Query 002211
Match_columns 953
No_of_seqs 664 out of 3833
Neff 9.5
Searched_HMMs 46136
Date Thu Mar 28 19:02:57 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/002211.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/002211hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1054 Glutamate-gated AMPA-t 100.0 9.4E-87 2E-91 697.1 47.3 778 46-876 23-846 (897)
2 KOG4440 NMDA selective glutama 100.0 2.5E-81 5.4E-86 659.1 41.4 750 43-875 29-857 (993)
3 KOG1053 Glutamate-gated NMDA-t 100.0 1.5E-74 3.3E-79 630.3 58.3 705 97-872 82-853 (1258)
4 KOG1052 Glutamate-gated kainat 100.0 1.8E-65 3.9E-70 615.1 55.8 594 232-875 4-624 (656)
5 cd06361 PBP1_GPC6A_like Ligand 100.0 7.1E-48 1.5E-52 433.2 40.5 337 63-439 34-396 (403)
6 cd06375 PBP1_mGluR_groupII Lig 100.0 1.5E-47 3.1E-52 438.1 41.8 365 48-436 1-454 (458)
7 cd06374 PBP1_mGluR_groupI Liga 100.0 1.4E-47 2.9E-52 442.6 40.9 375 45-442 5-469 (472)
8 cd06362 PBP1_mGluR Ligand bind 100.0 1.3E-47 2.8E-52 442.6 40.3 371 48-440 1-450 (452)
9 cd06364 PBP1_CaSR Ligand-bindi 100.0 2.6E-47 5.6E-52 440.4 42.5 373 45-437 8-494 (510)
10 cd06393 PBP1_iGluR_Kainate_Glu 100.0 2.9E-47 6.3E-52 428.9 39.8 366 49-442 2-383 (384)
11 cd06365 PBP1_Pheromone_recepto 100.0 4.6E-47 1E-51 435.9 39.5 369 48-437 1-453 (469)
12 cd06376 PBP1_mGluR_groupIII Li 100.0 7.3E-47 1.6E-51 435.9 41.3 367 48-436 1-452 (463)
13 cd06392 PBP1_iGluR_delta_1 N-t 100.0 1.2E-46 2.6E-51 414.8 40.0 363 51-441 1-399 (400)
14 cd06380 PBP1_iGluR_AMPA N-term 100.0 5.7E-45 1.2E-49 411.6 41.3 372 51-440 1-381 (382)
15 cd06390 PBP1_iGluR_AMPA_GluR1 100.0 5.5E-45 1.2E-49 402.5 39.0 355 51-440 1-363 (364)
16 cd06366 PBP1_GABAb_receptor Li 100.0 3.7E-45 7.9E-50 408.6 37.5 339 51-442 1-348 (350)
17 cd06379 PBP1_iGluR_NMDA_NR1 N- 100.0 1.3E-44 2.7E-49 407.4 41.0 334 45-437 15-364 (377)
18 cd06363 PBP1_Taste_receptor Li 100.0 9E-45 1.9E-49 412.5 39.5 353 46-437 3-396 (410)
19 cd06391 PBP1_iGluR_delta_2 N-t 100.0 1.4E-44 3E-49 403.5 40.1 365 51-440 1-398 (400)
20 cd06386 PBP1_NPR_C_like Ligand 100.0 2.7E-44 6E-49 404.5 39.1 352 53-437 3-379 (387)
21 cd06370 PBP1_Speract_GC_like L 100.0 2.1E-44 4.6E-49 408.5 38.5 349 50-427 1-386 (404)
22 cd06385 PBP1_NPR_A Ligand-bind 100.0 2E-44 4.3E-49 409.9 35.7 357 51-438 1-392 (405)
23 cd06367 PBP1_iGluR_NMDA N-term 100.0 3.5E-44 7.6E-49 402.0 36.7 339 49-436 2-351 (362)
24 cd06373 PBP1_NPR_like Ligand b 100.0 3.8E-44 8.2E-49 406.6 37.2 359 51-438 1-390 (396)
25 cd06352 PBP1_NPR_GC_like Ligan 100.0 1.1E-43 2.3E-48 403.0 39.0 361 51-439 1-384 (389)
26 cd06371 PBP1_sensory_GC_DEF_li 100.0 1E-43 2.2E-48 398.8 38.0 349 51-434 1-369 (382)
27 cd06372 PBP1_GC_G_like Ligand- 100.0 1.4E-43 2.9E-48 401.4 39.2 358 51-438 1-387 (391)
28 cd06387 PBP1_iGluR_AMPA_GluR3 100.0 1.1E-42 2.5E-47 382.6 40.3 360 52-440 2-371 (372)
29 cd06388 PBP1_iGluR_AMPA_GluR4 100.0 4E-42 8.6E-47 381.8 40.2 361 51-441 1-370 (371)
30 cd06389 PBP1_iGluR_AMPA_GluR2 100.0 5.1E-42 1.1E-46 382.1 39.2 360 51-441 1-369 (370)
31 cd06384 PBP1_NPR_B Ligand-bind 100.0 3.4E-42 7.4E-47 390.2 38.0 357 51-438 1-393 (399)
32 cd06382 PBP1_iGluR_Kainate N-t 100.0 8.4E-43 1.8E-47 385.5 32.0 316 51-440 1-326 (327)
33 PRK15404 leucine ABC transport 100.0 1.8E-41 4E-46 378.7 37.8 341 43-427 19-364 (369)
34 KOG1056 Glutamate-gated metabo 100.0 2.6E-41 5.6E-46 385.5 38.1 392 45-479 27-494 (878)
35 cd06394 PBP1_iGluR_Kainate_KA1 100.0 8.4E-42 1.8E-46 369.9 28.4 323 51-441 1-332 (333)
36 cd06368 PBP1_iGluR_non_NMDA_li 100.0 1.5E-39 3.3E-44 359.4 33.0 316 51-440 1-323 (324)
37 cd06342 PBP1_ABC_LIVBP_like Ty 100.0 6.8E-39 1.5E-43 356.2 35.6 328 51-422 1-334 (334)
38 cd06346 PBP1_ABC_ligand_bindin 100.0 6E-39 1.3E-43 351.9 30.8 304 51-419 1-310 (312)
39 cd06338 PBP1_ABC_ligand_bindin 100.0 2E-38 4.3E-43 353.9 34.6 329 51-422 1-345 (345)
40 cd06345 PBP1_ABC_ligand_bindin 100.0 3.3E-38 7.1E-43 351.5 34.5 320 51-413 1-337 (344)
41 PF01094 ANF_receptor: Recepto 100.0 4.1E-38 8.8E-43 352.4 33.5 334 66-423 2-348 (348)
42 cd06355 PBP1_FmdD_like Peripla 100.0 9.5E-38 2.1E-42 347.3 35.7 334 51-427 1-341 (348)
43 COG0683 LivK ABC-type branched 100.0 6.9E-38 1.5E-42 349.1 34.4 339 47-426 8-356 (366)
44 TIGR03669 urea_ABC_arch urea A 100.0 1.6E-37 3.4E-42 345.8 35.8 341 50-435 1-349 (374)
45 cd06348 PBP1_ABC_ligand_bindin 100.0 1.4E-37 3.1E-42 346.5 35.3 334 51-419 1-343 (344)
46 cd06350 PBP1_GPCR_family_C_lik 100.0 6.6E-38 1.4E-42 350.2 32.3 309 51-437 1-340 (348)
47 cd06344 PBP1_ABC_ligand_bindin 100.0 2.2E-37 4.7E-42 342.9 31.7 320 51-415 1-327 (332)
48 cd06381 PBP1_iGluR_delta_like 100.0 1.2E-36 2.6E-41 336.1 37.0 333 51-440 1-362 (363)
49 TIGR03407 urea_ABC_UrtA urea A 100.0 2.1E-36 4.5E-41 337.8 37.5 330 50-422 1-337 (359)
50 cd06340 PBP1_ABC_ligand_bindin 100.0 4.9E-37 1.1E-41 341.9 32.0 324 51-415 1-342 (347)
51 cd06329 PBP1_SBP_like_3 Peripl 100.0 8.6E-37 1.9E-41 339.4 32.3 316 51-411 1-334 (342)
52 cd06331 PBP1_AmiC_like Type I 100.0 4.5E-36 9.8E-41 332.6 33.6 319 51-412 1-325 (333)
53 cd06343 PBP1_ABC_ligand_bindin 100.0 1.6E-35 3.4E-40 332.5 36.2 340 47-426 4-361 (362)
54 cd06327 PBP1_SBP_like_1 Peripl 100.0 4.3E-36 9.4E-41 333.0 30.8 320 51-415 1-330 (334)
55 cd06349 PBP1_ABC_ligand_bindin 100.0 3.2E-35 7E-40 327.0 35.3 329 51-425 1-338 (340)
56 cd06357 PBP1_AmiC Periplasmic 100.0 6.1E-35 1.3E-39 326.1 36.9 341 51-432 1-347 (360)
57 cd06347 PBP1_ABC_ligand_bindin 100.0 3.4E-35 7.3E-40 326.6 34.6 321 51-416 1-330 (334)
58 cd06336 PBP1_ABC_ligand_bindin 100.0 1.4E-35 2.9E-40 330.3 30.4 325 51-418 1-345 (347)
59 cd06359 PBP1_Nba_like Type I p 100.0 3.6E-35 7.9E-40 325.2 33.6 324 51-420 1-331 (333)
60 cd06328 PBP1_SBP_like_2 Peripl 100.0 3.3E-35 7.3E-40 324.9 33.1 322 51-417 1-331 (333)
61 cd06378 PBP1_iGluR_NMDA_NR2 N- 100.0 3.5E-35 7.6E-40 323.9 29.4 304 96-442 43-355 (362)
62 cd06330 PBP1_Arsenic_SBP_like 100.0 7E-35 1.5E-39 325.3 31.7 320 51-409 1-333 (346)
63 cd06356 PBP1_Amide_Urea_BP_lik 100.0 2.1E-34 4.6E-39 318.7 33.1 317 51-411 1-325 (334)
64 cd06360 PBP1_alkylbenzenes_lik 100.0 3.1E-34 6.7E-39 319.0 34.5 325 51-417 1-332 (336)
65 PF13458 Peripla_BP_6: Peripla 100.0 1.5E-34 3.3E-39 322.6 31.6 335 49-426 1-342 (343)
66 cd06358 PBP1_NHase Type I peri 100.0 2.6E-34 5.6E-39 318.4 33.0 318 51-415 1-327 (333)
67 cd06334 PBP1_ABC_ligand_bindin 100.0 2.6E-34 5.6E-39 318.8 32.3 328 51-408 1-344 (351)
68 cd06335 PBP1_ABC_ligand_bindin 100.0 6.4E-34 1.4E-38 316.8 32.7 317 51-409 1-335 (347)
69 PF13433 Peripla_BP_5: Peripla 100.0 3E-33 6.5E-38 294.5 32.6 349 50-479 1-359 (363)
70 cd06383 PBP1_iGluR_AMPA_Like N 100.0 2.4E-33 5.1E-38 310.4 28.7 328 58-413 6-351 (368)
71 cd06332 PBP1_aromatic_compound 100.0 1.3E-32 2.9E-37 305.6 33.6 320 51-415 1-327 (333)
72 cd06337 PBP1_ABC_ligand_bindin 100.0 1E-32 2.2E-37 308.0 29.3 329 51-425 1-355 (357)
73 cd06351 PBP1_iGluR_N_LIVBP_lik 100.0 3.7E-32 8.1E-37 301.4 32.2 315 51-436 1-322 (328)
74 cd06377 PBP1_iGluR_NMDA_NR3 N- 100.0 2.4E-30 5.3E-35 279.7 37.5 341 47-441 16-375 (382)
75 KOG1055 GABA-B ion channel rec 100.0 1E-32 2.2E-37 303.8 19.1 370 46-438 38-431 (865)
76 TIGR03863 PQQ_ABC_bind ABC tra 100.0 3.5E-31 7.5E-36 290.4 26.2 296 61-415 8-309 (347)
77 cd06326 PBP1_STKc_like Type I 100.0 3.8E-30 8.3E-35 286.1 34.0 317 50-408 1-326 (336)
78 cd06339 PBP1_YraM_LppC_lipopro 100.0 3.2E-31 6.9E-36 292.9 25.1 302 51-412 1-329 (336)
79 cd06341 PBP1_ABC_ligand_bindin 100.0 1.7E-28 3.6E-33 273.3 30.3 308 51-402 1-318 (341)
80 cd06333 PBP1_ABC-type_HAAT_lik 100.0 6.5E-28 1.4E-32 264.9 30.6 278 51-345 1-293 (312)
81 cd06269 PBP1_glutamate_recepto 100.0 5.9E-28 1.3E-32 263.6 28.6 224 51-282 1-235 (298)
82 cd04509 PBP1_ABC_transporter_G 100.0 1.7E-27 3.6E-32 260.1 27.6 280 51-343 1-290 (299)
83 cd06268 PBP1_ABC_transporter_L 99.9 1.6E-25 3.4E-30 244.3 28.8 280 51-345 1-287 (298)
84 cd06369 PBP1_GC_C_enterotoxin_ 99.9 1.2E-22 2.7E-27 213.2 28.6 324 64-438 18-366 (380)
85 PRK09495 glnH glutamine ABC tr 99.9 2.5E-21 5.4E-26 204.6 22.0 219 483-824 23-243 (247)
86 PRK10797 glutamate and asparta 99.9 3.2E-21 6.9E-26 208.3 22.9 223 483-824 38-271 (302)
87 PF00497 SBP_bac_3: Bacterial 99.9 4.8E-21 1E-25 199.7 17.1 221 487-824 1-224 (225)
88 PRK11260 cystine transporter s 99.9 2.1E-20 4.6E-25 199.7 21.9 221 483-824 39-261 (266)
89 PRK15010 ABC transporter lysin 99.9 3.6E-20 7.7E-25 197.3 22.6 222 483-824 24-254 (260)
90 PRK11917 bifunctional adhesin/ 99.9 4.7E-20 1E-24 195.2 22.5 219 483-823 36-258 (259)
91 TIGR01096 3A0103s03R lysine-ar 99.8 6.4E-20 1.4E-24 194.6 21.4 219 484-823 23-250 (250)
92 PRK15007 putative ABC transpor 99.8 9.8E-20 2.1E-24 192.2 21.8 217 484-824 20-242 (243)
93 PRK15437 histidine ABC transpo 99.8 1.4E-19 3.1E-24 192.5 21.0 222 483-824 24-254 (259)
94 TIGR02995 ectoine_ehuB ectoine 99.8 2.4E-19 5.2E-24 192.4 20.3 223 483-824 31-261 (275)
95 PRK10859 membrane-bound lytic 99.8 3.8E-18 8.1E-23 196.4 20.0 221 483-824 41-266 (482)
96 PRK09959 hybrid sensory histid 99.8 2.4E-17 5.1E-22 214.0 23.7 216 484-824 301-520 (1197)
97 PF00060 Lig_chan: Ligand-gate 99.7 3.5E-19 7.6E-24 172.0 0.4 107 606-712 1-115 (148)
98 TIGR03870 ABC_MoxJ methanol ox 99.7 6.7E-17 1.4E-21 170.1 16.9 208 486-822 1-241 (246)
99 TIGR02285 conserved hypothetic 99.7 1E-16 2.2E-21 171.5 16.9 230 483-824 16-261 (268)
100 cd00134 PBPb Bacterial peripla 99.7 1E-15 2.2E-20 157.9 21.3 214 487-823 1-218 (218)
101 COG0834 HisJ ABC-type amino ac 99.7 7.1E-16 1.5E-20 166.2 20.5 225 483-824 32-264 (275)
102 smart00062 PBPb Bacterial peri 99.7 1.8E-15 3.9E-20 156.0 20.2 215 486-823 1-219 (219)
103 PRK09959 hybrid sensory histid 99.7 5.1E-16 1.1E-20 201.6 19.3 222 482-825 53-278 (1197)
104 cd01391 Periplasmic_Binding_Pr 99.7 7.7E-15 1.7E-19 156.7 24.2 257 51-343 1-261 (269)
105 TIGR03871 ABC_peri_MoxJ_2 quin 99.7 3.9E-15 8.5E-20 155.8 19.0 211 486-823 1-228 (232)
106 PF04348 LppC: LppC putative l 99.4 3.1E-11 6.7E-16 139.1 23.8 299 47-411 217-523 (536)
107 smart00079 PBPe Eukaryotic hom 99.4 1.9E-12 4.2E-17 122.5 11.4 123 701-824 1-133 (134)
108 COG4623 Predicted soluble lyti 99.3 3.7E-11 8.1E-16 123.5 14.3 220 483-824 21-247 (473)
109 cd01537 PBP1_Repressors_Sugar_ 99.0 1.7E-08 3.7E-13 107.6 20.6 205 51-275 1-211 (264)
110 TIGR01098 3A0109s03R phosphate 99.0 6.9E-09 1.5E-13 110.2 14.3 199 484-809 31-254 (254)
111 cd01536 PBP1_ABC_sugar_binding 98.9 1.7E-07 3.7E-12 100.2 24.2 205 51-276 1-214 (267)
112 cd06267 PBP1_LacI_sugar_bindin 98.9 1.8E-07 3.9E-12 99.7 20.3 205 51-275 1-210 (264)
113 PRK00489 hisG ATP phosphoribos 98.8 1.4E-08 3E-13 108.8 11.4 164 543-824 51-219 (287)
114 cd06325 PBP1_ABC_uncharacteriz 98.8 2.4E-07 5.3E-12 100.0 20.8 201 51-266 1-208 (281)
115 cd06300 PBP1_ABC_sugar_binding 98.8 6.8E-07 1.5E-11 95.9 23.7 202 51-269 1-211 (272)
116 PF10613 Lig_chan-Glu_bd: Liga 98.7 5.5E-09 1.2E-13 81.7 1.5 49 506-554 14-65 (65)
117 cd06320 PBP1_allose_binding Pe 98.7 5.2E-06 1.1E-10 89.2 23.8 199 51-267 1-207 (275)
118 PRK10653 D-ribose transporter 98.6 2.3E-05 5E-10 85.2 26.0 223 23-266 2-231 (295)
119 COG2984 ABC-type uncharacteriz 98.6 2.6E-05 5.6E-10 80.9 24.1 204 45-266 26-240 (322)
120 cd06282 PBP1_GntR_like_2 Ligan 98.6 6.8E-06 1.5E-10 87.7 21.3 201 51-273 1-207 (266)
121 COG3107 LppC Putative lipoprot 98.5 1.1E-05 2.4E-10 87.8 19.4 301 46-411 254-585 (604)
122 cd06323 PBP1_ribose_binding Pe 98.5 2.6E-05 5.6E-10 83.3 23.0 205 51-277 1-214 (268)
123 cd06317 PBP1_ABC_sugar_binding 98.4 3.8E-05 8.2E-10 82.5 22.3 208 51-275 1-219 (275)
124 cd06273 PBP1_GntR_like_1 This 98.4 2.6E-05 5.7E-10 83.3 20.7 200 51-272 1-208 (268)
125 cd06319 PBP1_ABC_sugar_binding 98.3 7.3E-05 1.6E-09 80.4 22.8 208 51-277 1-219 (277)
126 cd06312 PBP1_ABC_sugar_binding 98.3 0.00016 3.4E-09 77.6 23.6 200 51-267 1-208 (271)
127 TIGR03431 PhnD phosphonate ABC 98.3 1.6E-05 3.5E-10 86.0 15.2 117 700-818 125-258 (288)
128 cd06301 PBP1_rhizopine_binding 98.2 0.00019 4.2E-09 76.8 23.4 209 51-277 1-218 (272)
129 cd06305 PBP1_methylthioribose_ 98.2 0.00018 3.9E-09 77.1 22.9 208 51-277 1-217 (273)
130 cd06310 PBP1_ABC_sugar_binding 98.2 0.00034 7.4E-09 75.0 24.8 209 51-277 1-217 (273)
131 cd06309 PBP1_YtfQ_like Peripla 98.2 0.00024 5.1E-09 76.2 22.7 209 51-276 1-219 (273)
132 PF13407 Peripla_BP_4: Peripla 98.2 0.00015 3.3E-09 76.9 20.8 201 52-268 1-208 (257)
133 cd01545 PBP1_SalR Ligand-bindi 98.1 0.00024 5.2E-09 76.0 21.0 208 51-277 1-215 (270)
134 PRK10936 TMAO reductase system 98.0 0.002 4.4E-08 71.5 26.3 208 47-276 44-262 (343)
135 cd06298 PBP1_CcpA_like Ligand- 98.0 0.00057 1.2E-08 73.0 20.4 207 51-277 1-213 (268)
136 cd01539 PBP1_GGBP Periplasmic 98.0 0.0016 3.4E-08 71.1 24.0 208 51-269 1-228 (303)
137 PRK09701 D-allose transporter 98.0 0.0045 9.8E-08 67.7 27.5 213 51-277 26-250 (311)
138 cd06289 PBP1_MalI_like Ligand- 98.0 0.00063 1.4E-08 72.6 20.2 203 51-272 1-208 (268)
139 cd06284 PBP1_LacI_like_6 Ligan 97.9 0.001 2.2E-08 70.9 21.4 198 52-270 2-204 (267)
140 cd06303 PBP1_LuxPQ_Quorum_Sens 97.9 0.0022 4.8E-08 69.0 23.9 213 51-277 1-224 (280)
141 COG1879 RbsB ABC-type sugar tr 97.9 0.0033 7.2E-08 69.2 25.6 212 46-275 30-250 (322)
142 PRK15395 methyl-galactoside AB 97.9 0.0043 9.3E-08 68.5 26.2 209 45-266 20-249 (330)
143 cd01542 PBP1_TreR_like Ligand- 97.9 0.0011 2.4E-08 70.3 21.0 200 52-276 2-207 (259)
144 cd06311 PBP1_ABC_sugar_binding 97.9 0.0023 5.1E-08 68.5 23.5 211 52-277 2-219 (274)
145 cd06308 PBP1_sensor_kinase_lik 97.9 0.0026 5.5E-08 68.1 23.1 208 51-278 1-217 (270)
146 cd01540 PBP1_arabinose_binding 97.8 0.004 8.6E-08 67.3 23.7 215 51-277 1-229 (289)
147 PRK10355 xylF D-xylose transpo 97.8 0.0047 1E-07 68.1 24.4 203 46-267 22-236 (330)
148 cd06271 PBP1_AglR_RafR_like Li 97.8 0.0019 4E-08 68.9 20.8 203 52-275 2-214 (268)
149 TIGR01481 ccpA catabolite cont 97.8 0.0021 4.5E-08 71.1 21.7 203 48-272 58-266 (329)
150 cd06281 PBP1_LacI_like_5 Ligan 97.8 0.0017 3.6E-08 69.5 20.1 201 51-272 1-206 (269)
151 cd06288 PBP1_sucrose_transcrip 97.8 0.0016 3.5E-08 69.4 19.9 203 51-276 1-211 (269)
152 cd06321 PBP1_ABC_sugar_binding 97.8 0.0044 9.6E-08 66.2 23.2 206 51-277 1-214 (271)
153 cd06322 PBP1_ABC_sugar_binding 97.8 0.0062 1.3E-07 64.9 24.0 194 52-266 2-203 (267)
154 cd06313 PBP1_ABC_sugar_binding 97.8 0.0055 1.2E-07 65.6 23.5 197 61-277 12-216 (272)
155 PRK15408 autoinducer 2-binding 97.7 0.013 2.7E-07 64.7 26.1 199 50-266 24-233 (336)
156 cd06275 PBP1_PurR Ligand-bindi 97.7 0.0028 6E-08 67.7 20.4 206 51-275 1-211 (269)
157 cd06306 PBP1_TorT-like TorT-li 97.7 0.007 1.5E-07 64.6 23.2 196 51-266 1-207 (268)
158 cd06316 PBP1_ABC_sugar_binding 97.7 0.0082 1.8E-07 65.1 24.0 211 51-277 1-219 (294)
159 cd01575 PBP1_GntR Ligand-bindi 97.7 0.0042 9E-08 66.2 21.4 205 51-275 1-210 (268)
160 cd01538 PBP1_ABC_xylose_bindin 97.7 0.007 1.5E-07 65.4 23.3 199 51-268 1-216 (288)
161 cd06324 PBP1_ABC_sugar_binding 97.7 0.0081 1.8E-07 65.5 23.9 210 52-277 2-238 (305)
162 cd06295 PBP1_CelR Ligand bindi 97.7 0.0038 8.2E-08 66.9 20.8 204 50-277 4-222 (275)
163 cd06299 PBP1_LacI_like_13 Liga 97.7 0.0046 9.9E-08 65.8 21.0 205 51-275 1-208 (265)
164 cd06283 PBP1_RegR_EndR_KdgR_li 97.7 0.0059 1.3E-07 65.0 21.8 205 51-275 1-211 (267)
165 cd06278 PBP1_LacI_like_2 Ligan 97.7 0.0046 9.9E-08 65.8 20.7 191 52-265 2-197 (266)
166 cd06274 PBP1_FruR Ligand bindi 97.6 0.0069 1.5E-07 64.4 21.8 206 51-276 1-212 (264)
167 cd06270 PBP1_GalS_like Ligand 97.6 0.0076 1.7E-07 64.3 22.0 202 51-272 1-207 (268)
168 cd01574 PBP1_LacI Ligand-bindi 97.6 0.0098 2.1E-07 63.2 22.6 202 51-275 1-207 (264)
169 PF00532 Peripla_BP_1: Peripla 97.6 0.0035 7.5E-08 67.3 18.5 208 51-277 3-216 (279)
170 cd06285 PBP1_LacI_like_7 Ligan 97.6 0.0077 1.7E-07 64.1 21.3 203 51-276 1-210 (265)
171 PRK10703 DNA-binding transcrip 97.6 0.0063 1.4E-07 67.6 21.3 209 48-275 58-272 (341)
172 cd06293 PBP1_LacI_like_11 Liga 97.6 0.01 2.2E-07 63.4 21.9 205 51-275 1-210 (269)
173 PRK11303 DNA-binding transcrip 97.6 0.013 2.9E-07 64.5 23.4 206 48-275 60-271 (328)
174 cd06318 PBP1_ABC_sugar_binding 97.6 0.018 3.9E-07 61.9 23.6 198 51-267 1-215 (282)
175 PRK10014 DNA-binding transcrip 97.5 0.013 2.9E-07 65.0 22.6 203 48-269 63-270 (342)
176 COG1609 PurR Transcriptional r 97.5 0.022 4.8E-07 62.7 23.4 202 47-270 56-265 (333)
177 cd06292 PBP1_LacI_like_10 Liga 97.5 0.015 3.1E-07 62.3 21.7 206 52-275 2-214 (273)
178 cd06294 PBP1_ycjW_transcriptio 97.5 0.0091 2E-07 63.7 19.9 202 51-272 1-213 (270)
179 cd06302 PBP1_LsrB_Quorum_Sensi 97.5 0.028 6.2E-07 61.0 24.0 207 51-276 1-218 (298)
180 cd06296 PBP1_CatR_like Ligand- 97.5 0.011 2.3E-07 63.1 20.2 207 51-277 1-214 (270)
181 cd06314 PBP1_tmGBP Periplasmic 97.5 0.039 8.5E-07 58.9 24.4 206 51-277 1-213 (271)
182 cd01541 PBP1_AraR Ligand-bindi 97.4 0.011 2.3E-07 63.3 19.8 206 52-276 2-217 (273)
183 TIGR02955 TMAO_TorT TMAO reduc 97.4 0.031 6.8E-07 60.6 23.4 195 51-266 1-207 (295)
184 TIGR02417 fruct_sucro_rep D-fr 97.4 0.022 4.9E-07 62.7 22.6 205 48-275 59-270 (327)
185 PRK10423 transcriptional repre 97.4 0.021 4.6E-07 62.9 22.4 208 47-275 54-268 (327)
186 PF12974 Phosphonate-bd: ABC t 97.4 0.0012 2.6E-08 69.4 11.7 121 700-822 95-230 (243)
187 cd06354 PBP1_BmpA_PnrA_like Pe 97.4 0.018 3.8E-07 61.4 20.9 196 51-265 1-206 (265)
188 cd06291 PBP1_Qymf_like Ligand 97.4 0.019 4.2E-07 61.0 21.1 198 51-274 1-205 (265)
189 PRK11553 alkanesulfonate trans 97.4 0.0015 3.2E-08 71.7 12.3 110 701-812 120-236 (314)
190 cd06307 PBP1_uncharacterized_s 97.4 0.045 9.7E-07 58.6 23.5 210 51-277 1-219 (275)
191 cd06277 PBP1_LacI_like_1 Ligan 97.4 0.024 5.1E-07 60.4 21.3 198 52-270 2-205 (268)
192 cd06286 PBP1_CcpB_like Ligand- 97.4 0.017 3.8E-07 61.1 20.1 199 51-272 1-205 (260)
193 PRK10727 DNA-binding transcrip 97.3 0.026 5.7E-07 62.7 21.9 208 47-275 57-270 (343)
194 cd06290 PBP1_LacI_like_9 Ligan 97.3 0.022 4.7E-07 60.6 20.4 200 51-272 1-206 (265)
195 cd06304 PBP1_BmpA_like Peripla 97.3 0.024 5.3E-07 60.1 20.4 196 51-265 1-202 (260)
196 cd06272 PBP1_hexuronate_repres 97.3 0.019 4.1E-07 60.9 19.6 200 51-275 1-205 (261)
197 PRK09492 treR trehalose repres 97.2 0.038 8.2E-07 60.5 21.9 193 47-266 60-256 (315)
198 PF04392 ABC_sub_bind: ABC tra 97.2 0.019 4.2E-07 62.1 19.0 185 51-251 1-194 (294)
199 cd06280 PBP1_LacI_like_4 Ligan 97.2 0.037 8E-07 58.8 21.0 200 51-275 1-205 (263)
200 PRK09526 lacI lac repressor; R 97.2 0.052 1.1E-06 60.2 23.0 204 48-275 62-273 (342)
201 cd06279 PBP1_LacI_like_3 Ligan 97.2 0.031 6.7E-07 60.1 20.4 197 52-272 2-225 (283)
202 cd01543 PBP1_XylR Ligand-bindi 97.2 0.022 4.8E-07 60.6 18.8 203 51-277 1-207 (265)
203 TIGR01729 taurine_ABC_bnd taur 97.2 0.002 4.3E-08 70.2 10.7 71 700-772 90-164 (300)
204 PRK14987 gluconate operon tran 97.1 0.062 1.3E-06 59.4 22.0 207 48-275 62-272 (331)
205 cd06297 PBP1_LacI_like_12 Liga 97.1 0.051 1.1E-06 58.0 20.0 200 52-275 2-213 (269)
206 TIGR02637 RhaS rhamnose ABC tr 97.0 0.26 5.6E-06 53.6 25.2 198 52-267 1-210 (302)
207 PRK11041 DNA-binding transcrip 96.9 0.13 2.8E-06 56.0 21.7 208 47-275 33-246 (309)
208 TIGR02634 xylF D-xylose ABC tr 96.9 0.2 4.4E-06 54.4 22.8 197 52-267 1-209 (302)
209 PRK10401 DNA-binding transcrip 96.8 0.15 3.2E-06 56.7 22.0 207 48-275 58-270 (346)
210 TIGR02405 trehalos_R_Ecol treh 96.6 0.32 6.9E-06 53.1 22.2 191 48-266 58-253 (311)
211 cd01544 PBP1_GalR Ligand-bindi 96.6 0.2 4.4E-06 53.3 20.1 194 51-275 1-212 (270)
212 cd06353 PBP1_BmpA_Med_like Per 96.4 0.19 4.1E-06 53.1 18.1 196 51-266 1-201 (258)
213 cd06315 PBP1_ABC_sugar_binding 96.4 0.54 1.2E-05 50.4 22.1 203 51-269 2-216 (280)
214 PF13379 NMT1_2: NMT1-like fam 96.4 0.014 3.1E-07 61.6 9.1 74 700-774 104-189 (252)
215 COG3221 PhnD ABC-type phosphat 96.0 0.12 2.7E-06 55.1 14.1 110 700-811 134-260 (299)
216 TIGR03427 ABC_peri_uca ABC tra 96.0 0.033 7.2E-07 60.8 9.8 68 702-772 98-170 (328)
217 COG4213 XylF ABC-type xylose t 96.0 0.89 1.9E-05 47.4 19.0 208 44-268 20-243 (341)
218 PF09084 NMT1: NMT1/THI5 like; 95.3 0.11 2.3E-06 53.4 10.0 62 700-763 83-148 (216)
219 TIGR02122 TRAP_TAXI TRAP trans 94.9 0.087 1.9E-06 57.8 8.8 60 700-762 131-197 (320)
220 PF03466 LysR_substrate: LysR 94.9 0.77 1.7E-05 46.1 15.1 196 485-811 6-206 (209)
221 TIGR02990 ectoine_eutA ectoine 94.8 0.53 1.2E-05 48.6 13.4 92 169-263 107-203 (239)
222 cd05466 PBP2_LTTR_substrate Th 94.7 1.5 3.4E-05 42.7 16.6 70 512-593 13-82 (197)
223 TIGR01728 SsuA_fam ABC transpo 94.7 0.29 6.4E-06 52.6 11.9 71 700-772 91-165 (288)
224 cd06287 PBP1_LacI_like_8 Ligan 94.6 2.7 5.8E-05 44.7 19.0 183 65-275 24-211 (269)
225 cd08440 PBP2_LTTR_like_4 TThe 94.4 2.4 5.3E-05 41.6 17.3 70 512-593 13-82 (197)
226 cd08442 PBP2_YofA_SoxR_like Th 94.3 2.3 5E-05 41.7 16.8 70 512-593 13-82 (193)
227 COG1744 Med Uncharacterized AB 94.1 5.5 0.00012 43.9 20.2 205 46-267 32-245 (345)
228 cd08468 PBP2_Pa0477 The C-term 94.0 2.6 5.6E-05 42.0 16.6 73 512-593 13-85 (202)
229 cd08420 PBP2_CysL_like C-termi 93.9 3 6.6E-05 41.1 16.8 70 512-593 13-82 (201)
230 cd08421 PBP2_LTTR_like_1 The C 93.8 4.4 9.6E-05 39.9 17.8 70 512-593 13-82 (198)
231 cd08438 PBP2_CidR The C-termin 93.8 4.4 9.5E-05 39.8 17.6 70 512-593 13-82 (197)
232 PRK10339 DNA-binding transcrip 93.7 5.7 0.00012 43.5 19.8 194 48-273 62-265 (327)
233 CHL00180 rbcR LysR transcripti 93.7 3.4 7.3E-05 44.9 17.8 86 485-593 95-180 (305)
234 cd08433 PBP2_Nac The C-teminal 93.7 4.5 9.8E-05 39.9 17.6 70 512-593 13-82 (198)
235 PRK11151 DNA-binding transcrip 93.5 3.5 7.6E-05 44.7 17.6 194 485-810 91-290 (305)
236 PF07885 Ion_trans_2: Ion chan 93.4 0.16 3.5E-06 42.5 5.2 55 640-694 22-78 (79)
237 cd08412 PBP2_PAO1_like The C-t 93.4 5.6 0.00012 39.1 17.6 71 511-593 12-82 (198)
238 cd08459 PBP2_DntR_NahR_LinR_li 93.3 2.8 6.2E-05 41.6 15.5 70 512-593 13-82 (201)
239 PRK12684 transcriptional regul 93.3 3 6.6E-05 45.4 16.7 197 484-811 92-293 (313)
240 cd08418 PBP2_TdcA The C-termin 93.2 5.6 0.00012 39.2 17.4 72 512-593 13-84 (201)
241 cd08411 PBP2_OxyR The C-termin 93.1 3.6 7.9E-05 40.7 15.9 70 512-593 14-83 (200)
242 PRK11242 DNA-binding transcrip 93.0 4.3 9.4E-05 43.7 17.3 83 485-593 91-173 (296)
243 cd08415 PBP2_LysR_opines_like 92.9 5.2 0.00011 39.3 16.5 71 511-593 12-82 (196)
244 PRK12679 cbl transcriptional r 92.8 6.9 0.00015 42.7 18.6 208 484-824 92-306 (316)
245 cd08463 PBP2_DntR_like_4 The C 92.6 7.7 0.00017 38.7 17.5 71 512-593 13-83 (203)
246 PRK11480 tauA taurine transpor 92.5 0.47 1E-05 52.0 8.8 67 700-769 112-183 (320)
247 cd08434 PBP2_GltC_like The sub 92.5 7.2 0.00016 38.1 16.9 70 512-593 13-82 (195)
248 PF02608 Bmp: Basic membrane p 92.4 9.8 0.00021 41.3 18.9 202 50-266 2-212 (306)
249 PRK09791 putative DNA-binding 92.3 3.9 8.4E-05 44.3 15.8 86 484-593 94-179 (302)
250 cd08462 PBP2_NodD The C-termin 92.2 5.7 0.00012 39.4 15.9 68 513-593 14-81 (200)
251 cd08460 PBP2_DntR_like_1 The C 92.2 3.8 8.2E-05 40.7 14.5 70 511-593 12-81 (200)
252 PRK12681 cysB transcriptional 92.2 4.8 0.0001 44.2 16.3 85 484-593 92-176 (324)
253 cd08426 PBP2_LTTR_like_5 The C 92.1 8.7 0.00019 37.8 17.1 70 512-593 13-82 (199)
254 TIGR01256 modA molybdenum ABC 92.0 2.5 5.3E-05 43.2 13.0 73 738-811 132-205 (216)
255 PF12683 DUF3798: Protein of u 92.0 13 0.00028 38.5 17.2 208 49-266 2-224 (275)
256 cd08417 PBP2_Nitroaromatics_li 92.0 6.1 0.00013 39.0 15.8 70 512-593 13-82 (200)
257 TIGR00787 dctP tripartite ATP- 91.9 0.75 1.6E-05 48.6 9.2 103 700-810 126-231 (257)
258 cd06276 PBP1_FucR_like Ligand- 91.9 12 0.00025 39.2 18.3 144 107-273 45-193 (247)
259 TIGR00363 lipoprotein, YaeC fa 91.7 4.7 0.0001 42.3 14.7 120 700-822 106-250 (258)
260 PF13377 Peripla_BP_3: Peripla 91.7 0.78 1.7E-05 44.2 8.4 98 174-275 1-101 (160)
261 PRK11233 nitrogen assimilation 91.6 5 0.00011 43.6 15.6 84 484-592 90-173 (305)
262 cd08435 PBP2_GbpR The C-termin 91.6 13 0.00029 36.4 17.7 72 512-593 13-84 (201)
263 cd08466 PBP2_LeuO The C-termin 91.6 6.9 0.00015 38.6 15.6 70 512-593 13-82 (200)
264 cd08419 PBP2_CbbR_RubisCO_like 91.5 12 0.00026 36.6 17.2 70 512-593 12-81 (197)
265 PF13531 SBP_bac_11: Bacterial 91.2 2 4.4E-05 44.4 11.4 193 512-821 11-226 (230)
266 cd08461 PBP2_DntR_like_3 The C 91.1 9.1 0.0002 37.7 16.0 70 512-593 13-82 (198)
267 TIGR00035 asp_race aspartate r 90.8 2.4 5.2E-05 43.8 11.3 87 99-214 59-146 (229)
268 PRK10837 putative DNA-binding 90.8 15 0.00032 39.4 18.2 83 485-593 89-171 (290)
269 PRK11063 metQ DL-methionine tr 90.4 6.5 0.00014 41.7 14.4 120 700-822 119-263 (271)
270 PF03808 Glyco_tran_WecB: Glyc 90.3 3 6.5E-05 40.8 11.0 101 168-280 35-137 (172)
271 cd08443 PBP2_CysB The C-termin 90.1 21 0.00045 35.3 18.4 72 511-593 12-83 (198)
272 cd08425 PBP2_CynR The C-termin 90.0 14 0.00031 36.2 16.2 70 512-593 14-83 (197)
273 cd06353 PBP1_BmpA_Med_like Per 90.0 1.5 3.3E-05 46.3 9.3 86 51-145 122-207 (258)
274 TIGR02424 TF_pcaQ pca operon t 89.7 12 0.00026 40.4 16.4 86 484-593 92-177 (300)
275 cd08413 PBP2_CysB_like The C-t 89.7 14 0.00031 36.5 15.9 71 512-593 13-83 (198)
276 cd08467 PBP2_SyrM The C-termin 89.7 13 0.00028 36.9 15.6 70 512-593 13-82 (200)
277 cd08449 PBP2_XapR The C-termin 89.6 20 0.00044 34.9 17.0 72 512-593 13-84 (197)
278 COG3473 Maleate cis-trans isom 89.6 11 0.00025 37.0 13.6 90 171-263 107-201 (238)
279 PRK12682 transcriptional regul 89.4 19 0.00041 39.0 17.8 84 485-593 93-176 (309)
280 cd08423 PBP2_LTTR_like_6 The C 89.3 14 0.0003 36.2 15.6 73 512-593 13-87 (200)
281 PRK11482 putative DNA-binding 89.3 13 0.00028 40.6 16.3 82 484-593 116-197 (317)
282 cd08441 PBP2_MetR The C-termin 89.3 18 0.00038 35.6 16.3 69 513-593 14-82 (198)
283 cd08444 PBP2_Cbl The C-termina 89.0 22 0.00047 35.1 16.7 72 511-593 12-83 (198)
284 COG1910 Periplasmic molybdate- 88.8 6 0.00013 39.3 11.4 107 700-813 87-201 (223)
285 PRK09860 putative alcohol dehy 88.7 2.1 4.6E-05 48.0 9.7 88 171-260 20-109 (383)
286 cd08429 PBP2_NhaR The C-termin 88.7 26 0.00056 35.0 17.1 71 512-591 13-83 (204)
287 cd08464 PBP2_DntR_like_2 The C 88.6 19 0.00041 35.3 16.0 70 512-593 13-82 (200)
288 PF12727 PBP_like: PBP superfa 88.5 8.4 0.00018 38.5 12.8 102 700-807 81-190 (193)
289 PRK12683 transcriptional regul 88.5 24 0.00052 38.3 17.6 196 485-812 93-294 (309)
290 cd08427 PBP2_LTTR_like_2 The C 88.3 23 0.00051 34.4 16.4 72 512-593 13-84 (195)
291 cd08469 PBP2_PnbR The C-termin 88.3 16 0.00034 36.9 15.4 70 512-593 13-82 (221)
292 cd08456 PBP2_LysR The C-termin 88.3 19 0.00041 35.2 15.6 70 512-593 13-82 (196)
293 PRK12680 transcriptional regul 88.1 24 0.00053 38.6 17.5 84 485-593 93-176 (327)
294 cd08414 PBP2_LTTR_aromatics_li 88.0 27 0.00059 33.9 17.0 70 512-593 13-82 (197)
295 cd06533 Glyco_transf_WecG_TagA 88.0 5.3 0.00011 39.1 10.8 99 168-278 33-133 (171)
296 cd08486 PBP2_CbnR The C-termin 87.9 22 0.00048 35.1 15.9 70 512-593 14-83 (198)
297 COG1454 EutG Alcohol dehydroge 87.7 5.2 0.00011 44.2 11.5 92 171-264 18-111 (377)
298 cd08437 PBP2_MleR The substrat 87.7 29 0.00064 33.9 17.0 72 512-593 13-84 (198)
299 cd08448 PBP2_LTTR_aromatics_li 87.7 29 0.00062 33.8 16.7 70 512-593 13-82 (197)
300 cd08465 PBP2_ToxR The C-termin 87.6 15 0.00033 36.3 14.6 70 512-593 13-82 (200)
301 cd08445 PBP2_BenM_CatM_CatR Th 87.3 27 0.00059 34.4 16.3 70 512-593 14-83 (203)
302 PF03480 SBP_bac_7: Bacterial 87.3 1.1 2.3E-05 48.3 6.0 113 685-808 114-229 (286)
303 cd08436 PBP2_LTTR_like_3 The C 87.2 30 0.00065 33.5 17.7 71 512-593 13-83 (194)
304 PRK10341 DNA-binding transcrip 87.1 22 0.00047 38.7 16.3 85 485-593 97-181 (312)
305 PRK15454 ethanol dehydrogenase 87.1 2.7 5.9E-05 47.3 9.3 88 171-260 38-127 (395)
306 cd08189 Fe-ADH5 Iron-containin 86.7 5.4 0.00012 44.7 11.4 91 171-263 15-107 (374)
307 cd08192 Fe-ADH7 Iron-containin 86.7 5.5 0.00012 44.6 11.5 90 171-262 13-104 (370)
308 cd08451 PBP2_BudR The C-termin 86.5 34 0.00073 33.4 18.8 70 513-593 15-84 (199)
309 cd08457 PBP2_OccR The C-termin 85.9 36 0.00079 33.2 17.7 71 511-593 12-82 (196)
310 cd08190 HOT Hydroxyacid-oxoaci 85.8 3.6 7.8E-05 46.7 9.5 89 170-260 11-101 (414)
311 PRK10624 L-1,2-propanediol oxi 85.5 3.9 8.4E-05 46.0 9.5 88 170-259 18-107 (382)
312 cd08193 HVD 5-hydroxyvalerate 85.5 6.7 0.00015 44.0 11.4 89 171-261 15-105 (376)
313 cd08551 Fe-ADH iron-containing 85.4 6.8 0.00015 43.9 11.4 90 171-262 12-103 (370)
314 PRK11074 putative DNA-binding 85.4 24 0.00052 38.1 15.5 85 485-593 92-176 (300)
315 PRK15421 DNA-binding transcrip 84.8 33 0.00071 37.4 16.2 83 485-593 89-171 (317)
316 PRK10200 putative racemase; Pr 84.7 12 0.00026 38.6 11.9 88 98-214 58-147 (230)
317 PRK09861 cytoplasmic membrane 84.4 24 0.00052 37.4 14.3 120 700-822 120-264 (272)
318 cd08194 Fe-ADH6 Iron-containin 83.9 5.2 0.00011 44.8 9.6 87 171-259 12-100 (375)
319 COG0715 TauA ABC-type nitrate/ 83.8 7.1 0.00015 43.0 10.7 73 700-774 126-203 (335)
320 cd08458 PBP2_NocR The C-termin 83.8 45 0.00099 32.6 16.8 70 512-593 13-82 (196)
321 COG0725 ModA ABC-type molybdat 83.8 23 0.00049 37.2 13.6 116 701-822 123-252 (258)
322 TIGR02638 lactal_redase lactal 83.6 5.1 0.00011 45.0 9.3 88 171-260 18-107 (379)
323 cd08430 PBP2_IlvY The C-termin 83.3 47 0.001 32.3 18.0 72 511-593 12-83 (199)
324 PRK11062 nhaR transcriptional 83.2 27 0.00057 37.6 14.6 86 485-593 93-178 (296)
325 PF00465 Fe-ADH: Iron-containi 83.1 5.6 0.00012 44.4 9.5 89 171-263 12-102 (366)
326 PRK11013 DNA-binding transcrip 83.0 50 0.0011 35.7 16.8 83 485-593 94-176 (309)
327 PRK10094 DNA-binding transcrip 82.6 54 0.0012 35.5 16.8 87 484-593 91-177 (308)
328 PLN02245 ATP phosphoribosyl tr 82.5 13 0.00029 41.0 11.5 105 700-809 177-294 (403)
329 PRK09508 leuO leucine transcri 82.3 22 0.00047 38.7 13.6 84 484-593 111-194 (314)
330 COG1744 Med Uncharacterized AB 81.8 29 0.00064 38.2 14.1 92 49-147 161-252 (345)
331 cd08188 Fe-ADH4 Iron-containin 81.3 7.6 0.00016 43.6 9.6 88 171-260 17-106 (377)
332 COG1638 DctP TRAP-type C4-dica 81.0 6.1 0.00013 43.2 8.4 103 700-813 157-265 (332)
333 PRK13583 hisG ATP phosphoribos 80.9 24 0.00051 36.0 11.9 93 700-797 109-212 (228)
334 PRK10677 modA molybdate transp 80.9 17 0.00036 38.3 11.5 71 514-593 41-117 (257)
335 KOG3857 Alcohol dehydrogenase, 80.8 11 0.00023 40.0 9.5 97 154-252 38-138 (465)
336 COG1794 RacX Aspartate racemas 80.7 29 0.00063 34.9 12.0 86 99-214 59-146 (230)
337 cd08185 Fe-ADH1 Iron-containin 80.5 8.2 0.00018 43.4 9.6 88 171-261 15-105 (380)
338 cd08453 PBP2_IlvR The C-termin 80.5 60 0.0013 31.7 17.3 73 512-593 13-85 (200)
339 cd08176 LPO Lactadehyde:propan 79.7 7.7 0.00017 43.5 9.0 87 171-259 17-105 (377)
340 PF02608 Bmp: Basic membrane p 79.4 9.3 0.0002 41.5 9.3 89 51-146 128-221 (306)
341 cd08191 HHD 6-hydroxyhexanoate 79.4 17 0.00037 40.9 11.7 89 171-262 12-102 (386)
342 TIGR03339 phn_lysR aminoethylp 79.2 89 0.0019 32.9 17.3 69 513-593 98-166 (279)
343 cd08181 PPD-like 1,3-propanedi 79.1 10 0.00022 42.3 9.6 86 171-259 15-103 (357)
344 cd08170 GlyDH Glycerol dehydro 78.8 7.8 0.00017 43.0 8.6 84 171-259 12-97 (351)
345 PF06506 PrpR_N: Propionate ca 78.7 37 0.0008 33.3 12.5 128 98-267 17-145 (176)
346 cd08416 PBP2_MdcR The C-termin 78.6 68 0.0015 31.2 16.7 72 512-593 13-84 (199)
347 cd08182 HEPD Hydroxyethylphosp 78.5 17 0.00038 40.5 11.4 86 171-261 12-99 (367)
348 PRK09906 DNA-binding transcrip 78.4 75 0.0016 34.0 16.1 70 512-593 103-172 (296)
349 PRK03692 putative UDP-N-acetyl 78.1 26 0.00056 36.4 11.5 88 168-264 92-180 (243)
350 PF14503 YhfZ_C: YhfZ C-termin 77.5 7.8 0.00017 39.5 7.2 103 711-822 113-223 (232)
351 PRK10537 voltage-gated potassi 77.4 4.9 0.00011 45.0 6.4 54 638-691 164-219 (393)
352 TIGR00696 wecB_tagA_cpsF bacte 77.2 28 0.0006 34.2 10.9 98 168-278 35-134 (177)
353 PF13407 Peripla_BP_4: Peripla 77.1 7.6 0.00016 40.7 7.7 78 185-266 1-81 (257)
354 cd08428 PBP2_IciA_ArgP The C-t 76.4 78 0.0017 30.8 15.6 100 702-806 89-192 (195)
355 cd08186 Fe-ADH8 Iron-containin 76.3 21 0.00046 40.1 11.2 89 171-261 12-106 (383)
356 PRK07475 hypothetical protein; 76.2 17 0.00036 37.9 9.7 84 97-212 60-146 (245)
357 PF01177 Asp_Glu_race: Asp/Glu 76.1 65 0.0014 32.6 14.1 125 108-263 59-198 (216)
358 cd07766 DHQ_Fe-ADH Dehydroquin 75.6 22 0.00047 39.1 11.0 100 171-277 12-113 (332)
359 cd08187 BDH Butanol dehydrogen 75.4 13 0.00028 41.8 9.2 87 171-260 18-107 (382)
360 cd08446 PBP2_Chlorocatechol Th 75.3 83 0.0018 30.5 17.1 70 512-593 14-83 (198)
361 cd08171 GlyDH-like2 Glycerol d 74.7 14 0.0003 40.9 9.1 87 171-261 12-100 (345)
362 PF03401 TctC: Tripartite tric 74.3 76 0.0017 33.7 14.3 122 700-822 88-242 (274)
363 PF13685 Fe-ADH_2: Iron-contai 73.1 21 0.00046 37.2 9.3 100 172-277 9-108 (250)
364 KOG1419 Voltage-gated K+ chann 72.6 7.1 0.00015 44.0 5.9 89 607-695 234-324 (654)
365 cd08485 PBP2_ClcR The C-termin 72.4 1E+02 0.0022 30.2 16.6 70 512-593 14-83 (198)
366 PRK11716 DNA-binding transcrip 71.9 1.2E+02 0.0027 31.5 15.6 83 485-592 67-149 (269)
367 PRK09423 gldA glycerol dehydro 70.7 18 0.00038 40.4 8.8 84 171-259 19-104 (366)
368 PRK13348 chromosome replicatio 70.3 1.5E+02 0.0034 31.5 16.0 103 703-810 180-286 (294)
369 cd08450 PBP2_HcaR The C-termin 70.2 1.1E+02 0.0023 29.6 16.3 70 512-593 13-82 (196)
370 PRK09986 DNA-binding transcrip 70.1 1.6E+02 0.0034 31.4 17.1 85 485-593 97-181 (294)
371 PF00625 Guanylate_kin: Guanyl 69.9 32 0.0007 33.9 9.7 130 114-265 3-136 (183)
372 PRK05452 anaerobic nitric oxid 69.8 1.6E+02 0.0035 34.2 16.5 141 118-279 198-348 (479)
373 cd08183 Fe-ADH2 Iron-containin 69.8 36 0.00079 38.1 11.1 84 171-261 12-97 (374)
374 cd08432 PBP2_GcdR_TrpI_HvrB_Am 69.6 45 0.00097 32.3 10.9 65 513-592 14-78 (194)
375 PRK14498 putative molybdopteri 68.0 40 0.00086 40.9 11.7 67 180-251 184-262 (633)
376 PRK03635 chromosome replicatio 67.6 1.3E+02 0.0029 32.1 14.7 82 485-593 90-171 (294)
377 cd06305 PBP1_methylthioribose_ 67.3 24 0.00052 37.1 8.8 77 185-266 2-81 (273)
378 cd08431 PBP2_HupR The C-termin 66.3 1.3E+02 0.0028 29.1 14.3 71 512-593 13-83 (195)
379 cd08178 AAD_C C-terminal alcoh 66.3 41 0.00089 38.0 10.7 79 180-260 19-99 (398)
380 COG2358 Imp TRAP-type uncharac 65.8 31 0.00068 37.1 8.9 79 700-781 127-215 (321)
381 PLN03192 Voltage-dependent pot 65.8 6.6 0.00014 49.2 4.6 53 643-695 251-305 (823)
382 cd08550 GlyDH-like Glycerol_de 64.8 28 0.00061 38.6 8.8 84 171-259 12-97 (349)
383 cd08452 PBP2_AlsR The C-termin 64.2 1.5E+02 0.0031 28.9 17.9 70 512-593 13-82 (197)
384 cd06301 PBP1_rhizopine_binding 64.1 25 0.00055 37.0 8.2 78 184-266 1-82 (272)
385 PRK11139 DNA-binding transcrip 64.1 1E+02 0.0023 32.9 13.1 102 702-807 180-286 (297)
386 cd06312 PBP1_ABC_sugar_binding 63.8 27 0.00059 36.8 8.4 79 184-266 1-83 (271)
387 TIGR03298 argP transcriptional 63.5 2.1E+02 0.0045 30.4 16.4 64 516-592 107-170 (292)
388 PRK00865 glutamate racemase; P 63.2 82 0.0018 33.2 11.6 37 107-143 60-96 (261)
389 PF07287 DUF1446: Protein of u 63.0 2.3E+02 0.0049 31.4 15.0 173 60-268 6-187 (362)
390 cd01537 PBP1_Repressors_Sugar_ 62.8 25 0.00054 36.5 7.8 78 184-266 1-80 (264)
391 PRK15408 autoinducer 2-binding 62.8 36 0.00079 37.4 9.2 82 181-266 22-106 (336)
392 cd06267 PBP1_LacI_sugar_bindin 62.7 29 0.00063 36.1 8.3 76 185-266 2-79 (264)
393 TIGR03414 ABC_choline_bnd chol 61.9 2.1E+02 0.0045 30.7 14.6 41 514-563 23-63 (290)
394 cd08197 DOIS 2-deoxy-scyllo-in 61.8 96 0.0021 34.4 12.2 102 171-277 12-119 (355)
395 cd06306 PBP1_TorT-like TorT-li 61.4 31 0.00068 36.3 8.3 80 184-266 1-82 (268)
396 cd08422 PBP2_CrgA_like The C-t 61.3 42 0.00091 32.5 8.8 66 738-805 126-193 (197)
397 PRK01686 hisG ATP phosphoribos 60.9 1.7E+02 0.0038 29.6 12.7 93 711-810 114-208 (215)
398 PRK00945 acetyl-CoA decarbonyl 60.7 71 0.0015 31.0 9.5 120 108-238 28-168 (171)
399 PRK11119 proX glycine betaine 60.4 42 0.00092 36.7 9.1 62 481-565 25-87 (331)
400 cd08175 G1PDH Glycerol-1-phosp 60.2 41 0.00089 37.2 9.1 87 171-259 12-100 (348)
401 TIGR00070 hisG ATP phosphoribo 59.6 57 0.0012 32.1 8.8 74 701-782 100-173 (182)
402 cd06282 PBP1_GntR_like_2 Ligan 59.2 40 0.00088 35.2 8.7 77 185-266 2-80 (266)
403 COG2247 LytB Putative cell wal 58.6 1.2E+02 0.0026 32.4 11.2 50 160-215 104-159 (337)
404 cd02071 MM_CoA_mut_B12_BD meth 58.5 76 0.0016 28.9 9.1 62 197-266 14-79 (122)
405 PRK00002 aroB 3-dehydroquinate 57.5 96 0.0021 34.5 11.5 102 171-277 20-127 (358)
406 cd06318 PBP1_ABC_sugar_binding 57.1 40 0.00087 35.7 8.3 78 184-266 1-81 (282)
407 TIGR00315 cdhB CO dehydrogenas 56.7 1.3E+02 0.0028 29.0 10.5 120 109-238 22-160 (162)
408 cd08177 MAR Maleylacetate redu 56.3 30 0.00066 38.1 7.2 98 171-278 12-111 (337)
409 cd01536 PBP1_ABC_sugar_binding 56.1 46 0.001 34.6 8.5 78 184-266 1-81 (267)
410 cd06167 LabA_like LabA_like pr 56.0 1.7E+02 0.0037 27.4 11.6 95 171-266 27-124 (149)
411 cd08179 NADPH_BDH NADPH-depend 56.0 50 0.0011 37.0 9.0 80 179-260 20-102 (375)
412 cd01545 PBP1_SalR Ligand-bindi 55.2 51 0.0011 34.5 8.6 78 185-266 2-81 (270)
413 cd06310 PBP1_ABC_sugar_binding 55.2 46 0.001 35.0 8.3 80 184-266 1-83 (273)
414 cd06316 PBP1_ABC_sugar_binding 55.1 43 0.00093 35.8 8.1 79 184-266 1-82 (294)
415 cd01540 PBP1_arabinose_binding 54.8 40 0.00087 35.9 7.8 77 184-266 1-80 (289)
416 cd06302 PBP1_LsrB_Quorum_Sensi 54.8 51 0.0011 35.4 8.6 78 185-266 2-82 (298)
417 smart00072 GuKc Guanylate kina 54.6 2E+02 0.0044 28.2 12.2 130 114-265 3-136 (184)
418 cd06322 PBP1_ABC_sugar_binding 54.4 54 0.0012 34.3 8.7 77 185-266 2-81 (267)
419 cd06289 PBP1_MalI_like Ligand- 54.3 55 0.0012 34.2 8.7 77 185-266 2-80 (268)
420 cd06277 PBP1_LacI_like_1 Ligan 54.2 69 0.0015 33.5 9.4 75 185-266 2-81 (268)
421 TIGR00067 glut_race glutamate 53.3 1.7E+02 0.0037 30.6 11.8 40 105-144 51-91 (251)
422 PF04273 DUF442: Putative phos 53.3 1.4E+02 0.003 26.7 9.5 84 177-262 23-107 (110)
423 cd06304 PBP1_BmpA_like Peripla 53.1 1.8E+02 0.0039 30.3 12.4 126 50-184 121-246 (260)
424 PF02310 B12-binding: B12 bind 52.7 1.4E+02 0.0031 26.7 10.0 64 192-263 10-77 (121)
425 COG3340 PepE Peptidase E [Amin 52.7 1.4E+02 0.0031 30.0 10.1 85 171-267 22-108 (224)
426 cd08481 PBP2_GcdR_like The C-t 51.9 1.6E+02 0.0034 28.3 11.2 97 703-804 86-189 (194)
427 cd08549 G1PDH_related Glycerol 51.6 83 0.0018 34.5 9.7 98 171-277 12-113 (332)
428 cd01538 PBP1_ABC_xylose_bindin 51.6 71 0.0015 34.0 9.1 77 185-266 2-81 (288)
429 cd00886 MogA_MoaB MogA_MoaB fa 51.6 77 0.0017 30.2 8.2 63 184-250 2-70 (152)
430 cd08180 PDD 1,3-propanediol de 51.2 39 0.00086 37.1 7.1 79 178-259 18-98 (332)
431 TIGR02667 moaB_proteo molybden 51.1 90 0.0019 30.2 8.7 65 182-250 4-72 (163)
432 COG1922 WecG Teichoic acid bio 51.1 1.1E+02 0.0024 31.8 9.6 102 168-282 95-199 (253)
433 cd06299 PBP1_LacI_like_13 Liga 51.0 74 0.0016 33.2 9.0 76 185-266 2-79 (265)
434 PF01634 HisG: ATP phosphoribo 50.9 22 0.00047 34.3 4.3 102 701-810 57-160 (163)
435 PRK09701 D-allose transporter 50.6 74 0.0016 34.4 9.1 84 180-266 22-108 (311)
436 cd01391 Periplasmic_Binding_Pr 50.5 53 0.0012 33.8 7.8 78 184-266 1-83 (269)
437 cd06300 PBP1_ABC_sugar_binding 50.5 70 0.0015 33.6 8.8 80 184-266 1-86 (272)
438 PRK15424 propionate catabolism 50.5 2.7E+02 0.0058 32.9 13.9 129 98-268 47-176 (538)
439 COG1464 NlpA ABC-type metal io 50.3 69 0.0015 33.3 7.9 47 48-105 29-75 (268)
440 cd06303 PBP1_LuxPQ_Quorum_Sens 50.1 53 0.0011 34.8 7.8 81 184-265 1-84 (280)
441 PF00218 IGPS: Indole-3-glycer 49.5 1E+02 0.0022 32.2 9.3 88 170-267 70-160 (254)
442 PF13380 CoA_binding_2: CoA bi 49.4 23 0.0005 32.0 4.0 86 183-277 1-88 (116)
443 TIGR01744 XPRTase xanthine pho 49.4 48 0.001 33.0 6.6 70 74-144 5-79 (191)
444 cd08184 Fe-ADH3 Iron-containin 49.4 83 0.0018 34.7 9.1 85 171-261 12-103 (347)
445 TIGR00249 sixA phosphohistidin 49.2 95 0.0021 29.6 8.5 98 163-263 24-121 (152)
446 COG0563 Adk Adenylate kinase a 48.4 46 0.001 32.7 6.3 28 116-143 3-30 (178)
447 PRK09189 uroporphyrinogen-III 47.8 1.8E+02 0.0038 30.1 11.0 87 169-263 103-191 (240)
448 cd00758 MoCF_BD MoCF_BD: molyb 47.1 87 0.0019 29.0 7.7 48 198-250 20-67 (133)
449 cd08169 DHQ-like Dehydroquinat 47.0 1.5E+02 0.0033 32.6 10.8 101 171-277 12-118 (344)
450 cd06270 PBP1_GalS_like Ligand 46.9 96 0.0021 32.4 9.1 76 185-266 2-79 (268)
451 TIGR02329 propionate_PrpR prop 46.6 3.4E+02 0.0073 32.0 14.0 129 98-268 37-166 (526)
452 COG1880 CdhB CO dehydrogenase/ 46.6 2.6E+02 0.0057 26.5 10.7 124 106-238 27-168 (170)
453 COG0134 TrpC Indole-3-glycerol 46.6 48 0.001 34.4 6.1 86 172-267 70-158 (254)
454 PHA03239 envelope glycoprotein 46.2 44 0.00096 37.3 6.2 28 848-875 334-361 (429)
455 TIGR02637 RhaS rhamnose ABC tr 46.1 78 0.0017 34.0 8.4 77 186-266 2-82 (302)
456 cd06281 PBP1_LacI_like_5 Ligan 45.7 96 0.0021 32.5 8.9 77 185-266 2-80 (269)
457 cd06315 PBP1_ABC_sugar_binding 45.6 1.1E+02 0.0024 32.4 9.3 79 183-266 1-82 (280)
458 PF00532 Peripla_BP_1: Peripla 45.5 63 0.0014 34.4 7.4 73 183-261 2-76 (279)
459 PRK10936 TMAO reductase system 45.4 93 0.002 34.3 9.0 80 183-266 47-129 (343)
460 PRK15116 sulfur acceptor prote 45.4 3.3E+02 0.0071 28.8 12.3 79 61-151 80-159 (268)
461 TIGR00177 molyb_syn molybdenum 45.3 1E+02 0.0022 29.0 7.9 48 198-250 28-75 (144)
462 TIGR02370 pyl_corrinoid methyl 45.3 1.5E+02 0.0033 29.6 9.6 87 183-277 85-175 (197)
463 cd01324 cbb3_Oxidase_CcoQ Cyto 44.8 23 0.00049 26.2 2.6 27 608-634 12-38 (48)
464 cd01542 PBP1_TreR_like Ligand- 44.7 99 0.0021 32.0 8.8 75 185-265 2-78 (259)
465 PRK03601 transcriptional regul 44.4 4E+02 0.0087 28.0 15.3 84 484-593 88-171 (275)
466 cd08173 Gro1PDH Sn-glycerol-1- 44.3 1E+02 0.0022 34.0 9.0 95 172-277 14-111 (339)
467 COG0078 ArgF Ornithine carbamo 44.3 4.3E+02 0.0093 28.3 16.9 163 49-248 44-213 (310)
468 cd06320 PBP1_allose_binding Pe 44.1 90 0.002 32.8 8.4 80 184-266 1-83 (275)
469 cd06295 PBP1_CelR Ligand bindi 43.9 98 0.0021 32.5 8.7 77 182-266 3-88 (275)
470 PRK11303 DNA-binding transcrip 43.8 1.2E+02 0.0025 33.0 9.5 80 182-266 61-142 (328)
471 PRK10014 DNA-binding transcrip 43.8 1.3E+02 0.0028 32.9 9.9 79 183-266 65-145 (342)
472 PRK13010 purU formyltetrahydro 43.7 4.4E+02 0.0095 28.2 14.6 89 115-209 11-117 (289)
473 PRK10355 xylF D-xylose transpo 43.7 1.1E+02 0.0025 33.4 9.3 80 182-266 25-107 (330)
474 PF00072 Response_reg: Respons 43.7 1.6E+02 0.0034 25.6 8.7 58 197-265 9-69 (112)
475 PRK07377 hypothetical protein; 43.6 50 0.0011 32.0 5.3 61 485-562 75-135 (184)
476 PRK00843 egsA NAD(P)-dependent 43.5 1.3E+02 0.0029 33.2 9.8 97 171-278 22-121 (350)
477 KOG0025 Zn2+-binding dehydroge 43.3 1.1E+02 0.0024 32.3 8.0 97 157-266 162-258 (354)
478 cd06317 PBP1_ABC_sugar_binding 43.2 98 0.0021 32.4 8.5 77 185-266 2-82 (275)
479 cd08475 PBP2_CrgA_like_6 The C 43.1 2.1E+02 0.0046 27.5 10.5 67 738-806 128-196 (199)
480 PRK10653 D-ribose transporter 42.8 1.1E+02 0.0024 32.7 8.9 80 182-266 26-108 (295)
481 cd03522 MoeA_like MoeA_like. T 42.6 1.3E+02 0.0028 32.6 9.1 67 180-250 157-228 (312)
482 PF14981 FAM165: FAM165 family 42.4 62 0.0013 23.2 4.2 33 842-874 3-35 (51)
483 cd06323 PBP1_ribose_binding Pe 42.2 91 0.002 32.5 8.1 77 185-266 2-81 (268)
484 PF00448 SRP54: SRP54-type pro 42.1 2.3E+02 0.0049 28.4 10.2 65 182-251 29-93 (196)
485 cd01574 PBP1_LacI Ligand-bindi 41.8 1.3E+02 0.0028 31.3 9.1 77 185-266 2-80 (264)
486 cd06273 PBP1_GntR_like_1 This 41.2 1.2E+02 0.0027 31.5 8.9 76 185-266 2-79 (268)
487 PF00205 TPP_enzyme_M: Thiamin 40.9 35 0.00076 31.8 4.0 57 105-162 2-62 (137)
488 COG4521 TauA ABC-type taurine 40.8 2E+02 0.0044 29.3 9.2 106 700-807 120-237 (334)
489 cd06319 PBP1_ABC_sugar_binding 40.8 1.1E+02 0.0023 32.1 8.4 77 185-266 2-81 (277)
490 TIGR01276 thiB thiamine ABC tr 40.7 4.9E+02 0.011 27.9 15.7 83 740-822 175-261 (309)
491 cd01539 PBP1_GGBP Periplasmic 40.7 1.2E+02 0.0025 32.7 8.7 78 184-266 1-83 (303)
492 cd01575 PBP1_GntR Ligand-bindi 40.5 1.2E+02 0.0025 31.7 8.5 76 185-266 2-79 (268)
493 PRK14174 bifunctional 5,10-met 39.9 5E+02 0.011 27.8 14.9 175 51-251 33-216 (295)
494 cd00755 YgdL_like Family of ac 39.8 2.7E+02 0.0058 28.7 10.5 77 60-148 60-137 (231)
495 PRK02261 methylaspartate mutas 39.8 3E+02 0.0066 25.6 10.0 86 183-277 4-93 (137)
496 PF02310 B12-binding: B12 bind 39.6 1.2E+02 0.0026 27.2 7.4 73 169-251 16-89 (121)
497 cd00885 cinA Competence-damage 39.4 1.2E+02 0.0026 29.5 7.6 46 199-249 21-66 (170)
498 KOG3713 Voltage-gated K+ chann 39.3 41 0.00089 37.9 4.7 59 621-683 360-420 (477)
499 PRK14737 gmk guanylate kinase; 39.2 3.9E+02 0.0085 26.4 11.4 130 114-265 5-138 (186)
500 PRK11070 ssDNA exonuclease Rec 39.1 2.1E+02 0.0045 34.1 10.7 101 170-277 55-158 (575)
No 1
>KOG1054 consensus Glutamate-gated AMPA-type ion channel receptor subunit GluR2 and related subunits [Inorganic ion transport and metabolism; Amino acid transport and metabolism; Signal transduction mechanisms]
Probab=100.00 E-value=9.4e-87 Score=697.11 Aligned_cols=778 Identities=19% Similarity=0.320 Sum_probs=628.9
Q ss_pred CCceEEEeEEEecCCCchhHHHHHHHHHHHHHhcCCCCCC-CcEEEEEEecCC-CChHHHHHHHHHHHhcCcEEEEccCC
Q 002211 46 KPEVLNVGAIFSFGTVNGQVSRIAMKAAQDDINSDPRVLG-GRKLSITMHDAK-FNGFLSIMGALQFMETDTLAIVGPQS 123 (953)
Q Consensus 46 ~~~~i~IG~l~~~~~~~g~~~~~a~~lAve~iN~~g~il~-g~~l~l~~~D~~-~~~~~a~~~a~~li~~~v~aiiGp~~ 123 (953)
-+..|.||.+||.... +...|+++|+...|....--+ -.+|..++..-. .+......+.|...++||.||+|-+.
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 4678999999998764 467788888887776433210 134444433222 46677778889999999999999999
Q ss_pred hhhHHHHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecCccccchHHHHH
Q 002211 124 AVMAHVLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDDDQGRNGVTALG 203 (953)
Q Consensus 124 S~~a~av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~~~g~~~~~~l~ 203 (953)
-.....+..++...++|+|+++. |. +...++..++.|+-. .++++++.|++|.+++++| |.+-|....+++.
T Consensus 100 ~ks~~~ltsfc~aLh~~~vtpsf--p~--~~~~~Fviq~RP~l~---~al~s~i~hy~W~~fv~ly-D~~rg~s~Lqai~ 171 (897)
T KOG1054|consen 100 KKSVNTLTSFCGALHVSFVTPSF--PT--DGDNQFVIQMRPALK---GALLSLIDHYKWEKFVYLY-DTDRGLSILQAIM 171 (897)
T ss_pred ccchhhhhhhccceeeeeecccC--Cc--CCCceEEEEeCchHH---HHHHHHHHhcccceEEEEE-cccchHHHHHHHH
Confidence 99999999999999999998754 22 233467888888754 7899999999999999999 6667889999999
Q ss_pred HHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEEeCcccccc
Q 002211 204 DKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIATTWLSTFI 283 (953)
Q Consensus 204 ~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~ 283 (953)
+.+.++++.|.....-.+. +...+..+++.+...+.+.|++.|..+....++.|+-+.|-...+|+++..+..-...
T Consensus 172 ~~a~~~nw~VtA~~v~~~~---d~~~yr~~f~~l~~r~e~rv~iDce~~~~~~il~q~i~~~k~~~~YHYvlaNl~f~d~ 248 (897)
T KOG1054|consen 172 EAAAQNNWQVTAINVGNIN---DVKEYRMLFEMLDRRQENRVLIDCESERRNRILLQVIELGKHVKGYHYVLANLGFTDI 248 (897)
T ss_pred HHHHhcCceEEEEEcCCcc---cHHHHHHHHHHHhccccceEEEEcccHHHHHHHHHHHHHhhhccceEEEEeeCCCchh
Confidence 9999999998876544333 3566999999999999999999999999999999999988888999999988544443
Q ss_pred cCCCCCchhhhhhccceEEEEEecCCChhhHHHHHHHHhhcC------CCCCCCchhhHHhhHHHHHHHHHHHHHhcCCc
Q 002211 284 DSKSPLSLKTAKSILGALTLRQHTPDSKRRRDFVSRWNTLSN------GSIGLNPYGLYAYDTVWMIARALKLFLDQGNT 357 (953)
Q Consensus 284 ~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~F~~~~~~~~~------~~~~~~~~~~~~YDAv~~la~Al~~~~~~~~~ 357 (953)
+. ........++.+++...-+.|..++|.++|++... ...++...++.+|||+.++++|++.+..+...
T Consensus 249 dl-----~~f~~g~aNitgFqivn~~~~~~~k~~~~~~~l~~~~~~g~~~~~~k~tsAlthDailV~~eaf~~~~~q~~~ 323 (897)
T KOG1054|consen 249 DL-----ERFQHGGANITGFQIVNKNNPMVKKFIQRWKELDEREYPGASNDPIKYTSALTHDAILVMAEAFRSLRRQRID 323 (897)
T ss_pred hH-----HHHhcCCcceeEEEEecCCChHHHHHHHHHhhhcccccCCCCCCCcchhhhhhhhHHHHHHHHHHHHHHhhhc
Confidence 33 34455667789999999999999999999986542 22456677899999999999999999877543
Q ss_pred ccccCCCccCCCCCCcccCCCccccCchHHHHHHHHhcccCCcceeEEEccCCCCCCccEEEEEeecCCeeeEEEEecCC
Q 002211 358 ISFSNDTKLNGLGGGTLNLGALSIFDGGKKFLANILQTNMTGLSGPIHFNQDRSLLHPSYDIINVIEHGYPQQIGYWSNY 437 (953)
Q Consensus 358 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~f~G~tG~v~Fd~~g~~~~~~y~I~~~~~~~~~~~VG~w~~~ 437 (953)
... ++..|+++. .+..+|.+|..+-++|++++++|+||.|+||..|.|.+.+.+|+++..++. ++||+|+..
