIQYVLLKGEPGHPDAEARTTYVIKELNDKG--------IKTEQLQLDTAMWDTAQAKDKMDAWLSGPNANKIEVVIA 231 (330)
T ss_pred CCceEEEEEecCCCCchHHHHHHHHHHHHHhcC--------CCeeeeecccCCcCHHHHHHHHHHHHhhCcCCCeeEEEE
Confidence 4567777664432 2223344577877776632 222222222 334566777788888764 4789887
Q ss_pred cCchhhHHHHHHhhhcC---CccEEecccCCCCCCc-CCCCceEeecCChHHHHHHHHHHHHH
Q 003958 103 PQDAVTSHVVSHVANEL---QVPLLSFSATDPTLSS-LQFPYFVRTTQSDQYQMAAIAEIVDH 161 (784)
Q Consensus 103 p~~s~~~~~va~~~~~~---~ip~Is~~a~~~~l~~-~~~p~~~r~~ps~~~~~~ai~~~l~~ 161 (784)
..+ ..+..+...++.. .+|++++..+.....- ..-|.+.....+...++...++++..
T Consensus 232 ~~d-~~A~gvl~al~~~Gl~~vpVvg~D~~~~~~~~~~~g~~~ttv~~~~~~~G~~a~~~l~~ 293 (330)
T PRK15395 232 NND-AMAMGAVEALKAHNKSSIPVFGVDALPEALALVKSGAMAGTVLNDANNQAKATFDLAKN 293 (330)
T ss_pred CCc-hHHHHHHHHHHhcCCCCCeEEeeCCCHHHHHHHHhCCceEEEecCHHHHHHHHHHHHHH
Confidence 544 3344444444444 5588877554221111 11133555556667778777777544
No 379
>cd00001 PTS_IIB_man PTS_IIB, PTS system, Mannose/sorbose specific IIB subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family is one of four structurally and functionally distinct group IIB PTS system cytoplasmic enzymes, necessary for the uptake of carbohydrates across the cytoplasmic membrane and their phosphorylation. The active site histidine receives a phosphate group from the IIA subunit and transfers it to the substrate.
Probab=51.05 E-value=63 Score=29.46 Aligned_cols=82 Identities=7% Similarity=0.051 Sum_probs=57.1
Q ss_pred HHHHHHHHHHHHcCCcEEEEEEEcCCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEec
Q 003958 150 YQMAAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHT 229 (784)
Q Consensus 150 ~~~~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~ 229 (784)
.+++.+..|.++++-++|.++- |..-.....+.+.+...-.|+++... +.++....+++-+..+.++++++-
T Consensus 11 IHGQV~~~W~~~~~~~~IvVvd-D~~A~D~~~k~~l~ma~P~gvk~~i~-------sve~a~~~l~~~~~~~~~v~il~k 82 (151)
T cd00001 11 IHGQVATTWTKELNANRIIVVN-DEVANDELRKTLLKLAAPPGVKLRIF-------TVEKAIEAINSPKYDKQRVFLLFK 82 (151)
T ss_pred hhhHhhhhhhcccCCCEEEEEc-ccccCCHHHHHHHHhhCCCCCeEEEE-------EHHHHHHHHhCcCCCCceEEEEEC
Confidence 4788999999999999998885 33333445666666666678776642 234455556554556778999998
Q ss_pred cCCcHHHHHH
Q 003958 230 HYNRGPVVFH 239 (784)
Q Consensus 230 ~~~~~~~~~~ 239 (784)
++.++..+++
T Consensus 83 ~~~~~~~l~~ 92 (151)
T cd00001 83 NPQDVLRLVE 92 (151)
T ss_pred CHHHHHHHHH
Confidence 8888877654
No 380
>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=50.93 E-value=47 Score=35.08 Aligned_cols=76 Identities=9% Similarity=0.014 Sum_probs=52.6
Q ss_pred HHHHHHHHHcCCcEEEEEEEcCCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccC
Q 003958 153 AAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY 231 (784)
Q Consensus 153 ~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~ 231 (784)
..+.+.++.++.+++.+|+....+-. ..+.+.+.+++.+..+ ...+..+...+......+..++.++|.||-.+.+
T Consensus 12 ~~l~~~l~~~g~~~~livt~~~~~~~-~~~~v~~~l~~~~~~~--~~~~~~~p~~~~v~~~~~~~~~~~~d~IIaiGGG 87 (337)
T cd08177 12 AALAAELERLGASRALVLTTPSLATK-LAERVASALGDRVAGT--FDGAVMHTPVEVTEAAVAAAREAGADGIVAIGGG 87 (337)
T ss_pred HHHHHHHHHcCCCeEEEEcChHHHHH-HHHHHHHHhccCCcEE--eCCCCCCCCHHHHHHHHHHHHhcCCCEEEEeCCc
Confidence 45677889999999999986544333 6677888887765432 2233333456677788888888899999877543
No 381
>COG0563 Adk Adenylate kinase and related kinases [Nucleotide transport and metabolism]
Probab=50.54 E-value=39 Score=31.84 Aligned_cols=102 Identities=20% Similarity=0.185 Sum_probs=54.2
Q ss_pred eEEEccCchhhHHHHHHhhhcCCccEEecccC-----CC--CCCcCCCCceEe--ecCChHHHHHHHHHHHHHcCCcEEE
Q 003958 98 VAIIGPQDAVTSHVVSHVANELQVPLLSFSAT-----DP--TLSSLQFPYFVR--TTQSDQYQMAAIAEIVDHYGWREVI 168 (784)
Q Consensus 98 ~aiiGp~~s~~~~~va~~~~~~~ip~Is~~a~-----~~--~l~~~~~p~~~r--~~ps~~~~~~ai~~~l~~~~w~~v~ 168 (784)
..|+||++++-+.....+++.+++|+++.+-. .. .+....-.++-+ .+| +......+-+.+.+-.-.. +
T Consensus 3 iiilG~pGaGK~T~A~~La~~~~i~hlstgd~~r~~~~~~t~lg~~~k~~i~~g~lv~-d~i~~~~v~~rl~~~d~~~-~ 80 (178)
T COG0563 3 ILILGPPGAGKSTLAKKLAKKLGLPHLDTGDILRAAIAERTELGEEIKKYIDKGELVP-DEIVNGLVKERLDEADCKA-G 80 (178)
T ss_pred EEEECCCCCCHHHHHHHHHHHhCCcEEcHhHHhHhhhccCChHHHHHHHHHHcCCccc-hHHHHHHHHHHHHhhcccC-e
Confidence 57899999998888888999999999984321 00 010000011111 122 2222233333344432233 6
Q ss_pred EEEEcCCCcchhHHHHHHHHhccCcEEEEeecc
Q 003958 169 AIYVDDDHGRNGIAALGDTLAAKRCRISFKAPL 201 (784)
Q Consensus 169 ii~~d~~~g~~~~~~l~~~l~~~gi~v~~~~~~ 201 (784)
+|+.+.+-....++.++..+.+.|.+......+
T Consensus 81 ~I~dg~PR~~~qa~~l~r~l~~~g~~~d~v~~~ 113 (178)
T COG0563 81 FILDGFPRTLCQARALKRLLKELGVRLDMVIEL 113 (178)
T ss_pred EEEeCCCCcHHHHHHHHHHHHHcCCCcceEEee
Confidence 666665555555666666666655444443333
No 382
>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=50.26 E-value=1.3e+02 Score=25.68 Aligned_cols=81 Identities=12% Similarity=0.142 Sum_probs=41.6
Q ss_pred HHHHcCCcEEEEEEEcCCC-cchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHH
Q 003958 158 IVDHYGWREVIAIYVDDDH-GRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPV 236 (784)
Q Consensus 158 ~l~~~~w~~v~ii~~d~~~-g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~ 236 (784)
-+...|.+.|.-+..|.+- ++-..+.+++.+++.|+.....-.........++....+.+......|.+.|.++..+..
T Consensus 22 ~la~~GfktVInlRpd~E~~~qp~~~~~~~~a~~~Gl~y~~iPv~~~~~~~~~v~~f~~~l~~~~~Pvl~hC~sG~Ra~~ 101 (110)
T PF04273_consen 22 QLAAQGFKTVINLRPDGEEPGQPSSAEEAAAAEALGLQYVHIPVDGGAITEEDVEAFADALESLPKPVLAHCRSGTRASA 101 (110)
T ss_dssp HHHHCT--EEEE-S-TTSTTT-T-HHCHHHHHHHCT-EEEE----TTT--HHHHHHHHHHHHTTTTSEEEE-SCSHHHHH
T ss_pred HHHHCCCcEEEECCCCCCCCCCCCHHHHHHHHHHcCCeEEEeecCCCCCCHHHHHHHHHHHHhCCCCEEEECCCChhHHH
Confidence 4566999999999887653 455667788899999988664322222234456655555565554455444444444444
Q ss_pred HH
Q 003958 237 VF 238 (784)
Q Consensus 237 ~~ 238 (784)
+.
T Consensus 102 l~ 103 (110)
T PF04273_consen 102 LW 103 (110)
T ss_dssp HH
T ss_pred HH
Confidence 33
No 383
>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=50.12 E-value=58 Score=32.11 Aligned_cols=78 Identities=9% Similarity=0.080 Sum_probs=52.0
Q ss_pred EEEEEEEc---CCCcchhHHHHHHHHhc--cCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHH
Q 003958 166 EVIAIYVD---DDHGRNGIAALGDTLAA--KRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHV 240 (784)
Q Consensus 166 ~v~ii~~d---~~~g~~~~~~l~~~l~~--~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~ 240 (784)
+|++|..+ +.++....+.+++.+++ .++++..... ..+..+....++++...+.+.|++.........+...
T Consensus 1 ~Ig~i~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~d~ii~~~~~~~~~~~~~~ 77 (269)
T cd01391 1 KIGVLLPLSGSAPFGAQLLAGIELAAEEIGRGLEVILADS---QSDPERALEALRDLIQQGVDGIIGPPSSSSALAVVEL 77 (269)
T ss_pred CceEEeecCCCcHHHHHHHHHHHHHHHHhCCceEEEEecC---CCCHHHHHHHHHHHHHcCCCEEEecCCCHHHHHHHHH
Confidence 46777753 46777778888888888 7776654332 1233456677777777789999887665555446666
Q ss_pred HHHcCC
Q 003958 241 AQYLGM 246 (784)
Q Consensus 241 a~~~g~ 246 (784)
+.+.+.
T Consensus 78 ~~~~~i 83 (269)
T cd01391 78 AAAAGI 83 (269)
T ss_pred HHHcCC
Confidence 666553
No 384
>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=50.03 E-value=70 Score=32.07 Aligned_cols=77 Identities=8% Similarity=-0.003 Sum_probs=50.9
Q ss_pred EEEEEEc--CCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccC-CcHHHHHHHHHH
Q 003958 167 VIAIYVD--DDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY-NRGPVVFHVAQY 243 (784)
Q Consensus 167 v~ii~~d--~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~-~~~~~~~~~a~~ 243 (784)
|+++..+ +.|.....+.+++.+++.|..+..... . .+.......++.+...+++.|++.... ......++++.+
T Consensus 2 i~~~~~~~~~~~~~~~~~~i~~~~~~~g~~~~i~~~-~--~~~~~~~~~~~~~~~~~vdgiii~~~~~~~~~~~~~~~~~ 78 (267)
T cd06322 2 IGASLLTQQHPFYIELANAMKEEAKKQKVNLIVSIA-N--QDLNKQLSDVEDFITKKVDAIVLSPVDSKGIRAAIAKAKK 78 (267)
T ss_pred eeEeecCcccHHHHHHHHHHHHHHHhcCCEEEEecC-C--CCHHHHHHHHHHHHHcCCCEEEEcCCChhhhHHHHHHHHH
Confidence 5566654 567777889999999999988764321 1 233445566777777889999886433 333556777777
Q ss_pred cCC
Q 003958 244 LGM 246 (784)
Q Consensus 244 ~g~ 246 (784)
.|.
T Consensus 79 ~~i 81 (267)
T cd06322 79 AGI 81 (267)
T ss_pred CCC
Confidence 653
No 385
>COG0725 ModA ABC-type molybdate transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=49.11 E-value=2.9e+02 Score=27.78 Aligned_cols=95 Identities=12% Similarity=0.063 Sum_probs=54.8
Q ss_pred CCCChHhhhhC-CCceEEee------CchHHHHHHhhccc---CccCceeCCCHHHHHHHHhcCCcCCCeeEEEechhhh
Q 003958 683 PIKGIDSLRSS-NYPIGYQV------NSFARNYLVDELNI---DESRLVPLNSPEEYAKALKDGPHKGGVAAVVDDRAYA 752 (784)
Q Consensus 683 ~i~~~~dl~~~-~~~i~~~~------~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~l~~~~~~~~~~a~~~~~~~~ 752 (784)
.+.++++|.+. ..++++.. |.+.+..|++ .+. ...+++.-.+.++.+..|.+ |+.|+.+.=...+
T Consensus 123 ~~~~~~~l~~~~~~~lai~~p~~~P~G~ya~~~l~~-~g~~~~~~~k~v~~~~v~~~l~~V~~----G~ad~g~vy~sd~ 197 (258)
T COG0725 123 KIESLEDLLERPDVRLAIGDPKTVPAGKYAKEALEL-LGLWYTLKDKLVLATNVRQALAYVET----GEADAGFVYVSDA 197 (258)
T ss_pred CcccHHHHhcCcCcEEEecCCCCCCchHHHHHHHHH-hchhhhccccEEecCcHHHHHHHHHc----CCCCeEEEEEEhh
Confidence 34447777774 45577653 6677788754 222 22366666788899999999 7777644422211
Q ss_pred HHHHcCCCCeEEeCCccc-cceEEEEeeCCCC
Q 003958 753 ELFLSTRCEFSIVGQVFT-KNGWGFVSIVSSF 783 (784)
Q Consensus 753 ~~~~~~~c~l~~~~~~~~-~~~~~~~~~k~s~ 783 (784)
.. ..+.-....+.+... ...|.+++.++++
T Consensus 198 ~~-~~~~~~~~~~~~~~~~Pi~y~iav~~~~~ 228 (258)
T COG0725 198 LL-SKKVKIVGVFPEDLHSPIVYPIAVLKNAK 228 (258)
T ss_pred hc-cCCceEEEEcccccCCCeEEEEEEEcCCC
Confidence 11 111112333333333 4678999998875
No 386
>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=48.65 E-value=92 Score=31.19 Aligned_cols=75 Identities=7% Similarity=0.056 Sum_probs=50.0
Q ss_pred EEEEEE--cCCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHc
Q 003958 167 VIAIYV--DDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYL 244 (784)
Q Consensus 167 v~ii~~--d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~ 244 (784)
|+++.. ++.|.....+.+.+.+++.|+++.....- .+.......++.+.+.+.+.|++....... ..++.+.+.
T Consensus 2 i~vi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~~---~~~~~~~~~i~~l~~~~~dgiii~~~~~~~-~~~~~~~~~ 77 (270)
T cd06296 2 IGLVFPDLDSPWASEVLRGVEEAAAAAGYDVVLSESG---RRTSPERQWVERLSARRTDGVILVTPELTS-AQRAALRRT 77 (270)
T ss_pred eEEEECCCCCccHHHHHHHHHHHHHHcCCeEEEecCC---CchHHHHHHHHHHHHcCCCEEEEecCCCCh-HHHHHHhcC
Confidence 566664 46788888999999999999887654322 223345567777877889988876443222 346666665
Q ss_pred C
Q 003958 245 G 245 (784)
Q Consensus 245 g 245 (784)
+
T Consensus 78 ~ 78 (270)
T cd06296 78 G 78 (270)
T ss_pred C
Confidence 4
No 387
>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=48.61 E-value=1.3e+02 Score=30.33 Aligned_cols=68 Identities=18% Similarity=0.204 Sum_probs=41.0
Q ss_pred cCCCCChHhhhhCCCceEEeeCchHHHH----HHhhcccC------------------cc--CceeCCCHHHHHHHHhcC
Q 003958 681 SSPIKGIDSLRSSNYPIGYQVNSFARNY----LVDELNID------------------ES--RLVPLNSPEEYAKALKDG 736 (784)
Q Consensus 681 ~~~i~~~~dl~~~~~~i~~~~~~~~~~~----~~~~~~~~------------------~~--~~~~~~~~~~~~~~l~~~ 736 (784)
...|++++||++ |.+|++..+.+.... |++ .+.. +. ++++ -...+...++.+
T Consensus 105 s~~~~sl~dlk~-G~~IAip~d~~n~~raL~~L~~-aGLi~l~~~~~~~~t~~DI~~n~~~v~~ve-l~~~~~~~al~~- 180 (258)
T TIGR00363 105 SKKIKNVNELQD-GAKVAVPNDPTNLGRALLLLQK-QGLIKLKDGNGLLPTVLDIVENPKKLNITE-LETSQLPRALDD- 180 (258)
T ss_pred CcCCCCHHHcCC-CCEEEEeCCcchHHHHHHHHHH-cCCceecCCCCCcCChhhhhcCCCCCEEEE-cCHHHHHHHhhc-
Confidence 347999999964 788999865432222 422 1110 11 1112 234566778877
Q ss_pred CcCCCeeEEEechhhhHHH
Q 003958 737 PHKGGVAAVVDDRAYAELF 755 (784)
Q Consensus 737 ~~~~~~~a~~~~~~~~~~~ 755 (784)
++++|.+...+++.-.
T Consensus 181 ---g~vDaa~v~~~~~~~a 196 (258)
T TIGR00363 181 ---PKVDLAVINTTYAGQV 196 (258)
T ss_pred ---ccccEEEEChHHHHHc
Confidence 7899988887766543
No 388
>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=48.23 E-value=1.4e+02 Score=31.02 Aligned_cols=80 Identities=9% Similarity=0.053 Sum_probs=52.2
Q ss_pred CCcEEEEEEEc--CCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHH
Q 003958 163 GWREVIAIYVD--DDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHV 240 (784)
Q Consensus 163 ~w~~v~ii~~d--~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~ 240 (784)
.-+.|+++..+ +.|.....+.+.+.+++.|..+..... . .+.......++.+...+.+.||+..........+++
T Consensus 59 ~~~~Igvi~~~~~~~~~~~~~~~i~~~~~~~gy~~~i~~~-~--~~~~~~~~~~~~l~~~~vdgiIi~~~~~~~~~~~~~ 135 (327)
T TIGR02417 59 RSRTIGLVIPDLENYSYARIAKELEQQCREAGYQLLIACS-D--DNPDQEKVVIENLLARQVDALIVASCMPPEDAYYQK 135 (327)
T ss_pred CCceEEEEeCCCCCccHHHHHHHHHHHHHHCCCEEEEEeC-C--CCHHHHHHHHHHHHHcCCCEEEEeCCCCCChHHHHH
Confidence 34678888863 567777888999999999988765432 1 133334466777777889988886443223355666
Q ss_pred HHHcC
Q 003958 241 AQYLG 245 (784)
Q Consensus 241 a~~~g 245 (784)
+.+.+
T Consensus 136 l~~~~ 140 (327)
T TIGR02417 136 LQNEG 140 (327)
T ss_pred HHhcC
Confidence 66554
No 389
>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=48.20 E-value=99 Score=30.99 Aligned_cols=75 Identities=4% Similarity=-0.064 Sum_probs=49.7
Q ss_pred EEEEEE--cCCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHc
Q 003958 167 VIAIYV--DDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYL 244 (784)
Q Consensus 167 v~ii~~--d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~ 244 (784)
|++|.. ++.|.....+.+++.+++.|..+.....- .+...-...++.+...++|.|++....... ..++++.+.
T Consensus 2 igvi~p~~~~~~~~~~~~g~~~~a~~~g~~~~~~~~~---~~~~~~~~~i~~~~~~~vdgii~~~~~~~~-~~~~~~~~~ 77 (268)
T cd06270 2 IGLVVSDLDGPFFGPLLSGVESVARKAGKHLIITAGH---HSAEKEREAIEFLLERRCDALILHSKALSD-DELIELAAQ 77 (268)
T ss_pred EEEEEccccCcchHHHHHHHHHHHHHCCCEEEEEeCC---CchHHHHHHHHHHHHcCCCEEEEecCCCCH-HHHHHHhhC
Confidence 455654 46777888899999999999887653321 233334567777777889999987543232 236677665
Q ss_pred C
Q 003958 245 G 245 (784)
Q Consensus 245 g 245 (784)
|
T Consensus 78 ~ 78 (268)
T cd06270 78 V 78 (268)
T ss_pred C
Confidence 5
No 390
>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=47.97 E-value=72 Score=32.93 Aligned_cols=78 Identities=9% Similarity=0.078 Sum_probs=51.9
Q ss_pred EEEEEEEc--CCCcchhHHHHHHHHhc--cCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEec-cCCcHHHHHHH
Q 003958 166 EVIAIYVD--DDHGRNGIAALGDTLAA--KRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHT-HYNRGPVVFHV 240 (784)
Q Consensus 166 ~v~ii~~d--~~~g~~~~~~l~~~l~~--~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~-~~~~~~~~~~~ 240 (784)
+|++|..+ +.|.....+.+.+.+++ .|+.+..... ..+.......++.+...+++.|++.. ........+++
T Consensus 1 ~Igviv~~~~~~~~~~~~~gi~~~a~~~~~g~~~~~~~~---~~~~~~q~~~i~~l~~~~vdgiii~~~~~~~~~~~~~~ 77 (303)
T cd01539 1 KIGVFLYKFDDTFISLVRKNLEDIQKENGGKVEFTFYDA---KNNQSTQNEQIDTALAKGVDLLAVNLVDPTAAQTVINK 77 (303)
T ss_pred CeEEEeeCCCChHHHHHHHHHHHHHHhhCCCeeEEEecC---CCCHHHHHHHHHHHHHcCCCEEEEecCchhhHHHHHHH
Confidence 46777754 55667778889999988 7777654321 12334455677778888999888864 33334677788
Q ss_pred HHHcCC
Q 003958 241 AQYLGM 246 (784)
Q Consensus 241 a~~~g~ 246 (784)
+.+.|.
T Consensus 78 ~~~~gi 83 (303)
T cd01539 78 AKQKNI 83 (303)
T ss_pred HHHCCC
Confidence 877664
No 391
>PRK11425 PTS system N-acetylgalactosamine-specific transporter subunit IIB; Provisional
Probab=47.83 E-value=80 Score=28.99 Aligned_cols=81 Identities=15% Similarity=0.087 Sum_probs=56.1
Q ss_pred HHHHHHHHHHHHcCCcEEEEEEEcCCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEec
Q 003958 150 YQMAAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHT 229 (784)
Q Consensus 150 ~~~~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~ 229 (784)
.+++.+..|.++++-++|.++- |..-.....+.+.....-.|+++... +.++....+++ +..+.++++++-
T Consensus 14 IHGQV~~~W~~~~~~~~IvVvd-D~~A~D~~~k~~l~ma~P~gvk~~i~-------sv~~a~~~l~~-~~~~~~v~il~k 84 (157)
T PRK11425 14 IHGQVGVQWVGFAGANLVLVAN-DEVAEDPVQQNLMEMVLAEGIAVRFW-------TLQKVIDNIHR-AADRQKILLVCK 84 (157)
T ss_pred hhHHhhhhhhcccCCCEEEEEc-chhcCCHHHHHHHHhhCCCCCeEEEE-------EHHHHHHHHhc-cCCCceEEEEEC
Confidence 5788999999999999987774 33333345666666665678776542 33455566666 556678999998
Q ss_pred cCCcHHHHHH
Q 003958 230 HYNRGPVVFH 239 (784)
Q Consensus 230 ~~~~~~~~~~ 239 (784)
++.++..+++
T Consensus 85 ~~~d~~~l~~ 94 (157)
T PRK11425 85 TPADFLTLVK 94 (157)
T ss_pred CHHHHHHHHH
Confidence 8888776654
No 392
>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=47.68 E-value=80 Score=33.26 Aligned_cols=84 Identities=10% Similarity=0.090 Sum_probs=53.5
Q ss_pred HHHHHHHHcCC-cEEEEEEEcCCCcchhHHHHHHHHhccCcEEEEee-ccCCCCChhHHHHHHHHhhcCCceEEEEeccC
Q 003958 154 AIAEIVDHYGW-REVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKA-PLSVEATEDEITDLLVKVALTESRIIVVHTHY 231 (784)
Q Consensus 154 ai~~~l~~~~w-~~v~ii~~d~~~g~~~~~~l~~~l~~~gi~v~~~~-~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~ 231 (784)
.+.++++.++. +++.+|++...+.. ..+.+.+.+++.|+.+.... ....+++.......+..+++ +.++||-.+.+
T Consensus 13 ~l~~~~~~~~~~~kvlivtd~~~~~~-~~~~i~~~L~~~~~~~~i~~~~~~~~p~~~~v~~~~~~~~~-~~d~IIaiGGG 90 (332)
T cd08549 13 DIGPIINKIGVNSKIMIVCGNNTYKV-AGKEIIERLESNNFTKEVLERDSLLIPDEYELGEVLIKLDK-DTEFLLGIGSG 90 (332)
T ss_pred HHHHHHHHcCCCCcEEEEECCcHHHH-HHHHHHHHHHHcCCeEEEEecCCCCCCCHHHHHHHHHHhhc-CCCEEEEECCc
Confidence 45566777776 78888886554333 34788888988887554321 22222355667778888877 88998877543
Q ss_pred --CcHHHHHH
Q 003958 232 --NRGPVVFH 239 (784)
Q Consensus 232 --~~~~~~~~ 239 (784)
-++..++.