T Consensus 324 ~~r------RG~~GD~~a-n~~~p~~qG~~I~ralk~v~~eGLTGniqFd~~G~R~Nyt~~i~elk~~~~-rk~~~W~e~ 395 (897)
T KOG1054|consen 324 ISR------RGNAGDCLA-NPAVPWEQGIDIERALKQVQVEGLTGNIQFDKYGRRTNYTIDIVELKSNGS-RKVGYWNEG 395 (897)
T ss_pred hhc------cCCCccccC-CCCCchhcchhHHHHHHheeecccccceeecccCccccceEEEEEeccCCc-ceeeeeccc
Confidence 321 223343322 347789999999999999999999999999999999999999999999998 999999999
Q ss_pred CCccccCCcccccCCCCCCCCCCcceeeEeCCCcccCCCcccccCCCcceEEEecCcccccccEEe---eCCcceEEEee
Q 002211 438 SGLSVVPPEKLYRKPANRSSSNQHLYSVVWPGGVTSKPRGWVFPNNGRQLRIGVPNRVSYRDFVFK---VNGTDIVHGYC 514 (953)
Q Consensus 438 ~gl~~~~~~~~~~~~~~~~~~~~~l~~i~Wpg~~~~~P~~~~~~~~g~~lri~v~~~~~~~p~~~~---~~~~~~~~G~~ 514 (953)
.|+.....+. ...+. +. ..+.++..+.+.-..||..+... -.|+.++.|||
T Consensus 396 ~~fv~~~t~a----~~~~d---~~-------------------~~~n~tvvvttiL~spyvm~kkn~~~~egn~ryEGyC 449 (897)
T KOG1054|consen 396 EGFVPGSTVA----QSRND---QA-------------------SKENRTVVVTTILESPYVMLKKNHEQLEGNERYEGYC 449 (897)
T ss_pred Cceeeccccc----ccccc---cc-------------------ccccceEEEEEecCCchhHHHhhHHHhcCCcccceeH
Confidence 8865321100 00000 00 01123333333321133222221 13678999999
Q ss_pred HHHHHHHHHhCCCcccEEEeeCC---CCCCCCC-hHHHHHHHHcCceeEEEecEEEecCccceeeccccceecceEEEEe
Q 002211 515 IDVFLAAVRLLPYAVPYKFIPYG---DGHKNPT-YSELINQITTGVFDAAVGDIAIVTNRTKAVDFTQPYIESGLVVVAP 590 (953)
Q Consensus 515 ~dll~~la~~l~~~~~~~~~~~~---~~~~n~~-~~~~i~~l~~g~~Di~~~~~~~t~~r~~~vdft~p~~~~~~~~~v~ 590 (953)
+||+.++|++.++++++..+..| ..+..++ |+||+++|..|++|+++++++||..|++.+|||.|++..|++++.+
T Consensus 450 vdLa~~iAkhi~~~Y~l~iv~dgkyGardaD~k~WnGMvGeLv~grAdiavApLTIt~~REeviDFSKPfMslGISIMIK 529 (897)
T KOG1054|consen 450 VDLAAEIAKHIGIKYKLFIVGDGKYGARDADTKIWNGMVGELVYGRADIAVAPLTITLVREEVIDFSKPFMSLGISIMIK 529 (897)
T ss_pred HHHHHHHHHhcCceEEEEEecCCcccccCCCcccccchhHHHhcCccceEEeeeeeehhhhhhhccccchhhcCeEEEEe
Confidence 99999999999987666666533 3334455 9999999999999999999999999999999999999999999999
Q ss_pred ccc-CCcCcceeeccCchhHHHHHHHHHHHHHHHhhhhhcccCCCCC------CC-------CcccchhhHHHHHHHhhc
Q 002211 591 VRK-LNSSAWAFLRPFTPLMWAVTGVFFLVVGTVVWILEHRLNDEFR------GP-------PRKQIVTVLWFSFSTMFF 656 (953)
Q Consensus 591 ~~~-~~~~~~~~l~PF~~~vW~~i~~~~~~~~~~~~~l~~~~~~~~~------~~-------~~~~~~~~~~~~~~~l~~ 656 (953)
+|+ ..+..+.|+.|+..++|+|++..++-+++++++..+.++.+|+ |+ +-+++.+++||+++++++
T Consensus 530 KPqKsk~gVFSFldPLa~eIWm~ivfaYiGVSvvlFLVSrFSPYEwh~Ee~~rg~~t~~~~~NeFgifNsLWFsLgAFMQ 609 (897)
T KOG1054|consen 530 KPQKSKPGVFSFLDPLAYEIWMCIVFAYIGVSVVLFLVSRFSPYEWHTEEFERGRFTPSDPPNEFGIFNSLWFSLGAFMQ 609 (897)
T ss_pred CcccCCCCeeeecchhHHHHHHHHHHHHhcceEEEEEEeccCchheeccccccCCCCCCCCCccchhhHHHHHHHHHHHh
Confidence 998 6789999999999999999999999999999999999887653 22 224689999999999999
Q ss_pred cccC-CcccchhHHHHHHHHHHHHHhhhhcccceeeeeeeccccCCCCChHHhhhCCC-eEEEEeCchHHHHHHHhhCCC
Q 002211 657 AHRE-NTVSTLGRVVLIIWLFVVLIITSSYTASLTSILTVQQLSSPIKGIDTLMTSND-RVGYQVGSFAENYLIEELSIP 734 (953)
Q Consensus 657 ~~~~-~~~s~~~R~l~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~I~sl~dL~~~~~-~ig~~~~s~~~~~l~~~~~~~ 734 (953)
|+.+ .|+|.++||+..+||||+||++++|||||++|||++++.+||.+.|||++|.+ ..|+.++....+||+...-..
T Consensus 610 QG~DI~PRslSGRIvggvWWFFTlIIiSSYTANLAAFLTvErMvsPIESaEDLAkQteIaYGt~~~GSTkeFFr~Skiav 689 (897)
T KOG1054|consen 610 QGCDISPRSLSGRIVGGVWWFFTLIIISSYTANLAAFLTVERMVSPIESAEDLAKQTEIAYGTLDSGSTKEFFRRSKIAV 689 (897)
T ss_pred cCCCCCccccccceeccchhhhhhhhhhhhhhHHHHHHhHHhhcCcchhHHHHhhcceeeeeecCCCchHHHHhhhhHHH
Confidence 9988 89999999999999999999999999999999999999999999999998876 367788777788885421000
Q ss_pred ccce----------EeCCCHHHHHHHHHc-CCcEEEEccchhHHHHHhc-CcceEEeCCccccCccEEEecCCCcchHHH
Q 002211 735 KSRL----------VALGSPEEYAIALEN-RTVAAVVDERPYIDLFLSD-HCQFSVRGQEFTKSGWGFAFPRDSPLAIDM 802 (953)
Q Consensus 735 ~~~~----------~~~~~~~~~~~~l~~-g~~~a~~~~~~~~~~~~~~-~~~l~~~~~~~~~~~~~~~~~k~spl~~~~ 802 (953)
..++ +.+.+..|+++++++ .+.+||+.|...-+|.-++ +|+-..++..+.+.+||++.||||.|+..+
T Consensus 690 y~kMW~yM~SaepsVFv~t~aeGv~rVRksKGkyAfLLEsTmNey~eqRkPCDTMKVGgNLds~GYGiATp~Gsslr~~v 769 (897)
T KOG1054|consen 690 YEKMWTYMKSAEPSVFVRTTAEGVARVRKSKGKYAFLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGIATPKGSSLRNAV 769 (897)
T ss_pred HHHHHHHHhcCCcceeeehhhhHHHHHHhcCCceEeehHhhhhhhhhccCCccceecccccCCcceeecCCCCcccccch
Confidence 0111 345689999999998 7788999999988888765 899999999999999999999999999999
Q ss_pred HHHHHhhhccccHHHHHHHhcc-cCCCCCCCCCC--CCCccccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhccc
Q 002211 803 STAILTLSENGELQRIHDKWLR-KKACSSESSQS--DSEQLQIQSFRGLFLICGIACFLALLAYFCLMLRQFKKYSA 876 (953)
Q Consensus 803 n~~i~~l~e~G~~~~~~~~w~~-~~~c~~~~~~~--~~~~l~l~~~~g~f~il~~g~~lallvf~~e~~~~~~~~~~ 876 (953)
|.+++.|.|.|+++++++|||. ++.|....... ....|+|++..|+||||..|++||.++.++|++|+.|...+
T Consensus 770 NLAvLkL~E~G~LdKLkNKWWYDkGeC~sg~~ds~~ktsaLsLSnVAGvFYIL~gGl~laMlvALiEF~yksr~Eak 846 (897)
T KOG1054|consen 770 NLAVLKLNEQGLLDKLKNKWWYDKGECGSGGGDSKDKTSALSLSNVAGVFYILVGGLGLAMLVALIEFCYKSRAEAK 846 (897)
T ss_pred hhhhhhhcccchHHHhhhhhcccccccCCCCCCCCcchhhcchhhccceeeeehhhHHHHHHHHHHHHHHHhhHHHH
Confidence 9999999999999999999998 89999876543 45789999999999999999999999999999998766544
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=2.5e-81 Score=659.10 Aligned_cols=750 Identities=22% Similarity=0.391 Sum_probs=617.1
Q ss_pred cCCCCceEEEeEEEecCCCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEec--CCCChHHHHHHHH-HHHhcCcEEEE
Q 002211 43 GALKPEVLNVGAIFSFGTVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHD--AKFNGFLSIMGAL-QFMETDTLAIV 119 (953)
Q Consensus 43 ~~~~~~~i~IG~l~~~~~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D--~~~~~~~a~~~a~-~li~~~v~aii 119 (953)
++..+++++||.++... ....-+.-++.++|++.+ ..++.+...- -..++.+.+-.+| +|++..|.+|+
T Consensus 29 a~~np~t~nig~Vlst~-----~~ee~F~~t~~hln~~~~---s~k~~~~aksv~~d~n~i~t~~~VC~~li~~~vyav~ 100 (993)
T KOG4440|consen 29 AACNPKTVNIGAVLSTR-----KHEEMFRETVNHLNKRHG---SWKIQLNAKSVTHDPNAIQTALSVCEDLISSQVYAVL 100 (993)
T ss_pred cCCCccceeeeeeeech-----hHHHHHHHHHHHhhcccc---ceEEEEccccccCCCcHHHHHHHHHHHHHhhheeEEE
Confidence 34678899999998753 345668888999997764 2566653222 2235555555555 57888888877
Q ss_pred c--cCChhh---HHHHHHhhhhCCCcEEEeecCCCCCCC-CCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecCc
Q 002211 120 G--PQSAVM---AHVLSHLANELQVPLLSFTALDPTLSP-LQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDDD 193 (953)
Q Consensus 120 G--p~~S~~---a~av~~v~~~~~vP~Is~~at~~~ls~-~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~~ 193 (953)
- |.+|.. -.+++..+..+++|++.....+..+++ .-++.|.|+.|+.+.|+.+..+.+.+|.|++|.++.+||.
T Consensus 101 vSh~~Ts~d~f~p~~vSYT~gFY~iPV~G~~~Rda~fSdKnIh~sFlRtvpPyshqa~VwleMl~~~~y~~vi~l~s~d~ 180 (993)
T KOG4440|consen 101 VSHPPTSNDHFTPTPVSYTAGFYRIPVLGLTTRDAIFSDKNIHLSFLRTVPPYSHQASVWLEMLRVYSYNHVILLVSDDH 180 (993)
T ss_pred ecCCCCCCcccccccceeeccceeeeeeeeeehhhhhccCceeeeEeecCCCccchhHHHHHHHHHhhcceEEEEEcccc
Confidence 3 333332 235567788999999999999999999 6689999999999999999999999999999999999999
Q ss_pred cccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHHHcCCCCCceEE
Q 002211 194 QGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVW 273 (953)
Q Consensus 194 ~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~w 273 (953)
-|+.....++-.+++...++.....+.++ ..+++..|-.+|..++||+++....+++..+++.|.+++|++.||+|
T Consensus 181 ~gra~~~r~qt~~e~~~~~~e~v~~f~p~----~~~~t~~l~~~k~~~~rv~~~~as~dDA~~ifr~Ag~lnmTG~G~VW 256 (993)
T KOG4440|consen 181 EGRAAQKRLQTLLEERESKAEKVLQFDPG----TKNVTALLMEAKELEARVIILSASEDDAATIFRAAGMLNMTGSGYVW 256 (993)
T ss_pred cchhHHhHHHHHHHHHhhhhhhheecCcc----cchHHHHHhhhhhhhheeEEeecccchHHHHHHhhhhhcccCceEEE
Confidence 99988888888888777776666678877 78899999999999999999999999999999999999999999999
Q ss_pred EEeCcccccccCCCCCchhhhhhccceEEEEEecCCChhhHHHHHHHHhhcCCCCCCCchhhHHhhHHHHHHHHHHHHHh
Q 002211 274 IATTWLSTFIDSKSPLSLKTAKSILGALTLRQHTPDSKRRRDFVSRWNTLSNGSIGLNPYGLYAYDTVWMIARALKLFLD 353 (953)
Q Consensus 274 i~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~F~~~~~~~~~~~~~~~~~~~~~YDAv~~la~Al~~~~~ 353 (953)
|++....... ....|++|.+.-...+ -.++.-|++.++|.|++++..
T Consensus 257 iV~E~a~~~n-----------n~PdG~LGlqL~~~~~----------------------~~~hirDsv~vlasAv~e~~~ 303 (993)
T KOG4440|consen 257 IVGERAISGN-----------NLPDGILGLQLINGKN----------------------ESAHIRDSVGVLASAVHELLE 303 (993)
T ss_pred EEeccccccC-----------CCCCceeeeEeecCcc----------------------ccceehhhHHHHHHHHHHHHh
Confidence 9998544321 3367899987743211 134677999999999999986
Q ss_pred cCCcccccCCCccCCCCCCcccCCCccccCchHHHHHHHHhcc-cCCcceeEEEccCCCCCCccEEEEEeecCCeeeEEE
Q 002211 354 QGNTISFSNDTKLNGLGGGTLNLGALSIFDGGKKFLANILQTN-MTGLSGPIHFNQDRSLLHPSYDIINVIEHGYPQQIG 432 (953)
Q Consensus 354 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~-f~G~tG~v~Fd~~g~~~~~~y~I~~~~~~~~~~~VG 432 (953)
...-.. -+..||++...|..+..|.+.+...+ ..|.||+|.||++|||....|+|+|+..+...+.+|
T Consensus 304 ~e~I~~-----------~P~~c~d~~~~w~~g~~l~~~l~s~~~~~g~TgrV~Fnd~gdRi~a~YdiiN~hq~rk~Vg~~ 372 (993)
T KOG4440|consen 304 KENITD-----------PPRGCVDNTNIWKTGPLLKRVLMSSKYADGVTGRVEFNDDGDRIFANYDIINLHQNRKLVGVG 372 (993)
T ss_pred hccCCC-----------CCCcccCccchhcccHHHHHHHhhhcccCCcceeEEEcCCCceeeccceeEehhhhhhhhhhc
Confidence 533211 12346777788888888888888766 589999999999999999999999997544425555
Q ss_pred EecCCCCccccCCcccccCCCCCCCCCCcceeeEeCCCcccCCCcccccCCCcceEEEecCcccccccEEeeC-------
Q 002211 433 YWSNYSGLSVVPPEKLYRKPANRSSSNQHLYSVVWPGGVTSKPRGWVFPNNGRQLRIGVPNRVSYRDFVFKVN------- 505 (953)
Q Consensus 433 ~w~~~~gl~~~~~~~~~~~~~~~~~~~~~l~~i~Wpg~~~~~P~~~~~~~~g~~lri~v~~~~~~~p~~~~~~------- 505 (953)
.|+... ...+...|+||||.+..|++...| .+|||.+.+. +||+|..+
T Consensus 373 ~yd~~r-------------------~~~nd~~IiWpGg~~~KP~gi~~p---thLrivTi~~---~PFVYv~p~~sd~~c 427 (993)
T KOG4440|consen 373 IYDGTR-------------------VIPNDRKIIWPGGETEKPRGIQMP---THLRIVTIHQ---EPFVYVKPTLSDGTC 427 (993)
T ss_pred ccccee-------------------eccCCceeecCCCCcCCCcccccc---ceeEEEEecc---CCeEEEecCCCCcch
Confidence 554322 123456899999999999999988 5689888764 56666531
Q ss_pred ------------------------C------cceEEEeeHHHHHHHHHhCCCcccEEEeeCCC-CC----------CCCC
Q 002211 506 ------------------------G------TDIVHGYCIDVFLAAVRLLPYAVPYKFIPYGD-GH----------KNPT 544 (953)
Q Consensus 506 ------------------------~------~~~~~G~~~dll~~la~~l~~~~~~~~~~~~~-~~----------~n~~ 544 (953)
+ .-|+.|||||++-.+++.+||+++..+++.|. |. ...+
T Consensus 428 ~eef~~~~d~~~k~~c~gpn~s~p~s~~~t~~fCC~G~cIDLLi~Ls~~~Nftyd~~l~~dg~fg~~~~vnnsseT~~ke 507 (993)
T KOG4440|consen 428 KEEFTVNGDPVKKVICTGPNDSSPGSPRHTVPFCCYGFCIDLLIKLSRTMNFTYDVHLVADGKFGTQERVNNSSETNKKE 507 (993)
T ss_pred hhhccccCCcccceeecCCCCCCCCCcccCcchhhhHHHHHHHHHHHHhhcceEEEEEeecccccceeeeecccccccce
Confidence 0 12789999999999999999999999888542 11 2236
Q ss_pred hHHHHHHHHcCceeEEEecEEEecCccceeeccccceecceEEEEecccCCcCcceeeccCchhHHHHHHHHHHHHHHHh
Q 002211 545 YSELINQITTGVFDAAVGDIAIVTNRTKAVDFTQPYIESGLVVVAPVRKLNSSAWAFLRPFTPLMWAVTGVFFLVVGTVV 624 (953)
Q Consensus 545 ~~~~i~~l~~g~~Di~~~~~~~t~~r~~~vdft~p~~~~~~~~~v~~~~~~~~~~~~l~PF~~~vW~~i~~~~~~~~~~~ 624 (953)
|+|++++|.+|++||++++++|+++|.++++||.||...|+.++.+++.+.+....||+||+..+|+++++++.++++++
T Consensus 508 w~G~iGEL~~~~ADMivaplTINpERa~yieFskPfkYqGitILeKk~~r~Stl~SFlQPfqstLW~lv~~SVhvVal~l 587 (993)
T KOG4440|consen 508 WNGMIGELLSGQADMIVAPLTINPERAQYIEFSKPFKYQGITILEKKEIRRSTLDSFLQPFQSTLWLLVGLSVHVVALML 587 (993)
T ss_pred ehhhhhhhhCCccceEeeceeeChhhhhheeccCcccccceEEEeeCCCCCchHHHHHhHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhcccCC-CCCCC-------CcccchhhHHHHHHHhhccccC--CcccchhHHHHHHHHHHHHHhhhhcccceeeeee
Q 002211 625 WILEHRLND-EFRGP-------PRKQIVTVLWFSFSTMFFAHRE--NTVSTLGRVVLIIWLFVVLIITSSYTASLTSILT 694 (953)
Q Consensus 625 ~~l~~~~~~-~~~~~-------~~~~~~~~~~~~~~~l~~~~~~--~~~s~~~R~l~~~w~~~~lil~~~Yta~L~s~Lt 694 (953)
+++++.++. .|+-. ....++..+||+||.++..|.. .|+|.+.|++-++|+-|++|++++|||||++||.
T Consensus 588 YlLDrfSPFgRFk~~ds~~~ee~alnlssAmWF~WGVLLNSGigEgtPRSfSARvLGmVWaGFaMIiVASYTANLAAFLV 667 (993)
T KOG4440|consen 588 YLLDRFSPFGRFKVNDSEEEEEDALNLSSAMWFSWGVLLNSGIGEGTPRSFSARVLGMVWAGFAMIIVASYTANLAAFLV 667 (993)
T ss_pred HHHHhcCcccceeeccCccchhhhcchhhhHHHHhHhhhccccCCCCCcchhHHHHHHHHhhhheeeehhhhhhhhhhee
Confidence 999998875 34332 2346899999999999988743 8999999999999999999999999999999999
Q ss_pred eccccCCCCChHHhhhC----CCeEEEEeCchHHHHHHHhhCCC--ccce--EeCCCHHHHHHHHHcCCcEEEEccchhH
Q 002211 695 VQQLSSPIKGIDTLMTS----NDRVGYQVGSFAENYLIEELSIP--KSRL--VALGSPEEYAIALENRTVAAVVDERPYI 766 (953)
Q Consensus 695 ~~~~~~~I~sl~dL~~~----~~~ig~~~~s~~~~~l~~~~~~~--~~~~--~~~~~~~~~~~~l~~g~~~a~~~~~~~~ 766 (953)
..+.+..++++.|-.-. +...+.+.+|....||+++.... ..++ ..|.+.+|+++++++|..+||+-|..-+
T Consensus 668 LdrPe~~ltGinDpRLRNps~nf~~aTVk~SsVd~YFrRqVELS~MyR~ME~hNy~~A~eAiq~v~~gkL~AFIWDS~rL 747 (993)
T KOG4440|consen 668 LDRPEERLTGINDPRLRNPSDNFIYATVKQSSVDIYFRRQVELSTMYRHMEKHNYESAAEAIQAVRDGKLHAFIWDSARL 747 (993)
T ss_pred ecCccccccCCCCccccCcccceeEEEecCccHHHHHHHHhHHHHHHHhhhhcchhhHHHHHHHHHcCceeEEEeeccee
Confidence 99999999999884422 24578899999999997653221 1122 3478999999999999999999999999
Q ss_pred HHHHhcCcceEEeCCccccCccEEEecCCCcchHHHHHHHHhhhccccHHHHHHHhcc---cCCCCCCCCCCCCCccccc
Q 002211 767 DLFLSDHCQFSVRGQEFTKSGWGFAFPRDSPLAIDMSTAILTLSENGELQRIHDKWLR---KKACSSESSQSDSEQLQIQ 843 (953)
Q Consensus 767 ~~~~~~~~~l~~~~~~~~~~~~~~~~~k~spl~~~~n~~i~~l~e~G~~~~~~~~w~~---~~~c~~~~~~~~~~~l~l~ 843 (953)
+|..+++|++...|+.|...+||++++||||+.+.+..+|+++.|+|.|+++.++|+. ...|.... ..+..|+++
T Consensus 748 EfEAs~~CeLvT~GeLFgRSgyGIGlqK~SPWt~~vtlaIL~~hEsGfMEkLDk~Wi~~Ggpq~c~~~~--k~PatLgl~ 825 (993)
T KOG4440|consen 748 EFEASQKCELVTTGELFGRSGYGIGLQKDSPWTQNVTLAILKSHESGFMEKLDKTWIRYGGPQECDSRS--KAPATLGLE 825 (993)
T ss_pred eehhhcccceEeccccccccccccccccCCCCcchhhHHHHHhhhcchHHHHHHHHHhcCCcchhhhhc--cCccccccc
Confidence 9999999999999999999999999999999999999999999999999999999998 34454433 358899999
Q ss_pred cchHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q 002211 844 SFRGLFLICGIACFLALLAYFCLMLRQFKKYS 875 (953)
Q Consensus 844 ~~~g~f~il~~g~~lallvf~~e~~~~~~~~~ 875 (953)
++.|+|++.+.|+.+.+...++|+.|++++.+
T Consensus 826 NMagvFiLV~~Gia~GifLifiEv~Ykrh~~~ 857 (993)
T KOG4440|consen 826 NMAGVFILVAGGIAAGIFLIFIEVAYKRHKDA 857 (993)
T ss_pred ccccEEEEEecchhheeeEEEEeehhhhhhhh
Confidence 99999999999888888878889998776554
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=1.5e-74 Score=630.25 Aligned_cols=705 Identities=21% Similarity=0.367 Sum_probs=560.3
Q ss_pred CCChHHHHHHHHHHHhc-CcEEEEccCChh---hHHHHHHhhhhCCCcEEEeecCC-CCCCCC-CCCcEEEccCChHHHH
Q 002211 97 KFNGFLSIMGALQFMET-DTLAIVGPQSAV---MAHVLSHLANELQVPLLSFTALD-PTLSPL-QYPFFVQTAPNDLYLM 170 (953)
Q Consensus 97 ~~~~~~a~~~a~~li~~-~v~aiiGp~~S~---~a~av~~v~~~~~vP~Is~~at~-~~ls~~-~~p~~fr~~p~d~~~~ 170 (953)
..||..-+...|+++.. +|.+|+=-..|. ++..+--+....+||+|+..+.+ +.++++ ..-.|+++.++-.+|+
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 47999999999999976 888887544444 22233346678899999976554 444443 2347899999999999
Q ss_pred HHHHHHHHHcCCcEEEEEEecCccccchHHHHHHHHHhc--CcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEE
Q 002211 171 SAIAEMVSYFGWGEVIAIFNDDDQGRNGVTALGDKLAEI--RCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVH 248 (953)
Q Consensus 171 ~ai~~~l~~~~w~~vaii~~d~~~g~~~~~~l~~~l~~~--g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~ 248 (953)
+++.++|+.|+|..++++...-+..+.....+++..... |+++.......++ ++++......++|+-++.||+++
T Consensus 162 ~Vml~iL~~ydW~~Fs~vtt~~pg~~~f~~~ir~~~d~s~vgwe~i~v~~l~~s---~~d~~a~~q~qLkki~a~Villy 238 (1258)
T KOG1053|consen 162 QVMLKILEEYDWYNFSLVTTQFPGNRTFVSLIRQTNDNSHVGWEMINVLTLDPS---TDDLLAKLQAQLKKIQAPVILLY 238 (1258)
T ss_pred HHHHHHHHHcCcceeEEEEeecCchHHHHHHHHHhhhhccccceeeeeeecCCC---CCchHHHHHHHHHhcCCcEEEEE
Confidence 999999999999999999988877777888888777654 6666655555554 23334455566676779999999
Q ss_pred cchhhHHHHHHHHHHcCCCCCceEEEEeCcccccccCCCCCchhhhhhccceEEEEEecCCChhhHHHHHHHHhhcCCCC
Q 002211 249 GYSRTGLMVFDVAQRLGMMDSGYVWIATTWLSTFIDSKSPLSLKTAKSILGALTLRQHTPDSKRRRDFVSRWNTLSNGSI 328 (953)
Q Consensus 249 ~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~F~~~~~~~~~~~~ 328 (953)
|..+++..|+..|.++||++++|+||++....+. +. . -.+...|.+.+... .|+
T Consensus 239 C~~eea~~IF~~A~q~Gl~g~~y~Wi~pqlv~g~-~~---~---pa~~P~GLisv~~~------------~w~------- 292 (1258)
T KOG1053|consen 239 CSREEAERIFEEAEQAGLTGPGYVWIVPQLVEGL-EP---R---PAEFPLGLISVSYD------------TWR------- 292 (1258)
T ss_pred ecHHHHHHHHHHHHhcCCcCCceEEEeehhccCC-CC---C---CccCccceeeeecc------------chh-------
Confidence 9999999999999999999999999997654432 10 0 12334566665432 222
Q ss_pred CCCchhhHHhhHHHHHHHHHHHHHhcCCcccccCCCccCCCCCCcccCCCccccCchHHHHHHHHhcccCCcceeEEEcc
Q 002211 329 GLNPYGLYAYDTVWMIARALKLFLDQGNTISFSNDTKLNGLGGGTLNLGALSIFDGGKKFLANILQTNMTGLSGPIHFNQ 408 (953)
Q Consensus 329 ~~~~~~~~~YDAv~~la~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~f~G~tG~v~Fd~ 408 (953)
..+....-|+|-++|.|+..+...-+..+ ....++...... ....+..+...|.|+.|+| +.++|++
T Consensus 293 --~~l~~rVrdgvaiva~aa~s~~~~~~~lp--------~~~~~C~~~~~~-~~~~~~~l~r~l~NvT~~g--~~lsf~~ 359 (1258)
T KOG1053|consen 293 --YSLEARVRDGVAIVARAASSMLRIHGFLP--------EPKMDCREQEET-RLTSGETLHRFLANVTWDG--RDLSFNE 359 (1258)
T ss_pred --hhHHHHHhhhHHHHHHHHHHHHhhcccCC--------CcccccccccCc-cccchhhhhhhhheeeecc--cceeecC
Confidence 22346678999999999999877644332 122222211111 2224889999999999999 7899999
Q ss_pred CCCCCCccEEEEEeecCCeeeEEEEecCCCCccccCCcccccCCCCCCCCCCcceeeEeCCCcccCCCcccccCCCcceE
Q 002211 409 DRSLLHPSYDIINVIEHGYPQQIGYWSNYSGLSVVPPEKLYRKPANRSSSNQHLYSVVWPGGVTSKPRGWVFPNNGRQLR 488 (953)
Q Consensus 409 ~g~~~~~~y~I~~~~~~~~~~~VG~w~~~~gl~~~~~~~~~~~~~~~~~~~~~l~~i~Wpg~~~~~P~~~~~~~~g~~lr 488 (953)
+|-...+...|+-..++..|.+||.|.... |. +...+||.-.. .+.+ . .+..+|+
T Consensus 360 ~g~~v~p~lvvI~l~~~r~We~VG~We~~~-L~--------------------M~y~vWPr~~~-~~q~--~-~d~~HL~ 414 (1258)
T KOG1053|consen 360 DGYLVHPNLVVIDLNRDRTWERVGSWENGT-LV--------------------MKYPVWPRYHK-FLQP--V-PDKLHLT 414 (1258)
T ss_pred CceeeccceEEEecCCCcchheeceecCCe-EE--------------------EeccccccccC-ccCC--C-CCcceeE
Confidence 998889999999888888899999998764 33 34457773321 1111 1 1334677
Q ss_pred EEecCcccccccEEee---C-----------------------------CcceEEEeeHHHHHHHHHhCCCcccEEEeeC
Q 002211 489 IGVPNRVSYRDFVFKV---N-----------------------------GTDIVHGYCIDVFLAAVRLLPYAVPYKFIPY 536 (953)
Q Consensus 489 i~v~~~~~~~p~~~~~---~-----------------------------~~~~~~G~~~dll~~la~~l~~~~~~~~~~~ 536 (953)
|++-+. +||+... + -..|++|||||||+.|++.+||+++...+..
T Consensus 415 VvTLeE---~PFVive~vDP~t~~C~~ntvpc~s~~~~t~ss~~~~~~tvKkCCkGfCIDiLkKlA~~v~FtYDLYlVtn 491 (1258)
T KOG1053|consen 415 VVTLEE---RPFVIVEDVDPLTQTCVRNTVPCRSQLNSTFSSGDEANRTVKKCCKGFCIDILKKLARDVKFTYDLYLVTN 491 (1258)
T ss_pred EEEecc---CCeEEEecCCCCcCcCCCCCCcchhhhhhccCCCccCCchHHhhhhhhhHHHHHHHHhhcCcceEEEEecC
Confidence 776654 3444321 1 1348999999999999999999988888876
Q ss_pred C-CCC-CCCChHHHHHHHHcCceeEEEecEEEecCccceeeccccceecceEEEEecccCCcCcceeeccCchhHHHHHH
Q 002211 537 G-DGH-KNPTYSELINQITTGVFDAAVGDIAIVTNRTKAVDFTQPYIESGLVVVAPVRKLNSSAWAFLRPFTPLMWAVTG 614 (953)
Q Consensus 537 ~-~~~-~n~~~~~~i~~l~~g~~Di~~~~~~~t~~r~~~vdft~p~~~~~~~~~v~~~~~~~~~~~~l~PF~~~vW~~i~ 614 (953)
| .|+ .||.|+||+++|..+++||+++.++|+++|++.+|||.||.+++++++|...+...+.-+||.||++.+|++++
T Consensus 492 GKhGkk~ng~WnGmIGev~~~rA~MAVgSltINeeRSevVDFSvPFveTgIsVmV~rsngtvspsAFLePfs~svWVmmF 571 (1258)
T KOG1053|consen 492 GKHGKKINGVWNGMIGEVVYQRADMAVGSLTINEERSEVVDFSVPFVETGISVMVARSNGTVSPSAFLEPFSPSVWVMMF 571 (1258)
T ss_pred CcccceecCcchhhHHHHHhhhhheeeeeeEechhhhccccccccccccceEEEEEecCCccCchhhcCCcchHHHHHHH
Confidence 6 243 78999999999999999999999999999999999999999999999999999888899999999999999999
Q ss_pred HHHHHH-HHHhhhhhcccCCCC---------CCCCcccchhhHHHHHHHhhccc--cCCcccchhHHHHHHHHHHHHHhh
Q 002211 615 VFFLVV-GTVVWILEHRLNDEF---------RGPPRKQIVTVLWFSFSTMFFAH--RENTVSTLGRVVLIIWLFVVLIIT 682 (953)
Q Consensus 615 ~~~~~~-~~~~~~l~~~~~~~~---------~~~~~~~~~~~~~~~~~~l~~~~--~~~~~s~~~R~l~~~w~~~~lil~ 682 (953)
++++++ ++.++++|+.++-.| .|.+.++++.++|..|+.+|... .++|+++.+|+++.+|.||++|+.
T Consensus 572 Vm~livaai~vFlFEy~SPvgyn~~l~~gkkpggp~FtigkaiwllwaLvFnnsVpv~nPKgtTskiMv~VWAfFavifL 651 (1258)
T KOG1053|consen 572 VMCLIVAAITVFLFEYFSPVGYNRNLANGKKPGGPSFTIGKAIWLLWALVFNNSVPVENPKGTTSKIMVLVWAFFAVIFL 651 (1258)
T ss_pred HHHHHHHHHHHHHHhhcCcccccccccCCCCCCCcceehhhHHHHHHHHHhCCCcCCCCCCchHHHHHHHHHHHHHHHHH
Confidence 998866 455678899876433 23457889999999999999874 669999999999999999999999
Q ss_pred hhcccceeeeeeeccccCCCCChHHhhhC-------CCeEEEEeCchHHHHHHHhhCCCccceEeC--CCHHHHHHHHHc
Q 002211 683 SSYTASLTSILTVQQLSSPIKGIDTLMTS-------NDRVGYQVGSFAENYLIEELSIPKSRLVAL--GSPEEYAIALEN 753 (953)
Q Consensus 683 ~~Yta~L~s~Lt~~~~~~~I~sl~dL~~~-------~~~ig~~~~s~~~~~l~~~~~~~~~~~~~~--~~~~~~~~~l~~ 753 (953)
++|||||+|||..+++..++.++.|-+-+ +.++|.+.++..++++++++.....-++.| ...+++++.|++
T Consensus 652 AsYTANLAAfMIqE~~~d~vSGlsD~KfqrP~dq~PpFRFGTVpngSTE~niR~Nyp~MHeYM~kyNq~~v~dal~sLK~ 731 (1258)
T KOG1053|consen 652 ASYTANLAAFMIQEEYYDTVSGLSDPKFQRPHDQYPPFRFGTVPNGSTERNIRSNYPEMHEYMVKYNQPGVEDALESLKN 731 (1258)
T ss_pred HHHHHHHHHHHhhhhhhhhccccCcccccCccccCCCcccccCCCCchhhhHHhccHHHHHHHHHhccCchHHHHHHHhc
Confidence 99999999999999999999999886532 346888887778888876543222223333 588999999999
Q ss_pred CCcEEEEccchhHHHHHhc--CcceEEeC--CccccCccEEEecCCCcchHHHHHHHHhhhccccHHHHHHHhcccCCCC
Q 002211 754 RTVAAVVDERPYIDLFLSD--HCQFSVRG--QEFTKSGWGFAFPRDSPLAIDMSTAILTLSENGELQRIHDKWLRKKACS 829 (953)
Q Consensus 754 g~~~a~~~~~~~~~~~~~~--~~~l~~~~--~~~~~~~~~~~~~k~spl~~~~n~~i~~l~e~G~~~~~~~~w~~~~~c~ 829 (953)
|+.||||.|...++|...+ .|+|..+| ..|...+||++++||||++..+|.+|+++...|.++++++.|+. ..|.
T Consensus 732 gKLDAFIyDaAVLnY~agkDegCKLvTIGsgKvFAttGYGIal~k~Spwkr~IdlallQy~gdGeme~Le~~Wlt-gic~ 810 (1258)
T KOG1053|consen 732 GKLDAFIYDAAVLNYMAGKDEGCKLVTIGSGKVFATTGYGIALPKNSPWKRQIDLALLQYLGDGEMEMLETLWLT-GICH 810 (1258)
T ss_pred ccchhHHHHHHHHHHhhccCCCceEEEecCCceeeecceeeecCCCCcchhhHHHHHHHHhccchHHHHHHHHhh-cccc
Confidence 9999999999999999887 69999998 89999999999999999999999999999999999999999998 6777
Q ss_pred CCCCCCCCCccccccchHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 002211 830 SESSQSDSEQLQIQSFRGLFLICGIACFLALLAYFCLMLRQFK 872 (953)
Q Consensus 830 ~~~~~~~~~~l~l~~~~g~f~il~~g~~lallvf~~e~~~~~~ 872 (953)
+...+..+.+|++++|.|+|++|++|++||+++|++|-++.++
T Consensus 811 n~k~evmSsqLdIdnmaGvFymL~~amgLSllvfi~EHlvYw~ 853 (1258)
T KOG1053|consen 811 NSKNEVMSSQLDIDNMAGVFYMLAVAMGLSLLVFIWEHLVYWK 853 (1258)
T ss_pred cchhhhhhcccChhhhhhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 6666678999999999999999999999999999999775443
No 4
>KOG1052 consensus Glutamate-gated kainate-type ion channel receptor subunit GluR5 and related subunits [Inorganic ion transport and metabolism; Amino acid transport and metabolism; Signal transduction mechanisms]
Probab=100.00 E-value=1.8e-65 Score=615.11 Aligned_cols=594 Identities=36% Similarity=0.607 Sum_probs=507.2
Q ss_pred HHHHHHhcCCceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEEeCcccccccCCCCCchhhhhhccceEEEEEecCCCh
Q 002211 232 NELVKVRMMEARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIATTWLSTFIDSKSPLSLKTAKSILGALTLRQHTPDSK 311 (953)
Q Consensus 232 ~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~ 311 (953)
..+.+++....+++++++.+..+..++.++.+.||+..+|+|+.++......+.... ....+.++|.++...+.|.+.
T Consensus 4 ~~~~~~~~~~~~~~v~~~~~~~~~~~~~~a~~~~~~~~~~~~i~t~~~~~~~~~~~~--~~~~~~~~~~l~~~~~~~~s~ 81 (656)
T KOG1052|consen 4 KLLLKLKAMRTRVFVLHMFPILALAIFSQAEELGMMQFGYVWILTNLLTDALDLDEL--YSLIDVMNGVLGLRGHIPRSE 81 (656)
T ss_pred hHHHHhhccCceEEEEeCCHHHHHHHHHHHHHhCccccCeEEEEEecchhhhccccc--ccchhheeeEEeeccCCCccH
Confidence 345666778899999999999999999999999999999999999987766655432 345677889999999999999
Q ss_pred hhHHHHHHHHhhcCCCCCCCchhhHHhhHHHHHHHHHHHHHhcCCcccccCCCccCCCCCCcccCCCccccCchHHHHHH
Q 002211 312 RRRDFVSRWNTLSNGSIGLNPYGLYAYDTVWMIARALKLFLDQGNTISFSNDTKLNGLGGGTLNLGALSIFDGGKKFLAN 391 (953)
Q Consensus 312 ~~~~F~~~~~~~~~~~~~~~~~~~~~YDAv~~la~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~ 391 (953)
..++|..+|+.. + .....++.++||+++++|.|++.... ... ....|...+.|.++..+.+.
T Consensus 82 ~~~~~~~~~~~~-~--~~~~~~~~~~~D~~~~~a~~~~~~~~-~~~--------------~~~~~~~~~~~~~~~~~~~~ 143 (656)
T KOG1052|consen 82 LLQNFVTRWQTS-N--VELLVYALWAYDAIQALARAVESLLN-IGN--------------LSLSCGRNNSWLDALGVFNF 143 (656)
T ss_pred HHHHHHHHHhhc-c--ccccchhhHHHHHHHHHHHHHHHhhc-CCC--------------CceecCCCCcccchhHHHHH
Confidence 999999999876 2 45778899999999999999999764 111 22334444556678888888
Q ss_pred HHhcccC---CcceeEEEccCCCCCCccEEEEEeecCCeeeEEEEecCCCCccccCCcccccCCCCCCCCCCcceeeEeC
Q 002211 392 ILQTNMT---GLSGPIHFNQDRSLLHPSYDIINVIEHGYPQQIGYWSNYSGLSVVPPEKLYRKPANRSSSNQHLYSVVWP 468 (953)
Q Consensus 392 l~~~~f~---G~tG~v~Fd~~g~~~~~~y~I~~~~~~~~~~~VG~w~~~~gl~~~~~~~~~~~~~~~~~~~~~l~~i~Wp 468 (953)
+.+.... |.+|.+.++.++.+....|+|+|+.+++. +.||.|++..| ..|.||
T Consensus 144 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~n~~~~~~-~~ig~W~~~~~-----------------------~~i~~~ 199 (656)
T KOG1052|consen 144 GKKLLVVNLSGVTGQFQFFRGGLLEYFKYEILNLNGSGE-RRIGYWYPRGG-----------------------ENISWP 199 (656)
T ss_pred HHhhhhhccccceeEEEecCCCccccceEEEEEecCcCc-eeEEEecCCCC-----------------------ceeecc
Confidence 8887644 45678888888888999999999999999 88999998764 368899
Q ss_pred CCcccCCCcccccCCCcceEEEecCcccccccEEee---CCcceEEEeeHHHHHHHHHhCCCcccEEEeeCCCCC--CCC
Q 002211 469 GGVTSKPRGWVFPNNGRQLRIGVPNRVSYRDFVFKV---NGTDIVHGYCIDVFLAAVRLLPYAVPYKFIPYGDGH--KNP 543 (953)
Q Consensus 469 g~~~~~P~~~~~~~~g~~lri~v~~~~~~~p~~~~~---~~~~~~~G~~~dll~~la~~l~~~~~~~~~~~~~~~--~n~ 543 (953)
+.....|++|.++.+|+++||+++..+||..+.... .++..+.|+|+|+++++++++||+++++.++.+.|+ ++|
T Consensus 200 ~~~~~~~~~~~~~~~~~~l~v~~~~~~P~~~~~~~~~~~~~~~~~~G~~idll~~l~~~l~f~~~~~~~~~~~g~~~~~g 279 (656)
T KOG1052|consen 200 GKDYFVPKGWFFPTNGKPLRVGVVTEPPFVDLVEDLAILNGNDRIEGFEIDLLQALAKRLNFSYEIIFVPDGSGSRDPNG 279 (656)
T ss_pred CCcccCcCCccccCCCceEEEEEeccCCceeeeecccccCCCCccceEEehHHHHHHHhCCCceEEEEcCCCCCCCCCCC
Confidence 999999999999999999999999876665555542 145689999999999999999999999999876544 457
Q ss_pred ChHHHHHHHHcCceeEEEecEEEecCccceeeccccceecceEEEEecccCCcCcceeeccCchhHHHHHHHHHHHHHHH
Q 002211 544 TYSELINQITTGVFDAAVGDIAIVTNRTKAVDFTQPYIESGLVVVAPVRKLNSSAWAFLRPFTPLMWAVTGVFFLVVGTV 623 (953)
Q Consensus 544 ~~~~~i~~l~~g~~Di~~~~~~~t~~r~~~vdft~p~~~~~~~~~v~~~~~~~~~~~~l~PF~~~vW~~i~~~~~~~~~~ 623 (953)
+|+|++++|.+|++|++ ++++++.+|.+++|||.||++.++++++++++..+..|.|++||++++|+++++++++++++
T Consensus 280 ~~~g~v~~l~~~~advg-~~~tit~~R~~~vdfT~p~~~~~~~i~~~~~~~~~~~~~fl~Pf~~~vW~~i~~~~l~~~~~ 358 (656)
T KOG1052|consen 280 NWDGLVGQLVDGEADVG-ADITITPERSKYVDFTIPYLQFGIVIIVRKPDSRSKLWNFLAPFSPEVWLLILASLLLVGLL 358 (656)
T ss_pred ChhHHHHHHhcCccccc-cceEEeecccccEEeccceEeccEEEEEEecCCcccceEEecCCcHHHHHHHHHHHHHHHHH
Confidence 99999999999999999 89999999999999999999999999999999665599999999999999999999999999
Q ss_pred hhhhhcccCCCCCCCC-----cccchhhHHHHHHHhhcccc-CCcccchhHHHHHHHHHHHHHhhhhcccceeeeeeecc
Q 002211 624 VWILEHRLNDEFRGPP-----RKQIVTVLWFSFSTMFFAHR-ENTVSTLGRVVLIIWLFVVLIITSSYTASLTSILTVQQ 697 (953)
Q Consensus 624 ~~~l~~~~~~~~~~~~-----~~~~~~~~~~~~~~l~~~~~-~~~~s~~~R~l~~~w~~~~lil~~~Yta~L~s~Lt~~~ 697 (953)
+|+++++.+.++ .++ .....+++|+++++++.|+. +.|++.++|+++++||++++|++++|||+|+|+||+++
T Consensus 359 ~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~q~~~~~p~~~~~Rll~~~w~~~~lil~ssYTa~L~a~Lt~~~ 437 (656)
T KOG1052|consen 359 LWILERLSPYEL-PPRQIVTSLFSLLNCLWLTVGSLLQQGSDEIPRSLSTRLLLGAWWLFVLILISSYTANLTAFLTVPR 437 (656)
T ss_pred HHHHhccccccC-CccccceeEeecccchhhhhHHHhccCCCccccchhhhHHHHHHHHHHHHHHHHHHHHHHHHhcccc
Confidence 999999999888 222 11245578999999998875 48999999999999999999999999999999999999
Q ss_pred ccCCCCChHHhhh-CCCeEEEEeCchHHHHHHHh---hCCCcc-ceEeCCCHHHHHHHHHcCC--cEEEEccc-hhHHHH
Q 002211 698 LSSPIKGIDTLMT-SNDRVGYQVGSFAENYLIEE---LSIPKS-RLVALGSPEEYAIALENRT--VAAVVDER-PYIDLF 769 (953)
Q Consensus 698 ~~~~I~sl~dL~~-~~~~ig~~~~s~~~~~l~~~---~~~~~~-~~~~~~~~~~~~~~l~~g~--~~a~~~~~-~~~~~~ 769 (953)
+.++|++++||.+ ++.++|.+.+++...++.+. ...... +.+.+.+.+|+.+++++|. ..+++.+. ++.+++
T Consensus 438 ~~~~i~~~~dL~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~v~~~~~~~~~~~~~~~~~~~~~ 517 (656)
T KOG1052|consen 438 LRSPIDSLDDLADQSNIPYGTQRGSFTRIYLEESEDMWAFKVSQRSVPLASPEEGVERVRKGPSGGYAFASDELYLAYLF 517 (656)
T ss_pred cCCcccCHHHHHHhcCCeEEEEecchHHHHHHHHHHHHhhhccCCCccCCCHHHHHHHHHcCCCCceEEEeccHHHHHHH
Confidence 9999999999995 77899999999999999776 333444 6778999999999999984 34555444 444444
Q ss_pred Hhc-CcceEEeCCccccCccEEEecCCCcchHHHHHHHHhhhccccHHHHHHHhcccC----CCCCCCCCCCCCcccccc
Q 002211 770 LSD-HCQFSVRGQEFTKSGWGFAFPRDSPLAIDMSTAILTLSENGELQRIHDKWLRKK----ACSSESSQSDSEQLQIQS 844 (953)
Q Consensus 770 ~~~-~~~l~~~~~~~~~~~~~~~~~k~spl~~~~n~~i~~l~e~G~~~~~~~~w~~~~----~c~~~~~~~~~~~l~l~~ 844 (953)
.++ .|+++++++.+...+++ ++||||||++.++++|++++|.|.+++|+++|+... .|.... ....|++++
T Consensus 518 ~~~~~c~~~~v~~~~~~~~~~-~~~~~Spl~~~is~~Il~l~e~g~l~~~~~kw~~~~~~~~~~~~~~---~~~~l~~~~ 593 (656)
T KOG1052|consen 518 LRDEICDLTEVGEPFLYKGYG-AFPKGSPLRSLISRAILKLQETGILQKLKRKWFSKKPCLPKCSQTE---KTKALDLES 593 (656)
T ss_pred hhcCCCceEEeCCcccCCCcc-eecCCCccHHHHHHHHHhhccccHHHHHHHHhccCCCCCCCCCCcc---cccccchhh
Confidence 443 39999999999999999 999999999999999999999999999999999943 343333 467899999
Q ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q 002211 845 FRGLFLICGIACFLALLAYFCLMLRQFKKYS 875 (953)
Q Consensus 845 ~~g~f~il~~g~~lallvf~~e~~~~~~~~~ 875 (953)
++|+|+++++|+++|+++|++|++|++++..
T Consensus 594 ~~g~F~i~~~g~~lal~vfi~E~~~~~~~~~ 624 (656)
T KOG1052|consen 594 FWGLFLILLVGYLLALLVFILELLYSRRRTL 624 (656)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 9999999999999999999999999887775
No 5
>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=7.1e-48 Score=433.23 Aligned_cols=337 Identities=21% Similarity=0.278 Sum_probs=287.4
Q ss_pred hhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhc-------------------CcEEEEccCC
Q 002211 63 GQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMET-------------------DTLAIVGPQS 123 (953)
Q Consensus 63 g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~-------------------~v~aiiGp~~ 123 (953)
|.....|+++|+|+||+++ +|||++|+++++|+|++|..|+.++.+|+++ +|.|||||.+
T Consensus 34 g~~~~~am~~AieeIN~~~-~Lpg~~L~~~i~Dt~~~~~~a~~~a~~li~~~~~~~~~~~~~c~~~~~~~~V~aVIG~~~ 112 (403)
T cd06361 34 GFLQTLAMIHAIEMINNST-LLLGVTLGYEIYDTCSEVTTAMAAVLRFLSKFNCSRSTVEFKCDYSQYVPRIKAVIGAGY 112 (403)
T ss_pred HHHHHHHHHHHHHHHhCCC-CCCCCEEceEEEeCCCChHHHHHHHHHHHhhcccccccccccccCCCCCCCeEEEECCCc
Confidence 7788899999999999999 5689999999999999999999999999974 7999999999
Q ss_pred hhhHHHHHHhhhhCCCcEEEeecCCCCCCC-CCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecCccccchHHHH
Q 002211 124 AVMAHVLSHLANELQVPLLSFTALDPTLSP-LQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDDDQGRNGVTAL 202 (953)
Q Consensus 124 S~~a~av~~v~~~~~vP~Is~~at~~~ls~-~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~~~g~~~~~~l 202 (953)
|..+.+++++++.++||+||+++++|.+++ .+||||||+.|+|..|+++++++++++||++|++|++|++||++..+.|
T Consensus 113 S~~s~ava~v~~~~~IP~IS~~ats~~Ls~~~~~~~ffRt~p~D~~qa~ai~~li~~~~w~~Vaii~~~d~yG~~~~~~f 192 (403)
T cd06361 113 SEISMAVSRMLNLQLIPQVSYASTAEILSDKIRFPSFLRTVPSDFYQTKAMAHLIKKSGWNWVGIIITDDDYGRSALETF 192 (403)
T ss_pred chHHHHHHHHhccCCcceEecCcCCcccCCcccCCCeeECCCchHhHHHHHHHHHHHcCCcEEEEEEecCchHHHHHHHH
Confidence 999999999999999999999999999997 6899999999999999999999999999999999999999999999999
Q ss_pred HHHHHhcCcEEEEEEecCCCCCCC---hHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEEeCcc
Q 002211 203 GDKLAEIRCKISYKSALPPDQSVT---ETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIATTWL 279 (953)
Q Consensus 203 ~~~l~~~g~~v~~~~~~~~~~~~~---~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~ 279 (953)
++++++.|+||+..+.++.+.... ..++..+++.+++++|||||+.+...++..++++|+++|+ +++||++++|
T Consensus 193 ~~~~~~~GicIa~~e~~~~~~~~~~~~~~~~~~~~~~ik~~~a~vVvv~~~~~~~~~l~~~a~~~g~---~~~wigs~~w 269 (403)
T cd06361 193 IIQAEANGVCIAFKEILPASLSDNTKLNRIIRTTEKIIEENKVNVIVVFARQFHVFLLFNKAIERNI---NKVWIASDNW 269 (403)
T ss_pred HHHHHHCCeEEEEEEEecCccCcchhHHHHHHHHHHHHhcCCCeEEEEEeChHHHHHHHHHHHHhCC---CeEEEEECcc
Confidence 999999999999999888751111 1566777777899999999999999999999999999998 6899999998
Q ss_pred cccccCCCCCchhhhhhccceEEEEEecCCChhhHHHHHHHHhhcCCCCCCCchhhHHhhHHHHHHHHHHHHHhcCCccc
Q 002211 280 STFIDSKSPLSLKTAKSILGALTLRQHTPDSKRRRDFVSRWNTLSNGSIGLNPYGLYAYDTVWMIARALKLFLDQGNTIS 359 (953)
Q Consensus 280 ~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~F~~~~~~~~~~~~~~~~~~~~~YDAv~~la~Al~~~~~~~~~~~ 359 (953)
........ ........|++++.+..+..++ |.+.|++++ ..++||||+++|+||+++..+.
T Consensus 270 ~~~~~~~~---~~~~~~~~g~ig~~~~~~~~~~---F~~~~~~~~---------~~~v~~AVyaiA~Al~~~~~~~---- 330 (403)
T cd06361 270 STAKKILT---DPNVKKIGKVVGFTFKSGNISS---FHQFLKNLL---------IHSIQLAVFALAHAIRDLCQER---- 330 (403)
T ss_pred cCcccccc---CCcccccceEEEEEecCCccch---HHHHHHHhh---------HHHHHHHHHHHHHHHHHhccCC----
Confidence 76433321 1223567899999887755555 445555443 3468999999999999864321
Q ss_pred ccCCCccCCCCCCcccCCCccccCchHHHHHHHHhcccCCcceeEEEccCCCCCCccEEEEEeecCC---eeeEEEEecC
Q 002211 360 FSNDTKLNGLGGGTLNLGALSIFDGGKKFLANILQTNMTGLSGPIHFNQDRSLLHPSYDIINVIEHG---YPQQIGYWSN 436 (953)
Q Consensus 360 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~f~G~tG~v~Fd~~g~~~~~~y~I~~~~~~~---~~~~VG~w~~ 436 (953)
.|...... ++++|+++|++++|+|++|++.||++||. ...|+|+|++.++ .+++||.|++
T Consensus 331 ---------------~c~~~~~~-~~~~l~~~L~~~~f~g~~~~v~Fd~~gd~-~~~y~I~~~~~~~~~~~~~~vg~~~~ 393 (403)
T cd06361 331 ---------------QCQNPNAF-QPWELLGQLKNVTFEDGGNMYHFDANGDL-NLGYDVVLWKEDNGHMTVTIMAEYDP 393 (403)
T ss_pred ---------------CCCCCCCc-CHHHHHHHHheeEEecCCceEEECCCCCC-CcceEEEEeEecCCcEEEEEEEEEeC
Confidence 13332223 58999999999999999889999999995 7899999999432 3699999998
Q ss_pred CCC
Q 002211 437 YSG 439 (953)
Q Consensus 437 ~~g 439 (953)
.+.
T Consensus 394 ~~~ 396 (403)
T cd06361 394 QND 396 (403)
T ss_pred CCC
Confidence 763
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=1.5e-47 Score=438.14 Aligned_cols=365 Identities=22% Similarity=0.342 Sum_probs=311.5
Q ss_pred ceEEEeEEEecCC-------------CchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHh--
Q 002211 48 EVLNVGAIFSFGT-------------VNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFME-- 112 (953)
Q Consensus 48 ~~i~IG~l~~~~~-------------~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~-- 112 (953)
++|.||++||++. ..|.....|+.+|+|+||+++++|||++|+++++|+|+++..|++++.+++.
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 4789999999972 3588889999999999999999999999999999999999999999988883
Q ss_pred -----------------------cCcEEEEccCChhhHHHHHHhhhhCCCcEEEeecCCCCCCC-CCCCcEEEccCChHH
Q 002211 113 -----------------------TDTLAIVGPQSAVMAHVLSHLANELQVPLLSFTALDPTLSP-LQYPFFVQTAPNDLY 168 (953)
Q Consensus 113 -----------------------~~v~aiiGp~~S~~a~av~~v~~~~~vP~Is~~at~~~ls~-~~~p~~fr~~p~d~~ 168 (953)
.+|.|||||.+|+++.+++++++.++||+|+++++++.|++ .+||||||+.|+|..
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 679999999999999
Q ss_pred HHHHHHHHHHHcCCcEEEEEEecCccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhc-CCceEEEE
Q 002211 169 LMSAIAEMVSYFGWGEVIAIFNDDDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRM-MEARVIVV 247 (953)
Q Consensus 169 ~~~ai~~~l~~~~w~~vaii~~d~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~-~~~~vii~ 247 (953)
|+.+++++++++||++|++||.|++||+...+.|.+++++.|+||+..+.++.. .++.|+..+++++++ .++||||+
T Consensus 161 qa~ai~~ll~~~~W~~Vaii~~~~~yG~~~~~~~~~~~~~~gi~i~~~~~i~~~--~~~~d~~~~l~~l~~~~~a~vVvl 238 (458)
T cd06375 161 QAKAMAEILRFFNWTYVSTVASEGDYGETGIEAFEQEARLRNICIATSEKVGRS--ADRKSYDSVIRKLLQKPNARVVVL 238 (458)
T ss_pred HHHHHHHHHHHCCCeEEEEEEeCchHHHHHHHHHHHHHHHCCeeEEEEEEecCC--CCHHHHHHHHHHHhccCCCEEEEE
Confidence 999999999999999999999999999999999999999999999998888765 447899999999875 69999999
Q ss_pred EcchhhHHHHHHHHHHcCCCCCceEEEEeCcccccccCCCCCchhhhhhccceEEEEEecCCChhhHHHHHH--------
Q 002211 248 HGYSRTGLMVFDVAQRLGMMDSGYVWIATTWLSTFIDSKSPLSLKTAKSILGALTLRQHTPDSKRRRDFVSR-------- 319 (953)
Q Consensus 248 ~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~F~~~-------- 319 (953)
.+...++..++++|+++|+. ++||++++|....... ....+.++|++++.+.....+++++|++.
T Consensus 239 ~~~~~~~~~ll~~a~~~g~~---~~wigs~~~~~~~~~~----~~~~~~~~G~i~~~~~~~~i~~f~~yl~~l~p~~~~~ 311 (458)
T cd06375 239 FTRSEDARELLAAAKRLNAS---FTWVASDGWGAQESIV----KGSEDVAEGAITIELASHPIPDFDRYFQSLTPETNTR 311 (458)
T ss_pred ecChHHHHHHHHHHHHcCCc---EEEEEeccccccchhh----hccchhhceEEEEEeccccchhHHHHHHhCCcCcCCC
Confidence 99999999999999999985 7999999886432211 12346789999999998888888877654
Q ss_pred -------HHhhcCCCC----------------------CCCchhhHHhhHHHHHHHHHHHHHhcCCcccccCCCccCCCC
Q 002211 320 -------WNTLSNGSI----------------------GLNPYGLYAYDTVWMIARALKLFLDQGNTISFSNDTKLNGLG 370 (953)
Q Consensus 320 -------~~~~~~~~~----------------------~~~~~~~~~YDAv~~la~Al~~~~~~~~~~~~~~~~~~~~~~ 370 (953)
|+..|++.. ....+..+.||||+++|+|||+++.+.++.
T Consensus 312 n~w~~e~w~~~f~c~~~~~~~~~~~C~~~~~~~~~~~~~~~~~~~~v~~AVyA~AhaLh~~l~~~c~~------------ 379 (458)
T cd06375 312 NPWFKDFWEQKFQCSLQNRDCANTTTNDKERLLDKVNYEQESKIMFVVNAVYAMAHALHNMQRDLCPN------------ 379 (458)
T ss_pred CcHHHHHHHHHcCCCCCCCCccCCCCCchhcccccCcccccchHHHHHHHHHHHHHHHHHHHHhcCCC------------
Confidence 666654110 113467889999999999999998654321
Q ss_pred CCcccCCCccccCchHHHH-HHHHhcccC-----Ccce-eEEEccCCCCCCccEEEEEeec--CC---eeeEEEEecC
Q 002211 371 GGTLNLGALSIFDGGKKFL-ANILQTNMT-----GLSG-PIHFNQDRSLLHPSYDIINVIE--HG---YPQQIGYWSN 436 (953)
Q Consensus 371 ~~~~~~~~~~~~~~~~~l~-~~l~~~~f~-----G~tG-~v~Fd~~g~~~~~~y~I~~~~~--~~---~~~~VG~w~~ 436 (953)
....|.....+ ++++|+ +.|++++|. |.+| +|.||++|+ ....|+|+|++. ++ .+++||.|+.
T Consensus 380 -~~~~c~~~~~~-~~~~l~~~~L~~v~F~~~~~~~~~g~~v~Fd~nGd-~~~~YdI~n~q~~~~~~~~~~~~VG~w~~ 454 (458)
T cd06375 380 -TTKLCDAMKPL-DGKKLYKEYLLNVSFTAPFRPDLADSEVKFDSQGD-GLGRYNIFNYQRTGNSYGYRYVGVGAWAN 454 (458)
T ss_pred -CCCCCCCCCCC-CHHHHHHHHHHhccccccccCCCCCCeeEECCCCC-CCcceEEEEEEEcCCCCcEEEEEEEEEec
Confidence 11235555555 489999 599999999 9998 599999999 478999999993 22 2589999964
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=1.4e-47 Score=442.64 Aligned_cols=375 Identities=20% Similarity=0.313 Sum_probs=311.2
Q ss_pred CCCceEEEeEEEecCC-----------------CchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHH
Q 002211 45 LKPEVLNVGAIFSFGT-----------------VNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGA 107 (953)
Q Consensus 45 ~~~~~i~IG~l~~~~~-----------------~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a 107 (953)
..+++|.||++||.+. ..|.....|+.+|+|+||+++++|||++|+++++|+|+++..|++.+
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 4678999999999973 13677789999999999999999999999999999999999999999
Q ss_pred HHHHhc--------------------------CcEEEEccCChhhHHHHHHhhhhCCCcEEEeecCCCCCCC-CCCCcEE
Q 002211 108 LQFMET--------------------------DTLAIVGPQSAVMAHVLSHLANELQVPLLSFTALDPTLSP-LQYPFFV 160 (953)
Q Consensus 108 ~~li~~--------------------------~v~aiiGp~~S~~a~av~~v~~~~~vP~Is~~at~~~ls~-~~~p~~f 160 (953)
.+++.+ +|.|||||.+|.++.+++++++.+++|+|+++++++.+++ ..|||||
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 999852 7999999999999999999999999999999999999998 5799999
Q ss_pred EccCChHHHHHHHHHHHHHcCCcEEEEEEecCccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcC
Q 002211 161 QTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDDDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMM 240 (953)
Q Consensus 161 r~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~ 240 (953)
|+.|+|..|+.++++++++++|++|++||+|++||+...+.|.+.+++.|+||+..+.++.. ....|+..+|.+|+++
T Consensus 165 Rt~p~d~~~~~al~~l~~~~~W~~Vaii~~~~~yg~~~~~~~~~~~~~~gi~i~~~~~i~~~--~~~~d~~~~l~~lk~~ 242 (472)
T cd06374 165 RVVPSDTLQARAMLDIVKRYNWTYVSAVHTEGNYGESGMEAFKELAAHEGLCIAHSDKIYSN--AGEQSFDRLLRKLRSR 242 (472)
T ss_pred EcCCChHHHHHHHHHHHHHCCCcEEEEEEecchHHHHHHHHHHHHHHHCCeeEEEEEEecCC--CchHHHHHHHHHHHhc
Confidence 99999999999999999999999999999999999999999999999999999998887654 3478999999999976
Q ss_pred C--ceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEEeCcccccccCCCCCchhhhhhccceEEEEEecCCChhhHHHH-
Q 002211 241 E--ARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIATTWLSTFIDSKSPLSLKTAKSILGALTLRQHTPDSKRRRDFV- 317 (953)
Q Consensus 241 ~--~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~F~- 317 (953)
+ ++||++.+...++..++++|+++|+. .+++||++++|....... ....+.++|++++.++.+..+++++|+
T Consensus 243 ~~da~vvv~~~~~~~~~~~l~~a~~~g~~-~~~~wi~s~~~~~~~~~~----~~~~~~~~G~l~~~~~~~~~~~F~~~l~ 317 (472)
T cd06374 243 LPKARVVVCFCEGMTVRGLLMAMRRLGVG-GEFQLIGSDGWADRDDVV----EGYEEEAEGGITIKLQSPEVPSFDDYYL 317 (472)
T ss_pred CCCcEEEEEEechHHHHHHHHHHHHhcCC-CceEEEEecccccchHhh----hcchhhhheeEEEEecCCCCccHHHHHH
Confidence 5 45566667777899999999999986 568999999886532221 234567899999999988888887754
Q ss_pred --------------HHHHhhcCCCC------------------------CCCchhhHHhhHHHHHHHHHHHHHhcCCccc
Q 002211 318 --------------SRWNTLSNGSI------------------------GLNPYGLYAYDTVWMIARALKLFLDQGNTIS 359 (953)
Q Consensus 318 --------------~~~~~~~~~~~------------------------~~~~~~~~~YDAv~~la~Al~~~~~~~~~~~ 359 (953)
+.|+..|++.. ....++.++|||||++|+||+++..+.+..
T Consensus 318 ~l~~~~~~~~~~~~~~w~~~f~c~~~~~~~~~~~~~~~c~~~~~~~~~~~~~~~~~~vyDAVyaiA~ALh~~~~~~~~~- 396 (472)
T cd06374 318 KLRPETNTRNPWFREFWQHRFQCRLPGHPQENPNYIKICTGNESLDEQYVQDSKMGFVINAIYAMAHGLHNMHQDLCPG- 396 (472)
T ss_pred hCCcccCCCChHHHHHHHHhcCCCcCCccCcCCccCCCCCCcccccccccccceeHHHHHHHHHHHHHHHHHHHhhCCC-
Confidence 34665554210 011455689999999999999997653321
Q ss_pred ccCCCccCCCCCCcccCCCccccCchHHHHHHHHhcccCCcce-eEEEccCCCCCCccEEEEEeecC----CeeeEEEEe
Q 002211 360 FSNDTKLNGLGGGTLNLGALSIFDGGKKFLANILQTNMTGLSG-PIHFNQDRSLLHPSYDIINVIEH----GYPQQIGYW 434 (953)
Q Consensus 360 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~f~G~tG-~v~Fd~~g~~~~~~y~I~~~~~~----~~~~~VG~w 434 (953)
....|+..... ++.+|+++|++++|+|++| +|.||++|++ ...|+|+|++.. ..+++||.|
T Consensus 397 ------------~~~~c~~~~~~-~~~~l~~~l~~v~F~g~tG~~v~Fd~~G~~-~~~ydI~n~~~~~~~~~~~~~VG~w 462 (472)
T cd06374 397 ------------HVGLCDAMKPI-DGRKLLEYLLKTSFSGVSGEEVYFDENGDS-PGRYDIMNLQYTEDLRFDYINVGSW 462 (472)
T ss_pred ------------CCCCCcCCCCC-CHHHHHHHHHhCcccCCCCCeEEEcCCCCC-CCceEEEEEEECCCCCEEEEEEEEE
Confidence 11124333333 5999999999999999999 6999999996 569999999942 234999999
Q ss_pred cCCCCccc
Q 002211 435 SNYSGLSV 442 (953)
Q Consensus 435 ~~~~gl~~ 442 (953)
++ .+|.+
T Consensus 463 ~~-~~l~~ 469 (472)
T cd06374 463 HE-GDLGI 469 (472)
T ss_pred eC-Ccccc
Confidence 75 35543
No 8
>cd06362 PBP1_mGluR Ligand binding domain of the metabotropic glutamate receptors (mGluR). Ligand binding domain of the metabotropic glutamate receptors (mGluR), which are members of the family C of G-protein-coupled receptors that transduce extracellular signals into G-protein activation and ultimately into cellular responses. mGluRs bind to glutamate and function as an excitatory neurotransmitter; they are involved in learning, memory, anxiety, and the perception of pain. Eight subtypes of mGluRs have been cloned so far, and are classified into three groups according to their sequence similarities, transduction mechanisms, and pharmacological profiles. Group I is composed of mGlu1R and mGlu5R that both stimulate PLC hydrolysis. Group II includes mGlu2R and mGlu3R, which inhibit adenylyl cyclase, as do mGlu4R, mGlu6R, mGlu7R, and mGlu8R, which form group III.
Probab=100.00 E-value=1.3e-47 Score=442.59 Aligned_cols=371 Identities=22% Similarity=0.334 Sum_probs=312.0
Q ss_pred ceEEEeEEEecCC-------------CchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHh--
Q 002211 48 EVLNVGAIFSFGT-------------VNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFME-- 112 (953)
Q Consensus 48 ~~i~IG~l~~~~~-------------~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~-- 112 (953)
+++.||++||++. ..|.....|+++|+|+||+++++|||++|+++++|+|++|..|+..+.+++.
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 4789999999972 3577889999999999999999999999999999999999999999999985
Q ss_pred ---------------------cCcEEEEccCChhhHHHHHHhhhhCCCcEEEeecCCCCCCC-CCCCcEEEccCChHHHH
Q 002211 113 ---------------------TDTLAIVGPQSAVMAHVLSHLANELQVPLLSFTALDPTLSP-LQYPFFVQTAPNDLYLM 170 (953)
Q Consensus 113 ---------------------~~v~aiiGp~~S~~a~av~~v~~~~~vP~Is~~at~~~ls~-~~~p~~fr~~p~d~~~~ 170 (953)
.+|.|||||.+|+++.+++++++.+++|+|+++++++.+++ .+||||||+.|+|..|+
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 38999999999999999999999999999999999999997 68999999999999999
Q ss_pred HHHHHHHHHcCCcEEEEEEecCccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhc-CCceEEEEEc
Q 002211 171 SAIAEMVSYFGWGEVIAIFNDDDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRM-MEARVIVVHG 249 (953)
Q Consensus 171 ~ai~~~l~~~~w~~vaii~~d~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~-~~~~vii~~~ 249 (953)
.++++++++++|++|++|+.|++||++..+.|.+.+++.|+||+..+.++.. ....|+..++++|++ .++|+||+.+
T Consensus 161 ~a~~~~l~~~~w~~vaii~~~~~~G~~~~~~~~~~~~~~gi~i~~~~~~~~~--~~~~d~~~~l~~l~~~~~a~viil~~ 238 (452)
T cd06362 161 QAMVDIVKAFNWTYVSTVASEGNYGEKGIEAFEKLAAERGICIAGSEKIPSS--ATEEEFDNIIRKLLSKPNARVVVLFC 238 (452)
T ss_pred HHHHHHHHHCCCcEEEEEEeCCHHHHHHHHHHHHHHHHCCeeEEEEEEcCCC--CCHHHHHHHHHHHhhcCCCeEEEEEc
Confidence 9999999999999999999999999999999999999999999998888764 347899999999987 5899999999
Q ss_pred chhhHHHHHHHHHHcCCCCCceEEEEeCcccccccCCCCCchhhhhhccceEEEEEecCCChhhHHHH------------
Q 002211 250 YSRTGLMVFDVAQRLGMMDSGYVWIATTWLSTFIDSKSPLSLKTAKSILGALTLRQHTPDSKRRRDFV------------ 317 (953)
Q Consensus 250 ~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~F~------------ 317 (953)
...++..++++|+++|+. .+++||++++|....... ....+..+|++++.+.....+.+++|+
T Consensus 239 ~~~~~~~~~~~a~~~g~~-~~~~~i~~~~~~~~~~~~----~~~~~~~~g~~~~~~~~~~i~~f~~~l~~l~~~~~~~~~ 313 (452)
T cd06362 239 REDDIRGLLAAAKRLNAE-GHFQWIASDGWGARNSVV----EGLEDVAEGAITIELQSAEVPGFDEYFLSLTPENNSRNP 313 (452)
T ss_pred ChHHHHHHHHHHHHcCCc-CceEEEEeccccccchhh----cccccccceEEEEEecccccccHHHHhhhCCcCcCCCCh
Confidence 999999999999999997 568999999876542221 234467899999888776666655543
Q ss_pred ---HHHHhhcCCC----------------------CCCCchhhHHhhHHHHHHHHHHHHHhcCCcccccCCCccCCCCCC
Q 002211 318 ---SRWNTLSNGS----------------------IGLNPYGLYAYDTVWMIARALKLFLDQGNTISFSNDTKLNGLGGG 372 (953)
Q Consensus 318 ---~~~~~~~~~~----------------------~~~~~~~~~~YDAv~~la~Al~~~~~~~~~~~~~~~~~~~~~~~~ 372 (953)
+.|+..|++. .....+++++|||||++|+||+++..+.+...
T Consensus 314 ~~~~~w~~~~~c~~~~~~~~~~~~~c~~~~~~~~~~~~~~~~~~vyDAV~a~A~AL~~~l~~~~~~~------------- 380 (452)
T cd06362 314 WFREFWEQKFNCKLTGNGSTKDNTCCTERILLLSNYEQESKVQFVIDAVYAMAHALHNMHRDLCPGT------------- 380 (452)
T ss_pred HHHHHHHHhcCCCcCCCCccccCCCCccccccccccccccchhHHHHHHHHHHHHHHHHHHhhCCCC-------------
Confidence 3344434310 01244788999999999999999986543211
Q ss_pred cccCCCccccCchHHHHHHHHhcccCCcce-eEEEccCCCCCCccEEEEEeecC---CeeeEEEEecCCCCc
Q 002211 373 TLNLGALSIFDGGKKFLANILQTNMTGLSG-PIHFNQDRSLLHPSYDIINVIEH---GYPQQIGYWSNYSGL 440 (953)
Q Consensus 373 ~~~~~~~~~~~~~~~l~~~l~~~~f~G~tG-~v~Fd~~g~~~~~~y~I~~~~~~---~~~~~VG~w~~~~gl 440 (953)
...|.... +.++.+|+++|++++|.|++| +|.||++|++ ...|+|+|++.+ ..+++||+|++..||
T Consensus 381 ~~~c~~~~-~~~~~~l~~~l~~v~f~g~tg~~v~Fd~~G~~-~~~y~I~~~~~~~~~~~~~~VG~w~~~~~~ 450 (452)
T cd06362 381 TGLCDAMK-PIDGRKLLFYLRNVSFSGLAGGPVRFDANGDG-PGRYDIFNYQRTNGKYDYVKVGSWKGELSL 450 (452)
T ss_pred CCCCcCcc-CCCHHHHHHHHHhCCcCCCCCceEEECCCCCC-CCceEEEEEEEcCCceEEEEEEEEeccccc
Confidence 11244333 346999999999999999998 7999999996 569999999842 234999999887764
No 9
>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=2.6e-47 Score=440.36 Aligned_cols=373 Identities=22% Similarity=0.306 Sum_probs=313.4
Q ss_pred CCCceEEEeEEEecCC----------------------CchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHH
Q 002211 45 LKPEVLNVGAIFSFGT----------------------VNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFL 102 (953)
Q Consensus 45 ~~~~~i~IG~l~~~~~----------------------~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~ 102 (953)
..+++|.||++||++. ..|.....|+++|+|+||+++++||+++|+++++|+|+++..
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 4678999999999973 347788999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhc-C------------------cEEEEccCChhhHHHHHHhhhhCCCcEEEeecCCCCCCC-CCCCcEEEc
Q 002211 103 SIMGALQFMET-D------------------TLAIVGPQSAVMAHVLSHLANELQVPLLSFTALDPTLSP-LQYPFFVQT 162 (953)
Q Consensus 103 a~~~a~~li~~-~------------------v~aiiGp~~S~~a~av~~v~~~~~vP~Is~~at~~~ls~-~~~p~~fr~ 162 (953)
|+.++.+|+.+ + |.|||||.+|.++.+++++++.++||+|+++++++.+++ .+||||||+
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 2 469999999999999999999999999999999999998 689999999
Q ss_pred cCChHHHHHHHHHHHHHcCCcEEEEEEecCccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCc
Q 002211 163 APNDLYLMSAIAEMVSYFGWGEVIAIFNDDDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEA 242 (953)
Q Consensus 163 ~p~d~~~~~ai~~~l~~~~w~~vaii~~d~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~ 242 (953)
.|+|..|+.+++++++++||++|++|+.|++||+...+.|++.+++.|+||+..+.++.. ....|+..++.+++++++
T Consensus 168 ~psd~~q~~Ai~~l~~~f~wk~VaiI~~dd~yG~~~~~~~~~~~~~~Gi~I~~~~~i~~~--~~~~d~~~~l~klk~~~a 245 (510)
T cd06364 168 IPNDEHQATAMADIIEYFRWNWVGTIAADDDYGRPGIEKFREEAEERDICIDFSELISQY--SDEEEIQRVVEVIQNSTA 245 (510)
T ss_pred CCChHHHHHHHHHHHHHcCCeEEEEEEecCcchHHHHHHHHHHHHHCCcEEEEEEEeCCC--CCHHHHHHHHHHHHhcCC
Confidence 999999999999999999999999999999999999999999999999999998888763 347899999999999999
Q ss_pred eEEEEEcchhhHHHHHHHHHHcCCCCCceEEEEeCcccccccCCCCCchhhhhhccceEEEEEecCCChhhHHHHHH---
Q 002211 243 RVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIATTWLSTFIDSKSPLSLKTAKSILGALTLRQHTPDSKRRRDFVSR--- 319 (953)
Q Consensus 243 ~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~F~~~--- 319 (953)
||||+.+...++..++++|+++|+. +++||++++|........ ....+.+.|++++.+.....+++++|++.
T Consensus 246 ~vVvl~~~~~~~~~ll~qa~~~g~~--~~iwI~s~~w~~~~~~~~---~~~~~~~gg~lg~~~~~~~i~~f~~~l~~l~p 320 (510)
T cd06364 246 KVIVVFSSGPDLEPLIKEIVRRNIT--GKIWLASEAWASSSLIAM---PEYFDVMGGTIGFALKAGQIPGFREFLQKVHP 320 (510)
T ss_pred eEEEEEeCcHHHHHHHHHHHHhCCC--CcEEEEEchhhccccccc---CCccceeeEEEEEEECCCcCccHHHHHHhCCc
Confidence 9999999999999999999999985 569999998865432221 23457889999999988777776665543
Q ss_pred ------------HHhhcCCC-----CC---------------------------------------------CCchhhHH
Q 002211 320 ------------WNTLSNGS-----IG---------------------------------------------LNPYGLYA 337 (953)
Q Consensus 320 ------------~~~~~~~~-----~~---------------------------------------------~~~~~~~~ 337 (953)
|+..|++. .. ...++.+.
T Consensus 321 ~~~~~~~~~~~~we~~f~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~~~~~~~~~~~~~~~~~~~~~~~v 400 (510)
T cd06364 321 KKSSHNGFAKEFWEETFNCYLEDSPKNALPVDTFLGHEESGDDSENGSTAFRPLCTGDENIASVETPYLDYTHLRISYNV 400 (510)
T ss_pred ccCCCChHHHHHHHHhcCCCCCCCcccccccccccccccccccccccccccCCCCCChhhhcccCCccccccchhhHHHH
Confidence 55555421 00 11235679
Q ss_pred hhHHHHHHHHHHHHHhcCCc-ccccCCCccCCCCCCcccCCCccccCchHHHHHHHHhcccCCcce-eEEEccCCCCCCc
Q 002211 338 YDTVWMIARALKLFLDQGNT-ISFSNDTKLNGLGGGTLNLGALSIFDGGKKFLANILQTNMTGLSG-PIHFNQDRSLLHP 415 (953)
Q Consensus 338 YDAv~~la~Al~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~f~G~tG-~v~Fd~~g~~~~~ 415 (953)
|||||++|+|||+++.+... .++ ....|.....+ ++++|++.|++++|.|.+| +|.||++|+. ..
T Consensus 401 ~~AVyAvAhaLh~~~~c~~~~~~~-----------~~~~c~~~~~~-~~~~l~~~L~~v~F~~~~g~~v~Fd~~Gd~-~~ 467 (510)
T cd06364 401 YLAVYSIAHALQDIYTCTPGKGLF-----------TNGSCADIKKV-EAWQVLKHLRHLNFTDNMGEQVRFDEGGDL-VG 467 (510)
T ss_pred HHHHHHHHHHHHHHhcCCCCCCCc-----------cCCCCCCCCCC-CHHHHHHHHHhcEEecCCCCEEEEecCCCC-cc
Confidence 99999999999999876421 110 01235554445 4899999999999999998 5999999994 78
Q ss_pred cEEEEEeec---CC--eeeEEEEecCC
Q 002211 416 SYDIINVIE---HG--YPQQIGYWSNY 437 (953)
Q Consensus 416 ~y~I~~~~~---~~--~~~~VG~w~~~ 437 (953)
.|+|+|++. ++ .+++||.|++.
T Consensus 468 ~YdI~n~q~~~~~~~~~~v~VG~~~~~ 494 (510)
T cd06364 468 NYSIINWHLSPEDGSVVFKEVGYYNVY 494 (510)
T ss_pred ceeEEEeeecCCCCcEEEEEEEEEcCC
Confidence 999999993 23 24899999864
No 10
>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=2.9e-47 Score=428.92 Aligned_cols=366 Identities=21% Similarity=0.323 Sum_probs=309.7
Q ss_pred eEEEeEEEe-cC---CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCC-ChHHHHHHHHHHHhcCcEEEEccCC
Q 002211 49 VLNVGAIFS-FG---TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKF-NGFLSIMGALQFMETDTLAIVGPQS 123 (953)
Q Consensus 49 ~i~IG~l~~-~~---~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~-~~~~a~~~a~~li~~~v~aiiGp~~ 123 (953)
.|+||+++| ++ +..|...+.|+++|+++||+++++|++.+|.+.+.+.++ ++..+...+++++.++|.|||||.+
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 566888999999999999999999999999999999665 7767888888877789999999999
Q ss_pred hhhHHHHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecCccccchHHHHH
Q 002211 124 AVMAHVLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDDDQGRNGVTALG 203 (953)
Q Consensus 124 S~~a~av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~~~g~~~~~~l~ 203 (953)
|..+.++++++++++||+|++++++|.+++. .+|++|+.|++..++.++++++++++|++|++||++++ |....+.|.
T Consensus 82 S~~~~av~~i~~~~~iP~Is~~~t~~~lt~~-~~~~~~~~~~~~~~~~a~~~~~~~~~wk~vaily~~~~-g~~~l~~~~ 159 (384)
T cd06393 82 GSCTNAVQSICNALEVPHIQLRWKHHPLDNK-DTFYVNLYPDYASLSHAILDLVQYLKWRSATVVYDDST-GLIRLQELI 159 (384)
T ss_pred hHHHHHHHHHHhccCCCeEeccCCCcccCcc-ceeEEEeccCHHHHHHHHHHHHHHcCCcEEEEEEeCch-hHHHHHHHH
Confidence 9999999999999999999999999988864 35788888999899999999999999999999997654 666667888
Q ss_pred HHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEEeCcccccc
Q 002211 204 DKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIATTWLSTFI 283 (953)
Q Consensus 204 ~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~ 283 (953)
+.+++.|++|+. +.++.+ +.|++.+|++||+.++++||++++..++..+++||+++||+.+.|.|+.++......
T Consensus 160 ~~~~~~g~~v~~-~~~~~~----~~d~~~~L~~ik~~~~~~iil~~~~~~~~~il~qa~~~gm~~~~~~~~~~~~~~~~~ 234 (384)
T cd06393 160 MAPSRYNIRLKI-RQLPTD----SDDARPLLKEMKRGREFRIIFDCSHQMAAQILKQAMAMGMMTEYYHFIFTTLDLYAL 234 (384)
T ss_pred HhhhccCceEEE-EECCCC----chHHHHHHHHHhhcCceEEEEECCHHHHHHHHHHHHHhccccCceEEEEccCccccc
Confidence 888889999986 446655 789999999999999999999999999999999999999999999999887543333
Q ss_pred cCCCCCchhhhhhccceEEEEEecCCChhhHHHHHHHHhh-cCCCC---------CCCchhhHHhhHHHHHHHHHHHHHh
Q 002211 284 DSKSPLSLKTAKSILGALTLRQHTPDSKRRRDFVSRWNTL-SNGSI---------GLNPYGLYAYDTVWMIARALKLFLD 353 (953)
Q Consensus 284 ~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~F~~~~~~~-~~~~~---------~~~~~~~~~YDAv~~la~Al~~~~~ 353 (953)
+. +........+.+++...++.+..++|+++|+++ ++... .+..+++++||||+++|+|++++..
T Consensus 235 ~~-----~~~~~~~~~it~~~~~~~~~~~~~~f~~~~~~~~~~~~p~~~~~~~~~~~~~~aal~yDav~~~a~A~~~~~~ 309 (384)
T cd06393 235 DL-----EPYRYSGVNLTGFRILNVDNPHVSSIVEKWSMERLQAAPKPETGLLDGVMMTDAALLYDAVHMVSVCYQRAPQ 309 (384)
T ss_pred cc-----hhhhcCcceEEEEEecCCCcHHHHHHHHHHHhhhhccccccccccccccccchhHHhhhhHHHHHHHHhhhhh
Confidence 22 111112233578888888899999999999854 54211 1256899999999999999997633
Q ss_pred cCCcccccCCCccCCCCCCcccCCCccccCchHHHHHHHHhcccCCcceeEEEcc-CCCCCCccEEEEEeecCCeeeEEE
Q 002211 354 QGNTISFSNDTKLNGLGGGTLNLGALSIFDGGKKFLANILQTNMTGLSGPIHFNQ-DRSLLHPSYDIINVIEHGYPQQIG 432 (953)
Q Consensus 354 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~f~G~tG~v~Fd~-~g~~~~~~y~I~~~~~~~~~~~VG 432 (953)
. ....++|+...+|..|.+|+++|++++|+|+||+++||+ +|.|.+..|+|+|+.++|. ++||
T Consensus 310 ~---------------~~~~~~c~~~~~w~~G~~i~~~l~~~~~~GltG~i~Fd~~~g~r~~~~~~i~~~~~~g~-~~vg 373 (384)
T cd06393 310 M---------------TVNSLQCHRHKAWRFGGRFMNFIKEAQWEGLTGRIVFNKTSGLRTDFDLDIISLKEDGL-EKVG 373 (384)
T ss_pred c---------------CCCCCCCCCCCCCcccHHHHHHHhheeecccccceEecCCCCeeeeeEEEEEEecCCcc-eeeE
Confidence 2 112346777789999999999999999999999999996 6788999999999999999 9999
Q ss_pred EecCCCCccc
Q 002211 433 YWSNYSGLSV 442 (953)
Q Consensus 433 ~w~~~~gl~~ 442 (953)
+|++..||++
T Consensus 374 ~W~~~~g~~~ 383 (384)
T cd06393 374 VWNPNTGLNI 383 (384)
T ss_pred EEcCCCCcCC
Confidence 9999998753
No 11
>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=4.6e-47 Score=435.88 Aligned_cols=369 Identities=22% Similarity=0.337 Sum_probs=306.5
Q ss_pred ceEEEeEEEecCC----------------------CchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHH
Q 002211 48 EVLNVGAIFSFGT----------------------VNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIM 105 (953)
Q Consensus 48 ~~i~IG~l~~~~~----------------------~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~ 105 (953)
++|.||++||.+. ..|.+...|+.+|+|+||++..+|||++|++.++|+|+++..|+.
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 4689999999961 126677899999999999999999999999999999999999999
Q ss_pred HHHHHHh--------------cCcEEEEccCChhhHHHHHHhhhhCCCcEEEeecCCCCCCC-CCCCcEEEccCChHHHH
Q 002211 106 GALQFME--------------TDTLAIVGPQSAVMAHVLSHLANELQVPLLSFTALDPTLSP-LQYPFFVQTAPNDLYLM 170 (953)
Q Consensus 106 ~a~~li~--------------~~v~aiiGp~~S~~a~av~~v~~~~~vP~Is~~at~~~ls~-~~~p~~fr~~p~d~~~~ 170 (953)
++.+++. .+++|||||.+|..+.+++++++.++||+|+++++++.+++ .+||||||+.|+|..|+
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 67999999999999999
Q ss_pred HHHHHHHHHcCCcEEEEEEecCccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcc
Q 002211 171 SAIAEMVSYFGWGEVIAIFNDDDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGY 250 (953)
Q Consensus 171 ~ai~~~l~~~~w~~vaii~~d~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~ 250 (953)
.|+++++++|+|++|++|+.|++||+...+.|.+++++.|+||++.+.++........++...+++++++++||||+++.
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 99999999999999999999999999999999999999999999999898761112348899999999999999999999
Q ss_pred hhhHHHHHHHHHHcCCCCCceEEEEeCcccccccCCCCCchhhhhhccceEEEEEecCCChhhHHHHHH-----------
Q 002211 251 SRTGLMVFDVAQRLGMMDSGYVWIATTWLSTFIDSKSPLSLKTAKSILGALTLRQHTPDSKRRRDFVSR----------- 319 (953)
Q Consensus 251 ~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~F~~~----------- 319 (953)
..++..++.++.+.+. .+++||++++|....... ....+.++|++++.++.++.+++++|+++
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 8888766555555443 578999999886543221 23457899999999999999998888755
Q ss_pred ----HHhhcCCC----------C---------------C--CCchhhHHhhHHHHHHHHHHHHHhcCCcccccCCCccCC
Q 002211 320 ----WNTLSNGS----------I---------------G--LNPYGLYAYDTVWMIARALKLFLDQGNTISFSNDTKLNG 368 (953)
Q Consensus 320 ----~~~~~~~~----------~---------------~--~~~~~~~~YDAv~~la~Al~~~~~~~~~~~~~~~~~~~~ 368 (953)
|+..|++. . . ...++.+.||||+++|+||++++.+.+..
T Consensus 315 ~~efwe~~f~c~~~~~~~~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~v~dAVya~AhALh~~l~c~~~~---------- 384 (469)
T cd06365 315 LEKLWWIYFNCSLSKSSCKTLKNCLSNASLEWLPLHYFDMAMSEESYNVYNAVYAVAHALHEMLLQQVET---------- 384 (469)
T ss_pred HHhhHhHhcCcccCcCCccccCCCCCCccccccccccccchhhhhHHHHHHHHHHHHHHHHHHHHhhccC----------
Confidence 55444311 0 0 12356789999999999999999874421
Q ss_pred CCCCcccCCCccccCchHHHHHHHHhcccCCccee-EEEccCCCCCCccEEEEEeec--C--CeeeEEEEecCC
Q 002211 369 LGGGTLNLGALSIFDGGKKFLANILQTNMTGLSGP-IHFNQDRSLLHPSYDIINVIE--H--GYPQQIGYWSNY 437 (953)
Q Consensus 369 ~~~~~~~~~~~~~~~~~~~l~~~l~~~~f~G~tG~-v~Fd~~g~~~~~~y~I~~~~~--~--~~~~~VG~w~~~ 437 (953)
.+..+|.. ... ++.+|++.|++++|.|.+|. |.||+|||+ ...|+|+|++. + ..+++||.|++.
T Consensus 385 --~~~~~~~~-~~~-~~~~l~~~l~~v~F~~~~g~~v~Fd~nGd~-~~~YdI~n~q~~~~~~~~~~~VG~~~~~ 453 (469)
T cd06365 385 --QSENNGKR-LIF-LPWQLHSFLKNIQFKNPAGDEVNLNQKRKL-DTEYDILNYWNFPQGLGLKVKVGEFSPQ 453 (469)
T ss_pred --CCcCCCCC-CCc-cHHHHHHHHHhccccCCCCCEEEecCCCCc-CceeeEEEEEECCCCCEEEEEEEEEeCC
Confidence 01122322 233 48899999999999999995 999999995 78999999972 2 235999999764
No 12
>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=7.3e-47 Score=435.88 Aligned_cols=367 Identities=20% Similarity=0.334 Sum_probs=302.0
Q ss_pred ceEEEeEEEecC--C-----------CchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHH----HHH
Q 002211 48 EVLNVGAIFSFG--T-----------VNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGA----LQF 110 (953)
Q Consensus 48 ~~i~IG~l~~~~--~-----------~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a----~~l 110 (953)
++|+||++||++ . ..|.....|+++|+|+||+++++|||++|+++++|+|+++..+.+.+ .++
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 479999999997 1 25777899999999999999999999999999999999876555444 444
Q ss_pred Hh-------------------cCcEEEEccCChhhHHHHHHhhhhCCCcEEEeecCCCCCCC-CCCCcEEEccCChHHHH
Q 002211 111 ME-------------------TDTLAIVGPQSAVMAHVLSHLANELQVPLLSFTALDPTLSP-LQYPFFVQTAPNDLYLM 170 (953)
Q Consensus 111 i~-------------------~~v~aiiGp~~S~~a~av~~v~~~~~vP~Is~~at~~~ls~-~~~p~~fr~~p~d~~~~ 170 (953)
++ ++|+|||||.+|.++.+++++++.++||+|+++++++.+++ ..||||||+.|+|..|+
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 43 27999999999999999999999999999999999999987 67999999999999999
Q ss_pred HHHHHHHHHcCCcEEEEEEecCccccchHHHHHHHHHhcC-cEEEEEEecCCCCCCChHHHHHHHHHHhc-CCceEEEEE
Q 002211 171 SAIAEMVSYFGWGEVIAIFNDDDQGRNGVTALGDKLAEIR-CKISYKSALPPDQSVTETDVRNELVKVRM-MEARVIVVH 248 (953)
Q Consensus 171 ~ai~~~l~~~~w~~vaii~~d~~~g~~~~~~l~~~l~~~g-~~v~~~~~~~~~~~~~~~d~~~~l~~i~~-~~~~vii~~ 248 (953)
.+++++++++||++|++||.|++||....+.|.+.+++.| +||...+.++.. ..+.|+..+|++|++ .++|+||+.
T Consensus 161 ~ai~~~i~~~~w~~Vaii~~~~~yg~~~~~~~~~~~~~~g~~~v~~~~~i~~~--~~~~d~~~~l~~ik~~~~~~vIvl~ 238 (463)
T cd06376 161 QAMVDIVKALGWNYVSTLASEGNYGESGVEAFTQISREAGGVCIAQSIKIPRE--PRPGEFDKIIKRLLETPNARAVIIF 238 (463)
T ss_pred HHHHHHHHHcCCeEEEEEEeCChHHHHHHHHHHHHHHHcCCceEEEEEecCCC--CCHHHHHHHHHHHhccCCCeEEEEe
Confidence 9999999999999999999999999999999999999874 688766655544 447899999999987 799999999
Q ss_pred cchhhHHHHHHHHHHcCCCCCceEEEEeCcccccccCCCCCchhhhhhccceEEEEEecCCChhhHHHHH----------
Q 002211 249 GYSRTGLMVFDVAQRLGMMDSGYVWIATTWLSTFIDSKSPLSLKTAKSILGALTLRQHTPDSKRRRDFVS---------- 318 (953)
Q Consensus 249 ~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~F~~---------- 318 (953)
+...++..++++|+++|+.+ .|+||++++|........ ...+.+.|++++.+.....+++++|..
T Consensus 239 ~~~~~~~~ll~~a~~~~~~g-~~~wig~d~~~~~~~~~~----~~~~~~~G~~~~~~~~~~~~~F~~~~~~l~~~~~~~~ 313 (463)
T cd06376 239 ANEDDIRRVLEAAKRANQVG-HFLWVGSDSWGAKISPIL----QQEDVAEGAITILPKRASIEGFDAYFTSRTLENNRRN 313 (463)
T ss_pred cChHHHHHHHHHHHhcCCcC-ceEEEEeccccccccccc----cCcceeeeEEEEEeccccchhHHHHHHhCCcccCCCC
Confidence 99999999999999999875 599999998875433211 123568999999998888887777654
Q ss_pred -----HHHhhcCCCCC--------------------------CCchhhHHhhHHHHHHHHHHHHHhcCCcccccCCCccC
Q 002211 319 -----RWNTLSNGSIG--------------------------LNPYGLYAYDTVWMIARALKLFLDQGNTISFSNDTKLN 367 (953)
Q Consensus 319 -----~~~~~~~~~~~--------------------------~~~~~~~~YDAv~~la~Al~~~~~~~~~~~~~~~~~~~ 367 (953)
.|+..|++..+ ....++++|||||++|+||++++.+.+..
T Consensus 314 ~~~~~~w~~~f~c~~~~~~~~~~~~~~~C~~~~~~~~~~~~~~~~~~~~v~dAVyaiA~ALh~l~~~~c~~--------- 384 (463)
T cd06376 314 VWFAEFWEENFNCKLTISGSKKEDTDRKCTGQERIGRDSTYEQEGKVQFVIDAVYAMAHALHSMHKDLCPG--------- 384 (463)
T ss_pred cHHHHHHHHhCCCcccCCCCccccccCcCcchhhccccCcccccchhHHHHHHHHHHHHHHHHHHHhhCCC---------
Confidence 57665542210 11267899999999999999998654321
Q ss_pred CCCCCcccCCCccccCchHHHHHHHHhcccCCcce-eEEEccCCCCCCccEEEEEeec----CCeeeEEEEecC
Q 002211 368 GLGGGTLNLGALSIFDGGKKFLANILQTNMTGLSG-PIHFNQDRSLLHPSYDIINVIE----HGYPQQIGYWSN 436 (953)
Q Consensus 368 ~~~~~~~~~~~~~~~~~~~~l~~~l~~~~f~G~tG-~v~Fd~~g~~~~~~y~I~~~~~----~~~~~~VG~w~~ 436 (953)
....|.... +.++.+|+++|++++|+|.+| +|.||++|++ .+.|+|+|++- ...+++||.|++
T Consensus 385 ----~~~~C~~~~-~~~~~~l~~~L~~v~F~g~tg~~v~Fd~~G~~-~~~Ydi~n~q~~~~~~~~~~~VG~w~~ 452 (463)
T cd06376 385 ----YTGVCPEME-PADGKKLLKYIRAVNFNGSAGTPVMFNENGDA-PGRYDIFQYQITNTSSPGYRLIGQWTD 452 (463)
T ss_pred ----CCCCCccCC-CCCHHHHHHHHHhCCccCCCCCeEEeCCCCCC-CCceEEEEEEecCCCceeEEEEEEECC
Confidence 111344433 335999999999999999999 6999999995 56899999983 223499999976
No 13
>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=1.2e-46 Score=414.78 Aligned_cols=363 Identities=21% Similarity=0.334 Sum_probs=295.8
Q ss_pred EEeEEEecCCCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEE-ecCCCChHHHHHHHHHHHhcCcEEEEccCChhhHHH
Q 002211 51 NVGAIFSFGTVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITM-HDAKFNGFLSIMGALQFMETDTLAIVGPQSAVMAHV 129 (953)
Q Consensus 51 ~IG~l~~~~~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~-~D~~~~~~~a~~~a~~li~~~v~aiiGp~~S~~a~a 129 (953)
.||++|+..+. ..+.|+++||+++|.+..++++.+|.+++ +|+.+|++.+..++|+|+++||+|||||.++.++..
T Consensus 1 ~iG~if~~~~~---~~~~af~~Av~~~N~~~~~l~~~~L~~~~~~~~~~d~F~~~~~ac~l~~~gV~AI~Gp~s~~~a~~ 77 (400)
T cd06392 1 HIGAIFEENAA---KDDRVFQLAVSDLSLNDDILQSEKITYSIKSIEANNPFQAVQEACDLMTQGILALVTSTGCASANA 77 (400)
T ss_pred CeeeccCCCch---HHHHHHHHHHHHhccCccccCCceEEEEEEecCCCChhHHHHHHHHHHhcCeEEEECCCchhHHHH
Confidence 38999997653 46899999999999999999999999999 999999999999999999999999999999999999
Q ss_pred HHHhhhhCCCcEEEeec-----------CCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecCccccch
Q 002211 130 LSHLANELQVPLLSFTA-----------LDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDDDQGRNG 198 (953)
Q Consensus 130 v~~v~~~~~vP~Is~~a-----------t~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~~~g~~~ 198 (953)
++.+|+..+||+|++++ ++|.++..+||++.|+. ..+.+|+++++.+|+|++|++|| |++||...
T Consensus 78 v~sic~~l~VP~is~~~~~~~~~~~~~~~~p~~~~~~~~~~lrp~---~~~~~Ai~dlV~~~~W~~v~~iY-D~d~gl~~ 153 (400)
T cd06392 78 LQSLTDAMHIPHLFVQRNSGGSPRTACHLNPSPEGEEYTLAARPP---VRLNDVMLKLVTELRWQKFIVFY-DSEYDIRG 153 (400)
T ss_pred HHHHhccCcCCcEeecccccccccccccCCCCcCcCceeEEecCc---hHHHHHHHHHHHhCCCcEEEEEE-ECcccHHH
Confidence 99999999999999866 44655556777777764 36678999999999999999999 89999999
Q ss_pred HHHHHHHHHhcCcEEEEEEe-------cCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHHHcCCCCCce
Q 002211 199 VTALGDKLAEIRCKISYKSA-------LPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQRLGMMDSGY 271 (953)
Q Consensus 199 ~~~l~~~l~~~g~~v~~~~~-------~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~ 271 (953)
++.+.+++.+.+.+|.+... +++. -.+.....|.+++... ++||++|+++.+..+++||.++||+..+|
T Consensus 154 lq~L~~~~~~~~~~I~~~~v~~~~~~~~~~~---l~~~~~~~L~~~~~~~-r~iVv~~s~~~~~~il~qA~~lgM~~~~y 229 (400)
T cd06392 154 LQSFLDQASRLGLDVSLQKVDRNISRVFTNL---FTTMKTEELNRYRDTL-RRAILLLSPRGAQTFINEAVETNLASKDS 229 (400)
T ss_pred HHHHHHHHhhcCceEEEEEcccCcchhhhhH---HHHHHHhhhhhccccc-eEEEEEcCcHHHHHHHHHHHHhCcccCCe
Confidence 99999999999999987652 2221 1223344555555555 99999999999999999999999999999
Q ss_pred EEEEeCcccccccCCCCCchhhhhhcc-ceEEEEEecCCChhhHHHH----HHHHhhcCC---C--CCCCchhhHHhhHH
Q 002211 272 VWIATTWLSTFIDSKSPLSLKTAKSIL-GALTLRQHTPDSKRRRDFV----SRWNTLSNG---S--IGLNPYGLYAYDTV 341 (953)
Q Consensus 272 ~wi~~~~~~~~~~~~~~~~~~~~~~~~-g~~~~~~~~~~~~~~~~F~----~~~~~~~~~---~--~~~~~~~~~~YDAv 341 (953)
+||++++.....+. .+.....- ++.+++.+.|.+....+|. .+|++.... . ..+..+++++||||
T Consensus 230 ~wI~t~~~~~~~dl-----~~~~~g~~~niT~~r~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~l~~~aalayDaV 304 (400)
T cd06392 230 HWVFVNEEISDTEI-----LELVHSALGRMTVIRQIFPLSKDNNQRCIRNNHRISSLLCDPQEGYLQMLQVSNLYLYDSV 304 (400)
T ss_pred EEEEecCCcccccH-----HHHhcccccceeeEEEecCCcHHHHHHHHHHHHHHHhhhcccccccccccchhHHHHHHHH
Confidence 99999987765443 22333333 4555999888777555554 677644321 1 14678999999999
Q ss_pred HHHHHHHHHHHhcCCcccccCCCccCCCCCCcccC--CCccccCchHHHHHHHHhcccCCcceeEEEccCCCCCCccEEE
Q 002211 342 WMIARALKLFLDQGNTISFSNDTKLNGLGGGTLNL--GALSIFDGGKKFLANILQTNMTGLSGPIHFNQDRSLLHPSYDI 419 (953)
Q Consensus 342 ~~la~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~l~~~l~~~~f~G~tG~v~Fd~~g~~~~~~y~I 419 (953)
|++|+|+++++...... +.. .++| +...+|..|..|+++|++++|+|+||+|+||++|+|.++.|+|
T Consensus 305 ~~~A~Al~~ll~~~~~~---------~~~--~l~C~~~~~~~w~~G~~ll~~ik~v~f~GLTG~I~F~~~G~r~~~~ldI 373 (400)
T cd06392 305 LMLANAFHRKLEDRKWH---------SMA--SLNCIRKSTKPWNGGRSMLETIKKGHITGLTGVMEFKEDGANPHVQFEI 373 (400)
T ss_pred HHHHHHHHHHhhccccC---------CCC--CCccCCCCCCCCCChHHHHHHHHhCCCccCccceeECCCCCCcCCceEE
Confidence 99999999865322111 111 2456 5688999999999999999999999999999999999999999
Q ss_pred EEe-----ecCCeeeEEEEecCCCCcc
Q 002211 420 INV-----IEHGYPQQIGYWSNYSGLS 441 (953)
Q Consensus 420 ~~~-----~~~~~~~~VG~w~~~~gl~ 441 (953)
+|+ .|+|. ++||+|++.+||+
T Consensus 374 i~l~~~~~~g~g~-~~iG~W~~~~gl~ 399 (400)
T cd06392 374 LGTSYSETFGKDV-RRLATWDSEKGLN 399 (400)
T ss_pred EeccccccCCCCc-eEeEEecCCCCCC
Confidence 995 47778 9999999999864
No 14
>cd06380 PBP1_iGluR_AMPA N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the AMPA receptor. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the AMPA (alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid) receptor, a member of the glutamate-receptor ion channels (iGluRs). AMPA receptors are the major mediators of excitatory synaptic transmission in the central nervous system. While this N-terminal domain belongs to the periplasmic-binding fold type I superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type II. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR. AMPA receptors consist of four types of subunits (GluR1, GluR2, GluR3, and GluR4) which combine to form a tetramer and play an important roles in mediating the rapid excita
Probab=100.00 E-value=5.7e-45 Score=411.57 Aligned_cols=372 Identities=18% Similarity=0.276 Sum_probs=301.1
Q ss_pred EEeEEEecCCCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCC-CChHHHHHHHHHHHhcCcEEEEccCChhhHHH
Q 002211 51 NVGAIFSFGTVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAK-FNGFLSIMGALQFMETDTLAIVGPQSAVMAHV 129 (953)
Q Consensus 51 ~IG~l~~~~~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~-~~~~~a~~~a~~li~~~v~aiiGp~~S~~a~a 129 (953)
+||++|+.+ +...+.|+++|+++||++..++++.+|.+++.++. +|+.+++.++|+|++++|+|||||.+|.++.+
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 46889999999999999876767788888788776 79999999999999999999999999999999
Q ss_pred HHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecCccccchHHHHHHHHHhc
Q 002211 130 LSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDDDQGRNGVTALGDKLAEI 209 (953)
Q Consensus 130 v~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~~~g~~~~~~l~~~l~~~ 209 (953)
++++++.++||+|+++++++.++ ..+||+||+.|+. ..+++++++++||++|++||++++ |....+.+.+.+++.
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 99999999999999999988885 4679999998863 458899999999999999997665 667777888899988
Q ss_pred C--cEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEEeCcccccccCCC
Q 002211 210 R--CKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIATTWLSTFIDSKS 287 (953)
Q Consensus 210 g--~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~~~ 287 (953)
| ++|... .+... ....|++.+|++||+.++|+||+.++.+++..+++||+++||+.++|+||.+++.....+.
T Consensus 153 g~~i~v~~~-~~~~~--~~~~d~~~~L~~ik~~~~~~iil~~~~~~~~~i~~qa~~~gm~~~~y~~i~~~~~~~~~~~-- 227 (382)
T cd06380 153 DNKWQVTAR-RVDNV--TDEEEFLRLLEDLDRRKEKRIVLDCESERLNKILEQIVDVGKNRKGYHYILANLGFDDIDL-- 227 (382)
T ss_pred CCceEEEEE-EecCC--CcHHHHHHHHHHhhcccceEEEEECCHHHHHHHHHHHHHhhhcccceEEEEccCCcccccH--
Confidence 8 666543 23322 1257999999999999999999999999999999999999999999999998765443322
Q ss_pred CCchhhhhhccceEEEEEecCCChhhHHHHHHHHhhcCCC------CCCCchhhHHhhHHHHHHHHHHHHHhcCCccccc
Q 002211 288 PLSLKTAKSILGALTLRQHTPDSKRRRDFVSRWNTLSNGS------IGLNPYGLYAYDTVWMIARALKLFLDQGNTISFS 361 (953)
Q Consensus 288 ~~~~~~~~~~~g~~~~~~~~~~~~~~~~F~~~~~~~~~~~------~~~~~~~~~~YDAv~~la~Al~~~~~~~~~~~~~ 361 (953)
........++.++....+..+..++|.++|+++++.. ..+..+++++||||+++|+|++++++.++...+.
T Consensus 228 ---~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~aa~aYDav~~~a~Al~~~~~~~~~~~~~ 304 (382)
T cd06380 228 ---SKFLFGGVNITGFQLVDNTNPTVQKFLQRWKKLDPREWPGAGTSPIKYTAALAHDAVLVMAEAFRSLRRQRGSGRHR 304 (382)
T ss_pred ---HHhccCceeeEEEeccCCCCHHHHHHHHHHHhcCccccCcCCcCCcchHHHHHHHHHHHHHHHHHHHHHhccccccc
Confidence 1112233456777766777889999999999987521 2367799999999999999999997654321100
Q ss_pred CCCccCCCCCCcccCCCccccCchHHHHHHHHhcccCCcceeEEEccCCCCCCccEEEEEeecCCeeeEEEEecCCCCc
Q 002211 362 NDTKLNGLGGGTLNLGALSIFDGGKKFLANILQTNMTGLSGPIHFNQDRSLLHPSYDIINVIEHGYPQQIGYWSNYSGL 440 (953)
Q Consensus 362 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~f~G~tG~v~Fd~~g~~~~~~y~I~~~~~~~~~~~VG~w~~~~gl 440 (953)
.. ......+..|.-+...+|.+|.+|+++|++++|+|++|+++||++|++....++|+++++++. ++||+|++..|+
T Consensus 305 ~~-~~~~~~~~~C~~~~~~~~~~g~~i~~~l~~~~~~G~tG~i~Fd~~G~~~~~~~~i~~~~~~~~-~~vg~w~~~~g~ 381 (382)
T cd06380 305 ID-ISRRGNGGDCLANPAVPWEHGIDIERALKKVQFEGLTGNVQFDEFGQRTNYTLDVVELKTRGL-RKVGYWNEDDGL 381 (382)
T ss_pred cc-cccCCCCCcCCCCCCCCccchHHHHHHHHhcccCCcccceEECCCCCcccccEEEEEecCCCc-eEEEEECCCcCc
Confidence 00 000111222222345678889999999999999999999999999998888999999998888 999999998875
No 15
>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=5.5e-45 Score=402.52 Aligned_cols=355 Identities=19% Similarity=0.268 Sum_probs=298.3
Q ss_pred EEeEEEecCCCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEEccCChhhHHHH
Q 002211 51 NVGAIFSFGTVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIVGPQSAVMAHVL 130 (953)
Q Consensus 51 ~IG~l~~~~~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aiiGp~~S~~a~av 130 (953)
+||++|+.+. ...+.|+++|++++|.+..+++ .+. +-+..|...+.+++|+++++||+||+||.++..+..+
T Consensus 1 ~iG~if~~~~---~~~~~af~~av~~~N~~~~l~~--~~~---~~~~~dsf~~~~~~C~~~~~gV~AI~Gp~s~~~a~~v 72 (364)
T cd06390 1 QIGGLFPNQQ---SQEHAAFRFALSQLTEPPKLLP--QID---IVNISDSFEMTYTFCSQFSKGVYAIFGFYDRKTVNML 72 (364)
T ss_pred CCceeeCCCC---hHHHHHHHHHHHHhccCccccc--ceE---EeccccHHHHHHHHHHHhhcCceEEEccCChhHHHHH
Confidence 4899998754 3578999999999999875553 122 2244688999999999999999999999999999999
Q ss_pred HHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecCccccchHHHHHHHHHhcC
Q 002211 131 SHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDDDQGRNGVTALGDKLAEIR 210 (953)
Q Consensus 131 ~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~~~g~~~~~~l~~~l~~~g 210 (953)
+.+|+..+||+|+++. |..+ ..+|+.++.|+ +++|+++++++|||++|++||+++ ||....+.|.+.+++.|
T Consensus 73 ~sic~~~~vP~i~~~~--~~~~--~~~~~i~~~P~---~~~Ai~diI~~~~W~~v~iIYd~d-~g~~~lq~l~~~~~~~~ 144 (364)
T cd06390 73 TSFCGALHVCFITPSF--PVDT--SNQFVLQLRPE---LQDALISVIEHYKWQKFVYIYDAD-RGLSVLQKVLDTAAEKN 144 (364)
T ss_pred HHhhcCCCCCceecCC--CCCC--CCceEEEeChh---HHHHHHHHHHHcCCcEEEEEEeCC-ccHHHHHHHHHhhhccC
Confidence 9999999999999754 3332 33568999987 899999999999999999999655 99999999999999999
Q ss_pred cEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEEeCcccccccCCCCCc
Q 002211 211 CKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIATTWLSTFIDSKSPLS 290 (953)
Q Consensus 211 ~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~~~~~~ 290 (953)
++|.+...++.+ .+++..+|++++.+++++||++|..+.+..+++++.+.+|+..+|+||+++......+.
T Consensus 145 ~~I~~~~~~~~~----~~d~~~~L~~ik~~~~rvIVl~~~~~~~~~~L~~a~~~~~~~~gy~wI~t~l~~~~~~~----- 215 (364)
T cd06390 145 WQVTAVNILTTT----EEGYRKLFQDLDKKKERLIVVDCESERLNAILNQIIKLEKNGIGYHYILANLGFMDIDL----- 215 (364)
T ss_pred ceeeEEEeecCC----hHHHHHHHHhccccCCeEEEEECCHHHHHHHHHHHHHhhccCCceEEEecCCCcccccH-----
Confidence 999987776654 67999999999999999999999999999999999999999999999999833222222
Q ss_pred hhhhhhccceEEEEEecCCChhhHHHHHHHHhhcCC------CCCCCchhhHHhhHHHHHHHHHHHHHhcCCcccccCCC
Q 002211 291 LKTAKSILGALTLRQHTPDSKRRRDFVSRWNTLSNG------SIGLNPYGLYAYDTVWMIARALKLFLDQGNTISFSNDT 364 (953)
Q Consensus 291 ~~~~~~~~g~~~~~~~~~~~~~~~~F~~~~~~~~~~------~~~~~~~~~~~YDAv~~la~Al~~~~~~~~~~~~~~~~ 364 (953)
......++|++|++.+.|+++..++|.++|++.... ..+++.+++++|||||++|+|++++...+...++.
T Consensus 216 ~~~~~~~~nitg~r~~~~~~~~~~~~~~~w~~~~~~~~~~~~~~~~~~~~~l~yDaV~~~A~A~~~l~~~~~~~~~~--- 292 (364)
T cd06390 216 TKFRESGANVTGFQLVNYTDTTVSRIMQQWKNFDARDLPRVDWKRPKYTSALTYDGVRVMAEAFQNLRKQRIDISRR--- 292 (364)
T ss_pred HHHhcCCcCceEEEEecCCCHHHHHHHHHHHhhccccCCCCCcCCcchHHHHHHHHHHHHHHHHHHHHHcCCCcccC---
Confidence 445668999999999999999999999999876531 12467899999999999999999986554332211
Q ss_pred ccCCCCCCcccCC--CccccCchHHHHHHHHhcccCCcceeEEEccCCCCCCccEEEEEeecCCeeeEEEEecCCCCc
Q 002211 365 KLNGLGGGTLNLG--ALSIFDGGKKFLANILQTNMTGLSGPIHFNQDRSLLHPSYDIINVIEHGYPQQIGYWSNYSGL 440 (953)
Q Consensus 365 ~~~~~~~~~~~~~--~~~~~~~~~~l~~~l~~~~f~G~tG~v~Fd~~g~~~~~~y~I~~~~~~~~~~~VG~w~~~~gl 440 (953)
+....|. ...+|..|..|+++|++++|+|+||+++||++|+|.+..|+|+|+.++|. ++||+|++..||
T Consensus 293 ------~~~~~C~~~~~~~w~~G~~l~~~i~~~~f~GlTG~i~F~~~G~r~~~~~~I~~~~~~g~-~~vG~W~~~~g~ 363 (364)
T cd06390 293 ------GNAGDCLANPAVPWGQGIDIQRALQQVRFEGLTGNVQFNEKGRRTNYTLHVIEMKHDGI-RKIGYWNEDEKL 363 (364)
T ss_pred ------CCCCCCCCCCCCCCccHHHHHHHHHhhcccccccceeeCCCCCcccceEEEEEecCCcc-eEEEEECCCCCc
Confidence 1112332 34578899999999999999999999999999999999999999999999 999999998875
No 16
>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=3.7e-45 Score=408.63 Aligned_cols=339 Identities=40% Similarity=0.711 Sum_probs=305.0
Q ss_pred EEeEEEecC-CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhc-CcEEEEccCChhhHH
Q 002211 51 NVGAIFSFG-TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMET-DTLAIVGPQSAVMAH 128 (953)
Q Consensus 51 ~IG~l~~~~-~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~-~v~aiiGp~~S~~a~ 128 (953)
+||+++|++ +..|.....|+++|+|+||++||+++|++|+++++|++|+|..|++++++|+.+ +|.+||||.+|..+.
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 699999999 888999999999999999999977789999999999999999999999999988 999999999999999
Q ss_pred HHHHhhhhCCCcEEEeecCCCCCCC-CCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecCccccchHHHHHHHHH
Q 002211 129 VLSHLANELQVPLLSFTALDPTLSP-LQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDDDQGRNGVTALGDKLA 207 (953)
Q Consensus 129 av~~v~~~~~vP~Is~~at~~~ls~-~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~~~g~~~~~~l~~~l~ 207 (953)
++++++++++||+|+++++++.+++ ..+||+||+.|++..++.++++++++++|++|++|+.|++||+...+.+.+.++
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 9999999999999999999999965 678999999999999999999999999999999999999999999999999999
Q ss_pred hcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEEeCcccccccC-C
Q 002211 208 EIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIATTWLSTFIDS-K 286 (953)
Q Consensus 208 ~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~-~ 286 (953)
+.|++|+....++.+ .+..|+..++++|++++||+|++++.+.++..++++++++|+..++|+||.++++...++. .
T Consensus 161 ~~g~~v~~~~~~~~~--~~~~d~~~~l~~i~~~~~dvvi~~~~~~~~~~~~~~a~~~g~~~~~~~~i~~~~~~~~~~~~~ 238 (350)
T cd06366 161 EAGIEISYRAAFPPS--ANDDDITDALKKLKEKDSRVIVVHFSPDLARRVFCEAYKLGMMGKGYVWILTDWLSSNWWSSS 238 (350)
T ss_pred HcCCEEEEEeccCCC--CChhHHHHHHHHHhcCCCeEEEEECChHHHHHHHHHHHHcCCcCCCEEEEECcchhhhhccCC
Confidence 999999999888875 3468999999999999999999999999999999999999998889999999876544321 0
Q ss_pred CCCchhhhhhccceEEEEEecCC-ChhhHHHHHHHHhhcCCCC----CCCchhhHHhhHHHHHHHHHHHHHhcCCccccc
Q 002211 287 SPLSLKTAKSILGALTLRQHTPD-SKRRRDFVSRWNTLSNGSI----GLNPYGLYAYDTVWMIARALKLFLDQGNTISFS 361 (953)
Q Consensus 287 ~~~~~~~~~~~~g~~~~~~~~~~-~~~~~~F~~~~~~~~~~~~----~~~~~~~~~YDAv~~la~Al~~~~~~~~~~~~~ 361 (953)
........+..+|++++.++.+. .+..++|.++|+++++... .|+.+++++|||+++
T Consensus 239 ~~~~~~~~~~~~gv~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~p~~~a~~~YDav~~------------------ 300 (350)
T cd06366 239 DCTDEEMLEAMQGVIGVRSYVPNSSMTLQEFTSRWRKRFGNENPELTEPSIYALYAYDAVWA------------------ 300 (350)
T ss_pred CCChHHHHHhhceEEEEeecccccCccHHHHHHHHHHHhcccCcCcCCCCcccchhhhheee------------------
Confidence 11224556788999999998887 8889999999999986321 578899999999987
Q ss_pred CCCccCCCCCCcccCCCccccCchHHHHHHHHhcccCCcceeEEEccCCCCCCccEEEEEeecCCeeeEEEEecCCCCcc
Q 002211 362 NDTKLNGLGGGTLNLGALSIFDGGKKFLANILQTNMTGLSGPIHFNQDRSLLHPSYDIINVIEHGYPQQIGYWSNYSGLS 441 (953)
Q Consensus 362 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~f~G~tG~v~Fd~~g~~~~~~y~I~~~~~~~~~~~VG~w~~~~gl~ 441 (953)
+.+|+|++|+++||++|++....|+++++.+++. ++||+|++..|++
T Consensus 301 --------------------------------~~~~~G~~G~v~fd~~~~~~~~~~~~~~~~~~~~-~~vg~~~~~~~~~ 347 (350)
T cd06366 301 --------------------------------STNFNGLSGPVQFDGGRRLASPAFEIINIIGKGY-RKIGFWSSESGLS 347 (350)
T ss_pred --------------------------------eceEEeeeeeEEEcCCCccCCcceEEEEecCCce-EEEEEEeCCCCcc
Confidence 2368899999999999998889999999987777 9999999988875
Q ss_pred c
Q 002211 442 V 442 (953)
Q Consensus 442 ~ 442 (953)
.
T Consensus 348 ~ 348 (350)
T cd06366 348 V 348 (350)
T ss_pred c
Confidence 3
No 17
>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=1.3e-44 Score=407.41 Aligned_cols=334 Identities=21% Similarity=0.309 Sum_probs=277.2
Q ss_pred CCCceEEEeEEEecCCCchhHHHHHHHHHHHHHhcCCCC-----CCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEE
Q 002211 45 LKPEVLNVGAIFSFGTVNGQVSRIAMKAAQDDINSDPRV-----LGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIV 119 (953)
Q Consensus 45 ~~~~~i~IG~l~~~~~~~g~~~~~a~~lAve~iN~~g~i-----l~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aii 119 (953)
+.+.+|+||+++|. ...+.|+++|++++|++.+. ++|.++++ +++++..+...+.+|++++|+|||
T Consensus 15 ~~~~~i~IG~i~~~-----~~~~~~~~~Ai~~~N~~~~~~~~~~l~~~~i~~----~~~~~~~a~~~~~~Li~~~V~aii 85 (377)
T cd06379 15 CSPKTVNIGAVLSN-----KKHEQEFKEAVNAANVERHGSRKIKLNATTITH----DPNPIQTALSVCEQLISNQVYAVI 85 (377)
T ss_pred CCCcEEEEeEEecc-----hhHHHHHHHHHHHHhhhhcCCcceeeccceEee----cCChhhHHHHHHHHHhhcceEEEE
Confidence 34678999999984 35789999999999996543 33455555 334444455666678888999997
Q ss_pred c-cC-Chh---hHHHHHHhhhhCCCcEEEeecCCCCCCC-CCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecCc
Q 002211 120 G-PQ-SAV---MAHVLSHLANELQVPLLSFTALDPTLSP-LQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDDD 193 (953)
Q Consensus 120 G-p~-~S~---~a~av~~v~~~~~vP~Is~~at~~~ls~-~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~~ 193 (953)
| +. +|. .+.+++.+++.++||+|+++++++.+++ ..|||+||+.|+|..|+.++++++++++|++|++||++++
T Consensus 86 ~~~~~ss~~~~~~~~v~~~~~~~~iP~Is~~a~~~~ls~~~~~~~~~R~~psd~~~~~a~~~~l~~~~w~~vaii~~~~~ 165 (377)
T cd06379 86 VSHPPTSNDHLTPTSVSYTAGFYRIPVVGISTRDSIFSDKNIHLSFLRTVPPYSHQADVWLEMLRSFKWNKVILLVSDDH 165 (377)
T ss_pred EeCCCCCcccccHHHHHHHhhCCCCcEEecccCCccccCccccccEEEecCCHHHHHHHHHHHHHHcCCeEEEEEEEcCc
Confidence 4 33 443 4677888999999999999999999987 4699999999999999999999999999999999999999
Q ss_pred cccchHHHHHHHHHhcCc----EEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHHHcCCCCC
Q 002211 194 QGRNGVTALGDKLAEIRC----KISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQRLGMMDS 269 (953)
Q Consensus 194 ~g~~~~~~l~~~l~~~g~----~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~~~g~~~~ 269 (953)
||++..+.+++.+++.|+ +|+..+.++.+ ..|+..+++++++.++|+||++++.+++..++++|+++||+++
T Consensus 166 ~g~~~~~~~~~~~~~~g~~~~~~v~~~~~~~~~----~~d~~~~l~~ik~~~~~vIvl~~~~~~~~~l~~qa~~~g~~~~ 241 (377)
T cd06379 166 EGRAAQKRFETLLEEREIEFKIKVEKVVEFEPG----EKNVTSLLQEAKELTSRVILLSASEDDAAVIYRNAGMLNMTGE 241 (377)
T ss_pred chhHHHHHHHHHHHhcCCccceeeeEEEecCCc----hhhHHHHHHHHhhcCCeEEEEEcCHHHHHHHHHHHHHcCCCCC
Confidence 999999999999999999 88888888766 7899999999999999999999999999999999999999999
Q ss_pred ceEEEEeCcccccccCCCCCchhhhhhccceEEEEEecCCChhhHHHHHHHHhhcCCCCCCCchhhHHhhHHHHHHHHHH
Q 002211 270 GYVWIATTWLSTFIDSKSPLSLKTAKSILGALTLRQHTPDSKRRRDFVSRWNTLSNGSIGLNPYGLYAYDTVWMIARALK 349 (953)
Q Consensus 270 ~~~wi~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~F~~~~~~~~~~~~~~~~~~~~~YDAv~~la~Al~ 349 (953)
+|+||.++.+... .+...|++++++..+ ..+++++|||||++|+|++
T Consensus 242 ~~~wi~t~~~~~~-----------~~~~~g~~g~~~~~~----------------------~~~~~~~yDAV~~~A~Al~ 288 (377)
T cd06379 242 GYVWIVSEQAGAA-----------RNAPDGVLGLQLING----------------------KNESSHIRDAVAVLASAIQ 288 (377)
T ss_pred CEEEEEecccccc-----------ccCCCceEEEEECCC----------------------CCHHHHHHHHHHHHHHHHH
Confidence 9999999987322 134579999887542 1346789999999999999
Q ss_pred HHHhcCCcccccCCCccCCCCCCcccCCCc-cccCchHHHHHHHHhcccCCcceeEEEccCCCCCCccEEEEEeecCCee
Q 002211 350 LFLDQGNTISFSNDTKLNGLGGGTLNLGAL-SIFDGGKKFLANILQTNMTGLSGPIHFNQDRSLLHPSYDIINVIEHGYP 428 (953)
Q Consensus 350 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~l~~~l~~~~f~G~tG~v~Fd~~g~~~~~~y~I~~~~~~~~~ 428 (953)
++...... ......|... .+|.+|+.|+++|++++|+|++|+|+||++|++....|+|+|+++.++
T Consensus 289 ~~~~~~~~------------~~~~~~c~~~~~~~~~g~~l~~~l~~v~f~G~tg~i~Fd~~Gd~~~~~~~I~~~~~~~~- 355 (377)
T cd06379 289 ELFEKENI------------TEPPRECVGNTVIWETGPLFKRALMSSKYPGETGRVEFNDDGDRKFANYDIMNIQNRKL- 355 (377)
T ss_pred HHHcCCCC------------CCCCccccCCCCCCcchHHHHHHHHhCCcCCccCceEECCCCCccCccEEEEEecCCCc-
Confidence 98652111 0111233332 257789999999999999999999999999998778999999998887
Q ss_pred eEEEEecCC
Q 002211 429 QQIGYWSNY 437 (953)
Q Consensus 429 ~~VG~w~~~ 437 (953)
++||+|++.
T Consensus 356 ~~VG~w~~~ 364 (377)
T cd06379 356 VQVGLYNGD 364 (377)
T ss_pred eEeeEEcCc
Confidence 999999874
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=9e-45 Score=412.46 Aligned_cols=353 Identities=25% Similarity=0.361 Sum_probs=299.2
Q ss_pred CCceEEEeEEEecCC---------------------CchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHH
Q 002211 46 KPEVLNVGAIFSFGT---------------------VNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSI 104 (953)
Q Consensus 46 ~~~~i~IG~l~~~~~---------------------~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~ 104 (953)
.++++.||++||++. ..|.....|+++|+|+||++||+|+|++|+++++|+|+ +..|+
T Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~g~~~~~a~~lAv~~IN~~ggil~g~~l~~~~~D~~~-~~~a~ 81 (410)
T cd06363 3 LPGDYLLGGLFPLHYATSALPHRRPEPLDCSSYRFNLSGYRLFQAMRFAVEEINNSTSLLPGVTLGYEIFDHCS-DSANF 81 (410)
T ss_pred CCCCEEEEEEeECcccccccccCCCCCccCccCccCHHHHHHHHHHHHHHHHHhCCCccCCCCeeceEEEecCC-cHHHH
Confidence 578999999999973 23677899999999999999999999999999999977 77799
Q ss_pred HHHHHHHh----------------cCcEEEEccCChhhHHHHHHhhhhCCCcEEEeecCCCCCCC-CCCCcEEEccCChH
Q 002211 105 MGALQFME----------------TDTLAIVGPQSAVMAHVLSHLANELQVPLLSFTALDPTLSP-LQYPFFVQTAPNDL 167 (953)
Q Consensus 105 ~~a~~li~----------------~~v~aiiGp~~S~~a~av~~v~~~~~vP~Is~~at~~~ls~-~~~p~~fr~~p~d~ 167 (953)
+.+.+|++ ++|.|||||.+|+.+.+++++++++++|+|+++++++.+++ ..+||+||+.|++.
T Consensus 82 ~~~~~li~~~~~~~~~~c~~~~~~~~V~aIiGp~~S~~~~av~~i~~~~~vp~is~~~~~~~lt~~~~~~~~fr~~~~~~ 161 (410)
T cd06363 82 PPTLSLLSVNGSRIEPQCNYTNYQPRVVAVIGPDSSTLALTVAPLFSFFLIPQISYGASSEVLSNKELYPSFLRTVPSDK 161 (410)
T ss_pred HHHHHHHhccCcccCcccccccCCCCeEEEECCCccHHHHHHHHHhcccccccccccccCccccccccCCCeeEecCCcH
Confidence 99999985 48999999999999999999999999999999999999987 67899999999999
Q ss_pred HHHHHHHHHHHHcCCcEEEEEEecCccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEE
Q 002211 168 YLMSAIAEMVSYFGWGEVIAIFNDDDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVV 247 (953)
Q Consensus 168 ~~~~ai~~~l~~~~w~~vaii~~d~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~ 247 (953)
.++.++++++++++|++|++|+.|++||++..+.+.+.+++.|++|+..+.++... ..+.|+..+|.+|++++||+||+
T Consensus 162 ~~~~al~~~l~~~~~k~vaii~~~~~~g~~~~~~~~~~l~~~gi~i~~~~~~~~~~-~~~~d~~~~l~~i~~~~~dvIil 240 (410)
T cd06363 162 DQIEAMVQLLQEFGWNWVAFLGSDDEYGRDGLQLFSELIANTGICIAYQGLIPLDT-DPETDYQQILKQINQTKVNVIVV 240 (410)
T ss_pred HHHHHHHHHHHHCCCcEEEEEEeCChhHHHHHHHHHHHHHHCCeEEEEEEEecCCC-chHHHHHHHHHHHhcCCCeEEEE
Confidence 99999999999999999999999999999999999999999999999988887531 23789999999999999999999
Q ss_pred EcchhhHHHHHHHHHHcCCCCCceEEEEeCcccccccCCCCCchhhhhhccceEEEEEecCCChhhHHHHHHHHhhcCCC
Q 002211 248 HGYSRTGLMVFDVAQRLGMMDSGYVWIATTWLSTFIDSKSPLSLKTAKSILGALTLRQHTPDSKRRRDFVSRWNTLSNGS 327 (953)
Q Consensus 248 ~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~F~~~~~~~~~~~ 327 (953)
++.++++..++++|+++|+.. .+||+++++........ ....+...+++++....+..+++++|.++
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 48999877653221111 11223455778887777888888888877
Q ss_pred CCCCchhhHHhhHHHHHHHHHHHHHhcCCcccccCCCccCCCCCCcccCCCccccCchHHHHHHHHhcccCCcceeEEEc
Q 002211 328 IGLNPYGLYAYDTVWMIARALKLFLDQGNTISFSNDTKLNGLGGGTLNLGALSIFDGGKKFLANILQTNMTGLSGPIHFN 407 (953)
Q Consensus 328 ~~~~~~~~~~YDAv~~la~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~f~G~tG~v~Fd 407 (953)
+++.+||||+++|+|+++++.++.. .|...+ ..++++|+++|++++|+|++|++.||
T Consensus 308 -----~~~~~YDaV~~~a~Al~~a~~~~~~-----------------~~~~~~-~~~~~~l~~~L~~~~~~g~~g~i~fd 364 (410)
T cd06363 308 -----FAFSVYAAVYAVAHALHNVLQCGSG-----------------GCPKRV-PVYPWQLLEELKKVNFTLLGQTVRFD 364 (410)
T ss_pred -----HHHHHHHHHHHHHHHHHHHhCCCCC-----------------CCCCCC-CCCHHHHHHHHhccEEecCCcEEEeC
Confidence 4567999999999999999765321 122112 22588999999999999999999999
Q ss_pred cCCCCCCccEEEEEeecC---CeeeEEEEecCC
Q 002211 408 QDRSLLHPSYDIINVIEH---GYPQQIGYWSNY 437 (953)
Q Consensus 408 ~~g~~~~~~y~I~~~~~~---~~~~~VG~w~~~ 437 (953)
++|++ ...|.|++++.+ +.+++||+|++.
T Consensus 365 ~~G~~-~~~~~i~~~~~~~~~~~~~~vG~~~~~ 396 (410)
T cd06363 365 ENGDP-NFGYDIVVWWWDNSSGTFEEVGSYSFY 396 (410)
T ss_pred CCCCC-ccceEEEEEEEcCCceeEEEEEEEECC
Confidence 99994 668999999633 235999999884
No 19
>cd06391 PBP1_iGluR_delta_2 N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the delta2 receptor of an orphan glutamate receptor family. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the delta2 receptor of an orphan glutamate receptor family. While this N-terminal domain belongs to the periplasmic-binding fold type I superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type II. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR. Although the delta receptors are a member of the ionotropic glutamate receptor family, they cannot be activated by AMPA, kainate, NMDA, glutamate, or any other ligands. Phylogenetic analysis shows that both GluRdelta1 and GluRalpha2 are closer related to non-NMDA receptors. GluRdelta2 was shown to function as a
Probab=100.00 E-value=1.4e-44 Score=403.53 Aligned_cols=365 Identities=22% Similarity=0.328 Sum_probs=296.9
Q ss_pred EEeEEEecCCCchhHHHHHHHHHHHHHhcCCCCCCCcEEE--EEEecCCCChHHHHHHHHHHHhcCcEEEEccCChhhHH
Q 002211 51 NVGAIFSFGTVNGQVSRIAMKAAQDDINSDPRVLGGRKLS--ITMHDAKFNGFLSIMGALQFMETDTLAIVGPQSAVMAH 128 (953)
Q Consensus 51 ~IG~l~~~~~~~g~~~~~a~~lAve~iN~~g~il~g~~l~--l~~~D~~~~~~~a~~~a~~li~~~v~aiiGp~~S~~a~ 128 (953)
+||++|+.++..+ +.|+++|+++||++..+|+|++|+ ++..|++ |+..|..++++|++++|.||+||.++..+.
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 4899999988654 469999999999999999999555 4888995 999999999999999999999998888889
Q ss_pred HHHHhhhhCCCcEEEe----ecCC-----CCCCC--CCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecCccccc
Q 002211 129 VLSHLANELQVPLLSF----TALD-----PTLSP--LQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDDDQGRN 197 (953)
Q Consensus 129 av~~v~~~~~vP~Is~----~at~-----~~ls~--~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~~~g~~ 197 (953)
.++.+|+.++||+|++ ++++ |.+++ .+||+++| |+ ..+++++++++++|+|++|+++ .|++||..
T Consensus 77 ~v~~~~~~~~vP~i~~~~~~~~t~~~~~~~~~~~~~~~y~~~~r--p~-~~~~~ai~~li~~f~W~~v~i~-~d~~~~~~ 152 (400)
T cd06391 77 SLQSLADAMHIPHLFIQRSTAGTPRSSCGLTRSNRNDDYTLSVR--PP-VYLNDVILRVVTEYAWQKFIIF-YDTDYDIR 152 (400)
T ss_pred HHHHHhccCcCCeEEeecccccCccccCCCCCCCCcccceEEec--Ch-HHHHHHHHHHHHHcCCcEEEEE-EeCCccHH
Confidence 9999999999999985 4433 34443 56888888 43 6788999999999999999976 46778999
Q ss_pred hHHHHHHHHHhcCcEEEEEEecCCCCCCC---hHHHHH-HHHHHhc--CCceEEEEEcchhhHHHHHHHHHHcCCCCCce
Q 002211 198 GVTALGDKLAEIRCKISYKSALPPDQSVT---ETDVRN-ELVKVRM--MEARVIVVHGYSRTGLMVFDVAQRLGMMDSGY 271 (953)
Q Consensus 198 ~~~~l~~~l~~~g~~v~~~~~~~~~~~~~---~~d~~~-~l~~i~~--~~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~ 271 (953)
.++.+.+.+++.|+||..... ... .+ ...+.. .+++++. .+.++||+++..+.+..++++|+++||++.+|
T Consensus 153 ~l~~l~~~~~~~~i~I~~~~~-~~~--~~~~~~~~~~~~~~~~l~~~~~~~rviVl~~~~~~~~~ll~~a~~~gm~~~~y 229 (400)
T cd06391 153 GIQEFLDKVSQQGMDVALQKV-ENN--INKMITGLFRTMRIEELNRYRDTLRRAILVMNPATAKSFITEVVETNLVAFDC 229 (400)
T ss_pred HHHHHHHHHHHcCCeEEEEec-Ccc--hhhhhHHHHHHHHHHHHHhhcccccEEEEECCcHHHHHHHHHHHHcCCCCCCe
Confidence 999999999999999987442 221 11 112322 4556665 67799999999999999999999999999999
Q ss_pred EEEEeCcccccccCCCCCchhhhhhccceEEEEEecCCChhhHHHHHHHHhhcCCC---------CCCCchhhHHhhHHH
Q 002211 272 VWIATTWLSTFIDSKSPLSLKTAKSILGALTLRQHTPDSKRRRDFVSRWNTLSNGS---------IGLNPYGLYAYDTVW 342 (953)
Q Consensus 272 ~wi~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~F~~~~~~~~~~~---------~~~~~~~~~~YDAv~ 342 (953)
+||.+++....++.. +.....+.|+.+++++.|.+....+|..+|+.++... ..++.+++++|||||
T Consensus 230 ~wi~t~~~~~~~dl~----~~~~~~~~~v~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~alayDaV~ 305 (400)
T cd06391 230 HWIIINEEISDMDVQ----ELVRRSIGRLTIIRQTFPLPQNISQRCFRGNHRISSSLCDPKDPFAQMMEISNLYIYDTVL 305 (400)
T ss_pred EEEEeCccccccccc----hHHhcccceEEEeccCCchHHHHHHHHHHHhhhccccccCccccccccccchhhHHHHHHH
Confidence 999999988887763 2334567789999999998888899999998766310 135689999999999
Q ss_pred HHHHHHHHHHhcCCcccccCCCccCCCCCCcccCCCccccCchHHHHHHHHhcccCCcceeEEEccCCCCCCccEEEEEe
Q 002211 343 MIARALKLFLDQGNTISFSNDTKLNGLGGGTLNLGALSIFDGGKKFLANILQTNMTGLSGPIHFNQDRSLLHPSYDIINV 422 (953)
Q Consensus 343 ~la~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~f~G~tG~v~Fd~~g~~~~~~y~I~~~ 422 (953)
++|+|++++...+.... .....|..+...+|..|..|+++|++++|+|+||+++||++|+|.++.|+|+|+
T Consensus 306 ~~A~A~~~l~~~~~~~~---------~~~~~c~~~~~~~w~~G~~ll~~i~~~~f~GlTG~i~f~~~g~r~~~~~dIin~ 376 (400)
T cd06391 306 LLANAFHKKLEDRKWHS---------MASLSCIRKNSKPWQGGRSMLETIKKGGVSGLTGELEFNENGGNPNVHFEILGT 376 (400)
T ss_pred HHHHHHHHHHhhccccC---------CCCcccccCCCCCCCChHHHHHHHHhcCcccceeceEECCCCCccCCceEEEEe
Confidence 99999998753321111 111112223456899999999999999999999999999999999999999999
Q ss_pred e-----cCCeeeEEEEecCCCCc
Q 002211 423 I-----EHGYPQQIGYWSNYSGL 440 (953)
Q Consensus 423 ~-----~~~~~~~VG~w~~~~gl 440 (953)
. ++|. ++||+|++..||
T Consensus 377 ~~~~~~~~g~-rkiG~Ws~~~gl 398 (400)
T cd06391 377 NYGEDLGRGV-RKLGCWNPITGL 398 (400)
T ss_pred eccccCCCcc-eEEEEEcCCcCC
Confidence 6 8888 999999999886
No 20
>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=2.7e-44 Score=404.48 Aligned_cols=352 Identities=16% Similarity=0.232 Sum_probs=293.6
Q ss_pred eEEEecCC---CchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEEccCChhhHHH
Q 002211 53 GAIFSFGT---VNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIVGPQSAVMAHV 129 (953)
Q Consensus 53 G~l~~~~~---~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aiiGp~~S~~a~a 129 (953)
=+++|.+. ..+...+.|+++|+|+||+++++++|++|+++++|++|++..+..++.++++++|.|||||.||.++.+
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 35666542 235678999999999999999998999999999999999887888888888789999999999999999
Q ss_pred HHHhhhhCCCcEEEeecCCCCCCC--CCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecCccccch---HHHHHH
Q 002211 130 LSHLANELQVPLLSFTALDPTLSP--LQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDDDQGRNG---VTALGD 204 (953)
Q Consensus 130 v~~v~~~~~vP~Is~~at~~~ls~--~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~~~g~~~---~~~l~~ 204 (953)
++++++.++||+|+++++++.+++ ..|||+||+.|++..++.++++++++++|++|++||++++||++. .+.|.+
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 999999999999999999999986 368999999999999999999999999999999999999999886 899999
Q ss_pred HHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEEeCccccc-c
Q 002211 205 KLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIATTWLSTF-I 283 (953)
Q Consensus 205 ~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~-~ 283 (953)
.+++.|++|+....++.+ +.|+...|+++++.+ |+||+++....+..++++|+++||+..+|+||..+...+. .
T Consensus 163 ~~~~~gi~v~~~~~~~~~----~~d~~~~l~~ik~~~-rvii~~~~~~~~~~ll~~A~~~gm~~~~yv~i~~d~~~~~~~ 237 (387)
T cd06386 163 VFQEEGYHMSIYPFDETK----DLDLDEIIRAIQASE-RVVIMCAGADTIRSIMLAAHRRGLTSGDYIFFNIELFNSSSY 237 (387)
T ss_pred HHHhcCceEEEEecCCCC----cccHHHHHHHHHhcC-cEEEEecCHHHHHHHHHHHHHcCCCCCCEEEEEEeccccccc
Confidence 999999999877655544 679999999999887 9999999999999999999999999999999999865311 1
Q ss_pred -----cCCCCCc---hhhhhhccceEEEEEecCCChhhHHHHHHHHhhcCC------CCCCCchhhHHhhHHHHHHHHHH
Q 002211 284 -----DSKSPLS---LKTAKSILGALTLRQHTPDSKRRRDFVSRWNTLSNG------SIGLNPYGLYAYDTVWMIARALK 349 (953)
Q Consensus 284 -----~~~~~~~---~~~~~~~~g~~~~~~~~~~~~~~~~F~~~~~~~~~~------~~~~~~~~~~~YDAv~~la~Al~ 349 (953)
......+ ....+.++|+.++.++ .+.+++|.++|++++.. ...++.+++++||||+++|+|++
T Consensus 238 ~~~~w~~~~~~~~~~~~a~~~~~~v~~~~~~---~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~aa~~yDav~l~A~Al~ 314 (387)
T cd06386 238 GDGSWKRGDKHDFEAKQAYSSLNTVTLLRTV---KPEFEKFSMEVKSSVEKAGDLNDCDYVNMFVEGFHDAILLYALALH 314 (387)
T ss_pred CCCCCccCCCcCHHHHHHHHhheEEeccCCC---ChHHHHHHHHHHHHHHhCCCCcccccchHHHHHHHHHHHHHHHHHH
Confidence 0001111 2334556666665554 57788898888844321 12345889999999999999999
Q ss_pred HHHhcCCcccccCCCccCCCCCCcccCCCccccCchHHHHHHHHhcccCCcceeEEEccCCCCCCccEEEEEee--cCCe
Q 002211 350 LFLDQGNTISFSNDTKLNGLGGGTLNLGALSIFDGGKKFLANILQTNMTGLSGPIHFNQDRSLLHPSYDIINVI--EHGY 427 (953)
Q Consensus 350 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~f~G~tG~v~Fd~~g~~~~~~y~I~~~~--~~~~ 427 (953)
+++..++. +.+|..|+++|++++|+|++|++.||++|+| ...|.|+.++ +++.
T Consensus 315 ~~~~~g~~------------------------~~~g~~l~~~l~~~~f~G~tG~v~~d~~g~r-~~~~~v~~~~~~~~~~ 369 (387)
T cd06386 315 EVLKNGYS------------------------KKDGTKITQRMWNRTFEGIAGQVSIDANGDR-YGDFSVIAMTDVEAGT 369 (387)
T ss_pred HHhhCCCC------------------------CCCHHHHHHHHhCCceeeccccEEECCCCCc-cccEEEEEccCCCCcc
Confidence 98654321 2369999999999999999999999999997 6699999997 4455
Q ss_pred eeEEEEecCC
Q 002211 428 PQQIGYWSNY 437 (953)
Q Consensus 428 ~~~VG~w~~~ 437 (953)
++.||.|...
T Consensus 370 ~~~~~~~~~~ 379 (387)
T cd06386 370 YEVVGNYFGK 379 (387)
T ss_pred EEEEeEEccc
Confidence 5999999754
No 21
>cd06370 PBP1_Speract_GC_like Ligand-binding domain of membrane bound guanylyl cyclases. Ligand-binding domain of membrane bound guanylyl cyclases (GCs), which are known to be activated by sperm-activating peptides (SAPs), such as speract or resact. These ligand peptides are released by a range of invertebrates to stimulate the metabolism and motility of spermatozoa and are also potent chemoattractants. These GCs contain a single transmembrane segment, an extracellular ligand binding domain, and intracellular protein kinase-like and cyclase catalytic domains. GCs of insect and nematodes, which exhibit high sequence similarity to the speract receptor are also included in this model.
Probab=100.00 E-value=2.1e-44 Score=408.54 Aligned_cols=349 Identities=17% Similarity=0.290 Sum_probs=294.7
Q ss_pred EEEeEEEecCC----CchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEEccCChh
Q 002211 50 LNVGAIFSFGT----VNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIVGPQSAV 125 (953)
Q Consensus 50 i~IG~l~~~~~----~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aiiGp~~S~ 125 (953)
|+||+++|++. ..|.....|+++|+|+||++||+++|++|+++++|++|+|..|+.++++|++++|.+||||.+|.
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 68999999975 45899999999999999999999889999999999999999999999999999999999999985
Q ss_pred hHHHHHHhhhhCCCcEEEeecCCCCCCC-CCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecCccccchHHHHHH
Q 002211 126 MAHVLSHLANELQVPLLSFTALDPTLSP-LQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDDDQGRNGVTALGD 204 (953)
Q Consensus 126 ~a~av~~v~~~~~vP~Is~~at~~~ls~-~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~~~g~~~~~~l~~ 204 (953)
.+ ++.++++++||+|+++++++.+++ ..||+|||+.|++..++.++++++++++|++|++|+.+++||++..+.|++
T Consensus 81 ~~--~a~i~~~~~iP~Is~~a~~~~l~~~~~~~~f~r~~~~~~~~~~a~~~~~~~~~w~~vaii~~~~~~g~~~~~~~~~ 158 (404)
T cd06370 81 TT--EARLAAAWNLPMISYKCDEEPVSDKSKYPTFARTVPPSIQVVKSVIALLKHFNWNKFSVVYENDSKYSSVFETLKE 158 (404)
T ss_pred HH--HHHHHhhcCCcEEecccCCccccccccCCCeEEcCCCHHHHHHHHHHHHHHCCCcEEEEEEecCcccHHHHHHHHH
Confidence 44 567999999999999999999987 679999999999999999999999999999999999999999999999999
Q ss_pred HHHhcCcEEEEEEecCCCCC---CChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHHHcCCC-CCceEEEEeCccc
Q 002211 205 KLAEIRCKISYKSALPPDQS---VTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQRLGMM-DSGYVWIATTWLS 280 (953)
Q Consensus 205 ~l~~~g~~v~~~~~~~~~~~---~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~~~g~~-~~~~~wi~~~~~~ 280 (953)
.+++.|++|+..+.++.+.. ....++...|++++.. ++++|+++...++..+++||+++||+ ..+|+||.++...
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 99999999999988876410 0147889999998865 77888888888999999999999998 5789999876310
Q ss_pred c------c---------ccCCCCCchhhhhhccceEEEEEecCCChhhHHHHHHHHhhcCC------------CCCCCch
Q 002211 281 T------F---------IDSKSPLSLKTAKSILGALTLRQHTPDSKRRRDFVSRWNTLSNG------------SIGLNPY 333 (953)
Q Consensus 281 ~------~---------~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~F~~~~~~~~~~------------~~~~~~~ 333 (953)
. . ............++++|++.+.+..+ .+..++|.++|+++++. ...++.+
T Consensus 238 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 316 (404)
T cd06370 238 YDRDSQDYYSLHRGFQSREYNRSDDEKALEAMKSVLIIVPTPV-SPDYDSFSIFVRKYNLEPPFNGDLGESELVLEIDIE 316 (404)
T ss_pred ccccchhhhhhhhhhccccccccccHHHHHHhHheEEEecCCC-CchHHHHHHHHHHhccCCCCccccccccccccccee
Confidence 0 0 01011111355678899998876655 77788999999886431 1246778
Q ss_pred hhHHhhHHHHHHHHHHHHHhcCCcccccCCCccCCCCCCcccCCCccccCchHHHHHHHHhcccCCcce-eEEEccCCCC
Q 002211 334 GLYAYDTVWMIARALKLFLDQGNTISFSNDTKLNGLGGGTLNLGALSIFDGGKKFLANILQTNMTGLSG-PIHFNQDRSL 412 (953)
Q Consensus 334 ~~~~YDAv~~la~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~f~G~tG-~v~Fd~~g~~ 412 (953)
++++||||+++|+|++++.++++.. .++++|.++|++++|+|++| ++.||++|++
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 9999999999999999986653221 15899999999999999999 8999999996
Q ss_pred CCccEEEEEeecCCe
Q 002211 413 LHPSYDIINVIEHGY 427 (953)
Q Consensus 413 ~~~~y~I~~~~~~~~ 427 (953)
...|.|++++++.+
T Consensus 373 -~~~y~v~~~~~~~~ 386 (404)
T cd06370 373 -EGNYSVLALQPIPP 386 (404)
T ss_pred -ccceEEEEeccccc
Confidence 68999999976544
No 22
>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=2e-44 Score=409.89 Aligned_cols=357 Identities=17% Similarity=0.227 Sum_probs=293.0
Q ss_pred EEeEEEecCCC---ch-hHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHH-----HHHHH-HhcCcEEEEc
Q 002211 51 NVGAIFSFGTV---NG-QVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIM-----GALQF-METDTLAIVG 120 (953)
Q Consensus 51 ~IG~l~~~~~~---~g-~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~-----~a~~l-i~~~v~aiiG 120 (953)
+||+++|++.. +| .....|+++|+|+||++||+|+|++|++++.|+++++..+.. .+.++ ..++|.+|||
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 58999999844 44 778899999999999999999999999999999776654333 33332 3459999999
Q ss_pred cCChhhHHHHHHhhhhCCCcEEEeecCCCCCCC-CCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEE-EEecCc-cccc
Q 002211 121 PQSAVMAHVLSHLANELQVPLLSFTALDPTLSP-LQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIA-IFNDDD-QGRN 197 (953)
Q Consensus 121 p~~S~~a~av~~v~~~~~vP~Is~~at~~~ls~-~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vai-i~~d~~-~g~~ 197 (953)
|.||.++.+++++++.++||+|+++++++.+++ ..|||+||+.|++..++.++++++++++|+++++ +|.++. +++.