T Consensus 91 sv~D~aK~iA 100 (332)
T cd08549 91 TIIDLVKFVS 100 (332)
T ss_pred HHHHHHHHHH
Confidence 34444443
No 393
>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=47.67 E-value=2.3e+02 Score=26.03 Aligned_cols=68 Identities=12% Similarity=-0.030 Sum_probs=43.9
Q ss_pred eeeHHHHHHHHHHC-CCccceEEeeCCCCCCCCChhHHHHHHHcCcccEEEeeEEeecCccccceeccccccccEEEEEe
Q 003958 494 GFCIDVFTAAINLL-PYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAP 572 (784)
Q Consensus 494 G~~~dl~~~l~~~l-~f~~~~~~~~~~~~~~~~~~~g~i~~l~~~~~D~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~ 572 (784)
.+..+++..+.+.. +.+ +++.. +....+...+.+|++|+++.... .....+ -+.++....+.++++
T Consensus 13 ~~l~~~l~~~~~~~P~i~--i~i~~-------~~~~~~~~~l~~~~~Di~i~~~~---~~~~~~-~~~~l~~~~~~~~~~ 79 (197)
T cd08448 13 RGLPRILRAFRAEYPGIE--VALHE-------MSSAEQIEALLRGELDLGFVHSR---RLPAGL-SARLLHREPFVCCLP 79 (197)
T ss_pred HHHHHHHHHHHHHCCCCe--EEEEe-------CCHHHHHHHHHcCCcceEEEeCC---CCCcCc-eEEEEecCcEEEEee
Confidence 45567788887776 444 55442 45778899999999999885322 222223 235677777777765
Q ss_pred cc
Q 003958 573 VR 574 (784)
Q Consensus 573 ~~ 574 (784)
..
T Consensus 80 ~~ 81 (197)
T cd08448 80 AG 81 (197)
T ss_pred CC
Confidence 44
No 394
>PRK12679 cbl transcriptional regulator Cbl; Reviewed
Probab=47.57 E-value=3.4e+02 Score=28.09 Aligned_cols=70 Identities=20% Similarity=0.235 Sum_probs=43.3
Q ss_pred eeeHHHHHHHHHHCCCccceEEeeCCCCCCCCChhHHHHHHHcCcccEEEeeEEeecCccccceeccccccccEEEEEec
Q 003958 494 GFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPV 573 (784)
Q Consensus 494 G~~~dl~~~l~~~l~f~~~~~~~~~~~~~~~~~~~g~i~~l~~~~~D~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~ 573 (784)
.+..+++..+.+... .+++++.. +....++..|.+|++|+++...... . ...+. +.++....+++++++
T Consensus 106 ~~l~~~l~~f~~~~P-~i~l~l~~-------~~~~~~~~~L~~g~~Dl~i~~~~~~-~-~~~l~-~~~l~~~~~~~v~~~ 174 (316)
T PRK12679 106 YSLPEVIKAFRELFP-EVRLELIQ-------GTPQEIATLLQNGEADIGIASERLS-N-DPQLV-AFPWFRWHHSLLVPH 174 (316)
T ss_pred cchHHHHHHHHHHCC-CeEEEEec-------CCHHHHHHHHHcCCCCEEEecccCC-C-CCCce-EEEccCCcEEEEecC
Confidence 455667777777642 22344432 3466889999999999998532211 1 12233 356777888888765
Q ss_pred c
Q 003958 574 R 574 (784)
Q Consensus 574 ~ 574 (784)
.
T Consensus 175 ~ 175 (316)
T PRK12679 175 D 175 (316)
T ss_pred C
Confidence 5
No 395
>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=47.55 E-value=41 Score=36.15 Aligned_cols=70 Identities=4% Similarity=-0.070 Sum_probs=50.0
Q ss_pred cCCcEEEEEEEcCCCc-chhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccC
Q 003958 162 YGWREVIAIYVDDDHG-RNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY 231 (784)
Q Consensus 162 ~~w~~v~ii~~d~~~g-~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~ 231 (784)
++.+++.+|++...+- ....+.+.+.+++.|+.+.....+.+++..+.....++.+++.++|.||-.+.+
T Consensus 21 ~~~~r~livt~~~~~~~~g~~~~v~~~L~~~g~~~~~~~~v~~~p~~~~v~~~~~~~~~~~~D~IIavGGG 91 (375)
T cd08179 21 LKGKKAFIVTGGGSMKKFGFLDKVEAYLKEAGIEVEVFEGVEPDPSVETVLKGAEAMREFEPDWIIALGGG 91 (375)
T ss_pred hcCCeEEEEeCchHHHhCChHHHHHHHHHHcCCeEEEeCCCCCCcCHHHHHHHHHHHHhcCCCEEEEeCCc
Confidence 3458888887544332 245678888998889877644444445667778888889999999999987544
No 396
>PF14503 YhfZ_C: YhfZ C-terminal domain; PDB: 2OZZ_B.
Probab=47.55 E-value=61 Score=31.80 Aligned_cols=51 Identities=14% Similarity=0.261 Sum_probs=27.3
Q ss_pred CCceEEeeCchHHHHHHhhcccCccCceeC--CCHHHHHHHHhcCCcCCCeeEEEechh
Q 003958 694 NYPIGYQVNSFARNYLVDELNIDESRLVPL--NSPEEYAKALKDGPHKGGVAAVVDDRA 750 (784)
Q Consensus 694 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~a~~~~~~ 750 (784)
|++||+-..|.....+-+ .....++ ++| -+..+.++.|.+ |.+||.+.+..
T Consensus 114 GmRVGiD~~S~Dq~~LT~-~~~~gk~-Ve~Vei~Y~q~~~~l~~----g~IDA~IWN~d 166 (232)
T PF14503_consen 114 GMRVGIDPSSIDQKILTE-AEFEGKN-VEFVEIPYNQLLELLRS----GEIDAAIWNYD 166 (232)
T ss_dssp --EEEE-TT-HHHHHHHH-HHHTTS---EEEE--HHHHHHHHHH----TS--EEEEE--
T ss_pred eeEeecCCCCccHHHHHH-HHhCCCc-eEEEEecHHHHHHHHHC----CCccEEEECCc
Confidence 788999888866655532 2222222 222 245789999999 89999999866
No 397
>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=47.42 E-value=3.4e+02 Score=28.01 Aligned_cols=40 Identities=20% Similarity=0.149 Sum_probs=24.4
Q ss_pred CchhhHHHHH-HHHHHHHHHhhhccccCCCceEEEEEEeecC
Q 003958 1 MKLSGVMLLM-IFYCELFVYRITAQASGRPSVVNIGALLSFS 41 (784)
Q Consensus 1 M~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~i~IG~i~~~~ 41 (784)
||++.+++++ ++++++.+.+|... ...++.++||...+..
T Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~l~Ig~~~~~~ 41 (320)
T TIGR02122 1 MKKRLFLLGAALAIVGAALAACAGD-GGEPTFVTIGTGGTGG 41 (320)
T ss_pred CchHHHHHHHHHHHHHHHHHhhccC-CCCCceEEEEeCCCCC
Confidence 7777665543 34444445566543 3567789999876643
No 398
>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=47.41 E-value=2.3e+02 Score=26.09 Aligned_cols=71 Identities=13% Similarity=0.058 Sum_probs=43.5
Q ss_pred eeeeHHHHHHHHHHC-CCccceEEeeCCCCCCCCChhHHHHHHHcCcccEEEeeEEeecCccccceeccccccccEEEEE
Q 003958 493 SGFCIDVFTAAINLL-PYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVA 571 (784)
Q Consensus 493 ~G~~~dl~~~l~~~l-~f~~~~~~~~~~~~~~~~~~~g~i~~l~~~~~D~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~ 571 (784)
..+..+++..+.++. +.+ +++.. +....+...+.+|++|+++...... .....+ -+.++....+.+++
T Consensus 12 ~~~l~~~l~~~~~~~P~i~--l~i~~-------~~~~~~~~~l~~~~~Dl~i~~~~~~-~~~~~l-~~~~l~~~~~~~v~ 80 (199)
T cd08416 12 VNTVPRIIMGLKLRRPELD--IELTL-------GSNKDLLKKLKDGELDAILVATPEG-LNDPDF-EVVPLFEDDIFLAV 80 (199)
T ss_pred HhhhHHHHHHHHHhCCCeE--EEEEE-------cCcHHHHHHHhCCCCCEEEEecCCc-CCCCCe-EEEEeecceEEEEE
Confidence 345567777887776 444 44442 3456788999999999998643210 011222 24566777777777
Q ss_pred ecc
Q 003958 572 PVR 574 (784)
Q Consensus 572 ~~~ 574 (784)
++.
T Consensus 81 ~~~ 83 (199)
T cd08416 81 PAT 83 (199)
T ss_pred CCC
Confidence 554
No 399
>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=47.20 E-value=75 Score=32.53 Aligned_cols=79 Identities=8% Similarity=0.064 Sum_probs=50.3
Q ss_pred EEEEEEEc--CCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCC-cHHHHHHHHH
Q 003958 166 EVIAIYVD--DDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYN-RGPVVFHVAQ 242 (784)
Q Consensus 166 ~v~ii~~d--~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~-~~~~~~~~a~ 242 (784)
||++|..+ +.|.......+.+.+++.|..+.... ....+.......++.+...+++.|++..... .....++++.
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 46766643 44556677888899999998775321 1112334445667777677899888864332 2456778887
Q ss_pred HcCC
Q 003958 243 YLGM 246 (784)
Q Consensus 243 ~~g~ 246 (784)
+.|.
T Consensus 79 ~~~i 82 (294)
T cd06316 79 EAGI 82 (294)
T ss_pred HcCC
Confidence 7664
No 400
>COG1179 Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 1 [Coenzyme metabolism]
Probab=47.19 E-value=1.1e+02 Score=30.20 Aligned_cols=100 Identities=13% Similarity=0.182 Sum_probs=63.6
Q ss_pred cchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEccCchhhHH-HHHHhhhcCCc
Q 003958 43 NVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIGPQDAVTSH-VVSHVANELQV 121 (784)
Q Consensus 43 ~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiGp~~s~~~~-~va~~~~~~~i 121 (784)
..|+.-..+++-.+..||-+ . ++...|.--+ .+...+++..+...||-..++-.+. ++...|...++
T Consensus 80 ~iGk~Kv~vm~eri~~InP~------c--~V~~~~~f~t----~en~~~~~~~~~DyvIDaiD~v~~Kv~Li~~c~~~ki 147 (263)
T COG1179 80 DIGKPKVEVMKERIKQINPE------C--EVTAINDFIT----EENLEDLLSKGFDYVIDAIDSVRAKVALIAYCRRNKI 147 (263)
T ss_pred hcccHHHHHHHHHHHhhCCC------c--eEeehHhhhC----HhHHHHHhcCCCCEEEEchhhhHHHHHHHHHHHHcCC
Confidence 34666678888888888833 2 3344433333 3356677778899999877665554 46678999999
Q ss_pred cEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHH
Q 003958 122 PLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEI 158 (784)
Q Consensus 122 p~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~ 158 (784)
|+||.++....+. |+-+++.--.......+++.
T Consensus 148 ~vIss~Gag~k~D----PTri~v~DiskT~~DPLa~~ 180 (263)
T COG1179 148 PVISSMGAGGKLD----PTRIQVADISKTIQDPLAAK 180 (263)
T ss_pred CEEeeccccCCCC----CceEEeeechhhccCcHHHH
Confidence 9999876654443 66677654333333333333
No 401
>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=47.00 E-value=84 Score=31.58 Aligned_cols=77 Identities=5% Similarity=-0.078 Sum_probs=51.1
Q ss_pred EEEEEE---cCCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccC-CcHHHHHHHHH
Q 003958 167 VIAIYV---DDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY-NRGPVVFHVAQ 242 (784)
Q Consensus 167 v~ii~~---d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~-~~~~~~~~~a~ 242 (784)
|++|.. ++.|+....+.+.+.+++.|+.+..... ..+.......++.+...+++.|++.... +.....++++.
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 566664 3567778888999999999988765322 1244445566777777789998886543 33456677777
Q ss_pred HcCC
Q 003958 243 YLGM 246 (784)
Q Consensus 243 ~~g~ 246 (784)
+.+.
T Consensus 79 ~~~i 82 (275)
T cd06317 79 QAGI 82 (275)
T ss_pred HCCC
Confidence 7553
No 402
>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=46.94 E-value=43 Score=35.31 Aligned_cols=71 Identities=7% Similarity=0.009 Sum_probs=47.6
Q ss_pred HHcCCcEEEEEEEcCCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccC
Q 003958 160 DHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY 231 (784)
Q Consensus 160 ~~~~w~~v~ii~~d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~ 231 (784)
..++.+++.+|+....+.....+.+.+.+++. +.+.....+..++..+.....++.+++.++|.||-.+.+
T Consensus 18 ~~~~~~~~lvv~~~~~~~~g~~~~v~~~l~~~-~~~~~~~~v~~~p~~~~v~~~~~~~~~~~~d~IiaiGGG 88 (332)
T cd08180 18 KELKNKRVLIVTDPFMVKSGMLDKVTDHLDSS-IEVEIFSDVVPDPPIEVVAKGIKKFLDFKPDIVIALGGG 88 (332)
T ss_pred HHhCCCeEEEEeCchhhhCccHHHHHHHHHhc-CcEEEeCCCCCCcCHHHHHHHHHHHHhcCCCEEEEECCc
Confidence 45556899999854433333677788888776 554433334434556777788888888999999976543
No 403
>PRK00002 aroB 3-dehydroquinate synthase; Reviewed
Probab=46.79 E-value=1.2e+02 Score=32.42 Aligned_cols=92 Identities=7% Similarity=-0.014 Sum_probs=57.5
Q ss_pred HHHHHHHHHcCCcEEEEEEEcCCCcchhHHHHHHHHhccCcEEEEee--ccCCCCChhHHHHHHHHhhcCCc---eEEEE
Q 003958 153 AAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKA--PLSVEATEDEITDLLVKVALTES---RIIVV 227 (784)
Q Consensus 153 ~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~~l~~~gi~v~~~~--~~~~~~~~~d~~~~l~~l~~~~~---~vIvl 227 (784)
..+.++++.++++++.+|++... .....+.+.+.+++.|+.+.... ....+.+.+.....++.+++.+. +.||.
T Consensus 20 ~~l~~~l~~~~~~~~livtd~~~-~~~~~~~v~~~L~~~gi~~~~~~~~~~e~~~~~~~v~~~~~~~~~~~~~r~d~IIa 98 (358)
T PRK00002 20 SELGELLAPLKGKKVAIVTDETV-APLYLEKLRASLEAAGFEVDVVVLPDGEQYKSLETLEKIYDALLEAGLDRSDTLIA 98 (358)
T ss_pred HHHHHHHHhcCCCeEEEEECCch-HHHHHHHHHHHHHhcCCceEEEEeCCCCCCCCHHHHHHHHHHHHHcCCCCCCEEEE
Confidence 34666777778899999995544 33577888888988887655221 22222355667777777776544 88887
Q ss_pred eccC--CcHHHHHHHHHHcC
Q 003958 228 HTHY--NRGPVVFHVAQYLG 245 (784)
Q Consensus 228 ~~~~--~~~~~~~~~a~~~g 245 (784)
.+.+ -++..++......|
T Consensus 99 vGGGsv~D~aK~iA~~~~~g 118 (358)
T PRK00002 99 LGGGVIGDLAGFAAATYMRG 118 (358)
T ss_pred EcCcHHHHHHHHHHHHhcCC
Confidence 6543 44555544333433
No 404
>PF00625 Guanylate_kin: Guanylate kinase; InterPro: IPR008144 Guanylate kinase (2.7.4.8 from EC) (GK) [] catalyzes the ATP-dependent phosphorylation of GMP into GDP. It is essential for recycling GMP and indirectly, cGMP. In prokaryotes (such as Escherichia coli), lower eukaryotes (such as yeast) and in vertebrates, GK is a highly conserved monomeric protein of about 200 amino acids. GK has been shown [, , ] to be structurally similar to protein A57R (or SalG2R) from various strains of Vaccinia virus. Proteins containing one or more copies of the DHR domain, an SH3 domain as well as a C-terminal GK-like domain, are collectively termed MAGUKs (membrane-associated guanylate kinase homologs) [], and include Drosophila lethal(1)discs large-1 tumor suppressor protein (gene dlg1); mammalian tight junction protein Zo-1; a family of mammalian synaptic proteins that seem to interact with the cytoplasmic tail of NMDA receptor subunits (SAP90/PSD-95, CHAPSYN-110/PSD-93, SAP97/DLG1 and SAP102); vertebrate 55kDa erythrocyte membrane protein (p55); Caenorhabditis elegans protein lin-2; rat protein CASK; and human proteins DLG2 and DLG3. There is an ATP-binding site (P-loop) in the N-terminal section of GK, which is not conserved in the GK-like domain of the above proteins. However these proteins retain the residues known, in GK, to be involved in the binding of GMP.; GO: 0005515 protein binding; PDB: 3UAT_A 3KFV_A 2ANC_F 2F3T_E 2ANB_A 2AN9_A 1S96_A 2F3R_B 3TR0_A 1LVG_A ....
Probab=46.29 E-value=1.5e+02 Score=27.95 Aligned_cols=129 Identities=12% Similarity=0.155 Sum_probs=63.8
Q ss_pred CceEEEccCchhhHHHHHHhhhcCC--ccE-EecccCCCCCCc-CCCCceEeecCChHHHHHHHHHHHHHcCCcEEEEEE
Q 003958 96 QTVAIIGPQDAVTSHVVSHVANELQ--VPL-LSFSATDPTLSS-LQFPYFVRTTQSDQYQMAAIAEIVDHYGWREVIAIY 171 (784)
Q Consensus 96 ~v~aiiGp~~s~~~~~va~~~~~~~--ip~-Is~~a~~~~l~~-~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~v~ii~ 171 (784)
++.+++||.+++-......++.... ... +++..-.+...+ ++-.|.|-+ ......+.+-=+-..|.. +
T Consensus 3 r~ivl~Gpsg~GK~~l~~~L~~~~~~~~~~~v~~TTR~~r~~E~~g~~y~fvs----~~~f~~~~~~~~fie~~~----~ 74 (183)
T PF00625_consen 3 RPIVLVGPSGSGKSTLAKRLIQEFPDKFGRVVSHTTRPPRPGEVDGVDYHFVS----KEEFERMIKAGEFIEYGE----Y 74 (183)
T ss_dssp SEEEEESSTTSSHHHHHHHHHHHSTTTEEEEEEEESS-GGTTS-TTTSEEE------HHHHHHHHHTTHEEEEEE----E
T ss_pred CEEEEECCCCCCHHHHHHHHHHhcccccccceeecccCCcccccCCcceEEEe----echhhhhhccccEEEEee----e
Confidence 6789999999987666666666543 333 333332333333 334555531 222222221101111222 3
Q ss_pred EcCCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHc
Q 003958 172 VDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYL 244 (784)
Q Consensus 172 ~d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~ 244 (784)
.++.||.. .+.+++.+++...|+... . ..-+..+++...+.++++..+.....+-+.+.+.
T Consensus 75 ~g~~YGt~-~~~i~~~~~~gk~~il~~---~--------~~g~~~L~~~~~~~~~IfI~~~s~~~l~~~l~~r 135 (183)
T PF00625_consen 75 DGNYYGTS-KSAIDKVLEEGKHCILDV---D--------PEGVKQLKKAGFNPIVIFIKPPSPEVLKRRLRRR 135 (183)
T ss_dssp TTEEEEEE-HHHHHHHHHTTTEEEEEE---T--------HHHHHHHHHCTTTEEEEEEEESSHHHHHHHHHTT
T ss_pred cchhhhhc-cchhhHhhhcCCcEEEEc---c--------HHHHHHHHhcccCceEEEEEccchHHHHHHHhcc
Confidence 34566654 466777777666665432 1 1234555555666666665555555555444443
No 405
>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=45.71 E-value=1.1e+02 Score=30.30 Aligned_cols=75 Identities=8% Similarity=-0.026 Sum_probs=49.2
Q ss_pred EEEEEEc--CCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHc
Q 003958 167 VIAIYVD--DDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYL 244 (784)
Q Consensus 167 v~ii~~d--~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~ 244 (784)
|+++..+ +.|.....+.+++.+++.|.++..... ..+.......++++...+.+.||+...... ..++..+.+.
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 5666653 456667788999999999988764322 123444557777777789999998754322 3455666554
Q ss_pred C
Q 003958 245 G 245 (784)
Q Consensus 245 g 245 (784)
|
T Consensus 78 ~ 78 (259)
T cd01542 78 N 78 (259)
T ss_pred C
Confidence 4
No 406
>PF00205 TPP_enzyme_M: Thiamine pyrophosphate enzyme, central domain; InterPro: IPR012000 A number of enzymes require thiamine pyrophosphate (TPP) (vitamin B1) as a cofactor. It has been shown [] that some of these enzymes are structurally related. This central domain of TPP enzymes contains a 2-fold Rossman fold. ; GO: 0000287 magnesium ion binding, 0030976 thiamine pyrophosphate binding; PDB: 1OZH_C 1OZF_B 1OZG_B 2Q29_B 2Q28_A 2Q27_B 1OVM_B 1PVD_A 1PYD_B 2VK1_C ....
Probab=45.48 E-value=26 Score=31.26 Aligned_cols=57 Identities=18% Similarity=0.313 Sum_probs=39.7
Q ss_pred HHHHHHHhc--CceEEEccCch--hhHHHHHHhhhcCCccEEecccCCCCCCcCCCCceEee
Q 003958 87 AEALHLMEG--QTVAIIGPQDA--VTSHVVSHVANELQVPLLSFSATDPTLSSLQFPYFVRT 144 (784)
Q Consensus 87 ~~~~~li~~--~v~aiiGp~~s--~~~~~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~ 144 (784)
+++.+++++ ++..++|.... .....+.++++..++|+++....-..+ +...|.+.-.
T Consensus 2 ~~~~~~L~~A~rP~il~G~g~~~~~a~~~l~~lae~~~~Pv~~t~~~kg~i-~~~hp~~~G~ 62 (137)
T PF00205_consen 2 DEAADLLSSAKRPVILAGRGARRSGAAEELRELAEKLGIPVATTPMGKGVI-PEDHPLFLGY 62 (137)
T ss_dssp HHHHHHHHH-SSEEEEE-HHHHHTTCHHHHHHHHHHHTSEEEEEGGGTTSS-TTTSTTEEEE
T ss_pred HHHHHHHHhCCCEEEEEcCCcChhhHHHHHHHHHHHHCCCEEecCcccccc-CCCCchhccc
Confidence 345556654 89999998766 788899999999999999854443333 3345776653
No 407
>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=45.41 E-value=2.5e+02 Score=25.94 Aligned_cols=71 Identities=13% Similarity=0.091 Sum_probs=43.0
Q ss_pred eeeHHHHHHHHHHC-CCccceEEeeCCCCCCCCChhHHHHHHHcCcccEEEeeEEeecCccccceeccccccccEEEEEe
Q 003958 494 GFCIDVFTAAINLL-PYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAP 572 (784)
Q Consensus 494 G~~~dl~~~l~~~l-~f~~~~~~~~~~~~~~~~~~~g~i~~l~~~~~D~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~ 572 (784)
.+..+++..+.+.. +.+ +++.. +....+...+.+|++|+++............+ -+.+.....+.++++
T Consensus 13 ~~l~~~l~~~~~~~P~i~--l~i~~-------~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~~~-~~~~l~~~~~~~v~~ 82 (200)
T cd08453 13 SVLPELVRRFREAYPDVE--LQLRE-------ATSDVQLEALLAGEIDAGIVIPPPGASAPPAL-AYRPLLSEPLVLAVP 82 (200)
T ss_pred HHHHHHHHHHHHhCCCce--EEEEe-------CCHHHHHHHHHcCCCCEEEEecCcccCCCcce-eEEEeeeCceEEEEE
Confidence 35567777777765 334 55443 34667899999999999985322111011122 245666777777776
Q ss_pred cc
Q 003958 573 VR 574 (784)
Q Consensus 573 ~~ 574 (784)
..