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 999999999999999999999999999999998 6799999999999999999999999999999984 565543 3343
Q ss_pred ---hHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHHHcCCCCCceEEE
Q 002211 198 ---GVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWI 274 (953)
Q Consensus 198 ---~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi 274 (953)
..+.+.+.+++.|++|+..+..+.+ ..|+..+|+++++. .|+||++++..++..++++|+++||++++|+||
T Consensus 161 ~~~~~~~l~~~~~~~gi~v~~~~~~~~~----~~d~~~~l~~ik~~-~~iii~~~~~~~~~~i~~~a~~~g~~~~~y~~i 235 (405)
T cd06385 161 CYFAMEGLYMELKKNNITVVDLVFEEDD----LINYTTLLQDIKQK-GRVIYVCCSPDIFRRLMLQFWREGLPSEDYVFF 235 (405)
T ss_pred hHHHHHHHHHHHHhCCeEEEEeeccCCc----hhhHHHHHHHHhhc-ceEEEEeCCHHHHHHHHHHHHHcCCCCCcEEEE
Confidence 4688999999999999987644333 77999999999875 499999999999999999999999999999999
Q ss_pred EeCcccccccC---------CCCCchhhhhhccceEEEEEecCCChhhHHHHHHHHhh----cCCCC---CCCchhhHHh
Q 002211 275 ATTWLSTFIDS---------KSPLSLKTAKSILGALTLRQHTPDSKRRRDFVSRWNTL----SNGSI---GLNPYGLYAY 338 (953)
Q Consensus 275 ~~~~~~~~~~~---------~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~F~~~~~~~----~~~~~---~~~~~~~~~Y 338 (953)
.++++...+.. .+..+....+++++++....+.+.++.+++|.++|+++ |+... .++.+++++|
T Consensus 236 ~~~~~~~~~~~~~~~~~w~~~~~~~~~~~~a~~~v~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~aa~~Y 315 (405)
T cd06385 236 YIDLFGASLQGPDPKRPWYRGDADDAAAREAFQSVKILTYKEPQNPEYKEFLSDLKTDAKEMFNFTVEDSLMNIIAGGFY 315 (405)
T ss_pred EeecchhhccCCCCCCCCCCCCcccHHHHHhhheeEEEeCCCCCChhHHHHHHHHHHHhhccCCCccchhhHHHHHHHHH
Confidence 99765432221 01112344667899988877777788899999999985 54221 1568899999
Q ss_pred hHHHHHHHHHHHHHhcCCcccccCCCccCCCCCCcccCCCccccCchHHHHHHHHhcccCCcceeEEEccCCCCCCccEE
Q 002211 339 DTVWMIARALKLFLDQGNTISFSNDTKLNGLGGGTLNLGALSIFDGGKKFLANILQTNMTGLSGPIHFNQDRSLLHPSYD 418 (953)
Q Consensus 339 DAv~~la~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~f~G~tG~v~Fd~~g~~~~~~y~ 418 (953)
||||++|+|++++...++. +.+|++|.++|++++|+|++|++.||++|+| .+.|.
T Consensus 316 Dav~l~a~Al~~~~~~~~~------------------------~~~g~~i~~~l~~~~f~G~tG~v~fd~~G~r-~~~~~ 370 (405)
T cd06385 316 DGVMLYAHALNETMAKGGT------------------------RPPGTAITQRMWNRTFYGVTGFVKIDDNGDR-ETDFA 370 (405)
T ss_pred HHHHHHHHHHHHHHhcCCC------------------------CCCHHHHHHHhhCceEeeceeEEEEcCCCCE-eceeE
Confidence 9999999999998654332 2259999999999999999999999999997 57888
Q ss_pred EEEe---ecCCeeeEEEEecCCC
Q 002211 419 IINV---IEHGYPQQIGYWSNYS 438 (953)
Q Consensus 419 I~~~---~~~~~~~~VG~w~~~~ 438 (953)
|+++ +++.+ +.||+|+..+
T Consensus 371 ~~~~~~~~~g~~-~~v~~~~~~~ 392 (405)
T cd06385 371 LWDMTDTESGDF-QVVSVYNGTQ 392 (405)
T ss_pred EEEccCCCCCcE-EEEEEEcccC
Confidence 8866 34444 9999997654
No 23
>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=3.5e-44 Score=402.02 Aligned_cols=339 Identities=18% Similarity=0.256 Sum_probs=290.1
Q ss_pred eEEEeEEEecCCCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhc-CcEEEEccCChhh-
Q 002211 49 VLNVGAIFSFGTVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMET-DTLAIVGPQSAVM- 126 (953)
Q Consensus 49 ~i~IG~l~~~~~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~-~v~aiiGp~~S~~- 126 (953)
.|+||+++|.++ ...+++.|+..+|.+..+..+.+++++..|+++||.+++.++++++.+ +|.+|+||.+|+.
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 589999999884 347788888888876644468999999999999999999999998765 8999999999998
Q ss_pred --HHHHHHhhhhCCCcEEEeecCCCCC-CC-CCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecCccccchHHHH
Q 002211 127 --AHVLSHLANELQVPLLSFTALDPTL-SP-LQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDDDQGRNGVTAL 202 (953)
Q Consensus 127 --a~av~~v~~~~~vP~Is~~at~~~l-s~-~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~~~g~~~~~~l 202 (953)
+.+++++++.++||+|+++++++.+ ++ ..||||||+.|++..|+++++++++++||++|++||++++||++..+.+
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 9999999999999999999999998 77 6899999999999999999999999999999999999999999999999
Q ss_pred HHHHHhcCcE--EEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEEeCccc
Q 002211 203 GDKLAEIRCK--ISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIATTWLS 280 (953)
Q Consensus 203 ~~~l~~~g~~--v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~ 280 (953)
++.+++.|+| ++....++.. . .+++...+.++++.++|+||++++..++..++++|+++||++++|+||+++.+.
T Consensus 157 ~~~l~~~g~~~~i~~~~~~~~~--~-~~~~~~~l~~l~~~~~~vivl~~~~~~~~~il~~a~~~g~~~~~~~wI~~~~~~ 233 (362)
T cd06367 157 ETTLEESFVGWEFQLVLTLDLS--D-DDGDARLLRQLKKLESRVILLYCSKEEAERIFEAAASLGLTGPGYVWIVGELAL 233 (362)
T ss_pred HHHHHhcccceeeeeeEEeccC--C-CcchHHHHHHHHhcCCcEEEEeCCHHHHHHHHHHHHHcCCCCCCcEEEECcccc
Confidence 9999999999 7777777665 1 227889999999999999999999999999999999999999999999999886
Q ss_pred ccccCCCCCchhhhhhccceEEEEEecCCChhhHHHHHHHHhhcCCCCCCCchhhHHhhHHHHHHHHHHHHHhcCCcccc
Q 002211 281 TFIDSKSPLSLKTAKSILGALTLRQHTPDSKRRRDFVSRWNTLSNGSIGLNPYGLYAYDTVWMIARALKLFLDQGNTISF 360 (953)
Q Consensus 281 ~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~F~~~~~~~~~~~~~~~~~~~~~YDAv~~la~Al~~~~~~~~~~~~ 360 (953)
.... ...+...|++++++..+ ..+.+++||||+++|+|++++..+++...
T Consensus 234 ~~~~-------~~~~~~~G~~g~~~~~~----------------------~~~~~~~~Dav~~~a~Al~~~~~~~~~~~- 283 (362)
T cd06367 234 GSGL-------APEGLPVGLLGVGLDTW----------------------YSLEARVRDAVAIVARAAESLLRDKGALP- 283 (362)
T ss_pred cccC-------CccCCCCeeEEEEeccc----------------------ccHHHHHHHHHHHHHHHHHHHHHhcCCCC-
Confidence 4211 12356679999987542 24578899999999999999876533211
Q ss_pred cCCCccCCCCCCcccCCCccc--cCchHHHHHHHHhcccCCcceeEEEccCCCCCCccEEEEEee-cCCeeeEEEEecC
Q 002211 361 SNDTKLNGLGGGTLNLGALSI--FDGGKKFLANILQTNMTGLSGPIHFNQDRSLLHPSYDIINVI-EHGYPQQIGYWSN 436 (953)
Q Consensus 361 ~~~~~~~~~~~~~~~~~~~~~--~~~~~~l~~~l~~~~f~G~tG~v~Fd~~g~~~~~~y~I~~~~-~~~~~~~VG~w~~ 436 (953)
....+|..... |.+|..|.++|++++|.|++|+|+||++|++..+.|+|+|++ +.++ ++||.|++
T Consensus 284 ----------~~~~~C~~~~~~~~~~g~~l~~~l~~~~f~G~tg~v~F~~~G~~~~~~~~I~~l~~~~~~-~~VG~W~~ 351 (362)
T cd06367 284 ----------EPPVNCYDTANKRESSGQYLARFLMNVTFDGETGDVSFNEDGYLSNPKLVIINLRRNRKW-ERVGSWEN 351 (362)
T ss_pred ----------CCCCCcCCCCCCCCCchHHHHHHHhcccccCCCCceeECCCcccccceEEEEEecCCCcc-eEEEEEcC
Confidence 11224544432 677999999999999999999999999999888899999999 6566 99999975
No 24
>cd06373 PBP1_NPR_like Ligand binding domain of natriuretic peptide receptor (NPR) family. Ligand binding domain of natriuretic peptide receptor (NPR) family which consists of three different subtypes: type A natriuretic peptide receptor (NPR-A, or GC-A), type B natriuretic peptide receptors (NPR-B, or GC-B), and type C natriuretic peptide receptor (NPR-C). There are three types of natriuretic peptide (NP) ligands specific to the receptors: atrial NP (ANP), brain or B-type NP (BNP), and C-type NP (CNP). The NP family is thought to have arisen through gene duplication during evolution and plays an essential role in cardiovascular and body fluid homeostasis. ANP and BNP bind mainly to NPR-A, while CNP binds specifically to NPR-B. Both NPR-A and NPR-B have guanylyl cyclase catalytic activity and produces intracellular secondary messenger cGMP in response to peptide-ligand binding. Consequently, the NPR-A activation results in vasodilation and inhibition of vascular smooth muscle cell proli
Probab=100.00 E-value=3.8e-44 Score=406.63 Aligned_cols=359 Identities=17% Similarity=0.261 Sum_probs=300.7
Q ss_pred EEeEEEecCC----CchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCC----ChHHHHHHHHHHHh-cCcEEEEcc
Q 002211 51 NVGAIFSFGT----VNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKF----NGFLSIMGALQFME-TDTLAIVGP 121 (953)
Q Consensus 51 ~IG~l~~~~~----~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~----~~~~a~~~a~~li~-~~v~aiiGp 121 (953)
+||+++|.+. ..|.....|+++|+|+||++||+++|++|+++++|+++ ++..++..+.+++. ++|.|||||
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 5899999984 34678899999999999999999889999999999999 89999999999874 589999999
Q ss_pred CChhhHHHHHHhhhhCCCcEEEeecCCCCCCC-CCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecCccc----c
Q 002211 122 QSAVMAHVLSHLANELQVPLLSFTALDPTLSP-LQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDDDQG----R 196 (953)
Q Consensus 122 ~~S~~a~av~~v~~~~~vP~Is~~at~~~ls~-~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~~~g----~ 196 (953)
.||.++.+++++++.++||+|+++++++.+++ ..|||+||+.|++..++.++++++++++|++|++||.+++++ .
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 99999999999999999999999999999997 679999999999999999999999999999999999987774 5
Q ss_pred chHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEEe
Q 002211 197 NGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIAT 276 (953)
Q Consensus 197 ~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~ 276 (953)
...+.+.+.+++.|++|+.. .+... ....|+..+|+++++.. |+||+++...++..+++||+++||+..+|+||..
T Consensus 161 ~~~~~~~~~~~~~g~~v~~~-~~~~~--~~~~d~~~~l~~ik~~~-~vii~~~~~~~~~~~~~qa~~~g~~~~~yv~i~~ 236 (396)
T cd06373 161 FTLEGVYTVLKEENITVSDF-PFDED--KELDDYKELLRDISKKG-RVVIMCASPDTVREIMLAAHRLGLTSGEYVFFNI 236 (396)
T ss_pred HHHHHHHHHHhhcCceeeEE-eecCC--ccccCHHHHHHHHHhcC-cEEEEecCHHHHHHHHHHHHHcCCCCCcEEEEEE
Confidence 56788999999999998754 35443 11379999999999865 9999999999999999999999999999999997
Q ss_pred Ccccccc------c--CCCCCchhhhhhccceEEEEEecCCChhhHHHHHHHHhh----cCCC---CCCCchhhHHhhHH
Q 002211 277 TWLSTFI------D--SKSPLSLKTAKSILGALTLRQHTPDSKRRRDFVSRWNTL----SNGS---IGLNPYGLYAYDTV 341 (953)
Q Consensus 277 ~~~~~~~------~--~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~F~~~~~~~----~~~~---~~~~~~~~~~YDAv 341 (953)
+...... . ..........++.+|++++..+.++.+.+++|.++|+++ |+.. ..++.+++++||||
T Consensus 237 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~F~~~~~~~~~~~~~~~~~~~~~~~~a~~~YDav 316 (396)
T cd06373 237 DLFGSSLYGGGPWWWERGDEDDEKAKEAYQALMTITLREPDNPEYKEFSLEVKERAKKKFNTTSDDSLVNFFAGAFYDAV 316 (396)
T ss_pred ccchhhhccCCCCcCCCCCcccHHHHHHHHHheEEecCCCCChHHHHHHHHHHHHhhhcCCCCcchhHHHHHHHHHHHHH
Confidence 7543211 1 011111344566788998888888888899999999875 4311 13567899999999
Q ss_pred HHHHHHHHHHHhcCCcccccCCCccCCCCCCcccCCCccccCchHHHHHHHHhcccCCcceeEEEccCCCCCCccEEEEE
Q 002211 342 WMIARALKLFLDQGNTISFSNDTKLNGLGGGTLNLGALSIFDGGKKFLANILQTNMTGLSGPIHFNQDRSLLHPSYDIIN 421 (953)
Q Consensus 342 ~~la~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~f~G~tG~v~Fd~~g~~~~~~y~I~~ 421 (953)
+++|+|++++..+++. +.++++|+++|++++|+|++|++.||++|++ ...|.|++
T Consensus 317 ~~~a~Al~~~~~~~~~------------------------~~~~~~i~~~l~~~~f~G~tG~v~fd~~G~~-~~~~~v~~ 371 (396)
T cd06373 317 LLYALALNETLAEGGD------------------------PRDGTNITRRMWNRTFEGITGNVSIDENGDR-ESDFSLWD 371 (396)
T ss_pred HHHHHHHHHHHhccCC------------------------CCChHHHHHHhcCCceecccCceEeecCCcc-cceeeeee
Confidence 9999999998654321 1258999999999999999999999999996 67888877
Q ss_pred ee--cCCeeeEEEEecCCC
Q 002211 422 VI--EHGYPQQIGYWSNYS 438 (953)
Q Consensus 422 ~~--~~~~~~~VG~w~~~~ 438 (953)
+. ++|.++.||.|++.+
T Consensus 372 ~~~~~~g~~~~~~~~~~~~ 390 (396)
T cd06373 372 MTDTETGTFEVVANYNGSN 390 (396)
T ss_pred ccCCCCceEEEEeeccccc
Confidence 63 345559999998764
No 25
>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=1.1e-43 Score=402.96 Aligned_cols=361 Identities=20% Similarity=0.375 Sum_probs=315.5
Q ss_pred EEeEEEecC---CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhc-CcEEEEccCChhh
Q 002211 51 NVGAIFSFG---TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMET-DTLAIVGPQSAVM 126 (953)
Q Consensus 51 ~IG~l~~~~---~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~-~v~aiiGp~~S~~ 126 (953)
|||+++|++ +..|.....|+++|+|+||++|++++|++|+++++|++++|..+++.+.+|+.+ +|.+||||.+|++
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 699999998 556889999999999999999976679999999999999999999999999876 8999999999999
Q ss_pred HHHHHHhhhhCCCcEEEeecCCCCCCC-CCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecCc-cccchHHHHHH
Q 002211 127 AHVLSHLANELQVPLLSFTALDPTLSP-LQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDDD-QGRNGVTALGD 204 (953)
Q Consensus 127 a~av~~v~~~~~vP~Is~~at~~~ls~-~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~~-~g~~~~~~l~~ 204 (953)
+.+++++++++++|+|+++++++.+++ ..+||+||+.|++..++.+++++++++||++++++++++. ||....+.+.+
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 999999999999999999999999987 5789999999999999999999999999999999998888 99999999999
Q ss_pred HHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEEeCccccccc
Q 002211 205 KLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIATTWLSTFID 284 (953)
Q Consensus 205 ~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~ 284 (953)
++++.|++|+....++.+ .+..|+..+++++++.+ |+||+++.+.++..+++|++++|+...+++||.++.+.....
T Consensus 161 ~~~~~G~~v~~~~~~~~~--~~~~d~~~~l~~i~~~~-~vii~~~~~~~~~~~l~q~~~~g~~~~~~~~i~~~~~~~~~~ 237 (389)
T cd06352 161 ALREFNLTVSHVVFMEDN--SGAEDLLEILQDIKRRS-RIIIMCGSSEDVRELLLAAHDLGLTSGDYVFILIDLFNYSLP 237 (389)
T ss_pred HHHhcCCeEEEEEEecCC--ccchhHHHHHHHhhhcc-eEEEEECCHHHHHHHHHHHHHcCCCCCcEEEEEEehhccccc
Confidence 999999999998888765 12578999999999887 999999999999999999999999888899999887655421
Q ss_pred C--------CCCCchhhhhhccceEEEEEecCCChhhHHHHHHHHhhcCC--------CCCCCchhhHHhhHHHHHHHHH
Q 002211 285 S--------KSPLSLKTAKSILGALTLRQHTPDSKRRRDFVSRWNTLSNG--------SIGLNPYGLYAYDTVWMIARAL 348 (953)
Q Consensus 285 ~--------~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~F~~~~~~~~~~--------~~~~~~~~~~~YDAv~~la~Al 348 (953)
. .........+.++|++++.+..+.++..++|.++|+++++. ...++.+++++|||++++|+|+
T Consensus 238 ~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~a~~~YDav~~~a~Al 317 (389)
T cd06352 238 YQNSYPWERGDGDDEKAKEAYDAVLTITLRPPDNPEYEEFSEEVKEAAKRPPFNTDAEPEQVSPYAGYLYDAVLLYAHAL 317 (389)
T ss_pred cCCCCCcccCCcccHHHHHHHHhheEEEecCCCCchHHHHHHHHHHHHhcccCccCCCccccchhhhhHHHHHHHHHHHH
Confidence 1 11112345677899999988888888999999999998852 1245789999999999999999
Q ss_pred HHHHhcCCcccccCCCccCCCCCCcccCCCccccCchHHHHHHHHhcccCCcceeEEEccCCCCCCccEEEEEeecC-Ce
Q 002211 349 KLFLDQGNTISFSNDTKLNGLGGGTLNLGALSIFDGGKKFLANILQTNMTGLSGPIHFNQDRSLLHPSYDIINVIEH-GY 427 (953)
Q Consensus 349 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~f~G~tG~v~Fd~~g~~~~~~y~I~~~~~~-~~ 427 (953)
+++..+++. +.++.++.+.|++++|.|++|++.||++|++ ...|.|++++++ +.
T Consensus 318 ~~~~~~~~~------------------------~~~~~~v~~~l~~~~f~g~~G~v~fd~~G~~-~~~~~v~~~~~~~~~ 372 (389)
T cd06352 318 NETLAEGGD------------------------YNGGLIITRRMWNRTFSGITGPVTIDENGDR-EGDYSLLDLDSTGGQ 372 (389)
T ss_pred HHHHHhCCC------------------------CCchHHHHHHhcCcEEEeeeeeEEEcCCCCe-eeeEEEEEecCCCce
Confidence 998765322 1258889999999999999999999999996 678999999965 55
Q ss_pred eeEEEEecCCCC
Q 002211 428 PQQIGYWSNYSG 439 (953)
Q Consensus 428 ~~~VG~w~~~~g 439 (953)
...++.+.+.+|
T Consensus 373 ~~~~~~~~~~~~ 384 (389)
T cd06352 373 LEVVYLYDTSSG 384 (389)
T ss_pred EEEEEeccccce
Confidence 588888877654
No 26
>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=1e-43 Score=398.83 Aligned_cols=349 Identities=19% Similarity=0.275 Sum_probs=289.1
Q ss_pred EEeEEEecC---CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEEccCChhhH
Q 002211 51 NVGAIFSFG---TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIVGPQSAVMA 127 (953)
Q Consensus 51 ~IG~l~~~~---~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aiiGp~~S~~a 127 (953)
+||++.|++ +..|...+.|+++|+|+||+++++++|+++++++.|++|++..++.++.++ .++|.+||||.||.++
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 599999996 455788899999999999999999889999999999999988887655443 4699999999999999
Q ss_pred HHHHHhhhhCCCcEEEeecCCCCCCC-CCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecCccccchHHHHHHHH
Q 002211 128 HVLSHLANELQVPLLSFTALDPTLSP-LQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDDDQGRNGVTALGDKL 206 (953)
Q Consensus 128 ~av~~v~~~~~vP~Is~~at~~~ls~-~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~~~g~~~~~~l~~~l 206 (953)
.++++++++++||+|++++++|.+++ ..||+|+|+.|++ +.++++++++++|++|++||++++||.+..+.+.+.+
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 7799999999886 4678889999999999999999999999999999999
Q ss_pred HhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCC-ceEEEEEcch-----hhHHHHHHHHHHcCCCCCceEEEEeCccc
Q 002211 207 AEIRCKISYKSALPPDQSVTETDVRNELVKVRMME-ARVIVVHGYS-----RTGLMVFDVAQRLGMMDSGYVWIATTWLS 280 (953)
Q Consensus 207 ~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~-~~vii~~~~~-----~~~~~~~~~a~~~g~~~~~~~wi~~~~~~ 280 (953)
++.|++|+..+.++.+ +.|++.+|++||+.+ +||||++++. .++..+++||+++||++.+|+||.+++..
T Consensus 157 ~~~gi~v~~~~~~~~~----~~d~~~~L~~lk~~~~~~viv~~~~~~~~~~~~~~~i~~qa~~~Gm~~~~y~~i~~d~~~ 232 (382)
T cd06371 157 RAHGLPVGLVTSMGPD----EKGAREALKKVRSADRVRVVIMCMHSVLIGGEEQRLLLETALEMGMTDGRYVFIPYDTLL 232 (382)
T ss_pred HHCCCcEEEEEEecCC----HHHHHHHHHHHhcCCCcEEEEEEeeccccCcHHHHHHHHHHHHcCCcCCcEEEEEecccc
Confidence 9999999988888766 789999999999987 6999998876 67889999999999999999999998543
Q ss_pred cccc----CCC--CCchhhhhhccceEEEEEecCCChhhHHHHHHHHhh-cC---CCCCCCchhhHHhhHHHHHHHHHHH
Q 002211 281 TFID----SKS--PLSLKTAKSILGALTLRQHTPDSKRRRDFVSRWNTL-SN---GSIGLNPYGLYAYDTVWMIARALKL 350 (953)
Q Consensus 281 ~~~~----~~~--~~~~~~~~~~~g~~~~~~~~~~~~~~~~F~~~~~~~-~~---~~~~~~~~~~~~YDAv~~la~Al~~ 350 (953)
.... ... ..+....++.+|++.+.++.+..+..++|.++|+.. ++ +...++.+++++|||++++|+|+++
T Consensus 233 ~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~YDav~~~a~Al~~ 312 (382)
T cd06371 233 YSLPYRNVSYPALRNNSKLRRAYDAVLTITMDSGEQSFYEAFRAAQERGEIPSDLEPEQVSPLFGTIYNSIYLLAHAVEN 312 (382)
T ss_pred ccCCCCCccccCCCCCHHHHHHhHhhEEEEecCCCCcHHHHHHHHHhcCCCCCCCCccccchhHHHHHHHHHHHHHHHHH
Confidence 1110 000 112344467889888877655555556666665321 11 1112345667899999999999999
Q ss_pred HHhcCCcccccCCCccCCCCCCcccCCCccccCchHHHHHHHHhcccCCcceeEEEccCCCCCCccEEEEEeecCCeeeE
Q 002211 351 FLDQGNTISFSNDTKLNGLGGGTLNLGALSIFDGGKKFLANILQTNMTGLSGPIHFNQDRSLLHPSYDIINVIEHGYPQQ 430 (953)
Q Consensus 351 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~f~G~tG~v~Fd~~g~~~~~~y~I~~~~~~~~~~~ 430 (953)
+++.++. .++.+|+++|++++|+|++|+++||++|++ .+.|.|+++.++|. +-
T Consensus 313 a~~~g~~-------------------------~d~~~l~~~l~~~~f~GvtG~v~fd~~g~~-~~~~~v~~~~~~~~-~~ 365 (382)
T cd06371 313 ARAAGGG-------------------------VSGANLAQHTRNLEFQGFNQRLRTDSGGGG-QAPYVVLDTDGKGD-QL 365 (382)
T ss_pred HHHhCCC-------------------------ccHHHHHHHHhCccccccceEEEecCCCCc-ccceEEEecCCCCC-ee
Confidence 9765332 148999999999999999999999999995 79999999998877 55
Q ss_pred EEEe
Q 002211 431 IGYW 434 (953)
Q Consensus 431 VG~w 434 (953)
+-.+
T Consensus 366 ~~~~ 369 (382)
T cd06371 366 YPTY 369 (382)
T ss_pred eeeE
Confidence 4433
No 27
>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=1.4e-43 Score=401.38 Aligned_cols=358 Identities=18% Similarity=0.292 Sum_probs=291.3
Q ss_pred EEeEEEecC---CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhc-CcEEEEccCChhh
Q 002211 51 NVGAIFSFG---TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMET-DTLAIVGPQSAVM 126 (953)
Q Consensus 51 ~IG~l~~~~---~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~-~v~aiiGp~~S~~ 126 (953)
+||++.|.+ ...+.....|+++|+++||+++++++|++|++++.|++|++..|+.++++++.+ +|.|||||.||++
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 589999976 334677789999999999999999988999999999999999999999999975 9999999999999
Q ss_pred HHHHHHhhhhCCCcEEEeecCCCCCCC-CCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecC---cccc--chHH
Q 002211 127 AHVLSHLANELQVPLLSFTALDPTLSP-LQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDD---DQGR--NGVT 200 (953)
Q Consensus 127 a~av~~v~~~~~vP~Is~~at~~~ls~-~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~---~~g~--~~~~ 200 (953)
+.+++++++.++||+|+++++++.+++ ..||+++|+.|++..++.+++++++++||++|++||.++ .|++ ...+
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 999999999999999999999999997 678999999999999999999999999999999998542 3442 2344
Q ss_pred HHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEEeCccc
Q 002211 201 ALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIATTWLS 280 (953)
Q Consensus 201 ~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~ 280 (953)
.+.+.++ .+++++..+.++.+ +.|+...+.+.+.+++|+||++++..++..++++|+++||+.++|+||.+++..
T Consensus 161 ~~~~~~~-~~~~i~~~~~~~~~----~~d~~~~~l~~~~~~~~vii~~~~~~~~~~i~~~a~~~g~~~~~y~~i~~~~~~ 235 (391)
T cd06372 161 AVENQLK-FHFNITATVRYSSS----NPDLLQEKLRYISSVARVIILICSSEDAKAILQAAEKLGLMKGKFVFFLLQQFE 235 (391)
T ss_pred HHHHHHh-hCEEEEEEEecCCC----ChHHHHHHHHhhhccceEEEEEcChHHHHHHHHHHHHcCCCCCCEEEEEehhhc
Confidence 5555554 67899988888766 577777776777789999999999999999999999999988889999964322
Q ss_pred ccccCCCC---CchhhhhhccceEEEEEecCC-ChhhHHHHHHHHhhcCCCC---------CCCchhhHHhhHHHHHHHH
Q 002211 281 TFIDSKSP---LSLKTAKSILGALTLRQHTPD-SKRRRDFVSRWNTLSNGSI---------GLNPYGLYAYDTVWMIARA 347 (953)
Q Consensus 281 ~~~~~~~~---~~~~~~~~~~g~~~~~~~~~~-~~~~~~F~~~~~~~~~~~~---------~~~~~~~~~YDAv~~la~A 347 (953)
..+-.... ......+..+|++++.+..+. .+..++|.++|+++++... ..+.+++++|||||++|+|
T Consensus 236 ~~~w~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~f~~~~~~~~~~~p~~~~~~~~~~~~~~a~~~yDav~~~A~A 315 (391)
T cd06372 236 DNFWKEVLTDDQVQHLPKVYESVFLIAPSSYGGYSGGYEFRKQVYQKLKRPPFQSSLSSEEQVSPYSAYLHDAVLLYALA 315 (391)
T ss_pred CccccccCCCcchHHHHHHHhhEEEEecCCCCCCcchhHHHHHHHHHHhcCCccccccccccchHHHHHHHHHHHHHHHH
Confidence 11100000 012244567898888776543 3557788888887764111 2357899999999999999
Q ss_pred HHHHHhcCCcccccCCCccCCCCCCcccCCCccccCchHHHHHHHH---hcccCCcceeEEEccCCCCCCccEEEEEeec
Q 002211 348 LKLFLDQGNTISFSNDTKLNGLGGGTLNLGALSIFDGGKKFLANIL---QTNMTGLSGPIHFNQDRSLLHPSYDIINVIE 424 (953)
Q Consensus 348 l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~---~~~f~G~tG~v~Fd~~g~~~~~~y~I~~~~~ 424 (953)
++++++++.. +.+|.+|.++|+ +++|+|++|+|.||++|+| .+.|.|+++++
T Consensus 316 l~~~~~~g~~------------------------~~~g~~l~~~l~~~~~~~f~G~tG~v~fd~~G~r-~~~y~i~~~~~ 370 (391)
T cd06372 316 VKEMLKAGKD------------------------FRNGRQLVSTLRGANQVELQGITGLVLLDEQGKR-QMDYSVYALQK 370 (391)
T ss_pred HHHHHhcCCC------------------------CCCHHHHHHHHhhccCceEeccceeEEECCCCCc-ceeEEEEeccc
Confidence 9998764321 235889999999 6899999999999999996 88999999985
Q ss_pred CC---eeeEEEEecCCC
Q 002211 425 HG---YPQQIGYWSNYS 438 (953)
Q Consensus 425 ~~---~~~~VG~w~~~~ 438 (953)
.+ ..+.||+|+..+
T Consensus 371 ~~~~~~~~~vg~~~~~~ 387 (391)
T cd06372 371 SGNSSLFLPFLHYDSHQ 387 (391)
T ss_pred cCCccceeeEEEecchh
Confidence 32 248999998754
No 28
>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=1.1e-42 Score=382.57 Aligned_cols=360 Identities=15% Similarity=0.234 Sum_probs=298.6
Q ss_pred EeEEEecCCCchhHHHHHHHHHHHHHhcCCCCCCC-cEEEEEEecC-CCChHHHHHHHHHHHhcCcEEEEccCChhhHHH
Q 002211 52 VGAIFSFGTVNGQVSRIAMKAAQDDINSDPRVLGG-RKLSITMHDA-KFNGFLSIMGALQFMETDTLAIVGPQSAVMAHV 129 (953)
Q Consensus 52 IG~l~~~~~~~g~~~~~a~~lAve~iN~~g~il~g-~~l~l~~~D~-~~~~~~a~~~a~~li~~~v~aiiGp~~S~~a~a 129 (953)
||++|+.++ .....|+++|++++|.+..+++. .+|...+..- ..|..++.+++|+++++||.||+||.++..+..
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 35689999999999998877654 4777655433 468999999999999999999999999999999
Q ss_pred HHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecCccccchHHHHHHHHHhc
Q 002211 130 LSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDDDQGRNGVTALGDKLAEI 209 (953)
Q Consensus 130 v~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~~~g~~~~~~l~~~l~~~ 209 (953)
+..+|+..+||+|.+.-. .+...+|.+++.|+ ...|+++++++|||++|++|| |+++|...++.+.+.++..
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 LTSFCGALHTSFITPSFP----TDADVQFVIQMRPA---LKGAILSLLAHYKWEKFVYLY-DTERGFSILQAIMEAAVQN 150 (372)
T ss_pred HHHhhccccCCeeeeCCC----CCCCCceEEEEChh---HHHHHHHHHHhcCCCEEEEEe-cCchhHHHHHHHHHhhccC
Confidence 999999999999986322 12334778899988 689999999999999999999 7789999999999999999
Q ss_pred CcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEEeCcccccccCCCCC
Q 002211 210 RCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIATTWLSTFIDSKSPL 289 (953)
Q Consensus 210 g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~~~~~ 289 (953)
+..|......+.. ...++...+++++.++.++||++|.++.+..++++|.+.||+..+|+||+++......+.
T Consensus 151 ~~~V~~~~v~~~~---~~~~~~~~l~el~~~~~r~iIld~s~~~~~~il~~a~e~gM~~~~y~~ilt~ld~~~~dl---- 223 (372)
T cd06387 151 NWQVTARSVGNIK---DVQEFRRIIEEMDRRQEKRYLIDCEVERINTILEQVVILGKHSRGYHYMLANLGFTDISL---- 223 (372)
T ss_pred CceEEEEEeccCC---chHHHHHHHHHhccccceEEEEECCHHHHHHHHHHHHHcCccccceEEEEecCCcccccH----
Confidence 9998776544432 356899999999999999999999999999999999999999999999999844433333
Q ss_pred chhhhhhccceEEEEEecCCChhhHHHHHHHHhhcCC------CCCCCchhhHHhhHHHHHHHHHHHHHhcCCcccccCC
Q 002211 290 SLKTAKSILGALTLRQHTPDSKRRRDFVSRWNTLSNG------SIGLNPYGLYAYDTVWMIARALKLFLDQGNTISFSND 363 (953)
Q Consensus 290 ~~~~~~~~~g~~~~~~~~~~~~~~~~F~~~~~~~~~~------~~~~~~~~~~~YDAv~~la~Al~~~~~~~~~~~~~~~ 363 (953)
.+......+++|++.+.++++..++|.++|++.+.. ..+++.+++++|||||++|+|++++...+.....
T Consensus 224 -~~~~~g~~NItg~rl~~~~~~~~~~f~~~w~~~~~~~~~~~~~~~l~~~~al~yDaV~~~A~A~~~l~~~~~~~~~--- 299 (372)
T cd06387 224 -ERVMHGGANITGFQIVNNENPMVQQFLQRWVRLDEREFPEAKNSPLKYTSALTHDAILVIAEAFRYLRRQRVDVSR--- 299 (372)
T ss_pred -HHhccCCcceeEEEEecCCCchHHHHHHHHHhCCcccCCCCCCCCcchHHHHHHHHHHHHHHHHHHHHhcCCCccc---
Confidence 223333444999999999999999999999876531 1235678999999999999999998554332211
Q ss_pred CccCCCCCCcccCC--CccccCchHHHHHHHHhcccCCcceeEEEccCCCCCCccEEEEEeecCCeeeEEEEecCCCCc
Q 002211 364 TKLNGLGGGTLNLG--ALSIFDGGKKFLANILQTNMTGLSGPIHFNQDRSLLHPSYDIINVIEHGYPQQIGYWSNYSGL 440 (953)
Q Consensus 364 ~~~~~~~~~~~~~~--~~~~~~~~~~l~~~l~~~~f~G~tG~v~Fd~~g~~~~~~y~I~~~~~~~~~~~VG~w~~~~gl 440 (953)
.+...+|. ...+|..|..|+++|++++|+|+||+++||++|+|.+..|+|+|+.++|. ++||+|++..|+
T Consensus 300 ------~~~~~~C~~~~~~~W~~G~~l~~~ik~v~~~GLTG~i~F~~~G~R~~~~ldIinl~~~g~-~kIG~W~~~~g~ 371 (372)
T cd06387 300 ------RGSAGDCLANPAVPWSQGIDIERALKMVQVQGMTGNIQFDTYGRRTNYTIDVYEMKPSGS-RKAGYWNEYERF 371 (372)
T ss_pred ------CCCCCCcCCCCCCCccchHHHHHHHHhcccCCCccceeeCCCCCcccceEEEEEecCCCc-eeEEEECCCCCc
Confidence 01222342 35578999999999999999999999999999999999999999999998 999999999885
No 29
>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=4e-42 Score=381.77 Aligned_cols=361 Identities=16% Similarity=0.221 Sum_probs=288.7
Q ss_pred EEeEEEecCCCchhHHHHHHHHHHHHHhcCCCCCC-CcEEEEEEecC-CCChHHHHHHHHHHHhcCcEEEEccCChhhHH
Q 002211 51 NVGAIFSFGTVNGQVSRIAMKAAQDDINSDPRVLG-GRKLSITMHDA-KFNGFLSIMGALQFMETDTLAIVGPQSAVMAH 128 (953)
Q Consensus 51 ~IG~l~~~~~~~g~~~~~a~~lAve~iN~~g~il~-g~~l~l~~~D~-~~~~~~a~~~a~~li~~~v~aiiGp~~S~~a~ 128 (953)
+||++|+..+ .....|+++|++.+|.+..++. +.+|..++..- ..|...+.+++|+++++||.||+||.+|..+.
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 3467999999999998764432 24666655543 35899999999999999999999999999999
Q ss_pred HHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecCccccchHHHHHHHHHh
Q 002211 129 VLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDDDQGRNGVTALGDKLAE 208 (953)
Q Consensus 129 av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~~~g~~~~~~l~~~l~~ 208 (953)
++++++++.+||+|+++.+ +... +.||+...+. +..+++++++++||++|++||+ +++|....+.|.+.+++
T Consensus 78 ~v~~i~~~~~IP~I~~~~~----~~~~--~~f~i~~~p~-~~~a~~~~i~~~~wk~vaiiYd-~~~~~~~lq~l~~~~~~ 149 (371)
T cd06388 78 TLTSFCSALHISLITPSFP----TEGE--SQFVLQLRPS-LRGALLSLLDHYEWNRFVFLYD-TDRGYSILQAIMEKAGQ 149 (371)
T ss_pred HHHHHhhCCCCCeeecCcc----ccCC--CceEEEeChh-hhhHHHHHHHhcCceEEEEEec-CCccHHHHHHHHHhhHh
Confidence 9999999999999997543 1223 4444444444 4578888999999999999994 44566779999999999
Q ss_pred cCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEEeCcccccccCCCC
Q 002211 209 IRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIATTWLSTFIDSKSP 288 (953)
Q Consensus 209 ~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~~~~ 288 (953)
.|++|+.....+.+ +.|++.+|++|+.+++|+||+.|+++.+..+++||+++||+.++|+||+++......+.
T Consensus 150 ~g~~v~~~~~~~~~----~~d~~~~L~~ik~~~~~~iil~~~~~~~~~il~qa~~~gm~~~~y~~il~~~~~~~~~l--- 222 (371)
T cd06388 150 NGWQVSAICVENFN----DASYRRLLEDLDRRQEKKFVIDCEIERLQNILEQIVSVGKHVKGYHYIIANLGFKDISL--- 222 (371)
T ss_pred cCCeeeeEEeccCC----cHHHHHHHHHhcccccEEEEEECCHHHHHHHHHHHHhcCccccceEEEEccCccccccH---
Confidence 99999876655444 56999999999999999999999999999999999999999999999998753222221
Q ss_pred CchhhhhhccceEEEEEecCCChhhHHHHHHHHhhcC-----CCCCCCchhhHHhhHHHHHHHHHHHHHhcCCcccccCC
Q 002211 289 LSLKTAKSILGALTLRQHTPDSKRRRDFVSRWNTLSN-----GSIGLNPYGLYAYDTVWMIARALKLFLDQGNTISFSND 363 (953)
Q Consensus 289 ~~~~~~~~~~g~~~~~~~~~~~~~~~~F~~~~~~~~~-----~~~~~~~~~~~~YDAv~~la~Al~~~~~~~~~~~~~~~ 363 (953)
.+......++.+++...+..+..++|.++|++.+. ....|..+++++||||+++|.|++++.......+
T Consensus 223 --~~~~~g~~nitg~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~aAl~YDaV~l~a~A~~~l~~~~~~~~---- 296 (371)
T cd06388 223 --ERFMHGGANVTGFQLVDFNTPMVTKLMQRWKKLDQREYPGSESPPKYTSALTYDGVLVMAEAFRNLRRQKIDIS---- 296 (371)
T ss_pred --HHHhccCCceEEEEeecCCChhHHHHHHHHHhcCccccCCCCCCccchHHHHHHHHHHHHHHHHHHHhcCCCcc----
Confidence 12223344488898888888999999999987643 1135778999999999999999999754322111
Q ss_pred CccCCCCCCcccC--CCccccCchHHHHHHHHhcccCCcceeEEEccCCCCCCccEEEEEeecCCeeeEEEEecCCCCcc
Q 002211 364 TKLNGLGGGTLNL--GALSIFDGGKKFLANILQTNMTGLSGPIHFNQDRSLLHPSYDIINVIEHGYPQQIGYWSNYSGLS 441 (953)
Q Consensus 364 ~~~~~~~~~~~~~--~~~~~~~~~~~l~~~l~~~~f~G~tG~v~Fd~~g~~~~~~y~I~~~~~~~~~~~VG~w~~~~gl~ 441 (953)
..+.+..| +...+|..|..|+++|++++|+|+||+++||++|+|.+..++|+++.++|. ++||+|++..||.
T Consensus 297 -----~~~~~~~C~~~~~~~w~~G~~i~~~lk~~~~~GlTG~i~Fd~~G~r~~~~l~Ii~l~~~g~-~kvG~W~~~~g~~ 370 (371)
T cd06388 297 -----RRGNAGDCLANPAAPWGQGIDMERTLKQVRIQGLTGNIQFDHYGRRVNYTMDVFELKSNGP-RKIGYWNDMDKLV 370 (371)
T ss_pred -----cCCCCCCcCCCCCCCCcccHHHHHHHHhcCcCCCccceeECCCCCcccceEEEEEccCCCc-eEEEEEcCCCCcc
Confidence 01222244 346689999999999999999999999999999999888999999999998 9999999998864
No 30
>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=5.1e-42 Score=382.07 Aligned_cols=360 Identities=18% Similarity=0.281 Sum_probs=292.2
Q ss_pred EEeEEEecCCCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEec-CCCChHHHHHHHHHHHhcCcEEEEccCChhhHHH
Q 002211 51 NVGAIFSFGTVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHD-AKFNGFLSIMGALQFMETDTLAIVGPQSAVMAHV 129 (953)
Q Consensus 51 ~IG~l~~~~~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D-~~~~~~~a~~~a~~li~~~v~aiiGp~~S~~a~a 129 (953)
+||++|+... ...+.|+++|++.+|... .+|..++.. +..|...+.+++|+++++||.||+||.+|..+.+
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 4899998765 356899999999999862 566664443 4468899999999999999999999999999999
Q ss_pred HHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecCccccchHHHHHHHHHhc
Q 002211 130 LSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDDDQGRNGVTALGDKLAEI 209 (953)
Q Consensus 130 v~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~~~g~~~~~~l~~~l~~~ 209 (953)
++++|+..+||+|+++++. +..++|.+++.|+ ...++++++++++|++|++||+ ++||....+.+.+.+++.
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 9999999999999886542 3357888888887 4789999999999999999997 569999999999999999
Q ss_pred CcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEEeCcccccccCCCCC
Q 002211 210 RCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIATTWLSTFIDSKSPL 289 (953)
Q Consensus 210 g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~~~~~ 289 (953)
|++|+..............|++.+|++|+++++|+||+.|+++++..+++||+++||+.++|+||+++......+.
T Consensus 145 g~~V~~~~~~~i~~~~~~~d~~~~L~~ik~~~~~~Iil~~~~~~~~~il~qa~~~gm~~~~y~~il~~~~~~~~~l---- 220 (370)
T cd06389 145 KWQVTAINVGNINNDRKDEAYRSLFQDLENKKERRVILDCERDKVNDIVDQVITIGKHVKGYHYIIANLGFTDGDL---- 220 (370)
T ss_pred CceEEEEEeecCCCccchHHHHHHHHHhccccceEEEEECCHHHHHHHHHHHHHhCccccceEEEEccCCccccch----
Confidence 9888754421111012367999999999999999999999999999999999999999999999998753322222
Q ss_pred chhhhhhccceEEEEEecCCChhhHHHHHHHHh----hcCC--CCCCCchhhHHhhHHHHHHHHHHHHHhcCCcccccCC
Q 002211 290 SLKTAKSILGALTLRQHTPDSKRRRDFVSRWNT----LSNG--SIGLNPYGLYAYDTVWMIARALKLFLDQGNTISFSND 363 (953)
Q Consensus 290 ~~~~~~~~~g~~~~~~~~~~~~~~~~F~~~~~~----~~~~--~~~~~~~~~~~YDAv~~la~Al~~~~~~~~~~~~~~~ 363 (953)
........++.+++...+..+..++|.++|++ .+.. ...+..+++.+||||+++|.|++++...+.....
T Consensus 221 -~~~~~~~~nitg~~~~~~~~~~v~~f~~~~~~~~~~~~~~~~~~~~~~~aAl~yDAV~v~a~A~~~l~~~~~~~~~--- 296 (370)
T cd06389 221 -SKIQFGGANVSGFQIVDYDDPLVSKFIQRWSTLEEKEYPGAHTKTIKYTSALTYDAVQVMTEAFRNLRKQRIEISR--- 296 (370)
T ss_pred -hhhccCCcceEEEEEecCCCchHHHHHHHHHhcCccccCCCCCcCcchHHHHHHHHHHHHHHHHHHHHHcCCCccc---
Confidence 11112334678888888889999999999996 4411 1357789999999999999999998554322210
Q ss_pred CccCCCCCCcccC--CCccccCchHHHHHHHHhcccCCcceeEEEccCCCCCCccEEEEEeecCCeeeEEEEecCCCCcc
Q 002211 364 TKLNGLGGGTLNL--GALSIFDGGKKFLANILQTNMTGLSGPIHFNQDRSLLHPSYDIINVIEHGYPQQIGYWSNYSGLS 441 (953)
Q Consensus 364 ~~~~~~~~~~~~~--~~~~~~~~~~~l~~~l~~~~f~G~tG~v~Fd~~g~~~~~~y~I~~~~~~~~~~~VG~w~~~~gl~ 441 (953)
.++..+| +...+|.+|..|+++|++++|+|+||+++||++|+|.+..++|++++++|. ++||+|++..||.
T Consensus 297 ------~~~~~~C~~~~~~~w~~G~~i~~~l~~~~~~GlTG~i~Fd~~G~r~~~~~~ii~l~~~g~-~kvG~W~~~~~~~ 369 (370)
T cd06389 297 ------RGNAGDCLANPAVPWGQGVEIERALKQVQVEGLTGNIKFDQNGKRINYTINVMELKSNGP-RKIGYWSEVDKMV 369 (370)
T ss_pred ------CCCCCCcCCCCCCCCCCcHHHHHHHHhcccCccccceEeCCCCccccceEEEEEecCCcc-eEEEEEcCCCCcc
Confidence 1122234 345679999999999999999999999999999999888999999999998 9999999998864
No 31
>cd06384 PBP1_NPR_B Ligand-binding domain of type B natriuretic peptide receptor. Ligand-binding domain of type B natriuretic peptide receptor (NPR-B). NPR-B is one of three known single membrane-spanning natriuretic peptide receptors that have been identified. Natriuretic peptides are family of structurally related but genetically distinct hormones/paracrine factors that regulate blood volume, blood pressure, ventricular hypertrophy, pulmonary hypertension, fat metabolism, and long bone growth. In mammals there are three natriuretic peptides: ANP, BNP, and CNP. Like NPR-A (or GC-A), NPR-B (or GC-B) is a transmembrane guanylyl cyclase, an enzyme that catalyzes the synthesis of cGMP. NPR-B is the predominant natriuretic peptide receptor in the brain. The rank of order activation of NPR-B by natriuretic peptides is CNPANPBNP. Homozygous inactivating mutations in human NPR-B cause a form of short-limbed dwarfism known as acromesomelic dysplasia type Maroteaux.
Probab=100.00 E-value=3.4e-42 Score=390.16 Aligned_cols=357 Identities=16% Similarity=0.219 Sum_probs=286.6
Q ss_pred EEeEEEecCCC---c-hhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHH----HHHHHHH-HhcCcEEEEcc
Q 002211 51 NVGAIFSFGTV---N-GQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLS----IMGALQF-METDTLAIVGP 121 (953)
Q Consensus 51 ~IG~l~~~~~~---~-g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a----~~~a~~l-i~~~v~aiiGp 121 (953)
+||+++|.+.. + -.....|+++|+|+||++||+++|++|+++++|+++++..+ ...+..+ +.+++.+||||
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 47888886422 1 23556899999999999999888999999999987664333 3222211 23588999999
Q ss_pred CChhhHHHHHHhhhhCCCcEEEeecCCCCCCC--CCCCcEEEccCChHHHHHHHHHHHHHcCCc-EEEEEEecCcccc--
Q 002211 122 QSAVMAHVLSHLANELQVPLLSFTALDPTLSP--LQYPFFVQTAPNDLYLMSAIAEMVSYFGWG-EVIAIFNDDDQGR-- 196 (953)
Q Consensus 122 ~~S~~a~av~~v~~~~~vP~Is~~at~~~ls~--~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~-~vaii~~d~~~g~-- 196 (953)
.||.++.+++++++.++||+|+++++++.+++ ..|||+||+.|++..++.++..++++++|+ ++++||.++..+.
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 99999999999999999999999999999986 478999999999999999988889999999 6889997543221
Q ss_pred --chHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHHHcCCCCCceEEE
Q 002211 197 --NGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWI 274 (953)
Q Consensus 197 --~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi 274 (953)
...+.+.+.+++.|++|+....+..+ +.|+..+|++++. ++|+|+++++..++..+++||+++||+.++|+||
T Consensus 161 ~~~~~~~~~~~~~~~gi~v~~~~~~~~~----~~d~~~~l~~ik~-~~~vIi~~~~~~~~~~i~~qa~~~g~~~~~y~~i 235 (399)
T cd06384 161 HYFISEGVFLALQEENANVSAHPYHIEK----NSDIIEIIQFIKQ-NGRIVYICGPLETFLEIMLQAQREGLTPGDYVFF 235 (399)
T ss_pred ceEehHHHHHHHHhcCceEEEEEEeccc----hhhHHHHHHHHhh-cccEEEEeCCchHHHHHHHHHHHcCCCCCcEEEE
Confidence 13566788889999999987665555 7899999999997 8999999999999999999999999999999999
Q ss_pred EeCccccccc------C----CCCCchhhhhhccceEEEEEecCCChhhHHHHHHHHhh----cCCCCCC---CchhhHH
Q 002211 275 ATTWLSTFID------S----KSPLSLKTAKSILGALTLRQHTPDSKRRRDFVSRWNTL----SNGSIGL---NPYGLYA 337 (953)
Q Consensus 275 ~~~~~~~~~~------~----~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~F~~~~~~~----~~~~~~~---~~~~~~~ 337 (953)
..++....+. . .....+...+++++++++..+.+.++.+++|.++|+++ ++....| +.+++++
T Consensus 236 ~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~v~~~~~~~~~~~~~~~F~~~~~~~~~~~~~~~~~p~~~~~~aa~~ 315 (399)
T cd06384 236 YLDVFGESLRVKSPRESYKQMNHSSWTVLKEAFKSVFVITYREPENPEYKEFQRELHARAKEDFGVELEPSLMNFIAGCF 315 (399)
T ss_pred EehhcccccccCCCCccccCCCCcccHHHHHHHhheEEeecCCCCCchHHHHHHHHHHHHhhhcCCCcCcchHhhhhhhh
Confidence 9886543221 0 11112455668999999988888888899999999874 5432234 6679999
Q ss_pred hhHHHHHHHHHHHHHhcCCcccccCCCccCCCCCCcccCCCccccCchHHHHHHHHhcccCCcceeEEEccCCCCCCccE
Q 002211 338 YDTVWMIARALKLFLDQGNTISFSNDTKLNGLGGGTLNLGALSIFDGGKKFLANILQTNMTGLSGPIHFNQDRSLLHPSY 417 (953)
Q Consensus 338 YDAv~~la~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~f~G~tG~v~Fd~~g~~~~~~y 417 (953)
||||+++|.|++++...++. +.+|.+|+++|++++|+|++|++.||++|+| ...|
T Consensus 316 YDav~l~a~Al~~~~~~~~~------------------------~~~g~~i~~~l~~~~f~GvtG~v~fd~~G~r-~~~~ 370 (399)
T cd06384 316 YDGVMLYAMALNETLAEGGS------------------------QKDGLNITRKMQDRRFWGVTGLVSIDKNNDR-DIDF 370 (399)
T ss_pred HHHHHHHHHHHHHHHhcCCC------------------------CCCcHhHHHHHhCceeecceeEEEECCCCCc-ccce
Confidence 99999999999998654321 3358999999999999999999999999996 5677
Q ss_pred EEE---EeecCCeeeEEEEecCCC
Q 002211 418 DII---NVIEHGYPQQIGYWSNYS 438 (953)
Q Consensus 418 ~I~---~~~~~~~~~~VG~w~~~~ 438 (953)
.++ ++++++. +.||+|+..+
T Consensus 371 ~~~~~~~~~~g~~-~~v~~~~~~~ 393 (399)
T cd06384 371 DLWAMTDHETGKY-EVVAHYNGIT 393 (399)
T ss_pred EEEEeecCCCCeE-EEEEEEcCCC
Confidence 773 4456555 9999998754
No 32
>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=8.4e-43 Score=385.49 Aligned_cols=316 Identities=22% Similarity=0.350 Sum_probs=275.2
Q ss_pred EEeEEEecCCCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCC-CChHHHHHHHHHHHhcCcEEEEccCChhhHHH
Q 002211 51 NVGAIFSFGTVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAK-FNGFLSIMGALQFMETDTLAIVGPQSAVMAHV 129 (953)
Q Consensus 51 ~IG~l~~~~~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~-~~~~~a~~~a~~li~~~v~aiiGp~~S~~a~a 129 (953)
+||+++++ ..|...+.|+++|+|+||++||+|+|++|++++.|++ +++..++.++++|++++|.+||||.+|+.+.+
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 59999998 6688999999999999999999999999999999999 89999999999999889999999999999999
Q ss_pred HHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecCccccchHHHHHHHHHhc
Q 002211 130 LSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDDDQGRNGVTALGDKLAEI 209 (953)
Q Consensus 130 v~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~~~g~~~~~~l~~~l~~~ 209 (953)
+++++++++||+|+++++++.++ .++|+||+.|++..++.++++++++++|++|+++|++++++.. +.+.+++.
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 99999999999999988888776 4689999999999999999999999999999999998886544 44455555
Q ss_pred Cc---EEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEEeCcccccccCC
Q 002211 210 RC---KISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIATTWLSTFIDSK 286 (953)
Q Consensus 210 g~---~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~~ 286 (953)
|. .|.. +.++++ . |++.+|.+|++++||+|++++.+.++..+++||+++||+.+.|+|+.+++.....+..
T Consensus 153 ~~~g~~v~~-~~~~~~----~-d~~~~l~~i~~~~~d~vv~~~~~~~~~~~~~qa~~~g~~~~~~~~i~~~~~~~~~~l~ 226 (327)
T cd06382 153 GISGITITV-RQLDDD----L-DYRPLLKEIKNSGDNRIIIDCSADILIELLKQAQQVGMMSEYYHYIITNLDLHTLDLE 226 (327)
T ss_pred ccCCCeEEE-EEccCC----c-cHHHHHHHHHhcCceEEEEECCHHHHHHHHHHHHHhCccccceEEEEecCCccccchh
Confidence 44 4443 556665 5 9999999999999999999999999999999999999999999999988755443331
Q ss_pred CCCchhhhhhccceEEEEEecCCChhhHHHHHHHHhhcCCC------CCCCchhhHHhhHHHHHHHHHHHHHhcCCcccc
Q 002211 287 SPLSLKTAKSILGALTLRQHTPDSKRRRDFVSRWNTLSNGS------IGLNPYGLYAYDTVWMIARALKLFLDQGNTISF 360 (953)
Q Consensus 287 ~~~~~~~~~~~~g~~~~~~~~~~~~~~~~F~~~~~~~~~~~------~~~~~~~~~~YDAv~~la~Al~~~~~~~~~~~~ 360 (953)
.......++.++.++.++++..++|.++|+++++.. ..|+.+++.+|||++++
T Consensus 227 -----~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~p~~~~a~~yDav~~~---------------- 285 (327)
T cd06382 227 -----DYRYSGVNITGFRLVDPDSPEVKEVIRSLELSWDEGCRILPSTGVTTESALMYDAVYLF---------------- 285 (327)
T ss_pred -----hhccCceeEEEEEEecCCchhHHHHHHHHHhhcccccccCCCCCcchhhhhhhceEEEe----------------
Confidence 122234578888888888899999999999998621 12778899999998865
Q ss_pred cCCCccCCCCCCcccCCCccccCchHHHHHHHHhcccCCcceeEEEccCCCCCCccEEEEEeecCCeeeEEEEecCCCCc
Q 002211 361 SNDTKLNGLGGGTLNLGALSIFDGGKKFLANILQTNMTGLSGPIHFNQDRSLLHPSYDIINVIEHGYPQQIGYWSNYSGL 440 (953)
Q Consensus 361 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~f~G~tG~v~Fd~~g~~~~~~y~I~~~~~~~~~~~VG~w~~~~gl 440 (953)
|+||+|+||++|+|.+..|+|+|+.+++. ++||+|++..|+
T Consensus 286 --------------------------------------g~tG~v~f~~~g~r~~~~~~~~~~~~~~~-~~vg~w~~~~~~ 326 (327)
T cd06382 286 --------------------------------------GLTGRIEFDSSGQRSNFTLDVIELTESGL-RKVGTWNSSEGL 326 (327)
T ss_pred --------------------------------------ecccceeeCCCCCEeeeEEEEEeccccCc-eEEEEECCCCCc
Confidence 89999999999999999999999998888 999999998764
No 33
>PRK15404 leucine ABC transporter subunit substrate-binding protein LivK; Provisional
Probab=100.00 E-value=1.8e-41 Score=378.65 Aligned_cols=341 Identities=12% Similarity=0.161 Sum_probs=298.8
Q ss_pred cCCCCceEEEeEEEecC---CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEE
Q 002211 43 GALKPEVLNVGAIFSFG---TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIV 119 (953)
Q Consensus 43 ~~~~~~~i~IG~l~~~~---~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aii 119 (953)
++..+++|+||++.|++ +..|...+.|+++|+++||+.||+. |++|+++++|++++|..+++.+++|++++|.+||
T Consensus 19 ~~~~~~~I~IG~l~plSG~~a~~G~~~~~g~~~av~~iNa~GGi~-G~~ielv~~D~~~~p~~a~~~~~~Li~~~V~~ii 97 (369)
T PRK15404 19 HAALADDIKIAIVGPMSGPVAQYGDMEFTGARQAIEDINAKGGIK-GDKLEGVEYDDACDPKQAVAVANKVVNDGIKYVI 97 (369)
T ss_pred ccccCCceEEEEeecCCCcchhcCHhHHHHHHHHHHHHHhcCCCC-CeEEEEEeecCCCCHHHHHHHHHHHHhCCceEEE
Confidence 34556799999999998 4568899999999999999999996 8999999999999999999999999998999999
Q ss_pred ccCChhhHHHHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHH-HHcCCcEEEEEEecCccccch
Q 002211 120 GPQSAVMAHVLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMV-SYFGWGEVIAIFNDDDQGRNG 198 (953)
Q Consensus 120 Gp~~S~~a~av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l-~~~~w~~vaii~~d~~~g~~~ 198 (953)
||.+|..+.++++++++.+||+|++.+++|.+++..+||+||+.+.+..++.++++++ ++++|++|++|++|++||++.
T Consensus 98 G~~~s~~~~a~~~~~~~~~ip~i~~~s~~~~l~~~~~~~~fr~~~~~~~~~~~~~~~~~~~~~~k~va~i~~d~~~g~~~ 177 (369)
T PRK15404 98 GHLCSSSTQPASDIYEDEGILMITPAATAPELTARGYQLIFRTIGLDSDQGPTAAKYILEKVKPKRIAVLHDKQQYGEGL 177 (369)
T ss_pred cCCCchhHHHhHHHHHHCCCeEEecCCCCHHHhcCCCceEEeCCCCcHHHHHHHHHHHHHhcCCCEEEEEeCCCchhHHH
Confidence 9999999999999999999999999999999987678999999999999999999986 556999999999999999999
Q ss_pred HHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEEeCc
Q 002211 199 VTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIATTW 278 (953)
Q Consensus 199 ~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~ 278 (953)
.+.+.+.+++.|++++....++.+ ..|++.++.++++.+||+|++.+...+...++++++++|+.. .|+++++
T Consensus 178 ~~~~~~~~~~~G~~v~~~~~~~~g----~~D~~~~v~~l~~~~~d~v~~~~~~~~~~~~~k~~~~~G~~~---~~i~~~~ 250 (369)
T PRK15404 178 ARSVKDGLKKAGANVVFFEGITAG----DKDFSALIAKLKKENVDFVYYGGYHPEMGQILRQAREAGLKT---QFMGPEG 250 (369)
T ss_pred HHHHHHHHHHcCCEEEEEEeeCCC----CCchHHHHHHHHhcCCCEEEECCCchHHHHHHHHHHHCCCCC---eEEecCc
Confidence 999999999999999998889887 789999999999999999998888888999999999999854 3676654
Q ss_pred ccccccCCCCCchhhhhhccceEEEEEe-cCCChhhHHHHHHHHhhcCCCCCCCchhhHHhhHHHHHHHHHHHHHhcCCc
Q 002211 279 LSTFIDSKSPLSLKTAKSILGALTLRQH-TPDSKRRRDFVSRWNTLSNGSIGLNPYGLYAYDTVWMIARALKLFLDQGNT 357 (953)
Q Consensus 279 ~~~~~~~~~~~~~~~~~~~~g~~~~~~~-~~~~~~~~~F~~~~~~~~~~~~~~~~~~~~~YDAv~~la~Al~~~~~~~~~ 357 (953)
.... ... ....+..+|+++..++ ...+|..++|.++|+++++ .+++.++..+||++++++.|+++++..
T Consensus 251 ~~~~-~~~----~~~~~~~~Gv~~~~~~~~~~~~~~~~f~~~~~~~~~--~~~~~~~~~~Y~~~~~l~~Al~~aG~~--- 320 (369)
T PRK15404 251 VGNK-SLS----NIAGPASEGMLVTLPKRYDQDPANKAIVDAFKAKKQ--DPSGPFVWTTYAAVQSLAAGINRAGSD--- 320 (369)
T ss_pred CCCH-HHH----HhhhhhhcCcEEEccCCCccChhHHHHHHHHHHhcC--CCCccchHHHHHHHHHHHHHHHhhCCC---
Confidence 4322 110 1234567898876553 3346788999999999875 556678899999999999999986321
Q ss_pred ccccCCCccCCCCCCcccCCCccccCchHHHHHHHHhcccCCcceeEEEccCCCCCCccEEEEEeecCCe
Q 002211 358 ISFSNDTKLNGLGGGTLNLGALSIFDGGKKFLANILQTNMTGLSGPIHFNQDRSLLHPSYDIINVIEHGY 427 (953)
Q Consensus 358 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~f~G~tG~v~Fd~~g~~~~~~y~I~~~~~~~~ 427 (953)
+++.|.++|++.+|+|++|++.|+++|++....|.|++|++++.
T Consensus 321 --------------------------~~~~l~~al~~~~~~~~~G~~~~~~~g~~~~~~~~i~~~~~~~~ 364 (369)
T PRK15404 321 --------------------------DPAKVAKYLKANTFDTVIGPLSWDEKGDLKGFEFGVFEWHADGT 364 (369)
T ss_pred --------------------------CHHHHHHHHHhCCCCcceEeeEECCCCCcccCCEEEEEEEcCCe
Confidence 47899999999999999999999999998789999999998877
No 34
>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=2.6e-41 Score=385.49 Aligned_cols=392 Identities=22% Similarity=0.381 Sum_probs=337.2
Q ss_pred CCCceEEEeEEEecCC-------------CchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHH
Q 002211 45 LKPEVLNVGAIFSFGT-------------VNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFM 111 (953)
Q Consensus 45 ~~~~~i~IG~l~~~~~-------------~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li 111 (953)
.-+++|.||++||.+. ..|.....|+.+|+|+||+ +.+|||.||++.++|+|+++..|.++..+++
T Consensus 27 ~~~gdi~lgglFpvh~k~~~~~~cg~~~~~~gi~r~eAml~al~~iN~-~~lLp~~kLG~~i~DTCs~~t~aleqsl~Fv 105 (878)
T KOG1056|consen 27 RIPGDIILGGLFPVHEKGGGAPQCGRIREPRGIQRLEAMLFALDEINN-PDLLPNIKLGARILDTCSRSTYALEQSLSFV 105 (878)
T ss_pred cCCCCeEEcceeeecccCCCCCcccccccchhHHHHHHHHHHHHHhcC-cccCCCceeeeeEeeccCCcHHHHHhhHHHH
Confidence 4578999999999962 2366778999999999999 9999999999999999999999999999998
Q ss_pred hc-----------------CcEEEEccCChhhHHHHHHhhhhCCCcEEEeecCCCCCCC-CCCCcEEEccCChHHHHHHH
Q 002211 112 ET-----------------DTLAIVGPQSAVMAHVLSHLANELQVPLLSFTALDPTLSP-LQYPFFVQTAPNDLYLMSAI 173 (953)
Q Consensus 112 ~~-----------------~v~aiiGp~~S~~a~av~~v~~~~~vP~Is~~at~~~ls~-~~~p~~fr~~p~d~~~~~ai 173 (953)
.. .|.++|||..|+++.+++.+..-++||||+|+||+|.|++ .+|+||.|+.|+|..|++||
T Consensus 106 ~~~~~~~~~e~~c~~g~sp~v~~VIG~s~Ssvsi~vanlLrlf~ipQisyaSts~~LSdk~ry~~F~RtVP~D~~Qa~Am 185 (878)
T KOG1056|consen 106 RASLTSDDSEVRCPDGYSPPVVAVIGPSYSSVSIAVANLLRLFLIPQISYASTSPDLSDKTRYDYFLRTVPSDVFQAQAM 185 (878)
T ss_pred HhcccCCCcceecCCCCCCceeEEeCCCCchHHHHHHHHHHhhcCceeccccCCcccccchhhhceeeecCChHHHHHHH
Confidence 53 5899999999999999999999999999999999999999 89999999999999999999
Q ss_pred HHHHHHcCCcEEEEEEecCccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhc-CCceEEEEEcchh
Q 002211 174 AEMVSYFGWGEVIAIFNDDDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRM-MEARVIVVHGYSR 252 (953)
Q Consensus 174 ~~~l~~~~w~~vaii~~d~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~-~~~~vii~~~~~~ 252 (953)
++++++|+|.+|..++++++||+.+.++|++..+++|+||...+.++.. ..+..+...++++.. .++++||+.+..+
T Consensus 186 ~~il~~f~W~yVstv~s~~dYGE~Gieaf~~~a~~~~iCIa~s~ki~~~--~~~~~~~~~l~kl~~~~~a~vvV~F~~~~ 263 (878)
T KOG1056|consen 186 VDILKKFNWNYVSTVASEGDYGESGIEAFKEEAAERGICIAFSEKIYQL--SIEQEFDCVLRKLLETPNARVVVVFCRGE 263 (878)
T ss_pred HHHHHHhCeeEeeehhcCccchhhhHHHHHHhHHhcCceEEehhhcccc--cchhHHHHHHHHHhhcCCCeEEEEecCcc
Confidence 9999999999999999999999999999999999999999999777765 668889999999988 8999999999999
Q ss_pred hHHHHHHHHHHcCCCCCceEEEEeCcccccccCCCCCchhhhhhccceEEEEEecCCChhhHHHHHH-------------
Q 002211 253 TGLMVFDVAQRLGMMDSGYVWIATTWLSTFIDSKSPLSLKTAKSILGALTLRQHTPDSKRRRDFVSR------------- 319 (953)
Q Consensus 253 ~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~F~~~------------- 319 (953)
++..++++|+++++.+ .++||++|+|....+... ...+..+|++++....+..+.+++|.+.
T Consensus 264 ~~r~~~~aa~~~n~~g-~~~wiaSd~W~~~~~~~~----~~e~~a~g~i~i~l~~~~v~~F~~y~~s~~p~nn~~n~w~~ 338 (878)
T KOG1056|consen 264 DARRLLKAARRANLTG-EFLWIASDGWASQNSPTE----APEREAEGAITIKLASPQVPGFDRYFQSLHPENNRRNPWFA 338 (878)
T ss_pred hHHHHHHHHHHhCCCc-ceEEEecchhhccCChhh----hhhhhhceeEEEEecCCcchhHHHHHHhcCccccccCcccc
Confidence 9999999999988865 589999999987655432 2334789999999999888888877655
Q ss_pred --HHhhcCCC---------------------CCC-----CchhhHHhhHHHHHHHHHHHHHhcCCcccccCCCccCCCCC
Q 002211 320 --WNTLSNGS---------------------IGL-----NPYGLYAYDTVWMIARALKLFLDQGNTISFSNDTKLNGLGG 371 (953)
Q Consensus 320 --~~~~~~~~---------------------~~~-----~~~~~~~YDAv~~la~Al~~~~~~~~~~~~~~~~~~~~~~~ 371 (953)
|+..|++. ... ..-....+|||+++|+||+.+..+... +
T Consensus 339 e~w~~~f~C~l~~~~~~~~~~~~~Ct~~e~~~~~~~~~q~~k~~~Vi~aVya~A~aLh~m~~~lc~-------------~ 405 (878)
T KOG1056|consen 339 EFWEDKFNCSLPNSAFKNENLIRLCTAVERITLDSAYEQDSKVQFVIDAVYAMAHALHNMHQDLCP-------------G 405 (878)
T ss_pred hhhhhcccCCCCcccccchhhhhhcccchhhccccchhhhcccccHHHHHHHHHHHHHHHHHhhcC-------------C
Confidence 44444311 011 112457999999999999999766332 2
Q ss_pred CcccCCCccccCchHHHHHHHHhcccCCcceeEEEccCCCCCCccEEEEEeecCC---eeeEEEEecCCCCccccCCccc
Q 002211 372 GTLNLGALSIFDGGKKFLANILQTNMTGLSGPIHFNQDRSLLHPSYDIINVIEHG---YPQQIGYWSNYSGLSVVPPEKL 448 (953)
Q Consensus 372 ~~~~~~~~~~~~~~~~l~~~l~~~~f~G~tG~v~Fd~~g~~~~~~y~I~~~~~~~---~~~~VG~w~~~~gl~~~~~~~~ 448 (953)
....|+.+... +|.+|.+.+++++|.|..|.+.||++|| ....|+|++++..+ .+..||+|++...
T Consensus 406 ~~~~C~~m~~~-dg~~L~~~l~~vnF~~~~~~v~Fd~~gD-~~~~y~I~~~~~~~~~~~y~~vg~w~~~~~--------- 474 (878)
T KOG1056|consen 406 TSGLCSAMKAI-DGSLLLKYLLNVNFTGPAGSVRFDENGD-GPGRYDILNYQLTNGSYTYKEVGYWSEGLS--------- 474 (878)
T ss_pred ccccCcCcccc-CHHHHHhhhheeEEecCCCceeecCCCC-CccceeEEEeeccCCCccceeeeeeccccc---------
Confidence 33457777766 5999999999999999999999999999 68999999999655 5599999988652
Q ss_pred ccCCCCCCCCCCcceeeEeCCCcccCCCccc
Q 002211 449 YRKPANRSSSNQHLYSVVWPGGVTSKPRGWV 479 (953)
Q Consensus 449 ~~~~~~~~~~~~~l~~i~Wpg~~~~~P~~~~ 479 (953)
.+...+.|.++...+|++.|
T Consensus 475 -----------l~i~~~~w~~~~~~v~~S~C 494 (878)
T KOG1056|consen 475 -----------LNIEDLDWTTKPSGVPKSVC 494 (878)
T ss_pred -----------ccceeeeeccCCCCCccccc
Confidence 33456789999999999998
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=8.4e-42 Score=369.88 Aligned_cols=323 Identities=20% Similarity=0.301 Sum_probs=263.4
Q ss_pred EEeEEEecCCCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChH-HHHHHHHHHHhcCcEEEEccCChhh-HH
Q 002211 51 NVGAIFSFGTVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGF-LSIMGALQFMETDTLAIVGPQSAVM-AH 128 (953)
Q Consensus 51 ~IG~l~~~~~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~-~a~~~a~~li~~~v~aiiGp~~S~~-a~ 128 (953)
+||++++..+..|+..+.|+++|++++|++++++++++|++++.|++.++. .+..+++++++++|.|||||.+|.. +.
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 489999999999999999999999999999999866799999999999875 7788889999889999999999975 67
Q ss_pred HHHHhhhhCCCcEEEeecCC-CCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecCccccchHHHHHHHHH
Q 002211 129 VLSHLANELQVPLLSFTALD-PTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDDDQGRNGVTALGDKLA 207 (953)
Q Consensus 129 av~~v~~~~~vP~Is~~at~-~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~~~g~~~~~~l~~~l~ 207 (953)
++++++++.+||+|+++... |.+...++++ .++.|++..|++|+++++++|||++|++||+++++ ...|++.++
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 3333344444 89999999999999999999999999999999987 445555555
Q ss_pred hcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEEeCcccccccCCC
Q 002211 208 EIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIATTWLSTFIDSKS 287 (953)
Q Consensus 208 ~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~~~ 287 (953)
..+. +...++.....++.|++++|++|+.+++|+||++++++.+..+++||+++||+.++|+||+++......+.