T Consensus 83 ~~ 84 (200)
T cd08453 83 AA 84 (200)
T ss_pred CC
Confidence 54
No 408
>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=45.40 E-value=83 Score=32.37 Aligned_cols=78 Identities=9% Similarity=0.003 Sum_probs=51.2
Q ss_pred EEEEEE--cCCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccC-CcHHHHHHHHHH
Q 003958 167 VIAIYV--DDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY-NRGPVVFHVAQY 243 (784)
Q Consensus 167 v~ii~~--d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~-~~~~~~~~~a~~ 243 (784)
|++|.. ++.|.....+.+++.+++.|..+....... .+.......++.+...+++.||+.... ......++++.+
T Consensus 2 I~vi~~~~~~~f~~~i~~gi~~~a~~~g~~v~~~~~~~--~d~~~~~~~i~~~~~~~~DgiIi~~~~~~~~~~~~~~~~~ 79 (298)
T cd06302 2 IAFVPKVTGIPYFNRMEEGAKEAAKELGVDAIYVGPTT--ADAAGQVQIIEDLIAQGVDAIAVVPNDPDALEPVLKKARE 79 (298)
T ss_pred EEEEEcCCCChHHHHHHHHHHHHHHHhCCeEEEECCCC--CCHHHHHHHHHHHHhcCCCEEEEecCCHHHHHHHHHHHHH
Confidence 566664 456777788899999999998876421111 234445567777777789999986433 223567777776
Q ss_pred cCC
Q 003958 244 LGM 246 (784)
Q Consensus 244 ~g~ 246 (784)
.+.
T Consensus 80 ~~i 82 (298)
T cd06302 80 AGI 82 (298)
T ss_pred CCC
Confidence 553
No 409
>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=45.35 E-value=28 Score=30.11 Aligned_cols=85 Identities=19% Similarity=0.223 Sum_probs=45.0
Q ss_pred cEEEEEEEcCCCcchhHHHHHHHHhccCcEEEEeeccCCC-CChhHHHHHHHHhh--cCCceEEEEeccCCcHHHHHHHH
Q 003958 165 REVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVE-ATEDEITDLLVKVA--LTESRIIVVHTHYNRGPVVFHVA 241 (784)
Q Consensus 165 ~~v~ii~~d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~-~~~~d~~~~l~~l~--~~~~~vIvl~~~~~~~~~~~~~a 241 (784)
|+|++|...+.-+.-. ..+-..+.++|.+|.....-... .+.. ....+. ....|.++++..++....+++++
T Consensus 1 ksiAVvGaS~~~~~~g-~~v~~~l~~~G~~v~~Vnp~~~~i~G~~----~y~sl~e~p~~iDlavv~~~~~~~~~~v~~~ 75 (116)
T PF13380_consen 1 KSIAVVGASDNPGKFG-YRVLRNLKAAGYEVYPVNPKGGEILGIK----CYPSLAEIPEPIDLAVVCVPPDKVPEIVDEA 75 (116)
T ss_dssp -EEEEET--SSTTSHH-HHHHHHHHHTT-EEEEESTTCSEETTEE-----BSSGGGCSST-SEEEE-S-HHHHHHHHHHH
T ss_pred CEEEEEcccCCCCChH-HHHHHHHHhCCCEEEEECCCceEECcEE----eeccccCCCCCCCEEEEEcCHHHHHHHHHHH
Confidence 5678887544433333 33334444477666543211100 1111 222233 36789999999999999999999
Q ss_pred HHcCCCCCCeEEEecC
Q 003958 242 QYLGMLGTGYVWIATS 257 (784)
Q Consensus 242 ~~~g~~~~~~~wi~~~ 257 (784)
.++| .+.+|+.++
T Consensus 76 ~~~g---~~~v~~~~g 88 (116)
T PF13380_consen 76 AALG---VKAVWLQPG 88 (116)
T ss_dssp HHHT----SEEEE-TT
T ss_pred HHcC---CCEEEEEcc
Confidence 9987 567898877
No 410
>cd03770 SR_TndX_transposase Serine Recombinase (SR) family, TndX-like transposase subfamily, catalytic domain; composed of large serine recombinases similar to Clostridium TndX and TnpX transposases. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining mechanism which involves a transient phosphoserine linkage between DNA and the enzyme. They are functionally versatile and include resolvases, invertases, integrases, and transposases. TndX mediates the excision and circularization of the conjugative transposon Tn5397 from Clostridium difficile. TnpX is responsible for the movement of the nonconjugative chloramphenicol resistance elements of the Tn4451/3 family. Mobile genetic elements such as transposons are important vehicles for the transmission of virulence and antibiotic resistance in many microorganisms.
Probab=45.31 E-value=2.3e+02 Score=25.34 Aligned_cols=20 Identities=20% Similarity=0.275 Sum_probs=11.4
Q ss_pred HHHHHHHHHHHHHcCCcEEE
Q 003958 149 QYQMAAIAEIVDHYGWREVI 168 (784)
Q Consensus 149 ~~~~~ai~~~l~~~~w~~v~ 168 (784)
+.|-.++-++.+..||.-+.
T Consensus 21 e~Q~~~l~~~a~~~g~~i~~ 40 (140)
T cd03770 21 ENQKAILEEYAKENGLENIR 40 (140)
T ss_pred HHHHHHHHHHHHHCCCEEEE
Confidence 44555555666666776444
No 411
>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=45.24 E-value=1.5e+02 Score=28.38 Aligned_cols=87 Identities=10% Similarity=0.010 Sum_probs=50.5
Q ss_pred cEEEEEEEcCCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccC----CcHHHHHHH
Q 003958 165 REVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY----NRGPVVFHV 240 (784)
Q Consensus 165 ~~v~ii~~d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~----~~~~~~~~~ 240 (784)
.+|.+....++.-.-....+...++.+|++|..-. .......+++.+++.++++|.+.+.. ..+..++++
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------RDVPIDTVVEKVKKEKPLMLTGSALMTTTMYGQKDINDK 158 (197)
T ss_pred CeEEEEeCCCchhHHHHHHHHHHHHhCCcEEEECC------CCCCHHHHHHHHHHcCCCEEEEccccccCHHHHHHHHHH
Confidence 35555555555555556667777777887776422 11123456666667778888776442 345666677
Q ss_pred HHHcCCCCCCeEEEecC
Q 003958 241 AQYLGMLGTGYVWIATS 257 (784)
Q Consensus 241 a~~~g~~~~~~~wi~~~ 257 (784)
+++.+....-.+|++..
T Consensus 159 l~~~~~~~~v~i~vGG~ 175 (197)
T TIGR02370 159 LKEEGYRDSVKFMVGGA 175 (197)
T ss_pred HHHcCCCCCCEEEEECh
Confidence 77766543334555544
No 412
>PRK10653 D-ribose transporter subunit RbsB; Provisional
Probab=45.16 E-value=96 Score=31.77 Aligned_cols=80 Identities=3% Similarity=-0.046 Sum_probs=53.5
Q ss_pred CcEEEEEEEc--CCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCC-cHHHHHHH
Q 003958 164 WREVIAIYVD--DDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYN-RGPVVFHV 240 (784)
Q Consensus 164 w~~v~ii~~d--~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~-~~~~~~~~ 240 (784)
-+.|+++..+ +.|.....+.+++.+++.|+.+...... .+.......++++...+.+.|++..... .....++.
T Consensus 26 ~~~I~vi~~~~~~~f~~~~~~~i~~~~~~~G~~~~~~~~~---~d~~~~~~~~~~l~~~~~dgiii~~~~~~~~~~~l~~ 102 (295)
T PRK10653 26 KDTIALVVSTLNNPFFVSLKDGAQKEADKLGYNLVVLDSQ---NNPAKELANVQDLTVRGTKILLINPTDSDAVGNAVKM 102 (295)
T ss_pred CCeEEEEecCCCChHHHHHHHHHHHHHHHcCCeEEEecCC---CCHHHHHHHHHHHHHcCCCEEEEcCCChHHHHHHHHH
Confidence 5678888853 5677788889999999999887653221 2334455677777777888887764332 22356667
Q ss_pred HHHcCC
Q 003958 241 AQYLGM 246 (784)
Q Consensus 241 a~~~g~ 246 (784)
+.+.|.
T Consensus 103 ~~~~~i 108 (295)
T PRK10653 103 ANQANI 108 (295)
T ss_pred HHHCCC
Confidence 766553
No 413
>PRK10355 xylF D-xylose transporter subunit XylF; Provisional
Probab=45.12 E-value=1e+02 Score=32.43 Aligned_cols=79 Identities=6% Similarity=-0.005 Sum_probs=56.2
Q ss_pred CcEEEEEEE--cCCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCc-HHHHHHH
Q 003958 164 WREVIAIYV--DDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNR-GPVVFHV 240 (784)
Q Consensus 164 w~~v~ii~~--d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~-~~~~~~~ 240 (784)
-.+|+++.. ++.|.....+.+++++++.|..+..... . .+......+++.+.+.++|.||+...... ....++.
T Consensus 25 ~~~Ig~i~~~~~~~f~~~~~~gi~~~a~~~g~~l~i~~~-~--~~~~~~~~~i~~l~~~~vDGiIi~~~~~~~~~~~l~~ 101 (330)
T PRK10355 25 EVKIGMAIDDLRLERWQKDRDIFVKKAESLGAKVFVQSA-N--GNEETQMSQIENMINRGVDVLVIIPYNGQVLSNVIKE 101 (330)
T ss_pred CceEEEEecCCCchHHHHHHHHHHHHHHHcCCEEEEECC-C--CCHHHHHHHHHHHHHcCCCEEEEeCCChhhHHHHHHH
Confidence 467787774 5678888999999999999988775422 1 24455667788888889999998754322 3455667
Q ss_pred HHHcC
Q 003958 241 AQYLG 245 (784)
Q Consensus 241 a~~~g 245 (784)
+.+.+
T Consensus 102 ~~~~~ 106 (330)
T PRK10355 102 AKQEG 106 (330)
T ss_pred HHHCC
Confidence 66655
No 414
>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=44.19 E-value=1.4e+02 Score=29.89 Aligned_cols=75 Identities=5% Similarity=-0.032 Sum_probs=50.4
Q ss_pred EEEEEEc--CCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHc
Q 003958 167 VIAIYVD--DDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYL 244 (784)
Q Consensus 167 v~ii~~d--~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~ 244 (784)
|+++..+ +.|.....+.+.+.+++.|..+..... ..+.......++.+...++|.|++....... ..++++.+.
T Consensus 2 igvi~p~~~~~~~~~~~~gi~~~~~~~~~~~~~~~~---~~~~~~~~~~i~~l~~~~~dgiii~~~~~~~-~~~~~~~~~ 77 (265)
T cd06285 2 IGVLVPRLTDTVMATMYEGIEEAAAERGYSTFVANT---GDNPDAQRRAIEMLLDRRVDGLILGDARSDD-HFLDELTRR 77 (265)
T ss_pred EEEEeCCCCCccHHHHHHHHHHHHHHCCCEEEEEeC---CCCHHHHHHHHHHHHHcCCCEEEEecCCCCh-HHHHHHHHc
Confidence 5677754 567778889999999999988754221 1233445577777888899988887543333 346677665
Q ss_pred C
Q 003958 245 G 245 (784)
Q Consensus 245 g 245 (784)
+
T Consensus 78 ~ 78 (265)
T cd06285 78 G 78 (265)
T ss_pred C
Confidence 5
No 415
>PRK10936 TMAO reductase system periplasmic protein TorT; Provisional
Probab=44.14 E-value=92 Score=32.91 Aligned_cols=81 Identities=7% Similarity=-0.094 Sum_probs=53.4
Q ss_pred CcEEEEEEEc--CCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccC-CcHHHHHHH
Q 003958 164 WREVIAIYVD--DDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY-NRGPVVFHV 240 (784)
Q Consensus 164 w~~v~ii~~d--~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~-~~~~~~~~~ 240 (784)
-+.|++|..+ +.|.....+.+++.+++.|..+....... ..+.......++.+.+.+++.||+.... ......+ +
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 3788888854 56777778899999999998876543221 1133444567777777889999987543 3333455 6
Q ss_pred HHHcCC
Q 003958 241 AQYLGM 246 (784)
Q Consensus 241 a~~~g~ 246 (784)
+.+.|.
T Consensus 124 ~~~~gi 129 (343)
T PRK10936 124 LQAANI 129 (343)
T ss_pred HHHCCC
Confidence 666553
No 416
>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=44.00 E-value=96 Score=30.99 Aligned_cols=80 Identities=8% Similarity=0.154 Sum_probs=46.7
Q ss_pred hHHHHHHHHHHHHHcCCcEEEEEEEcCCCcchhHHHHHHHHh---ccCcEEE-EeeccCCCCChhHHHHHHHHhhcCCce
Q 003958 148 DQYQMAAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLA---AKRCRIS-FKAPLSVEATEDEITDLLVKVALTESR 223 (784)
Q Consensus 148 ~~~~~~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~~l~---~~gi~v~-~~~~~~~~~~~~d~~~~l~~l~~~~~~ 223 (784)
.+...++.-+++++||-..|..++--+.|....-..+.+.+. +..++.. .....+ -....++++|+.++|
T Consensus 15 ~ed~~r~Ae~l~~~Yg~~~I~h~tyPdnf~~e~EttIskI~~lAdDp~mKaIVv~q~vp------Gt~~af~kIkekRpD 88 (275)
T PF12683_consen 15 SEDEYRGAEELIKKYGDVMIKHVTYPDNFMSEQETTISKIVSLADDPDMKAIVVSQAVP------GTAEAFRKIKEKRPD 88 (275)
T ss_dssp -HHHHHHHHHHHHHHHHHEEEEEE--TTGGGCHHHHHHHHHGGGG-TTEEEEEEE-SS---------HHHHHHHHHH-TT
T ss_pred ChHHHHHHHHHHHHhCcceEEEEeCCCcccchHHHHHHHHHHhccCCCccEEEEeCCCc------chHHHHHHHHhcCCC
Confidence 445567777788888876666555445566665556666555 5555433 333333 356889999999999
Q ss_pred EEEEeccCCc
Q 003958 224 IIVVHTHYNR 233 (784)
Q Consensus 224 vIvl~~~~~~ 233 (784)
++++.+.+.+
T Consensus 89 Il~ia~~~~E 98 (275)
T PF12683_consen 89 ILLIAGEPHE 98 (275)
T ss_dssp SEEEESS--S
T ss_pred eEEEcCCCcC
Confidence 9999877543
No 417
>cd00423 Pterin_binding Pterin binding enzymes. This family includes dihydropteroate synthase (DHPS) and cobalamin-dependent methyltransferases such as methyltetrahydrofolate, corrinoid iron-sulfur protein methyltransferase (MeTr) and methionine synthase (MetH). DHPS, a functional homodimer, catalyzes the condensation of p-aminobenzoic acid (pABA) in the de novo biosynthesis of folate, which is an essential cofactor in both nucleic acid and protein biosynthesis. Prokaryotes (and some lower eukaryotes) must synthesize folate de novo, while higher eukaryotes are able to utilize dietary folate and therefore lack DHPS. Sulfonamide drugs, which are substrate analogs of pABA, target DHPS. Cobalamin-dependent methyltransferases catalyze the transfer of a methyl group via a methyl- cob(III)amide intermediate. These include MeTr, a functional heterodimer, and the folate binding domain of MetH.
Probab=43.93 E-value=2.5e+02 Score=28.21 Aligned_cols=18 Identities=22% Similarity=0.431 Sum_probs=11.2
Q ss_pred HHHHHHHHHcCCcEEEEEE
Q 003958 153 AAIAEIVDHYGWREVIAIY 171 (784)
Q Consensus 153 ~ai~~~l~~~~w~~v~ii~ 171 (784)
..+++++++++.. +.+++
T Consensus 110 ~~~~~l~~~~~~~-vV~m~ 127 (258)
T cd00423 110 PEMAPLAAEYGAP-VVLMH 127 (258)
T ss_pred hHHHHHHHHcCCC-EEEEC
Confidence 4667778888763 33344
No 418
>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=43.86 E-value=1.4e+02 Score=30.11 Aligned_cols=77 Identities=10% Similarity=0.069 Sum_probs=48.0
Q ss_pred CcEEEEEEEc---------CCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcH
Q 003958 164 WREVIAIYVD---------DDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRG 234 (784)
Q Consensus 164 w~~v~ii~~d---------~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~ 234 (784)
.+.|++|..+ +.|.....+.+.+.+++.|+.+.... .. .. +.....+.+.+.+++.|++......
T Consensus 3 s~~i~vi~p~~~~~~~~~~~~~~~~~~~gi~~~~~~~g~~~~v~~-~~--~~--~~~~~~~~l~~~~~dgiii~~~~~~- 76 (275)
T cd06295 3 TDTIALVVPEPHERDQSFSDPFFLSLLGGIADALAERGYDLLLSF-VS--SP--DRDWLARYLASGRADGVILIGQHDQ- 76 (275)
T ss_pred ceEEEEEecCccccccccCCchHHHHHHHHHHHHHHcCCEEEEEe-CC--ch--hHHHHHHHHHhCCCCEEEEeCCCCC-
Confidence 5678888853 34566677888899999998876532 11 11 2334445556678998888654323
Q ss_pred HHHHHHHHHcCC
Q 003958 235 PVVFHVAQYLGM 246 (784)
Q Consensus 235 ~~~~~~a~~~g~ 246 (784)
...++++.+.|.
T Consensus 77 ~~~~~~~~~~~i 88 (275)
T cd06295 77 DPLPERLAETGL 88 (275)
T ss_pred hHHHHHHHhCCC
Confidence 244677766554
No 419
>cd00338 Ser_Recombinase Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or C-terminal to the catalytic domain. These enzymes perform site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining mechanism which involves a transient phosphoserine linkage between DNA and serine recombinase. Serine recombinases demonstrate functional versatility and include resolvases, invertases, integrases, and transposases. Resolvases and invertases (i.e. Tn3, gamma-delta, Tn5044 resolvases, Gin and Hin invertases) in this family contain a C-terminal DNA binding domain and comprise a major phylogenic group. Also included are phage- and bacterial-encoded recombinases such as phiC31 integrase, SpoIVCA excisionase, and Tn4451 TnpX transposase. These integrases and transposases have larger C-terminal domains compared to resolvases/invertases and are referred to as large serine recombinases. Also belonging to this family are protei
Probab=43.56 E-value=2.3e+02 Score=24.87 Aligned_cols=26 Identities=23% Similarity=0.036 Sum_probs=16.9
Q ss_pred ChHHHHHHHHHHHHHcCCcEEEEEEE
Q 003958 147 SDQYQMAAIAEIVDHYGWREVIAIYV 172 (784)
Q Consensus 147 s~~~~~~ai~~~l~~~~w~~v~ii~~ 172 (784)
+.+.|-..+-++....||.-+.++.+
T Consensus 15 s~~~Q~~~~~~~a~~~g~~i~~~~~d 40 (137)
T cd00338 15 SLERQREALREYAARNGLEVVGEYED 40 (137)
T ss_pred CHHHHHHHHHHHHHHCCCEEEEEEEe
Confidence 34466677777777778876554443
No 420
>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=43.40 E-value=93 Score=31.31 Aligned_cols=76 Identities=8% Similarity=-0.081 Sum_probs=49.4
Q ss_pred EEEEEE--cCCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCc-HHHHHHHHHH
Q 003958 167 VIAIYV--DDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNR-GPVVFHVAQY 243 (784)
Q Consensus 167 v~ii~~--d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~-~~~~~~~a~~ 243 (784)
|++|.. ++.|.....+.+.+.+++.|+++..... ..+.......++++...+++.|++...... ....++.+.+
T Consensus 2 i~vi~~~~~~~~~~~~~~~i~~~~~~~g~~~~~~~~---~~~~~~~~~~i~~~~~~~~dgiii~~~~~~~~~~~l~~~~~ 78 (277)
T cd06319 2 IAYIVSDLRIPFWQIMGRGVKSKAKALGYDAVELSA---ENSAKKELENLRTAIDKGVSGIIISPTNSSAAVTLLKLAAQ 78 (277)
T ss_pred eEEEeCCCCchHHHHHHHHHHHHHHhcCCeEEEecC---CCCHHHHHHHHHHHHhcCCCEEEEcCCchhhhHHHHHHHHH
Confidence 566664 3667777788888999999988764321 123344456677777788999987643322 3456667766
Q ss_pred cC
Q 003958 244 LG 245 (784)
Q Consensus 244 ~g 245 (784)
.|
T Consensus 79 ~~ 80 (277)
T cd06319 79 AK 80 (277)
T ss_pred CC
Confidence 55
No 421
>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=43.40 E-value=1.2e+02 Score=30.28 Aligned_cols=75 Identities=11% Similarity=0.008 Sum_probs=43.6
Q ss_pred EEEEEEc------CCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHH
Q 003958 167 VIAIYVD------DDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHV 240 (784)
Q Consensus 167 v~ii~~d------~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~ 240 (784)
|++|..+ +.|.....+.+.+.+++.|+.+.....-. .........+.+.+.+.+.|++....... ..++.
T Consensus 2 igvi~p~~~~~~~~~~~~~~~~~i~~~~~~~g~~~~~~~~~~---~~~~~~~~~~~~~~~~vdgiii~~~~~~~-~~~~~ 77 (268)
T cd06271 2 IGLVLPTGEREEGDPFFAEFLSGLSEALAEHGYDLVLLPVDP---DEDPLEVYRRLVESGLVDGVIISRTRPDD-PRVAL 77 (268)
T ss_pred eEEEeCCcccccCCccHHHHHHHHHHHHHHCCceEEEecCCC---cHHHHHHHHHHHHcCCCCEEEEecCCCCC-hHHHH
Confidence 4566654 67777888899999999998876543221 22222233333455678888886433222 23455
Q ss_pred HHHcC
Q 003958 241 AQYLG 245 (784)
Q Consensus 241 a~~~g 245 (784)
+.+.+
T Consensus 78 ~~~~~ 82 (268)
T cd06271 78 LLERG 82 (268)
T ss_pred HHhcC
Confidence 55544
No 422
>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=43.25 E-value=1.3e+02 Score=29.95 Aligned_cols=75 Identities=7% Similarity=0.029 Sum_probs=48.8
Q ss_pred EEEEEE--cCCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHc
Q 003958 167 VIAIYV--DDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYL 244 (784)
Q Consensus 167 v~ii~~--d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~ 244 (784)
|+++.. ++.|.....+.+.+.+++.|..+...... .+.......++.+...+.+.|++........ .++++.+.
T Consensus 2 igvi~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~---~~~~~~~~~i~~l~~~~vdgiii~~~~~~~~-~~~~~~~~ 77 (264)
T cd06274 2 IGLIIPDLENRSFARIAKRLEALARERGYQLLIACSD---DDPETERETVETLIARQVDALIVAGSLPPDD-PYYLCQKA 77 (264)
T ss_pred EEEEeccccCchHHHHHHHHHHHHHHCCCEEEEEeCC---CCHHHHHHHHHHHHHcCCCEEEEcCCCCchH-HHHHHHhc
Confidence 456664 35677777888889898999887654322 2334455677778888999988875433322 25566665
Q ss_pred C
Q 003958 245 G 245 (784)
Q Consensus 245 g 245 (784)
+
T Consensus 78 ~ 78 (264)
T cd06274 78 G 78 (264)
T ss_pred C
Confidence 5
No 423
>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=43.25 E-value=1.2e+02 Score=30.10 Aligned_cols=75 Identities=12% Similarity=0.105 Sum_probs=49.2
Q ss_pred EEEEEE--cCCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHc
Q 003958 167 VIAIYV--DDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYL 244 (784)
Q Consensus 167 v~ii~~--d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~ 244 (784)
|+++.. ++.|.....+.+.+.+++.|..+..... . ... +....++++.+.+.+.|++....... ..++.+.+.
T Consensus 2 I~~i~~~~~~~~~~~~~~~i~~~~~~~g~~~~~~~~-~--~~~-~~~~~i~~~~~~~vdgiii~~~~~~~-~~~~~~~~~ 76 (266)
T cd06278 2 IGVVVADLDNPFYSELLEALSRALQARGYQPLLINT-D--DDE-DLDAALRQLLQYRVDGVIVTSGTLSS-ELAEECRRN 76 (266)
T ss_pred EEEEeCCCCCchHHHHHHHHHHHHHHCCCeEEEEcC-C--CCH-HHHHHHHHHHHcCCCEEEEecCCCCH-HHHHHHhhc
Confidence 455654 3567777888899999999988764421 1 122 56677777777889988886443222 446677665
Q ss_pred CC
Q 003958 245 GM 246 (784)
Q Consensus 245 g~ 246 (784)
|.
T Consensus 77 ~i 78 (266)
T cd06278 77 GI 78 (266)
T ss_pred CC
Confidence 53
No 424
>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=43.18 E-value=88 Score=31.80 Aligned_cols=77 Identities=9% Similarity=0.056 Sum_probs=52.3
Q ss_pred EEEEEEEc--CCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccC-CcHHHHHHHHH
Q 003958 166 EVIAIYVD--DDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY-NRGPVVFHVAQ 242 (784)
Q Consensus 166 ~v~ii~~d--~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~-~~~~~~~~~a~ 242 (784)
+|++|..+ +.|.....+.+.+.+++.|..+.... . . +.......++++...+++.||+.... +.....++++.
T Consensus 1 ~Ig~v~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~--~-~-~~~~~~~~i~~~~~~~~dgiii~~~~~~~~~~~~~~~~ 76 (289)
T cd01540 1 KIGFIVKQPEEPWFQTEWKFAKKAAKEKGFTVVKID--V-P-DGEKVLSAIDNLGAQGAKGFVICVPDVKLGPAIVAKAK 76 (289)
T ss_pred CeeeecCCCCCcHHHHHHHHHHHHHHHcCCEEEEcc--C-C-CHHHHHHHHHHHHHcCCCEEEEccCchhhhHHHHHHHH
Confidence 36667653 55777788889999999998876432 1 1 33344567777777889998887543 34566778887
Q ss_pred HcCC
Q 003958 243 YLGM 246 (784)
Q Consensus 243 ~~g~ 246 (784)
+.|.
T Consensus 77 ~~~i 80 (289)
T cd01540 77 AYNM 80 (289)
T ss_pred hCCC
Confidence 7663
No 425
>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=43.16 E-value=1.4e+02 Score=29.91 Aligned_cols=75 Identities=19% Similarity=0.075 Sum_probs=50.1
Q ss_pred EEEEEE--cCCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHc
Q 003958 167 VIAIYV--DDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYL 244 (784)
Q Consensus 167 v~ii~~--d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~ 244 (784)
|+++.. ++.|.......+.+.+++.|..+... ....+.......++++.+.+.+.|++..... ....++.+.+.
T Consensus 2 i~vv~p~~~~~~~~~~~~~i~~~~~~~g~~~~~~---~~~~~~~~~~~~~~~l~~~~vdgiii~~~~~-~~~~~~~l~~~ 77 (268)
T cd06273 2 IGAIVPTLDNAIFARVIQAFQETLAAHGYTLLVA---SSGYDLDREYAQARKLLERGVDGLALIGLDH-SPALLDLLARR 77 (268)
T ss_pred eEEEeCCCCCchHHHHHHHHHHHHHHCCCEEEEe---cCCCCHHHHHHHHHHHHhcCCCEEEEeCCCC-CHHHHHHHHhC
Confidence 567775 36677778889999999999887652 2122444556777788777888888764432 33556666665
Q ss_pred C
Q 003958 245 G 245 (784)
Q Consensus 245 g 245 (784)
+
T Consensus 78 ~ 78 (268)
T cd06273 78 G 78 (268)
T ss_pred C
Confidence 5
No 426
>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=43.10 E-value=1.4e+02 Score=26.92 Aligned_cols=60 Identities=17% Similarity=0.071 Sum_probs=40.3
Q ss_pred hHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEecc-CCcHHHHHHHHH
Q 003958 180 GIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTH-YNRGPVVFHVAQ 242 (784)
Q Consensus 180 ~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~-~~~~~~~~~~a~ 242 (784)
....+.+.+++.|.++.....++ .+..++...++++.+ +.|+||..+. .....++..++.
T Consensus 28 n~~~l~~~l~~~G~~v~~~~~v~--Dd~~~i~~~l~~~~~-~~DliIttGG~g~g~~D~t~~ai 88 (144)
T TIGR00177 28 NGPLLAALLEEAGFNVSRLGIVP--DDPEEIREILRKAVD-EADVVLTTGGTGVGPRDVTPEAL 88 (144)
T ss_pred cHHHHHHHHHHCCCeEEEEeecC--CCHHHHHHHHHHHHh-CCCEEEECCCCCCCCCccHHHHH
Confidence 35678888999999988777676 355667777777653 7899998743 333344444443
No 427
>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=42.83 E-value=1.3e+02 Score=30.11 Aligned_cols=77 Identities=10% Similarity=-0.029 Sum_probs=50.0
Q ss_pred EEEEEE--cCCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEecc-CC---cHHHHHHH
Q 003958 167 VIAIYV--DDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTH-YN---RGPVVFHV 240 (784)
Q Consensus 167 v~ii~~--d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~-~~---~~~~~~~~ 240 (784)
|++|.. ++.|.....+.+.+.+++.|..+...... .+.......++.+.+.++|.|++... .. .....+.+
T Consensus 2 Igvi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~~---~~~~~~~~~i~~l~~~~vdgiIi~~~~~~~~~~~~~~i~~ 78 (273)
T cd06292 2 VGLLVPELSNPIFPAFAEAIEAALAQYGYTVLLCNTY---RGGVSEADYVEDLLARGVRGVVFISSLHADTHADHSHYER 78 (273)
T ss_pred EEEEeCCCcCchHHHHHHHHHHHHHHCCCEEEEEeCC---CChHHHHHHHHHHHHcCCCEEEEeCCCCCcccchhHHHHH
Confidence 466664 45677788899999999999887643221 23344557788888888998888642 22 22344566
Q ss_pred HHHcCC
Q 003958 241 AQYLGM 246 (784)
Q Consensus 241 a~~~g~ 246 (784)
+.+.|.
T Consensus 79 ~~~~~i 84 (273)
T cd06292 79 LAERGL 84 (273)
T ss_pred HHhCCC
Confidence 666553
No 428
>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=42.78 E-value=1e+02 Score=31.75 Aligned_cols=77 Identities=6% Similarity=0.045 Sum_probs=49.3
Q ss_pred EEEEEE---cCCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcC--CceEEEEeccCCcHHHHHHHH
Q 003958 167 VIAIYV---DDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALT--ESRIIVVHTHYNRGPVVFHVA 241 (784)
Q Consensus 167 v~ii~~---d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~--~~~vIvl~~~~~~~~~~~~~a 241 (784)
|+++.. ++.|.....+.+++.+++.|..+..... . .+.......++.+... ++|.||+.........+++.+
T Consensus 2 Igvi~~~~~~~~~~~~~~~gi~~~~~~~g~~v~~~~~-~--~~~~~~~~~i~~~~~~~~~vdgiIi~~~~~~~~~~~~~~ 78 (305)
T cd06324 2 VVFLNPGKSDEPFWNSVARFMQAAADDLGIELEVLYA-E--RDRFLMLQQARTILQRPDKPDALIFTNEKSVAPELLRLA 78 (305)
T ss_pred eEEecCCCCCCcHHHHHHHHHHHHHHhcCCeEEEEeC-C--CCHHHHHHHHHHHHHhccCCCEEEEcCCccchHHHHHHH
Confidence 566663 3456677788888888888887765421 1 2333345667777777 899988864333345566777
Q ss_pred HHcCC
Q 003958 242 QYLGM 246 (784)
Q Consensus 242 ~~~g~ 246 (784)
.+.|.
T Consensus 79 ~~~gi 83 (305)
T cd06324 79 EGAGV 83 (305)
T ss_pred HhCCC
Confidence 76553
No 429
>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=42.72 E-value=1.3e+02 Score=30.56 Aligned_cols=78 Identities=13% Similarity=0.033 Sum_probs=51.9
Q ss_pred cEEEEEEEc--CCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCc-HHHHHHHH
Q 003958 165 REVIAIYVD--DDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNR-GPVVFHVA 241 (784)
Q Consensus 165 ~~v~ii~~d--~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~-~~~~~~~a 241 (784)
++|++|..+ +.|.....+.+.+.+++.|..+..... ..+.+.....++.+...+.+.||+...... ....++.+
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 467877764 556667788899999999987765321 124444567788888889999998754322 23455666
Q ss_pred HHcC
Q 003958 242 QYLG 245 (784)
Q Consensus 242 ~~~g 245 (784)
.+.+
T Consensus 78 ~~~~ 81 (280)
T cd06315 78 QKAG 81 (280)
T ss_pred HHCC
Confidence 6654
No 430
>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=42.59 E-value=1e+02 Score=30.88 Aligned_cols=79 Identities=8% Similarity=-0.031 Sum_probs=49.6
Q ss_pred EEEEEEE--cCCCcchhHHHHHHHHhcc---CcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccC-CcHHHHHH
Q 003958 166 EVIAIYV--DDDHGRNGIAALGDTLAAK---RCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY-NRGPVVFH 239 (784)
Q Consensus 166 ~v~ii~~--d~~~g~~~~~~l~~~l~~~---gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~-~~~~~~~~ 239 (784)
||+++.. ++.|.....+.+++.+++. |.++.... +....+.......++++...+.+.||+.... ......+.
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 4666664 3456667788888888888 86432222 1211244556677888777899999987543 33345667
Q ss_pred HHHHcC
Q 003958 240 VAQYLG 245 (784)
Q Consensus 240 ~a~~~g 245 (784)
.+.+.|
T Consensus 80 ~~~~~~ 85 (272)
T cd06300 80 EACEAG 85 (272)
T ss_pred HHHHCC
Confidence 776655
No 431
>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=42.52 E-value=1.3e+02 Score=26.52 Aligned_cols=61 Identities=15% Similarity=0.149 Sum_probs=40.1
Q ss_pred hhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEecc-CCcHHHHHHHHH
Q 003958 179 NGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTH-YNRGPVVFHVAQ 242 (784)
Q Consensus 179 ~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~-~~~~~~~~~~a~ 242 (784)
.....+.+.+++.|.++......+ .+...+.+.+++..+. +|+|+..+. .....++..++-
T Consensus 19 ~n~~~l~~~l~~~G~~v~~~~~v~--Dd~~~i~~~i~~~~~~-~DlvittGG~g~g~~D~t~~ai 80 (133)
T cd00758 19 TNGPALEALLEDLGCEVIYAGVVP--DDADSIRAALIEASRE-ADLVLTTGGTGVGRRDVTPEAL 80 (133)
T ss_pred chHHHHHHHHHHCCCEEEEeeecC--CCHHHHHHHHHHHHhc-CCEEEECCCCCCCCCcchHHHH
Confidence 345678888889998887765665 4556677777776544 899998743 333444444443
No 432
>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=42.28 E-value=1.3e+02 Score=30.08 Aligned_cols=75 Identities=9% Similarity=0.096 Sum_probs=48.7
Q ss_pred EEEEEEc--CCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHc
Q 003958 167 VIAIYVD--DDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYL 244 (784)
Q Consensus 167 v~ii~~d--~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~ 244 (784)
|++|..+ +.|.....+.+.+.+++.|.++..... . .+..+....++.+...+++.|++...... ...++.+.+.
T Consensus 2 Ig~i~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~-~--~~~~~~~~~~~~l~~~~vdgiii~~~~~~-~~~~~~~~~~ 77 (268)
T cd01575 2 VAVLVPSLSNSVFADVLQGISDVLEAAGYQLLLGNT-G--YSPEREEELLRTLLSRRPAGLILTGLEHT-ERTRQLLRAA 77 (268)
T ss_pred EEEEeCCCcchhHHHHHHHHHHHHHHcCCEEEEecC-C--CCchhHHHHHHHHHHcCCCEEEEeCCCCC-HHHHHHHHhc
Confidence 5666643 456667778888999999988765322 1 23344567778887788999888754332 3455555555
Q ss_pred C
Q 003958 245 G 245 (784)
Q Consensus 245 g 245 (784)
+
T Consensus 78 ~ 78 (268)
T cd01575 78 G 78 (268)
T ss_pred C
Confidence 4
No 433
>PF03830 PTSIIB_sorb: PTS system sorbose subfamily IIB component; InterPro: IPR004720 Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains.The Man family is unique in several respects among PTS permease families: It is the only PTS family in which members possess a IID protein. It is the only PTS family in which the IIB constituent is phosphorylated on a histidyl rather than a cysteyl residue. Its permease members exhibit broad specificity for a range of sugars, rather than being specific for just one or a few sugars. The mannose permease of Escherichia coli, for example, can transport and phosphorylate glucose, mannose, fructose, glucosamine, N-acetylglucosamine, and other sugars. Other members of this can transport sorbose, fructose and N-acetylglucosamine. This entry is specific for the IIB components of this family of PTS transporters [].; GO: 0008982 protein-N(PI)-phosphohistidine-sugar phosphotransferase activity, 0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system, 0005737 cytoplasm; PDB: 3LFJ_B 1BLE_A 3P3V_B 1NRZ_C 3EYE_A 1VSQ_C 2JZH_A 2JZN_C 2JZO_D.
Probab=42.00 E-value=29 Score=31.63 Aligned_cols=83 Identities=11% Similarity=0.109 Sum_probs=57.6
Q ss_pred HHHHHHHHHHHcCCcEEEEEEEcCCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEecc
Q 003958 151 QMAAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTH 230 (784)
Q Consensus 151 ~~~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~ 230 (784)
+++.+..|.++++-++|.++- |........+.+.+...-.|+++... +.++....+++....+.++++++-+
T Consensus 13 HGQV~~~W~~~~~~~~IiVvd-D~~A~D~~~k~~l~ma~P~gvk~~i~-------sv~~a~~~l~~~~~~~~~v~ii~k~ 84 (151)
T PF03830_consen 13 HGQVATAWVKKLNANRIIVVD-DEVANDPFQKMILKMAAPAGVKLSIF-------SVEEAIEKLKKPEYSKKRVLIIVKS 84 (151)
T ss_dssp CTTHHHHHHHHHTTSEEEEE--HHHHHSHHHHHHHHHTSHTTSEEEEE--------HHHHHHHHCGGGGTTEEEEEEESS
T ss_pred eeeeeEEEhhhcccCEEEEEC-HHHhcCHHHHHHHHHhhcCCCceEEE-------EHHHHHHHHHhcccCCceEEEEECC
Confidence 567889999999999999885 33333445666666665678777642 3445666666666678899999988
Q ss_pred CCcHHHHHHHH
Q 003958 231 YNRGPVVFHVA 241 (784)
Q Consensus 231 ~~~~~~~~~~a 241 (784)
+.++..++++-
T Consensus 85 ~~d~~~l~~~g 95 (151)
T PF03830_consen 85 PEDALRLVEAG 95 (151)
T ss_dssp HHHHHHHHHTT
T ss_pred HHHHHHHHhcC
Confidence 88877666443
No 434
>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=41.99 E-value=99 Score=31.14 Aligned_cols=80 Identities=8% Similarity=-0.007 Sum_probs=50.1
Q ss_pred EEEEEEE--cCCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccC-CcHHHHHHHHH
Q 003958 166 EVIAIYV--DDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY-NRGPVVFHVAQ 242 (784)
Q Consensus 166 ~v~ii~~--d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~-~~~~~~~~~a~ 242 (784)
+|++|.. ++.|.....+.+++.+++.|..+.....-. ..+...-...+.++...+.+.||+.... ......++++.
T Consensus 1 ~igvi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~~~-~~~~~~~~~~i~~l~~~~vdgiIi~~~~~~~~~~~~~~~~ 79 (275)
T cd06320 1 KYGVVLKTLSNEFWRSLKEGYENEAKKLGVSVDIQAAPS-EGDQQGQLSIAENMINKGYKGLLFSPISDVNLVPAVERAK 79 (275)
T ss_pred CeeEEEecCCCHHHHHHHHHHHHHHHHhCCeEEEEccCC-CCCHHHHHHHHHHHHHhCCCEEEECCCChHHhHHHHHHHH
Confidence 3667764 456677778889999999998876532211 1233334566777777788988876432 22345566776
Q ss_pred HcCC
Q 003958 243 YLGM 246 (784)
Q Consensus 243 ~~g~ 246 (784)
+.+.
T Consensus 80 ~~~i 83 (275)
T cd06320 80 KKGI 83 (275)
T ss_pred HCCC
Confidence 6553
No 435
>COG1419 FlhF Flagellar GTP-binding protein [Cell motility and secretion]
Probab=41.91 E-value=1.8e+02 Score=31.14 Aligned_cols=84 Identities=12% Similarity=0.010 Sum_probs=56.4
Q ss_pred HHHHHHHHHHHcCCcEEEEEEEcCCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEecc
Q 003958 151 QMAAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTH 230 (784)
Q Consensus 151 ~~~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~ 230 (784)
.+.-.+.+....+-++|++|+.|. |=.+..++++...+-.|+.+.... +..|+...+..+++ .|+|++...
T Consensus 220 lAKLAar~~~~~~~~kVaiITtDt-YRIGA~EQLk~Ya~im~vp~~vv~------~~~el~~ai~~l~~--~d~ILVDTa 290 (407)
T COG1419 220 LAKLAARYVMLKKKKKVAIITTDT-YRIGAVEQLKTYADIMGVPLEVVY------SPKELAEAIEALRD--CDVILVDTA 290 (407)
T ss_pred HHHHHHHHHhhccCcceEEEEecc-chhhHHHHHHHHHHHhCCceEEec------CHHHHHHHHHHhhc--CCEEEEeCC
Confidence 343334444456789999999764 777788999999988887766432 44677777777764 499999865
Q ss_pred CCcHH--HHHHHHHH
Q 003958 231 YNRGP--VVFHVAQY 243 (784)
Q Consensus 231 ~~~~~--~~~~~a~~ 243 (784)
+.... ..+.++.+
T Consensus 291 Grs~~D~~~i~el~~ 305 (407)
T COG1419 291 GRSQYDKEKIEELKE 305 (407)
T ss_pred CCCccCHHHHHHHHH
Confidence 54333 33444444
No 436
>PRK10677 modA molybdate transporter periplasmic protein; Provisional
Probab=41.77 E-value=1.9e+02 Score=29.08 Aligned_cols=92 Identities=9% Similarity=0.004 Sum_probs=46.1
Q ss_pred CCChHhhhhCCCceEEee------CchHHHHHHhhccc---CccCceeCCCHHHHHHHHhcCCcCCCeeEEEechhhhHH
Q 003958 684 IKGIDSLRSSNYPIGYQV------NSFARNYLVDELNI---DESRLVPLNSPEEYAKALKDGPHKGGVAAVVDDRAYAEL 754 (784)
Q Consensus 684 i~~~~dl~~~~~~i~~~~------~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~l~~~~~~~~~~a~~~~~~~~~~ 754 (784)
.++++||.+. .+|++.. |.+....+++ .+. -..++....+..+....+.+ ++.++.+.-...+
T Consensus 127 ~~~~~dLl~~-~~iai~dP~~~p~G~~a~~~l~~-~g~~~~l~~k~~~~~~v~~~~~~v~~----G~ad~gi~~~s~a-- 198 (257)
T PRK10677 127 KTDWKSLLNG-GRLAVGDPDHVPAGIYAKEALQK-LGAWDTLSPKLARAEDVRGALALVER----NEAPLGIVYGSDA-- 198 (257)
T ss_pred ccCHHHhcCC-CeEEEcCCCCChHHHHHHHHHHH-cCCHHHHHhhhcccccHHHHHHHHHc----CCCCEEEEEeeee--
Confidence 3578888753 3566653 2234445532 211 01123323566778888888 6777655321211
Q ss_pred HHcCCCCeE-EeCC-ccccceEEEEeeCCCC
Q 003958 755 FLSTRCEFS-IVGQ-VFTKNGWGFVSIVSSF 783 (784)
Q Consensus 755 ~~~~~c~l~-~~~~-~~~~~~~~~~~~k~s~ 783 (784)
...+..+.. .+.+ ......|++++.|+++
T Consensus 199 ~~~~~~~~~~~~P~e~~~~i~~~~avlk~~~ 229 (257)
T PRK10677 199 VASKKVKVVGTFPEDSHKPVEYPMAIVKGHN 229 (257)
T ss_pred eccCCCeEEEECCcccCCcceeeEEEEcCCC
Confidence 122233332 2232 2334567888888764
No 437
>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=41.67 E-value=1.8e+02 Score=28.35 Aligned_cols=74 Identities=16% Similarity=0.109 Sum_probs=48.0
Q ss_pred cEEEEEEEcCCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccC--CcHHHHHHHHH
Q 003958 165 REVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY--NRGPVVFHVAQ 242 (784)
Q Consensus 165 ~~v~ii~~d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~--~~~~~~~~~a~ 242 (784)
.++++|....+. .+...+..+..+..+.+...-|+..+..++...-+++++.++++|++.|-+ ...+++++++.
T Consensus 126 ~~vGVivP~~eQ----~~~~~~kW~~l~~~~~~a~asPy~~~~~~l~~Aa~~L~~~gadlIvLDCmGYt~~~r~~~~~~~ 201 (221)
T PF07302_consen 126 HQVGVIVPLPEQ----IAQQAEKWQPLGNPVVVAAASPYEGDEEELAAAARELAEQGADLIVLDCMGYTQEMRDIVQRAL 201 (221)
T ss_pred CeEEEEecCHHH----HHHHHHHHHhcCCCeEEEEeCCCCCCHHHHHHHHHHHHhcCCCEEEEECCCCCHHHHHHHHHHh
Confidence 799999987653 222223333343334333333332577889999999999999999998654 55666666653
No 438
>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=41.35 E-value=2.1e+02 Score=24.48 Aligned_cols=67 Identities=10% Similarity=0.010 Sum_probs=37.4
Q ss_pred cCCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEecc-C---CcHHHHHHHHHHcC
Q 003958 173 DDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTH-Y---NRGPVVFHVAQYLG 245 (784)
Q Consensus 173 d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~-~---~~~~~~~~~a~~~g 245 (784)
..+.-.-....+...++..|+++..-. .. ......++.+.+.++++|.+.+. . ..+..++++.++.+
T Consensus 8 ~~e~H~lG~~~~~~~l~~~G~~V~~lg---~~---~~~~~l~~~~~~~~pdvV~iS~~~~~~~~~~~~~i~~l~~~~ 78 (119)
T cd02067 8 GGDGHDIGKNIVARALRDAGFEVIDLG---VD---VPPEEIVEAAKEEDADAIGLSGLLTTHMTLMKEVIEELKEAG 78 (119)
T ss_pred CCchhhHHHHHHHHHHHHCCCEEEECC---CC---CCHHHHHHHHHHcCCCEEEEeccccccHHHHHHHHHHHHHcC
Confidence 333334445667777777887774322 11 11335556666677888888755 2 23445555555543
No 439
>TIGR01744 XPRTase xanthine phosphoribosyltransferase. This model represent a xanthine-specific phosphoribosyltransferase of Bacillus subtilis and closely related proteins from other species, mostly from other Gram-positive bacteria. The adjacent gene is a xanthine transporter; B. subtilis can import xanthine for the purine salvage pathway or for catabolism to obtain nitrogen.
Probab=41.31 E-value=74 Score=30.36 Aligned_cols=71 Identities=13% Similarity=0.106 Sum_probs=49.2
Q ss_pred HHHHHhcCCCCCCCCEEEEEEe-cCCCCHHHHHHHHHHHHhc----CceEEEccCchhhHHHHHHhhhcCCccEEec
Q 003958 55 AVDDVNSDPTTLGGTKLKLQMQ-DCNHSGFLALAEALHLMEG----QTVAIIGPQDAVTSHVVSHVANELQVPLLSF 126 (784)
Q Consensus 55 Ave~IN~~~~il~g~~l~~~~~-D~~~~~~~a~~~~~~li~~----~v~aiiGp~~s~~~~~va~~~~~~~ip~Is~ 126 (784)
-.+.||+.+-++||--|....+ |.+.+|......+..+.+. ++.+|+|+.......+. .++...++|++-.
T Consensus 4 l~~~~~~~~~~~~~~~i~~~~~~~~~~~p~~l~~v~~~l~~~~~~~~~d~Vv~~ea~Gi~la~-~lA~~Lg~p~v~v 79 (191)
T TIGR01744 4 LKQKIKEEGVVLPGGILKVDSFLNHQIDPKLMQEVGEEFARRFADDGITKIVTIEASGIAPAI-MTGLKLGVPVVFA 79 (191)
T ss_pred HHHHHhcCCEEcCCCEEEEehhhccccCHHHHHHHHHHHHHHhccCCCCEEEEEccccHHHHH-HHHHHHCCCEEEE
Confidence 3578999999999877777554 5556887665555554433 78999998777654442 3566678998863
No 440
>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=41.26 E-value=2.3e+02 Score=24.23 Aligned_cols=17 Identities=18% Similarity=0.249 Sum_probs=8.5
Q ss_pred hHHHHHHHHhccCcEEE
Q 003958 180 GIAALGDTLAAKRCRIS 196 (784)
Q Consensus 180 ~~~~l~~~l~~~gi~v~ 196 (784)
....+...+++.|.++.