T Consensus 156 ~~~~---~~~~i~~~~~~~~~d~~~~L~~ik~~~~~~iVv~~~~~~a~~il~qa~~lGm~~~~y~~i~T~l~~~~~~L-- 230 (333)
T cd06394 156 QFLI---SKETLSVRMLDDSRDPTPLLKEIRDDKTATIIIDANASMSHTILLKASELGMTSAFYKYILTTMDFPLLRL-- 230 (333)
T ss_pred hhcc---cCCceeeEEccCcccHHHHHHHHHhcCCCEEEEECChHHHHHHHHHHHHcCCCCCceEEEEecCCcccccH--
Confidence 4432 12222221112367899999999999999999999999999999999999999999999999876654433
Q ss_pred CCchhhhhhccceEEEEEecCCChhhHHHHHHHHhhcCCC--C----CCCchhhHHhhHHHHHHHHHHHHHhcCCccccc
Q 002211 288 PLSLKTAKSILGALTLRQHTPDSKRRRDFVSRWNTLSNGS--I----GLNPYGLYAYDTVWMIARALKLFLDQGNTISFS 361 (953)
Q Consensus 288 ~~~~~~~~~~~g~~~~~~~~~~~~~~~~F~~~~~~~~~~~--~----~~~~~~~~~YDAv~~la~Al~~~~~~~~~~~~~ 361 (953)
.+.......+.+++...++.+..++|+++|++++.+. . .....++.+||||+++
T Consensus 231 ---~~~~~~~~niTgF~l~d~~~~~v~~f~~~~~~~~~~~~~~~~~~~~~~~~al~~D~v~~~----------------- 290 (333)
T cd06394 231 ---DSIVDDRSNILGFSMFNQSHAFYQEFIRSLNQSWRENCDHSPYTGPALSSALLFDAVYAV----------------- 290 (333)
T ss_pred ---HHhhcCCcceEEEEeecCCcHHHHHHHHHHHHhhhhhcccccCCCcccceeeecceEEEE-----------------
Confidence 2233335568888999999999999999888765211 1 1123455566665542
Q ss_pred CCCccCCCCCCcccCCCccccCchHHHHHHHHhcccCCcceeEEEccCCCCCCccEEEEEeecCCeeeEEEEecCCCCcc
Q 002211 362 NDTKLNGLGGGTLNLGALSIFDGGKKFLANILQTNMTGLSGPIHFNQDRSLLHPSYDIINVIEHGYPQQIGYWSNYSGLS 441 (953)
Q Consensus 362 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~f~G~tG~v~Fd~~g~~~~~~y~I~~~~~~~~~~~VG~w~~~~gl~ 441 (953)
|+||+|+||++|.|.+...+|+++..+|. ++||+|++..||+
T Consensus 291 -------------------------------------glTg~i~f~~~g~R~~~~l~v~~l~~~g~-~kig~W~~~~gl~ 332 (333)
T cd06394 291 -------------------------------------GLTGRIEFNSKGQRSNYTLKILQKTRSGF-RQIGQWHSNETLS 332 (333)
T ss_pred -------------------------------------eeecceecCCCCcCcccEEEEEEecCCcc-eEEEEEeCCCCcC
Confidence 99999999999999999999999999999 9999999998875
No 36
>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=1.5e-39 Score=359.41 Aligned_cols=316 Identities=21% Similarity=0.348 Sum_probs=270.8
Q ss_pred EEeEEEecCCCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecC-CCChHHHHHHHHHHHhcCcEEEEccCChhhHHH
Q 002211 51 NVGAIFSFGTVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDA-KFNGFLSIMGALQFMETDTLAIVGPQSAVMAHV 129 (953)
Q Consensus 51 ~IG~l~~~~~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~-~~~~~~a~~~a~~li~~~v~aiiGp~~S~~a~a 129 (953)
+||+++|.++ ...+.|+++|+|+||++||++++.++++++.|+ ++++..++.++++|++++|.+||||.+|..+.+
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 5999999987 788999999999999999999767999999998 599999999999999989999999999999999
Q ss_pred HHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecCccccchHHHHHHHHHhc
Q 002211 130 LSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDDDQGRNGVTALGDKLAEI 209 (953)
Q Consensus 130 v~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~~~g~~~~~~l~~~l~~~ 209 (953)
+++++++++||+|+++++++.++ ..++|.| .|++..++.++++++++++|++|++||++++++ ...+.+.+.+++.
T Consensus 78 v~~i~~~~~ip~is~~~~~~~~~-~~~~~~~--~~~~~~~~~a~~~~~~~~~w~~vaii~~~~~~~-~~l~~~~~~~~~~ 153 (324)
T cd06368 78 VQSICDALEIPHITTSWSPNPKP-RQFTINL--YPSMRDLSDALLDLIKYFGWRKFVYIYDSDEGL-LRLQELLDALSPK 153 (324)
T ss_pred HHHHHhccCCCcEEecCCcCCCC-CcceEEe--cCCHHHHHHHHHHHHHhcCCCEEEEEECCcHhH-HHHHHHHHhhccC
Confidence 99999999999999999998876 2344444 577779999999999999999999999877654 4456677778888
Q ss_pred CcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEEeCcccccccCCCCC
Q 002211 210 RCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIATTWLSTFIDSKSPL 289 (953)
Q Consensus 210 g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~~~~~ 289 (953)
|++|+.....+ . .+|++.+|.++++.++|+||+.+.+.++..+++||+++||+.++|+||+++......+.
T Consensus 154 g~~v~~~~~~~-~----~~d~~~~l~~i~~~~~d~Vi~~~~~~~~~~i~~qa~~~g~~~~~~~~i~~~~~~~~~~~---- 224 (324)
T cd06368 154 GIQVTVRRLDD-D----TDMYRPLLKEIKREKERRIILDCSPERLKEFLEQAVEVGMMSEYYHYILTNLDFHTLDL---- 224 (324)
T ss_pred CceEEEEEecC-C----chHHHHHHHHHhhccCceEEEECCHHHHHHHHHHHHHhccccCCcEEEEccCCccccch----
Confidence 99998765444 3 23899999999999999999999999999999999999999899999998764433221
Q ss_pred chhhhhhccceEEEEEecCCChhhHHHHHHHHhhcCCC------CCCCchhhHHhhHHHHHHHHHHHHHhcCCcccccCC
Q 002211 290 SLKTAKSILGALTLRQHTPDSKRRRDFVSRWNTLSNGS------IGLNPYGLYAYDTVWMIARALKLFLDQGNTISFSND 363 (953)
Q Consensus 290 ~~~~~~~~~g~~~~~~~~~~~~~~~~F~~~~~~~~~~~------~~~~~~~~~~YDAv~~la~Al~~~~~~~~~~~~~~~ 363 (953)
........++.++....++++..++|.++|+++++.. ..|+.+++.+||||+++
T Consensus 225 -~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~p~~~aa~~yDav~~~------------------- 284 (324)
T cd06368 225 -ELFRYGGVNITGFRLVDPDNPEVQKFIQRWERSDHRICPGSGLKPIKTESALTYDAVLLF------------------- 284 (324)
T ss_pred -hhhhcCCceEEEEEEecCCChHHHHHHHHHHhccccccCCCCCCCcchhhHhhhcEEEEe-------------------
Confidence 1222344567777778888999999999999998631 26888999999999864
Q ss_pred CccCCCCCCcccCCCccccCchHHHHHHHHhcccCCcceeEEEccCCCCCCccEEEEEeecCCeeeEEEEecCCCCc
Q 002211 364 TKLNGLGGGTLNLGALSIFDGGKKFLANILQTNMTGLSGPIHFNQDRSLLHPSYDIINVIEHGYPQQIGYWSNYSGL 440 (953)
Q Consensus 364 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~f~G~tG~v~Fd~~g~~~~~~y~I~~~~~~~~~~~VG~w~~~~gl 440 (953)
||+++||++|+|.+..++|+++.+++. +.||+|++..|+
T Consensus 285 -------------------------------------tg~~~f~~~g~~~~~~~~i~~~~~~~~-~~~g~W~~~~~~ 323 (324)
T cd06368 285 -------------------------------------TGRIQFDENGQRSNFTLDILELKEGGL-RKVGTWNPEDGL 323 (324)
T ss_pred -------------------------------------eeeeEeCCCCcCcceEEEEEEEcCCCc-eEEEEECCCCCC
Confidence 899999999999999999999998888 999999998764
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=6.8e-39 Score=356.19 Aligned_cols=328 Identities=17% Similarity=0.213 Sum_probs=290.3
Q ss_pred EEeEEEecC---CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEEccCChhhH
Q 002211 51 NVGAIFSFG---TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIVGPQSAVMA 127 (953)
Q Consensus 51 ~IG~l~~~~---~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aiiGp~~S~~a 127 (953)
+||++.|++ +..|.....|+++|++++|++||+ +|++|++++.|++++|..+++.+.+|++++|.+|+||.+|..+
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 599999998 456889999999999999999988 4999999999999999999999999999999999999999999
Q ss_pred HHHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHH-HHcCCcEEEEEEecCccccchHHHHHHHH
Q 002211 128 HVLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMV-SYFGWGEVIAIFNDDDQGRNGVTALGDKL 206 (953)
Q Consensus 128 ~av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l-~~~~w~~vaii~~d~~~g~~~~~~l~~~l 206 (953)
.+++++++..+||+|+++++++.+.+..||++||+.|++..++.++++++ ++++|++|++++.|++||+...+.+++.+
T Consensus 80 ~~~~~~~~~~~ip~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~v~~~~~~g~~~~~~~~~~~ 159 (334)
T cd06342 80 IPASPIYADAGIVMISPAATNPKLTERGYKNVFRVVARDDQQGPAAAKYAVETLKAKKVAIIDDKTAYGQGLADEFKKAL 159 (334)
T ss_pred HHhHHHHHhCCCeEEecCCCCchhhcCCCceEEeccCCcHHHHHHHHHHHHHhcCCCEEEEEeCCcchhhHHHHHHHHHH
Confidence 99999999999999999888777776678999999999999999999985 57889999999999999999999999999
Q ss_pred HhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEEeCcccccccCC
Q 002211 207 AEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIATTWLSTFIDSK 286 (953)
Q Consensus 207 ~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~~ 286 (953)
++.|++|+....++.+ ..|+...+.++++.++|+|++.+...++..+++++++.|+.. .|+.++++... ..
T Consensus 160 ~~~g~~v~~~~~~~~~----~~d~~~~l~~i~~~~~~~vi~~~~~~~~~~~~~~~~~~g~~~---~~~~~~~~~~~-~~- 230 (334)
T cd06342 160 KAAGGKVVAREGTTDG----ATDFSAILTKIKAANPDAVFFGGYYPEAGPLVRQMRQLGLKA---PFMGGDGLCDP-EF- 230 (334)
T ss_pred HHcCCEEEEEecCCCC----CccHHHHHHHHHhcCCCEEEEcCcchhHHHHHHHHHHcCCCC---cEEecCccCCH-HH-
Confidence 9999999999888876 789999999999999999999999999999999999999843 57776644321 10
Q ss_pred CCCchhhhhhccceEEEEEecC--CChhhHHHHHHHHhhcCCCCCCCchhhHHhhHHHHHHHHHHHHHhcCCcccccCCC
Q 002211 287 SPLSLKTAKSILGALTLRQHTP--DSKRRRDFVSRWNTLSNGSIGLNPYGLYAYDTVWMIARALKLFLDQGNTISFSNDT 364 (953)
Q Consensus 287 ~~~~~~~~~~~~g~~~~~~~~~--~~~~~~~F~~~~~~~~~~~~~~~~~~~~~YDAv~~la~Al~~~~~~~~~~~~~~~~ 364 (953)
.....+..+|++...++.+ ..+..++|.++|+++++ ..++.++..+||+++++++|++++..
T Consensus 231 ---~~~~~~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~~--~~~~~~~~~~yda~~~~~~al~~~~~----------- 294 (334)
T cd06342 231 ---IKIAGDAAEGTYATFPGGPLEKMPAGKAFVARYKAKFG--DPPGAYAPYAYDAANVLAEAIKKAGS----------- 294 (334)
T ss_pred ---HHHhhHhhCCcEEEecCCCCCCChHHHHHHHHHHHHhC--CCCchhHHHHHHHHHHHHHHHHHhCC-----------
Confidence 0223456789888877665 46889999999999886 55688999999999999999998621
Q ss_pred ccCCCCCCcccCCCccccCchHHHHHHHHhcccCCcceeEEEccCCCCCCccEEEEEe
Q 002211 365 KLNGLGGGTLNLGALSIFDGGKKFLANILQTNMTGLSGPIHFNQDRSLLHPSYDIINV 422 (953)
Q Consensus 365 ~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~f~G~tG~v~Fd~~g~~~~~~y~I~~~ 422 (953)
.+++.|+++|++++|+|++|+++|+++|++....|+|+||
T Consensus 295 ------------------~~~~~v~~~l~~~~~~g~~g~i~f~~~g~~~~~~~~~~~~ 334 (334)
T cd06342 295 ------------------TDPAKVADALRKVDFDGVTGKISFDAKGDLKGAAVTVYQV 334 (334)
T ss_pred ------------------CCHHHHHHHHHhCCCCCcceeeEECCCCCcccCcEEEEeC
Confidence 1488999999999999999999999999999999999986
No 38
>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=6e-39 Score=351.85 Aligned_cols=304 Identities=18% Similarity=0.256 Sum_probs=267.7
Q ss_pred EEeEEEecC---CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhc-CcEEEEccCChhh
Q 002211 51 NVGAIFSFG---TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMET-DTLAIVGPQSAVM 126 (953)
Q Consensus 51 ~IG~l~~~~---~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~-~v~aiiGp~~S~~ 126 (953)
|||++.|++ +..|+....|+++|+++||++||+ .|++|+++++|++++|..+++++++|+++ +|.+||||.+|..
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 699999998 456888999999999999999999 49999999999999999999999999987 9999999999999
Q ss_pred HHHH-HHhhhhCCCcEEEeecCCCCCCC-CCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecCccccchHHHHHH
Q 002211 127 AHVL-SHLANELQVPLLSFTALDPTLSP-LQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDDDQGRNGVTALGD 204 (953)
Q Consensus 127 a~av-~~v~~~~~vP~Is~~at~~~ls~-~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~~~g~~~~~~l~~ 204 (953)
+.++ ++++++.++|+|+++++++.+++ ..++|+||+.|++..++.++++++.+++|+++++|+.|++||++..+.+++
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 99999999999999999999987 557999999999999999999999999999999999999999999999999
Q ss_pred HHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEEeCccccccc
Q 002211 205 KLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIATTWLSTFID 284 (953)
Q Consensus 205 ~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~ 284 (953)
.+++.|++|+....++++ ++|++++++++++.+||+|++.+.+.++..++++++++|+.. .|++++++.....
T Consensus 160 ~~~~~G~~vv~~~~~~~~----~~d~~~~v~~l~~~~pd~v~~~~~~~~~~~~~~~~~~~G~~~---~~~~~~~~~~~~~ 232 (312)
T cd06346 160 AFEALGGTVTNVVAHEEG----KSSYSSEVAAAAAGGPDALVVIGYPETGSGILRSAYEQGLFD---KFLLTDGMKSDSF 232 (312)
T ss_pred HHHHcCCEEEEEEeeCCC----CCCHHHHHHHHHhcCCCEEEEecccchHHHHHHHHHHcCCCC---ceEeeccccChHH
Confidence 999999999999999887 889999999999999999999999999999999999999843 3666655332210
Q ss_pred CCCCCchhhhhhccceEEEEEecCCChhhHHHHHHHHhhcCCCCCCCchhhHHhhHHHHHHHHHHHHHhcCCcccccCCC
Q 002211 285 SKSPLSLKTAKSILGALTLRQHTPDSKRRRDFVSRWNTLSNGSIGLNPYGLYAYDTVWMIARALKLFLDQGNTISFSNDT 364 (953)
Q Consensus 285 ~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~F~~~~~~~~~~~~~~~~~~~~~YDAv~~la~Al~~~~~~~~~~~~~~~~ 364 (953)
. .......++|+++..+..+. +..++|.++|+++|+ ..|+.+++.+||+++++++|
T Consensus 233 ~----~~~~~~~~~g~~~~~~~~~~-~~~~~f~~~~~~~~g--~~p~~~~~~~Yd~~~~l~~A----------------- 288 (312)
T cd06346 233 L----PADGGYILAGSYGTSPGAGG-PGLEAFTSAYKAAYG--ESPSAFADQSYDAAALLALA----------------- 288 (312)
T ss_pred H----HhhhHHHhCCcEEccCCCCc-hhHHHHHHHHHHHhC--CCCCccchhhHHHHHHHHHH-----------------
Confidence 1 01223567888877665544 888999999999997 56889999999999999855
Q ss_pred ccCCCCCCcccCCCccccCchHHHHHHHHhcccCCcceeEEEccCCCCCCccEEE
Q 002211 365 KLNGLGGGTLNLGALSIFDGGKKFLANILQTNMTGLSGPIHFNQDRSLLHPSYDI 419 (953)
Q Consensus 365 ~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~f~G~tG~v~Fd~~g~~~~~~y~I 419 (953)
|.|++|+++||++|++. ..|+-
T Consensus 289 --------------------------------~~g~~g~~~f~~~g~~~-~~~~~ 310 (312)
T cd06346 289 --------------------------------YQGASGVVDFDENGDVA-GSYDE 310 (312)
T ss_pred --------------------------------hCCCccceeeCCCCCcc-cceee
Confidence 67899999999999853 35553
No 39
>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=2e-38 Score=353.85 Aligned_cols=329 Identities=15% Similarity=0.191 Sum_probs=283.2
Q ss_pred EEeEEEecC---CCchhHHHHHHHHHHHHHhcCCCCC---CCcEEEEEEecCCCChHHHHHHHHHHHhc-CcEEEEccCC
Q 002211 51 NVGAIFSFG---TVNGQVSRIAMKAAQDDINSDPRVL---GGRKLSITMHDAKFNGFLSIMGALQFMET-DTLAIVGPQS 123 (953)
Q Consensus 51 ~IG~l~~~~---~~~g~~~~~a~~lAve~iN~~g~il---~g~~l~l~~~D~~~~~~~a~~~a~~li~~-~v~aiiGp~~ 123 (953)
+||+++|++ +..|.....|+++|+++||++||+. .|++|+++.+|++++|..+++.+++|+++ +|.+||||.+
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 699999998 5568889999999999999988763 47999999999999999999999999987 9999999999
Q ss_pred hhhHHHHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcC--CcEEEEEEecCccccchHHH
Q 002211 124 AVMAHVLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFG--WGEVIAIFNDDDQGRNGVTA 201 (953)
Q Consensus 124 S~~a~av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~--w~~vaii~~d~~~g~~~~~~ 201 (953)
|..+.++++++++.+||+|+++++++.++...+||+||+.|++..++.++++++++++ |+++++++.|++||+...+.
T Consensus 81 s~~~~a~~~~~~~~~vp~i~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~v~~v~~~~~~g~~~~~~ 160 (345)
T cd06338 81 SGLTLAAAPVAEKYGVPMVAGSGASDSIFAQGFKYVFGTLPPASQYAKSLLEMLVALDPRPKKVAILYADDPFSQDVAEG 160 (345)
T ss_pred chhHHHHHHHHHHhCCcEEecCCCCchHhhcCCceEEEecCchHHHHHHHHHHHHhcCCCCceEEEEecCCcccHHHHHH
Confidence 9999999999999999999999888888766689999999999999999999999987 99999999999999999999
Q ss_pred HHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEEeCcccc
Q 002211 202 LGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIATTWLST 281 (953)
Q Consensus 202 l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~ 281 (953)
+.+.+++.|++|+....++.+ .+|+++++++|++.++|+|++.+...+...+++++++.|+..+ . ...+.+...
T Consensus 161 ~~~~~~~~g~~v~~~~~~~~~----~~d~~~~v~~l~~~~~d~i~~~~~~~~~~~~~~~~~~~g~~~~-~-~~~~~~~~~ 234 (345)
T cd06338 161 AREKAEAAGLEVVYDETYPPG----TADLSPLISKAKAAGPDAVVVAGHFPDAVLLVRQMKELGYNPK-A-LYMTVGPAF 234 (345)
T ss_pred HHHHHHHcCCEEEEEeccCCC----ccchHHHHHHHHhcCCCEEEECCcchhHHHHHHHHHHcCCCCC-E-EEEecCCCc
Confidence 999999999999988888876 6899999999999999999999999999999999999998654 2 222232221
Q ss_pred cccCCCCCchhhhhhccceEEEEEecCC-------ChhhHHHHHHHHhhcCCCCCCCchhhHHhhHHHHHHHHHHHHHhc
Q 002211 282 FIDSKSPLSLKTAKSILGALTLRQHTPD-------SKRRRDFVSRWNTLSNGSIGLNPYGLYAYDTVWMIARALKLFLDQ 354 (953)
Q Consensus 282 ~~~~~~~~~~~~~~~~~g~~~~~~~~~~-------~~~~~~F~~~~~~~~~~~~~~~~~~~~~YDAv~~la~Al~~~~~~ 354 (953)
.... .......+|+++...+.+. .+..++|.++|+++|+ ..|+.++..+||+++++++|+++++..
T Consensus 235 ~~~~-----~~~g~~~~g~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~--~~p~~~~~~~y~a~~~~~~a~~~ag~~ 307 (345)
T cd06338 235 PAFV-----KALGADAEGVFGPTQWTPALDYKDDLFPSAAEFAAAYKEKYG--KAPDYHAAGAYAAGQVLQEAVERAGSL 307 (345)
T ss_pred HHHH-----HHHhhhhCceeecceeccCcccccccCccHHHHHHHHHHHhC--CCCCcccHHHHHHHHHHHHHHHHhCCC
Confidence 1000 2234556888887766554 3678999999999987 557788899999999999999986321
Q ss_pred CCcccccCCCccCCCCCCcccCCCccccCchHHHHHHHHhcccCCcceeEEEccCCCCCCccEEEEEe
Q 002211 355 GNTISFSNDTKLNGLGGGTLNLGALSIFDGGKKFLANILQTNMTGLSGPIHFNQDRSLLHPSYDIINV 422 (953)
Q Consensus 355 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~f~G~tG~v~Fd~~g~~~~~~y~I~~~ 422 (953)
+++.|.++|++++|+|++|++.|+++|++.. .+.|++|
T Consensus 308 -----------------------------~~~~v~~al~~~~~~~~~G~~~f~~~~~~~~-~~~~~~~ 345 (345)
T cd06338 308 -----------------------------DPAAVRDALASNDFDTFYGPIKFDETGQNNH-PMTVVQW 345 (345)
T ss_pred -----------------------------CHHHHHHHHHhCCCcccccCeeECCCCCcCC-CceeeeC
Confidence 4789999999999999999999999998644 5555543
No 40
>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=3.3e-38 Score=351.45 Aligned_cols=320 Identities=18% Similarity=0.248 Sum_probs=277.5
Q ss_pred EEeEEEecC---CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhc-CcEEEEccCChhh
Q 002211 51 NVGAIFSFG---TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMET-DTLAIVGPQSAVM 126 (953)
Q Consensus 51 ~IG~l~~~~---~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~-~v~aiiGp~~S~~ 126 (953)
+||++.|++ +..|+....|+++|++++|++||+. |++|++++.|++++|..+++.+++|+++ +|.+||||.+|..
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 KIGVLAPLSGGASTTGEAMWNGAELAAEEINAAGGIL-GRKVELVFEDTEGSPEDAVRAFERLVSQDKVDAVVGGYSSEV 79 (344)
T ss_pred CeeEEEecCCcccccCHHHHHHHHHHHHHHHHcCCCC-CceEEEEEecCCCCHHHHHHHHHHHhccCCceEEECCcchHH
Confidence 599999998 5679999999999999999999985 8999999999999999999999999987 9999999999999
Q ss_pred HHHHHHhhhhCCCcEEEeecCCCCCCC----CCCCcEEEccCChHHHHHHHHHHHHH-----cCCcEEEEEEecCccccc
Q 002211 127 AHVLSHLANELQVPLLSFTALDPTLSP----LQYPFFVQTAPNDLYLMSAIAEMVSY-----FGWGEVIAIFNDDDQGRN 197 (953)
Q Consensus 127 a~av~~v~~~~~vP~Is~~at~~~ls~----~~~p~~fr~~p~d~~~~~ai~~~l~~-----~~w~~vaii~~d~~~g~~ 197 (953)
+.++++++++++||+|+++++++.+++ ..+||+||+.|++..++.++++++.+ ++|++|++++.+++||+.
T Consensus 80 ~~a~~~~~~~~~vp~i~~~~~~~~~t~~~~~~~~~~~fr~~~~~~~~~~~~~~~~~~~~~~~~~~~~va~l~~~~~~g~~ 159 (344)
T cd06345 80 VLALQDVAAENKVPFIVTGAASPEITTADDYETYKYVFRAGPTNSSYAQSVADALKETLVDKHGFKTAAIVAEDAAWGKG 159 (344)
T ss_pred HHHHHHHHHHcCCcEEeccCCCCcccccccccCCceEEecCCCcHHHHHHHHHHHHHhhcccCCCceEEEEecCchhhhH
Confidence 999999999999999999888888873 46899999999999999999999876 899999999999999999
Q ss_pred hHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEEeC
Q 002211 198 GVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIATT 277 (953)
Q Consensus 198 ~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~ 277 (953)
..+.+++.+++.|++|+....++.+ ..|+..++.+|++.++|+|++.+.+.++..++++++++|+..+ ++..+
T Consensus 160 ~~~~~~~~~~~~G~~vv~~~~~~~~----~~d~~~~v~~l~~~~~d~v~~~~~~~~~~~~~~~~~~~g~~~~---~~~~~ 232 (344)
T cd06345 160 IDAGIKALLPEAGLEVVSVERFSPD----TTDFTPILQQIKAADPDVIIAGFSGNVGVLFTQQWAEQKVPIP---TIGIS 232 (344)
T ss_pred HHHHHHHHHHHcCCeEEEEEecCCC----CCchHHHHHHHHhcCCCEEEEeecCchHHHHHHHHHHcCCCCc---eEEec
Confidence 9999999999999999998888876 7799999999999999999999999999999999999998532 33332
Q ss_pred cccccccCCCCCchhhhhhccceEEEEEecC----CChhhHHHHHHHHhhcCCCCCCCchhhHHhhHHHHHHHHHHHHHh
Q 002211 278 WLSTFIDSKSPLSLKTAKSILGALTLRQHTP----DSKRRRDFVSRWNTLSNGSIGLNPYGLYAYDTVWMIARALKLFLD 353 (953)
Q Consensus 278 ~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~----~~~~~~~F~~~~~~~~~~~~~~~~~~~~~YDAv~~la~Al~~~~~ 353 (953)
.+....... .......+|++....+.+ .++..++|.++|+++|+ ..|+.+++.+||+++++++|+++++.
T Consensus 233 ~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~y~~~~g--~~p~~~~~~~yda~~~l~~A~~~ag~ 306 (344)
T cd06345 233 VEGNSPAFW----KATNGAGNYVITAESGAPGVEAITDKTVPFTEAYEAKFG--GPPNYMGASTYDSIYILAEAIERAGS 306 (344)
T ss_pred CCcCCHHHH----HhhchhcceEEeecccccCccCCCHHHHHHHHHHHHHhC--CCCcccchHHHHHHHHHHHHHHHhcC
Confidence 221110000 122345677766555443 56788999999999987 66889999999999999999998632
Q ss_pred cCCcccccCCCccCCCCCCcccCCCccccCchHHHHHHHHhcccCCcceeEEEccCCCCC
Q 002211 354 QGNTISFSNDTKLNGLGGGTLNLGALSIFDGGKKFLANILQTNMTGLSGPIHFNQDRSLL 413 (953)
Q Consensus 354 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~f~G~tG~v~Fd~~g~~~ 413 (953)
. +++.|.++|++++|+|++|+++||++||+.
T Consensus 307 ~-----------------------------~~~~i~~al~~~~~~g~~G~i~f~~~g~~~ 337 (344)
T cd06345 307 T-----------------------------DGDALVEALEKTDFVGTAGRIQFYGDDSAF 337 (344)
T ss_pred C-----------------------------CHHHHHHHHHhCCCcCCceeEEECCCCCcC
Confidence 1 478899999999999999999999999964
No 41
>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=4.1e-38 Score=352.36 Aligned_cols=334 Identities=26% Similarity=0.450 Sum_probs=281.4
Q ss_pred HHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHH-HhcCcEEEEccCChhhHHHHHHhhhhCCCcEEEe
Q 002211 66 SRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQF-METDTLAIVGPQSAVMAHVLSHLANELQVPLLSF 144 (953)
Q Consensus 66 ~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~l-i~~~v~aiiGp~~S~~a~av~~v~~~~~vP~Is~ 144 (953)
...|+++|+++||+++++++|.+|++++.|+++++..+...+... ..++|.+||||.|+..+.+++.+++.++||+|++
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 578999999999999999999999999999996666666655544 4569999999999999999999999999999999
Q ss_pred ecCCCCCCC--CCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecCccccchHHHHHHHHHhcCcEEEEE-EecCC
Q 002211 145 TALDPTLSP--LQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDDDQGRNGVTALGDKLAEIRCKISYK-SALPP 221 (953)
Q Consensus 145 ~at~~~ls~--~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~~~g~~~~~~l~~~l~~~g~~v~~~-~~~~~ 221 (953)
+++++.+++ ..||+|+|+.|++..+++++++++++++|++|++||+++++|.+....+.+.+++.++.+... ...+.
T Consensus 82 ~~~~~~ls~~~~~~~~~~r~~p~~~~~~~a~~~~l~~~~w~~v~vv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 161 (348)
T PF01094_consen 82 GSTSPSLSDRKTRYPTFFRTVPSDSSQARALVDLLKHFGWTRVSVVYSDDDYGNSLADSFQDLLRERGGICVAFISVVIS 161 (348)
T ss_dssp SGGSGGGGSTTTTTTTEEESSB-HHHHHHHHHHHHHHTTSSEEEEEEESSHHHHHHHHHHHHHHHHHTTCEEEEEEEEET
T ss_pred cccccccccchhhccccccccccHHHHHHHHHHhhhcCCCceeeeeccccccccccchhhhhhhcccccceecccccccc
Confidence 999999988 479999999999999999999999999999999999999999999999999999975444433 33333
Q ss_pred CCCCChHHHHHHHHHHhc--CCceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEEeCcccccccCCCCCchhhhhhccc
Q 002211 222 DQSVTETDVRNELVKVRM--MEARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIATTWLSTFIDSKSPLSLKTAKSILG 299 (953)
Q Consensus 222 ~~~~~~~d~~~~l~~i~~--~~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~~~~~~~~~~~~~~g 299 (953)
. ..++...+.++++ .++++||+++...++..++++|.++||...+|+||.++.+...... ..........|
T Consensus 162 ~----~~~~~~~~~~l~~~~~~~rvvil~~~~~~~~~~l~~a~~~~~~~~~~~~i~~~~~~~~~~~---~~~~~~~~~~~ 234 (348)
T PF01094_consen 162 S----DSDAEELLKKLKEIKSGARVVILCSSPEDARQFLEAAYELGMTSGDYVWILTDLDNSSFWQ---NNEDFREAFQG 234 (348)
T ss_dssp T----TSHHHHHHHHHHHHTTTTSEEEEESBHHHHHHHHHHHHHTTTSSTTSEEEEETTTTTTHTS---THCHHHCCHTT
T ss_pred c----ccchhhhhhhhhhccccceeeeeecccccccccccchhhhhccccceeEEeeccccccccc---ccccccccccc
Confidence 3 3455555555555 9999999999999999999999999999999999999987665321 11466788999
Q ss_pred eEEEEEecCCChhhHHHHHHHHhhc------CCCCCCCchhhHHhhHHHHHHHHHHHHHhcCCcccccCCCccCCCCCCc
Q 002211 300 ALTLRQHTPDSKRRRDFVSRWNTLS------NGSIGLNPYGLYAYDTVWMIARALKLFLDQGNTISFSNDTKLNGLGGGT 373 (953)
Q Consensus 300 ~~~~~~~~~~~~~~~~F~~~~~~~~------~~~~~~~~~~~~~YDAv~~la~Al~~~~~~~~~~~~~~~~~~~~~~~~~ 373 (953)
++++.++.+..+.+++|.++|++.. .....+..+++++|||++++|+|++++...++....
T Consensus 235 ~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~yDAv~~~a~al~~~~~~~~~~~~------------- 301 (348)
T PF01094_consen 235 VLGFTPPPPSSPEFEDFMKKWKESNNQSSTSGSDQEPSPYAAYAYDAVYLLAHALNRALQDGGPVTN------------- 301 (348)
T ss_dssp EEEEEESTTTSHHHHHHHHHHHTTTHTTTTTTTTSSGCHHHHHHHHHHHHHHHHHHHHHHHHSTTTS-------------
T ss_pred eeeeeeecccccchhhhhcccChhhccCcccccccccceeeeeehhhhHHHHHHHHHHHHhccCCCC-------------
Confidence 9999999999999999999999752 133567889999999999999999999876443210
Q ss_pred ccCCCccccCchHHHHHHHHhcccCCcceeEEEcc-CCCCCCccEEEEEee
Q 002211 374 LNLGALSIFDGGKKFLANILQTNMTGLSGPIHFNQ-DRSLLHPSYDIINVI 423 (953)
Q Consensus 374 ~~~~~~~~~~~~~~l~~~l~~~~f~G~tG~v~Fd~-~g~~~~~~y~I~~~~ 423 (953)
....|.+|..|.++|++++|+|++|++.||+ +|++....|.|+|++
T Consensus 302 ----~~~~~~~g~~l~~~l~~~~f~G~tG~v~f~~~~G~~~~~~~~i~~~~ 348 (348)
T PF01094_consen 302 ----GRNPWQNGSQLLKYLRNVSFEGLTGRVSFDSNDGDRTNYDYDILNMQ 348 (348)
T ss_dssp ----SSGTSTTHHHHHHHHHTEEEEETTEEEEEETTTSBEESEEEEEEEE-
T ss_pred ----CccccccHHHHHHHHhheeeeCCCCCEEEeCCCCCcCCCEEEEEECC
Confidence 0044667999999999999999999999999 999889999999975
No 42
>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=9.5e-38 Score=347.27 Aligned_cols=334 Identities=15% Similarity=0.125 Sum_probs=279.1
Q ss_pred EEeEEEecC---CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhc-CcEEEEccCChhh
Q 002211 51 NVGAIFSFG---TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMET-DTLAIVGPQSAVM 126 (953)
Q Consensus 51 ~IG~l~~~~---~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~-~v~aiiGp~~S~~ 126 (953)
+||++.|+| +..|+...+|+++|+++||++||++ |++|+++.+|++++|.++++++++|+++ +|.+|+|+.+|+.
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 699999998 5568999999999999999999997 8999999999999999999999999976 8999999999999
Q ss_pred HHHHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHH-cCCcEEEEEEecCccccchHHHHHHH
Q 002211 127 AHVLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSY-FGWGEVIAIFNDDDQGRNGVTALGDK 205 (953)
Q Consensus 127 a~av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~-~~w~~vaii~~d~~~g~~~~~~l~~~ 205 (953)
+.++.+++++.++|++++.+... ....||+||+.+.+..++..+++++.. .|+++|++++.|++||++..+.+++.
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 99999999999999998653321 135699999999999999999998765 57999999999999999999999999
Q ss_pred HHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEEeCcccccccC
Q 002211 206 LAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIATTWLSTFIDS 285 (953)
Q Consensus 206 l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~ 285 (953)
+++.|++|+....++.+ ..|+++++.++++.+||+|++...+.++..+++++++.|+..+...++........+.
T Consensus 157 ~~~~G~~vv~~~~~~~~----~~D~~~~v~~l~~~~pd~v~~~~~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~~~~- 231 (348)
T cd06355 157 LESLGGEVVGEEYLPLG----HTDFQSIINKIKAAKPDVVVSTVNGDSNVAFFKQLKAAGITASKVPVLSFSVAEEELR- 231 (348)
T ss_pred HHHcCCeEEeeEEecCC----hhhHHHHHHHHHHhCCCEEEEeccCCchHHHHHHHHHcCCCccCCeeEEccccHHHHh-
Confidence 99999999999989877 8999999999999999999999999999999999999998754445555432221111
Q ss_pred CCCCchhhhhhccceEEEEEe--cCCChhhHHHHHHHHhhcCCCCCCCchhhHHhhHHHHHHHHHHHHHhcCCcccccCC
Q 002211 286 KSPLSLKTAKSILGALTLRQH--TPDSKRRRDFVSRWNTLSNGSIGLNPYGLYAYDTVWMIARALKLFLDQGNTISFSND 363 (953)
Q Consensus 286 ~~~~~~~~~~~~~g~~~~~~~--~~~~~~~~~F~~~~~~~~~~~~~~~~~~~~~YDAv~~la~Al~~~~~~~~~~~~~~~ 363 (953)
....+..+|++....+ ..+.|..++|.++|+++|+....++.+++.+||+++++++|++++++.
T Consensus 232 -----~~g~~~~~g~~~~~~~~~~~~~~~~~~f~~~y~~~~g~~~~~~~~a~~~Y~a~~~~~~Al~~ag~~--------- 297 (348)
T cd06355 232 -----GIGPENLAGHYAAWNYFQSVDTPENKKFVAAFKARYGQDRVTNDPMEAAYIGVYLWKQAVEKAGSF--------- 297 (348)
T ss_pred -----hcChHhhcCCEEeccchhhcCCHHHHHHHHHHHHHcCCCCCCCcHHHHHHHHHHHHHHHHHHhCCC---------
Confidence 1112456787765544 335678899999999999743345667889999999999999997321
Q ss_pred CccCCCCCCcccCCCccccCchHHHHHHHHhcccCCcceeEEEccCCCCCCccEEEEEeecCCe
Q 002211 364 TKLNGLGGGTLNLGALSIFDGGKKFLANILQTNMTGLSGPIHFNQDRSLLHPSYDIINVIEHGY 427 (953)
Q Consensus 364 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~f~G~tG~v~Fd~~g~~~~~~y~I~~~~~~~~ 427 (953)
++++|.++|++++|+++.|+++|+++++.....+.|.+++.+|.
T Consensus 298 --------------------~~~~i~~aL~~~~~~~~~g~~~f~~~~~~~~~~~~i~~~~~~g~ 341 (348)
T cd06355 298 --------------------DVDKVRAALPGQSFDAPEGPVTVDPANHHLWKPVRIGRIQADGQ 341 (348)
T ss_pred --------------------CHHHHHHHhccCcccCCCcceEeecCCCeeeeeeEEEEEcCCCc
Confidence 48899999999999999999999984433455566777764444
No 43
>COG0683 LivK ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]
Probab=100.00 E-value=6.9e-38 Score=349.12 Aligned_cols=339 Identities=20% Similarity=0.281 Sum_probs=284.5
Q ss_pred CceEEEeEEEecC---CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhc-CcEEEEccC
Q 002211 47 PEVLNVGAIFSFG---TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMET-DTLAIVGPQ 122 (953)
Q Consensus 47 ~~~i~IG~l~~~~---~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~-~v~aiiGp~ 122 (953)
.++|+||++.|+| +.+|+....|+++|+|+||+.||++ |++|+++++|+++||..+++.+++|+.+ +|.+|+|+.
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 4589999999998 6679999999999999999999986 7889999999999999999999999985 999999999
Q ss_pred ChhhHHHHHHhhhhCCCcEEEeecCCCCCCCCCC-CcEEEccCChHHHHHHHHHHHHH-cCCcEEEEEEecCccccchHH
Q 002211 123 SAVMAHVLSHLANELQVPLLSFTALDPTLSPLQY-PFFVQTAPNDLYLMSAIAEMVSY-FGWGEVIAIFNDDDQGRNGVT 200 (953)
Q Consensus 123 ~S~~a~av~~v~~~~~vP~Is~~at~~~ls~~~~-p~~fr~~p~d~~~~~ai~~~l~~-~~w~~vaii~~d~~~g~~~~~ 200 (953)
+|+.+.++.+++++.++|+|++++++|.++...+ +++||++|++.+|+.++++++.. .+.|+|++|+.|+.||++..+
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 9999999999999999999999999999877444 55999999999999999999765 455599999999999999999
Q ss_pred HHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEEeCccc
Q 002211 201 ALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIATTWLS 280 (953)
Q Consensus 201 ~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~ 280 (953)
.+++.+++.|++++..+.+.+. +.++..++.++++++||+|++.+.++++..++++++++|+... ..++......
T Consensus 167 ~~~~~l~~~G~~~~~~~~~~~~----~~~~~~~v~~i~~~~~d~v~~~~~~~~~~~~~r~~~~~G~~~~-~~~~~~~~~~ 241 (366)
T COG0683 167 AFKAALKALGGEVVVEEVYAPG----DTDFSALVAKIKAAGPDAVLVGGYGPDAALFLRQAREQGLKAK-LIGGDGAGTA 241 (366)
T ss_pred HHHHHHHhCCCeEEEEEeeCCC----CCChHHHHHHHHhcCCCEEEECCCCccchHHHHHHHHcCCCCc-cccccccCch
Confidence 9999999999986666777776 5569999999999999999999999999999999999998653 2222222111
Q ss_pred ccccCCCCCchhhhhhccc-eEE-EEEecC-CChhhHHHHHHHHhhcCCCCCCCchhhHHhhHHHHHHHHHHHHHhcCCc
Q 002211 281 TFIDSKSPLSLKTAKSILG-ALT-LRQHTP-DSKRRRDFVSRWNTLSNGSIGLNPYGLYAYDTVWMIARALKLFLDQGNT 357 (953)
Q Consensus 281 ~~~~~~~~~~~~~~~~~~g-~~~-~~~~~~-~~~~~~~F~~~~~~~~~~~~~~~~~~~~~YDAv~~la~Al~~~~~~~~~ 357 (953)
.... .......+ ... ...+.+ ..|..+.|+++|+++++....++.++..+||+++++++|++++...
T Consensus 242 ~~~~-------~~~~~~~~~~~~~~~~~~~~~~p~~~~f~~~~~~~~g~~~~~~~~~~~~y~a~~~~~~ai~~a~~~--- 311 (366)
T COG0683 242 EFEE-------IAGAGGAGAGLLATAYSTPDDSPANKKFVEAYKAKYGDPAAPSYFAAAAYDAVKLLAKAIEKAGKS--- 311 (366)
T ss_pred hhhh-------hcccCccccEEEEecccccccCcchHHHHHHHHHHhCCCCCcccchHHHHHHHHHHHHHHHHHhcC---
Confidence 1111 11122233 322 223332 4567888999999999855667779999999999999999998530
Q ss_pred ccccCCCccCCCCCCcccCCCccccCchHHHHHHHHhcc-cCCcceeEEEccCCCCCCccEEEEEeecCC
Q 002211 358 ISFSNDTKLNGLGGGTLNLGALSIFDGGKKFLANILQTN-MTGLSGPIHFNQDRSLLHPSYDIINVIEHG 426 (953)
Q Consensus 358 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~-f~G~tG~v~Fd~~g~~~~~~y~I~~~~~~~ 426 (953)
. +++++.++|+... +.+.+|++.||++|++....+.|.+++..+
T Consensus 312 ------------------------~-d~~~v~~al~~~~~~~~~~G~v~~~~~~~~~~~~~~i~~~~~~~ 356 (366)
T COG0683 312 ------------------------S-DREAVAEALKGGKFFDTAGGPVTFDEKGDRGSKPVYVGQVQKGG 356 (366)
T ss_pred ------------------------C-CHHHHHHHHhhCCCCccCCcceeECCCCCcCCCceEEEEEEecC
Confidence 1 3788999999988 689999999999999999999999998543
No 44
>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=1.6e-37 Score=345.83 Aligned_cols=341 Identities=9% Similarity=0.049 Sum_probs=280.6
Q ss_pred EEEeEEEecC---CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhc-CcEEEEccCChh
Q 002211 50 LNVGAIFSFG---TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMET-DTLAIVGPQSAV 125 (953)
Q Consensus 50 i~IG~l~~~~---~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~-~v~aiiGp~~S~ 125 (953)
|+||++.|+| +..|...++|+++|+++||++||++ |++|+++++|++++|..|+.++++|+++ +|.+||||.+|+
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 5678999999999999999999997 8999999999999999999999999985 899999999999
Q ss_pred hHHHHHHhhhhCCCcEEEeecCCCCCCC-CCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecCccccchHHHHHH
Q 002211 126 MAHVLSHLANELQVPLLSFTALDPTLSP-LQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDDDQGRNGVTALGD 204 (953)
Q Consensus 126 ~a~av~~v~~~~~vP~Is~~at~~~ls~-~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~~~g~~~~~~l~~ 204 (953)
.+.++.+++++.++|+|.... ++. ...||+||+.+++..++.++++++....-+++++|+.|++||+...+.+++
T Consensus 80 ~~~A~~~~~~~~~~~~i~~~~----~~~~~~~~~~Fr~~~~~~~~~~~~~~~~~~~~g~~va~l~~d~~~g~~~~~~~~~ 155 (374)
T TIGR03669 80 TREAIRPIIDRNEQLYFYTNQ----YEGGVCDEYTFAVGATARQQLGTVVPYMVEEYGKKIYTIAADYNFGQLSADWVRV 155 (374)
T ss_pred HHHHHHHHHHhcCceEEcCcc----cccccCCCCEEEcCCChHHHHHHHHHHHHHcCCCeEEEEcCCcHHHHHHHHHHHH
Confidence 999999999999999996422 222 346899999999999999999997654337899999999999999999999
Q ss_pred HHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEEeCccccccc
Q 002211 205 KLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIATTWLSTFID 284 (953)
Q Consensus 205 ~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~ 284 (953)
.+++.|++|+....++.+ ..||++++.+|++++||+|++...+.+...+++|++++|+..+ ++..........
T Consensus 156 ~~~~~G~~vv~~~~~~~g----~~Df~~~l~~i~~~~pD~V~~~~~g~~~~~~~kq~~~~G~~~~---~~~~~~~~~~~~ 228 (374)
T TIGR03669 156 IAKENGAEVVGEEFIPLS----VSQFSSTIQNIQKADPDFVMSMLVGANHASFYEQAASANLNLP---MGTSTAMAQGYE 228 (374)
T ss_pred HHHHcCCeEEeEEecCCC----cchHHHHHHHHHHcCCCEEEEcCcCCcHHHHHHHHHHcCCCCc---ccchhhhhhhhh
Confidence 999999999999999887 8999999999999999999999999999999999999998643 222221111111
Q ss_pred CCCCCchhhhhhccceEEEEEecC--CChhhHHHHHHHHhhcCCCCCCCchhhHHhhHHHHHHHHHHHHHhcCCcccccC
Q 002211 285 SKSPLSLKTAKSILGALTLRQHTP--DSKRRRDFVSRWNTLSNGSIGLNPYGLYAYDTVWMIARALKLFLDQGNTISFSN 362 (953)
Q Consensus 285 ~~~~~~~~~~~~~~g~~~~~~~~~--~~~~~~~F~~~~~~~~~~~~~~~~~~~~~YDAv~~la~Al~~~~~~~~~~~~~~ 362 (953)
.. ........|+++..++.+ +.+..++|.++|+++|+....++.+++.+||+++++++|++++++.
T Consensus 229 ~~----~~~~~~~~g~~~~~~~~~~~~~~~~~~F~~~y~~~~g~~p~~~~~a~~~Yda~~~l~~Ai~~AGs~-------- 296 (374)
T TIGR03669 229 HK----RFEPPALKDVYAGVNYMEEIDTPENEAFVERFYAKFPDAPYINQEAENNYFSVYMYKQAVEEAGTT-------- 296 (374)
T ss_pred hh----hcCchhhCCcEEeeeccccCCCHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHHhCCC--------
Confidence 00 011234677776666544 4678899999999999733334677889999999999999997432
Q ss_pred CCccCCCCCCcccCCCccccCchHHHHHHHHh-cccCCcceeEEEccCCCCCCccEEEEEeecCCeeeEEEEec
Q 002211 363 DTKLNGLGGGTLNLGALSIFDGGKKFLANILQ-TNMTGLSGPIHFNQDRSLLHPSYDIINVIEHGYPQQIGYWS 435 (953)
Q Consensus 363 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~-~~f~G~tG~v~Fd~~g~~~~~~y~I~~~~~~~~~~~VG~w~ 435 (953)
++++|+++|++ .+|+|+.|+++||++++.....+.|.++..++....+..|.
T Consensus 297 ---------------------d~~av~~aL~~~~~~~~~~G~i~fd~~~~~~~~~~~v~~~~~~~~~~~~~~~~ 349 (374)
T TIGR03669 297 ---------------------DQDAVRDVLESGVEMDAPEGKVCIDGATHHMSHTMRLARADADHNITFVKEQE 349 (374)
T ss_pred ---------------------CHHHHHHHHHcCCeEECCCccEEEcCCCCeeeeeeEEEEEcCCCCEEEEEecC
Confidence 58999999997 57999999999997665455566777777665446666665
No 45
>cd06348 PBP1_ABC_ligand_binding_like_13 Type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine/isoleucine/valine binding protein (LIVBP); however its ligand specificity has not been determined experimentally.
Probab=100.00 E-value=1.4e-37 Score=346.48 Aligned_cols=334 Identities=18% Similarity=0.249 Sum_probs=279.2
Q ss_pred EEeEEEecC---CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhc-CcEEEEccCChhh
Q 002211 51 NVGAIFSFG---TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMET-DTLAIVGPQSAVM 126 (953)
Q Consensus 51 ~IG~l~~~~---~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~-~v~aiiGp~~S~~ 126 (953)
+||++.|+| +..|+..+.|+++|+++||++||++ |++|+++++|++++|..+++++++|+++ +|++|+||.+|.+
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 699999998 5569999999999999999999995 8999999999999999999999999987 8999999999999
Q ss_pred HHHHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHH-HHHHHHHc-CCcEEEEEEecC-ccccchHHHHH
Q 002211 127 AHVLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSA-IAEMVSYF-GWGEVIAIFNDD-DQGRNGVTALG 203 (953)
Q Consensus 127 a~av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~a-i~~~l~~~-~w~~vaii~~d~-~~g~~~~~~l~ 203 (953)
+.++.+++++.++|+|+++++++.+.. .+||+||+.+++..+... +..+++++ ||+++++||.++ .||+...+.++
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 999999999999999999887776643 468999998777655544 44567777 999999999754 49999999999
Q ss_pred HHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEEeCcccccc
Q 002211 204 DKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIATTWLSTFI 283 (953)
Q Consensus 204 ~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~ 283 (953)
+.+++.|++|+....++.+ +.|+..++.+++++++|+|++.+.+.++..+++++++.|+..+ ++.++++....
T Consensus 159 ~~~~~~g~~v~~~~~~~~~----~~d~~~~v~~i~~~~~d~vi~~~~~~~~~~~~~~~~~~g~~~~---~~~~~~~~~~~ 231 (344)
T cd06348 159 KALRDQGLNLVTVQTFQTG----DTDFQAQITAVLNSKPDLIVISALAADGGNLVRQLRELGYNGL---IVGGNGFNTPN 231 (344)
T ss_pred HHHHHcCCEEEEEEeeCCC----CCCHHHHHHHHHhcCCCEEEECCcchhHHHHHHHHHHcCCCCc---eeccccccCHH
Confidence 9999999999999889877 7899999999999999999999999999999999999998642 55555433211
Q ss_pred cCCCCCchhhhhhccceEEEEEecC--CChhhHHHHHHHHhhcCCCCCCCchhhHHhhHHHHHHHHHHHHHhcCCccccc
Q 002211 284 DSKSPLSLKTAKSILGALTLRQHTP--DSKRRRDFVSRWNTLSNGSIGLNPYGLYAYDTVWMIARALKLFLDQGNTISFS 361 (953)
Q Consensus 284 ~~~~~~~~~~~~~~~g~~~~~~~~~--~~~~~~~F~~~~~~~~~~~~~~~~~~~~~YDAv~~la~Al~~~~~~~~~~~~~ 361 (953)
.. ....+..+|++...++.+ +.+..++|.++|+++|+ ..++.++..+||+++++++|+++++..+....
T Consensus 232 -~~----~~~g~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~g--~~p~~~~~~~yda~~~~~~A~~~a~~~~~~~~-- 302 (344)
T cd06348 232 -VF----PVCQAACDGVLVAQAYSPENDTPVNRDFVEAYKKKYG--KAPPQFSAQAFDAVQVVAEALKRLNQKQKLAE-- 302 (344)
T ss_pred -HH----HhhhHhhcCeEEEeeccCCCCCHHHHHHHHHHHHHHC--CCccHHHHHHHHHHHHHHHHHHHhcCCCcccc--
Confidence 10 234467789888777654 45678999999999987 56788899999999999999999864321100
Q ss_pred CCCccCCCCCCcccCCCccccCchHHHHHHHHhcccCCcceeEEEccCCCCCCccEEE
Q 002211 362 NDTKLNGLGGGTLNLGALSIFDGGKKFLANILQTNMTGLSGPIHFNQDRSLLHPSYDI 419 (953)
Q Consensus 362 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~f~G~tG~v~Fd~~g~~~~~~y~I 419 (953)
+. ....++.|.++|++++|+|++|++.||++|++....|.|
T Consensus 303 --------------~~---~~~~~~~l~~~l~~~~~~g~~G~v~f~~~g~~~~~~~~~ 343 (344)
T cd06348 303 --------------LP---LPELRTALNAALLSGQYDTPLGEISFTPDGEVLQKAFYV 343 (344)
T ss_pred --------------ch---hhhHHHHHHHHHhccCCccceeeeEECCCCCcccCceec
Confidence 00 001367899999999999999999999999987776643
No 46
>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=6.6e-38 Score=350.23 Aligned_cols=309 Identities=31% Similarity=0.508 Sum_probs=268.5
Q ss_pred EEeEEEecCCC-------------chhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhc----
Q 002211 51 NVGAIFSFGTV-------------NGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMET---- 113 (953)
Q Consensus 51 ~IG~l~~~~~~-------------~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~---- 113 (953)
.||++||++.. .|.....++.+|+++||+++++++|++|+++++|++|+|.+|++++.+|+.+
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 48999999752 3567789999999999999999999999999999999999999999999985
Q ss_pred ----------CcEEEEccCChhhHHHHHHhhhhCCCcEEEeecCCCCCCC-CCCCcEEEccCChHHHHHHHHHHHHHcCC
Q 002211 114 ----------DTLAIVGPQSAVMAHVLSHLANELQVPLLSFTALDPTLSP-LQYPFFVQTAPNDLYLMSAIAEMVSYFGW 182 (953)
Q Consensus 114 ----------~v~aiiGp~~S~~a~av~~v~~~~~vP~Is~~at~~~ls~-~~~p~~fr~~p~d~~~~~ai~~~l~~~~w 182 (953)
+|.+||||.+|..+.++++++++++||+|+++++++.+++ ..|||+||+.|++..++.+++++++++||
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 8999999999999999999999999999999999999976 67899999999999999999999999999
Q ss_pred cEEEEEEecCccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHH
Q 002211 183 GEVIAIFNDDDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQ 262 (953)
Q Consensus 183 ~~vaii~~d~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~ 262 (953)
++|++++.+++||....+.|.+.+++.|++|+..+.++.+ .+..|+..++++++++++|+|++++.+.++..++++++
T Consensus 161 ~~v~~l~~~~~~g~~~~~~~~~~~~~~gi~v~~~~~~~~~--~~~~d~~~~l~~l~~~~~~vvv~~~~~~~~~~~~~~a~ 238 (348)
T cd06350 161 TWVGLVYSDDDYGRSGLSDLEEELEKNGICIAFVEAIPPS--STEEDIKRILKKLKSSTARVIVVFGDEDDALRLFCEAY 238 (348)
T ss_pred eEEEEEEecchhHHHHHHHHHHHHHHCCCcEEEEEEccCC--CcHHHHHHHHHHHHhCCCcEEEEEeCcHHHHHHHHHHH
Confidence 9999999999999999999999999999999999988875 34689999999999999999999999999999999999
Q ss_pred HcCCCCCceEEEEeCcccccccCCCCCchhhhhhccceEEEEEecCCChhhHHHHHHHHhhcCCCCCCCchhhHHhhHHH
Q 002211 263 RLGMMDSGYVWIATTWLSTFIDSKSPLSLKTAKSILGALTLRQHTPDSKRRRDFVSRWNTLSNGSIGLNPYGLYAYDTVW 342 (953)
Q Consensus 263 ~~g~~~~~~~wi~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~F~~~~~~~~~~~~~~~~~~~~~YDAv~ 342 (953)
++|+ ...+ |+.++.+....... ....+.++|++++.++.+.....++|.+.|++ +++++|||+|
T Consensus 239 ~~g~-~~~~-~i~~~~~~~~~~~~----~~~~~~~~g~~~~~~~~~~~~~~~~f~~~~~~----------~~~~~YDav~ 302 (348)
T cd06350 239 KLGM-TGKY-WIISTDWDTSTCLL----LFTLDAFQGVLGFSGHAPRSGEIPGFKDFLRK----------YAYNVYDAVY 302 (348)
T ss_pred HhCC-CCeE-EEEEccccCccccc----cCCcceeeeEEEEEEEeecCCcCCChHHHHHH----------HHHHHHhhee
Confidence 9999 4444 44554443321111 23446789999999988766666667777765 6789999998
Q ss_pred HHHHHHHHHHhcCCcccccCCCccCCCCCCcccCCCccccCchHHHHHHHHhcccCCcceeEEEccCCCCCCccEEEEEe
Q 002211 343 MIARALKLFLDQGNTISFSNDTKLNGLGGGTLNLGALSIFDGGKKFLANILQTNMTGLSGPIHFNQDRSLLHPSYDIINV 422 (953)
Q Consensus 343 ~la~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~f~G~tG~v~Fd~~g~~~~~~y~I~~~ 422 (953)
+ .+.||++|++ ...|.|+++
T Consensus 303 ~-----------------------------------------------------------~v~f~~~gd~-~~~~~i~~~ 322 (348)
T cd06350 303 A-----------------------------------------------------------EVKFDENGDR-LASYDIINW 322 (348)
T ss_pred E-----------------------------------------------------------EEEecCCCCc-ccceeEEEE
Confidence 6 6999999995 778999999
Q ss_pred ec---CCeeeEEEEecCC
Q 002211 423 IE---HGYPQQIGYWSNY 437 (953)
Q Consensus 423 ~~---~~~~~~VG~w~~~ 437 (953)
+. ++.+++||.|++.
T Consensus 323 ~~~~~~~~~~~vg~~~~~ 340 (348)
T cd06350 323 QIFPGGGGFVKVGFWDPQ 340 (348)
T ss_pred EEcCCcEEEEEEEEEcCC
Confidence 75 3445999999874
No 47
>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=2.2e-37 Score=342.88 Aligned_cols=320 Identities=17% Similarity=0.144 Sum_probs=274.1
Q ss_pred EEeEEEecC--CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhc-CcEEEEccCChhhH
Q 002211 51 NVGAIFSFG--TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMET-DTLAIVGPQSAVMA 127 (953)
Q Consensus 51 ~IG~l~~~~--~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~-~v~aiiGp~~S~~a 127 (953)
+||++.|++ +..|....+|+++|+++||++||++ |++|+++++|++++|..+++++++|+++ +|++|+|+.+|+.+
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 TIAVVVPIGKNPNLAEEILRGVAQAQTEINLQGGIN-GKLLKVVIANDGNDPEIAKKVADELVKDPEILGVVGHYSSDAT 79 (332)
T ss_pred CeEEEEecCCChhhHHHHHHHHHHHHHHHHhcCCCC-CCeEEEEEECCCCChHHHHHHHHHHhcccCceEEEcCCCcHHH
Confidence 489999998 6678899999999999999999985 9999999999999999999999999987 99999999999999
Q ss_pred HHHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcC-CcEEEEEEecCc-cccchHHHHHHH
Q 002211 128 HVLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFG-WGEVIAIFNDDD-QGRNGVTALGDK 205 (953)
Q Consensus 128 ~av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~-w~~vaii~~d~~-~g~~~~~~l~~~ 205 (953)
.++++++++.++|+|+++++++.++ ..+||+||+.+++..++.++++++++.+ |++|++|+.|++ ||+...+.+.+.
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 9999999999999999988888887 4679999999999999999999998876 999999998876 999999999999
Q ss_pred HHh-cCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEEeCccccccc
Q 002211 206 LAE-IRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIATTWLSTFID 284 (953)
Q Consensus 206 l~~-~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~ 284 (953)
+++ .|++++....++.. +.++..++.++++.+||+|++.+.......+++++++.|. ...+++++.+... +
T Consensus 159 ~~~~~g~~v~~~~~~~~~----~~~~~~~v~~i~~~~~d~v~~~~~~~~~~~~~~~~~~~~~---~~~i~~~~~~~~~-~ 230 (332)
T cd06344 159 LLERGGGIVVTPCDLSSP----DFNANTAVSQAINNGATVLVLFPDTDTLDKALEVAKANKG---RLTLLGGDSLYTP-D 230 (332)
T ss_pred HHHhcCCeeeeeccCCCC----CCCHHHHHHHHHhcCCCEEEEeCChhHHHHHHHHHHhcCC---CceEEecccccCH-H
Confidence 999 59998876555544 6678899999999999999999998889999999998774 2335555544322 1
Q ss_pred CCCCCchhhhhhccceEEEEEecCCChhhHHHHHHHHhhcCCCCCCCchhhHHhhHHHHHHHHHHHHHhcCCcccccCCC
Q 002211 285 SKSPLSLKTAKSILGALTLRQHTPDSKRRRDFVSRWNTLSNGSIGLNPYGLYAYDTVWMIARALKLFLDQGNTISFSNDT 364 (953)
Q Consensus 285 ~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~F~~~~~~~~~~~~~~~~~~~~~YDAv~~la~Al~~~~~~~~~~~~~~~~ 364 (953)
.. .......+|+++..++.++.+..++|.++|+++++ .+++.++..+||+++++++|++++++.
T Consensus 231 ~~----~~~~~~~~G~~~~~~~~~~~~~~~~f~~~~~~~~~--~~~~~~a~~~Yda~~~l~~A~~~ag~~---------- 294 (332)
T cd06344 231 TL----LDGGKDLEGLVLAVPWHPLASPNSPFAKLAQQLWG--GDVSWRTATAYDATKALIAALSQGPTR---------- 294 (332)
T ss_pred HH----HhchhhhcCeEEEEecccccccchHHHHHHHHHhc--CCchHHHHhHHHHHHHHHHHHHhCCCh----------
Confidence 11 12235678999988888877888999999999997 578899999999999999999986321
Q ss_pred ccCCCCCCcccCCCccccCchHHHH-HHHHhcccCCcceeEEEccCCCCCCc
Q 002211 365 KLNGLGGGTLNLGALSIFDGGKKFL-ANILQTNMTGLSGPIHFNQDRSLLHP 415 (953)
Q Consensus 365 ~~~~~~~~~~~~~~~~~~~~~~~l~-~~l~~~~f~G~tG~v~Fd~~g~~~~~ 415 (953)
++..+. .++++..|+|+.|+++||++|++..+
T Consensus 295 -------------------~~~~~~~~~~~~~~~~g~~g~i~f~~~g~~~~~ 327 (332)
T cd06344 295 -------------------EGVQQVELSLRNFSVQGATGKIKFLPSGDRNGQ 327 (332)
T ss_pred -------------------hhhhhhhhhcccccccCCCceeEeCCCCcccCc
Confidence 244455 67888889999999999999997544
No 48
>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=1.2e-36 Score=336.12 Aligned_cols=333 Identities=17% Similarity=0.200 Sum_probs=257.6
Q ss_pred EEeEEEecCCCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEEccCChhhHHHH
Q 002211 51 NVGAIFSFGTVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIVGPQSAVMAHVL 130 (953)
Q Consensus 51 ~IG~l~~~~~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aiiGp~~S~~a~av 130 (953)
+||++|+.++.. ....-++.+|++++|+++|+ .|+.++++.+|+.+||.+|+.++|+|++++|.|||||.+|..+.++
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 599999987543 34456667777888998887 4788899999999999999999999999999999999999999999
Q ss_pred HHhhhhCCCcEEEeecCC---CC-----CCC-CCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecCccccchHHH
Q 002211 131 SHLANELQVPLLSFTALD---PT-----LSP-LQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDDDQGRNGVTA 201 (953)
Q Consensus 131 ~~v~~~~~vP~Is~~at~---~~-----ls~-~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~~~g~~~~~~ 201 (953)
+++++..+||+|++.+.. |. +.+ ...+|.|++.|++ .+..+++++++++||++|+++|++++ |....+.
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 999999999999975321 11 111 1224555555664 68899999999999999999998776 5555677
Q ss_pred HHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHh-------cCCceEEEEEcchhhHHHHHHHHHHcCCCCCceEEE
Q 002211 202 LGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVR-------MMEARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWI 274 (953)
Q Consensus 202 l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~-------~~~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi 274 (953)
+.+++++.|+.+.... ...+ ....+...++.++ ..+.++||++|.++.+..++++|.++||+..+|+||
T Consensus 157 ~~~~~~~~g~~v~~~~-~~~~---~~~~~~~l~~~~~~~~l~~~~~~~~~vIl~~~~~~~~~~l~~a~~~gm~~~~~~wi 232 (363)
T cd06381 157 FLDQLSRQGIDVLLQK-VDLN---ISKMATALFTTMRCEELNRYRDTLRRALLLLSPNGAYTFIDASVETNLAIKDSHWF 232 (363)
T ss_pred HHHHHHhcCceEEEEe-cccc---cchhhhhhhhHHHHHHHHhhcccceEEEEEcCcHHHHHHHHHHHHcCCCcCceEEE
Confidence 8888999998766432 2222 1223344443332 345568999999999999999999999999999999
Q ss_pred EeCcccccccCCCCCchhhhhhccceEEEEEecCCChhhH----HHHHHHHhhcCCC----CCCCchhhHHhhHHHHHHH
Q 002211 275 ATTWLSTFIDSKSPLSLKTAKSILGALTLRQHTPDSKRRR----DFVSRWNTLSNGS----IGLNPYGLYAYDTVWMIAR 346 (953)
Q Consensus 275 ~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~----~F~~~~~~~~~~~----~~~~~~~~~~YDAv~~la~ 346 (953)
+++.+....... ........|+++++...+..+..+ +|.+.|+...... ..+...++++|||||++
T Consensus 233 ~~~~l~~~~~~l----~~~~~~~~nitgfrl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~al~yDaV~~~-- 306 (363)
T cd06381 233 LINEEISDTEID----ELVRYAHGRMTVIRQTFSKEKTNQRCLRNNHRISSLLCDPKDGYLQMLEISNLYIYDSVLLL-- 306 (363)
T ss_pred Eeccccccchhh----HHHhhcCccEEEEEEecCCcCchHHHHHHHHHHHHhhcCCCCCCCCChhHHHHHHHHHHHHH--
Confidence 887766532211 456678899999999988777766 5556675433211 23456799999999998
Q ss_pred HHHHHHhcCCcccccCCCccCCCCCCcccCCCccccCchHHHHHHHHhcccCCcceeEEEccCCCCCCccEEEEEeecCC
Q 002211 347 ALKLFLDQGNTISFSNDTKLNGLGGGTLNLGALSIFDGGKKFLANILQTNMTGLSGPIHFNQDRSLLHPSYDIINVIEHG 426 (953)
Q Consensus 347 Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~f~G~tG~v~Fd~~g~~~~~~y~I~~~~~~~ 426 (953)
+++|++++|+|+||+|+||++|.|.+..++|+++.-++
T Consensus 307 ------------------------------------------~~~~~~~~~~GLTG~i~F~~~g~r~~~~l~i~~~~~~~ 344 (363)
T cd06381 307 ------------------------------------------LETIKKGPITGLTGKLEFNEGGDNSNVQFEILGTGYSE 344 (363)
T ss_pred ------------------------------------------HHHHHhcCccCcceeEEeCCCCCccccEEEEEEeccCC
Confidence 34578889999999999999999999999999999554
Q ss_pred -----eeeEEEEecCCCCc
Q 002211 427 -----YPQQIGYWSNYSGL 440 (953)
Q Consensus 427 -----~~~~VG~w~~~~gl 440 (953)
. +.||+|++..||
T Consensus 345 ~~~~~~-~~~~~w~~~~~~ 362 (363)
T cd06381 345 TLGKDG-RWLATWNPSKGL 362 (363)
T ss_pred ccccce-EEeeeccCCCCC
Confidence 6 889999998875
No 49
>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=2.1e-36 Score=337.78 Aligned_cols=330 Identities=13% Similarity=0.106 Sum_probs=270.8
Q ss_pred EEEeEEEecC---CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhc-CcEEEEccCChh
Q 002211 50 LNVGAIFSFG---TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMET-DTLAIVGPQSAV 125 (953)
Q Consensus 50 i~IG~l~~~~---~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~-~v~aiiGp~~S~ 125 (953)
|+||++.|++ +..|...++|+++|+++||++||++ |++|+++++|++++|.+|+.++++|+++ +|.+|+||.+|.
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 4668889999999999999999997 8999999999999999999999999975 899999999999
Q ss_pred hHHHHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHH-cCCcEEEEEEecCccccchHHHHHH
Q 002211 126 MAHVLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSY-FGWGEVIAIFNDDDQGRNGVTALGD 204 (953)
Q Consensus 126 ~a~av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~-~~w~~vaii~~d~~~g~~~~~~l~~ 204 (953)
.+.++.+++++.++|++++.... .....||+||+.+++..++.++++++.. .|.++|++++.|++||++..+.+++
T Consensus 80 ~~~a~~~~~~~~~~~~i~~~~~~---~~~~~~~~F~~~~~~~~~~~~~~~~~~~~~g~k~v~~l~~d~~~g~~~~~~~~~ 156 (359)
T TIGR03407 80 SRKAVLPVFEENNGLLFYPVQYE---GEECSPNIFYTGAAPNQQIIPAVDYLLSKKGAKRFFLLGSDYVFPRTANKIIKA 156 (359)
T ss_pred HHHHHHHHHhccCCceEeCCccc---CcccCCCEEEcCCChHHHHHHHHHHHHhccCCceEEEecCccHHHHHHHHHHHH
Confidence 99999999999999999764221 1245689999999999999999998776 5999999999999999999999999
Q ss_pred HHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEEeCccccccc
Q 002211 205 KLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIATTWLSTFID 284 (953)
Q Consensus 205 ~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~ 284 (953)
.+++.|++|+....++.+ ..|+++++++|++.+||+|++.....+...++++++++|+..+...++.+......+.
T Consensus 157 ~~~~~G~~vv~~~~~~~~----~~D~s~~v~~l~~~~pDav~~~~~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~~~~ 232 (359)
T TIGR03407 157 YLKSLGGTVVGEDYTPLG----HTDFQTIINKIKAFKPDVVFNTLNGDSNVAFFKQLKNAGITAKDVPVVSFSVAEEEIR 232 (359)
T ss_pred HHHHcCCEEEeeEEecCC----hHhHHHHHHHHHHhCCCEEEEeccCCCHHHHHHHHHHcCCCccCCcEEEeecCHHHHh
Confidence 999999999998889887 8999999999999999999988888888899999999998644333444332211111
Q ss_pred CCCCCchhhhhhccceEEEEEe--cCCChhhHHHHHHHHhhcCCCCCCCchhhHHhhHHHHHHHHHHHHHhcCCcccccC
Q 002211 285 SKSPLSLKTAKSILGALTLRQH--TPDSKRRRDFVSRWNTLSNGSIGLNPYGLYAYDTVWMIARALKLFLDQGNTISFSN 362 (953)
Q Consensus 285 ~~~~~~~~~~~~~~g~~~~~~~--~~~~~~~~~F~~~~~~~~~~~~~~~~~~~~~YDAv~~la~Al~~~~~~~~~~~~~~ 362 (953)
....+.++|+++...+ ..+.+..++|.++|+++++....+..+++.+||+++++++|++++++.
T Consensus 233 ------~~g~~~~~G~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~y~a~~~~~~A~~~ag~~-------- 298 (359)
T TIGR03407 233 ------GIGPENLVGHLAAWNYFQSVDTPANKKFVKAFKAKYGDDRVTNDPMEAAYLGVYLWKAAVEKAGSF-------- 298 (359)
T ss_pred ------hcChHhhCCeEEeccchhcCCCHHHHHHHHHHHHHcCCCCCCCcHHHHHHHHHHHHHHHHHHhCCC--------
Confidence 1112456887654333 345688899999999998633334556678999999999999997321
Q ss_pred CCccCCCCCCcccCCCccccCchHHHHHHHHhcccCCcceeEEEccCCCCCCccEEEEEe
Q 002211 363 DTKLNGLGGGTLNLGALSIFDGGKKFLANILQTNMTGLSGPIHFNQDRSLLHPSYDIINV 422 (953)
Q Consensus 363 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~f~G~tG~v~Fd~~g~~~~~~y~I~~~ 422 (953)
+++.++++|++++|+++.|+++|+++++.....+.+.++
T Consensus 299 ---------------------~~~~i~~al~~~~~~~~~G~i~f~~~~~~~~~~~~~~~~ 337 (359)
T TIGR03407 299 ---------------------DVDAVRDAAIGIEFDAPEGKVKVDGKNHHLTKTVRIGEI 337 (359)
T ss_pred ---------------------CHHHHHHHhcCCcccCCCccEEEeCCCCeeeeeeEEEEE
Confidence 488999999999999999999999733323334444444
No 50
>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=4.9e-37 Score=341.87 Aligned_cols=324 Identities=18% Similarity=0.257 Sum_probs=278.5
Q ss_pred EEeEEEecC---CCchhHHHHHHHHHHHHHhcCCCC--CCCcEEEEEEecCCCChHHHHHHHHHHHhc-CcEEEEccCCh
Q 002211 51 NVGAIFSFG---TVNGQVSRIAMKAAQDDINSDPRV--LGGRKLSITMHDAKFNGFLSIMGALQFMET-DTLAIVGPQSA 124 (953)
Q Consensus 51 ~IG~l~~~~---~~~g~~~~~a~~lAve~iN~~g~i--l~g~~l~l~~~D~~~~~~~a~~~a~~li~~-~v~aiiGp~~S 124 (953)
+||++.|++ +..|.....|+++|+++||++||+ ++|++|+++++|++++|..+++++++|+++ +|.+|+||.+|
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 466889999999999999999973 469999999999999999999999999988 99999999999
Q ss_pred hhHHHHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHc------CCcEEEEEEecCccccch
Q 002211 125 VMAHVLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYF------GWGEVIAIFNDDDQGRNG 198 (953)
Q Consensus 125 ~~a~av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~------~w~~vaii~~d~~~g~~~ 198 (953)
..+.++++++++.++|+|+++++++.++...+||+||+.|++..++.++++++.++ +|+++++|+.|++||...
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 99999999999999999999988888887778999999999999999999998876 469999999999999999
Q ss_pred HHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEEeCc
Q 002211 199 VTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIATTW 278 (953)
Q Consensus 199 ~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~ 278 (953)
.+.+++.+++.|++|+..+.++.+ +.|++.++.+++++++|+|++.+...++..+++++++.|+..+ .++...++
T Consensus 161 ~~~~~~~~~~~G~~vv~~~~~~~~----~~d~~~~i~~l~~~~~d~v~~~~~~~~~~~~~~~~~~~G~~~~-~~~~~~~~ 235 (347)
T cd06340 161 AEAIKKFAKERGFEIVEDISYPAN----ARDLTSEVLKLKAANPDAILPASYTNDAILLVRTMKEQRVEPK-AVYSVGGG 235 (347)
T ss_pred HHHHHHHHHHcCCEEEEeeccCCC----CcchHHHHHHHHhcCCCEEEEcccchhHHHHHHHHHHcCCCCc-EEEecCCC
Confidence 999999999999999998888876 7899999999999999999999999999999999999998643 22222222
Q ss_pred ccccccCCCCCchhhhhhccceEEEEEecCC-ChhhHHHHHHHHhhcCCCCCCCchhhHHhhHHHHHHHHHHHHHhcCCc
Q 002211 279 LSTFIDSKSPLSLKTAKSILGALTLRQHTPD-SKRRRDFVSRWNTLSNGSIGLNPYGLYAYDTVWMIARALKLFLDQGNT 357 (953)
Q Consensus 279 ~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~-~~~~~~F~~~~~~~~~~~~~~~~~~~~~YDAv~~la~Al~~~~~~~~~ 357 (953)
..... .. ....+..+|++...++.+. .+..++|.++|+++|+ ..++.++..+||+++++++|++++.+.
T Consensus 236 ~~~~~-~~----~~~g~~~~g~~~~~~~~~~~~~~~~~f~~~y~~~~~--~~~~~~~~~~Y~a~~~l~~A~~~ag~~--- 305 (347)
T cd06340 236 AEDPS-FV----KALGKDAEGILTRNEWSDPKDPMAKDLNKRFKARFG--VDLSGNSARAYTAVLVIADALERAGSA--- 305 (347)
T ss_pred cCcHH-HH----HHhhHhhheEEeccccCCCCChHHHHHHHHHHHHhC--CCCChHHHHHHHHHHHHHHHHHHhcCC---
Confidence 22111 10 2344667899888776654 6788999999999987 558899999999999999999997422
Q ss_pred ccccCCCccCCCCCCcccCCCccccCchHHHH--HHHHhcccC---CcceeEEEccCCCCCCc
Q 002211 358 ISFSNDTKLNGLGGGTLNLGALSIFDGGKKFL--ANILQTNMT---GLSGPIHFNQDRSLLHP 415 (953)
Q Consensus 358 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~--~~l~~~~f~---G~tG~v~Fd~~g~~~~~ 415 (953)
+++.+. .+|++..+. ++.|+++||++|+..++
T Consensus 306 --------------------------~~~~v~~~~~~~~~~~~~~~~~~g~~~f~~~g~~~~~ 342 (347)
T cd06340 306 --------------------------DPEKIRDLAALASTSGEDLIMPYGPIKFDAKGQNTNA 342 (347)
T ss_pred --------------------------CHHHHHHHHHhccCCccccccCCCCeeECCCCCcccc
Confidence 477888 488877765 56899999999986444
No 51
>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=8.6e-37 Score=339.41 Aligned_cols=316 Identities=18% Similarity=0.192 Sum_probs=276.4
Q ss_pred EEeEEEecC---CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEEccCChhhH
Q 002211 51 NVGAIFSFG---TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIVGPQSAVMA 127 (953)
Q Consensus 51 ~IG~l~~~~---~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aiiGp~~S~~a 127 (953)
+||++.|++ +..|...+.|+++|+++||++||+. |++|+++++|++++|.++++.+++|++++|++||||.+|..+
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 599999998 4578999999999999999999996 899999999999999999999999999999999999999999
Q ss_pred HHH-------HHhhhhCCCcEEEeecCCCCCCC-CCCCcEEEccCChHHHHHHHHHHHHHcC-CcEEEEEEecCccccch
Q 002211 128 HVL-------SHLANELQVPLLSFTALDPTLSP-LQYPFFVQTAPNDLYLMSAIAEMVSYFG-WGEVIAIFNDDDQGRNG 198 (953)
Q Consensus 128 ~av-------~~v~~~~~vP~Is~~at~~~ls~-~~~p~~fr~~p~d~~~~~ai~~~l~~~~-w~~vaii~~d~~~g~~~ 198 (953)
.++ +++++++++|+|+++++++.+++ ..+||+||+.|++..++.++++++.+.+ |++|++++.|+.||+..
T Consensus 80 ~~~~~~~~~~~~~~~~~~ip~i~~~~~~~~~~~~~~~~~~fr~~~~~~~~~~~l~~~~~~~~~~k~v~i~~~~~~~g~~~ 159 (342)
T cd06329 80 LALTEAVRKHNQRNPGKEVLYLNYASVAPALTGEKCSFWHFRTDANTDMKMEALASYIKKQPDGKKVYLINQDYSWGQDV 159 (342)
T ss_pred HHhhhhhhhhhhhhccCCeEEEecCCCCchhhhccCcceEEEecCChHHHHHHHHHHHHhcccCceEEEEeCChHHHHHH
Confidence 999 78889999999999888888887 5679999999999999999999998876 99999999999999999
Q ss_pred HHHHHHHHHh--cCcEEEEEEecCCCCCCCh-HHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEE
Q 002211 199 VTALGDKLAE--IRCKISYKSALPPDQSVTE-TDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIA 275 (953)
Q Consensus 199 ~~~l~~~l~~--~g~~v~~~~~~~~~~~~~~-~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~ 275 (953)
.+.+.+.+++ .|++|+....++.+ . +|+.+++.++++.+||+|++...+.++..++++++++|+..+ ++.
T Consensus 160 ~~~~~~~~~~~~~G~~vv~~~~~~~~----~~~d~~~~i~~l~~~~~d~v~~~~~~~~~~~~~~~~~~~g~~~~---~~~ 232 (342)
T cd06329 160 AAAFKAMLAAKRPDIQIVGEDLHPLG----KVKDFSPYVAKIKASGADTVITGNWGNDLLLLVKQAADAGLKLP---FYT 232 (342)
T ss_pred HHHHHHHHHhhcCCcEEeceeccCCC----CCCchHHHHHHHHHcCCCEEEEcccCchHHHHHHHHHHcCCCce---EEe
Confidence 9999999999 99999988888876 6 899999999999999999999988899999999999998543 454
Q ss_pred eCcccccccCCCCCchhhhhhccceEEEEEecC--CChhhHHHHHHHHhhcCCCCCCCchhhHHhhHHHHHHHHHHHHHh
Q 002211 276 TTWLSTFIDSKSPLSLKTAKSILGALTLRQHTP--DSKRRRDFVSRWNTLSNGSIGLNPYGLYAYDTVWMIARALKLFLD 353 (953)
Q Consensus 276 ~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~--~~~~~~~F~~~~~~~~~~~~~~~~~~~~~YDAv~~la~Al~~~~~ 353 (953)
..+.... .. ....+..+|++...++.+ +++..++|.++|+++++ ..|+.++..+||+++++++|+++++.
T Consensus 233 ~~~~~~~--~~----~~~g~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~~--~~~~~~~~~~y~~~~~~~~a~~~ag~ 304 (342)
T cd06329 233 PYLDQPG--NP----AALGEAGLGLVVAVAYWHPNDTPANRAFVEAFKAKYG--RVPDYYEGQAYNGIQMLADAIEKAGS 304 (342)
T ss_pred ccccchh--HH----HhhcccccceEEeeeccCCCCCHHHHHHHHHHHHHhC--CCCCchHHHHHHHHHHHHHHHHHhCC
Confidence 4433222 10 234456788887766543 36788999999999987 57788899999999999999998532
Q ss_pred cCCcccccCCCccCCCCCCcccCCCccccCchHHHHHHHHhcccCCcceeEEEcc-CCC
Q 002211 354 QGNTISFSNDTKLNGLGGGTLNLGALSIFDGGKKFLANILQTNMTGLSGPIHFNQ-DRS 411 (953)
Q Consensus 354 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~f~G~tG~v~Fd~-~g~ 411 (953)
. +++.+.++|++++|+|+.|+++|++ +++
T Consensus 305 ~-----------------------------~~~~v~~al~~~~~~~~~g~~~~~~~~~~ 334 (342)
T cd06329 305 T-----------------------------DPEAVAKALEGMEVDTPVGPVTMRASDHQ 334 (342)
T ss_pred C-----------------------------CHHHHHHHHhCCccccCCCCeEEcccCcc
Confidence 1 4889999999999999999999985 444
No 52
>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=4.5e-36 Score=332.64 Aligned_cols=319 Identities=15% Similarity=0.151 Sum_probs=272.3
Q ss_pred EEeEEEecC---CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhc-CcEEEEccCChhh
Q 002211 51 NVGAIFSFG---TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMET-DTLAIVGPQSAVM 126 (953)
Q Consensus 51 ~IG~l~~~~---~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~-~v~aiiGp~~S~~ 126 (953)
+||+++|++ +..|...+.|+++|+++||++||+. |++|+++++|+++||..+++++++|+++ +|.+|+||.+|..
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 KIGLLFSLSGPAAISEPSLRNAALLAIEEINAAGGIL-GRPLELVVEDPASDPAFAAKAARRLIRDDKVDAVFGCYTSAS 79 (333)
T ss_pred CeEEEecCCCccccccHHHHHHHHHHHHHHHhcCCCC-CeEEEEEEECCCCCHHHHHHHHHHHHhccCCcEEEecccHHH
Confidence 599999998 4568899999999999999999985 8999999999999999999999999988 9999999999999
Q ss_pred HHHHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecCccccchHHHHHHHH
Q 002211 127 AHVLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDDDQGRNGVTALGDKL 206 (953)
Q Consensus 127 a~av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~~~g~~~~~~l~~~l 206 (953)
+.++++++++.++|+|++++.+.. ...||+||+.+++..++.++++++...+|++|++|+.|+.||+...+.+++.+
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 999999999999999987543321 24589999999999999999999877679999999999999999999999999
Q ss_pred HhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEEeCcccccccCC
Q 002211 207 AEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIATTWLSTFIDSK 286 (953)
Q Consensus 207 ~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~~ 286 (953)
++.|++|+....++.+ ..|+++++.++++.++|+|++.+.+.++..+++++++.|+...... +.+...... ...
T Consensus 157 ~~~G~~vv~~~~~~~~----~~d~~~~v~~~~~~~~d~v~~~~~~~~~~~~~~~~~~~g~~~~~~~-~~~~~~~~~-~~~ 230 (333)
T cd06331 157 EELGGEVVGEEYLPLG----TSDFGSVIEKIKAAGPDVVLSTLVGDSNVAFYRQFAAAGLDADRIP-ILSLTLDEN-ELA 230 (333)
T ss_pred HHcCCEEEEEEEecCC----cccHHHHHHHHHHcCCCEEEEecCCCChHHHHHHHHHcCCCcCCCe-eEEcccchh-hhh
Confidence 9999999999999987 7899999999999999999999999999999999999999643333 333322221 111
Q ss_pred CCCchhhhhhccceEEEEEecC--CChhhHHHHHHHHhhcCCCCCCCchhhHHhhHHHHHHHHHHHHHhcCCcccccCCC
Q 002211 287 SPLSLKTAKSILGALTLRQHTP--DSKRRRDFVSRWNTLSNGSIGLNPYGLYAYDTVWMIARALKLFLDQGNTISFSNDT 364 (953)
Q Consensus 287 ~~~~~~~~~~~~g~~~~~~~~~--~~~~~~~F~~~~~~~~~~~~~~~~~~~~~YDAv~~la~Al~~~~~~~~~~~~~~~~ 364 (953)
.......+|++...++.+ +.+..++|.++|+++++....++.+++.+||+++++++|++++.+.
T Consensus 231 ----~~~~~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~yda~~~~~~A~~~ag~~---------- 296 (333)
T cd06331 231 ----AIGAEAAEGHYSAASYFQSLDTPENKAFVARYRARYGDDAVINSPAEAAYEAVYLWAAAVEKAGST---------- 296 (333)
T ss_pred ----ccChhhhCCcEeechhhhhcCChhHHHHHHHHHHHcCCCcCCCchhHHHHHHHHHHHHHHHHcCCC----------
Confidence 112345788888776644 4677899999999988643357889999999999999999985321
Q ss_pred ccCCCCCCcccCCCccccCchHHHHHHHHhcccCCcceeEEEccCCCC
Q 002211 365 KLNGLGGGTLNLGALSIFDGGKKFLANILQTNMTGLSGPIHFNQDRSL 412 (953)
Q Consensus 365 ~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~f~G~tG~v~Fd~~g~~ 412 (953)
+++.|.++|++++|+|++|+++|++++++
T Consensus 297 -------------------~~~~l~~al~~~~~~~~~G~i~f~~~~~~ 325 (333)
T cd06331 297 -------------------DPEAVRAALEGVSFDAPQGPVRIDPDNHH 325 (333)
T ss_pred -------------------CHHHHHHHhhcCcccCCCCceEecCCCCc
Confidence 48899999999999999999999987764
No 53
>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=1.6e-35 Score=332.52 Aligned_cols=340 Identities=15% Similarity=0.195 Sum_probs=287.6
Q ss_pred CceEEEeEEEecC---CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhc-CcEEEEccC
Q 002211 47 PEVLNVGAIFSFG---TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMET-DTLAIVGPQ 122 (953)
Q Consensus 47 ~~~i~IG~l~~~~---~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~-~v~aiiGp~ 122 (953)
+++|+||+++|++ +..|.....|+++|++++|+.||++ |++|+++++|+++++..+++.+++|+++ +|.+||||.
T Consensus 4 ~~~i~iG~~~~~sG~~a~~g~~~~~g~~~a~~~~Na~gGi~-G~~i~l~~~D~~~~~~~a~~~a~~li~~~~v~avvG~~ 82 (362)
T cd06343 4 DTEIKIGNTMPLSGPASAYGVIGRTGAAYFFMINNDQGGIN-GRKIELIVEDDGYSPPKTVEQTRKLVESDEVFAMVGGL 82 (362)
T ss_pred CceEEEeeccCCCCchhhhcHHHHHHHHHHHHHHHhcCCcC-CeEEEEEEecCCCChHHHHHHHHHHHhhcCeEEEEecC
Confidence 5789999999998 4568899999999999999999996 8999999999999999999999999985 999999999
Q ss_pred ChhhHHHHHHhhhhCCCcEEEeecCCCCCCC-CCCCcEEEccCChHHHHHHHHHH-HHHcCCcEEEEEEecCccccchHH
Q 002211 123 SAVMAHVLSHLANELQVPLLSFTALDPTLSP-LQYPFFVQTAPNDLYLMSAIAEM-VSYFGWGEVIAIFNDDDQGRNGVT 200 (953)
Q Consensus 123 ~S~~a~av~~v~~~~~vP~Is~~at~~~ls~-~~~p~~fr~~p~d~~~~~ai~~~-l~~~~w~~vaii~~d~~~g~~~~~ 200 (953)
+|..+.++++++++.+||+|++.++++.+++ ..+||+||+.|++..++.+++++ ++++||++|++|+.|++||+...+
T Consensus 83 ~s~~~~~~~~~~~~~~ip~i~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~g~~~v~ii~~~~~~g~~~~~ 162 (362)
T cd06343 83 GTPTNLAVQKYLNEKKVPQLFPASGASKWNDPKPFPWTFGWQPSYQDEARIYAKYLVEEKPNAKIAVLYQNDDFGKDYLK 162 (362)
T ss_pred CcHHHHHhHHHHHhcCCceEecccccHhhhCCCCCCceEecCCChHHHHHHHHHHHHHhCCCceEEEEEeccHHHHHHHH
Confidence 9999999999999999999998888888877 47899999999999999999997 456799999999999999999999
Q ss_pred HHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEEeCccc
Q 002211 201 ALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIATTWLS 280 (953)
Q Consensus 201 ~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~ 280 (953)
.+++.+++.|++++....++.+ .+|+.++++++++.++|+|++.+...++..+++++++.|+... ++.++++.
T Consensus 163 ~~~~~~~~~G~~vv~~~~~~~~----~~d~~~~v~~i~~~~~d~v~~~~~~~~~~~~~~~~~~~g~~~~---~~~~~~~~ 235 (362)
T cd06343 163 GLKDGLGDAGLEIVAETSYEVT----EPDFDSQVAKLKAAGADVVVLATTPKFAAQAIRKAAELGWKPT---FLLSSVSA 235 (362)
T ss_pred HHHHHHHHcCCeEEEEeeecCC----CccHHHHHHHHHhcCCCEEEEEcCcHHHHHHHHHHHHcCCCce---EEEEeccc
Confidence 9999999999999999889877 7899999999999999999999999999999999999998643 55555443
Q ss_pred cccc-CCCCCchhhhhhccceEEEEEec-------CCChhhHHHHHHHHhhcCCCCCCCchhhHHhhHHHHHHHHHHHHH
Q 002211 281 TFID-SKSPLSLKTAKSILGALTLRQHT-------PDSKRRRDFVSRWNTLSNGSIGLNPYGLYAYDTVWMIARALKLFL 352 (953)
Q Consensus 281 ~~~~-~~~~~~~~~~~~~~g~~~~~~~~-------~~~~~~~~F~~~~~~~~~~~~~~~~~~~~~YDAv~~la~Al~~~~ 352 (953)
.... .. ....+..+|++....+. ...+..++|.++|+++++...+++.++..+||++.++++|++++.
T Consensus 236 ~~~~~~~----~~~~~~~~g~~~~~~~~~~~~p~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~y~a~~~~~~a~~~ag 311 (362)
T cd06343 236 SVASVLK----PAGLEAAEGVIAAAYLKDPTDPAWADDPGVKEFIAFYKKYFPEGDPPDTYAVYGYAAAETLVKVLKQAG 311 (362)
T ss_pred ccHHHHH----HhhhHhhCceEEEEEecCCCccccccCHHHHHHHHHHHHhcCCCCCCchhhhHHHHHHHHHHHHHHHhC
Confidence 2211 10 12235678887766542 246778999999999986333588899999999999999999863
Q ss_pred hcCCcccccCCCccCCCCCCcccCCCccccCchHHHHHHHHhccc---CC-cceeEEEccCCCCCCccEEEEEeecCC
Q 002211 353 DQGNTISFSNDTKLNGLGGGTLNLGALSIFDGGKKFLANILQTNM---TG-LSGPIHFNQDRSLLHPSYDIINVIEHG 426 (953)
Q Consensus 353 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~f---~G-~tG~v~Fd~~g~~~~~~y~I~~~~~~~ 426 (953)
.. . +++.|+++|+++++ .+ ..|++.|++++++....+.|.++++++
T Consensus 312 ~~---------------------------~-~~~~v~~aL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~ 361 (362)
T cd06343 312 DD---------------------------L-TRENIMKQAESLKDVLPDLLPGIRINTSPDDHLPIEQMQLMRFEGGR 361 (362)
T ss_pred CC---------------------------C-CHHHHHHHHHhCCCCCccccCccceecCccccccceeEEEEEEecCc
Confidence 11 1 48899999999997 33 345899987655556677788776543
No 54
>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=4.3e-36 Score=332.95 Aligned_cols=320 Identities=17% Similarity=0.151 Sum_probs=275.7
Q ss_pred EEeEEEecCCC----chhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhc-CcEEEEccCChh
Q 002211 51 NVGAIFSFGTV----NGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMET-DTLAIVGPQSAV 125 (953)
Q Consensus 51 ~IG~l~~~~~~----~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~-~v~aiiGp~~S~ 125 (953)
+||+++|++.. .|.....|+++|+++|| ||++ |++|+++++|++++|.++++++++|+++ +|.+||||.+|.
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--GGVL-GRPIELVVADHQNKADVAAAKAREWIDRDGVDMIVGGPNSA 77 (334)
T ss_pred CcccccCCCCcCccccCHHHHHHHHHHHHHhc--CCcc-CeEEEEEEecCCCCchHHHHHHHHHHhhcCceEEECCccHH
Confidence 58999999744 48889999999999999 8885 8999999999999999999999999987 999999999999
Q ss_pred hHHHHHHhhhhCCCcEEEeecCCCCCCC-CCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecCccccchHHHHHH
Q 002211 126 MAHVLSHLANELQVPLLSFTALDPTLSP-LQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDDDQGRNGVTALGD 204 (953)
Q Consensus 126 ~a~av~~v~~~~~vP~Is~~at~~~ls~-~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~~~g~~~~~~l~~ 204 (953)
.+.++++++++.++|+|+++++++.++. ..+||+||+.+++..++.++++++...+++++++++.|++||+...+.+++
T Consensus 78 ~~~a~~~~~~~~~vp~i~~~s~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~v~~i~~~~~~g~~~~~~~~~ 157 (334)
T cd06327 78 VALAVQEVAREKKKIYIVTGAGSDDLTGKDCSPYTFHWAYDTYMLANGTAPALVKAGGKKWFFLTADYAFGHSLERDARK 157 (334)
T ss_pred HHHHHHHHHHHhCceEEecCCCccccccCCCCCceEEccCChHHHHHHHHHHHHHhcCCeEEEEecchHHhHHHHHHHHH
Confidence 9999999999999999999999988887 457999999999999999999998888899999999999999999999999
Q ss_pred HHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEEeCccccccc
Q 002211 205 KLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIATTWLSTFID 284 (953)
Q Consensus 205 ~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~ 284 (953)
.+++.|++|+....++.+ .+|+.+++.++++.+||+|++.+.+.++..+++++++.|+.. +..++..........
T Consensus 158 ~~~~~G~~vv~~~~~~~~----~~d~~~~v~~l~~~~~d~v~~~~~~~~~~~~~~~~~~~g~~~-~~~~~~~~~~~~~~~ 232 (334)
T cd06327 158 VVKANGGKVVGSVRHPLG----TSDFSSYLLQAQASGADVLVLANAGADTVNAIKQAAEFGLTK-GQKLAGLLLFLTDVH 232 (334)
T ss_pred HHHhcCCEEcCcccCCCC----CccHHHHHHHHHhCCCCEEEEeccchhHHHHHHHHHHhCCcc-CCcEEEecccHHHHH
Confidence 999999999998888877 789999999999999999999999999999999999999862 223333322211110
Q ss_pred CCCCCchhhhhhccceEEEEEecC--CChhhHHHHHHHHhhcCCCCCCCchhhHHhhHHHHHHHHHHHHHhcCCcccccC
Q 002211 285 SKSPLSLKTAKSILGALTLRQHTP--DSKRRRDFVSRWNTLSNGSIGLNPYGLYAYDTVWMIARALKLFLDQGNTISFSN 362 (953)
Q Consensus 285 ~~~~~~~~~~~~~~g~~~~~~~~~--~~~~~~~F~~~~~~~~~~~~~~~~~~~~~YDAv~~la~Al~~~~~~~~~~~~~~ 362 (953)
....+..+|++...++.+ +.+..++|.++|+++++ ..|+.++..+||+++++++|++++++.
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 122346789888777643 36788999999999987 558889999999999999999997432
Q ss_pred CCccCCCCCCcccCCCccccCchHHHHHHHHhcc-cCCcceeEEEcc-CCCCCCc
Q 002211 363 DTKLNGLGGGTLNLGALSIFDGGKKFLANILQTN-MTGLSGPIHFNQ-DRSLLHP 415 (953)
Q Consensus 363 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~-f~G~tG~v~Fd~-~g~~~~~ 415 (953)
++++|.++|++++ ++++.|+++|+. +|+...+
T Consensus 297 ---------------------~~~~v~~al~~~~~~~~~~g~~~~~~~~~~~~~~ 330 (334)
T cd06327 297 ---------------------DADKVVAKMKETPIYDLFAGNGYIRACDHQMVHD 330 (334)
T ss_pred ---------------------ChHHHHHhccccceeccCCCCceeeccccchhcc
Confidence 4677999999986 688999999986 6765444
No 55
>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=3.2e-35 Score=326.97 Aligned_cols=329 Identities=18% Similarity=0.230 Sum_probs=277.0
Q ss_pred EEeEEEecC---CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhc-CcEEEEccCChhh
Q 002211 51 NVGAIFSFG---TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMET-DTLAIVGPQSAVM 126 (953)
Q Consensus 51 ~IG~l~~~~---~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~-~v~aiiGp~~S~~ 126 (953)
|||++.|++ +..|.....|+++|++++|++||+ +|++|+++++|++++|..+.+.+++|+++ +|.+|+||.+|+.
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 699999998 556899999999999999999999 59999999999999999999999999987 7999999999999
Q ss_pred HHHHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHH-HHcCCcEEEEEEecCccccchHHHHHHH
Q 002211 127 AHVLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMV-SYFGWGEVIAIFNDDDQGRNGVTALGDK 205 (953)
Q Consensus 127 a~av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l-~~~~w~~vaii~~d~~~g~~~~~~l~~~ 205 (953)
+.++++++++.++|+|+++++++.+++ ..+|+||+.+++..++.++++++ ++++|++|++++.|++||+...+.+++.
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 999999999999999999888887765 36899999999999999999995 6789999999999999999999999999
Q ss_pred HHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEEeCcccccccC
Q 002211 206 LAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIATTWLSTFIDS 285 (953)
Q Consensus 206 l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~ 285 (953)
+++.|++|+....++++ ..|++.++.++++++||+|++.+.+.+...+++++++.|+..+ ++..+........
T Consensus 159 ~~~~g~~v~~~~~~~~~----~~d~~~~v~~l~~~~~d~v~~~~~~~~~~~~~~~~~~~g~~~~---~~~~~~~~~~~~~ 231 (340)
T cd06349 159 AEKLGGQVVAHEEYVPG----EKDFRPTITRLRDANPDAIILISYYNDGAPIARQARAVGLDIP---VVASSSVYSPKFI 231 (340)
T ss_pred HHHcCCEEEEEEEeCCC----CCcHHHHHHHHHhcCCCEEEEccccchHHHHHHHHHHcCCCCc---EEccCCcCCHHHH
Confidence 99999999998888877 7899999999999999999999999999999999999998643 4444332211100
Q ss_pred CCCCchhhhhhccceEEEEEecCC--ChhhHHHHHHHHhhcCCCCCCCchhhHHhhHHHHHHHHHHHHHhcCCcccccCC
Q 002211 286 KSPLSLKTAKSILGALTLRQHTPD--SKRRRDFVSRWNTLSNGSIGLNPYGLYAYDTVWMIARALKLFLDQGNTISFSND 363 (953)
Q Consensus 286 ~~~~~~~~~~~~~g~~~~~~~~~~--~~~~~~F~~~~~~~~~~~~~~~~~~~~~YDAv~~la~Al~~~~~~~~~~~~~~~ 363 (953)
.......+|++...++.+. .+..++|.++|+++|+ ..|+.++..+||+++++++|+++++..
T Consensus 232 -----~~~~~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~~--~~p~~~~~~~y~~~~~~~~a~~~ag~~--------- 295 (340)
T cd06349 232 -----ELGGDAVEGVYTPTAFFPGDPRPEVQSFVSAYEAKYG--AQPDAFAAQAYDAVGILAAAVRRAGTD--------- 295 (340)
T ss_pred -----HHhHHHhCCcEEecccCCCCCCHHHHHHHHHHHHHHC--CCcchhhhhHHHHHHHHHHHHHHhCCC---------
Confidence 1223467898887776553 5778999999998887 567889999999999999999986321
Q ss_pred CccCCCCCCcccCCCccccCchHHHHHH-HHhcccCCcceeEEEccC-CCCCCccEEEEEeecC
Q 002211 364 TKLNGLGGGTLNLGALSIFDGGKKFLAN-ILQTNMTGLSGPIHFNQD-RSLLHPSYDIINVIEH 425 (953)
Q Consensus 364 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~-l~~~~f~G~tG~v~Fd~~-g~~~~~~y~I~~~~~~ 425 (953)
+...+.+. +.+..+.|++|++.|+++ |+ ....|.++.++++
T Consensus 296 --------------------~~~~~~~~~~~~~~~~~~~g~i~~~~~~~~-~~~~~~~~~~~~g 338 (340)
T cd06349 296 --------------------RRAARDGFAKAEDVYSGVTGSTKFDPNTRR-VIKRFVPLVVRNG 338 (340)
T ss_pred --------------------CHHHHHHHHHhccCcccceEeEEECCCCCC-ccCceEEEEEeCC
Confidence 12223333 245568899999999987 65 4457888777654
No 56
>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=6.1e-35 Score=326.07 Aligned_cols=341 Identities=17% Similarity=0.123 Sum_probs=277.0
Q ss_pred EEeEEEecC---CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhc-CcEEEEccCChhh
Q 002211 51 NVGAIFSFG---TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMET-DTLAIVGPQSAVM 126 (953)
Q Consensus 51 ~IG~l~~~~---~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~-~v~aiiGp~~S~~ 126 (953)
+||++.|+| +..|+..+.|+++|+++||++||++ |++|+++++|++++|..++.++++|+++ +|.+|+||.+|..
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 699999998 5679999999999999999999996 8999999999999999999999999975 8999999999999
Q ss_pred HHHHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecCccccchHHHHHHHH
Q 002211 127 AHVLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDDDQGRNGVTALGDKL 206 (953)
Q Consensus 127 a~av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~~~g~~~~~~l~~~l 206 (953)
+.++++++++.++|++++++... + ...|++|++.+++..++.++++++.+.+-+++++|+.|++||++..+.+.+.+
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 99999999999999998654321 1 22378888888888888899999877666899999999999999999999999
Q ss_pred HhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEEeCcccccccCC
Q 002211 207 AEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIATTWLSTFIDSK 286 (953)
Q Consensus 207 ~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~~ 286 (953)
++.|++|+....++.+ ..+.||++++.++++++||+|++.+.+.++..++++++++|+..+. +.+.+...... ...
T Consensus 157 ~~~G~~vv~~~~~~~~--~~~~d~s~~v~~l~~~~pd~V~~~~~~~~~~~~~~~~~~~G~~~~~-~~~~~~~~~~~-~~~ 232 (360)
T cd06357 157 EQRGGEVLGERYLPLG--ASDEDFARIVEEIREAQPDFIFSTLVGQSSYAFYRAYAAAGFDPAR-MPIASLTTSEA-EVA 232 (360)
T ss_pred HHcCCEEEEEEEecCC--CchhhHHHHHHHHHHcCCCEEEEeCCCCChHHHHHHHHHcCCCccC-ceeEEeeccHH-HHh
Confidence 9999999886656644 4488999999999999999999999999999999999999987542 23333322111 110
Q ss_pred CCCchhhhhhccceEEEEEecC--CChhhHHHHHHHHhhcCCCCCCCchhhHHhhHHHHHHHHHHHHHhcCCcccccCCC
Q 002211 287 SPLSLKTAKSILGALTLRQHTP--DSKRRRDFVSRWNTLSNGSIGLNPYGLYAYDTVWMIARALKLFLDQGNTISFSNDT 364 (953)
Q Consensus 287 ~~~~~~~~~~~~g~~~~~~~~~--~~~~~~~F~~~~~~~~~~~~~~~~~~~~~YDAv~~la~Al~~~~~~~~~~~~~~~~ 364 (953)
....+..+|+++..++.+ ++|..++|.++|+++|+....++.+++.+||+++++++|++++++.
T Consensus 233 ----~~~g~~~~g~~~~~~~~~~~~~p~~~~f~~~~~~~~g~~~~~~~~~~~~yda~~~l~~Al~~ag~~---------- 298 (360)
T cd06357 233 ----AMGAEAAAGHITAAPYFSSIDTPANRAFVARYRARFGEDAPVSACAEAAYFQVHLFARALQRAGSD---------- 298 (360)
T ss_pred ----hcchHhhCCcEEecccccccCChhHHHHHHHHHHHcCCCCCCCcHHHHHHHHHHHHHHHHHHcCCC----------
Confidence 122356789888766533 5688999999999999733346778999999999999999986321
Q ss_pred ccCCCCCCcccCCCccccCchHHHHHHHHhcccCCcceeEEEccCCCCCCccEEEEEeecCCeeeEEE
Q 002211 365 KLNGLGGGTLNLGALSIFDGGKKFLANILQTNMTGLSGPIHFNQDRSLLHPSYDIINVIEHGYPQQIG 432 (953)
Q Consensus 365 ~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~f~G~tG~v~Fd~~g~~~~~~y~I~~~~~~~~~~~VG 432 (953)
+++.|+++|++++|+|+.|.+.||..++.......+.++..+|.+..|.
T Consensus 299 -------------------~~~~v~~aL~~~~~~~~~g~~~f~~~~~~~~~~~~~~~~~~~G~~~~~~ 347 (360)
T cd06357 299 -------------------DPEDVLAALLGFSFDAPQGPVRIDPDNNHTYLWPRIARVNADGQFDIVR 347 (360)
T ss_pred -------------------CHHHHHHHhccCcccCCCcceEEeCCCCeeeeeeEEEEEcCCCCEEEEE
Confidence 4788999999999999999999987655344445555663344334444
No 57
>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=3.4e-35 Score=326.60 Aligned_cols=321 Identities=16% Similarity=0.284 Sum_probs=276.3
Q ss_pred EEeEEEecCC---CchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhc-CcEEEEccCChhh
Q 002211 51 NVGAIFSFGT---VNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMET-DTLAIVGPQSAVM 126 (953)
Q Consensus 51 ~IG~l~~~~~---~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~-~v~aiiGp~~S~~ 126 (953)
+||+++|++. ..|.....|+++|+|+||++||+. |++|++++.|++++|.++++.+++|+++ +|++||||.+|..
T Consensus 1 ~iG~~~~~sG~~~~~g~~~~~g~~~a~~~iN~~ggi~-g~~l~~~~~D~~~~~~~~~~~~~~li~~~~v~aiiG~~~s~~ 79 (334)
T cd06347 1 KIGVNLPLTGDVAAYGQSEKNGAKLAVKEINAAGGVL-GKKIELVVEDNKSDKEEAANAATRLIDQDKVVAIIGPVTSGA 79 (334)
T ss_pred CeeEEecCCchhhhcCHhHHHHHHHHHHHHHhcCCCC-CeeEEEEEecCCCChHHHHHHHHHHhcccCeEEEEcCCccHh
Confidence 5999999984 567889999999999999999984 8999999999999999999999999998 9999999999999
Q ss_pred HHHHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHH-HHcCCcEEEEEEecC-ccccchHHHHHH
Q 002211 127 AHVLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMV-SYFGWGEVIAIFNDD-DQGRNGVTALGD 204 (953)
Q Consensus 127 a~av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l-~~~~w~~vaii~~d~-~~g~~~~~~l~~ 204 (953)
+.++++++++.+||+|+++++.+.+++. .+|+||+.+++..++.++++++ ++++|++|++|+.++ +|+....+.+++
T Consensus 80 ~~~v~~~~~~~~ip~i~~~~~~~~~~~~-~~~~fr~~~~~~~~~~~~~~~~~~~~~~~~v~ii~~~~~~~~~~~~~~~~~ 158 (334)
T cd06347 80 TLAAGPIAEDAKVPMITPSATNPKVTQG-KDYVFRVCFIDPFQGTVMAKFATENLKAKKAAVLYDNSSDYSKGLAKAFKE 158 (334)
T ss_pred HHHhHHHHHHCCCeEEcCCCCCCCcccC-CCeEEEeeCCcHHHHHHHHHHHHHhcCCcEEEEEEeCCCchhHHHHHHHHH
Confidence 9999999999999999998888777653 3599999999999999999996 667999999999875 899999999999
Q ss_pred HHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEEeCccccccc
Q 002211 205 KLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIATTWLSTFID 284 (953)
Q Consensus 205 ~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~ 284 (953)
.+++.|++++....++.+ ..|+...++++++.++|+|++.+...+...+++++++.|+.. .|+.++.+.....
T Consensus 159 ~~~~~g~~v~~~~~~~~~----~~d~~~~~~~~~~~~~d~i~~~~~~~~~~~~~~~~~~~g~~~---~i~~~~~~~~~~~ 231 (334)
T cd06347 159 AFKKLGGEIVAEETFNAG----DTDFSAQLTKIKAKNPDVIFLPGYYTEVGLIAKQARELGIKV---PILGGDGWDSPKL 231 (334)
T ss_pred HHHHcCCEEEEEEEecCC----CCcHHHHHHHHHhcCCCEEEEcCchhhHHHHHHHHHHcCCCC---cEEecccccCHHH
Confidence 999999999988888876 678999999999999999999999999999999999999743 4777665543211
Q ss_pred CCCCCchhhhhhccceEEEEEecCC--ChhhHHHHHHHHhhcCCCCCCCchhhHHhhHHHHHHHHHHHHHhcCCcccccC
Q 002211 285 SKSPLSLKTAKSILGALTLRQHTPD--SKRRRDFVSRWNTLSNGSIGLNPYGLYAYDTVWMIARALKLFLDQGNTISFSN 362 (953)
Q Consensus 285 ~~~~~~~~~~~~~~g~~~~~~~~~~--~~~~~~F~~~~~~~~~~~~~~~~~~~~~YDAv~~la~Al~~~~~~~~~~~~~~ 362 (953)
. ....+..+|++...++.+. .+..++|.++|+++++ ..++.++..+||+++++++|+++++..
T Consensus 232 ~-----~~~~~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~~--~~~~~~~~~~yda~~~~~~Al~~ag~~-------- 296 (334)
T cd06347 232 E-----EAGGAAAEGVYFTTHFSADDPTPKAKKFVKAYKAKYG--KEPDAFAALGYDAYYLLADAIERAGST-------- 296 (334)
T ss_pred H-----HHHHHHhCCcEEecccCCCCCCHHHHHHHHHHHHHHC--CCcchhHHHHHHHHHHHHHHHHHhCCC--------
Confidence 1 2234678888877776553 5778999999999886 678889999999999999999985321
Q ss_pred CCccCCCCCCcccCCCccccCchHHHHHHHHhc-ccCCcceeEEEccCCCCCCcc
Q 002211 363 DTKLNGLGGGTLNLGALSIFDGGKKFLANILQT-NMTGLSGPIHFNQDRSLLHPS 416 (953)
Q Consensus 363 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~-~f~G~tG~v~Fd~~g~~~~~~ 416 (953)
+++.+.++|.+. +|+|++|+++|+++|+.....
T Consensus 297 ---------------------~~~~v~~~l~~~~~~~g~~G~v~f~~~g~~~~~~ 330 (334)
T cd06347 297 ---------------------DPEAIRDALAKTKDFDGVTGKITIDENGNPVKSA 330 (334)
T ss_pred ---------------------CHHHHHHHHHhCCCcccceeeeEECCCCCcCCCc
Confidence 378899998865 699999999999999864443
No 58
>cd06336 PBP1_ABC_ligand_binding_like_3 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. This group includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. Members of this group are sequence-similar to members of the family of ABC-type hydrophobic amino acid transporters (HAAT), such as leucine-isoleucine-valine-binding protein (LIVBP); however their ligand specificity has not been determined experimentally.
Probab=100.00 E-value=1.4e-35 Score=330.29 Aligned_cols=325 Identities=17% Similarity=0.180 Sum_probs=275.2
Q ss_pred EEeEEEecC---CCchhHHHHHHHHHHHHHhcCCCCC-CC--cEEEEEEecCCCChHHHHHHHHHHHhc-CcEEEEccCC
Q 002211 51 NVGAIFSFG---TVNGQVSRIAMKAAQDDINSDPRVL-GG--RKLSITMHDAKFNGFLSIMGALQFMET-DTLAIVGPQS 123 (953)
Q Consensus 51 ~IG~l~~~~---~~~g~~~~~a~~lAve~iN~~g~il-~g--~~l~l~~~D~~~~~~~a~~~a~~li~~-~v~aiiGp~~ 123 (953)
+||++.|++ +..|.....|+++|++++|++||++ +| ++|+++++|++++|..+.+.+++|+++ +|.+|+||.+
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 599999998 4568899999999999999999986 45 489999999999999999999999987 9999999999
Q ss_pred hhhHHHHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecCccccchHHHHH
Q 002211 124 AVMAHVLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDDDQGRNGVTALG 203 (953)
Q Consensus 124 S~~a~av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~~~g~~~~~~l~ 203 (953)
|.++.+ ++++++.++|+|+++++++.++...+||+||+.|++..++.++++++.+.+|++|++|+.|++||+...+.++
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 999988 9999999999999999999887656799999999999999999999888999999999999999999999999
Q ss_pred HHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchh-hHHHHHHHHHHcCCCCCceEEEEeCccccc
Q 002211 204 DKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSR-TGLMVFDVAQRLGMMDSGYVWIATTWLSTF 282 (953)
Q Consensus 204 ~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~-~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~ 282 (953)
+.+++.|++|+....++.+ ..|++.++.+++++++|+|++.+... ++..++++++++|+..+ ..++........
T Consensus 160 ~~l~~~G~~vv~~~~~~~~----~~D~s~~i~~i~~~~~d~v~~~~~~~~~~~~~~~~~~~~g~~~~-~~~~~~~~~~~~ 234 (347)
T cd06336 160 AAWEAAGGKVVSEEPYDPG----TTDFSPIVTKLLAEKPDVIFLGGPSPAPAALVIKQARELGFKGG-FLSCTGDKYDEL 234 (347)
T ss_pred HHHHHcCCEEeeecccCCC----CcchHHHHHHHHhcCCCEEEEcCCCchHHHHHHHHHHHcCCCcc-EEeccCCCchHH
Confidence 9999999999998888877 78999999999999999999999998 99999999999998653 222222111111
Q ss_pred ccCCCCCchhhhhhccceEEEEEecC----CChhhHHHHHHHHhhcCCCCCCCchhhHHhhHHHHHHHHHHHHHhcCCcc
Q 002211 283 IDSKSPLSLKTAKSILGALTLRQHTP----DSKRRRDFVSRWNTLSNGSIGLNPYGLYAYDTVWMIARALKLFLDQGNTI 358 (953)
Q Consensus 283 ~~~~~~~~~~~~~~~~g~~~~~~~~~----~~~~~~~F~~~~~~~~~~~~~~~~~~~~~YDAv~~la~Al~~~~~~~~~~ 358 (953)
.. ....+.++|++...++.+ .+|..++|.++|+++++ ..++.++..+||+++++++|+++++..
T Consensus 235 ~~------~~~~~~~~g~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~--~~p~~~~~~~y~~~~~~~~Al~~ag~~---- 302 (347)
T cd06336 235 LV------ATGADFMEGVYFQFPDVDDPALAFPRAKAFVEEYKKRYG--EPPNSEAAVSYDAVYILKAAMEAAGSV---- 302 (347)
T ss_pred HH------HhcHHhhCceEEEeecccccccCCHHHHHHHHHHHHHHC--CCCcHHHHHHHHHHHHHHHHHHhcCCC----
Confidence 10 122356789888877654 47788999999999987 458889999999999999999986422
Q ss_pred cccCCCccCCCCCCcccCCCccccCchHHHHHHHHh--------cccCCcceeEEEccCCCCCCccEE
Q 002211 359 SFSNDTKLNGLGGGTLNLGALSIFDGGKKFLANILQ--------TNMTGLSGPIHFNQDRSLLHPSYD 418 (953)
Q Consensus 359 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~--------~~f~G~tG~v~Fd~~g~~~~~~y~ 418 (953)
++..+.+++.. ..|.++.|.+.||++|+...+.+.
T Consensus 303 -------------------------~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~ 345 (347)
T cd06336 303 -------------------------DDTAAVAALAAMLGVGKPAFGYARWWGKELFGVNGALVGPWPV 345 (347)
T ss_pred -------------------------CcHHHHHHHhhccCCCcCccccccccccccccCCCccccCccc
Confidence 13344444432 568899999999999997666543
No 59
>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=3.6e-35 Score=325.24 Aligned_cols=324 Identities=14% Similarity=0.191 Sum_probs=272.9
Q ss_pred EEeEEEecC---CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhc-CcEEEEccCChhh
Q 002211 51 NVGAIFSFG---TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMET-DTLAIVGPQSAVM 126 (953)
Q Consensus 51 ~IG~l~~~~---~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~-~v~aiiGp~~S~~ 126 (953)
+||+++|++ +..|.....|+++|++++| ||+ .|++|+++++|++++|..+++.+++|+++ +|.+|+||.+|..
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 599999998 4568889999999999998 677 59999999999999999999999999977 9999999999999
Q ss_pred HHHHHHhhhhCCCcEEEeecCCCCCCC-CCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecCccccchHHHHHHH
Q 002211 127 AHVLSHLANELQVPLLSFTALDPTLSP-LQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDDDQGRNGVTALGDK 205 (953)
Q Consensus 127 a~av~~v~~~~~vP~Is~~at~~~ls~-~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~~~g~~~~~~l~~~ 205 (953)
+.++++++++.++|+|+++++++.+.+ ..+||+||+.+++..++.++++++...||++|++++.|++||+...+.+++.
T Consensus 78 ~~a~~~~~~~~~ip~i~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~g~~~vail~~~~~~g~~~~~~~~~~ 157 (333)
T cd06359 78 LLAVVPPVLESGTFYISTNAGPSQLAGKQCSPYFFSTSWQNDQVHEAMGKYAQDKGYKRVFLIAPNYQAGKDALAGFKRT 157 (333)
T ss_pred HHHHHHHHHHcCCeEEecCCCccccccccCCCcEEEeeCChHhhHHHHHHHHHHhCCCeEEEEecCchhhHHHHHHHHHH
Confidence 999999999999999998777666665 4589999999999999999999999999999999999999999999988887
Q ss_pred HHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEEeCcccccccC
Q 002211 206 LAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIATTWLSTFIDS 285 (953)
Q Consensus 206 l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~ 285 (953)
++ .+++....++.+ .+|+.+++.++++++||+|++...+.++..++++++++|+.. ...++.+++.... +.
T Consensus 158 ~~---~~v~~~~~~~~~----~~d~~~~i~~l~~~~pd~v~~~~~~~~~~~~~~~~~~~G~~~-~~~~~~~~~~~~~-~~ 228 (333)
T cd06359 158 FK---GEVVGEVYTKLG----QLDFSAELAQIRAAKPDAVFVFLPGGMGVNFVKQYRQAGLKK-DIPLYSPGFSDEE-DT 228 (333)
T ss_pred hC---ceeeeeecCCCC----CcchHHHHHHHHhCCCCEEEEEccCccHHHHHHHHHHcCccc-CCeeeccCcccCH-HH
Confidence 74 467766666665 789999999999999999999888888999999999999853 3345555443322 11
Q ss_pred CCCCchhhhhhccceEEEEEecC--CChhhHHHHHHHHhhcCCCCCCCchhhHHhhHHHHHHHHHHHHHhcCCcccccCC
Q 002211 286 KSPLSLKTAKSILGALTLRQHTP--DSKRRRDFVSRWNTLSNGSIGLNPYGLYAYDTVWMIARALKLFLDQGNTISFSND 363 (953)
Q Consensus 286 ~~~~~~~~~~~~~g~~~~~~~~~--~~~~~~~F~~~~~~~~~~~~~~~~~~~~~YDAv~~la~Al~~~~~~~~~~~~~~~ 363 (953)
. ....+..+|++...++.+ +++..++|.++|+++++ ..++.++..+||+++++++|+++++..
T Consensus 229 ~----~~~g~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~~--~~~~~~~~~~yda~~~~~~A~~~ag~~--------- 293 (333)
T cd06359 229 L----PAVGDAALGLYNTAQWAPDLDNPANKKFVADFEKKYG--RLPTLYAAQAYDAAQLLDSAVRKVGGN--------- 293 (333)
T ss_pred H----HhcchhhcCeeeccccCCCCCCHHHHHHHHHHHHHhC--CCCcHHHHHHHHHHHHHHHHHHHhcCC---------
Confidence 0 233456789888777765 46889999999999987 578899999999999999999987321
Q ss_pred CccCCCCCCcccCCCccccCchHHHHHHHHhcccCCcceeEEEccCCCCCCccEEEE
Q 002211 364 TKLNGLGGGTLNLGALSIFDGGKKFLANILQTNMTGLSGPIHFNQDRSLLHPSYDII 420 (953)
Q Consensus 364 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~f~G~tG~v~Fd~~g~~~~~~y~I~ 420 (953)
..+++.|.++|++++|+|++|+++|+++|+. ...+.|+
T Consensus 294 ------------------~~~~~~v~~al~~~~~~~~~G~~~~~~~~~~-~~~~~~~ 331 (333)
T cd06359 294 ------------------LSDKDALRAALRAADFKSVRGAFRFGTNHFP-IQDFYLR 331 (333)
T ss_pred ------------------CCCHHHHHHHHhcCccccCccceEECCCCCc-ceeEEEE
Confidence 0147899999999999999999999998874 3334443
No 60
>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=3.3e-35 Score=324.93 Aligned_cols=322 Identities=16% Similarity=0.138 Sum_probs=269.3
Q ss_pred EEeEEEecC---CCchhHHHHHHHHHHHHHh-cCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhc-CcEEEEccCChh
Q 002211 51 NVGAIFSFG---TVNGQVSRIAMKAAQDDIN-SDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMET-DTLAIVGPQSAV 125 (953)
Q Consensus 51 ~IG~l~~~~---~~~g~~~~~a~~lAve~iN-~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~-~v~aiiGp~~S~ 125 (953)
+||++.|++ +..|....+|+++|++++| +.||+ +|++|++++.|++++|..++.++++|+++ +|.+|+||.+|+
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 699999998 4568899999999999995 56777 49999999999999999999999999998 999999999999
Q ss_pred hHHHHHHhhhhCCCcEEEeecCCCCCCC-CCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecCccccchHHHHHH
Q 002211 126 MAHVLSHLANELQVPLLSFTALDPTLSP-LQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDDDQGRNGVTALGD 204 (953)
Q Consensus 126 ~a~av~~v~~~~~vP~Is~~at~~~ls~-~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~~~g~~~~~~l~~ 204 (953)
.+.++.+++++.++|+|+++++++.++. ..++|+||+.+++..++.++++++... +++|++|+.|++||++..+.+++
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 9999999999999999999888898886 346999999998888999988887766 89999999999999999999999
Q ss_pred HHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchh-hHHHHHHHHHHcCCCCCceEEEEeCcccccc
Q 002211 205 KLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSR-TGLMVFDVAQRLGMMDSGYVWIATTWLSTFI 283 (953)
Q Consensus 205 ~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~-~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~ 283 (953)
.+++.|++|+....++++ ..|+.+++.++++++||+|++...+. +...+++++.+.|+... ...........
T Consensus 159 ~~~~~G~~vv~~~~~~~~----~~d~~~~v~~l~~~~pd~V~~~~~~~~~~~~~~~~~~~~g~~~~---~~~~~~~~~~~ 231 (333)
T cd06328 159 ALEKLGAAIVTEEYAPTD----TTDFTPYAQRLLDALKKVLFVIWAGAGGPWPKLQQMGVLGYGIE---ITLAGDILANL 231 (333)
T ss_pred HHHhCCCEEeeeeeCCCC----CcchHHHHHHHHhcCCCEEEEEecCchhHHHHHHHhhhhcCCCe---EEecccccCcc
Confidence 999999999999999887 88999999999999999998876655 67778888888776532 22222221111
Q ss_pred cCCCCCchhhhhhccceEEEEEec-CCChhhHHHHHHHHhhcCCCCCCCchhhHHhhHHHHHHHHHHHHHhcCCcccccC
Q 002211 284 DSKSPLSLKTAKSILGALTLRQHT-PDSKRRRDFVSRWNTLSNGSIGLNPYGLYAYDTVWMIARALKLFLDQGNTISFSN 362 (953)
Q Consensus 284 ~~~~~~~~~~~~~~~g~~~~~~~~-~~~~~~~~F~~~~~~~~~~~~~~~~~~~~~YDAv~~la~Al~~~~~~~~~~~~~~ 362 (953)
.. .......+|+....++. +.+|..+.|.++|+++|+ ..|+.+++.+||++.++++|++++...
T Consensus 232 ~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~y~~~~g--~~p~~~~~~~y~a~~~l~~Ai~~ag~~-------- 296 (333)
T cd06328 232 TM-----YKAGPGMSGASYYYHYFLPKNPVNDWLVEEHKARFG--SPPDLFTAGGMSAAIAVVEALEETGDT-------- 296 (333)
T ss_pred cc-----ccccccccceeeeecCCCCCCHHHHHHHHHHHHHhC--CCcchhhHHHHHHHHHHHHHHHHhCCC--------
Confidence 10 11234456766655554 677888999999999987 668889999999999999999987311
Q ss_pred CCccCCCCCCcccCCCccccCchHHHHHHHHhcccCCcceeEEEcc-CCCCCCccE
Q 002211 363 DTKLNGLGGGTLNLGALSIFDGGKKFLANILQTNMTGLSGPIHFNQ-DRSLLHPSY 417 (953)
Q Consensus 363 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~f~G~tG~v~Fd~-~g~~~~~~y 417 (953)
+++.+.++|++..|+++.|+++|+. +++...+.|
T Consensus 297 ---------------------~~~~v~~aL~~~~~~~~~g~~~f~~~~~~~~~~~~ 331 (333)
T cd06328 297 ---------------------DTEALIAAMEGMSFETPKGTMTFRKEDHQALQPMY 331 (333)
T ss_pred ---------------------CHHHHHHHHhCCeeecCCCceEECcccchhhhccc
Confidence 4889999999999999999999985 555444433
No 61
>cd06378 PBP1_iGluR_NMDA_NR2 N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the NR2 subunit of NMDA receptor family. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the NR2 subunit of NMDA receptor family. The ionotropic N-methyl-d-asparate (NMDA) subtype of glutamate receptor serves critical functions in neuronal development, functioning, and degeneration in the mammalian central nervous system. The functional NMDA receptor is a heterotetramer composed of two NR1 and two NR2 (A, B, C, and D) or of NR3 (A and B) subunits. The receptor controls a cation channel that is highly permeable to monovalent ions and calcium and exhibits voltage-dependent inhibition by magnesium. Dual agonists, glutamate and glycine, are required for efficient activation of the NMDA receptor. Among NMDA receptor subtypes, the NR2B subunit containing receptors appear particularly important for pain perception; thus NR2B-selective antagonists may be useful in
Probab=100.00 E-value=3.5e-35 Score=323.85 Aligned_cols=304 Identities=15% Similarity=0.226 Sum_probs=240.2
Q ss_pred CCCChHHHHHHHHHHHhc-CcEEEE-ccCChh--hHHHHHHhhhhCCCcEEEeecCCC-CCCC-CCCCcEEEccCChHHH
Q 002211 96 AKFNGFLSIMGALQFMET-DTLAIV-GPQSAV--MAHVLSHLANELQVPLLSFTALDP-TLSP-LQYPFFVQTAPNDLYL 169 (953)
Q Consensus 96 ~~~~~~~a~~~a~~li~~-~v~aii-Gp~~S~--~a~av~~v~~~~~vP~Is~~at~~-~ls~-~~~p~~fr~~p~d~~~ 169 (953)
...||...+.+.|+++.+ +|.|+| ||.++. .+..++.++++++||+|+++++++ .+++ ..+|||+|+.|++..|
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 557999999999999977 699866 999997 556788899999999999977665 5666 6799999999999999
Q ss_pred HHHHHHHHHHcCCcEEEEEEecCccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEc
Q 002211 170 MSAIAEMVSYFGWGEVIAIFNDDDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHG 249 (953)
Q Consensus 170 ~~ai~~~l~~~~w~~vaii~~d~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~ 249 (953)
+.|+++++++|+|++|++||++++.+..+.+.+++.+.+.++|+.....++... ....++...+.+++..+++|||++|
T Consensus 123 ~~Ai~~Ii~~f~W~~v~iV~~~~~g~~~~~~~l~~~~~~~~~~~~i~~~~~~~~-~~~~~~~~~l~~lk~~~arViVl~~ 201 (362)
T cd06378 123 AAVMLKIMEEYDWHAFSVVTSRFPGYDDFVSAVRTTVDNSFVGWELQSVLTLDM-SDDDGDARTQRQLKKLESQVILLYC 201 (362)
T ss_pred HHHHHHHHHHCCCeEEEEEEEcCCCHHHHHHHHHHHHhhcccceeEEEEEeecc-CCCcchHHHHHHHHhcCCCEEEEEC
Confidence 999999999999999999999988777788888887777666654443333321 1133478899999999999999999
Q ss_pred chhhHHHHHHHHHHcCCCCCceEEEEeCcccccccCCCCCchhhhhhccceEEEEEecCCChhhHHHHHHHHhhcCCCCC
Q 002211 250 YSRTGLMVFDVAQRLGMMDSGYVWIATTWLSTFIDSKSPLSLKTAKSILGALTLRQHTPDSKRRRDFVSRWNTLSNGSIG 329 (953)
Q Consensus 250 ~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~F~~~~~~~~~~~~~ 329 (953)
+.+.+..++++|+++||++++|+||++++.....+. ...+..+|++++.. ++|+..
T Consensus 202 s~~~a~~if~~A~~~gm~g~~yvWI~t~~~~~~~~~------~~~~~~~G~i~v~~------------~~w~~~------ 257 (362)
T cd06378 202 SKEEAEYIFRAARSAGLTGPGYVWIVPSLVLGNTDL------GPSEFPVGLISVSY------------DGWRYS------ 257 (362)
T ss_pred CHHHHHHHHHHHHHcCCcCCCeEEEecccccCCCcc------ccccCCcceEeecc------------cccccc------
Confidence 999999999999999999999999999987655321 01234467777553 233321
Q ss_pred CCchhhHHhhHHHHHHHHHHHHHhcCCcccccCCCccCCCCCCcccCCC-cc-ccCchHHHHHHHHhcccCCcceeEEEc
Q 002211 330 LNPYGLYAYDTVWMIARALKLFLDQGNTISFSNDTKLNGLGGGTLNLGA-LS-IFDGGKKFLANILQTNMTGLSGPIHFN 407 (953)
Q Consensus 330 ~~~~~~~~YDAv~~la~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~-~~~~~~~l~~~l~~~~f~G~tG~v~Fd 407 (953)
+.+..||||+++|+|++.+...++..+ ....+|.. .. .|..|..|+++|++++|+|+ +++||
T Consensus 258 ---~~a~~~DaV~vva~Al~~l~~~~~~~~-----------~~~~~C~~~~~~~~~~G~~l~~~l~~v~~~G~--~i~F~ 321 (362)
T cd06378 258 ---LRARVRDGVAIIATGASAMLRQHGFIP-----------EAKGSCYGQAEKRDLPPNTLHRYMMNVTWEGR--DLSFT 321 (362)
T ss_pred ---HHHHHHHHHHHHHHHHHHHHhccCCCC-----------CCCCCcCCCCCCCCCchHHHHHHhhcceECCC--ceeEC
Confidence 356789999999999998865433322 11223432 22 37789999999999999996 99999
Q ss_pred cCCCCCCccEEEEEeecC-CeeeEEEEecCCCCccc
Q 002211 408 QDRSLLHPSYDIINVIEH-GYPQQIGYWSNYSGLSV 442 (953)
Q Consensus 408 ~~g~~~~~~y~I~~~~~~-~~~~~VG~w~~~~gl~~ 442 (953)
++|++.++.|+|+|++++ |+ ++||+|++. +|.+
T Consensus 322 ~~G~r~~~~ldIinl~~~~g~-~kVG~W~~~-~L~~ 355 (362)
T cd06378 322 EDGYLVNPKLVVISLNKERVW-EEVGKWENG-SLRL 355 (362)
T ss_pred CCCeEccceEEEEEecCCCCc-eEEEEEcCC-eEEE
Confidence 999999999999999974 77 999999854 3443
No 62
>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=7e-35 Score=325.29 Aligned_cols=320 Identities=16% Similarity=0.144 Sum_probs=272.0
Q ss_pred EEeEEEecCC---CchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhc-CcEEEEccCChhh
Q 002211 51 NVGAIFSFGT---VNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMET-DTLAIVGPQSAVM 126 (953)
Q Consensus 51 ~IG~l~~~~~---~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~-~v~aiiGp~~S~~ 126 (953)
+||++.|++. ..|.....|+++|+++||++||+. |++|+++++|+++++..+++++++|+++ +|.+||||.+|..
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 KIGVITFLSGRAAIFGEPARNGAELAVEEINAAGGIG-GRKIELVVRDEAGKPDEAIREARELVENEGVDMLIGLISSGV 79 (346)
T ss_pred CeeEEeecCCchhhhcHHHHHHHHHHHHHHhhcCCcC-CeEEEEEEecCCCCHHHHHHHHHHHHhccCCcEEEcccchHH
Confidence 6999999984 458889999999999999999985 8999999999999999999999999997 9999999999999
Q ss_pred HHHHHHhhhhCCCcEEEeecCCCCCCC-CCCCcEEEccCChHHHHHHHHHHHHHc--CCcEEEEEEecCccccchHHHHH
Q 002211 127 AHVLSHLANELQVPLLSFTALDPTLSP-LQYPFFVQTAPNDLYLMSAIAEMVSYF--GWGEVIAIFNDDDQGRNGVTALG 203 (953)
Q Consensus 127 a~av~~v~~~~~vP~Is~~at~~~ls~-~~~p~~fr~~p~d~~~~~ai~~~l~~~--~w~~vaii~~d~~~g~~~~~~l~ 203 (953)
+.++++++++.+||+|++.++++.+++ ..+||+||+.|++..+..++++++++. +|++|++++.|++||....+.++
T Consensus 80 ~~~~~~~~~~~~ip~i~~~s~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~v~~l~~~~~~g~~~~~~~~ 159 (346)
T cd06330 80 ALAVAPVAEELKVFFIATDPGTPRLTEEPDNPYVFRTRNSTIMDAVAGALYAAKLDKKAKTWATINPDYAYGQDAWADFK 159 (346)
T ss_pred HHHHHHHHHHcCCeEEEcCCCCcccccCCCCCceEEecCChHHHHHHHHHHHHHhCcCccEEEEECCchHHHHHHHHHHH
Confidence 999999999999999999888888876 578999999999999999999998887 49999999999999999999999
Q ss_pred HHHHhc--CcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEEeCcccc
Q 002211 204 DKLAEI--RCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIATTWLST 281 (953)
Q Consensus 204 ~~l~~~--g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~ 281 (953)
+.+++. |++++....++.+ .+|+..++.+|++.++|+|++.+.+.+...+++++++.|+.. +..|+.+.+...
T Consensus 160 ~~~~~~g~~~~~v~~~~~~~~----~~d~~~~v~~i~~~~~d~ii~~~~~~~~~~~~~~~~~~g~~~-~~~~~~~~~~~~ 234 (346)
T cd06330 160 AALKRLRPDVEVVSEQWPKLG----APDYGSEITALLAAKPDAIFSSLWGGDLVTFVRQANARGLFD-GTTVVLTLTGAP 234 (346)
T ss_pred HHHHHhCCCCeecccccCCCC----CcccHHHHHHHHhcCCCEEEEecccccHHHHHHHHHhcCccc-CceEEeeccchh
Confidence 999998 4666665555544 789999999999999999999999999999999999999864 566777665433
Q ss_pred cccCCCCCchhhhhhccceEEEEEe--cC--CChhhHHHHHHHHhhcCCCCCCCchhhHHhhHHHHHHHHHHHHHhcCCc
Q 002211 282 FIDSKSPLSLKTAKSILGALTLRQH--TP--DSKRRRDFVSRWNTLSNGSIGLNPYGLYAYDTVWMIARALKLFLDQGNT 357 (953)
Q Consensus 282 ~~~~~~~~~~~~~~~~~g~~~~~~~--~~--~~~~~~~F~~~~~~~~~~~~~~~~~~~~~YDAv~~la~Al~~~~~~~~~ 357 (953)
.+. ....+..+|++....+ .. +.+..++|.++|+++++ ..|+.++..+||+++++++|++++......
T Consensus 235 ~~~------~~~~~~~~g~~~~~~~~~~~~~~~~~~~~f~~~~~~~~g--~~p~~~~~~~y~a~~~l~~a~~~a~~~~~~ 306 (346)
T cd06330 235 ELA------PLGDEMPEGVIIGGRGPYFIPPDTPENKAFVDAYQEKYG--DYPTYGAYGAYQAVMALAAAVEKAGATDGG 306 (346)
T ss_pred hhh------hhhcccCCceEEeccccCCCCCCChHHHHHHHHHHHHHC--CCCChHHHHHHHHHHHHHHHHHHhcCCCCC
Confidence 211 1223556777654432 21 47789999999999987 677888999999999999999997543110
Q ss_pred ccccCCCccCCCCCCcccCCCccccCchHHHHHHHHhcccCCcceeEEEccC
Q 002211 358 ISFSNDTKLNGLGGGTLNLGALSIFDGGKKFLANILQTNMTGLSGPIHFNQD 409 (953)
Q Consensus 358 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~f~G~tG~v~Fd~~ 409 (953)
.+ .+.+.++|++++|.|+.|++.|+++
T Consensus 307 ------------------------~~-~~~v~~al~~~~~~~~~G~~~f~~~ 333 (346)
T cd06330 307 ------------------------AP-PEQIAAALEGLSFETPGGPITMRAA 333 (346)
T ss_pred ------------------------Cc-HHHHHHHHcCCCccCCCCceeeecC
Confidence 11 2579999999999999999999874
No 63
>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=2.1e-34 Score=318.70 Aligned_cols=317 Identities=13% Similarity=0.097 Sum_probs=264.4
Q ss_pred EEeEEEecC---CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhc-CcEEEEccCChhh
Q 002211 51 NVGAIFSFG---TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMET-DTLAIVGPQSAVM 126 (953)
Q Consensus 51 ~IG~l~~~~---~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~-~v~aiiGp~~S~~ 126 (953)
+||++.|+| +..|+..+.|+++|+++||++||++ |++|+++++|++++|..++..+++|+++ +|.+|||+.+|.+
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 699999998 5669999999999999999999996 8999999999999999999999999976 8999999999999
Q ss_pred HHHHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecCccccchHHHHHHHH
Q 002211 127 AHVLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDDDQGRNGVTALGDKL 206 (953)
Q Consensus 127 a~av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~~~g~~~~~~l~~~l 206 (953)
+.++.+++++.++|+|+..+... ....||+||+.+++..++.++++++...+-+++++|+.|++||++..+.+.+.+
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 99999999999999998533322 223589999999999999999999877655899999999999999999999999
Q ss_pred HhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHHHcCC-CCCceEEEEeCcccccccC
Q 002211 207 AEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQRLGM-MDSGYVWIATTWLSTFIDS 285 (953)
Q Consensus 207 ~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~~~g~-~~~~~~wi~~~~~~~~~~~ 285 (953)
++.|++++....++.+ ..||+++++++++.+||+|++...+.+...+++++++.|+ ..+ .+...+.......
T Consensus 157 ~~~G~~vv~~~~~~~~----~~d~~~~v~~l~~~~pd~v~~~~~~~~~~~~~~~~~~~G~~~~~---~~~~~~~~~~~~~ 229 (334)
T cd06356 157 EENGGEVVGEEFIPLD----VSDFGSTIQKIQAAKPDFVMSILVGANHLSFYRQWAAAGLGNIP---MASSTLGAQGYEH 229 (334)
T ss_pred HHcCCEEEeeeecCCC----chhHHHHHHHHHhcCCCEEEEeccCCcHHHHHHHHHHcCCccCc---eeeeecccchhHH
Confidence 9999999999999887 8899999999999999999999999899999999999998 222 2222111111100
Q ss_pred CCCCchhhhhhccceEEEEEecC--CChhhHHHHHHHHhhcCCCCCCCchhhHHhhHHHHHHHHHHHHHhcCCcccccCC
Q 002211 286 KSPLSLKTAKSILGALTLRQHTP--DSKRRRDFVSRWNTLSNGSIGLNPYGLYAYDTVWMIARALKLFLDQGNTISFSND 363 (953)
Q Consensus 286 ~~~~~~~~~~~~~g~~~~~~~~~--~~~~~~~F~~~~~~~~~~~~~~~~~~~~~YDAv~~la~Al~~~~~~~~~~~~~~~ 363 (953)
. .......+|++....+.+ ..|..++|.++|+++++....++.+++.+||+++++++|++++++.
T Consensus 230 ~----~~~~~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~p~~~~~~~~~y~a~~~~~~A~~~ag~~--------- 296 (334)
T cd06356 230 K----RLKPPALKDMYATANYIEELDTPANKAFVERFRAKFPDAPYINEEAENNYEAIYLYKEAVEKAGTT--------- 296 (334)
T ss_pred h----ccCchhcCCeEEecchhhhcCCHHHHHHHHHHHHHcCCCCCCCchhHHHHHHHHHHHHHHHHHCCC---------
Confidence 0 011245678877766543 3677899999999999732223678999999999999999997421
Q ss_pred CccCCCCCCcccCCCccccCchHHHHHHHHh-cccCCcceeEEEccCCC
Q 002211 364 TKLNGLGGGTLNLGALSIFDGGKKFLANILQ-TNMTGLSGPIHFNQDRS 411 (953)
Q Consensus 364 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~-~~f~G~tG~v~Fd~~g~ 411 (953)
+++.|.++|++ ..|+|+.|++.|+++++
T Consensus 297 --------------------~~~~v~~aL~~~~~~~~~~g~~~~~~~~h 325 (334)
T cd06356 297 --------------------DRDAVIEALESGLVCDGPEGKVCIDGKTH 325 (334)
T ss_pred --------------------CHHHHHHHHHhCCceeCCCceEEEecCCC
Confidence 48899999997 56899999999997443
No 64
>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=3.1e-34 Score=319.00 Aligned_cols=325 Identities=16% Similarity=0.223 Sum_probs=281.0
Q ss_pred EEeEEEecCCC---chhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhc-CcEEEEccCChhh
Q 002211 51 NVGAIFSFGTV---NGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMET-DTLAIVGPQSAVM 126 (953)
Q Consensus 51 ~IG~l~~~~~~---~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~-~v~aiiGp~~S~~ 126 (953)
+||+++|++.. .|.....|+++|++++| +++ .|++|+++++|++++|..+++++.+|+++ +|.+||||.+|..
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 69999999844 46899999999999986 455 69999999999999999999999999975 8999999999999
Q ss_pred HHHHHHhhhhCCCcEEEeecCCCCCCC-CCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecCccccchHHHHHHH
Q 002211 127 AHVLSHLANELQVPLLSFTALDPTLSP-LQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDDDQGRNGVTALGDK 205 (953)
Q Consensus 127 a~av~~v~~~~~vP~Is~~at~~~ls~-~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~~~g~~~~~~l~~~ 205 (953)
+.++.+++++.++|+|+++++++.+++ ..+||+||+.+++..++..+++++.+.+|+++++++.++.||+...+.+++.
T Consensus 78 ~~~~~~~~~~~~ip~v~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~l~~~~~~~v~~l~~~~~~g~~~~~~~~~~ 157 (336)
T cd06360 78 ALAMVKVLREPGTPLINPNAGADDLTGRLCAPNFFRTSFSNAQWAAPMGKYAADDGYKKVVTVAWDYAFGYEVVEGFKEA 157 (336)
T ss_pred HHHHHHHHHhcCceEEecCCCCccccccCCCCcEEEEeCchHHHHHHHHHHHHHcCCCeEEEEeccchhhHHHHHHHHHH
Confidence 999999999999999999888888887 4489999999999999999999999999999999999999999999999999
Q ss_pred HHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEEeCcccccccC
Q 002211 206 LAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIATTWLSTFIDS 285 (953)
Q Consensus 206 l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~ 285 (953)
+++.|++++....++.+ .+||+++++++++.+||+|++.+.+.++..+++++++.|+.+ +..++.++++.+....
T Consensus 158 ~~~~G~~v~~~~~~~~~----~~d~~~~v~~~~~~~pd~v~~~~~~~~~~~~~~~~~~~g~~~-~~~~~~~~~~~~~~~~ 232 (336)
T cd06360 158 FTEAGGKIVKELWVPFG----TSDFASYLAQIPDDVPDAVFVFFAGGDAIKFVKQYDAAGLKA-KIPLIGSGFLTDGTTL 232 (336)
T ss_pred HHHcCCEEEEEEecCCC----CcchHHHHHHHHhcCCCEEEEecccccHHHHHHHHHHcCCcc-CCeEEecccccCHHHH
Confidence 99999999988888876 789999999999999999999999999999999999999853 3346666554332111
Q ss_pred CCCCchhhhhhccceEEEEEecC--CChhhHHHHHHHHhhcCCCCCCCchhhHHhhHHHHHHHHHHHHHhcCCcccccCC
Q 002211 286 KSPLSLKTAKSILGALTLRQHTP--DSKRRRDFVSRWNTLSNGSIGLNPYGLYAYDTVWMIARALKLFLDQGNTISFSND 363 (953)
Q Consensus 286 ~~~~~~~~~~~~~g~~~~~~~~~--~~~~~~~F~~~~~~~~~~~~~~~~~~~~~YDAv~~la~Al~~~~~~~~~~~~~~~ 363 (953)
....+..+|++...++.+ +.+..++|.++|+++++ ..|+.++..+||+++++++|++++.+..
T Consensus 233 -----~~~g~~~~g~~~~~~~~~~~~~~~~~~f~~~y~~~~~--~~~~~~~~~~yda~~~~~~A~~~a~~~~-------- 297 (336)
T cd06360 233 -----GAAGEAAEGVITALHYADTLDNPANQAFVKAYRAAYP--DTPSVYAVQGYDAGQALILALEAVGGDL-------- 297 (336)
T ss_pred -----HhhHhhhcCceeccccCCCCCCHHHHHHHHHHHHHhC--CCccHHHHHHHHHHHHHHHHHHHhCCCC--------
Confidence 234567889888777654 46889999999999987 5788999999999999999999974220
Q ss_pred CccCCCCCCcccCCCccccCchHHHHHHHHhcccCCcceeEEEccCCCCCCccE
Q 002211 364 TKLNGLGGGTLNLGALSIFDGGKKFLANILQTNMTGLSGPIHFNQDRSLLHPSY 417 (953)
Q Consensus 364 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~f~G~tG~v~Fd~~g~~~~~~y 417 (953)
.+++.|.++|++++|.|+.|+++|+++|++..+.|
T Consensus 298 -------------------~~~~~v~~al~~~~~~~~~g~~~f~~~~~~~~~~~ 332 (336)
T cd06360 298 -------------------SDGQALIAAMAAAKIDSPRGPFTLDKAHNPIQDNY 332 (336)
T ss_pred -------------------CCHHHHHHHHhcCCccCCCcceEECCCCCcccceE
Confidence 13788999999999999999999999998765543
No 65
>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=1.5e-34 Score=322.61 Aligned_cols=335 Identities=21% Similarity=0.300 Sum_probs=281.9
Q ss_pred eEEEeEEEecCC---CchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHh-cCcEEEEccCCh
Q 002211 49 VLNVGAIFSFGT---VNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFME-TDTLAIVGPQSA 124 (953)
Q Consensus 49 ~i~IG~l~~~~~---~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~-~~v~aiiGp~~S 124 (953)
+|+||++.|++. ..|.....|+++|++++|++||++ |++|+++++|+++++..+++.+.+|++ ++|.+|+||.+|
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 589999999984 457889999999999999999996 899999999999999999999999999 699999999999
Q ss_pred hhHHHHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHH-HHcCCcEEEEEEecCccccchHHHHH
Q 002211 125 VMAHVLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMV-SYFGWGEVIAIFNDDDQGRNGVTALG 203 (953)
Q Consensus 125 ~~a~av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l-~~~~w~~vaii~~d~~~g~~~~~~l~ 203 (953)
..+.++++++++.++|+|++++.++ ...+||+||+.|++..++.++++++ +++|.+++++|+.+++||+...+.+.
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 2567999999999999999999985 55899999999999999999999999
Q ss_pred HHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEEeCcccccc
Q 002211 204 DKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIATTWLSTFI 283 (953)
Q Consensus 204 ~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~ 283 (953)
+.+++.|++++....++.+ ..|+...++++++.++|+|++.+.+.+...++++++++|+..+.+....+......+
T Consensus 157 ~~~~~~G~~vv~~~~~~~~----~~d~~~~~~~l~~~~~d~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l 232 (343)
T PF13458_consen 157 KALEAAGGKVVGEIRYPPG----DTDFSALVQQLKSAGPDVVVLAGDPADAAAFLRQLRQLGLKPPRIPLFGTSLDDASL 232 (343)
T ss_dssp HHHHHTTCEEEEEEEE-TT----SSHHHHHHHHHHHTTTSEEEEESTHHHHHHHHHHHHHTTGCSCTEEEEEGGGSSHHH
T ss_pred HHHhhcCceeccceecccc----cccchHHHHHHhhcCCCEEEEeccchhHHHHHHHHHhhccccccceeeccccCcHHH
Confidence 9999999999988889877 789999999999999999999999999999999999999865434444333222221
Q ss_pred cCCCCCchhhhhhccceEEEEEecC--CChhhHHHHHHHHhhcCCCCCCCchhhHHhhHHHHHHHHHHHHHhcCCccccc
Q 002211 284 DSKSPLSLKTAKSILGALTLRQHTP--DSKRRRDFVSRWNTLSNGSIGLNPYGLYAYDTVWMIARALKLFLDQGNTISFS 361 (953)
Q Consensus 284 ~~~~~~~~~~~~~~~g~~~~~~~~~--~~~~~~~F~~~~~~~~~~~~~~~~~~~~~YDAv~~la~Al~~~~~~~~~~~~~ 361 (953)
. ....+..+|++...++.+ +.+..++|.++|+++++....++.++..+||++.++++|++++...