T Consensus 16 Gl~~la~~l~~~G~~v~ 32 (121)
T PF02310_consen 16 GLLYLAAYLRKAGHEVD 32 (121)
T ss_dssp HHHHHHHHHHHTTBEEE
T ss_pred HHHHHHHHHHHCCCeEE
Confidence 34445555555555544
No 441
>cd03364 TOPRIM_DnaG_primases TOPRIM_DnaG_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of proteins similar to Escherichia coli DnaG. Primases synthesize RNA primers for the initiation of DNA replication. DnaG type primases are often closely associated with DNA helicases in primosome assemblies. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function. E. coli DnaG is a single subunit enzyme.
Probab=41.09 E-value=56 Score=25.76 Aligned_cols=42 Identities=19% Similarity=0.244 Sum_probs=33.7
Q ss_pred HHHHHHHcCCcEEEEEEEcCCCcchhHHHHHHHHhccCcEEEE
Q 003958 155 IAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISF 197 (784)
Q Consensus 155 i~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~~l~~~gi~v~~ 197 (784)
..++|+.+ -++|.+.+++|.-|+...+.+.+.+.+.|..+..
T Consensus 35 ~~~~L~~~-~~~vii~~D~D~aG~~a~~~~~~~l~~~g~~~~~ 76 (79)
T cd03364 35 QAELLKRL-AKEVILAFDGDEAGQKAALRALELLLKLGLNVRV 76 (79)
T ss_pred HHHHHHhc-CCeEEEEECCCHHHHHHHHHHHHHHHHCCCeEEE
Confidence 35555555 6889999999999999999999999998877653
No 442
>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=40.95 E-value=1e+02 Score=30.99 Aligned_cols=76 Identities=5% Similarity=-0.029 Sum_probs=49.0
Q ss_pred EEEEEE--cCCCcchhHHHHHHHHhc--cCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCc-HHHHHHHH
Q 003958 167 VIAIYV--DDDHGRNGIAALGDTLAA--KRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNR-GPVVFHVA 241 (784)
Q Consensus 167 v~ii~~--d~~~g~~~~~~l~~~l~~--~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~-~~~~~~~a 241 (784)
|+++.. ++.|.....+.+.+.+++ .|.++..... ..+.......++.+...+++.||+...... ....++.+
T Consensus 2 Ig~v~~~~~~~~~~~~~~gi~~~~~~~~~~~~~~~~~~---~~~~~~~~~~i~~~~~~~~dgiIi~~~~~~~~~~~i~~~ 78 (271)
T cd06321 2 IGVSVGDLGNPFFVALAKGAEAAAKKLNPGVKVTVVSA---DYDLNKQVSQIDNFIAAKVDLILLNAVDSKGIAPAVKRA 78 (271)
T ss_pred eEEEecccCCHHHHHHHHHHHHHHHHhCCCeEEEEccC---CCCHHHHHHHHHHHHHhCCCEEEEeCCChhHhHHHHHHH
Confidence 567775 356777888899999999 6766554321 123334456677777778998888643322 35666777
Q ss_pred HHcC
Q 003958 242 QYLG 245 (784)
Q Consensus 242 ~~~g 245 (784)
.+.+
T Consensus 79 ~~~~ 82 (271)
T cd06321 79 QAAG 82 (271)
T ss_pred HHCC
Confidence 6655
No 443
>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=40.53 E-value=1.2e+02 Score=32.07 Aligned_cols=81 Identities=9% Similarity=-0.011 Sum_probs=53.5
Q ss_pred HHHHHHH-HcCCcEEEEEEEcCCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccC-
Q 003958 154 AIAEIVD-HYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY- 231 (784)
Q Consensus 154 ai~~~l~-~~~w~~v~ii~~d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~- 231 (784)
.+.++++ ..+.+++.+|++...+ +...+.+++.+++.| .+... +..+.+.+.....++.+++.++++||-.+.+
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 3556666 3567899999854433 356778888888887 44322 2233466778888888888899998876543
Q ss_pred -CcHHHHH
Q 003958 232 -NRGPVVF 238 (784)
Q Consensus 232 -~~~~~~~ 238 (784)
-++..++
T Consensus 90 ~~D~aK~~ 97 (339)
T cd08173 90 VIDVAKVA 97 (339)
T ss_pred HHHHHHHH
Confidence 3444444
No 444
>PRK09701 D-allose transporter subunit; Provisional
Probab=40.47 E-value=1.2e+02 Score=31.44 Aligned_cols=84 Identities=10% Similarity=-0.011 Sum_probs=56.1
Q ss_pred cCCcEEEEEEEc--CCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccC-CcHHHHH
Q 003958 162 YGWREVIAIYVD--DDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY-NRGPVVF 238 (784)
Q Consensus 162 ~~w~~v~ii~~d--~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~-~~~~~~~ 238 (784)
+.-..|++|..+ +.|.....+.+++.+++.|..+..... +...+.......++.+...+++.||+.... ......+
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 455799999964 667778889999999999988765321 111233445567777777889999987543 2333446
Q ss_pred HHHHHcCC
Q 003958 239 HVAQYLGM 246 (784)
Q Consensus 239 ~~a~~~g~ 246 (784)
.++.+.|.
T Consensus 101 ~~~~~~gi 108 (311)
T PRK09701 101 ARAWKKGI 108 (311)
T ss_pred HHHHHCCC
Confidence 66666553
No 445
>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=40.46 E-value=1.4e+02 Score=29.56 Aligned_cols=73 Identities=4% Similarity=-0.022 Sum_probs=48.4
Q ss_pred EEEEEE--cCCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHH
Q 003958 167 VIAIYV--DDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQY 243 (784)
Q Consensus 167 v~ii~~--d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~ 243 (784)
|+++.. ++.|.....+.+++.+++.|.++...... .+.......++.+.+.+++.|++....... ..++.+.+
T Consensus 2 i~~i~~~~~~~~~~~i~~gi~~~~~~~g~~~~~~~~~---~~~~~~~~~i~~l~~~~vdgiii~~~~~~~-~~~~~~~~ 76 (260)
T cd06286 2 IGVVLPYINHPYFSQLVDGIEKAALKHGYKVVLLQTN---YDKEKELEYLELLKTKQVDGLILCSRENDW-EVIEPYTK 76 (260)
T ss_pred EEEEeCCCCCchHHHHHHHHHHHHHHcCCEEEEEeCC---CChHHHHHHHHHHHHcCCCEEEEeCCCCCH-HHHHHHhc
Confidence 566765 36677888899999999999888654321 233444567777777889988886543332 34555544
No 446
>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=40.45 E-value=23 Score=34.90 Aligned_cols=92 Identities=12% Similarity=0.098 Sum_probs=58.7
Q ss_pred cCChHHHHHHHHHHHHH-cCCcEEEEEEEcCCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCce
Q 003958 145 TQSDQYQMAAIAEIVDH-YGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESR 223 (784)
Q Consensus 145 ~ps~~~~~~ai~~~l~~-~~w~~v~ii~~d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~ 223 (784)
.|+....+..+++.+.. ..-+++.++..+.. ...+.+.+++.|..|.....|.. ..........+.++..+.+
T Consensus 97 ~~~~~~~s~~L~~~l~~~~~~~~vl~~~g~~~-----~~~l~~~L~~~g~~v~~~~vY~~-~~~~~~~~~~~~l~~~~~~ 170 (231)
T PF02602_consen 97 VPSSEGSSEGLAELLKEQLRGKRVLILRGEGG-----RPDLPEKLREAGIEVTEVIVYET-PPEELSPELKEALDRGEID 170 (231)
T ss_dssp E-TTSSSHHHHHGGHHHCCTTEEEEEEESSSS-----CHHHHHHHHHTTEEEEEEECEEE-EEHHHHHHHHHHHHHTTTS
T ss_pred cCCCCCCHHHHHHHHHhhCCCCeEEEEcCCCc-----cHHHHHHHHHCCCeEEEEEEeec-ccccchHHHHHHHHcCCCC
Confidence 45434446778887764 44488888775543 56688889999988877666653 2233444555666666777
Q ss_pred EEEEeccCCcHHHHHHHHHH
Q 003958 224 IIVVHTHYNRGPVVFHVAQY 243 (784)
Q Consensus 224 vIvl~~~~~~~~~~~~~a~~ 243 (784)
+|++ .++..+..+++...+
T Consensus 171 ~v~f-tS~~~~~~~~~~~~~ 189 (231)
T PF02602_consen 171 AVVF-TSPSAVRAFLELLKK 189 (231)
T ss_dssp EEEE-SSHHHHHHHHHHSSG
T ss_pred EEEE-CCHHHHHHHHHHhHh
Confidence 6555 556667777766654
No 447
>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=40.37 E-value=68 Score=32.01 Aligned_cols=19 Identities=11% Similarity=-0.092 Sum_probs=14.4
Q ss_pred HHHHHHHhhcCCceEEEEe
Q 003958 210 ITDLLVKVALTESRIIVVH 228 (784)
Q Consensus 210 ~~~~l~~l~~~~~~vIvl~ 228 (784)
....++.+...+.|+.+..
T Consensus 183 ~~~~~~al~~G~~Da~~~~ 201 (254)
T TIGR01098 183 HDASALAVANGKVDAATNN 201 (254)
T ss_pred hHHHHHHHHcCCCCeEEec
Confidence 4467778888889988764
No 448
>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=40.28 E-value=3e+02 Score=25.29 Aligned_cols=70 Identities=20% Similarity=0.267 Sum_probs=42.6
Q ss_pred eeHHHHHHHHHHCCCccceEEeeCCCCCCCCChhHHHHHHHcCcccEEEeeEEeecCccccceeccccccccEEEEEecc
Q 003958 495 FCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPVR 574 (784)
Q Consensus 495 ~~~dl~~~l~~~l~f~~~~~~~~~~~~~~~~~~~g~i~~l~~~~~D~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~~ 574 (784)
+..+++..+.+... ++++++.. +....++..+.+|++|+++..... ..+...+. ..|+....++++++..
T Consensus 14 ~l~~~l~~~~~~~P-~v~i~i~~-------~~~~~~~~~l~~~~~Dl~i~~~~~-~~~~~~~~-~~~l~~~~~~~~~~~~ 83 (201)
T cd08435 14 LLPPAIARLLARHP-RLTVRVVE-------GTSDELLEGLRAGELDLAIGRLAD-DEQPPDLA-SEELADEPLVVVARPG 83 (201)
T ss_pred HHHHHHHHHHHHCC-CeEEEEEe-------CCHHHHHHHHHcCCccEEEEecCc-ccCCCCcE-EEEcccCcEEEEEeCC
Confidence 44566777766643 33355432 345678999999999999854221 11122232 3567778888887654
No 449
>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=40.20 E-value=1e+02 Score=30.80 Aligned_cols=76 Identities=4% Similarity=-0.069 Sum_probs=49.9
Q ss_pred EEEEEE--cCCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCc-HHHHHHHHHH
Q 003958 167 VIAIYV--DDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNR-GPVVFHVAQY 243 (784)
Q Consensus 167 v~ii~~--d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~-~~~~~~~a~~ 243 (784)
|++|.. ++.|.....+.+.+.+++.|+.+.... ...+..+....++++...+++.|++...... ....++++.+
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 455664 466777888899999999998876422 1224445567777777788998888643222 3456677766
Q ss_pred cC
Q 003958 244 LG 245 (784)
Q Consensus 244 ~g 245 (784)
.+
T Consensus 79 ~~ 80 (268)
T cd06323 79 AG 80 (268)
T ss_pred CC
Confidence 54
No 450
>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=40.19 E-value=1.1e+02 Score=31.26 Aligned_cols=76 Identities=9% Similarity=0.017 Sum_probs=52.6
Q ss_pred cEEEEEEEc--CCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHH
Q 003958 165 REVIAIYVD--DDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQ 242 (784)
Q Consensus 165 ~~v~ii~~d--~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~ 242 (784)
+.|++|.++ +.|.......+.+.++++|..+.....-. + .+....++.+.+.+.|.||+.+...+-..+. ...
T Consensus 2 ~~IGvivp~~~npff~~ii~gIe~~a~~~Gy~l~l~~t~~---~-~~~e~~i~~l~~~~vDGiI~~s~~~~~~~l~-~~~ 76 (279)
T PF00532_consen 2 KTIGVIVPDISNPFFAEIIRGIEQEAREHGYQLLLCNTGD---D-EEKEEYIELLLQRRVDGIILASSENDDEELR-RLI 76 (279)
T ss_dssp CEEEEEESSSTSHHHHHHHHHHHHHHHHTTCEEEEEEETT---T-HHHHHHHHHHHHTTSSEEEEESSSCTCHHHH-HHH
T ss_pred CEEEEEECCCCCcHHHHHHHHHHHHHHHcCCEEEEecCCC---c-hHHHHHHHHHHhcCCCEEEEecccCChHHHH-HHH
Confidence 468888875 56777888999999999998876533222 2 2333888889999999999986665533443 443
Q ss_pred HcC
Q 003958 243 YLG 245 (784)
Q Consensus 243 ~~g 245 (784)
+.+
T Consensus 77 ~~~ 79 (279)
T PF00532_consen 77 KSG 79 (279)
T ss_dssp HTT
T ss_pred HcC
Confidence 333
No 451
>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=39.88 E-value=1.4e+02 Score=31.74 Aligned_cols=75 Identities=15% Similarity=0.046 Sum_probs=49.1
Q ss_pred HHHHHHHHHcCC--cEEEEEEEcCCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcC---CceEEEE
Q 003958 153 AAIAEIVDHYGW--REVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALT---ESRIIVV 227 (784)
Q Consensus 153 ~ai~~~l~~~~w--~~v~ii~~d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~---~~~vIvl 227 (784)
..+.++++.++. +++.+++ |...-+ ..+.+.+++.|+.+.....+..++..++.....+..++. ++|.||-
T Consensus 12 ~~l~~~~~~~g~~~~~~lvvt-d~~~~~---~~v~~~L~~~g~~~~~f~~v~~nPt~~~v~~~~~~~~~~~~~~~D~IIa 87 (347)
T cd08184 12 DQLNDLLAPKRKNKDPAVFFV-DDVFQG---KDLISRLPVESEDMIIWVDATEEPKTDQIDALTAQVKSFDGKLPCAIVG 87 (347)
T ss_pred HHHHHHHHHcCCCCCeEEEEE-Ccchhh---hHHHHHHHhcCCcEEEEcCCCCCcCHHHHHHHHHHHHhhCCCCCCEEEE
Confidence 356666777763 5566666 322211 566777888787655444555556677788888888876 8999997
Q ss_pred eccC
Q 003958 228 HTHY 231 (784)
Q Consensus 228 ~~~~ 231 (784)
.+.+
T Consensus 88 iGGG 91 (347)
T cd08184 88 IGGG 91 (347)
T ss_pred eCCc
Confidence 6543
No 452
>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=39.85 E-value=1.5e+02 Score=27.07 Aligned_cols=63 Identities=19% Similarity=0.202 Sum_probs=42.2
Q ss_pred EEEEEEEcCC--Ccc---hhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhc-CCceEEEEecc
Q 003958 166 EVIAIYVDDD--HGR---NGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVAL-TESRIIVVHTH 230 (784)
Q Consensus 166 ~v~ii~~d~~--~g~---~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~-~~~~vIvl~~~ 230 (784)
++++|...++ .|+ .....+.+.+++.|.++.....++ .+..++.+.+++..+ +++|+||..+.
T Consensus 2 ~~~ii~~~~e~~~g~i~d~n~~~l~~~l~~~G~~v~~~~~v~--Dd~~~i~~~l~~~~~~~~~DlVittGG 70 (152)
T cd00886 2 RAAVLTVSDTRSAGEAEDRSGPALVELLEEAGHEVVAYEIVP--DDKDEIREALIEWADEDGVDLILTTGG 70 (152)
T ss_pred EEEEEEEcCcccCCCCccchHHHHHHHHHHcCCeeeeEEEcC--CCHHHHHHHHHHHHhcCCCCEEEECCC
Confidence 5677765542 222 234568888999998888777676 455667777776543 37899998743
No 453
>PRK11063 metQ DL-methionine transporter substrate-binding subunit; Provisional
Probab=39.74 E-value=1.6e+02 Score=29.93 Aligned_cols=39 Identities=15% Similarity=0.144 Sum_probs=26.2
Q ss_pred HHHHHHH-HHHCCCccceEEeeCCCCCCCCChhHHHHHHHcCcccEEE
Q 003958 497 IDVFTAA-INLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAV 543 (784)
Q Consensus 497 ~dl~~~l-~~~l~f~~~~~~~~~~~~~~~~~~~g~i~~l~~~~~D~~~ 543 (784)
.++.+.+ .++.|.+ ++++.+ ..+..+...|.+|++|+..
T Consensus 46 ~~~~~~~l~~~~G~~--Vel~~f------~~~~~~~~ALa~GdID~~~ 85 (271)
T PRK11063 46 AEVAQKVAKEKYGLD--VELVTF------NDYVLPNEALSKGDIDANA 85 (271)
T ss_pred HHHHHHHHHHhcCCe--EEEEEe------cCcHHHHHHHHcCCcceec
Confidence 3344444 4556988 555544 3567889999999999854
No 454
>PF07172 GRP: Glycine rich protein family; InterPro: IPR010800 This family consists of glycine rich proteins. Some of them may be involved in resistance to environmental stress [].
Probab=39.71 E-value=28 Score=28.77 Aligned_cols=20 Identities=20% Similarity=0.368 Sum_probs=10.8
Q ss_pred CchhhHHHHHHHHHHHHHHh
Q 003958 1 MKLSGVMLLMIFYCELFVYR 20 (784)
Q Consensus 1 M~~~~~~~~~~~~~~~~~~~ 20 (784)
|..|..++|+++|+++++++
T Consensus 1 MaSK~~llL~l~LA~lLlis 20 (95)
T PF07172_consen 1 MASKAFLLLGLLLAALLLIS 20 (95)
T ss_pred CchhHHHHHHHHHHHHHHHH
Confidence 66666556555555444433
No 455
>PRK05928 hemD uroporphyrinogen-III synthase; Reviewed
Probab=39.62 E-value=85 Score=31.14 Aligned_cols=87 Identities=17% Similarity=0.199 Sum_probs=49.5
Q ss_pred HHHHHHHHH--cCCcEEEEEEEcCCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEecc
Q 003958 153 AAIAEIVDH--YGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTH 230 (784)
Q Consensus 153 ~ai~~~l~~--~~w~~v~ii~~d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~ 230 (784)
..+++.+.. ...+++.++..+. ....+.+.+++.|..+.....+.......+.......+.+.+.++|++ .+
T Consensus 112 ~~l~~~l~~~~~~~~~ili~~~~~-----~~~~l~~~L~~~G~~v~~~~~Y~~~~~~~~~~~~~~~~~~~~~d~ivf-tS 185 (249)
T PRK05928 112 SELLLELPELLLKGKRVLYLRGNG-----GREVLGDTLEERGAEVDECEVYERVPPKLDGAELLARLQSGEVDAVIF-TS 185 (249)
T ss_pred hHHHHhChhhhcCCCEEEEECCCC-----CHHHHHHHHHHCCCEEeEEEEEEeeCCCCChHHHHHHHHhCCCCEEEE-CC
Confidence 344444332 3566777776543 356788888888887765554432222222333444444456776554 55
Q ss_pred CCcHHHHHHHHHHcC
Q 003958 231 YNRGPVVFHVAQYLG 245 (784)
Q Consensus 231 ~~~~~~~~~~a~~~g 245 (784)
+..+..+++.+.+.+
T Consensus 186 ~~~v~~~~~~~~~~~ 200 (249)
T PRK05928 186 PSTVRAFFSLAPELG 200 (249)
T ss_pred HHHHHHHHHHhcccc
Confidence 667777777765544
No 456
>PRK15421 DNA-binding transcriptional regulator MetR; Provisional
Probab=39.38 E-value=4.6e+02 Score=27.20 Aligned_cols=68 Identities=9% Similarity=0.062 Sum_probs=41.9
Q ss_pred eeHHHHHHHHHHCCCccceEEeeCCCCCCCCChhHHHHHHHcCcccEEEeeEEeecCccccceeccccccccEEEEEecc
Q 003958 495 FCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPVR 574 (784)
Q Consensus 495 ~~~dl~~~l~~~l~f~~~~~~~~~~~~~~~~~~~g~i~~l~~~~~D~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~~ 574 (784)
+..+++..+.+..- .+++++.. +.-..+...|.+|++|+++..-. .....+.+ .++....+.++++..
T Consensus 103 ~l~~~l~~~~~~~P-~i~l~~~~-------~~~~~~~~~L~~g~~Dl~i~~~~---~~~~~~~~-~~l~~~~~~lv~~~~ 170 (317)
T PRK15421 103 WLTPALENFHKNWP-QVEMDFKS-------GVTFDPQPALQQGELDLVMTSDI---LPRSGLHY-SPMFDYEVRLVLAPD 170 (317)
T ss_pred HHHHHHHHHHHHCC-CceEEEEe-------CccHHHHHHHHCCCcCEEEecCc---ccCCCceE-EEeccceEEEEEcCC
Confidence 34566777776642 23354432 23457789999999999985422 22223433 667778888887555
No 457
>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=39.04 E-value=2.9e+02 Score=24.75 Aligned_cols=92 Identities=13% Similarity=-0.018 Sum_probs=55.6
Q ss_pred HHHHHHHHcCCcEEEEEEEcCCCcchhHHHHHHHHhccCcEEEEeeccC--CCCChhHH---HHHHHHhhcCCceEEEEe
Q 003958 154 AIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLS--VEATEDEI---TDLLVKVALTESRIIVVH 228 (784)
Q Consensus 154 ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~--~~~~~~d~---~~~l~~l~~~~~~vIvl~ 228 (784)
.+.+.+...+-....-+|.+.... .....+.+.++..|+.+....... ......|. .+.+..+.+.+.+.|++.
T Consensus 28 ~l~~~~~~~~~~~~~r~y~~~~~~-~~~~~~~~~L~~~g~~~~~~~~~~~~~~~~~~D~~l~~d~~~~~~~~~~d~ivLv 106 (149)
T cd06167 28 KLLEFLRDGGEIVLARAYGNWTSP-ERQRGFLDALRRLGFEPIQKPLRTRGSGKKGVDVALAIDALELAYKRRIDTIVLV 106 (149)
T ss_pred HHHHHHHhCCeEEEEEEEEecCCc-hhHHHHHHHHHHCCcEEEEEcceecCCcccCccHHHHHHHHHHhhhcCCCEEEEE
Confidence 444444443323333444433211 356778888999998887654321 11222333 333444444578999999
Q ss_pred ccCCcHHHHHHHHHHcCC
Q 003958 229 THYNRGPVVFHVAQYLGM 246 (784)
Q Consensus 229 ~~~~~~~~~~~~a~~~g~ 246 (784)
+...+...+++++++.|.
T Consensus 107 SgD~Df~~~i~~lr~~G~ 124 (149)
T cd06167 107 SGDSDFVPLVERLRELGK 124 (149)
T ss_pred ECCccHHHHHHHHHHcCC
Confidence 888899999999999863
No 458
>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=38.81 E-value=1.5e+02 Score=29.56 Aligned_cols=75 Identities=8% Similarity=-0.058 Sum_probs=48.5
Q ss_pred EEEEEE--cCCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHc
Q 003958 167 VIAIYV--DDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYL 244 (784)
Q Consensus 167 v~ii~~--d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~ 244 (784)
|++|.. ++.|.....+.+++.+++.|..+..... . .+...-...++++.+.+.+.|++..... ....++.+.+.