T Consensus 233 ~------~~~~~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~yda~~~~~~al~~~g~~------- 299 (343)
T PF13458_consen 233 Q------QLGGDALEGVYIVSPWFPDPDSPAVKQFQERYRAAYGEEPPPSLYAAQGYDAARLLAQALERAGSL------- 299 (343)
T ss_dssp H------HHHGGGGTTEEEEESGGGTGGSHHHHHHHHHHHHHHSSTGGTCHHHHHHHHHHHHHHHHHHHHTSH-------
T ss_pred H------HhhhhhccCceeecccCCCCCCHHHHHHHHHHHHHcCCCCCCchhHHHHHHHHHHHHHHHHHhCCC-------
Confidence 1 223347889998888765 4678899999999999743348999999999999999999997211
Q ss_pred CCCccCCCCCCcccCCCccccCchHHHHHHHHhcccCCcceeEEEccCCCCCCccEEEEEeecCC
Q 002211 362 NDTKLNGLGGGTLNLGALSIFDGGKKFLANILQTNMTGLSGPIHFNQDRSLLHPSYDIINVIEHG 426 (953)
Q Consensus 362 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~f~G~tG~v~Fd~~g~~~~~~y~I~~~~~~~ 426 (953)
+++.+.++|++++|+|+.|++.|++.++.....+.|++++.+|
T Consensus 300 ----------------------~~~~v~~al~~~~~~g~~g~~~~~~~~~~~~~~~~i~~v~~~G 342 (343)
T PF13458_consen 300 ----------------------DREAVREALESLKYDGLFGPISFDPPDHQANKPVYIVQVKSDG 342 (343)
T ss_dssp ----------------------HHHHHHHHHHTSEEEETTEEEEEETTTSBEEEEEEEEEEETTT
T ss_pred ----------------------CHHHHHHHHHhCCCcccccceEEeCCCCccccCeEEEEEecCC
Confidence 5899999999999999999999976555568888999988444
No 66
>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=2.6e-34 Score=318.42 Aligned_cols=318 Identities=15% Similarity=0.165 Sum_probs=267.4
Q ss_pred EEeEEEecC---CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhc-CcEEEEccCChhh
Q 002211 51 NVGAIFSFG---TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMET-DTLAIVGPQSAVM 126 (953)
Q Consensus 51 ~IG~l~~~~---~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~-~v~aiiGp~~S~~ 126 (953)
|||++.|+| +..|.....|+++|+++||+.||+. |++|+++++|++++|..++..+++|+++ +|.+||||.+|.+
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 699999998 4478999999999999999999995 8999999999999999999999999987 8999999999999
Q ss_pred HHHHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHH-HHcCCcEEEEEEecCccccchHHHHHHH
Q 002211 127 AHVLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMV-SYFGWGEVIAIFNDDDQGRNGVTALGDK 205 (953)
Q Consensus 127 a~av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l-~~~~w~~vaii~~d~~~g~~~~~~l~~~ 205 (953)
+.++.++++ .+||+|++.+.+.. ...||+||+.+++..++.++++++ +..||++|++++.|++||+...+.+++.
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 346899999999999988888875 5579999999999999999999999999
Q ss_pred HHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEE-eCccccccc
Q 002211 206 LAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIA-TTWLSTFID 284 (953)
Q Consensus 206 l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~-~~~~~~~~~ 284 (953)
+++.|++|+....++.+ ..|+++++.++++.+||+|++.+...+...+++++++.|+..+ ++. ...+.....
T Consensus 156 ~~~~G~~v~~~~~~~~~----~~d~~~~v~~l~~~~pd~v~~~~~~~~~~~~~~~~~~~G~~~~---~~~~~~~~~~~~~ 228 (333)
T cd06358 156 IAELGGEVVGEEYVPLG----TTDFTSVLERIAASGADAVLSTLVGQDAVAFNRQFAAAGLRDR---ILRLSPLMDENML 228 (333)
T ss_pred HHHcCCEEeeeeeecCC----hHHHHHHHHHHHHcCCCEEEEeCCCCchHHHHHHHHHcCCCcc---CceeecccCHHHH
Confidence 99999999998889877 8999999999999999999999999899999999999999754 222 222221110
Q ss_pred CCCCCchhhhhhccceEEEEEecC--CChhhHHHHHHHHhhcCCC-CCCCchhhHHhhHHHHHHHHHHHHHhcCCccccc
Q 002211 285 SKSPLSLKTAKSILGALTLRQHTP--DSKRRRDFVSRWNTLSNGS-IGLNPYGLYAYDTVWMIARALKLFLDQGNTISFS 361 (953)
Q Consensus 285 ~~~~~~~~~~~~~~g~~~~~~~~~--~~~~~~~F~~~~~~~~~~~-~~~~~~~~~~YDAv~~la~Al~~~~~~~~~~~~~ 361 (953)
. .......+|++....+.+ ..+..++|.++|+++|+.. ..++.++..+||+++++++|+++++..
T Consensus 229 ~-----~~~~~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~g~~~~~~~~~~~~~yda~~~~~~A~~~ag~~------- 296 (333)
T cd06358 229 L-----ASGAEAAEGLYSSSGYFASLQTPANAAFLARYRARFGDDAPPLNSLSESCYEAVHALAAAAERAGSL------- 296 (333)
T ss_pred H-----hcChHhhCCcEEeccchhhcCCHHHHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHHHHHHHhCCC-------
Confidence 0 112245688877665533 5688999999999998732 246778899999999999999975321
Q ss_pred CCCccCCCCCCcccCCCccccCchHHHHHHHHhcccCCcceeEEEccCCCCCCc
Q 002211 362 NDTKLNGLGGGTLNLGALSIFDGGKKFLANILQTNMTGLSGPIHFNQDRSLLHP 415 (953)
Q Consensus 362 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~f~G~tG~v~Fd~~g~~~~~ 415 (953)
++++|.++|++++|+|++|++.|++++. ..+
T Consensus 297 ----------------------~~~~v~~al~~~~~~~~~G~~~~~~~~~-~~~ 327 (333)
T cd06358 297 ----------------------DPEALIAALEDVSYDGPRGTVTMRGRHA-RQP 327 (333)
T ss_pred ----------------------CHHHHHHHhccCeeeCCCcceEEccccc-ccc
Confidence 4789999999999999999999998764 444
No 67
>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=2.6e-34 Score=318.79 Aligned_cols=328 Identities=14% Similarity=0.172 Sum_probs=269.5
Q ss_pred EEeEEEecC---CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhc-CcEEEEccCChhh
Q 002211 51 NVGAIFSFG---TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMET-DTLAIVGPQSAVM 126 (953)
Q Consensus 51 ~IG~l~~~~---~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~-~v~aiiGp~~S~~ 126 (953)
|||++.|+| +..|.....|+++|+++||+.|||+ |++|+++++|++++|..++..+++|+++ +|.+|+ +.+|+.
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 689999998 5678999999999999999999995 8999999999999999999999999988 677765 688999
Q ss_pred HHHHHHhhhhCCCcEEEeecCCCCCCC-CCCCcEEEccCChHHHHHHHHHHHHHcC-----CcEEEEEEecCccccchHH
Q 002211 127 AHVLSHLANELQVPLLSFTALDPTLSP-LQYPFFVQTAPNDLYLMSAIAEMVSYFG-----WGEVIAIFNDDDQGRNGVT 200 (953)
Q Consensus 127 a~av~~v~~~~~vP~Is~~at~~~ls~-~~~p~~fr~~p~d~~~~~ai~~~l~~~~-----w~~vaii~~d~~~g~~~~~ 200 (953)
+.++++++++.+||+|+++++++.+++ ..+||+||+.|++..++.++++++.+.+ .++|++|+.|++||+...+
T Consensus 79 ~~a~~~~~~~~~vp~i~~~~~~~~~~~~~~~~~~Fr~~~~~~~~~~~l~~~~~~~~~~~~~~~kvaiv~~~~~~g~~~~~ 158 (351)
T cd06334 79 TEALIPKIAADKIPLMSGSYGATLADDGAVFPYNFPVGPTYSDQARALVQYIAEQEGGKLKGKKIALVYHDSPFGKEPIE 158 (351)
T ss_pred HHHhhHHHhhcCCcEEecccchhhccCCCCCCeeeeCCCCHHHHHHHHHHHHHHhcccCCCCCeEEEEeCCCccchhhHH
Confidence 999999999999999998877777764 6689999999999999999999987654 7999999999999999999
Q ss_pred HHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEEeCccc
Q 002211 201 ALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIATTWLS 280 (953)
Q Consensus 201 ~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~ 280 (953)
.+++.+++.|++|+....++.+ .+|+++++.++++.+||+|++.+.+.++..++++++++|+.. .++.+++..
T Consensus 159 ~~~~~~~~~G~~vv~~~~~~~~----~~D~~~~v~~i~~~~pd~V~~~~~~~~~~~~~~~~~~~G~~~---~~~~~~~~~ 231 (351)
T cd06334 159 ALKALAEKLGFEVVLEPVPPPG----PNDQKAQWLQIRRSGPDYVILWGWGVMNPVAIKEAKRVGLDD---KFIGNWWSG 231 (351)
T ss_pred HHHHHHHHcCCeeeeeccCCCC----cccHHHHHHHHHHcCCCEEEEecccchHHHHHHHHHHcCCCc---eEEEeeccC
Confidence 9999999999999999888877 789999999999999999999999999999999999999843 255444322
Q ss_pred ccccCCCCCchhhhhhccceEEEEEecC--CChhhHHHHHHHHhhcCCCC----CCCchhhHHhhHHHHHHHHHHHHHhc
Q 002211 281 TFIDSKSPLSLKTAKSILGALTLRQHTP--DSKRRRDFVSRWNTLSNGSI----GLNPYGLYAYDTVWMIARALKLFLDQ 354 (953)
Q Consensus 281 ~~~~~~~~~~~~~~~~~~g~~~~~~~~~--~~~~~~~F~~~~~~~~~~~~----~~~~~~~~~YDAv~~la~Al~~~~~~ 354 (953)
.. ... ....+..+|+++..++.+ ++|..++|.+.|+++++... .++.++..+||+++++++|++++++.
T Consensus 232 ~~-~~~----~~~g~~~~g~~~~~~~~~~~~~p~~~~f~~~~~~~~~~~~~~~~~~~~~~~~gy~a~~~l~~Al~~ag~~ 306 (351)
T cd06334 232 DE-EDV----KPAGDAAKGYKGVTPFAGGADDPVGKEIVKEVYDKGKGSGNDKEIGSVYYNRGVVNAMIMVEAIRRAQEK 306 (351)
T ss_pred cH-HHH----HHhhhhhcCcEEeecccCCCCchHHHHHHHHHHHccCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHh
Confidence 21 110 234466789888776654 67889999999999986221 34678999999999999999999876
Q ss_pred CCcccccCCCccCCCCCCcccCCCccccCchHHHHHHHHhcccCCcceeEEEcc
Q 002211 355 GNTISFSNDTKLNGLGGGTLNLGALSIFDGGKKFLANILQTNMTGLSGPIHFNQ 408 (953)
Q Consensus 355 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~f~G~tG~v~Fd~ 408 (953)
.......+ .....+-+.-++.+++....|+.|+++|..
T Consensus 307 ~~~~~~~~----------------~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~ 344 (351)
T cd06334 307 GGETTIAG----------------EEQLENLKLDAARLEELGAEGLGPPVSVSC 344 (351)
T ss_pred cCCCCCcH----------------HHHHHhhhhhhhhhhhcCcccccCCceecc
Confidence 43211100 000000123355666777889999999975
No 68
>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=6.4e-34 Score=316.80 Aligned_cols=317 Identities=18% Similarity=0.225 Sum_probs=264.7
Q ss_pred EEeEEEecC---CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhc-CcEEEEccCChhh
Q 002211 51 NVGAIFSFG---TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMET-DTLAIVGPQSAVM 126 (953)
Q Consensus 51 ~IG~l~~~~---~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~-~v~aiiGp~~S~~ 126 (953)
+||++.|++ +..|.....|+++|++++|++||+. |++|+++++|++++|..+.+.+++|+++ +|.+|+||.+|+.
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 699999998 4678999999999999999999995 8999999999999999999999999987 8999999999999
Q ss_pred HHHHHHhhhhCCCcEEEeecCCCCCCC--CCCCcEEEccCChHHHHHHHHHHH-HHcCCcEEEEEEecCccccchHHHHH
Q 002211 127 AHVLSHLANELQVPLLSFTALDPTLSP--LQYPFFVQTAPNDLYLMSAIAEMV-SYFGWGEVIAIFNDDDQGRNGVTALG 203 (953)
Q Consensus 127 a~av~~v~~~~~vP~Is~~at~~~ls~--~~~p~~fr~~p~d~~~~~ai~~~l-~~~~w~~vaii~~d~~~g~~~~~~l~ 203 (953)
+.++.+++++.+||+|++.++++.+++ ..++|+||+.+++..++.++++++ ++.+|++|+++|.|++||+...+.++
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 999999999999999998888777765 346899999999999999999986 45669999999999999999999999
Q ss_pred HHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEEeCcccccc
Q 002211 204 DKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIATTWLSTFI 283 (953)
Q Consensus 204 ~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~ 283 (953)
+.+++.|++++....++.+ ..|+++.+++|++.+||+|++.+.+.+...+++++++.|+..+ ++...+.. ..
T Consensus 160 ~~~~~~G~~v~~~~~~~~~----~~d~s~~i~~i~~~~~d~v~~~~~~~~~~~~~~~~~~~g~~~~---~~~~~~~~-~~ 231 (347)
T cd06335 160 AALAARGLKPVAVEWFNWG----DKDMTAQLLRAKAAGADAIIIVGNGPEGAQIANGMAKLGWKVP---IISHWGLS-GG 231 (347)
T ss_pred HHHHHcCCeeEEEeeecCC----CccHHHHHHHHHhCCCCEEEEEecChHHHHHHHHHHHcCCCCc---EecccCCc-Cc
Confidence 9999999999998888877 7899999999999999999999999999999999999998542 23222211 11
Q ss_pred cCCCCCchhhhhhccceEEEEEec---CCChhhHHHHHHHHhhcCCCC----CCCchhhHHhhHHHHHHHHHHHHHhcCC
Q 002211 284 DSKSPLSLKTAKSILGALTLRQHT---PDSKRRRDFVSRWNTLSNGSI----GLNPYGLYAYDTVWMIARALKLFLDQGN 356 (953)
Q Consensus 284 ~~~~~~~~~~~~~~~g~~~~~~~~---~~~~~~~~F~~~~~~~~~~~~----~~~~~~~~~YDAv~~la~Al~~~~~~~~ 356 (953)
+.. ....+..+|++....+. +.++..++|.++|+++++... .++.+++.+||+++++++|++++...
T Consensus 232 ~~~----~~~g~~~~g~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~aYd~~~~l~~A~~~ag~~-- 305 (347)
T cd06335 232 NFI----EGAGPAANDALMIQTFIFEPPSNPKAKAFLAAYHKKYPEKKPADIPAPVGAAHAYDAVHLLAAAIKQAGST-- 305 (347)
T ss_pred hhh----hccchhhcCcEEEEeeccccCCCHHHHHHHHHHHHHhCCCcccccCcchhHHHHHHHHHHHHHHHHHhcCC--
Confidence 111 12334567877665443 356889999999999987322 34566788999999999999986322
Q ss_pred cccccCCCccCCCCCCcccCCCccccCchHHHHHHHHhcc--cCCccee--EEEccC
Q 002211 357 TISFSNDTKLNGLGGGTLNLGALSIFDGGKKFLANILQTN--MTGLSGP--IHFNQD 409 (953)
Q Consensus 357 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~--f~G~tG~--v~Fd~~ 409 (953)
.++.+.++|+++. +.|+.|. +.|++.
T Consensus 306 ---------------------------~~~~v~~al~~~~~~~~G~~~~~~~~~~~~ 335 (347)
T cd06335 306 ---------------------------DGRAIKRALENLKKPVEGLVKTYDKPFSKE 335 (347)
T ss_pred ---------------------------CHHHHHHHHHhccCCceeeecccCCCCChh
Confidence 2478999998764 6787774 457543
No 69
>PF13433 Peripla_BP_5: Periplasmic binding protein domain; PDB: 1QNL_A 1QO0_A 1PEA_A.
Probab=100.00 E-value=3e-33 Score=294.46 Aligned_cols=349 Identities=16% Similarity=0.150 Sum_probs=249.8
Q ss_pred EEEeEEEecCCCc---hhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhc-CcEEEEccCChh
Q 002211 50 LNVGAIFSFGTVN---GQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMET-DTLAIVGPQSAV 125 (953)
Q Consensus 50 i~IG~l~~~~~~~---g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~-~v~aiiGp~~S~ 125 (953)
|+||+++++++.. +.....|+.||++|||++||++ |++|+.+++|.++|+....+.|.+|+.+ +|.+|+|.++|.
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 6899999998655 5678999999999999999998 8999999999999999999999999875 999999999999
Q ss_pred hHHHHHHhhhhCCCcEEEeecCCCCCCC--CCCCcEEEccCChHHHHHHHHHH-HHHcCCcEEEEEEecCccccchHHHH
Q 002211 126 MAHVLSHLANELQVPLLSFTALDPTLSP--LQYPFFVQTAPNDLYLMSAIAEM-VSYFGWGEVIAIFNDDDQGRNGVTAL 202 (953)
Q Consensus 126 ~a~av~~v~~~~~vP~Is~~at~~~ls~--~~~p~~fr~~p~d~~~~~ai~~~-l~~~~w~~vaii~~d~~~g~~~~~~l 202 (953)
+..++.++.++.+-++..+. ..+ ...|++|-+.....+|...++++ +.++|.+++.+|.+|+.|++.....+
T Consensus 80 sRKaVlPvvE~~~~LL~Yp~-----~YEG~E~S~nviYtGa~PNQ~~~pl~~~~~~~~G~~r~~lvGSdYv~pre~Nri~ 154 (363)
T PF13433_consen 80 SRKAVLPVVERHNALLFYPT-----QYEGFECSPNVIYTGAAPNQQLLPLIDYLLENFGAKRFYLVGSDYVYPRESNRII 154 (363)
T ss_dssp HHHHHHHHHHHCT-EEEE-S-------------TTEEE-S--GGGTHHHHHHHHHHHS--SEEEEEEESSHHHHHHHHHH
T ss_pred hHHHHHHHHHhcCceEEecc-----ccccccCCCceEEcCCCchhhHHHHHHHHHhccCCceEEEecCCccchHHHHHHH
Confidence 99999999999999999642 222 45689999999999999999999 67789999999999999999999999
Q ss_pred HHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEEeCcccc-
Q 002211 203 GDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIATTWLST- 281 (953)
Q Consensus 203 ~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~- 281 (953)
++.+++.|++|+.+..+|.+ .+|+...+.+|++.+||+|+-...++....|+++++++|+... .+-|.+....+
T Consensus 155 r~~l~~~GgevvgE~Y~plg----~td~~~ii~~I~~~~Pd~V~stlvG~s~~aF~r~~~~aG~~~~-~~Pi~S~~~~E~ 229 (363)
T PF13433_consen 155 RDLLEARGGEVVGERYLPLG----ATDFDPIIAEIKAAKPDFVFSTLVGDSNVAFYRAYAAAGLDPE-RIPIASLSTSEA 229 (363)
T ss_dssp HHHHHHTT-EEEEEEEE-S-----HHHHHHHHHHHHHHT-SEEEEE--TTCHHHHHHHHHHHH-SSS----EEESS--HH
T ss_pred HHHHHHcCCEEEEEEEecCC----chhHHHHHHHHHhhCCCEEEEeCcCCcHHHHHHHHHHcCCCcc-cCeEEEEecCHH
Confidence 99999999999999999998 8999999999999999999999999999999999999998754 44555544332
Q ss_pred cccCCCCCchhhhhhccceEEEEEecC--CChhhHHHHHHHHhhcCCCCCCCchhhHHhhHHHHHHHHHHHHHhcCCccc
Q 002211 282 FIDSKSPLSLKTAKSILGALTLRQHTP--DSKRRRDFVSRWNTLSNGSIGLNPYGLYAYDTVWMIARALKLFLDQGNTIS 359 (953)
Q Consensus 282 ~~~~~~~~~~~~~~~~~g~~~~~~~~~--~~~~~~~F~~~~~~~~~~~~~~~~~~~~~YDAv~~la~Al~~~~~~~~~~~ 359 (953)
..... ..+...|.++..+|.. ++|..++|+++|+++|+.+..++.....+|.+|+++|+|++++++.
T Consensus 230 E~~~~------g~~~~~Gh~~~~~YFqsidtp~N~~Fv~~~~~~~g~~~v~s~~~eaaY~~v~l~a~Av~~ags~----- 298 (363)
T PF13433_consen 230 ELAAM------GAEAAAGHYTSAPYFQSIDTPENQAFVARFRARYGDDRVTSDPMEAAYFQVHLWAQAVEKAGSD----- 298 (363)
T ss_dssp HHTTS-------HHHHTT-EEEES--TT-SSHHHHHHHHHHHTTS-TT----HHHHHHHHHHHHHHHHHHHHTS------
T ss_pred HHhhc------ChhhcCCcEEeehhhhhCCcHHHHHHHHHHHHHhCCCCCCCcHHHHHHHHHHHHHHHHHHhCCC-----
Confidence 22221 2357899999988754 6899999999999999876667888888999999999999998432
Q ss_pred ccCCCccCCCCCCcccCCCccccCchHHHHHHHHhcccCCcceeEEEccCCCCCCccEEEEEeecCCeeeEEEEecCCCC
Q 002211 360 FSNDTKLNGLGGGTLNLGALSIFDGGKKFLANILQTNMTGLSGPIHFNQDRSLLHPSYDIINVIEHGYPQQIGYWSNYSG 439 (953)
Q Consensus 360 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~f~G~tG~v~Fd~~g~~~~~~y~I~~~~~~~~~~~VG~w~~~~g 439 (953)
+.++++++|.+.+|+++.|.+++|++.+...- +..||..++..
T Consensus 299 ------------------------d~~~vr~al~g~~~~aP~G~v~id~~n~H~~l------------~~rIg~~~~dG- 341 (363)
T PF13433_consen 299 ------------------------DPEAVREALAGQSFDAPQGRVRIDPDNHHTWL------------PPRIGRVNADG- 341 (363)
T ss_dssp -------------------------HHHHHHHHTT--EEETTEEEEE-TTTSBEEB--------------EEEEE-TTS-
T ss_pred ------------------------CHHHHHHHhcCCeecCCCcceEEcCCCCeecc------------cceEEEEcCCC-
Confidence 58999999999999999999999973321111 25677765542
Q ss_pred ccccCCcccccCCCCCCCCCCcceeeEeCCCcccCCCccc
Q 002211 440 LSVVPPEKLYRKPANRSSSNQHLYSVVWPGGVTSKPRGWV 479 (953)
Q Consensus 440 l~~~~~~~~~~~~~~~~~~~~~l~~i~Wpg~~~~~P~~~~ 479 (953)
...|+|-...+..|.+|.
T Consensus 342 ----------------------~f~Iv~~s~~pv~PdPyl 359 (363)
T PF13433_consen 342 ----------------------QFDIVWESDEPVKPDPYL 359 (363)
T ss_dssp -----------------------EEEEEE-SS-B---TT-
T ss_pred ----------------------CEEEEEeCCCCCCCCCCC
Confidence 245777766666676664
No 70
>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=2.4e-33 Score=310.43 Aligned_cols=328 Identities=16% Similarity=0.158 Sum_probs=242.9
Q ss_pred cCCCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecC------CC-ChHHHHHHHHHHHhcCc--EEEEccCChhhHH
Q 002211 58 FGTVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDA------KF-NGFLSIMGALQFMETDT--LAIVGPQSAVMAH 128 (953)
Q Consensus 58 ~~~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~------~~-~~~~a~~~a~~li~~~v--~aiiGp~~S~~a~ 128 (953)
.+...|+..+.|+++|++++|++. |.+|.+.+.|. .+ |...+.+++|+++++++ .|||||.+|..+.
T Consensus 6 ~~~~~~~~~~~A~~~Av~~~N~~~----~~~l~~~~~~~~~~~~~~~~d~~~~~~~~C~~~~~gv~~~AIiGp~ss~~a~ 81 (368)
T cd06383 6 MTEDDNDVYKQIIDDALSYINRNI----GTGLSVVHQQVETNAEVNRNDVKVALIEVCDKADSAIVPHLVLDTTTCGDAS 81 (368)
T ss_pred ecccchHHHHHHHHHHHHHHhcCC----CCceEEEEecccccccccCCcHHHHHHHHHHHHHccCCcEEEECCCcchhHH
Confidence 345578899999999999999985 67888888887 55 56666667999999988 8999999999999
Q ss_pred HHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecCccccchHH-HHHHHHH
Q 002211 129 VLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDDDQGRNGVT-ALGDKLA 207 (953)
Q Consensus 129 av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~~~g~~~~~-~l~~~l~ 207 (953)
.++.+++.++||+|+++.. ..++.++|||+|+.|++..+++|+++++++|+|++|++||++++++..... .+++...
T Consensus 82 ~V~si~~~~~IP~Is~s~~--~~~~~~~p~~ir~~Ps~~~~~~Ai~dlI~~f~W~~v~iIYddd~gl~~~l~~~l~~~~~ 159 (368)
T cd06383 82 EIKSVTGALGIPTFSASYG--QEGDLEQPYLIQLMPPADDIVEAIRDIVSYYNITNAAILYDDDFVMDHKYKSLLQNWPT 159 (368)
T ss_pred HHHHHHhccCCCEEEccCC--CcCcccCceEEEEeCChHHHHHHHHHHHHHCCCcEEEEEEEcCchhhHHHHHHHHhHHh
Confidence 9999999999999997443 333457999999999999999999999999999999999977664432333 3333333
Q ss_pred hcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcc-hhhHHHHHHHHHHcCCCCCceEEEEeCcccccccCC
Q 002211 208 EIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGY-SRTGLMVFDVAQRLGMMDSGYVWIATTWLSTFIDSK 286 (953)
Q Consensus 208 ~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~-~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~~ 286 (953)
..+.++. +.. ..++...|++++.++.+.||+.+. ++.+..++++|.++||++.+|+||++++.....+.
T Consensus 160 ~~~~~v~-----~~~----~~~~~~~Lk~lk~~~~~rIIi~~s~~~~~~~il~qA~~lgm~~~~y~wilt~ld~~~~dl- 229 (368)
T cd06383 160 RHVITII-----NSI----IDEVREQIKRLRNLDIKNIFILGSTEEIIRYVLDQALAEGFMGRKYAWFLGNPDLGIYDD- 229 (368)
T ss_pred cCCEEEE-----ecc----chhHHHHHHHHHhCCCeEEEEEeCCHHHHHHHHHHHHHcCCcCCceEEEEcCCCchhhhh-
Confidence 3344443 112 456889999999998855555555 59999999999999999999999999986655443
Q ss_pred CCCchhhhhhccceEEEEEecCCChhhHHHHHHHHhhc--C-CCCCCCchhhHHhhHHHHHHHHHHHHHhcCCcccccCC
Q 002211 287 SPLSLKTAKSILGALTLRQHTPDSKRRRDFVSRWNTLS--N-GSIGLNPYGLYAYDTVWMIARALKLFLDQGNTISFSND 363 (953)
Q Consensus 287 ~~~~~~~~~~~~g~~~~~~~~~~~~~~~~F~~~~~~~~--~-~~~~~~~~~~~~YDAv~~la~Al~~~~~~~~~~~~~~~ 363 (953)
......-.++.+++...+.....+.+.++|.+.. + ...+...-++.+||||++++.|++.+..+....
T Consensus 230 ----~~~~~~~~Nitgfrl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~aL~~Dav~~~~~a~~~l~~~~~~~----- 300 (368)
T cd06383 230 ----LSCQLRNASIFVTRPMMDYQSSVRGALLRTDEPTLRPVFYFEWAFRLFLAYDAVLAVGEWPRRMRKKRVED----- 300 (368)
T ss_pred ----hhhccccCcEEEeeccccchhhhccceeeccCCccCchhHHHHHHHHHHHHHHHHHhccccchhheeeccC-----
Confidence 2233445678999997666666688887774321 0 001123358899999999999999763211110
Q ss_pred CccCCCCCCcccCCCc---ccc-CchHHHHHHHHhcccCCcceeEEEccCCCCC
Q 002211 364 TKLNGLGGGTLNLGAL---SIF-DGGKKFLANILQTNMTGLSGPIHFNQDRSLL 413 (953)
Q Consensus 364 ~~~~~~~~~~~~~~~~---~~~-~~~~~l~~~l~~~~f~G~tG~v~Fd~~g~~~ 413 (953)
.+.......|... -+| ..|..+.++|+.++|+|+||+|+||++|.|.
T Consensus 301 ---~~~~~~~~~~~g~~~~~~w~~~g~~~~~~~k~~~~~gltG~i~f~~~g~R~ 351 (368)
T cd06383 301 ---GSTGTSVLPGFGISPESPLMTLQSSPFNGSSEIKFEMLAGRVAIDEGSSVS 351 (368)
T ss_pred ---CCcCccccCCCCCCcccchhhcccccccCccceeEeeecCeEEEecCceee
Confidence 0111112233322 134 5566999999999999999999999999864
No 71
>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=100.00 E-value=1.3e-32 Score=305.63 Aligned_cols=320 Identities=17% Similarity=0.250 Sum_probs=271.9
Q ss_pred EEeEEEecCCC---chhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhc-CcEEEEccCChhh
Q 002211 51 NVGAIFSFGTV---NGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMET-DTLAIVGPQSAVM 126 (953)
Q Consensus 51 ~IG~l~~~~~~---~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~-~v~aiiGp~~S~~ 126 (953)
+||+++|++.. .|.....|+++|++++| +++ .|++++++++|++++|..+.+.+.+|+++ +|.+||||.+|..
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 69999999844 57789999999999997 566 59999999999999999999999999987 9999999999998
Q ss_pred HHHHHHhhhhCCCcEEEeecCCCCCCCC-CCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecCccccchHHHHHHH
Q 002211 127 AHVLSHLANELQVPLLSFTALDPTLSPL-QYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDDDQGRNGVTALGDK 205 (953)
Q Consensus 127 a~av~~v~~~~~vP~Is~~at~~~ls~~-~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~~~g~~~~~~l~~~ 205 (953)
+.++.+.+++.++|+|+++++++.+++. .+||+||+.+++..++..+++++...||+++++++.++.||++..+.+.+.
T Consensus 78 ~~~~~~~~~~~~ip~v~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~l~~~g~~~v~il~~~~~~~~~~~~~~~~~ 157 (333)
T cd06332 78 ALAVVPSLTESGTFLISPNAGPSDLAGKLCSPNFFRTSWQNDQVHEAMGKYAADKGYKKVVIIAPDYAAGKDAVAGFKRT 157 (333)
T ss_pred HHHHHHHHhhcCCeEEecCCCCccccccCCCCcEEEeeCChHHhHHHHHHHHHHhCCceEEEEecCcchhHHHHHHHHHh
Confidence 9999999999999999998888877763 479999999999999999999999999999999999999999999999999
Q ss_pred HHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEEeCcccccccC
Q 002211 206 LAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIATTWLSTFIDS 285 (953)
Q Consensus 206 l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~ 285 (953)
++ +.++....++.+ ..|+..+++++++.+||+|++...+..+..++++++++|+.. ...++.++.+......
T Consensus 158 ~~---~~~~~~~~~~~~----~~d~~~~i~~l~~~~~d~i~~~~~~~~~~~~~~~~~~~g~~~-~~~~~~~~~~~~~~~~ 229 (333)
T cd06332 158 FK---GEVVEEVYTPLG----QLDFSAELAQIRAAKPDAVFVFLPGGMAVNFVKQYDQAGLKK-KIPLYGPGFLTDQDTL 229 (333)
T ss_pred hc---EEEeeEEecCCC----CcchHHHHHHHHhcCCCEEEEecccchHHHHHHHHHHcCccc-CCceeccCCCCCHHHH
Confidence 87 466666667665 678999999999999999999988889999999999999843 3446666554432111
Q ss_pred CCCCchhhhhhccceEEEEEecC--CChhhHHHHHHHHhhcCCCCCCCchhhHHhhHHHHHHHHHHHHHhcCCcccccCC
Q 002211 286 KSPLSLKTAKSILGALTLRQHTP--DSKRRRDFVSRWNTLSNGSIGLNPYGLYAYDTVWMIARALKLFLDQGNTISFSND 363 (953)
Q Consensus 286 ~~~~~~~~~~~~~g~~~~~~~~~--~~~~~~~F~~~~~~~~~~~~~~~~~~~~~YDAv~~la~Al~~~~~~~~~~~~~~~ 363 (953)
....+..+|++...++.+ +++..++|.++|+++++ ..++.++..+||+++++++|++++...
T Consensus 230 -----~~~~~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~~--~~~~~~~~~~yda~~~~~~a~~~ag~~--------- 293 (333)
T cd06332 230 -----PAQGDAAVGVLTALHWAPDLDNPANKRFVAAYKAAYG--RVPSVYAAQGYDAAQLLDAALRAVGGD--------- 293 (333)
T ss_pred -----HhhchhhcCeeeeeccCCCCCCHHHHHHHHHHHHHhC--CCCcHHHHHHHHHHHHHHHHHHHhcCC---------
Confidence 234466789888877765 35788999999999987 557889999999999999999997321
Q ss_pred CccCCCCCCcccCCCccccCchHHHHHHHHhcccCCcceeEEEccCCCCCCc
Q 002211 364 TKLNGLGGGTLNLGALSIFDGGKKFLANILQTNMTGLSGPIHFNQDRSLLHP 415 (953)
Q Consensus 364 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~f~G~tG~v~Fd~~g~~~~~ 415 (953)
..+++.|.++|++++|+|+.|++.|+++|+...+
T Consensus 294 ------------------~~~~~~v~~al~~~~~~~~~g~i~f~~~~~~~~~ 327 (333)
T cd06332 294 ------------------LSDKDALRAALRAADFDSPRGPFKFNPNHNPIQD 327 (333)
T ss_pred ------------------CCCHHHHHHHHhcCceecCccceeECCCCCcccc
Confidence 1136789999999999999999999999985444
No 72
>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=100.00 E-value=1e-32 Score=307.99 Aligned_cols=329 Identities=12% Similarity=0.092 Sum_probs=263.9
Q ss_pred EEeEEEecC---CCchhHHHHHHHHHHHHHhcCCCCCCC--cEEEEEEecCCCChHHHHHHHHHHHhc-CcEEEEccCCh
Q 002211 51 NVGAIFSFG---TVNGQVSRIAMKAAQDDINSDPRVLGG--RKLSITMHDAKFNGFLSIMGALQFMET-DTLAIVGPQSA 124 (953)
Q Consensus 51 ~IG~l~~~~---~~~g~~~~~a~~lAve~iN~~g~il~g--~~l~l~~~D~~~~~~~a~~~a~~li~~-~v~aiiGp~~S 124 (953)
+||++.|+| +..|.....++++|+++||..+++ .| ++|+++++|++++|.+|+.++++|+++ +|.+|||+.+|
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 599999998 566888899999999999965544 35 589999999999999999999999987 99999999999
Q ss_pred hhHHHHHHhhhhCCCcEEEeecCCCCC------C-CCCCCcEEEccCChHHHHHHHHHHHHHcC-CcEEEEEEecCcccc
Q 002211 125 VMAHVLSHLANELQVPLLSFTALDPTL------S-PLQYPFFVQTAPNDLYLMSAIAEMVSYFG-WGEVIAIFNDDDQGR 196 (953)
Q Consensus 125 ~~a~av~~v~~~~~vP~Is~~at~~~l------s-~~~~p~~fr~~p~d~~~~~ai~~~l~~~~-w~~vaii~~d~~~g~ 196 (953)
..+.++++++++.+||+|++.+..+.+ . ...+||+||+.+++..++.+++++++..+ +++|++++.|++||+
T Consensus 80 ~~~~a~~~~~~~~~ip~i~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~k~v~ii~~~~~~g~ 159 (357)
T cd06337 80 DTTNPVSDQCEANGVPCISTMAPWQAWFFGRGGNPATGFKWTYHFFWGAEDVVATYVGMWKQLETNKKVGILYPNDPDGN 159 (357)
T ss_pred chhhHHHHHHHHhCCCeEEeccchhhhhccCCCCcccCCceeEEecCCHHHHHHHHHHHHHhCCCCceEEEEeecCchhH
Confidence 999999999999999999875432221 1 13478999999999888899998888887 999999999999999
Q ss_pred chHHHHH---HHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHHHcCCCCCceEE
Q 002211 197 NGVTALG---DKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVW 273 (953)
Q Consensus 197 ~~~~~l~---~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~w 273 (953)
...+.+. +.+++.|++|+..+.++++ ..||++++++|++++||+|++.+.+.++..++++++++|+..+ +
T Consensus 160 ~~~~~~~~~~~~~~~~G~~vv~~~~~~~~----~~D~~~~v~~ik~a~pD~v~~~~~~~~~~~~~~~~~~~G~~~~---~ 232 (357)
T cd06337 160 AFADPVIGLPAALADAGYKLVDPGRFEPG----TDDFSSQINAFKREGVDIVTGFAIPPDFATFWRQAAQAGFKPK---I 232 (357)
T ss_pred HHHHhhhcccHHHHhCCcEEecccccCCC----CCcHHHHHHHHHhcCCCEEEeCCCccHHHHHHHHHHHCCCCCC---e
Confidence 8877654 5777899999999999987 7899999999999999999999999999999999999998654 3
Q ss_pred EEe-CcccccccCCCCCchhhhhhccceEEEEEecCC--------ChhhHHHHHHHHhhcCCCCCCCchhhHHhhHHHHH
Q 002211 274 IAT-TWLSTFIDSKSPLSLKTAKSILGALTLRQHTPD--------SKRRRDFVSRWNTLSNGSIGLNPYGLYAYDTVWMI 344 (953)
Q Consensus 274 i~~-~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~--------~~~~~~F~~~~~~~~~~~~~~~~~~~~~YDAv~~l 344 (953)
+.. .+.... ... ....+..+|++....+.+. ++..++|.++|+++++ ..+.....++||+++++
T Consensus 233 ~~~~~~~~~~-~~~----~~~g~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~~~~g--~~~~~~~~~~~~~~~~l 305 (357)
T cd06337 233 VTIAKALLFP-EDV----EALGDRGDGMSTEVWWSPSHPFRSSLTGQSAAELADAYEAATG--RQWTQPLGYAHALFEVG 305 (357)
T ss_pred EEEeccccCH-HHH----HHhhhhhcCccccceeccCCCcccccCCccHHHHHHHHHHHhC--CCccCcchHHHHHHHHH
Confidence 332 222111 010 1223345777665444443 2357899999999987 45666778899999999
Q ss_pred HHHHHHHHhcCCcccccCCCccCCCCCCcccCCCccccCchHHHHHHHHhcccCCcceeEEEccCCCCCCccEEEEEeec
Q 002211 345 ARALKLFLDQGNTISFSNDTKLNGLGGGTLNLGALSIFDGGKKFLANILQTNMTGLSGPIHFNQDRSLLHPSYDIINVIE 424 (953)
Q Consensus 345 a~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~f~G~tG~v~Fd~~g~~~~~~y~I~~~~~ 424 (953)
++|++++++. .+++.|+++|++++++++.|++.||++ . .....|+.+.|
T Consensus 306 ~~Ai~~Ags~----------------------------~d~~~v~~aL~~~~~~~~~G~~~f~~~--~-~~~~~~~~~~~ 354 (357)
T cd06337 306 VKALVRADDP----------------------------DDPAAVADAIATLKLDTVVGPVDFGNS--P-IKNVAKTPLVG 354 (357)
T ss_pred HHHHHHcCCC----------------------------CCHHHHHHHHHcCCcccceeeeecCCC--C-Ccccccccccc
Confidence 9999987432 147899999999999999999999865 2 33455666655
Q ss_pred C
Q 002211 425 H 425 (953)
Q Consensus 425 ~ 425 (953)
+
T Consensus 355 ~ 355 (357)
T cd06337 355 G 355 (357)
T ss_pred C
Confidence 3
No 73
>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=3.7e-32 Score=301.39 Aligned_cols=315 Identities=23% Similarity=0.360 Sum_probs=254.6
Q ss_pred EEeEEEecCCCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCC-CChHHHHHHHHHHH-hcCcEEEEccCChhhHH
Q 002211 51 NVGAIFSFGTVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAK-FNGFLSIMGALQFM-ETDTLAIVGPQSAVMAH 128 (953)
Q Consensus 51 ~IG~l~~~~~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~-~~~~~a~~~a~~li-~~~v~aiiGp~~S~~a~ 128 (953)
+||++++... ...+.|+++|++++|..++++++.++.+.+.+.+ ++|..++.++|+++ .++|.+|+||.+|..+.
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 4889988765 6789999999999999999877777776666655 79999999999999 67999999999999999
Q ss_pred HHHHhhhhCCCcEEEeecCCCCCCC-CCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecCccccchHHHHHHHHH
Q 002211 129 VLSHLANELQVPLLSFTALDPTLSP-LQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDDDQGRNGVTALGDKLA 207 (953)
Q Consensus 129 av~~v~~~~~vP~Is~~at~~~ls~-~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~~~g~~~~~~l~~~l~ 207 (953)
+++++++.++||+|+++++++.+++ ..+||+||+.|++..+++++++++.+++|++|++||++++++... +.+.+...
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 9999999999999999998888876 678999999999999999999999999999999999988855443 33333333
Q ss_pred hcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCc-eEEEEEcchhhHHHHHHHHHHcCCCCCceEEEEeCcccccccCC
Q 002211 208 EIRCKISYKSALPPDQSVTETDVRNELVKVRMMEA-RVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIATTWLSTFIDSK 286 (953)
Q Consensus 208 ~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~-~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~~ 286 (953)
..+..+.. ..+..+ .+++...++++++.++ ++|+.++...++..++++|+++||++++|+||.++......+.
T Consensus 157 ~~~~~v~~-~~~~~~----~~~~~~~l~~l~~~~~~~vil~~~~~~~~~~~l~~a~~~gm~~~~~~~i~~~~~~~~~d~- 230 (328)
T cd06351 157 IKGIQVTV-RRLDLD----DDNYRQLLKELKRSESRRIILDCSSEEEAKEILEQAVELGMMGYGYHWILTNLDLSDIDL- 230 (328)
T ss_pred ccCceEEE-EEecCC----chhHHHHHHHHhhcccceEEEECCcHHHHHHHHHHHHHhccccCCcEEEEecCCccccch-
Confidence 33444443 345544 3489999999999999 6666555559999999999999999999999999976655433
Q ss_pred CCCchhhhhhccceEEEEEecCCChhhHHHHHHHHhhcC--CCCCCCchhhHHhhHHHHHHHHHHHHHhcCCcccccCCC
Q 002211 287 SPLSLKTAKSILGALTLRQHTPDSKRRRDFVSRWNTLSN--GSIGLNPYGLYAYDTVWMIARALKLFLDQGNTISFSNDT 364 (953)
Q Consensus 287 ~~~~~~~~~~~~g~~~~~~~~~~~~~~~~F~~~~~~~~~--~~~~~~~~~~~~YDAv~~la~Al~~~~~~~~~~~~~~~~ 364 (953)
........|+++++...+..+..+.|..+|..... ....+...++.+||+++++
T Consensus 231 ----~~~~~~~~~i~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~-------------------- 286 (328)
T cd06351 231 ----EPFQYGPANITGFRLVDPDSPDVSQFLQRWLEESPGVNLRAPIYDAALLYDAVLLL-------------------- 286 (328)
T ss_pred ----hhhccCCcceEEEEEeCCCchHHHHHHHhhhhccCCCCcCccchhhHhhhcEEEEE--------------------
Confidence 23456779999999999999999999999944332 1112233344444443321
Q ss_pred ccCCCCCCcccCCCccccCchHHHHHHHHhcccCCcceeEEEccCCCCCCccEEEEEee-cCCeeeEEEEecC
Q 002211 365 KLNGLGGGTLNLGALSIFDGGKKFLANILQTNMTGLSGPIHFNQDRSLLHPSYDIINVI-EHGYPQQIGYWSN 436 (953)
Q Consensus 365 ~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~f~G~tG~v~Fd~~g~~~~~~y~I~~~~-~~~~~~~VG~w~~ 436 (953)
||++.||++|+|.+..++|+++. +.++ ++||.|++
T Consensus 287 ------------------------------------tg~i~f~~~g~r~~~~l~i~~l~~~~~~-~~vg~W~~ 322 (328)
T cd06351 287 ------------------------------------TGTVSFDEDGVRSNFTLDIIELNRSRGW-RKVGTWNG 322 (328)
T ss_pred ------------------------------------EeeEEECCCCcccceEEEEEEecCCCCc-eEEEEecC
Confidence 99999999999999999999999 6777 99999984
No 74
>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=2.4e-30 Score=279.67 Aligned_cols=341 Identities=16% Similarity=0.163 Sum_probs=248.4
Q ss_pred CceEEEeEEEecCCCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCC-CChHHHHHHHHHH-HhcCcEEEEcc-CC
Q 002211 47 PEVLNVGAIFSFGTVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAK-FNGFLSIMGALQF-METDTLAIVGP-QS 123 (953)
Q Consensus 47 ~~~i~IG~l~~~~~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~-~~~~~a~~~a~~l-i~~~v~aiiGp-~~ 123 (953)
+..|+||++|+.. ...+.|+++|++.+|.+..++++.+|+.++..-. .|+..+....|++ +++||.||+|| .+
T Consensus 16 ~~~i~iG~if~~~----~~~~~af~~Av~~~N~~~~l~~~~~L~~~~~~~~~~dsf~~~~~vC~~ll~~GV~AIfg~p~s 91 (382)
T cd06377 16 GHTVRLGALLVRA----PAPRDRVLAALARANRAPLLPYNLSLEVVAAAAPSRDPASLLRSVCQTVVVQGVSALLAFPQT 91 (382)
T ss_pred CCceeeeEEecCC----chHHHHHHHHHHHhccccccccCceeEEeEEEcCCCChHHHHHHHHHhHhhCCeEEEEecCCC
Confidence 4579999999965 3579999999999999988888889998888755 4999999999999 59999999994 88
Q ss_pred hhhHHHHHHhhhhCCCcEEEeecCCCCC-CCCCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecCccccchHHHH
Q 002211 124 AVMAHVLSHLANELQVPLLSFTALDPTL-SPLQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDDDQGRNGVTAL 202 (953)
Q Consensus 124 S~~a~av~~v~~~~~vP~Is~~at~~~l-s~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~~~g~~~~~~l 202 (953)
+..+..+..+++.++||+|+++..++.. ++..+.+..++.|+...++.|+.+++++|+|++|++||+.+..... |
T Consensus 92 ~~~~~~v~sic~~l~IP~I~~~~~~~~~~~~~~~~l~L~l~P~~~~l~~a~~~ll~~~~W~~f~~iy~~~~gl~~----l 167 (382)
T cd06377 92 RPELVQLDFVSAALEIPVVSIVRREFPRGSQNPFHLQMSWASPLSTLLDVLLSVLQRNGWEDVSLVLCRERDPTG----L 167 (382)
T ss_pred HHHHHHHHHHhcCCCCCEEEecCCcccccCCCceeEEEEecCCHHHHHHHHHHHHHHCCCcEEEEEEecCcCHHH----H
Confidence 8888999999999999999986655333 2233333446799999999999999999999999999988774433 3
Q ss_pred HHHHHhcCc----EEEEEEecCCCCCCChHHH-HHHHHHHhcCC-ceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEEe
Q 002211 203 GDKLAEIRC----KISYKSALPPDQSVTETDV-RNELVKVRMME-ARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIAT 276 (953)
Q Consensus 203 ~~~l~~~g~----~v~~~~~~~~~~~~~~~d~-~~~l~~i~~~~-~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~ 276 (953)
++.++..+. .+......+..+ .+..++ +..|+++++.. +++|+++|+.+.+..+++++.+ +|+||++
T Consensus 168 q~l~~~~~~~~~~~~i~v~~~~~~~-~d~~~~~~~~L~~i~~~~~~~~ill~cs~e~~~~il~~~~~------~y~wIv~ 240 (382)
T cd06377 168 LLLWTNHARFHLGSVLNLSRNDPST-ADLLDFLRAQLELLKDPPGPAVVLFGCDVARARRVLELTPP------GPHWILG 240 (382)
T ss_pred HHHHHHhcccccCceEEEEeccCcc-CChhHHHHHHHHHhhcccCceEEEEECCHHHHHHHHHhhcc------ceEEEEc
Confidence 333333321 122222233210 124455 99999999999 9999999999999999988754 4999998
Q ss_pred CcccccccCCCCCchhhhhhccceEEEEEecCCChhhHHHHHHHHhhcCCCCCCCchhhHHhhHHHHHHHHHHHHHhcCC
Q 002211 277 TWLSTFIDSKSPLSLKTAKSILGALTLRQHTPDSKRRRDFVSRWNTLSNGSIGLNPYGLYAYDTVWMIARALKLFLDQGN 356 (953)
Q Consensus 277 ~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~F~~~~~~~~~~~~~~~~~~~~~YDAv~~la~Al~~~~~~~~ 356 (953)
+.. +.... .....-.|+++ |.+. ......++.||||+++|+|++.+.....
T Consensus 241 ~~~----~le~~---~~~g~nigLl~-----------------~~~~-----~~~~l~ali~DAV~lvA~a~~~l~~~~~ 291 (382)
T cd06377 241 DPL----PPEAL---RTEGLPPGLLA-----------------HGET-----TQPPLEAYVQDALELVARAVGSATLVQP 291 (382)
T ss_pred CCc----Chhhc---cCCCCCceEEE-----------------Eeec-----ccccHHHHHHHHHHHHHHHHHHhhhccc
Confidence 721 11100 00111223331 2111 1113388999999999999998632111
Q ss_pred cccccCCCccCCCCCCcccCCCc--c-ccCchHHHHHHHHhcccCCcceeEEEccCCCC--CCccEEEEEee--cCC--e
Q 002211 357 TISFSNDTKLNGLGGGTLNLGAL--S-IFDGGKKFLANILQTNMTGLSGPIHFNQDRSL--LHPSYDIINVI--EHG--Y 427 (953)
Q Consensus 357 ~~~~~~~~~~~~~~~~~~~~~~~--~-~~~~~~~l~~~l~~~~f~G~tG~v~Fd~~g~~--~~~~y~I~~~~--~~~--~ 427 (953)
... ..-...+|... + +|..|..|.++|++++|+|.||+|.|+ .|.| .+..++|++++ ..| .
T Consensus 292 ~~~---------l~~~~~~C~~~~~~~~W~~G~~l~~~Lknv~~eGlTG~I~F~-~g~R~~~~~~l~I~~L~~~~~G~~~ 361 (382)
T cd06377 292 ELA---------LIPATVNCMDLPTKGNESSGQYLARFLANTSFDGRTGPVWVT-GSSQVHSSRHFKVWSLRRDPVGQPT 361 (382)
T ss_pred ccc---------cCCCCCCcccCCCCCCCCchHHHHHHHHhCcccccceeEEEc-cCeeecccceEEEEEeccccCCCcc
Confidence 110 11122456543 5 899999999999999999999999994 5777 78999999998 333 4
Q ss_pred eeEEEEecCCCCcc
Q 002211 428 PQQIGYWSNYSGLS 441 (953)
Q Consensus 428 ~~~VG~w~~~~gl~ 441 (953)
|++||+|++...+.
T Consensus 362 W~kVG~W~~~~~~~ 375 (382)
T cd06377 362 WTTVGSWQGGRKIV 375 (382)
T ss_pred ceEEEEecCCCcee
Confidence 79999999874433
No 75
>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=1e-32 Score=303.84 Aligned_cols=370 Identities=19% Similarity=0.300 Sum_probs=302.2
Q ss_pred CCceEEEeEEEecC-----CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhc--CcEEE
Q 002211 46 KPEVLNVGAIFSFG-----TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMET--DTLAI 118 (953)
Q Consensus 46 ~~~~i~IG~l~~~~-----~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~--~v~ai 118 (953)
...+..+++++|+. ...|+....|+++|++++|+.+.||||++|.++..|++|++..+.++..+++.. ..+++
T Consensus 38 ~~~~~~~~~~~~~~~~~~~~~~g~~~~Pav~~Al~~vn~~~~ilp~y~L~~~~~ds~C~~~~g~k~~fdll~~~p~k~ml 117 (865)
T KOG1055|consen 38 SRCPRRIVGIGPLGPGSGGWPGGQACLPAVELALEDVNSRSDILPGYRLKLIHHDSECDPGQGTKALYDLLYNGPNKLML 117 (865)
T ss_pred CCCCceeeeeecCccccCCCcCcccccHHHHHHHHHhhccccccCCcEEEEEeccccCCccccHHHHHHHHHcCCchhee
Confidence 34568888899985 334788899999999999999999999999999999999999999999999987 67778
Q ss_pred EccCChhhHHHHHHhhhhCCCcEEEeecCCCCCCC-CCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecCccccc
Q 002211 119 VGPQSAVMAHVLSHLANELQVPLLSFTALDPTLSP-LQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDDDQGRN 197 (953)
Q Consensus 119 iGp~~S~~a~av~~v~~~~~vP~Is~~at~~~ls~-~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~~~g~~ 197 (953)
+|+ ||+++..++.-+..++.-++||++++|.+++ ..||+|||+.|++......+.+++++++|++|+.++++..-...
T Consensus 118 l~G-Cs~v~~~iaea~~~w~l~~lsy~~ssp~ls~r~rfp~~frt~PS~~~~np~rl~l~~~~~w~rvgt~~q~e~~f~~ 196 (865)
T KOG1055|consen 118 LGG-CSSVTTLIAEAAKMWNLIVLSYGASSPALSNRKRFPTFFRTHPSANAHNPTRIKLLKKFGWKRVATLQQTEEVFSS 196 (865)
T ss_pred ccC-CCCcchHHHhhccccceeeecccCCCccccchhhcchhhhcCCccccCCcceeeechhcCcceeeeeeeehhhhcc
Confidence 888 9999999999999999999999999999998 78999999999999999999999999999999999999888888
Q ss_pred hHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEEeC
Q 002211 198 GVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIATT 277 (953)
Q Consensus 198 ~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~ 277 (953)
..+.+...+.+.|++++..+.+.. |....+.+++..++|+|+...+...+..++++++..+|.+..|+|+...
T Consensus 197 ~~~dl~~~~~~~~ieiv~~qsf~~-------dp~~~vk~l~~~D~RiI~g~f~~~~Arkv~C~~Y~~~myg~ky~w~~~g 269 (865)
T KOG1055|consen 197 TLNDLEARLKEAGIEIVFRQSFSS-------DPADSVKNLKRQDARIIVGLFYETEARKVFCEAYKERLYGRKYVWFLIG 269 (865)
T ss_pred hHHHHHHhhhccccEEEEeecccc-------CHHHHHhhccccchhheeccchHhhhhHHHHhhchhhcccceeEEEEEE
Confidence 999999999999999998876643 4556789999999999999999999999999999999999999999987
Q ss_pred cccccc-----cCCCCCchhhhhhccceEEEEEec--CCC------hhhHHHHHHHHhhcC---CCCCCCchhhHHhhHH
Q 002211 278 WLSTFI-----DSKSPLSLKTAKSILGALTLRQHT--PDS------KRRRDFVSRWNTLSN---GSIGLNPYGLYAYDTV 341 (953)
Q Consensus 278 ~~~~~~-----~~~~~~~~~~~~~~~g~~~~~~~~--~~~------~~~~~F~~~~~~~~~---~~~~~~~~~~~~YDAv 341 (953)
|....+ +...|+-.++..+++|.+++.... +.. -..+.|...+.++.+ ..........++|||+
T Consensus 270 ~y~d~w~ev~~~~~~ctveem~~A~eg~~s~e~~pl~~~~~~tisg~T~~~~l~~~~~~r~~~~~~~~~~~~~~~ayd~I 349 (865)
T KOG1055|consen 270 WYADNWWEITHPSENCTVEEMTEAAEGHITTEFVMLSPANITTISGMTAQEFLEELTKYRKRHPEETGGFQEAPLAYDAI 349 (865)
T ss_pred eeccchhhccCchhhhhHHHHHHHHhhheeeeeeccccccceeeccchhHHHHHHHHhhhccccccccCcccCchHHHHH
Confidence 655433 222344467888999988876532 211 123556655544432 2234566788999999
Q ss_pred HHHHHHHHHHHhcCCcccccCCCccCCCCCCcccCCCccccCchHHHHHHHHhcccCCcceeEEEccCCCCCCccEEEEE
Q 002211 342 WMIARALKLFLDQGNTISFSNDTKLNGLGGGTLNLGALSIFDGGKKFLANILQTNMTGLSGPIHFNQDRSLLHPSYDIIN 421 (953)
Q Consensus 342 ~~la~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~f~G~tG~v~Fd~~g~~~~~~y~I~~ 421 (953)
|++|+|++++....+.... + ..+.+..... -.++|++++.+++|.|++|.|.|.+ |+| ...-.|-|
T Consensus 350 wa~ala~n~t~e~l~~~~~----~-------l~~f~y~~k~-i~d~i~eamn~tsF~GvsG~V~F~~-geR-~a~t~ieQ 415 (865)
T KOG1055|consen 350 WALALALNKTMEGLGRSHV----R-------LEDFNYNNKT-IADQIYEAMNSTSFEGVSGHVVFSN-GER-MALTLIEQ 415 (865)
T ss_pred HHHHHHHHHHHhcCCccce----e-------ccccchhhhH-HHHHHHHHhhcccccccccceEecc-hhh-HHHHHHHH
Confidence 9999999999765431110 0 0011111111 2678999999999999999999976 986 56668888
Q ss_pred eecCCeeeEEEEecCCC
Q 002211 422 VIEHGYPQQIGYWSNYS 438 (953)
Q Consensus 422 ~~~~~~~~~VG~w~~~~ 438 (953)
++++.. +++|+|+...
T Consensus 416 ~qdg~y-~k~g~Yds~~ 431 (865)
T KOG1055|consen 416 FQDGKY-KKIGYYDSTK 431 (865)
T ss_pred HhCCce-Eeeccccccc
Confidence 888888 9999998775
No 76
>TIGR03863 PQQ_ABC_bind ABC transporter, substrate binding protein, PQQ-dependent alcohol dehydrogenase system. Members of this protein family are putative substrate-binding proteins of an ABC transporter family that associates, in gene neighborhood and phylogenomic profile, with pyrroloquinoline-quinone (PQQ)-dependent degradation of certain alcohols, such as 2-phenylethanol in Pseudomonas putida U.
Probab=99.98 E-value=3.5e-31 Score=290.38 Aligned_cols=296 Identities=16% Similarity=0.118 Sum_probs=235.7
Q ss_pred CchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEEccCChhhHHHHHHhhhhCCCc
Q 002211 61 VNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIVGPQSAVMAHVLSHLANELQVP 140 (953)
Q Consensus 61 ~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aiiGp~~S~~a~av~~v~~~~~vP 140 (953)
..+...++|++||+||||+.||++ |++|+++..|. ++|..++..+++|++++|.+|+|+.+|+++.++.+++++.++|
T Consensus 8 ~~~~~~~~ga~lAveeiNaaGGv~-G~~ielv~~D~-~~p~~a~~~a~~Li~~~V~~vvG~~~S~~~~Av~~~a~~~~vp 85 (347)
T TIGR03863 8 PPEDRGLDGARLAIEDNNTTGRFL-GQTFTLDEVAV-RTPEDLVAALKALLAQGVRFFVLDLPAAALLALADAAKAKGAL 85 (347)
T ss_pred CCcchHHHHHHHHHHHHHhhCCcC-CceEEEEEccC-CCHHHHHHHHHHHHHCCCCEEEecCChHHHHHHHHHHHhCCcE
Confidence 345678999999999999999997 89999999985 7899999999999988999999999999999999999999999
Q ss_pred EEEeecCCCCCCC-CCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecCccccchHHHHHHHHHhcCcEEEEEEec
Q 002211 141 LLSFTALDPTLSP-LQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDDDQGRNGVTALGDKLAEIRCKISYKSAL 219 (953)
Q Consensus 141 ~Is~~at~~~ls~-~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~~~g~~~~~~l~~~l~~~g~~v~~~~~~ 219 (953)
+|+++++++.++. ..+||+||+.+++..++.++++++...+.|+|++|+.|++||+...+.+++.+++.|++|+..+.+
T Consensus 86 ~i~~~a~~~~lt~~~c~~~~Fr~~~~~~~~~~ala~~~~~~g~kkvaii~~~~~~g~~~~~~~~~~~~~~G~~vv~~~~~ 165 (347)
T TIGR03863 86 LFNAGAPDDALRGADCRANLLHTLPSRAMLADALAQYLAAKRWRRILLIQGPLPADALYADAFRRSAKRFGAKIVAERPF 165 (347)
T ss_pred EEeCCCCChHHhCCCCCCCEEEecCChHhHHHHHHHHHHHcCCCEEEEEeCCCcccHHHHHHHHHHHHHCCCEEEEeEEe
Confidence 9999999999987 567999999999999999999998888999999999999999999999999999999999999988
Q ss_pred CCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEEeCcccccccCCCCCchhhhhhccc
Q 002211 220 PPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIATTWLSTFIDSKSPLSLKTAKSILG 299 (953)
Q Consensus 220 ~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~~~~~~~~~~~~~~g 299 (953)
+.+......|++......+.++||+|++.....+....+.... +. .... ....|
T Consensus 166 ~~~~~~~~~d~s~~~~~~~~s~pDvv~~~~~~~~~~~~~~~~~--~~---~~~~---------------------~g~~G 219 (347)
T TIGR03863 166 TFSGDPRRTDQSEVPLFTQGADYDVVVVADEAGEFARYLPYAT--WL---PRPV---------------------AGSAG 219 (347)
T ss_pred ccCCchhhhhcccCceeecCCCCCEEEEecchhhHhhhccccc--cc---cccc---------------------ccccC
Confidence 8652122345553233334489999999766544322111000 00 0000 11123
Q ss_pred eEEEEEe-cCCChhhHHHHHHHHhhcCCCCCCCchhhHHhhHHHHHHHHHHHHHhcCCcccccCCCccCCCCCCcccCCC
Q 002211 300 ALTLRQH-TPDSKRRRDFVSRWNTLSNGSIGLNPYGLYAYDTVWMIARALKLFLDQGNTISFSNDTKLNGLGGGTLNLGA 378 (953)
Q Consensus 300 ~~~~~~~-~~~~~~~~~F~~~~~~~~~~~~~~~~~~~~~YDAv~~la~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 378 (953)
+....++ ..+.+..++|.++|+++|+ ..|+.+++.+||++++++.|++++++.
T Consensus 220 ~~~~~~~~~~~~~~~~~f~~~f~~~~g--~~p~~~~a~aY~av~~~a~Ai~~AGs~------------------------ 273 (347)
T TIGR03863 220 LVPTAWHRAWERWGATQLQSRFEKLAG--RPMTELDYAAWLAVRAVGEAVTRTRSA------------------------ 273 (347)
T ss_pred ccccccCCcccchhHHHHHHHHHHHhC--CCCChHHHHHHHHHHHHHHHHHHhcCC------------------------
Confidence 2222221 2234678999999999997 677888999999999999999998543
Q ss_pred ccccCchHHHHHHHHhccc--CCcce-eEEEcc-CCCCCCc
Q 002211 379 LSIFDGGKKFLANILQTNM--TGLSG-PIHFNQ-DRSLLHP 415 (953)
Q Consensus 379 ~~~~~~~~~l~~~l~~~~f--~G~tG-~v~Fd~-~g~~~~~ 415 (953)
++++|+++|+++++ .+..| +++|.+ ||+...+
T Consensus 274 -----d~~aV~~aL~~~~~~~~~~~g~~~~~R~~Dhq~~~~ 309 (347)
T TIGR03863 274 -----DPATLRDYLLSDEFELAGFKGRPLSFRPWDGQLRQP 309 (347)
T ss_pred -----CHHHHHHHHcCCCceecccCCCcceeeCCCcccccc
Confidence 59999999999887 57887 699985 7775444
No 77
>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=99.98 E-value=3.8e-30 Score=286.13 Aligned_cols=317 Identities=14% Similarity=0.162 Sum_probs=262.9
Q ss_pred EEEeEEEecCC---CchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhc-CcEEEEccCChh
Q 002211 50 LNVGAIFSFGT---VNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMET-DTLAIVGPQSAV 125 (953)
Q Consensus 50 i~IG~l~~~~~---~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~-~v~aiiGp~~S~ 125 (953)
|+||++.|+|. ..|+....|+++|+++||++||+. |++|+++..|+++||..+.+.+++|+++ +|.+|||+.+|.
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 IVLGQSAPLSGPAAALGRAYRAGAQAYFDAVNAAGGVN-GRKIELVTLDDGYEPERTVANTRKLIEDDKVFALFGYVGTP 79 (336)
T ss_pred CEEEEeccCCCcchhhHHHHHHHHHHHHHHHHhcCCcC-CceEEEEEeCCCCChHHHHHHHHHHHhhcCcEEEEeCCCch
Confidence 68999999984 458889999999999999999985 9999999999999999999999999996 999999999888
Q ss_pred hHHHHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecCccccchHHHHHHH
Q 002211 126 MAHVLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDDDQGRNGVTALGDK 205 (953)
Q Consensus 126 ~a~av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~~~g~~~~~~l~~~ 205 (953)
.+.++.+++.+.++|+|+++++++.++....|++||+.+++..++..+++++.+.||+++++++.++.||+...+.+++.
T Consensus 80 ~~~~~~~~~~~~~iP~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~g~~~v~~l~~~~~~~~~~~~~~~~~ 159 (336)
T cd06326 80 TTAAALPLLEEAGVPLVGPFTGASSLRDPPDRNVFNVRASYADEIAAIVRHLVTLGLKRIAVFYQDDAFGKDGLAGVEKA 159 (336)
T ss_pred hHHHHHHHHHHcCCeEEEecCCcHHhcCCCCCceEEeCCChHHHHHHHHHHHHHhCCceEEEEEecCcchHHHHHHHHHH
Confidence 88888899999999999987766656544468999999999999999999999999999999999999999999999999
Q ss_pred HHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEEeCcccccccC
Q 002211 206 LAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIATTWLSTFIDS 285 (953)
Q Consensus 206 l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~ 285 (953)
+++.|++++....++.+ ..|+..++.++++.++|+|++......+..++++++++|+..+ ++...+..... .
T Consensus 160 ~~~~G~~~~~~~~~~~~----~~d~~~~~~~l~~~~~dav~~~~~~~~a~~~i~~~~~~G~~~~---~~~~~~~~~~~-~ 231 (336)
T cd06326 160 LAARGLKPVATASYERN----TADVAAAVAQLAAARPQAVIMVGAYKAAAAFIRALRKAGGGAQ---FYNLSFVGADA-L 231 (336)
T ss_pred HHHcCCCeEEEEeecCC----cccHHHHHHHHHhcCCCEEEEEcCcHHHHHHHHHHHhcCCCCc---EEEEeccCHHH-H
Confidence 99999998887777765 6789999999999999999999988889999999999998542 22222222110 0
Q ss_pred CCCCchhhhhhccceEEEEEe----cCCChhhHHHHHHHHhhcCCCCCCCchhhHHhhHHHHHHHHHHHHHhcCCccccc
Q 002211 286 KSPLSLKTAKSILGALTLRQH----TPDSKRRRDFVSRWNTLSNGSIGLNPYGLYAYDTVWMIARALKLFLDQGNTISFS 361 (953)
Q Consensus 286 ~~~~~~~~~~~~~g~~~~~~~----~~~~~~~~~F~~~~~~~~~~~~~~~~~~~~~YDAv~~la~Al~~~~~~~~~~~~~ 361 (953)
........+|++..... ....|..++|.++|+++++. .+++.++..+||+++++++|++++...
T Consensus 232 ----~~~~g~~~~g~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~-~~~~~~~~~~y~~~~~~~~a~~~~g~~------- 299 (336)
T cd06326 232 ----ARLLGEYARGVIVTQVVPNPWSRTLPIVREYQAAMKAYGPG-APPSYVSLEGYIAAKVLVEALRRAGPD------- 299 (336)
T ss_pred ----HHHhhhhhcceEEEEEecCccccCCHHHHHHHHHHHhhCCC-CCCCeeeehhHHHHHHHHHHHHHcCCC-------
Confidence 02234566787654321 23467889999999998752 367888999999999999999986321
Q ss_pred CCCccCCCCCCcccCCCccccCchHHHHHHHHhccc-CCcceeEEEcc
Q 002211 362 NDTKLNGLGGGTLNLGALSIFDGGKKFLANILQTNM-TGLSGPIHFNQ 408 (953)
Q Consensus 362 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~f-~G~tG~v~Fd~ 408 (953)
.+++.|+++|++++. .+..|.+.|++
T Consensus 300 ---------------------~~~~~v~~al~~~~~~~~~g~~~~~~~ 326 (336)
T cd06326 300 ---------------------PTRESLLAALEAMGKFDLGGFRLDFSP 326 (336)
T ss_pred ---------------------CCHHHHHHHHHhcCCCCCCCeEEecCc
Confidence 148899999999885 55545899975
No 78
>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=99.98 E-value=3.2e-31 Score=292.91 Aligned_cols=302 Identities=15% Similarity=0.130 Sum_probs=248.9
Q ss_pred EEeEEEecCC---CchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEEccCChhhH
Q 002211 51 NVGAIFSFGT---VNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIVGPQSAVMA 127 (953)
Q Consensus 51 ~IG~l~~~~~---~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aiiGp~~S~~a 127 (953)
+||++.|++. .+|.....|+++|++++| |++++++++|+++ |..++..+.+|++++|.+||||.+|..+
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 5999999985 468899999999999999 6889999999999 9999999999999899999999999999
Q ss_pred HHHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecCccccchHHHHHHHHH
Q 002211 128 HVLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDDDQGRNGVTALGDKLA 207 (953)
Q Consensus 128 ~av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~~~g~~~~~~l~~~l~ 207 (953)
.++++++.+.+||+|+++++++ +.. .||+||+.+++..++.++++++.+.|++++++++.+++||++..+.|.+.++
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 9999999999999999765543 322 5899999999999999999999888999999999999999999999999999
Q ss_pred hcCcEEEEEEecCCCCCCChHHHHHHHHHHhcC---------------------CceEEEEEcchh-hHHHHHHHHHHcC
Q 002211 208 EIRCKISYKSALPPDQSVTETDVRNELVKVRMM---------------------EARVIVVHGYSR-TGLMVFDVAQRLG 265 (953)
Q Consensus 208 ~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~---------------------~~~vii~~~~~~-~~~~~~~~a~~~g 265 (953)
+.|++|+..+.++.+ ..||+.++++|++. +||+|++.+.+. ++..+.++++..+
T Consensus 150 ~~G~~vv~~~~~~~~----~~d~~~~i~~i~~~~~~~~~~~~~~~~~~~~~~~~~~d~v~~~~~~~~~~~~~~~~~~~~~ 225 (336)
T cd06339 150 QLGGTVVAIESYDPS----PTDLSDAIRRLLGVDDSEQRIAQLKSLESEPRRRQDIDAIDAVALPDGEARLIKPQLLFYY 225 (336)
T ss_pred HcCCceeeeEecCCC----HHHHHHHHHHHhccccchhhhhhhhhcccCccccCCCCcEEEEecChhhhhhhcchhhhhc
Confidence 999999999999887 89999999999998 999999988886 7777777777665
Q ss_pred CCCCceEEEEeCcccccccCCCCCchhhhhhccceEEEEEecCCChhhHHHHHHHHhhcCCCCCC-CchhhHHhhHHHHH
Q 002211 266 MMDSGYVWIATTWLSTFIDSKSPLSLKTAKSILGALTLRQHTPDSKRRRDFVSRWNTLSNGSIGL-NPYGLYAYDTVWMI 344 (953)
Q Consensus 266 ~~~~~~~wi~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~F~~~~~~~~~~~~~~-~~~~~~~YDAv~~l 344 (953)
....+-.+++++++.+.... ....+..+|++...+.. ....+|.++|+++|+ ..| +.+++.+|||+.++
T Consensus 226 ~~~~~~~~~g~~~~~~~~~~-----~~~g~~~~g~~~~~~~~---~~~~~f~~~y~~~~~--~~p~~~~~a~~YDa~~l~ 295 (336)
T cd06339 226 GVPGDVPLYGTSRWYSGTPA-----PLRDPDLNGAWFADPPW---LLDANFELRYRAAYG--WPPLSRLAALGYDAYALA 295 (336)
T ss_pred cCcCCCCEEEeccccCCCCC-----cccCcccCCcEEeCCCc---ccCcchhhhHHHHhc--CCCCchHHHHHHhHHHHH
Confidence 31113347777766643111 12335677876554421 223489999999987 567 89999999999999
Q ss_pred HHHHHHHHhcCCcccccCCCccCCCCCCcccCCCccccCchHHHHHHHHh-cccCCcceeEEEccCCCC
Q 002211 345 ARALKLFLDQGNTISFSNDTKLNGLGGGTLNLGALSIFDGGKKFLANILQ-TNMTGLSGPIHFNQDRSL 412 (953)
Q Consensus 345 a~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~-~~f~G~tG~v~Fd~~g~~ 412 (953)
+.++++... +. +|.+ ..|+|++|+++||++|+.
T Consensus 296 ~~~~~~~~~------------------------------~~-----al~~~~~~~g~~G~~~f~~~g~~ 329 (336)
T cd06339 296 AALAQLGQG------------------------------DA-----ALTPGAGFSGVTGVLRLDPDGVI 329 (336)
T ss_pred HHHHHcccc------------------------------cc-----ccCCCCccccCcceEEECCCCeE
Confidence 987776311 11 3333 359999999999999973
No 79
>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=99.97 E-value=1.7e-28 Score=273.27 Aligned_cols=308 Identities=12% Similarity=0.083 Sum_probs=253.7
Q ss_pred EEeEEEecC---CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhc-CcEEEEccCChhh
Q 002211 51 NVGAIFSFG---TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMET-DTLAIVGPQSAVM 126 (953)
Q Consensus 51 ~IG~l~~~~---~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~-~v~aiiGp~~S~~ 126 (953)
+||+++|++ +..|.....|+++|++++|+.||+. |+++++++.|++++|..+.+.+.+|+++ +|.+|||+.+|..
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 KIGLLYPDTGVAAVSFPGARAGADAAAGYANAAGGIA-GRPIEYVWCDDQGDPASAAACARDLVEDDKVVAVVGGSSGAG 79 (341)
T ss_pred CeEEEecCCCchhhccHHHHHHHHHHHHHHHhcCCcC-CceEEEEEecCCCChhHHHHHHHHHHHhcCceEEEecccccc
Confidence 699999998 4678999999999999999999995 8999999999999999999999999998 9999999999888
Q ss_pred HHHHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecCc-cccchHHHHHHH
Q 002211 127 AHVLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDDD-QGRNGVTALGDK 205 (953)
Q Consensus 127 a~av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~~-~g~~~~~~l~~~ 205 (953)
+.++ +++++.++|+|+++++++.++. .|++|++.+++..++.++++++...+.+++++++.++. ||+...+.+++.
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 7766 8999999999998777766553 57889999999999999999999989999999987665 999999999999
Q ss_pred HHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEEeCcccccccC
Q 002211 206 LAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIATTWLSTFIDS 285 (953)
Q Consensus 206 l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~ 285 (953)
+++.|++++....++.+ ..|+...+.++++.+||+|++......+..++++++++|+..+.. +......... .