T Consensus 2 i~vi~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~-~--~~~~~~~~~i~~l~~~~vdgiii~~~~~-~~~~~~~l~~~ 77 (268)
T cd06298 2 VGVIIPDITNSYFAELARGIDDIATMYKYNIILSNS-D--NDKEKELKVLNNLLAKQVDGIIFMGGKI-SEEHREEFKRS 77 (268)
T ss_pred EEEEECCCcchHHHHHHHHHHHHHHHcCCeEEEEeC-C--CCHHHHHHHHHHHHHhcCCEEEEeCCCC-cHHHHHHHhcC
Confidence 566664 3567777888899999888887765432 1 2344455677777778899988864321 23455555554
Q ss_pred C
Q 003958 245 G 245 (784)
Q Consensus 245 g 245 (784)
+
T Consensus 78 ~ 78 (268)
T cd06298 78 P 78 (268)
T ss_pred C
Confidence 4
No 459
>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=38.78 E-value=2e+02 Score=25.43 Aligned_cols=74 Identities=9% Similarity=0.133 Sum_probs=47.6
Q ss_pred EEEEEEcCCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccC----CcHHHHHHHHH
Q 003958 167 VIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY----NRGPVVFHVAQ 242 (784)
Q Consensus 167 v~ii~~d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~----~~~~~~~~~a~ 242 (784)
|.+-....+--....+.+...|+..|++|.....+. .....++..++.++++|.+++.. +.+..++++++
T Consensus 5 v~~a~~g~D~Hd~g~~iv~~~l~~~GfeVi~lg~~~------s~e~~v~aa~e~~adii~iSsl~~~~~~~~~~~~~~L~ 78 (132)
T TIGR00640 5 ILVAKMGQDGHDRGAKVIATAYADLGFDVDVGPLFQ------TPEEIARQAVEADVHVVGVSSLAGGHLTLVPALRKELD 78 (132)
T ss_pred EEEEeeCCCccHHHHHHHHHHHHhCCcEEEECCCCC------CHHHHHHHHHHcCCCEEEEcCchhhhHHHHHHHHHHHH
Confidence 333333333334456677778889999987644332 23456777788999999998654 34556666677
Q ss_pred HcCC
Q 003958 243 YLGM 246 (784)
Q Consensus 243 ~~g~ 246 (784)
+.|.
T Consensus 79 ~~g~ 82 (132)
T TIGR00640 79 KLGR 82 (132)
T ss_pred hcCC
Confidence 7664
No 460
>KOG1545 consensus Voltage-gated shaker-like K+ channel KCNA [Inorganic ion transport and metabolism]
Probab=38.37 E-value=23 Score=36.35 Aligned_cols=40 Identities=18% Similarity=0.254 Sum_probs=32.3
Q ss_pred cCCceeehhhhhhhhhcc--cccccccchhhHHHHHHHHHHH
Q 003958 622 KRQVVTIFWFSFSTMFFA--HKEKTVSALGRLVLIIWLFVVL 661 (784)
Q Consensus 622 ~~~~~~~~~~~~~~~~~~--~~~~p~~~~~R~~~~~w~~~~l 661 (784)
..++.+++||++.+|..- |.-.|.+..|+|+.....+.+.
T Consensus 391 F~SIPdaFWwavVTMTTVGYGDm~P~TvgGKIVGslCAiaGV 432 (507)
T KOG1545|consen 391 FSSIPDAFWWAVVTMTTVGYGDMVPVTVGGKIVGSLCAIAGV 432 (507)
T ss_pred CCcCcccceEEEEEEEeeccccceecccCceehhhHHhhhhh
Confidence 346889999999999754 5668999999998887776665
No 461
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=38.24 E-value=2.5e+02 Score=29.19 Aligned_cols=79 Identities=6% Similarity=0.034 Sum_probs=51.3
Q ss_pred CcEEEEEEEc--CCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHH
Q 003958 164 WREVIAIYVD--DDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVA 241 (784)
Q Consensus 164 w~~v~ii~~d--~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a 241 (784)
-+.|+++..+ +.|.....+.+.+.+++.|..+..... . .+.......+..+...+.+.||+.... .....++.+
T Consensus 63 ~~~Igvi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~-~--~~~~~~~~~~~~~~~~~vdgiI~~~~~-~~~~~~~~l 138 (331)
T PRK14987 63 SRAIGVLLPSLTNQVFAEVLRGIESVTDAHGYQTMLAHY-G--YKPEMEQERLESMLSWNIDGLILTERT-HTPRTLKMI 138 (331)
T ss_pred CCEEEEEeCCCcchhHHHHHHHHHHHHHHCCCEEEEecC-C--CCHHHHHHHHHHHHhcCCCEEEEcCCC-CCHHHHHHH
Confidence 3578888754 557777888999999999988765321 1 123333456667777889999986432 223556666
Q ss_pred HHcCC
Q 003958 242 QYLGM 246 (784)
Q Consensus 242 ~~~g~ 246 (784)
.+.|.
T Consensus 139 ~~~~i 143 (331)
T PRK14987 139 EVAGI 143 (331)
T ss_pred HhCCC
Confidence 66553
No 462
>COG1638 DctP TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]
Probab=38.22 E-value=2.1e+02 Score=30.16 Aligned_cols=170 Identities=12% Similarity=0.061 Sum_probs=0.0
Q ss_pred HHHHHHHHHCCCccceEEeeCCCCCCCCChhHHHHHHHcCcccEEEeeEEeecCccccceeccccccccEEEEEeccCCc
Q 003958 498 DVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPVRKLD 577 (784)
Q Consensus 498 dl~~~l~~~l~f~~~~~~~~~~~~~~~~~~~g~i~~l~~~~~D~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~~~~~ 577 (784)
.+-+++.++.|=.+++++.+.+.- |.-..+++.|+.|..|+...+...-.. |...+....+=|+++-..
T Consensus 48 ~fa~~v~ekt~G~l~i~vfP~~qL---G~~~~~ie~l~~G~id~~~~s~~~l~~------~~P~~~v~~lPflf~d~~-- 116 (332)
T COG1638 48 KFAELVEEKTGGRLKIEVFPNSQL---GGEAEMIEQLRSGTLDIGVVSLGFLAG------LVPEFGVFDLPFLFRDEE-- 116 (332)
T ss_pred HHHHHHHHHhCCeEEEEECCCccc---CcHHHHHHHHhcCCeeEEeccchhhcc------cCCcceeecCCeeeCCHH--
Q ss_pred cccccccccccHHHHHHHHHHHHHHHHHhhheecccCCCCCCCccCCceeehhhhhhhhhcccccccccchhhHHHHHHH
Q 003958 578 SNAWAFLSPFTPMMWGVTAIFFLAVGAVVWILEHRLNDEFRGPPKRQVVTIFWFSFSTMFFAHKEKTVSALGRLVLIIWL 657 (784)
Q Consensus 578 ~~~~~~~~pf~~~~W~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~R~~~~~w~ 657 (784)
...+-++.++.--+.-.+---++...-....=.+.+...
T Consensus 117 ----~~~~~~~~~~g~~l~~~~e~~g~~~l~~~~~G~R~~t~~------------------------------------- 155 (332)
T COG1638 117 ----HARRVLDSEFGEELLKSLEAKGLKGLAFWENGFRQFTSN------------------------------------- 155 (332)
T ss_pred ----HHHHHHccHHHHHHHHHHHHcCCEEEEEecCceeeeecC-------------------------------------
Q ss_pred HHHHHHHhhccccceeeEeeccccCCCCChHhhhhCCCceEEeeCchHHHHHHhhcccCccCceeCCCHHHHHHHHhcCC
Q 003958 658 FVVLIINSSYTASLTSILTVQKLSSPIKGIDSLRSSNYPIGYQVNSFARNYLVDELNIDESRLVPLNSPEEYAKALKDGP 737 (784)
Q Consensus 658 ~~~lvl~~~Yta~L~s~l~~~~~~~~i~~~~dl~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~ 737 (784)
..||.+++||+ |.++-+..+.....+| +..+..+..| ...|.+.+|++
T Consensus 156 -----------------------k~PI~~peDlk--GlkiRv~~s~~~~~~~-~a~GA~P~pm----~f~Evy~aLqt-- 203 (332)
T COG1638 156 -----------------------KRPIKTPEDLK--GLKIRVPQSPLLLAMF-KALGANPTPM----PFAEVYTALQT-- 203 (332)
T ss_pred -----------------------CCCCCChHHhC--CCeeecCCCHHHHHHH-HHcCCCCCCC----CHHHHHHHHHc--
Q ss_pred cCCCeeEEEechhhhH
Q 003958 738 HKGGVAAVVDDRAYAE 753 (784)
Q Consensus 738 ~~~~~~a~~~~~~~~~ 753 (784)
|-+|+.-.....+.
T Consensus 204 --GvVDGqEnp~~~i~ 217 (332)
T COG1638 204 --GVVDGQENPLSNIY 217 (332)
T ss_pred --CCcccccCCHHHHh
No 463
>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=37.99 E-value=4.2e+02 Score=26.43 Aligned_cols=122 Identities=11% Similarity=0.014 Sum_probs=62.6
Q ss_pred eEEEEEEeecCCcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhcCceEEEccCchhhHH
Q 003958 31 VVNIGALLSFSTNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEGQTVAIIGPQDAVTSH 110 (784)
Q Consensus 31 ~i~IG~i~~~~~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~~v~aiiGp~~s~~~~ 110 (784)
.=+||.+.+...........|++-++++.|... + ..+..........+...+.+.+.+++++++.+|+.. ....+.
T Consensus 121 ~~~I~~i~~~~~~~~~~r~~gf~~~~~~~g~~~-~--~~~~~~~~~~~~~~~~~~~~~~~~ll~~~pdaI~~~-nd~~A~ 196 (265)
T cd06354 121 TGKVGFIGGMDIPLIRRFEAGFEAGVKYVNPGV-P--DIEVLVQYAGSFNDPAKGKEIAQAMYDQGADVIFAA-AGGTGN 196 (265)
T ss_pred CCeEEEEecccChHHHHHHHHHHHHHHHHhccC-C--CceEEEEEcCcccCHHHHHHHHHHHHHCCCcEEEEC-CCCCch
Confidence 345777654322222222368888887765221 1 122222222112234556667778887677888875 444455
Q ss_pred HHHHhhhcCCccEEecccCCCCCCcCCCCceEeecCChHHHHHHHHHH
Q 003958 111 VVSHVANELQVPLLSFSATDPTLSSLQFPYFVRTTQSDQYQMAAIAEI 158 (784)
Q Consensus 111 ~va~~~~~~~ip~Is~~a~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~ 158 (784)
.+...+...++.++++.... +.....|.+..+...-..++.-++..
T Consensus 197 gv~~al~~~gisIvGfD~~~--~~~~~~p~lttv~~~~~~~~~~~~~~ 242 (265)
T cd06354 197 GVFQAAKEAGVYAIGVDSDQ--YYLAPGVVLTSMVKRVDVAVYDAIKS 242 (265)
T ss_pred HHHHHHHhcCCeEEEecCcc--cccCCCcEEEEEeehhHHHHHHHHHH
Confidence 55566777777777765532 22223455555544334444333333
No 464
>KOG0498 consensus K+-channel ERG and related proteins, contain PAS/PAC sensor domain [Inorganic ion transport and metabolism; Signal transduction mechanisms]
Probab=37.81 E-value=21 Score=41.32 Aligned_cols=53 Identities=13% Similarity=0.157 Sum_probs=46.7
Q ss_pred ceeehhhhhhhhh--cccccccccchhhHHHHHHHHHHHHHHhhccccceeeEee
Q 003958 625 VVTIFWFSFSTMF--FAHKEKTVSALGRLVLIIWLFVVLIINSSYTASLTSILTV 677 (784)
Q Consensus 625 ~~~~~~~~~~~~~--~~~~~~p~~~~~R~~~~~w~~~~lvl~~~Yta~L~s~l~~ 677 (784)
+.-|+|+++.+|. +||...|..++..++.++.++++++|.++--+|+++++..
T Consensus 295 Y~~aLyw~l~tLstvG~g~~~s~~~~E~iFsi~~mi~GllL~A~lIGNmt~~iqs 349 (727)
T KOG0498|consen 295 YVYALYWGLSTLSTVGYGLVHANNMGEKIFSIFIMLFGLLLFAYLIGNMTALLQS 349 (727)
T ss_pred HHHHHHHHhhHhhhccCCccCCCCcHHHHHHHHHHHHhHHHHHHHHhhHHHhHHH
Confidence 5568999999987 5566688999999999999999999999999999999853
No 465
>cd06578 HemD Uroporphyrinogen-III synthase (HemD) catalyzes the asymmetrical cyclization of tetrapyrrole (linear) to uroporphyrinogen-III, the fourth step in the biosynthesis of heme. This ubiquitous enzyme is present in eukaryotes, bacteria and archaea. Mutations in the human uroporphyrinogen-III synthase gene cause congenital erythropoietic porphyria, a recessive inborn error of metabolism also known as Gunther disease.
Probab=37.50 E-value=3.9e+02 Score=25.92 Aligned_cols=117 Identities=7% Similarity=0.009 Sum_probs=64.5
Q ss_pred cCCccEEecccCC-CCCCcCCCCceEeecCChHHHHHHHHHHHHHc--CCcEEEEEEEcCCCcchhHHHHHHHHhccCcE
Q 003958 118 ELQVPLLSFSATD-PTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHY--GWREVIAIYVDDDHGRNGIAALGDTLAAKRCR 194 (784)
Q Consensus 118 ~~~ip~Is~~a~~-~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~--~w~~v~ii~~d~~~g~~~~~~l~~~l~~~gi~ 194 (784)
..+++.++.|... ..+...+++-.+. ++...+..+++++... .-.+|.++..+. ....+.+.+++.|..
T Consensus 76 ~~~~~~~avG~~Ta~~l~~~g~~~~~~---~~~~~~~~L~~~i~~~~~~~~~il~~~g~~-----~~~~l~~~L~~~g~~ 147 (239)
T cd06578 76 LAGLKIAAVGPKTAEALREAGLTADFV---PEEGDSEGLLELLELQDGKGKRILRPRGGR-----AREDLAEALRERGAE 147 (239)
T ss_pred ccCCEEEEECHHHHHHHHHcCCCceeC---CCccCHHHHHHHHHhcCCCCCEEEEEcCcc-----hhHHHHHHHHHCCCE
Confidence 3567777665432 2333333333332 2333467788887765 445555554332 356778888888887
Q ss_pred EEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHc
Q 003958 195 ISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYL 244 (784)
Q Consensus 195 v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~ 244 (784)
+.....+...... +.....+.+.+...+ +|++.++..+..+++...+.
T Consensus 148 v~~~~~Y~~~~~~-~~~~~~~~l~~~~~~-~iiftS~~~v~~f~~~~~~~ 195 (239)
T cd06578 148 VDEVEVYRTVPPD-LDAELLELLEEGAID-AVLFTSPSTVRNLLELLGKE 195 (239)
T ss_pred EEEEEEEEEECCC-CcHHHHHHHHcCCCc-EEEEeCHHHHHHHHHHHhhh
Confidence 7655544322111 112333444444444 56667778888888877654
No 466
>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=37.49 E-value=3.3e+02 Score=24.95 Aligned_cols=69 Identities=19% Similarity=0.164 Sum_probs=42.3
Q ss_pred eeeHHHHHHHHHHCCCccceEEeeCCCCCCCCChhHHHHHHHcCcccEEEeeEEeecCccccceeccccccccEEEEEec
Q 003958 494 GFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPV 573 (784)
Q Consensus 494 G~~~dl~~~l~~~l~f~~~~~~~~~~~~~~~~~~~g~i~~l~~~~~D~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~ 573 (784)
.+..+++..+.++.- .+++++.. +....++..+.+|++|+++...... ...+ ...++....++++++.
T Consensus 13 ~~l~~~l~~~~~~~P-~i~l~i~~-------~~~~~~~~~l~~~~~Dl~i~~~~~~---~~~~-~~~~l~~~~~~~~~~~ 80 (196)
T cd08450 13 QWLPEVLPILREEHP-DLDVELSS-------LFSPQLAEALMRGKLDVAFMRPEIQ---SDGI-DYQLLLKEPLIVVLPA 80 (196)
T ss_pred hhHHHHHHHHHhhCC-CcEEEEEe-------cChHHHHHHHhcCCccEEEEeCCCC---CCCc-EEEEEEccceEEEecC
Confidence 445667777777652 22355443 3466889999999999998542211 1223 2355667777777755
Q ss_pred c
Q 003958 574 R 574 (784)
Q Consensus 574 ~ 574 (784)
.
T Consensus 81 ~ 81 (196)
T cd08450 81 D 81 (196)
T ss_pred C
Confidence 4
No 467
>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=37.37 E-value=1.7e+02 Score=26.90 Aligned_cols=90 Identities=10% Similarity=-0.008 Sum_probs=45.9
Q ss_pred ChHhhhhCCCceEEeeCchHHHHHHhh---cccCccCceeCCCHHHHHHHHhcCCcCCCeeEEEechhhhHHHHcCCCCe
Q 003958 686 GIDSLRSSNYPIGYQVNSFARNYLVDE---LNIDESRLVPLNSPEEYAKALKDGPHKGGVAAVVDDRAYAELFLSTRCEF 762 (784)
Q Consensus 686 ~~~dl~~~~~~i~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~a~~~~~~~~~~~~~~~c~l 762 (784)
+++||.+... +....+......+.+. .+.........++.+...+.++. +...+++-+.. +....... .+
T Consensus 87 ~~~~l~~~~~-i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~----g~gi~~lp~~~-~~~~~~~~-~l 159 (194)
T cd08432 87 SPADLARHTL-LHDATRPEAWQWWLWAAGVADVDARRGPRFDDSSLALQAAVA----GLGVALAPRAL-VADDLAAG-RL 159 (194)
T ss_pred CHHHhhcCce-EEecCcccccHHHHhcCCeeccccCCeEEECCHHHHHHHHHh----CCCeEEeeHHH-hhhhhcCC-ce
Confidence 7889985443 3333333233433221 11222344456888888888888 55567777643 33333322 22
Q ss_pred E-EeCC-ccccceEEEEeeCCC
Q 003958 763 S-IVGQ-VFTKNGWGFVSIVSS 782 (784)
Q Consensus 763 ~-~~~~-~~~~~~~~~~~~k~s 782 (784)
. .... ......+.++.+++.
T Consensus 160 ~~~~~~~~~~~~~~~~~~~~~~ 181 (194)
T cd08432 160 VRPFDLPLPSGGAYYLVYPPGR 181 (194)
T ss_pred EeccccccCCCCCEEEEecccc
Confidence 2 1222 223456677777654
No 468
>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=37.28 E-value=2.3e+02 Score=25.06 Aligned_cols=99 Identities=12% Similarity=0.076 Sum_probs=47.2
Q ss_pred HHHHHHHHHHcCCcEEEEEEEcCCCcchhHHHHHHHHhccCcEEEEeeccC---CCCChhHHH---HHHHHhhcCCceEE
Q 003958 152 MAAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLS---VEATEDEIT---DLLVKVALTESRII 225 (784)
Q Consensus 152 ~~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~---~~~~~~d~~---~~l~~l~~~~~~vI 225 (784)
...+.+.+...+--....+|.+ ........+.+.++..|+.+....... ......|.. .++....+...+.+
T Consensus 22 ~~~l~~~i~~~~~~~~~~~y~~--~~~~~~~~~~~~L~~~g~~v~~~~~~~~~~~~k~~~D~~l~~d~~~~~~~~~~d~i 99 (146)
T PF01936_consen 22 FERLLEEIRKYGPLVRIRAYGN--WDDPNQKSFQEALQRAGIKVRHFPLRKRGGGGKKGVDVALAVDILELAYENPPDTI 99 (146)
T ss_dssp HHHHHHHHTTTEEEEEEEEEE------HHHHHHHHHHHHHT-EEEE------S---S---HHHHHHHHHHHG--GG-SEE
T ss_pred HHHHHHHHHhcCCeEEEEEEee--ccccchhhHHHHHHhCeeeEEeeecccccccccCCcHHHHHHHHHHHhhccCCCEE
Confidence 4556666655443323445544 222335777788888898776543321 112333332 22233323445888
Q ss_pred EEeccCCcHHHHHHHHHHcCCCCCCeEEEec
Q 003958 226 VVHTHYNRGPVVFHVAQYLGMLGTGYVWIAT 256 (784)
Q Consensus 226 vl~~~~~~~~~~~~~a~~~g~~~~~~~wi~~ 256 (784)
++.+...+...+++.+++.|. .+++..
T Consensus 100 vLvSgD~Df~~~v~~l~~~g~----~V~v~~ 126 (146)
T PF01936_consen 100 VLVSGDSDFAPLVRKLRERGK----RVIVVG 126 (146)
T ss_dssp EEE---GGGHHHHHHHHHH------EEEEEE
T ss_pred EEEECcHHHHHHHHHHHHcCC----EEEEEE
Confidence 888888889999999998773 345554
No 469
>PF00072 Response_reg: Response regulator receiver domain; InterPro: IPR001789 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. Bipartite response regulator proteins are involved in a two-component signal transduction system in bacteria, and certain eukaryotes like protozoa, that functions to detect and respond to environmental changes []. These systems have been detected during host invasion, drug resistance, motility, phosphate uptake, osmoregulation, and nitrogen fixation, amongst others []. The two-component system consists of a histidine protein kinase environmental sensor that phosphorylates the receiver domain of a response regulator protein; phosphorylation induces a conformational change in the response regulator, which activates the effector domain, triggering the cellular response []. The domains of the two-component proteins are highly modular, but the core structures and activities are maintained. The response regulators act as phosphorylation-activated switches to affect a cellular response, usually by transcriptional regulation. Most of these proteins consist of two domains, an N-terminal response regulator receiver domain, and a variable C-terminal effector domain with DNA-binding activity. This entry represents the response regulator receiver domain, which belongs to the CheY family, and receives the signal from the sensor partner in the two-component system.; GO: 0000156 two-component response regulator activity, 0000160 two-component signal transduction system (phosphorelay), 0006355 regulation of transcription, DNA-dependent; PDB: 2QR3_A 2QXY_A 1I3C_A 1JLK_A 2PKX_A 2PL1_A 3H1F_A 3H1E_A 3GWG_A 3H1G_A ....
Probab=37.19 E-value=2.1e+02 Score=23.61 Aligned_cols=58 Identities=10% Similarity=0.070 Sum_probs=37.9
Q ss_pred hhHHHHHHHHhccCc-EEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEec--cCCcHHHHHHHHHHcC
Q 003958 179 NGIAALGDTLAAKRC-RISFKAPLSVEATEDEITDLLVKVALTESRIIVVHT--HYNRGPVVFHVAQYLG 245 (784)
Q Consensus 179 ~~~~~l~~~l~~~gi-~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~--~~~~~~~~~~~a~~~g 245 (784)
...+.+++.++..|. .+.. .. +....++.+++..+++|++.. .......++++.++.+
T Consensus 9 ~~~~~l~~~l~~~~~~~v~~---~~------~~~~~~~~~~~~~~d~iiid~~~~~~~~~~~~~~i~~~~ 69 (112)
T PF00072_consen 9 EIRELLEKLLERAGYEEVTT---AS------SGEEALELLKKHPPDLIIIDLELPDGDGLELLEQIRQIN 69 (112)
T ss_dssp HHHHHHHHHHHHTTEEEEEE---ES------SHHHHHHHHHHSTESEEEEESSSSSSBHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHhCCCCEEEE---EC------CHHHHHHHhcccCceEEEEEeeecccccccccccccccc
Confidence 356677777777776 4432 21 234556666667788988873 3456778888887766
No 470
>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=37.02 E-value=4.4e+02 Score=26.38 Aligned_cols=119 Identities=14% Similarity=0.018 Sum_probs=63.9
Q ss_pred EEEEEeec-CCcchhhHHHHHHHHHHHHhcCCCCCCCCEEEEEEecCCCCHHHHHHHHHHHHhc--CceEEEccCchhhH
Q 003958 33 NIGALLSF-STNVGKVAKLAIKAAVDDVNSDPTTLGGTKLKLQMQDCNHSGFLALAEALHLMEG--QTVAIIGPQDAVTS 109 (784)
Q Consensus 33 ~IG~i~~~-~~~~g~~~~~a~~~Ave~IN~~~~il~g~~l~~~~~D~~~~~~~a~~~~~~li~~--~v~aiiGp~~s~~~ 109 (784)
+||.+... ..........|++-|+++.+ + +..+.......+...+.+.+.+++.+ ++.+|+.. +...+
T Consensus 120 ~I~~i~~~~~~~~~~~R~~gf~~a~~~~g----~----~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~-~d~~A 190 (269)
T cd06287 120 QIALIVGSARRNSYLEAEAAYRAFAAEHG----M----PPVVLRVDEAGGEEAGYAACAQLLAQHPDLDALCVP-VDAFA 190 (269)
T ss_pred cEEEEeCCcccccHHHHHHHHHHHHHHcC----C----CcceeEecCCCChHHHHHHHHHHHhCCCCCCEEEEc-CcHHH
Confidence 46666432 22223345577777777622 2 11112122233445566777777765 57888874 44555
Q ss_pred HHHHHhhhcCCc--cE-Eeccc-CCCCCCcCCCCceEeecCChHHHHHHHHHHHH
Q 003958 110 HVVSHVANELQV--PL-LSFSA-TDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVD 160 (784)
Q Consensus 110 ~~va~~~~~~~i--p~-Is~~a-~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~ 160 (784)
..+...+...++ |- |+..+ .+...+.-..|.+.....+....++..+++|.
T Consensus 191 ~gvl~al~~~gl~vP~dvsvig~~d~~~~~~~~p~ltti~~~~~~~g~~A~~~l~ 245 (269)
T cd06287 191 VGAVRAATELGRAVPDQLRVVTRYDGLRARTSEPPLTAVDLHLDEVAEQAVDLLF 245 (269)
T ss_pred HHHHHHHHHcCCCCCCceEEEeccCchhhccCCCCcccccCCHHHHHHHHHHHHH
Confidence 556666665554 42 33222 23223333346666667777788887777653
No 471
>COG1922 WecG Teichoic acid biosynthesis proteins [Cell envelope biogenesis, outer membrane]
Probab=36.80 E-value=2.5e+02 Score=28.02 Aligned_cols=99 Identities=13% Similarity=0.044 Sum_probs=54.7
Q ss_pred HHHHHHHHHHHcCCcEEEEEEEcCCCcchhHHHHHHHHhccCcEEEEee-ccCCCCChhHHHHHHHHhhcCCceEEEEec
Q 003958 151 QMAAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKA-PLSVEATEDEITDLLVKVALTESRIIVVHT 229 (784)
Q Consensus 151 ~~~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~~l~~~gi~v~~~~-~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~ 229 (784)
...++.+.+..- -++|.++....+-.....+.++.... +..|+... -+. ...++ ..++++|+++++|++++..
T Consensus 96 l~~~Ll~~a~~~-~~~vfllGgkp~V~~~a~~~l~~~~p--~l~ivg~h~GYf--~~~e~-~~i~~~I~~s~pdil~Vgm 169 (253)
T COG1922 96 LVEALLKRAAEE-GKRVFLLGGKPGVAEQAAAKLRAKYP--GLKIVGSHDGYF--DPEEE-EAIVERIAASGPDILLVGM 169 (253)
T ss_pred HHHHHHHHhCcc-CceEEEecCCHHHHHHHHHHHHHHCC--CceEEEecCCCC--ChhhH-HHHHHHHHhcCCCEEEEeC
Confidence 345555555444 45677777655433344444444333 34555443 222 12333 6899999999999999986
Q ss_pred cCCcHHHHHHHHHHcCCCCCCeEEEecCc
Q 003958 230 HYNRGPVVFHVAQYLGMLGTGYVWIATSW 258 (784)
Q Consensus 230 ~~~~~~~~~~~a~~~g~~~~~~~wi~~~~ 258 (784)
..+.-..++..-++.- +.-++++.++
T Consensus 170 G~P~QE~wi~~~~~~~---~~~v~igVGg 195 (253)
T COG1922 170 GVPRQEIWIARNRQQL---PVAVAIGVGG 195 (253)
T ss_pred CCchhHHHHHHhHHhc---CCceEEeccc
Confidence 5555445554444321 2335666553
No 472
>PRK05569 flavodoxin; Provisional
Probab=36.76 E-value=2.4e+02 Score=25.05 Aligned_cols=85 Identities=8% Similarity=0.052 Sum_probs=0.0
Q ss_pred cEEEEEE-EcCCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccC--------CcHH
Q 003958 165 REVIAIY-VDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY--------NRGP 235 (784)
Q Consensus 165 ~~v~ii~-~d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~--------~~~~ 235 (784)
+++.|+| +..-..+..++.+.+.+++.|..+.....-. .+..++ .+.+.|++.+.. ....
T Consensus 2 ~ki~iiY~S~tGnT~~iA~~i~~~~~~~g~~v~~~~~~~--~~~~~~---------~~~d~iilgsPty~~~~~~~~~~~ 70 (141)
T PRK05569 2 KKVSIIYWSCGGNVEVLANTIADGAKEAGAEVTIKHVAD--AKVEDV---------LEADAVAFGSPSMDNNNIEQEEMA 70 (141)
T ss_pred CeEEEEEECCCCHHHHHHHHHHHHHHhCCCeEEEEECCc--CCHHHH---------hhCCEEEEECCCcCCCcCChHHHH
Q ss_pred HHHHHHHHcCCCCCCeEEEecCccc
Q 003958 236 VVFHVAQYLGMLGTGYVWIATSWLS 260 (784)
Q Consensus 236 ~~~~~a~~~g~~~~~~~wi~~~~~~ 260 (784)
.++.........+.....+.+.+|.
T Consensus 71 ~~~~~l~~~~~~~K~v~~f~t~g~~ 95 (141)
T PRK05569 71 PFLDQFKLTPNENKKCILFGSYGWD 95 (141)
T ss_pred HHHHHhhccCcCCCEEEEEeCCCCC
No 473
>TIGR00067 glut_race glutamate racemase. The most closely related proteins differing in function are aspartate racemases.
Probab=36.59 E-value=2.6e+02 Score=27.99 Aligned_cols=126 Identities=7% Similarity=0.006 Sum_probs=66.1
Q ss_pred HHHH-hcCceEEEccCchhhHHHHHHhhhcCCccEEecc-cCCCCCCc-CCCCceEeecCChHHHHHHHHHHHHHcCCcE
Q 003958 90 LHLM-EGQTVAIIGPQDAVTSHVVSHVANELQVPLLSFS-ATDPTLSS-LQFPYFVRTTQSDQYQMAAIAEIVDHYGWRE 166 (784)
Q Consensus 90 ~~li-~~~v~aiiGp~~s~~~~~va~~~~~~~ip~Is~~-a~~~~l~~-~~~p~~~r~~ps~~~~~~ai~~~l~~~~w~~ 166 (784)
..|. +.++.+|+=+-.+.++.....+-+..++|+|+.. .+...... .....+-=+..+.+......-+.+++++.+-
T Consensus 54 ~~L~~~~g~d~ivIaCNTA~a~~~~~l~~~~~iPii~iie~~v~~a~~~~~~~~IgvLAT~~Ti~s~~y~~~i~~~~~~~ 133 (251)
T TIGR00067 54 TFLKERHNIKLLVVACNTASALALEDLQRNFDFPVVGVIEPAIKAAIRLTANGRVLVIATNATIKSNAYHEALKEIANDL 133 (251)
T ss_pred HHHHHhCCCCEEEEeCchHHHHHHHHHHHHCCCCEEeecHHHHHHHHHhCCCCeEEEEeCHHHHhhhHHHHHHHHhCCCC
Confidence 3454 4589888876666665667777778899999832 11111111 1111233334444555666667777766552
Q ss_pred EEEEEEcCCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccC
Q 003958 167 VIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY 231 (784)
Q Consensus 167 v~ii~~d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~ 231 (784)
. +.+.. . ..+-... +.|. .........+...++.+++.+++.||+.|..
T Consensus 134 ~--v~~~~--~----~~lv~~I-e~g~-------~~~~~~~~~l~~~l~~l~~~~~d~lILGCTh 182 (251)
T TIGR00067 134 L--VEMLA--C----PELVPLA-EAGL-------LGEDYALECLKRYLRPLLDTLPDTVVLGCTH 182 (251)
T ss_pred E--EEecC--C----HHHHHHH-HcCC-------cCCHHHHHHHHHHHHHHhcCCCCEEEECcCC
Confidence 2 22211 1 1111112 2231 1100122346777777777789999998764
No 474
>PRK09189 uroporphyrinogen-III synthase; Validated
Probab=36.52 E-value=86 Score=31.10 Aligned_cols=114 Identities=12% Similarity=0.067 Sum_probs=63.5
Q ss_pred CccEEeccc-CCCCCCcCCCCceEeecCChHHHHHHHHHHHHHc--CCcEEEEEEEcCCCcchhHHHHHHHHhccCcEEE
Q 003958 120 QVPLLSFSA-TDPTLSSLQFPYFVRTTQSDQYQMAAIAEIVDHY--GWREVIAIYVDDDHGRNGIAALGDTLAAKRCRIS 196 (784)
Q Consensus 120 ~ip~Is~~a-~~~~l~~~~~p~~~r~~ps~~~~~~ai~~~l~~~--~w~~v~ii~~d~~~g~~~~~~l~~~l~~~gi~v~ 196 (784)
+++.+..|. |...+.+.++..+ .|. ...+..+++++... .-++|.++..+. ..+.+.+.+++.|+.|.
T Consensus 75 ~~~~~aVG~~Ta~~l~~~G~~~~---~~~-~~~~e~L~~~~~~~~~~~~~vL~~rg~~-----~r~~l~~~L~~~G~~v~ 145 (240)
T PRK09189 75 ALPLFAVGEATAEAARELGFRHV---IEG-GGDGVRLAETVAAALAPTARLLYLAGRP-----RAPVFEDRLAAAGIPFR 145 (240)
T ss_pred CCeEEEEcHHHHHHHHHcCCCCC---cCC-CCCHHHHHHHHHHhcCCCCcEEEeccCc-----ccchhHHHHHhCCCeeE
Confidence 456655543 2333333333322 232 23467777776543 457777777443 35678888999998876
Q ss_pred EeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHH
Q 003958 197 FKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQY 243 (784)
Q Consensus 197 ~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~ 243 (784)
....|.......+.......+++.+.++|++.+ +..+..|++....
T Consensus 146 ~~~vY~~~~~~~~~~~~~~~l~~~~~d~i~f~S-~~~~~~f~~~~~~ 191 (240)
T PRK09189 146 VAECYDMLPVMYSPATLSAILGGAPFDAVLLYS-RVAARRFFALMRL 191 (240)
T ss_pred EEEEEEeecCCCChHHHHHHHhcCCCCEEEEeC-HHHHHHHHHHHhh
Confidence 655443211112223444555666777766654 5567778776643
No 475
>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=36.39 E-value=1.2e+02 Score=31.21 Aligned_cols=77 Identities=8% Similarity=0.044 Sum_probs=45.9
Q ss_pred EEEEE--cCCCcchhHHHHHHHHhccCc-EEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccC-CcHHHHHHHHHH
Q 003958 168 IAIYV--DDDHGRNGIAALGDTLAAKRC-RISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY-NRGPVVFHVAQY 243 (784)
Q Consensus 168 ~ii~~--d~~~g~~~~~~l~~~l~~~gi-~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~-~~~~~~~~~a~~ 243 (784)
++|.. ++.|.....+.+++.+++.|. .+.....- ..+......+++.+...+++.|++.... +.....++++.+
T Consensus 2 gvi~~~~~~~f~~~~~~gi~~~a~~~g~~~~i~~~~~--~~d~~~q~~~i~~l~~~~vdgiIi~~~~~~~~~~~l~~~~~ 79 (302)
T TIGR02637 2 GLVVKSLGNPFFEAANKGAEEAAKELGSVYIIYTGPT--GTTAEGQIEVVNSLIAQKVDAIAISANDPDALVPALKKAMK 79 (302)
T ss_pred EEEeccCCCHHHHHHHHHHHHHHHHhCCeeEEEECCC--CCCHHHHHHHHHHHHHcCCCEEEEeCCChHHHHHHHHHHHH
Confidence 44443 355666777888888888884 33321111 1233445567777777788888886432 334456777777
Q ss_pred cCC
Q 003958 244 LGM 246 (784)
Q Consensus 244 ~g~ 246 (784)
.|.
T Consensus 80 ~gi 82 (302)
T TIGR02637 80 RGI 82 (302)
T ss_pred CCC
Confidence 653
No 476
>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=36.37 E-value=4.5e+02 Score=26.26 Aligned_cols=68 Identities=13% Similarity=0.100 Sum_probs=42.2
Q ss_pred eeHHHHHHHHHHCCCccceEEeeCCCCCCCCChhHHHHHHHcCcccEEEeeEEeecCccccceeccccccccEEEEEecc
Q 003958 495 FCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPVR 574 (784)
Q Consensus 495 ~~~dl~~~l~~~l~f~~~~~~~~~~~~~~~~~~~g~i~~l~~~~~D~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~~ 574 (784)
+..+++..+.+... .+++++.. +....++..+.+|++|+++..-..+. ..+ -..|+....+++++++.
T Consensus 98 ~~~~~l~~~~~~~p-~v~l~i~~-------~~~~~~~~~l~~g~~Dl~i~~~~~~~---~~~-~~~~l~~~~~~lv~s~~ 165 (279)
T TIGR03339 98 YVLDLVARFRQRYP-GIEVSVRI-------GNSQEVLQALQSYRVDVAVSSEVVDD---PRL-DRVVLGNDPLVAVVHRQ 165 (279)
T ss_pred HHHHHHHHHHHHCC-CcEEEEEE-------CCHHHHHHHHHcCCCcEEEEecccCC---Cce-EEEEcCCceEEEEECCC
Confidence 45567777776653 22344432 34678899999999999986433221 122 23566777788877554
No 477
>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=36.09 E-value=2e+02 Score=28.57 Aligned_cols=75 Identities=11% Similarity=0.104 Sum_probs=48.1
Q ss_pred EEEEEE--cCCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHc
Q 003958 167 VIAIYV--DDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYL 244 (784)
Q Consensus 167 v~ii~~--d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~ 244 (784)
|++|.. ++.|.....+.+++.+++.|+.+.... . ..+.......++.+...+.|.|++....... ..++++.+.
T Consensus 2 igvi~~~~~~~~~~~~~~~i~~~a~~~g~~~~~~~--~-~~~~~~~~~~~~~l~~~~~dgiii~~~~~~~-~~l~~~~~~ 77 (267)
T cd06283 2 IGVIVADITNPFSSLVLKGIEDVCRAHGYQVLVCN--S-DNDPEKEKEYLESLLAYQVDGLIVNPTGNNK-ELYQRLAKN 77 (267)
T ss_pred EEEEecCCccccHHHHHHHHHHHHHHcCCEEEEEc--C-CCCHHHHHHHHHHHHHcCcCEEEEeCCCCCh-HHHHHHhcC
Confidence 455553 456777888899999999998775422 1 1233445567777777888988886543333 235666554
Q ss_pred C
Q 003958 245 G 245 (784)
Q Consensus 245 g 245 (784)
+
T Consensus 78 ~ 78 (267)
T cd06283 78 G 78 (267)
T ss_pred C
Confidence 4
No 478
>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=35.97 E-value=1.3e+02 Score=30.97 Aligned_cols=71 Identities=6% Similarity=0.039 Sum_probs=48.2
Q ss_pred cCCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccC-CcHHHHHHHHHHcCC
Q 003958 173 DDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY-NRGPVVFHVAQYLGM 246 (784)
Q Consensus 173 d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~-~~~~~~~~~a~~~g~ 246 (784)
+++|.....+.+++.+++.|..+..... ..+......+++.+...++|.|++.... ......++++.+.+.
T Consensus 9 ~~~~~~~~~~~i~~~a~~~g~~v~~~~~---~~~~~~q~~~i~~l~~~~vDgIIi~~~~~~~~~~~l~~~~~~~i 80 (302)
T TIGR02634 9 RLERWQKDRDIFVAAAESLGAKVFVQSA---NGNEAKQISQIENLIARGVDVLVIIPQNGQVLSNAVQEAKDEGI 80 (302)
T ss_pred chhhHHHHHHHHHHHHHhcCCEEEEEeC---CCCHHHHHHHHHHHHHcCCCEEEEeCCChhHHHHHHHHHHHCCC
Confidence 5667778888899999999988765321 1233445567777777889988887543 334567777777653
No 479
>PF02401 LYTB: LytB protein; InterPro: IPR003451 Terpenes are among the largest groups of natural products and include compounds such as vitamins, cholesterol and carotenoids. The biosynthesis of all terpenoids begins with one or both of the two C5 precursors of the pathway: isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). In animals, fungi, and certain bacteria, the synthesis of IPP and DMAPP occurs via the well-known mevalonate pathway, however, a second, nonmevalonate terpenoid pathway has been identified in many eubacteria, algae and the chloroplasts of higher plants []. LytB(IspH) catalyses the conversion of 1-hydroy-2-methyl-2-(E)-butenyl 4-diphosphate into IPP and DMAPP in this second pathway The enzyme appears to be responsible for a branch-step in the nonmevalonate pathway, in that IPP and DMAPP are produced in parallel from a single precursor although the exact mechanism of this is not currently fully understood []. Escherichia coli LytB protein had been found to regulate the activity of RelA (guanosine 3',5'-bispyrophosphate synthetase I), which in turn controls the level of a regulatory metabolite. It is involved in penicillin tolerance and the stringent response [].; GO: 0019288 isopentenyl diphosphate biosynthetic process, mevalonate-independent pathway, 0055114 oxidation-reduction process; PDB: 3DNF_B 3SZL_B 3KE8_B 3KEF_B 3SZU_A 3KEL_A 3F7T_B 3KE9_B 3KEM_B 3T0G_A ....
Probab=35.68 E-value=2.1e+02 Score=29.23 Aligned_cols=55 Identities=15% Similarity=0.178 Sum_probs=37.4
Q ss_pred EEEEecCCCCHHHHHHHHH-HHHhc-CceEEEccCchhhHHHHHHhhhcCCccEEec
Q 003958 72 KLQMQDCNHSGFLALAEAL-HLMEG-QTVAIIGPQDAVTSHVVSHVANELQVPLLSF 126 (784)
Q Consensus 72 ~~~~~D~~~~~~~a~~~~~-~li~~-~v~aiiGp~~s~~~~~va~~~~~~~ip~Is~ 126 (784)
+..+.|+=|+...-.+.+. +|..+ .+..|||+..|+.+..++++|...+.|.+-.
T Consensus 185 ~~~~~nTIC~aT~~RQ~a~~~La~~vD~miVIGg~~SsNT~kL~eia~~~~~~t~~I 241 (281)
T PF02401_consen 185 EGPVFNTICYATQNRQEAARELAKEVDAMIVIGGKNSSNTRKLAEIAKEHGKPTYHI 241 (281)
T ss_dssp E-SCC-S--CHHHHHHHHHHHHHCCSSEEEEES-TT-HHHHHHHHHHHHCTTCEEEE
T ss_pred cCCCCCCCCHhHHHHHHHHHHHHhhCCEEEEecCCCCccHHHHHHHHHHhCCCEEEe
Confidence 3357888887776665444 55444 7888899999999999999999998877654
No 480
>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=35.63 E-value=2.2e+02 Score=28.27 Aligned_cols=76 Identities=8% Similarity=0.064 Sum_probs=46.8
Q ss_pred EEEEEE--cCCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHHHHHc
Q 003958 167 VIAIYV--DDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHVAQYL 244 (784)
Q Consensus 167 v~ii~~--d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~a~~~ 244 (784)
|++|.. ++.+.....+.+++.+++.|..+.....-. .+.......++.+.+.+.+.|++........ .+.++.+.
T Consensus 2 i~vi~~~~~~~~~~~~~~gi~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~l~~~~vdgiii~~~~~~~~-~~~~~~~~ 78 (264)
T cd01574 2 IGVVTTDLALHGPSSTLAAIESAAREAGYAVTLSMLAE--ADEEALRAAVRRLLAQRVDGVIVNAPLDDAD-AALAAAPA 78 (264)
T ss_pred EEEEeCCCCcccHHHHHHHHHHHHHHCCCeEEEEeCCC--CchHHHHHHHHHHHhcCCCEEEEeCCCCChH-HHHHHHhc
Confidence 566664 355677788899999999888766432111 1224455667777777889988865443333 23344444
Q ss_pred C
Q 003958 245 G 245 (784)
Q Consensus 245 g 245 (784)
|
T Consensus 79 ~ 79 (264)
T cd01574 79 D 79 (264)
T ss_pred C
Confidence 4
No 481
>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=35.54 E-value=3.6e+02 Score=24.82 Aligned_cols=71 Identities=8% Similarity=0.034 Sum_probs=43.7
Q ss_pred eeeHHHHHHHHHHCCCccceEEeeCCCCCCCCChhHHHHHHHcCcccEEEeeEEeecCccccceeccccccccEEEEEec
Q 003958 494 GFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPV 573 (784)
Q Consensus 494 G~~~dl~~~l~~~l~f~~~~~~~~~~~~~~~~~~~g~i~~l~~~~~D~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~ 573 (784)
.+..+++..+.++.- ++++++.. +....+++.|.+|++|+++.... .......++ ..++....++++++.
T Consensus 13 ~~l~~~l~~~~~~~P-~v~i~~~~-------~~~~~~~~~l~~g~~Dl~i~~~~-~~~~~~~l~-~~~l~~~~~~~~~~~ 82 (198)
T cd08437 13 YYFPKLAKDLIKTGL-MIQIDTYE-------GGSAELLEQLLQGDLDIALLGSL-TPLENSALH-SKIIKTQHFMIIVSK 82 (198)
T ss_pred HHhHHHHHHHHHhCC-ceEEEEEE-------cCHHHHHHHHHcCCCCEEEecCC-CCCCcccce-EEEeecceEEEEecC
Confidence 345677777777753 33355543 34678899999999999985321 111222333 356777777777755
Q ss_pred c
Q 003958 574 R 574 (784)
Q Consensus 574 ~ 574 (784)
.
T Consensus 83 ~ 83 (198)
T cd08437 83 D 83 (198)
T ss_pred C
Confidence 4
No 482
>PRK00843 egsA NAD(P)-dependent glycerol-1-phosphate dehydrogenase; Reviewed
Probab=35.50 E-value=1.6e+02 Score=31.29 Aligned_cols=82 Identities=9% Similarity=0.028 Sum_probs=53.5
Q ss_pred HHHHHHHHHcCC-cEEEEEEEcCCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccC
Q 003958 153 AAIAEIVDHYGW-REVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY 231 (784)
Q Consensus 153 ~ai~~~l~~~~w-~~v~ii~~d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~ 231 (784)
..+.++++.++. +++.+|++...+. ...+.+++.+++.| .+... +.+..+.+.....++.+++.+.++||-.+.+
T Consensus 22 ~~l~~~l~~~~~~~~~livtd~~~~~-~~~~~l~~~l~~~~-~~~~~--~~~~~t~~~v~~~~~~~~~~~~d~IIaiGGG 97 (350)
T PRK00843 22 DDIGDVCSDLKLTGRALIVTGPTTKK-IAGDRVEENLEDAG-DVEVV--IVDEATMEEVEKVEEKAKDVNAGFLIGVGGG 97 (350)
T ss_pred HHHHHHHHHhCCCCeEEEEECCcHHH-HHHHHHHHHHHhcC-CeeEE--eCCCCCHHHHHHHHHHhhccCCCEEEEeCCc
Confidence 345667777775 7888888655543 34567888887776 44322 3333566778888888888889998876543
Q ss_pred --CcHHHHH
Q 003958 232 --NRGPVVF 238 (784)
Q Consensus 232 --~~~~~~~ 238 (784)
-++..++
T Consensus 98 sv~D~ak~v 106 (350)
T PRK00843 98 KVIDVAKLA 106 (350)
T ss_pred hHHHHHHHH
Confidence 3344444
No 483
>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=35.48 E-value=3.5e+02 Score=24.72 Aligned_cols=71 Identities=13% Similarity=-0.002 Sum_probs=42.5
Q ss_pred eeeHHHHHHHHHHCCCccceEEeeCCCCCCCCChhHHHHHHHcCcccEEEeeEEeecCccccceeccccccccEEEEEec
Q 003958 494 GFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDIAIITNRTKMADFTQPYIESGLVVVAPV 573 (784)
Q Consensus 494 G~~~dl~~~l~~~l~f~~~~~~~~~~~~~~~~~~~g~i~~l~~~~~D~~~~~~~~t~~r~~~~~fs~p~~~~~~~~~~~~ 573 (784)
.+...++..+.++.. .+++++.. +....++..+.+|++|+++....... +...+. ..++....+.++++.
T Consensus 13 ~~l~~~l~~~~~~~P-~i~i~~~~-------~~~~~~~~~l~~~~~Dl~i~~~~~~~-~~~~~~-~~~l~~~~~~~v~~~ 82 (197)
T cd08449 13 GGLGPALRRFKRQYP-NVTVRFHE-------LSPEAQKAALLSKRIDLGFVRFADTL-NDPPLA-SELLWREPMVVALPE 82 (197)
T ss_pred hhHHHHHHHHHHHCC-CeEEEEEE-------CCHHHHHHHHhCCCccEEEecccccC-CCCCce-EEEEEEeeEEEEecC
Confidence 345677777777752 23355442 34678899999999999985332210 112222 345666777777654
Q ss_pred c
Q 003958 574 R 574 (784)
Q Consensus 574 ~ 574 (784)
.
T Consensus 83 ~ 83 (197)
T cd08449 83 E 83 (197)
T ss_pred C
Confidence 3
No 484
>PF13155 Toprim_2: Toprim-like
Probab=35.05 E-value=51 Score=27.05 Aligned_cols=41 Identities=12% Similarity=0.314 Sum_probs=34.6
Q ss_pred HHHHHHHHHHcCCcEEEEEEEcCCCcchhHHHHHHHHhccC
Q 003958 152 MAAIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKR 192 (784)
Q Consensus 152 ~~ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~~l~~~g 192 (784)
...+.++++..+-++|.+..++|.-|+...+.+.+.+...+
T Consensus 35 ~~~~~~~l~~~~~~~i~l~~DnD~aG~~~~~~~~~~l~~~~ 75 (96)
T PF13155_consen 35 EKQQIKFLKENPYKKIVLAFDNDEAGRKAAEKLQKELKEEG 75 (96)
T ss_pred HHHHHHHHHhCCCCcEEEEeCCCHHHHHHHHHHHHHHHhhC
Confidence 35788888776668888888999999999999999998876
No 485
>TIGR03850 bind_CPR_0540 carbohydrate ABC transporter substrate-binding protein, CPR_0540 family. Members of this protein are the substrate-binding protein of a predicted carbohydrate transporter operon, together with permease subunits of ABC transporter homology families. This substrate-binding protein frequently co-occurs in genomes with a family of disaccharide phosphorylases, TIGR02336, suggesting that the molecule transported will include beta-D-galactopyranosyl-(1-3)-N-acetyl-D-glucosamine and related carbohydrates. Members of this family are sporadically strain by strain, often in species with a human host association, including Propionibacterium acnes and Clostridium perfringens, and Bacillus cereus.
Probab=34.98 E-value=1.2e+02 Score=33.30 Aligned_cols=24 Identities=17% Similarity=0.291 Sum_probs=17.2
Q ss_pred HHHHHHHHHHhcCCCCCCCCEEEEEEe
Q 003958 50 LAIKAAVDDVNSDPTTLGGTKLKLQMQ 76 (784)
Q Consensus 50 ~a~~~Ave~IN~~~~il~g~~l~~~~~ 76 (784)
..++-.+++.|+.. ||+++++...
T Consensus 48 ~~~~~~~~~F~~~~---~~i~V~~~~~ 71 (437)
T TIGR03850 48 KMWEEVVEAFEKSH---EGVKVELTVS 71 (437)
T ss_pred HHHHHHHHHHHHHC---CCceEEEEeC
Confidence 45667888888874 5778888754
No 486
>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=34.77 E-value=1.2e+02 Score=30.49 Aligned_cols=71 Identities=8% Similarity=0.130 Sum_probs=49.2
Q ss_pred cCCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccC-CcHHHHHHHHHHcCC
Q 003958 173 DDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY-NRGPVVFHVAQYLGM 246 (784)
Q Consensus 173 d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~-~~~~~~~~~a~~~g~ 246 (784)
++.|.....+.+.+.+++.|+.+.....- .+.......++.+...+++.||+.... ......++++.+.+.
T Consensus 10 ~~~~~~~~~~~~~~~a~~~g~~~~~~~~~---~~~~~~~~~i~~l~~~~vdgiIi~~~~~~~~~~~i~~~~~~~i 81 (273)
T cd06309 10 ESPWRTAETKSIKDAAEKRGFDLKFADAQ---QKQENQISAIRSFIAQGVDVIILAPVVETGWDPVLKEAKAAGI 81 (273)
T ss_pred CCHHHHHHHHHHHHHHHhcCCEEEEeCCC---CCHHHHHHHHHHHHHcCCCEEEEcCCccccchHHHHHHHHCCC
Confidence 46677788899999999999988764321 234455577778877889998886433 223456777777653
No 487
>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=34.49 E-value=2e+02 Score=28.72 Aligned_cols=62 Identities=10% Similarity=-0.001 Sum_probs=44.4
Q ss_pred EEEEEEc--CCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccC
Q 003958 167 VIAIYVD--DDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY 231 (784)
Q Consensus 167 v~ii~~d--~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~ 231 (784)
|+++..+ +.|.....+.+.+.+++.|..+...... .+...-...++.+...+.|.||+....
T Consensus 2 Ig~i~~~~~~~~~~~~~~gi~~~~~~~gy~v~~~~~~---~~~~~~~~~i~~~~~~~~dgiii~~~~ 65 (269)
T cd06293 2 IGLVVPDIANPFFAELADAVEEEADARGLSLVLCATR---NRPERELTYLRWLDTNHVDGLIFVTNR 65 (269)
T ss_pred EEEEeCCCCCCcHHHHHHHHHHHHHHCCCEEEEEeCC---CCHHHHHHHHHHHHHCCCCEEEEeCCC
Confidence 6777753 5677788899999999999887654322 233445577777888899999987543
No 488
>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=34.26 E-value=3e+02 Score=29.13 Aligned_cols=91 Identities=10% Similarity=-0.028 Sum_probs=54.3
Q ss_pred HHHHHHHHcCCcEEEEEEEcCCCcchhHHHHHHHHhc-cCcEEEEeeccCCCCChhHHHHHHHHhhc---CCceEEEEec
Q 003958 154 AIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAA-KRCRISFKAPLSVEATEDEITDLLVKVAL---TESRIIVVHT 229 (784)
Q Consensus 154 ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~~l~~-~gi~v~~~~~~~~~~~~~d~~~~l~~l~~---~~~~vIvl~~ 229 (784)
.+.++++.++-+++.+|++..... ...+.+.+.+++ .++.+..........+.+.....+..+++ .+.+.||..+
T Consensus 13 ~l~~~~~~~~~~k~livtd~~v~~-~~~~~v~~~L~~~~~~~~~~~~~~e~~k~~~~v~~~~~~~~~~~~~r~d~IIaiG 91 (344)
T cd08169 13 SVESYTTRDLFDQYFFISDSGVAD-LIAHYIAEYLSKILPVHILVIEGGEEYKTFETVTRILERAIALGANRRTAIVAVG 91 (344)
T ss_pred HHHHHHHhcCCCeEEEEECccHHH-HHHHHHHHHHHhhcCceEEEeCCCCCCCCHHHHHHHHHHHHHcCCCCCcEEEEEC
Confidence 455667777778998888554432 566778888876 56654332222223355566777777765 4488888765
Q ss_pred cC--CcHHHHHHHHHHcC
Q 003958 230 HY--NRGPVVFHVAQYLG 245 (784)
Q Consensus 230 ~~--~~~~~~~~~a~~~g 245 (784)
.+ -++..++......|
T Consensus 92 GGsv~D~ak~vA~~~~rg 109 (344)
T cd08169 92 GGATGDVAGFVASTLFRG 109 (344)
T ss_pred CcHHHHHHHHHHHHhccC
Confidence 43 44555554443334
No 489
>PLN02821 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate reductase
Probab=34.18 E-value=1.8e+02 Score=31.71 Aligned_cols=57 Identities=9% Similarity=0.102 Sum_probs=43.8
Q ss_pred CEEEEEEecCCCCHHHHHH-HHHHHHhc--CceEEEccCchhhHHHHHHhhhcCCccEEe
Q 003958 69 TKLKLQMQDCNHSGFLALA-EALHLMEG--QTVAIIGPQDAVTSHVVSHVANELQVPLLS 125 (784)
Q Consensus 69 ~~l~~~~~D~~~~~~~a~~-~~~~li~~--~v~aiiGp~~s~~~~~va~~~~~~~ip~Is 125 (784)
..-++.++|+=|++..-.+ ++.+|..+ .+..|||+..|+.+..++++|...++|..-
T Consensus 334 ~~~~~~vfnTIC~ATqeRQdA~~~L~~~~vDlmiVVGG~NSSNT~~L~eIa~~~g~~sy~ 393 (460)
T PLN02821 334 VNDHFMSFNTICDATQERQDAMYKLVEEKLDLMLVVGGWNSSNTSHLQEIAEHKGIPSYW 393 (460)
T ss_pred cCccccccCCcchhHHHHHHHHHHHhhcCCCEEEEECCCCCccHHHHHHHHHHhCCCEEE
Confidence 3345677899887766554 45566543 788889999999999999999999998654
No 490
>COG5510 Predicted small secreted protein [Function unknown]
Probab=34.15 E-value=51 Score=22.46 Aligned_cols=21 Identities=10% Similarity=0.252 Sum_probs=10.5
Q ss_pred CchhhHHHHHHHHHHHHHHhh
Q 003958 1 MKLSGVMLLMIFYCELFVYRI 21 (784)
Q Consensus 1 M~~~~~~~~~~~~~~~~~~~~ 21 (784)
||+...+..+++++++++.+|
T Consensus 2 mk~t~l~i~~vll~s~llaaC 22 (44)
T COG5510 2 MKKTILLIALVLLASTLLAAC 22 (44)
T ss_pred chHHHHHHHHHHHHHHHHHHh
Confidence 444444444445555555555
No 491
>cd03522 MoeA_like MoeA_like. This domain is similar to a domain found in a variety of proteins involved in biosynthesis of molybdopterin cofactor, like MoaB, MogA, and MoeA. There this domain is presumed to bind molybdopterin. The exact function of this subgroup is unknown.
Probab=34.13 E-value=2.5e+02 Score=29.20 Aligned_cols=80 Identities=14% Similarity=0.042 Sum_probs=54.2
Q ss_pred cCCcEEEEEEEcCC--Cc---chhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEecc-CCcHH
Q 003958 162 YGWREVIAIYVDDD--HG---RNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTH-YNRGP 235 (784)
Q Consensus 162 ~~w~~v~ii~~d~~--~g---~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~-~~~~~ 235 (784)
|.-.++++|...++ .| ......+++.+++.|.++......+ .+...+...+.++.+.++|+||+.+. ...-.
T Consensus 157 ~r~~rv~II~TG~Ev~~G~i~D~~~~~l~~~L~~~G~~v~~~~iv~--Dd~~~I~~ai~~~~~~g~DlIItTGGtsvg~~ 234 (312)
T cd03522 157 FRPLRVGLIVTGSEVYGGRIEDKFGPVLRARLAALGVELVEQVIVP--HDEAAIAAAIAEALEAGAELLILTGGASVDPD 234 (312)
T ss_pred cCCCEEEEEEcCCcCCCCcEEEhHHHHHHHHHHHCCCEEEEEEEcC--CCHHHHHHHHHHHhcCCCCEEEEeCCcccCCc
Confidence 44568888886543 22 2345678888999999988877777 45667788888776666899998744 34445
Q ss_pred HHHHHHHH
Q 003958 236 VVFHVAQY 243 (784)
Q Consensus 236 ~~~~~a~~ 243 (784)
++..++.+
T Consensus 235 D~tp~Ai~ 242 (312)
T cd03522 235 DVTPAAIR 242 (312)
T ss_pred chHHHHHH
Confidence 55555433
No 492
>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=34.03 E-value=1.7e+02 Score=29.36 Aligned_cols=77 Identities=5% Similarity=-0.015 Sum_probs=47.4
Q ss_pred EEEEEEc--CCCcchhHHHHHHHHhcc-CcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccC-CcHHHHHHHHH
Q 003958 167 VIAIYVD--DDHGRNGIAALGDTLAAK-RCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY-NRGPVVFHVAQ 242 (784)
Q Consensus 167 v~ii~~d--~~~g~~~~~~l~~~l~~~-gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~-~~~~~~~~~a~ 242 (784)
|+++..+ +.|.......+.+.+++. |..+..... . .+..+....++.+...+++.|++.... +.....++.+.
T Consensus 2 ig~~~~~~~~~~~~~~~~~i~~~~~~~~g~~~~~~~~-~--~~~~~~~~~i~~~~~~~vdgiii~~~~~~~~~~~~~~~~ 78 (270)
T cd06308 2 IGFSQCNLADPWRAAMNDEIQREASNYPDVELIIADA-A--DDNSKQVADIENFIRQGVDLLIISPNEAAPLTPVVEEAY 78 (270)
T ss_pred EEEEeeCCCCHHHHHHHHHHHHHHHhcCCcEEEEEcC-C--CCHHHHHHHHHHHHHhCCCEEEEecCchhhchHHHHHHH
Confidence 5666654 445667778888888885 777764322 1 233444566676667788988886433 32345566666
Q ss_pred HcCC
Q 003958 243 YLGM 246 (784)
Q Consensus 243 ~~g~ 246 (784)
+.|.
T Consensus 79 ~~~i 82 (270)
T cd06308 79 RAGI 82 (270)
T ss_pred HCCC
Confidence 6553
No 493
>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=33.93 E-value=3.8e+02 Score=28.48 Aligned_cols=99 Identities=11% Similarity=0.044 Sum_probs=60.4
Q ss_pred HHHHHHHHcCCcEEEEEEEcCCCcchhHHHHHHHHhccCcEEEEee--ccCCCCChhHHHHHHHHhhcCCce---EEEEe
Q 003958 154 AIAEIVDHYGWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKA--PLSVEATEDEITDLLVKVALTESR---IIVVH 228 (784)
Q Consensus 154 ai~~~l~~~~w~~v~ii~~d~~~g~~~~~~l~~~l~~~gi~v~~~~--~~~~~~~~~d~~~~l~~l~~~~~~---vIvl~ 228 (784)
-+.++++.++-+++.++++...+ ....+.+.+.+++.|+.+.... ......+.+.....+..+++.+++ +||..
T Consensus 13 ~l~~~l~~~g~~rvlvVtd~~v~-~~~~~~l~~~L~~~g~~~~~~~~~~~e~~k~~~~v~~~~~~~~~~~~dr~~~IIAv 91 (355)
T cd08197 13 SVLGYLPELNADKYLLVTDSNVE-DLYGHRLLEYLREAGAPVELLSVPSGEEHKTLSTLSDLVERALALGATRRSVIVAL 91 (355)
T ss_pred HHHHHHHhcCCCeEEEEECccHH-HHHHHHHHHHHHhcCCceEEEEeCCCCCCCCHHHHHHHHHHHHHcCCCCCcEEEEE
Confidence 35566777777899988865543 3366788889988887653221 122223456677888888887777 77766
Q ss_pred ccC--CcHHHHHHHHHHcCCCCCCeEEEec
Q 003958 229 THY--NRGPVVFHVAQYLGMLGTGYVWIAT 256 (784)
Q Consensus 229 ~~~--~~~~~~~~~a~~~g~~~~~~~wi~~ 256 (784)
+.+ -++..++......| ..++.|-|
T Consensus 92 GGGsv~D~ak~~A~~~~rg---ip~I~IPT 118 (355)
T cd08197 92 GGGVVGNIAGLLAALLFRG---IRLVHIPT 118 (355)
T ss_pred CCcHHHHHHHHHHHHhccC---CCEEEecC
Confidence 443 44555554433333 34455544
No 494
>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=33.89 E-value=3.4e+02 Score=26.05 Aligned_cols=86 Identities=13% Similarity=0.059 Sum_probs=49.6
Q ss_pred cEEEEEEEcCCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccC----CcHHHHHHH
Q 003958 165 REVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY----NRGPVVFHV 240 (784)
Q Consensus 165 ~~v~ii~~d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~----~~~~~~~~~ 240 (784)
.+|.+.....+.-.-+...+...++..|++|..-. .+ .....++..+++.++++|.+.+.. ..+..++++
T Consensus 83 ~~vl~~~~~gd~H~lG~~~v~~~l~~~G~~vi~lG---~~---~p~~~l~~~~~~~~~d~v~lS~~~~~~~~~~~~~i~~ 156 (201)
T cd02070 83 GKVVIGTVEGDIHDIGKNLVATMLEANGFEVIDLG---RD---VPPEEFVEAVKEHKPDILGLSALMTTTMGGMKEVIEA 156 (201)
T ss_pred CeEEEEecCCccchHHHHHHHHHHHHCCCEEEECC---CC---CCHHHHHHHHHHcCCCEEEEeccccccHHHHHHHHHH
Confidence 45555555555545556777778888888875321 11 123456666677788888887532 345566666
Q ss_pred HHHcCCCCCCeEEEec
Q 003958 241 AQYLGMLGTGYVWIAT 256 (784)
Q Consensus 241 a~~~g~~~~~~~wi~~ 256 (784)
.++.+....-.+|++.
T Consensus 157 lr~~~~~~~~~i~vGG 172 (201)
T cd02070 157 LKEAGLRDKVKVMVGG 172 (201)
T ss_pred HHHCCCCcCCeEEEEC
Confidence 6666532222344544
No 495
>cd06294 PBP1_ycjW_transcription_regulator_like Ligand-binding domain of uncharacterized transcription regulator ycjW which is a member of the LacI-GalR family repressors. This group includes the ligand-binding domain of uncharacterized transcription regulator ycjW which is a member of the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=33.77 E-value=2.2e+02 Score=28.38 Aligned_cols=68 Identities=7% Similarity=0.038 Sum_probs=39.5
Q ss_pred CCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHH-hhcCCceEEEEeccCCcHHHHHHHHHHcCC
Q 003958 174 DDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVK-VALTESRIIVVHTHYNRGPVVFHVAQYLGM 246 (784)
Q Consensus 174 ~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~-l~~~~~~vIvl~~~~~~~~~~~~~a~~~g~ 246 (784)
+.|.....+.+++.+++.|.++...... +..+....+.+ +...+.+.||+...... ...++.+.+.|.
T Consensus 16 ~~~~~~~~~~~~~~~~~~g~~~~~~~~~----~~~~~~~~~~~~~~~~~~dgiii~~~~~~-~~~~~~~~~~~i 84 (270)
T cd06294 16 NPFFIEVLRGISAVANENGYDISLATGK----NEEELLEEVKKMIQQKRVDGFILLYSRED-DPIIDYLKEEKF 84 (270)
T ss_pred CCCHHHHHHHHHHHHHHCCCEEEEecCC----CcHHHHHHHHHHHHHcCcCEEEEecCcCC-cHHHHHHHhcCC
Confidence 4566677888888888888887643211 12222233333 44456888888643222 345666666553
No 496
>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=33.63 E-value=3.4e+02 Score=28.12 Aligned_cols=79 Identities=9% Similarity=-0.068 Sum_probs=50.2
Q ss_pred CCcEEEEEEEc--CCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcHHHHHHH
Q 003958 163 GWREVIAIYVD--DDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRGPVVFHV 240 (784)
Q Consensus 163 ~w~~v~ii~~d--~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~~~~~~~ 240 (784)
.-+.|+++..+ +.|.....+.+++.+++.|..+..... . .+.......++.+...+.+.||+...... ..+.+.
T Consensus 58 ~~~~Igvv~~~~~~~f~~~l~~~i~~~~~~~g~~~~i~~~-~--~~~~~~~~~~~~l~~~~vdGiIi~~~~~~-~~~~~~ 133 (329)
T TIGR01481 58 RTTTVGVIIPDISNIYYAELARGIEDIATMYKYNIILSNS-D--EDPEKEVQVLNTLLSKQVDGIIFMGGTIT-EKLREE 133 (329)
T ss_pred CCCEEEEEeCCCCchhHHHHHHHHHHHHHHcCCEEEEEeC-C--CCHHHHHHHHHHHHhCCCCEEEEeCCCCC-hHHHHH
Confidence 34678888863 567777788888999989987765321 1 23333456677777788999888643222 234455
Q ss_pred HHHcC
Q 003958 241 AQYLG 245 (784)
Q Consensus 241 a~~~g 245 (784)
+.+.+
T Consensus 134 l~~~~ 138 (329)
T TIGR01481 134 FSRSP 138 (329)
T ss_pred HHhcC
Confidence 55544
No 497
>PRK10481 hypothetical protein; Provisional
Probab=33.60 E-value=3e+02 Score=27.03 Aligned_cols=75 Identities=13% Similarity=0.046 Sum_probs=46.2
Q ss_pred HHHHHHc-CCcEEEEEEEcCCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccCCcH
Q 003958 156 AEIVDHY-GWREVIAIYVDDDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHYNRG 234 (784)
Q Consensus 156 ~~~l~~~-~w~~v~ii~~d~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~~ 234 (784)
..++..+ +-++++++....+.. .+..++.. ..|..+.....-|.......+....++++..++|+|++.|.+-..
T Consensus 120 ~~lv~Al~~g~riGVitP~~~qi---~~~~~kw~-~~G~~v~~~~aspy~~~~~~l~~aa~~L~~~gaD~Ivl~C~G~~~ 195 (224)
T PRK10481 120 PPLVAAIVGGHQVGVIVPVEEQL---AQQAQKWQ-VLQKPPVFALASPYHGSEEELIDAGKELLDQGADVIVLDCLGYHQ 195 (224)
T ss_pred HHHHHHhcCCCeEEEEEeCHHHH---HHHHHHHH-hcCCceeEeecCCCCCCHHHHHHHHHHhhcCCCCEEEEeCCCcCH
Confidence 4444433 348999999765432 23333333 347766544332322344567778888888999999999876444
No 498
>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=33.59 E-value=1.3e+02 Score=30.21 Aligned_cols=80 Identities=11% Similarity=-0.060 Sum_probs=49.2
Q ss_pred EEEEEEEc--CCCcchhHHHHHHHHhccCcEEEEeecc-CCCCChhHHHHHHHHhhcCCceEEEEeccCCc-HHHHHHHH
Q 003958 166 EVIAIYVD--DDHGRNGIAALGDTLAAKRCRISFKAPL-SVEATEDEITDLLVKVALTESRIIVVHTHYNR-GPVVFHVA 241 (784)
Q Consensus 166 ~v~ii~~d--~~~g~~~~~~l~~~l~~~gi~v~~~~~~-~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~~~-~~~~~~~a 241 (784)
+|+++..+ +.|.....+.+.+.+++.|.++...... ....+.......++.+.. +.|.|++...... ....++++
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 46777754 4577777888888888887543322211 111233445577777777 8998888654323 34667787
Q ss_pred HHcCC
Q 003958 242 QYLGM 246 (784)
Q Consensus 242 ~~~g~ 246 (784)
.+.|.
T Consensus 80 ~~~~i 84 (275)
T cd06307 80 AAAGV 84 (275)
T ss_pred HHCCC
Confidence 77553
No 499
>PRK07377 hypothetical protein; Provisional
Probab=33.49 E-value=1.1e+02 Score=28.48 Aligned_cols=63 Identities=14% Similarity=0.153 Sum_probs=44.5
Q ss_pred ccEEEEecCCCccceeEeeCCCcceeeeeHHHHHHHHHHCCCccceEEeeCCCCCCCCChhHHHHHHHcCcccEEEeeE
Q 003958 468 RHLRIGVPNRVSFREFVSVKGSEMTSGFCIDVFTAAINLLPYAVPYKLIPFGDGHNNPSCTELVRLITAGVYDAAVGDI 546 (784)
Q Consensus 468 ~~l~v~~~~~~~~~~~~~~~~~~~~~G~~~dl~~~l~~~l~f~~~~~~~~~~~~~~~~~~~g~i~~l~~~~~D~~~~~~ 546 (784)
-.+|+++... . ...+...+-.++.++.+.++++.. ++++++ ++-..+.+.+.+|++|++++.-
T Consensus 75 ~~~Rlgv~~~--~------~~~~~~~~~l~~~l~~~~~~y~~r--lElv~y------~~~~~l~~aL~~~eVh~~c~~~ 137 (184)
T PRK07377 75 LVMRLGVLEI--E------TETSSVFDQLIDQLRTILDKYHLR--LELVVY------PDLQALEQALRDKEVHAICLES 137 (184)
T ss_pred cEEEEEEEec--c------ccccccHHHHHHHHHHHHHHhCce--eeEEec------CCHHHHHHHHhcCCccEEecCC
Confidence 3567776553 0 112224445778889999999988 666666 5678899999999999988743
No 500
>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=33.37 E-value=1.3e+02 Score=30.44 Aligned_cols=70 Identities=10% Similarity=-0.020 Sum_probs=47.1
Q ss_pred CCCcchhHHHHHHHHhccCcEEEEeeccCCCCChhHHHHHHHHhhcCCceEEEEeccC-CcHHHHHHHHHHcCC
Q 003958 174 DDHGRNGIAALGDTLAAKRCRISFKAPLSVEATEDEITDLLVKVALTESRIIVVHTHY-NRGPVVFHVAQYLGM 246 (784)
Q Consensus 174 ~~~g~~~~~~l~~~l~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~vIvl~~~~-~~~~~~~~~a~~~g~ 246 (784)
+.|.....+.+.+.+++.|..+.....- .+.......++.+...+++.|++.... ......++++.+.+.
T Consensus 11 ~~f~~~~~~gi~~~~~~~G~~~~~~~~~---~d~~~~~~~i~~~~~~~vdgiii~~~~~~~~~~~i~~~~~~~i 81 (272)
T cd06313 11 ATWCAQGKQAADEAGKLLGVDVTWYGGA---LDAVKQVAAIENMASQGWDFIAVDPLGIGTLTEAVQKAIARGI 81 (272)
T ss_pred ChHHHHHHHHHHHHHHHcCCEEEEecCC---CCHHHHHHHHHHHHHcCCCEEEEcCCChHHhHHHHHHHHHCCC
Confidence 4566677788888888899887754322 234445567777777889988886432 334566777777653
Done!