T Consensus 157 ~~~~G~~v~~~~~~~~~----~~d~~~~~~~i~~~~pdaV~~~~~~~~a~~~~~~~~~~G~~~~~~--~~~~~~~~~~-~ 229 (341)
T cd06341 157 LAAAGVSVAGIVVITAT----APDPTPQAQQAAAAGADAIITVLDAAVCASVLKAVRAAGLTPKVV--LSGTCYDPAL-L 229 (341)
T ss_pred HHHcCCccccccccCCC----CCCHHHHHHHHHhcCCCEEEEecChHHHHHHHHHHHHcCCCCCEE--EecCCCCHHH-H
Confidence 99999999887777665 678999999999999999999999889999999999999876522 2222221111 0
Q ss_pred CCCCchhhhhhccceEEEEEecC---CChhhHHHHHHHHhhcC-CCCCCCchhhHHhhHHHHHHHHHHHHHhcCCccccc
Q 002211 286 KSPLSLKTAKSILGALTLRQHTP---DSKRRRDFVSRWNTLSN-GSIGLNPYGLYAYDTVWMIARALKLFLDQGNTISFS 361 (953)
Q Consensus 286 ~~~~~~~~~~~~~g~~~~~~~~~---~~~~~~~F~~~~~~~~~-~~~~~~~~~~~~YDAv~~la~Al~~~~~~~~~~~~~ 361 (953)
....+..+|++...++.| +.|..+.|.+.+++... ....++.++..+||+++++++|++++...
T Consensus 230 -----~~~g~~~~g~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~yda~~~~~~a~~~ag~~------- 297 (341)
T cd06341 230 -----AAPGPALAGVYIAVFYRPFESGTPAVALYLAAMARYAPQLDPPEQGFALIGYIAADLFLRGLSGAGGC------- 297 (341)
T ss_pred -----HhcCcccCceEEEeeeccccCCCHHHHHHHHHHHHhCCCCCCCcchHHHHHHHHHHHHHHHHHhcCCC-------
Confidence 234467899888877765 46778888876654332 11468899999999999999999997321
Q ss_pred CCCccCCCCCCcccCCCccccCchHH-HHHHHHhcccCCcce
Q 002211 362 NDTKLNGLGGGTLNLGALSIFDGGKK-FLANILQTNMTGLSG 402 (953)
Q Consensus 362 ~~~~~~~~~~~~~~~~~~~~~~~~~~-l~~~l~~~~f~G~tG 402 (953)
.+++. ++++|++++.....|
T Consensus 298 ---------------------~~~~~~v~~al~~~~~~~~~g 318 (341)
T cd06341 298 ---------------------PTRASQFLRALRAVTDYDAGG 318 (341)
T ss_pred ---------------------CChHHHHHHHhhcCCCCCCCC
Confidence 13666 999999998544444
No 80
>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=99.96 E-value=6.5e-28 Score=264.94 Aligned_cols=278 Identities=20% Similarity=0.284 Sum_probs=233.6
Q ss_pred EEeEEEecC---CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhc-CcEEEEccCChhh
Q 002211 51 NVGAIFSFG---TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMET-DTLAIVGPQSAVM 126 (953)
Q Consensus 51 ~IG~l~~~~---~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~-~v~aiiGp~~S~~ 126 (953)
+||+++|++ +..|.....|+++|+++||+ ||+. |+++++++.|+++++..+.+.+.+|+++ +|.+|||+.+|..
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-GGIG-GEKVELIVLDDGSDPTKAVTNARKLIEEDKVDAIIGPSTTPA 78 (312)
T ss_pred CeeEEeecCCcchhhCHHHHHHHHHHHHHHhc-CCcC-CeEEEEEEecCCCCHHHHHHHHHHHHhhCCeEEEECCCCCHH
Confidence 699999998 55688899999999999999 8885 9999999999999999999999999986 9999999998888
Q ss_pred HHHHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecCccccchHHHHHHHH
Q 002211 127 AHVLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDDDQGRNGVTALGDKL 206 (953)
Q Consensus 127 a~av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~~~g~~~~~~l~~~l 206 (953)
+.++.+++.+.++|+|+++++++.+. ...+|+||+.+++..++..+++++.+.||++|++++.++.+|+...+.+.+.+
T Consensus 79 ~~~~~~~~~~~~vP~v~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~l~~~g~~~vail~~~~~~~~~~~~~~~~~~ 157 (312)
T cd06333 79 TMAVAPVAEEAKTPMISLAPAAAIVE-PKRKWVFKTPQNDRLMAEAILADMKKRGVKTVAFIGFSDAYGESGLKELKALA 157 (312)
T ss_pred HHHHHHHHHhcCCCEEEccCCccccC-CCCCcEEEcCCCcHHHHHHHHHHHHHcCCCEEEEEecCcHHHHHHHHHHHHHH
Confidence 88889999999999999877665443 34689999999999999999999999999999999999999999999999999
Q ss_pred HhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEEeCcccccccCC
Q 002211 207 AEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIATTWLSTFIDSK 286 (953)
Q Consensus 207 ~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~~ 286 (953)
++.|++++....++.+ ..|+...+.++++.+||+|++......+..+++++++.|+..+ ++++++.... +..
T Consensus 158 ~~~G~~v~~~~~~~~~----~~d~~~~~~~l~~~~pdaIi~~~~~~~~~~~~~~l~~~g~~~p---~~~~~~~~~~-~~~ 229 (312)
T cd06333 158 PKYGIEVVADERYGRT----DTSVTAQLLKIRAARPDAVLIWGSGTPAALPAKNLRERGYKGP---IYQTHGVASP-DFL 229 (312)
T ss_pred HHcCCEEEEEEeeCCC----CcCHHHHHHHHHhCCCCEEEEecCCcHHHHHHHHHHHcCCCCC---EEeecCcCcH-HHH
Confidence 9999999887777765 5678999999988899999999888888889999999998654 3344333221 110
Q ss_pred CCCchhhhhhccceEEEEEe------cC----CChhhHHHHHHHHhhcCCCCC-CCchhhHHhhHHHHHH
Q 002211 287 SPLSLKTAKSILGALTLRQH------TP----DSKRRRDFVSRWNTLSNGSIG-LNPYGLYAYDTVWMIA 345 (953)
Q Consensus 287 ~~~~~~~~~~~~g~~~~~~~------~~----~~~~~~~F~~~~~~~~~~~~~-~~~~~~~~YDAv~~la 345 (953)
....+..+|++.+..+ .| ..+..++|.++|+++|+ .. |..+++.+|||+++++
T Consensus 230 ----~~~g~~~~g~~~~~~~~~~~~~~p~~~~~~~~~~~f~~~~~~~~g--~~~~~~~~~~~Yda~~~~~ 293 (312)
T cd06333 230 ----RLAGKAAEGAILPAGPVLVADQLPDSDPQKKVALDFVKAYEAKYG--AGSVSTFGGHAYDALLLLA 293 (312)
T ss_pred ----HHhhHhhcCcEeecccceeeeeCCCCCcchHHHHHHHHHHHHHhC--CCCCCchhHHHHHHHHHHH
Confidence 2334567887665321 22 24578999999999986 44 8889999999999999
No 81
>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=5.9e-28 Score=263.59 Aligned_cols=224 Identities=30% Similarity=0.499 Sum_probs=208.5
Q ss_pred EEeEEEecCC-----CchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhc-----CcEEEEc
Q 002211 51 NVGAIFSFGT-----VNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMET-----DTLAIVG 120 (953)
Q Consensus 51 ~IG~l~~~~~-----~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~-----~v~aiiG 120 (953)
+||++++.+. ..+.....++.+|++++|++ ++|++|++++.|+++++..+...+.+++++ ++.+|+|
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 4899999875 34667789999999999998 579999999999999999999999999975 8999999
Q ss_pred cCChhhHHHHHHhhhhCCCcEEEeecCCCCCCC-CCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecCccccchH
Q 002211 121 PQSAVMAHVLSHLANELQVPLLSFTALDPTLSP-LQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDDDQGRNGV 199 (953)
Q Consensus 121 p~~S~~a~av~~v~~~~~vP~Is~~at~~~ls~-~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~~~g~~~~ 199 (953)
|.+|..+.+++++++.+++|+|+++++++.+++ ..+||+||+.|++..++.+++++++++||++|+++|+++++|....
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 999999999999999999999999999999887 6789999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEEeCcc
Q 002211 200 TALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIATTWL 279 (953)
Q Consensus 200 ~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~ 279 (953)
+.+++.+++.|+++.....++.+ ..++...+++++..+++|||+++.+.++..++++++++||+ .+++||.++.+
T Consensus 158 ~~~~~~~~~~~~~v~~~~~~~~~----~~~~~~~l~~l~~~~~~viv~~~~~~~~~~~l~~a~~~g~~-~~~~~i~~~~~ 232 (298)
T cd06269 158 ELLEEELEKNGICVAFVESIPDG----SEDIRRLLKELKSSTARVIVVFSSEEDALRLLEEAVELGMM-TGYHWIITDLW 232 (298)
T ss_pred HHHHHHHHHCCeeEEEEEEcCCC----HHHHHHHHHHHHhcCCcEEEEEechHHHHHHHHHHHHcCCC-CCeEEEEEChh
Confidence 99999999999999999888876 68999999999999999999999999999999999999998 89999999977
Q ss_pred ccc
Q 002211 280 STF 282 (953)
Q Consensus 280 ~~~ 282 (953)
...
T Consensus 233 ~~~ 235 (298)
T cd06269 233 LTS 235 (298)
T ss_pred hcc
Confidence 643
No 82
>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=99.96 E-value=1.7e-27 Score=260.10 Aligned_cols=280 Identities=23% Similarity=0.351 Sum_probs=241.5
Q ss_pred EEeEEEecC---CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhc-CcEEEEccCChhh
Q 002211 51 NVGAIFSFG---TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMET-DTLAIVGPQSAVM 126 (953)
Q Consensus 51 ~IG~l~~~~---~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~-~v~aiiGp~~S~~ 126 (953)
+||+++|++ +..|.....|+++|++++|+++|+ .|+++++++.|+++++..+.+.+.+++++ +|.+||||.++..
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 456888999999999999999977 58999999999999999999999999998 9999999999999
Q ss_pred HHHHHHhhhhCCCcEEEeecCCCCCCC-CCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecCccccchHHHHHHH
Q 002211 127 AHVLSHLANELQVPLLSFTALDPTLSP-LQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDDDQGRNGVTALGDK 205 (953)
Q Consensus 127 a~av~~v~~~~~vP~Is~~at~~~ls~-~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~~~g~~~~~~l~~~ 205 (953)
+.+++++++..+||+|++.+.++.+.+ ..+|++||+.|++..++..+++++.++||+++++++.++.++....+.+++.
T Consensus 80 ~~~~~~~~~~~~iP~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~v~iv~~~~~~~~~~~~~~~~~ 159 (299)
T cd04509 80 ALAVAPVAEALKIPLISPGATAPGLTDKKGYPYLFRTGPSDEQQAEALADYIKEYNWKKVAILYDDDSYGRGLLEAFKAA 159 (299)
T ss_pred HHHHHHHHhhCCceEEeccCCCcccccccCCCCEEEecCCcHHHHHHHHHHHHHcCCcEEEEEecCchHHHHHHHHHHHH
Confidence 999999999999999999888777665 5689999999999999999999999999999999999999999999999999
Q ss_pred HHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEEeCcccccccC
Q 002211 206 LAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIATTWLSTFIDS 285 (953)
Q Consensus 206 l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~ 285 (953)
+++.|++++....++.+ .+++...++++++.++|+|++++.+..+..++++++++|+. .++.|+..+.+......
T Consensus 160 ~~~~g~~i~~~~~~~~~----~~~~~~~~~~l~~~~~~~v~~~~~~~~~~~~~~~~~~~g~~-~~~~~i~~~~~~~~~~~ 234 (299)
T cd04509 160 FKKKGGTVVGEEYYPLG----TTDFTSLLQKLKAAKPDVIVLCGSGEDAATILKQAAEAGLT-GGYPILGITLGLSDVLL 234 (299)
T ss_pred HHHcCCEEEEEecCCCC----CccHHHHHHHHHhcCCCEEEEcccchHHHHHHHHHHHcCCC-CCCcEEecccccCHHHH
Confidence 99999999877777665 46889999999988899999999889999999999999998 78899998876543221
Q ss_pred CCCCchhhhhhccceEEEEEecCCCh--hhHHHH---HHHHhhcCCCCCCCchhhHHhhHHHH
Q 002211 286 KSPLSLKTAKSILGALTLRQHTPDSK--RRRDFV---SRWNTLSNGSIGLNPYGLYAYDTVWM 343 (953)
Q Consensus 286 ~~~~~~~~~~~~~g~~~~~~~~~~~~--~~~~F~---~~~~~~~~~~~~~~~~~~~~YDAv~~ 343 (953)
....+..+|+++..++.+..+ ..+.|. ..+++.++ ..++.+++++|||+++
T Consensus 235 -----~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~yda~~~ 290 (299)
T cd04509 235 -----EAGGEAAEGVLTGTPYFPGDPPPESFFFVRAAAREKKKYE--DQPDYFAALAYDAVLL 290 (299)
T ss_pred -----HHhHHhhcCcEEeeccCCCCCChHHHHHHhHHHHHHHHhC--CCCChhhhhhcceeee
Confidence 134567889988887765433 334443 44555544 6788999999999998
No 83
>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=99.95 E-value=1.6e-25 Score=244.34 Aligned_cols=280 Identities=21% Similarity=0.327 Sum_probs=241.1
Q ss_pred EEeEEEecC---CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEEccCChhhH
Q 002211 51 NVGAIFSFG---TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIVGPQSAVMA 127 (953)
Q Consensus 51 ~IG~l~~~~---~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aiiGp~~S~~a 127 (953)
+||+++|++ +..|.....|+++|++++|+.||+ +|++++++++|+++++..+.+.++++++++|.+||||.++..+
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 589999997 567889999999999999999988 4899999999999999999999999999999999999999888
Q ss_pred HHHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcC-CcEEEEEEecCccccchHHHHHHHH
Q 002211 128 HVLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFG-WGEVIAIFNDDDQGRNGVTALGDKL 206 (953)
Q Consensus 128 ~av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~-w~~vaii~~d~~~g~~~~~~l~~~l 206 (953)
.++.+.+.+.+||+|++.+.++.+.+..+|++|++.+++..++.++++++.+.+ |+++++++.+++++....+.+.+.+
T Consensus 80 ~~~~~~~~~~~ip~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~v~~~~~~~~~~~~~~~~~~ 159 (298)
T cd06268 80 LAAAPVAEEAGVPLISPGATSPALTGKGNPYVFRTAPSDAQQAAALADYLAEKGKVKKVAIIYDDYAYGRGLAAAFREAL 159 (298)
T ss_pred HhhHHHHHhCCCcEEccCCCCcccccCCCceEEEcccCcHHHHHHHHHHHHHhcCCCEEEEEEcCCchhHHHHHHHHHHH
Confidence 899999999999999998887766544579999999999999999999998888 9999999999999999999999999
Q ss_pred HhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEEeCcccccccCC
Q 002211 207 AEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIATTWLSTFIDSK 286 (953)
Q Consensus 207 ~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~~ 286 (953)
++.|++++....++.+ ..++...++++++.++|+|++.+.+..+..+++++++.|+ +..|+..+.+......
T Consensus 160 ~~~g~~i~~~~~~~~~----~~~~~~~~~~l~~~~~~~vi~~~~~~~~~~~~~~~~~~g~---~~~~~~~~~~~~~~~~- 231 (298)
T cd06268 160 KKLGGEVVAEETYPPG----ATDFSPLIAKLKAAGPDAVFLAGYGGDAALFLKQAREAGL---KVPIVGGDGAAAPALL- 231 (298)
T ss_pred HHcCCEEEEEeccCCC----CccHHHHHHHHHhcCCCEEEEccccchHHHHHHHHHHcCC---CCcEEecCccCCHHHH-
Confidence 9999999887777655 5688999999999999999999988999999999999997 3457777765443211
Q ss_pred CCCchhhhhhccceEEEEEecCC--ChhhHHHH-HHHHhhcCCCCCCCchhhHHhhHHHHHH
Q 002211 287 SPLSLKTAKSILGALTLRQHTPD--SKRRRDFV-SRWNTLSNGSIGLNPYGLYAYDTVWMIA 345 (953)
Q Consensus 287 ~~~~~~~~~~~~g~~~~~~~~~~--~~~~~~F~-~~~~~~~~~~~~~~~~~~~~YDAv~~la 345 (953)
....+..+|++...++.+. .+....|. ++|++.++ ..++.++..+||++++++
T Consensus 232 ----~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~y~~~~~~~ 287 (298)
T cd06268 232 ----ELAGDAAEGVLGTTPYAPDDDDPAAAAFFQKAFKAKYG--RPPDSYAAAAYDAVRLLA 287 (298)
T ss_pred ----HhhhHhhCCcEEeccCCCCCCChhhhHHHHHHHHHHhC--CCcccchHHHHHHHHHHc
Confidence 1234567898888877654 33445565 78888876 788999999999999998
No 84
>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=99.92 E-value=1.2e-22 Score=213.24 Aligned_cols=324 Identities=13% Similarity=0.176 Sum_probs=246.7
Q ss_pred hHHHHHHHHHHHHHhcCCCCCCCcEEEE----------EEecCCC--ChHHHHHHHHHHHhc--CcEEEEccCChhhHHH
Q 002211 64 QVSRIAMKAAQDDINSDPRVLGGRKLSI----------TMHDAKF--NGFLSIMGALQFMET--DTLAIVGPQSAVMAHV 129 (953)
Q Consensus 64 ~~~~~a~~lAve~iN~~g~il~g~~l~l----------~~~D~~~--~~~~a~~~a~~li~~--~v~aiiGp~~S~~a~a 129 (953)
+..+.|++.|++.+++.. ..+|..+.+ +..+..| +.=+++++..+|+.+ .-.+++||.|.-++.+
T Consensus 18 ~~v~~av~~a~~~~~~~~-~~~g~~f~~~a~~~~~~~~~y~~~~C~sstceg~~~l~~l~~~~~~gcv~lGP~CtYat~~ 96 (380)
T cd06369 18 KFVKEAVEEAIEIVAERL-AEAGLNVTVNANFEGFNTSLYRSRGCRSSTCEGVELLKKLSVTGRLGCVLLGPSCTYATFQ 96 (380)
T ss_pred HHHHHHHHHHHHHHHhhh-hccCceEEEEEeeeccccceeccCCCCcccchHHHHHHHHHhcCccCcEEEcCccceehhh
Confidence 456889999999887755 335777777 6665554 455788888888876 6888999999999999
Q ss_pred HHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHH------HHcCCcEEEEEEecCccccc---hHH
Q 002211 130 LSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMV------SYFGWGEVIAIFNDDDQGRN---GVT 200 (953)
Q Consensus 130 v~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l------~~~~w~~vaii~~d~~~g~~---~~~ 200 (953)
++.+...+++|+||.++-. ++-...+++-|+.|+....+..+.++. ++++|+++. ||.+++-.++ .++
T Consensus 97 ~~~~~~~~~~P~ISaGsfg--lscd~k~~LTR~~pparK~~~~~~~f~~~~~~~~~~~W~~ay-vyk~~~~~edCf~~i~ 173 (380)
T cd06369 97 MVDDEFNLSLPIISAGSFG--LSCDYKENLTRLLPPARKISDFFVDFWKEKNFPKKPKWETAY-VYKKQENTEDCFWYIN 173 (380)
T ss_pred hhhhhhcCCCceEeccccc--cCCCchhhhhhcCchHHHHHHHHHHHHhcccccCCCCCceeE-EEcCCCCccceeeEhH
Confidence 9999999999999976644 332344689999999999999999998 489998665 9977643332 245
Q ss_pred HHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEEeCccc
Q 002211 201 ALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIATTWLS 280 (953)
Q Consensus 201 ~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~ 280 (953)
++....+..+..+...+.... .+++...+++++ .++||||+|+.+.+.+.++.+ |+...+|++|..|...
T Consensus 174 al~a~~~~f~~~~~~~~~l~~-----~~~~~~il~~~~-~~sRIiImCG~p~~ir~lm~~----~~~~gDYVf~~IDlF~ 243 (380)
T cd06369 174 ALEAGVAYFSSALKFKELLRT-----EEELQKLLTDKN-RKSNVIIMCGTPEDIVNLKGD----RAVAEDIVIILIDLFN 243 (380)
T ss_pred hhhhhhhhhhhcccceeeecC-----chhHHHHHHHhc-cCccEEEEeCCHHHHHHHHhc----CccCCCEEEEEEeccc
Confidence 555555555555554433322 578888888876 679999999999999999886 4445799999998765
Q ss_pred ccccCCCCCchhhhhhccceEEEEEecCCChhhHHHHHHHHhhcCCCCCCC-chhhHHhhHHHHHHHHHHHHHhcCCccc
Q 002211 281 TFIDSKSPLSLKTAKSILGALTLRQHTPDSKRRRDFVSRWNTLSNGSIGLN-PYGLYAYDTVWMIARALKLFLDQGNTIS 359 (953)
Q Consensus 281 ~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~F~~~~~~~~~~~~~~~-~~~~~~YDAv~~la~Al~~~~~~~~~~~ 359 (953)
..+.. +....++++.++.+++..|+.+.++++ ..++ .... .+++..||||.++|+||++++..+++.
T Consensus 244 ~sy~~----d~~a~~amqsVLvIT~~~p~~~~~~~~-----~~fn--~~l~~~~aa~fyDaVLLYa~AL~EtL~~G~~~- 311 (380)
T cd06369 244 DVYYE----NTTSPPYMRNVLVLTLPPRNSTNNSSF-----TTDN--SLLKDDYVAAYHDGVLLFGHVLKKFLESQEGV- 311 (380)
T ss_pred chhcc----CcchHHHHhceEEEecCCCCCcccccC-----CCCC--cchHHHHHHHHHHHHHHHHHHHHHHHHhCCCC-
Confidence 44321 134567899999999888876655441 1222 2222 889999999999999999998876542
Q ss_pred ccCCCccCCCCCCcccCCCccccCchHHHHHHHHhcccCCcceeEEEccCCCCCCccEEEEEee-cCCeeeEEEEecCCC
Q 002211 360 FSNDTKLNGLGGGTLNLGALSIFDGGKKFLANILQTNMTGLSGPIHFNQDRSLLHPSYDIINVI-EHGYPQQIGYWSNYS 438 (953)
Q Consensus 360 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~f~G~tG~v~Fd~~g~~~~~~y~I~~~~-~~~~~~~VG~w~~~~ 438 (953)
.+.++.+.++|.+|.|++|++++|++||| ..+|.++-+. +++.++.||.|+-..
T Consensus 312 ------------------------~~~~I~~~m~NrTF~GitG~V~IDeNGDR-d~dfsLl~ms~~tg~y~vV~~y~t~~ 366 (380)
T cd06369 312 ------------------------QTFSFINEFRNISFEGAGGPYTLDEYGDR-DVNFTLLYTSTDTSKYKVLFEFDTST 366 (380)
T ss_pred ------------------------CcHHHHHHHhCcceecCCCceEeCCCCCc-cCceEEEEeeCCCCCeEEEEEEECCC
Confidence 24789999999999999999999999996 8999999886 345559999997754
No 85
>PRK09495 glnH glutamine ABC transporter periplasmic protein; Reviewed
Probab=99.88 E-value=2.5e-21 Score=204.61 Aligned_cols=219 Identities=27% Similarity=0.453 Sum_probs=189.5
Q ss_pred CCcceEEEecCcccccccEEeeCCcceEEEeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEe
Q 002211 483 NGRQLRIGVPNRVSYRDFVFKVNGTDIVHGYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVG 562 (953)
Q Consensus 483 ~g~~lri~v~~~~~~~p~~~~~~~~~~~~G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~ 562 (953)
+.++|+|++.. +|+||.+.+ ++.+.|+++|+++++++++|.+++++ + .+|.+++..+.+|++|++++
T Consensus 23 ~~~~l~v~~~~--~~~P~~~~~--~g~~~G~~vdl~~~ia~~lg~~~~~~--~-------~~~~~~~~~l~~G~vDi~~~ 89 (247)
T PRK09495 23 ADKKLVVATDT--AFVPFEFKQ--GDKYVGFDIDLWAAIAKELKLDYTLK--P-------MDFSGIIPALQTKNVDLALA 89 (247)
T ss_pred cCCeEEEEeCC--CCCCeeecC--CCceEEEeHHHHHHHHHHhCCceEEE--e-------CCHHHHHHHHhCCCcCEEEe
Confidence 34689999875 799998864 57799999999999999999765554 3 34999999999999999988
Q ss_pred cEEEecCccceeeccccceecceEEEEecccCCcCcceeeccCchhHHHHHHHHHHHHHHHhhhhhcccCCCCCCCCccc
Q 002211 563 DIAIVTNRTKAVDFTQPYIESGLVVVAPVRKLNSSAWAFLRPFTPLMWAVTGVFFLVVGTVVWILEHRLNDEFRGPPRKQ 642 (953)
Q Consensus 563 ~~~~t~~r~~~vdft~p~~~~~~~~~v~~~~~~~~~~~~l~PF~~~vW~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~ 642 (953)
+++.+++|.+.++||.||..+++.+++++..
T Consensus 90 ~~~~t~~R~~~~~fs~p~~~~~~~~~~~~~~------------------------------------------------- 120 (247)
T PRK09495 90 GITITDERKKAIDFSDGYYKSGLLVMVKANN------------------------------------------------- 120 (247)
T ss_pred cCccCHHHHhhccccchheecceEEEEECCC-------------------------------------------------
Confidence 7999999999999999999999999998665
Q ss_pred chhhHHHHHHHhhccccCCcccchhHHHHHHHHHHHHHhhhhcccceeeeeeeccccCCCCChHHhhhCCCeEEEEeCch
Q 002211 643 IVTVLWFSFSTMFFAHRENTVSTLGRVVLIIWLFVVLIITSSYTASLTSILTVQQLSSPIKGIDTLMTSNDRVGYQVGSF 722 (953)
Q Consensus 643 ~~~~~~~~~~~l~~~~~~~~~s~~~R~l~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~I~sl~dL~~~~~~ig~~~~s~ 722 (953)
..+++++||. +++||+..|+.
T Consensus 121 ---------------------------------------------------------~~~~~~~dL~--g~~I~v~~g~~ 141 (247)
T PRK09495 121 ---------------------------------------------------------NDIKSVKDLD--GKVVAVKSGTG 141 (247)
T ss_pred ---------------------------------------------------------CCCCChHHhC--CCEEEEecCch
Confidence 5688999996 88999999998
Q ss_pred HHHHHHHhhCCCccceEeCCCHHHHHHHHHcCCcEEEEccchhHHHHHhcCc--ceEEeCCccccCccEEEecCCCcchH
Q 002211 723 AENYLIEELSIPKSRLVALGSPEEYAIALENRTVAAVVDERPYIDLFLSDHC--QFSVRGQEFTKSGWGFAFPRDSPLAI 800 (953)
Q Consensus 723 ~~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~g~~~a~~~~~~~~~~~~~~~~--~l~~~~~~~~~~~~~~~~~k~spl~~ 800 (953)
...++.+.. +..+++.+++.++++++|.+|++|+++.+.....+++++.. ++..++......+++++++|++.+++
T Consensus 142 ~~~~l~~~~--~~~~i~~~~~~~~~~~~L~~grvDa~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~l~~ 219 (247)
T PRK09495 142 SVDYAKANI--KTKDLRQFPNIDNAYLELGTGRADAVLHDTPNILYFIKTAGNGQFKAVGDSLEAQQYGIAFPKGSELRE 219 (247)
T ss_pred HHHHHHhcC--CCCceEEcCCHHHHHHHHHcCceeEEEeChHHHHHHHHhCCCCceEEecCcccccceEEEEcCcHHHHH
Confidence 888885532 44577889999999999999999999999988888877643 57777766666788999999999999
Q ss_pred HHHHHHHhhhccccHHHHHHHhcc
Q 002211 801 DMSTAILTLSENGELQRIHDKWLR 824 (953)
Q Consensus 801 ~~n~~i~~l~e~G~~~~~~~~w~~ 824 (953)
.+|++|.++.++|.++++.++|+.
T Consensus 220 ~~n~al~~~~~~g~~~~i~~k~~~ 243 (247)
T PRK09495 220 KVNGALKTLKENGTYAEIYKKWFG 243 (247)
T ss_pred HHHHHHHHHHHCCcHHHHHHHHcC
Confidence 999999999999999999999997
No 86
>PRK10797 glutamate and aspartate transporter subunit; Provisional
Probab=99.88 E-value=3.2e-21 Score=208.34 Aligned_cols=223 Identities=21% Similarity=0.272 Sum_probs=188.1
Q ss_pred CCcceEEEecCcccccccEEeeCCcceEEEeeHHHHHHHHH----hCCC-cccEEEeeCCCCCCCCChHHHHHHHHcCce
Q 002211 483 NGRQLRIGVPNRVSYRDFVFKVNGTDIVHGYCIDVFLAAVR----LLPY-AVPYKFIPYGDGHKNPTYSELINQITTGVF 557 (953)
Q Consensus 483 ~g~~lri~v~~~~~~~p~~~~~~~~~~~~G~~~dll~~la~----~l~~-~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~ 557 (953)
..++|+||+.. +|+||.+.++ ++.+.||++|+++++++ ++|. .+++++++ .+|..++..|.+|++
T Consensus 38 ~~g~L~Vg~~~--~~pP~~f~~~-~g~~~G~didl~~~ia~~l~~~lg~~~~~~~~v~-------~~~~~~i~~L~~G~~ 107 (302)
T PRK10797 38 KNGVIVVGHRE--SSVPFSYYDN-QQKVVGYSQDYSNAIVEAVKKKLNKPDLQVKLIP-------ITSQNRIPLLQNGTF 107 (302)
T ss_pred hCCeEEEEEcC--CCCCcceECC-CCCEeeecHHHHHHHHHHHHHhhCCCCceEEEEE-------cChHhHHHHHHCCCc
Confidence 34679999986 7999998865 67899999998777765 6664 36677777 458889999999999
Q ss_pred eEEEecEEEecCccceeeccccceecceEEEEecccCCcCcceeeccCchhHHHHHHHHHHHHHHHhhhhhcccCCCCCC
Q 002211 558 DAAVGDIAIVTNRTKAVDFTQPYIESGLVVVAPVRKLNSSAWAFLRPFTPLMWAVTGVFFLVVGTVVWILEHRLNDEFRG 637 (953)
Q Consensus 558 Di~~~~~~~t~~r~~~vdft~p~~~~~~~~~v~~~~~~~~~~~~l~PF~~~vW~~i~~~~~~~~~~~~~l~~~~~~~~~~ 637 (953)
|++++++++|++|.+.++||.||...+..+++++..
T Consensus 108 Di~~~~~~~t~eR~~~~~fS~Py~~~~~~lv~r~~~-------------------------------------------- 143 (302)
T PRK10797 108 DFECGSTTNNLERQKQAAFSDTIFVVGTRLLTKKGG-------------------------------------------- 143 (302)
T ss_pred cEEecCCccCcchhhcceecccEeeccEEEEEECCC--------------------------------------------
Confidence 999988999999999999999999999999998755
Q ss_pred CCcccchhhHHHHHHHhhccccCCcccchhHHHHHHHHHHHHHhhhhcccceeeeeeeccccCCCCChHHhhhCCCeEEE
Q 002211 638 PPRKQIVTVLWFSFSTMFFAHRENTVSTLGRVVLIIWLFVVLIITSSYTASLTSILTVQQLSSPIKGIDTLMTSNDRVGY 717 (953)
Q Consensus 638 ~~~~~~~~~~~~~~~~l~~~~~~~~~s~~~R~l~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~I~sl~dL~~~~~~ig~ 717 (953)
.|++++||. |++||+
T Consensus 144 ---------------------------------------------------------------~i~sl~dL~--Gk~V~v 158 (302)
T PRK10797 144 ---------------------------------------------------------------DIKDFADLK--GKAVVV 158 (302)
T ss_pred ---------------------------------------------------------------CCCChHHcC--CCEEEE
Confidence 478999996 899999
Q ss_pred EeCchHHHHHHHhhC--CCccceEeCCCHHHHHHHHHcCCcEEEEccchhHHHHHhc--C-cceEEeCCccccCccEEEe
Q 002211 718 QVGSFAENYLIEELS--IPKSRLVALGSPEEYAIALENRTVAAVVDERPYIDLFLSD--H-CQFSVRGQEFTKSGWGFAF 792 (953)
Q Consensus 718 ~~~s~~~~~l~~~~~--~~~~~~~~~~~~~~~~~~l~~g~~~a~~~~~~~~~~~~~~--~-~~l~~~~~~~~~~~~~~~~ 792 (953)
..|+....++.+... .+..+++.+++.++.+++|.+|++|+++.+...+.+.+.+ . ..++++++.+...++++++
T Consensus 159 ~~gs~~~~~l~~~~~~~~~~~~i~~~~~~~~~l~~L~~GrvDa~i~d~~~~~~~~~~~~~~~~l~i~~~~~~~~~~~~a~ 238 (302)
T PRK10797 159 TSGTTSEVLLNKLNEEQKMNMRIISAKDHGDSFRTLESGRAVAFMMDDALLAGERAKAKKPDNWEIVGKPQSQEAYGCML 238 (302)
T ss_pred eCCCcHHHHHHHHhhhcCCceEEEEeCCHHHHHHHHHcCCceEEEccHHHHHHHHHcCCCCcceEECCccCCcCceeEEE
Confidence 999998888754221 1235678899999999999999999999998776654332 2 2578888777778899999
Q ss_pred cCCCc-chHHHHHHHHhhhccccHHHHHHHhcc
Q 002211 793 PRDSP-LAIDMSTAILTLSENGELQRIHDKWLR 824 (953)
Q Consensus 793 ~k~sp-l~~~~n~~i~~l~e~G~~~~~~~~w~~ 824 (953)
+|+++ +++.+|.+|.++.++|.+++|.++|+.
T Consensus 239 ~k~~~~L~~~in~~L~~l~~~G~l~~i~~kw~~ 271 (302)
T PRK10797 239 RKDDPQFKKLMDDTIAQAQTSGEAEKWFDKWFK 271 (302)
T ss_pred eCCCHHHHHHHHHHHHHHHhCchHHHHHHHHcC
Confidence 99988 999999999999999999999999998
No 87
>PF00497 SBP_bac_3: Bacterial extracellular solute-binding proteins, family 3; InterPro: IPR001638 Bacterial high affinity transport systems are involved in active transport of solutes across the cytoplasmic membrane. The protein components of these traffic systems include one or two transmembrane protein components, one or two membrane-associated ATP-binding proteins (ABC transporters; see IPR003439 from INTERPRO) and a high affinity periplasmic solute-binding protein. The latter are thought to bind the substrate in the vicinity of the inner membrane, and to transfer it to a complex of inner membrane proteins for concentration into the cytoplasm. In Gram-positive bacteria which are surrounded by a single membrane and have therefore no periplasmic region, the equivalent proteins are bound to the membrane via an N-terminal lipid anchor. These homologue proteins do not play an integral role in the transport process per se, but probably serve as receptors to trigger or initiate translocation of the solute throught the membrane by binding to external sites of the integral membrane proteins of the efflux system. In addition, at least some solute-binding proteins function in the initiation of sensory transduction pathways. On the basis of sequence similarities, the vast majority of these solute-binding proteins can be grouped [] into eight families or clusters, which generally correlate with the nature of the solute bound. Family 3 groups together specific amino acids and opine-binding periplasmic proteins and a periplasmic homologue with catalytic activity.; GO: 0005215 transporter activity, 0006810 transport, 0030288 outer membrane-bounded periplasmic space; PDB: 3N26_A 3QAX_A 3I6V_A 2VHA_B 2IA4_B 2Q89_A 2Q88_A 2YJP_C 1II5_A 1IIW_A ....
Probab=99.86 E-value=4.8e-21 Score=199.68 Aligned_cols=221 Identities=28% Similarity=0.422 Sum_probs=185.8
Q ss_pred eEEEecCcccccccEEeeCCcceEEEeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEecEEE
Q 002211 487 LRIGVPNRVSYRDFVFKVNGTDIVHGYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGDIAI 566 (953)
Q Consensus 487 lri~v~~~~~~~p~~~~~~~~~~~~G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~~~~ 566 (953)
||||+.. +++||.+.+. +++..|+++|+++++++++|+++++...+ |.+++..|.+|++|+++++++.
T Consensus 1 l~V~~~~--~~~P~~~~~~-~~~~~G~~~dl~~~i~~~~g~~~~~~~~~---------~~~~~~~l~~g~~D~~~~~~~~ 68 (225)
T PF00497_consen 1 LRVGVDE--DYPPFSYIDE-DGEPSGIDVDLLRAIAKRLGIKIEFVPMP---------WSRLLEMLENGKADIIIGGLSI 68 (225)
T ss_dssp EEEEEES--EBTTTBEEET-TSEEESHHHHHHHHHHHHHTCEEEEEEEE---------GGGHHHHHHTTSSSEEESSEB-
T ss_pred CEEEEcC--CCCCeEEECC-CCCEEEEhHHHHHHHHhhcccccceeecc---------cccccccccccccccccccccc
Confidence 6899965 7999999986 78999999999999999999886666544 9999999999999999988999
Q ss_pred ecCccceeeccccceecceEEEEecccCCcCcceeeccCchhHHHHHHHHHHHHHHHhhhhhcccCCCCCCCCcccchhh
Q 002211 567 VTNRTKAVDFTQPYIESGLVVVAPVRKLNSSAWAFLRPFTPLMWAVTGVFFLVVGTVVWILEHRLNDEFRGPPRKQIVTV 646 (953)
Q Consensus 567 t~~r~~~vdft~p~~~~~~~~~v~~~~~~~~~~~~l~PF~~~vW~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~ 646 (953)
+++|.+.++||.||.....++++++.+..
T Consensus 69 ~~~r~~~~~~s~p~~~~~~~~~~~~~~~~--------------------------------------------------- 97 (225)
T PF00497_consen 69 TPERAKKFDFSDPYYSSPYVLVVRKGDAP--------------------------------------------------- 97 (225)
T ss_dssp BHHHHTTEEEESESEEEEEEEEEETTSTC---------------------------------------------------
T ss_pred cccccccccccccccchhheeeecccccc---------------------------------------------------
Confidence 99999999999999999999999975310
Q ss_pred HHHHHHHhhccccCCcccchhHHHHHHHHHHHHHhhhhcccceeeeeeeccccCCCCChHHhhhCCCeEEEEeCchHHHH
Q 002211 647 LWFSFSTMFFAHRENTVSTLGRVVLIIWLFVVLIITSSYTASLTSILTVQQLSSPIKGIDTLMTSNDRVGYQVGSFAENY 726 (953)
Q Consensus 647 ~~~~~~~l~~~~~~~~~s~~~R~l~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~I~sl~dL~~~~~~ig~~~~s~~~~~ 726 (953)
....+++++||. +.+||+..|+...++
T Consensus 98 ---------------------------------------------------~~~~~~~~~dl~--~~~i~~~~g~~~~~~ 124 (225)
T PF00497_consen 98 ---------------------------------------------------PIKTIKSLDDLK--GKRIGVVRGSSYADY 124 (225)
T ss_dssp ---------------------------------------------------STSSHSSGGGGT--TSEEEEETTSHHHHH
T ss_pred ---------------------------------------------------ccccccchhhhc--CcccccccchhHHHH
Confidence 014677788994 789999999998888
Q ss_pred HHHhhCCCccceEeCCCHHHHHHHHHcCCcEEEEccchhHHHHHhcCc--ceEEeCCccccCccEEEecCCCc-chHHHH
Q 002211 727 LIEELSIPKSRLVALGSPEEYAIALENRTVAAVVDERPYIDLFLSDHC--QFSVRGQEFTKSGWGFAFPRDSP-LAIDMS 803 (953)
Q Consensus 727 l~~~~~~~~~~~~~~~~~~~~~~~l~~g~~~a~~~~~~~~~~~~~~~~--~l~~~~~~~~~~~~~~~~~k~sp-l~~~~n 803 (953)
+.+.... ..+++.+.+.++++++|.+|++|+++.+...+.+++++.. ............+++++++++.+ +++.||
T Consensus 125 l~~~~~~-~~~~~~~~~~~~~~~~l~~g~~d~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~n 203 (225)
T PF00497_consen 125 LKQQYPS-NINIVEVDSPEEALEALLSGRIDAFIVDESTAEYLLKRHPLENIVVIPPPISPSPVYFAVRKKNPELLEIFN 203 (225)
T ss_dssp HHHHTHH-TSEEEEESSHHHHHHHHHTTSSSEEEEEHHHHHHHHHHTTTCEEEEEEEEEEEEEEEEEEETTTHHHHHHHH
T ss_pred hhhhccc-hhhhcccccHHHHHHHHhcCCeeeeeccchhhhhhhhhcccccccccccccccceeEEeecccccHHHHHHH
Confidence 8653311 4567789999999999999999999999999999988754 23332445556677788877655 999999
Q ss_pred HHHHhhhccccHHHHHHHhcc
Q 002211 804 TAILTLSENGELQRIHDKWLR 824 (953)
Q Consensus 804 ~~i~~l~e~G~~~~~~~~w~~ 824 (953)
++|.++.++|.++++.+||++
T Consensus 204 ~~i~~l~~~G~~~~i~~ky~g 224 (225)
T PF00497_consen 204 KAIRELKQSGEIQKILKKYLG 224 (225)
T ss_dssp HHHHHHHHTTHHHHHHHHHHS
T ss_pred HHHHHHHhCcHHHHHHHHHcC
Confidence 999999999999999999986
No 88
>PRK11260 cystine transporter subunit; Provisional
Probab=99.86 E-value=2.1e-20 Score=199.72 Aligned_cols=221 Identities=19% Similarity=0.364 Sum_probs=190.8
Q ss_pred CCcceEEEecCcccccccEEeeCCcceEEEeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEe
Q 002211 483 NGRQLRIGVPNRVSYRDFVFKVNGTDIVHGYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVG 562 (953)
Q Consensus 483 ~g~~lri~v~~~~~~~p~~~~~~~~~~~~G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~ 562 (953)
..++|+|++.. +++||.+.++ ++.+.|+.+|+++++++++|.++++.. ..|.+++.++.+|++|++++
T Consensus 39 ~~~~l~v~~~~--~~~P~~~~~~-~g~~~G~~~dl~~~i~~~lg~~~e~~~---------~~~~~~~~~l~~G~~D~~~~ 106 (266)
T PRK11260 39 ERGTLLVGLEG--TYPPFSFQGE-DGKLTGFEVEFAEALAKHLGVKASLKP---------TKWDGMLASLDSKRIDVVIN 106 (266)
T ss_pred cCCeEEEEeCC--CcCCceEECC-CCCEEEehHHHHHHHHHHHCCeEEEEe---------CCHHHHHHHHhcCCCCEEEe
Confidence 46789999875 7899988765 678999999999999999997755544 34999999999999999998
Q ss_pred cEEEecCccceeeccccceecceEEEEecccCCcCcceeeccCchhHHHHHHHHHHHHHHHhhhhhcccCCCCCCCCccc
Q 002211 563 DIAIVTNRTKAVDFTQPYIESGLVVVAPVRKLNSSAWAFLRPFTPLMWAVTGVFFLVVGTVVWILEHRLNDEFRGPPRKQ 642 (953)
Q Consensus 563 ~~~~t~~r~~~vdft~p~~~~~~~~~v~~~~~~~~~~~~l~PF~~~vW~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~ 642 (953)
+++.+++|.+.+.||.||...+..+++++...
T Consensus 107 ~~~~~~~r~~~~~fs~p~~~~~~~~~~~~~~~------------------------------------------------ 138 (266)
T PRK11260 107 QVTISDERKKKYDFSTPYTVSGIQALVKKGNE------------------------------------------------ 138 (266)
T ss_pred ccccCHHHHhccccCCceeecceEEEEEcCCc------------------------------------------------
Confidence 88999999999999999999999999887651
Q ss_pred chhhHHHHHHHhhccccCCcccchhHHHHHHHHHHHHHhhhhcccceeeeeeeccccCCCCChHHhhhCCCeEEEEeCch
Q 002211 643 IVTVLWFSFSTMFFAHRENTVSTLGRVVLIIWLFVVLIITSSYTASLTSILTVQQLSSPIKGIDTLMTSNDRVGYQVGSF 722 (953)
Q Consensus 643 ~~~~~~~~~~~l~~~~~~~~~s~~~R~l~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~I~sl~dL~~~~~~ig~~~~s~ 722 (953)
..+++++||. +++||+..|+.
T Consensus 139 ---------------------------------------------------------~~~~~~~dL~--g~~Igv~~G~~ 159 (266)
T PRK11260 139 ---------------------------------------------------------GTIKTAADLK--GKKVGVGLGTN 159 (266)
T ss_pred ---------------------------------------------------------CCCCCHHHcC--CCEEEEecCCc
Confidence 3678899995 88999999998
Q ss_pred HHHHHHHhhCCCccceEeCCCHHHHHHHHHcCCcEEEEccchhHHHHHhcCcc-eEEeCCccccCccEEEecCCCc-chH
Q 002211 723 AENYLIEELSIPKSRLVALGSPEEYAIALENRTVAAVVDERPYIDLFLSDHCQ-FSVRGQEFTKSGWGFAFPRDSP-LAI 800 (953)
Q Consensus 723 ~~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~g~~~a~~~~~~~~~~~~~~~~~-l~~~~~~~~~~~~~~~~~k~sp-l~~ 800 (953)
...++.+. .+..++..+++..+++++|.+|++|+++.+...+.+++.+... +.+....+...+++++++|++| +++
T Consensus 160 ~~~~l~~~--~~~~~i~~~~~~~~~l~~L~~GrvD~~i~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~l~~ 237 (266)
T PRK11260 160 YEQWLRQN--VQGVDVRTYDDDPTKYQDLRVGRIDAILVDRLAALDLVKKTNDTLAVAGEAFSRQESGVALRKGNPDLLK 237 (266)
T ss_pred HHHHHHHh--CCCCceEecCCHHHHHHHHHcCCCCEEEechHHHHHHHHhCCCcceecCCccccCceEEEEeCCCHHHHH
Confidence 88888553 3456778899999999999999999999999888888777553 5555666677889999999988 999
Q ss_pred HHHHHHHhhhccccHHHHHHHhcc
Q 002211 801 DMSTAILTLSENGELQRIHDKWLR 824 (953)
Q Consensus 801 ~~n~~i~~l~e~G~~~~~~~~w~~ 824 (953)
.||++|.++.++|.++++.++|+.
T Consensus 238 ~ln~~l~~~~~~g~~~~i~~k~~~ 261 (266)
T PRK11260 238 AVNQAIAEMQKDGTLKALSEKWFG 261 (266)
T ss_pred HHHHHHHHHHhCCcHHHHHHHhcC
Confidence 999999999999999999999987
No 89
>PRK15010 ABC transporter lysine/arginine/ornithine binding periplasmic protein; Provisional
Probab=99.86 E-value=3.6e-20 Score=197.26 Aligned_cols=222 Identities=19% Similarity=0.290 Sum_probs=181.3
Q ss_pred CCcceEEEecCcccccccEEeeCCcceEEEeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEe
Q 002211 483 NGRQLRIGVPNRVSYRDFVFKVNGTDIVHGYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVG 562 (953)
Q Consensus 483 ~g~~lri~v~~~~~~~p~~~~~~~~~~~~G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~ 562 (953)
..++|+|++.. +|+||.+.++ ++.+.|+++|+++++++++|.+++++. .+|+.++.++..|++|++++
T Consensus 24 ~~~~l~v~~~~--~~pPf~~~~~-~g~~~G~~vdl~~~ia~~lg~~~~~~~---------~~~~~~~~~l~~g~~Di~~~ 91 (260)
T PRK15010 24 LPETVRIGTDT--TYAPFSSKDA-KGDFVGFDIDLGNEMCKRMQVKCTWVA---------SDFDALIPSLKAKKIDAIIS 91 (260)
T ss_pred cCCeEEEEecC--CcCCceeECC-CCCEEeeeHHHHHHHHHHhCCceEEEe---------CCHHHHHHHHHCCCCCEEEe
Confidence 45789999875 6899999875 678999999999999999997755543 34999999999999999998
Q ss_pred cEEEecCccceeeccccceecceEEEEecccCCcCcceeeccCchhHHHHHHHHHHHHHHHhhhhhcccCCCCCCCCccc
Q 002211 563 DIAIVTNRTKAVDFTQPYIESGLVVVAPVRKLNSSAWAFLRPFTPLMWAVTGVFFLVVGTVVWILEHRLNDEFRGPPRKQ 642 (953)
Q Consensus 563 ~~~~t~~r~~~vdft~p~~~~~~~~~v~~~~~~~~~~~~l~PF~~~vW~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~ 642 (953)
++..+++|.+.++||.||..+..++++++..
T Consensus 92 ~~~~t~eR~~~~~fs~p~~~~~~~~~~~~~~------------------------------------------------- 122 (260)
T PRK15010 92 SLSITDKRQQEIAFSDKLYAADSRLIAAKGS------------------------------------------------- 122 (260)
T ss_pred cCcCCHHHHhhcccccceEeccEEEEEECCC-------------------------------------------------
Confidence 8999999999999999999999999998776
Q ss_pred chhhHHHHHHHhhccccCCcccchhHHHHHHHHHHHHHhhhhcccceeeeeeeccccCCCCChHHhhhCCCeEEEEeCch
Q 002211 643 IVTVLWFSFSTMFFAHRENTVSTLGRVVLIIWLFVVLIITSSYTASLTSILTVQQLSSPIKGIDTLMTSNDRVGYQVGSF 722 (953)
Q Consensus 643 ~~~~~~~~~~~l~~~~~~~~~s~~~R~l~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~I~sl~dL~~~~~~ig~~~~s~ 722 (953)
+...+++||. |++||+..|+.
T Consensus 123 ---------------------------------------------------------~~~~~~~dl~--g~~Igv~~gs~ 143 (260)
T PRK15010 123 ---------------------------------------------------------PIQPTLDSLK--GKHVGVLQGST 143 (260)
T ss_pred ---------------------------------------------------------CCCCChhHcC--CCEEEEecCch
Confidence 2234688995 88999999998
Q ss_pred HHHHHHHhhCCCccceEeCCCHHHHHHHHHcCCcEEEEccchhHHH-HHhcC--cceEEeCCcc-----ccCccEEEecC
Q 002211 723 AENYLIEELSIPKSRLVALGSPEEYAIALENRTVAAVVDERPYIDL-FLSDH--CQFSVRGQEF-----TKSGWGFAFPR 794 (953)
Q Consensus 723 ~~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~g~~~a~~~~~~~~~~-~~~~~--~~l~~~~~~~-----~~~~~~~~~~k 794 (953)
...++.........+++.+++.++++++|.+|++|+++.+...+.+ +..+. .++...+..+ ...++++++++
T Consensus 144 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~griDa~i~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~ 223 (260)
T PRK15010 144 QEAYANETWRSKGVDVVAYANQDLVYSDLAAGRLDAALQDEVAASEGFLKQPAGKDFAFAGPSVKDKKYFGDGTGVGLRK 223 (260)
T ss_pred HHHHHHHhcccCCceEEecCCHHHHHHHHHcCCccEEEeCcHHHHHHHHhCCCCCceEEecCccccccccCCceEEEEeC
Confidence 8777755433233456778899999999999999999999877654 33432 2455554322 12346789999
Q ss_pred CCc-chHHHHHHHHhhhccccHHHHHHHhcc
Q 002211 795 DSP-LAIDMSTAILTLSENGELQRIHDKWLR 824 (953)
Q Consensus 795 ~sp-l~~~~n~~i~~l~e~G~~~~~~~~w~~ 824 (953)
+.+ |+..||++|.++.++|.++++.+||+.
T Consensus 224 ~~~~L~~~ln~~l~~l~~~G~~~~i~~ky~~ 254 (260)
T PRK15010 224 DDAELTAAFNKALGELRQDGTYDKMAKKYFD 254 (260)
T ss_pred CCHHHHHHHHHHHHHHHhCCcHHHHHHHhcC
Confidence 877 999999999999999999999999987
No 90
>PRK11917 bifunctional adhesin/ABC transporter aspartate/glutamate-binding protein; Reviewed
Probab=99.85 E-value=4.7e-20 Score=195.24 Aligned_cols=219 Identities=16% Similarity=0.276 Sum_probs=182.2
Q ss_pred CCcceEEEecCcccccccEEeeCCcceEEEeeHHHHHHHHHhC-CCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEE
Q 002211 483 NGRQLRIGVPNRVSYRDFVFKVNGTDIVHGYCIDVFLAAVRLL-PYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAV 561 (953)
Q Consensus 483 ~g~~lri~v~~~~~~~p~~~~~~~~~~~~G~~~dll~~la~~l-~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~ 561 (953)
..++|+||+.. +++||.+.++.++++.||++|+++++++++ |..+++++.+ .+|......|.+|++|+++
T Consensus 36 ~~g~l~vg~~~--~~pP~~~~~~~~g~~~G~~vdl~~~ia~~llg~~~~~~~~~-------~~~~~~~~~l~~g~~D~~~ 106 (259)
T PRK11917 36 SKGQLIVGVKN--DVPHYALLDQATGEIKGFEIDVAKLLAKSILGDDKKIKLVA-------VNAKTRGPLLDNGSVDAVI 106 (259)
T ss_pred hCCEEEEEECC--CCCCceeeeCCCCceeEeeHHHHHHHHHHhcCCCccEEEEE-------cChhhHHHHHHCCCccEEE
Confidence 46789999986 899999876446899999999999999994 8655666665 3477778999999999999
Q ss_pred ecEEEecCccceeeccccceecceEEEEecccCCcCcceeeccCchhHHHHHHHHHHHHHHHhhhhhcccCCCCCCCCcc
Q 002211 562 GDIAIVTNRTKAVDFTQPYIESGLVVVAPVRKLNSSAWAFLRPFTPLMWAVTGVFFLVVGTVVWILEHRLNDEFRGPPRK 641 (953)
Q Consensus 562 ~~~~~t~~r~~~vdft~p~~~~~~~~~v~~~~~~~~~~~~l~PF~~~vW~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~ 641 (953)
+++++|++|.+.++||.||+.++..+++++..
T Consensus 107 ~~~~~t~eR~~~~~fs~py~~~~~~lvv~~~~------------------------------------------------ 138 (259)
T PRK11917 107 ATFTITPERKRIYNFSEPYYQDAIGLLVLKEK------------------------------------------------ 138 (259)
T ss_pred ecccCChhhhheeeeccCceeeceEEEEECCC------------------------------------------------
Confidence 99999999999999999999999999998765
Q ss_pred cchhhHHHHHHHhhccccCCcccchhHHHHHHHHHHHHHhhhhcccceeeeeeeccccCCCCChHHhhhCCCeEEEEeCc
Q 002211 642 QIVTVLWFSFSTMFFAHRENTVSTLGRVVLIIWLFVVLIITSSYTASLTSILTVQQLSSPIKGIDTLMTSNDRVGYQVGS 721 (953)
Q Consensus 642 ~~~~~~~~~~~~l~~~~~~~~~s~~~R~l~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~I~sl~dL~~~~~~ig~~~~s 721 (953)
++++++||. |++||+..|+
T Consensus 139 -----------------------------------------------------------~~~s~~dL~--g~~V~v~~gs 157 (259)
T PRK11917 139 -----------------------------------------------------------NYKSLADMK--GANIGVAQAA 157 (259)
T ss_pred -----------------------------------------------------------CCCCHHHhC--CCeEEEecCC
Confidence 478899996 8999999999
Q ss_pred hHHHHHHHhhCC--CccceEeCCCHHHHHHHHHcCCcEEEEccchhHHHHHhcCcceEEeCCccccCccEEEecCCCc-c
Q 002211 722 FAENYLIEELSI--PKSRLVALGSPEEYAIALENRTVAAVVDERPYIDLFLSDHCQFSVRGQEFTKSGWGFAFPRDSP-L 798 (953)
Q Consensus 722 ~~~~~l~~~~~~--~~~~~~~~~~~~~~~~~l~~g~~~a~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~k~sp-l 798 (953)
...+.+.+.... ...+++.+++..+.+++|..|++|+++.+...+.++..+ +..++++.+...+++++++|+++ +
T Consensus 158 ~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~l~~GrvDa~~~d~~~~~~~~~~--~~~~~~~~~~~~~~~~a~~k~~~~l 235 (259)
T PRK11917 158 TTKKAIGEAAKKIGIDVKFSEFPDYPSIKAALDAKRVDAFSVDKSILLGYVDD--KSEILPDSFEPQSYGIVTKKDDPAF 235 (259)
T ss_pred cHHHHHHHhhHhcCCceeEEecCCHHHHHHHHHcCCCcEEEecHHHHHHhhhc--CCeecCCcCCCCceEEEEeCCCHHH
Confidence 877766443211 123567789999999999999999999998877665544 24566667777789999999988 9
Q ss_pred hHHHHHHHHhhhccccHHHHHHHhc
Q 002211 799 AIDMSTAILTLSENGELQRIHDKWL 823 (953)
Q Consensus 799 ~~~~n~~i~~l~e~G~~~~~~~~w~ 823 (953)
++.+|+.|.++.. .+++|.+||-
T Consensus 236 ~~~ln~~l~~~~~--~~~~i~~kw~ 258 (259)
T PRK11917 236 AKYVDDFVKEHKN--EIDALAKKWG 258 (259)
T ss_pred HHHHHHHHHHHHH--HHHHHHHHhC
Confidence 9999999999864 7999999993
No 91
>TIGR01096 3A0103s03R lysine-arginine-ornithine-binding periplasmic protein.
Probab=99.85 E-value=6.4e-20 Score=194.61 Aligned_cols=219 Identities=22% Similarity=0.389 Sum_probs=185.4
Q ss_pred CcceEEEecCcccccccEEeeCCcceEEEeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEec
Q 002211 484 GRQLRIGVPNRVSYRDFVFKVNGTDIVHGYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGD 563 (953)
Q Consensus 484 g~~lri~v~~~~~~~p~~~~~~~~~~~~G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~ 563 (953)
+++|+|++.. +|+||.+.++ +++++|+++|+++.+++++|.++++ ++ .+|++++..+.+|++|+++++
T Consensus 23 ~~~l~v~~~~--~~~P~~~~~~-~g~~~G~~~dl~~~i~~~lg~~~~~--~~-------~~~~~~~~~l~~G~~D~~~~~ 90 (250)
T TIGR01096 23 EGSVRIGTET--GYPPFESKDA-NGKLVGFDVDLAKALCKRMKAKCKF--VE-------QNFDGLIPSLKAKKVDAIMAT 90 (250)
T ss_pred CCeEEEEECC--CCCCceEECC-CCCEEeehHHHHHHHHHHhCCeEEE--Ee-------CCHHHHHHHHhCCCcCEEEec
Confidence 3789999964 7899998765 6899999999999999999966554 44 459999999999999999888
Q ss_pred EEEecCccceeeccccceecceEEEEecccCCcCcceeeccCchhHHHHHHHHHHHHHHHhhhhhcccCCCCCCCCcccc
Q 002211 564 IAIVTNRTKAVDFTQPYIESGLVVVAPVRKLNSSAWAFLRPFTPLMWAVTGVFFLVVGTVVWILEHRLNDEFRGPPRKQI 643 (953)
Q Consensus 564 ~~~t~~r~~~vdft~p~~~~~~~~~v~~~~~~~~~~~~l~PF~~~vW~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~ 643 (953)
+..+.+|.+.+.||.|+...+..++++...
T Consensus 91 ~~~~~~r~~~~~~s~p~~~~~~~~~~~~~~-------------------------------------------------- 120 (250)
T TIGR01096 91 MSITPKRQKQIDFSDPYYATGQGFVVKKGS-------------------------------------------------- 120 (250)
T ss_pred CccCHHHhhccccccchhcCCeEEEEECCC--------------------------------------------------
Confidence 889999999999999999999999998766
Q ss_pred hhhHHHHHHHhhccccCCcccchhHHHHHHHHHHHHHhhhhcccceeeeeeeccccCCCCChHHhhhCCCeEEEEeCchH
Q 002211 644 VTVLWFSFSTMFFAHRENTVSTLGRVVLIIWLFVVLIITSSYTASLTSILTVQQLSSPIKGIDTLMTSNDRVGYQVGSFA 723 (953)
Q Consensus 644 ~~~~~~~~~~l~~~~~~~~~s~~~R~l~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~I~sl~dL~~~~~~ig~~~~s~~ 723 (953)
+.+.+++||. +++||+..|+..
T Consensus 121 --------------------------------------------------------~~~~~~~dl~--g~~i~~~~g~~~ 142 (250)
T TIGR01096 121 --------------------------------------------------------DLAKTLEDLD--GKTVGVQSGTTH 142 (250)
T ss_pred --------------------------------------------------------CcCCChHHcC--CCEEEEecCchH
Confidence 3356788995 889999999988
Q ss_pred HHHHHHhhCCCccceEeCCCHHHHHHHHHcCCcEEEEccchhHHHHHhcCc---ceEEeCCcccc-----CccEEEecCC
Q 002211 724 ENYLIEELSIPKSRLVALGSPEEYAIALENRTVAAVVDERPYIDLFLSDHC---QFSVRGQEFTK-----SGWGFAFPRD 795 (953)
Q Consensus 724 ~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~g~~~a~~~~~~~~~~~~~~~~---~l~~~~~~~~~-----~~~~~~~~k~ 795 (953)
..++.+.... ..++..+.+.++++++|.+|++|+++.+...+.+++++.. ++.+++..+.. ..++++++++
T Consensus 143 ~~~l~~~~~~-~~~~~~~~s~~~~~~~L~~g~vD~~v~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~ 221 (250)
T TIGR01096 143 EQYLKDYFKP-GVDIVEYDSYDNANMDLKAGRIDAVFTDASVLAEGFLKPPNGKDFKFVGPSVTDEKYFGDGYGIGLRKG 221 (250)
T ss_pred HHHHHHhccC-CcEEEEcCCHHHHHHHHHcCCCCEEEeCHHHHHHHHHhCCCCCceEEeccccccccccCCceEEEEeCC
Confidence 8888654421 4567788999999999999999999999999988877643 37766544332 2478999999
Q ss_pred Cc-chHHHHHHHHhhhccccHHHHHHHhc
Q 002211 796 SP-LAIDMSTAILTLSENGELQRIHDKWL 823 (953)
Q Consensus 796 sp-l~~~~n~~i~~l~e~G~~~~~~~~w~ 823 (953)
++ ++..||++|.+|.++|.+++|.+||+
T Consensus 222 ~~~l~~~ln~~l~~l~~~g~~~~i~~kw~ 250 (250)
T TIGR01096 222 DTELKAAFNKALAAIRADGTYQKISKKWF 250 (250)
T ss_pred CHHHHHHHHHHHHHHHHCCcHHHHHHhhC
Confidence 88 99999999999999999999999996
No 92
>PRK15007 putative ABC transporter arginine-biding protein; Provisional
Probab=99.84 E-value=9.8e-20 Score=192.21 Aligned_cols=217 Identities=21% Similarity=0.403 Sum_probs=181.4
Q ss_pred CcceEEEecCcccccccEEeeCCcceEEEeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEec
Q 002211 484 GRQLRIGVPNRVSYRDFVFKVNGTDIVHGYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGD 563 (953)
Q Consensus 484 g~~lri~v~~~~~~~p~~~~~~~~~~~~G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~ 563 (953)
.++|+|++.. +++||.+.+. ++.+.|+++|+++++++++|.+++|.. .+|++++..+.+|++|+++++
T Consensus 20 ~~~l~v~~~~--~~~P~~~~~~-~g~~~G~~~dl~~~i~~~lg~~~~~~~---------~~~~~~~~~l~~g~~D~~~~~ 87 (243)
T PRK15007 20 AETIRFATEA--SYPPFESIDA-NNQIVGFDVDLAQALCKEIDATCTFSN---------QAFDSLIPSLKFRRVEAVMAG 87 (243)
T ss_pred CCcEEEEeCC--CCCCceeeCC-CCCEEeeeHHHHHHHHHHhCCcEEEEe---------CCHHHHhHHHhCCCcCEEEEc
Confidence 4689999975 7999998764 688999999999999999997755543 459999999999999998887
Q ss_pred EEEecCccceeeccccceecceEEEEecccCCcCcceeeccCchhHHHHHHHHHHHHHHHhhhhhcccCCCCCCCCcccc
Q 002211 564 IAIVTNRTKAVDFTQPYIESGLVVVAPVRKLNSSAWAFLRPFTPLMWAVTGVFFLVVGTVVWILEHRLNDEFRGPPRKQI 643 (953)
Q Consensus 564 ~~~t~~r~~~vdft~p~~~~~~~~~v~~~~~~~~~~~~l~PF~~~vW~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~ 643 (953)
++.+++|.+.++||.||+..+..++.+..
T Consensus 88 ~~~~~~r~~~~~fs~p~~~~~~~~v~~~~--------------------------------------------------- 116 (243)
T PRK15007 88 MDITPEREKQVLFTTPYYDNSALFVGQQG--------------------------------------------------- 116 (243)
T ss_pred CccCHHHhcccceecCccccceEEEEeCC---------------------------------------------------
Confidence 88999999999999999998877765422
Q ss_pred hhhHHHHHHHhhccccCCcccchhHHHHHHHHHHHHHhhhhcccceeeeeeeccccCCCCChHHhhhCCCeEEEEeCchH
Q 002211 644 VTVLWFSFSTMFFAHRENTVSTLGRVVLIIWLFVVLIITSSYTASLTSILTVQQLSSPIKGIDTLMTSNDRVGYQVGSFA 723 (953)
Q Consensus 644 ~~~~~~~~~~l~~~~~~~~~s~~~R~l~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~I~sl~dL~~~~~~ig~~~~s~~ 723 (953)
.+++++||. +++||+..|+..
T Consensus 117 ---------------------------------------------------------~~~~~~dL~--g~~Igv~~g~~~ 137 (243)
T PRK15007 117 ---------------------------------------------------------KYTSVDQLK--GKKVGVQNGTTH 137 (243)
T ss_pred ---------------------------------------------------------CCCCHHHhC--CCeEEEecCcHH
Confidence 356789995 889999999988
Q ss_pred HHHHHHhhCCCccceEeCCCHHHHHHHHHcCCcEEEEccchhHHHHHhcCcceEEeCCc-----cccCccEEEecCCCc-
Q 002211 724 ENYLIEELSIPKSRLVALGSPEEYAIALENRTVAAVVDERPYIDLFLSDHCQFSVRGQE-----FTKSGWGFAFPRDSP- 797 (953)
Q Consensus 724 ~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~g~~~a~~~~~~~~~~~~~~~~~l~~~~~~-----~~~~~~~~~~~k~sp- 797 (953)
.+++.+. .+..+++.+++.++++++|.+|++|+++.+...+.+++.+..++..++.. ....+++++++++.+
T Consensus 138 ~~~l~~~--~~~~~~~~~~~~~~~~~~L~~grvDa~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 215 (243)
T PRK15007 138 QKFIMDK--HPEITTVPYDSYQNAKLDLQNGRIDAVFGDTAVVTEWLKDNPKLAAVGDKVTDKDYFGTGLGIAVRQGNTE 215 (243)
T ss_pred HHHHHHh--CCCCeEEEcCCHHHHHHHHHcCCCCEEEeCHHHHHHHHhcCCCceeecCcccccccCCcceEEEEeCCCHH
Confidence 8888653 24456778899999999999999999999998888887776665554432 223357899998876
Q ss_pred chHHHHHHHHhhhccccHHHHHHHhcc
Q 002211 798 LAIDMSTAILTLSENGELQRIHDKWLR 824 (953)
Q Consensus 798 l~~~~n~~i~~l~e~G~~~~~~~~w~~ 824 (953)
++..||++|.++.++|.++++.++|+.
T Consensus 216 l~~~ln~~l~~l~~~g~~~~i~~~w~~ 242 (243)
T PRK15007 216 LQQKLNTALEKVKKDGTYETIYNKWFQ 242 (243)
T ss_pred HHHHHHHHHHHHHhCCcHHHHHHHhcC
Confidence 999999999999999999999999985
No 93
>PRK15437 histidine ABC transporter substrate-binding protein HisJ; Provisional
Probab=99.84 E-value=1.4e-19 Score=192.52 Aligned_cols=222 Identities=17% Similarity=0.276 Sum_probs=180.0
Q ss_pred CCcceEEEecCcccccccEEeeCCcceEEEeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEe
Q 002211 483 NGRQLRIGVPNRVSYRDFVFKVNGTDIVHGYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVG 562 (953)
Q Consensus 483 ~g~~lri~v~~~~~~~p~~~~~~~~~~~~G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~ 562 (953)
...+|++++.. +|+||.+.++ ++++.|+++|+++++++++|.+++++.. .|++++.++.+|++|++++
T Consensus 24 ~~~~l~v~~~~--~~~P~~~~~~-~g~~~G~~vdi~~~ia~~lg~~i~~~~~---------pw~~~~~~l~~g~~D~~~~ 91 (259)
T PRK15437 24 IPQNIRIGTDP--TYAPFESKNS-QGELVGFDIDLAKELCKRINTQCTFVEN---------PLDALIPSLKAKKIDAIMS 91 (259)
T ss_pred cCCeEEEEeCC--CCCCcceeCC-CCCEEeeeHHHHHHHHHHcCCceEEEeC---------CHHHHHHHHHCCCCCEEEe
Confidence 45789999864 6899998765 6789999999999999999977666554 3999999999999999998
Q ss_pred cEEEecCccceeeccccceecceEEEEecccCCcCcceeeccCchhHHHHHHHHHHHHHHHhhhhhcccCCCCCCCCccc
Q 002211 563 DIAIVTNRTKAVDFTQPYIESGLVVVAPVRKLNSSAWAFLRPFTPLMWAVTGVFFLVVGTVVWILEHRLNDEFRGPPRKQ 642 (953)
Q Consensus 563 ~~~~t~~r~~~vdft~p~~~~~~~~~v~~~~~~~~~~~~l~PF~~~vW~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~ 642 (953)
+++.+++|.+.++||.||...+.++++++..
T Consensus 92 ~~~~t~eR~~~~~fs~p~~~~~~~~~~~~~~------------------------------------------------- 122 (259)
T PRK15437 92 SLSITEKRQQEIAFTDKLYAADSRLVVAKNS------------------------------------------------- 122 (259)
T ss_pred cCCCCHHHhhhccccchhhcCceEEEEECCC-------------------------------------------------
Confidence 8999999999999999999999999998766
Q ss_pred chhhHHHHHHHhhccccCCcccchhHHHHHHHHHHHHHhhhhcccceeeeeeeccccCCCCChHHhhhCCCeEEEEeCch
Q 002211 643 IVTVLWFSFSTMFFAHRENTVSTLGRVVLIIWLFVVLIITSSYTASLTSILTVQQLSSPIKGIDTLMTSNDRVGYQVGSF 722 (953)
Q Consensus 643 ~~~~~~~~~~~l~~~~~~~~~s~~~R~l~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~I~sl~dL~~~~~~ig~~~~s~ 722 (953)
+...+++||. +++||+..|+.
T Consensus 123 ---------------------------------------------------------~~~~~~~dl~--g~~Igv~~g~~ 143 (259)
T PRK15437 123 ---------------------------------------------------------DIQPTVESLK--GKRVGVLQGTT 143 (259)
T ss_pred ---------------------------------------------------------CCCCChHHhC--CCEEEEecCcH
Confidence 2234788985 88999999998
Q ss_pred HHHHHHHhhCCCccceEeCCCHHHHHHHHHcCCcEEEEccchhHHH-HHhcC--cceEEeCC-----ccccCccEEEecC
Q 002211 723 AENYLIEELSIPKSRLVALGSPEEYAIALENRTVAAVVDERPYIDL-FLSDH--CQFSVRGQ-----EFTKSGWGFAFPR 794 (953)
Q Consensus 723 ~~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~g~~~a~~~~~~~~~~-~~~~~--~~l~~~~~-----~~~~~~~~~~~~k 794 (953)
.+.++.+.......+++.+.+.++.+++|.+|++|+++.+.....+ +..+. .++.+.+. .+...++++++++
T Consensus 144 ~~~~~~~~~~~~~~~~~~~~~~~~~i~~L~~grvD~~v~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~ia~~~ 223 (259)
T PRK15437 144 QETFGNEHWAPKGIEIVSYQGQDNIYSDLTAGRIDAAFQDEVAASEGFLKQPVGKDYKFGGPSVKDEKLFGVGTGMGLRK 223 (259)
T ss_pred HHHHHHhhccccCceEEecCCHHHHHHHHHcCCccEEEechHHHHHHHHhCCCCCceEEecCccccccccCcceEEEEeC
Confidence 8888754332223567888999999999999999999988876643 33332 23443322 2223346788888
Q ss_pred CCc-chHHHHHHHHhhhccccHHHHHHHhcc
Q 002211 795 DSP-LAIDMSTAILTLSENGELQRIHDKWLR 824 (953)
Q Consensus 795 ~sp-l~~~~n~~i~~l~e~G~~~~~~~~w~~ 824 (953)
+.+ +++.+|+++.++.++|.++++.+||++
T Consensus 224 ~~~~l~~~~n~~l~~~~~~G~~~~i~~k~~~ 254 (259)
T PRK15437 224 EDNELREALNKAFAEMRADGTYEKLAKKYFD 254 (259)
T ss_pred CCHHHHHHHHHHHHHHHHCCcHHHHHHHhcC
Confidence 766 999999999999999999999999997
No 94
>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=99.83 E-value=2.4e-19 Score=192.37 Aligned_cols=223 Identities=19% Similarity=0.211 Sum_probs=182.8
Q ss_pred CCcceEEEecCcccccccEEeeCCcceEEEeeHHHHHHHHHhCCCc-ccEEEeeCCCCCCCCChHHHHHHHHcCceeEEE
Q 002211 483 NGRQLRIGVPNRVSYRDFVFKVNGTDIVHGYCIDVFLAAVRLLPYA-VPYKFIPYGDGHKNPTYSELINQITTGVFDAAV 561 (953)
Q Consensus 483 ~g~~lri~v~~~~~~~p~~~~~~~~~~~~G~~~dll~~la~~l~~~-~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~ 561 (953)
..++|+|++. +++||.+.+. ++++.|+++|+++++++++|.. +++.. .+|++++..+.+|++|+++
T Consensus 31 ~~~~l~v~~~---~~pP~~~~~~-~g~~~G~~~dl~~~i~~~lg~~~~~~~~---------~~w~~~~~~l~~G~~Di~~ 97 (275)
T TIGR02995 31 EQGFARIAIA---NEPPFTYVGA-DGKVSGAAPDVARAIFKRLGIADVNASI---------TEYGALIPGLQAGRFDAIA 97 (275)
T ss_pred hCCcEEEEcc---CCCCceeECC-CCceecchHHHHHHHHHHhCCCceeecc---------CCHHHHHHHHHCCCcCEEe
Confidence 4578999986 5889998765 6788999999999999999975 34444 3499999999999999998
Q ss_pred ecEEEecCccceeeccccceecceEEEEecccCCcCcceeeccCchhHHHHHHHHHHHHHHHhhhhhcccCCCCCCCCcc
Q 002211 562 GDIAIVTNRTKAVDFTQPYIESGLVVVAPVRKLNSSAWAFLRPFTPLMWAVTGVFFLVVGTVVWILEHRLNDEFRGPPRK 641 (953)
Q Consensus 562 ~~~~~t~~r~~~vdft~p~~~~~~~~~v~~~~~~~~~~~~l~PF~~~vW~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~ 641 (953)
++++++++|...++||.||..+..++++++...
T Consensus 98 ~~~~~t~eR~~~~~fs~py~~~~~~~~~~~~~~----------------------------------------------- 130 (275)
T TIGR02995 98 AGLFIKPERCKQVAFTQPILCDAEALLVKKGNP----------------------------------------------- 130 (275)
T ss_pred ecccCCHHHHhccccccceeecceeEEEECCCC-----------------------------------------------
Confidence 889999999999999999999999999987661
Q ss_pred cchhhHHHHHHHhhccccCCcccchhHHHHHHHHHHHHHhhhhcccceeeeeeeccccCCCCChHHhhh-CCCeEEEEeC
Q 002211 642 QIVTVLWFSFSTMFFAHRENTVSTLGRVVLIIWLFVVLIITSSYTASLTSILTVQQLSSPIKGIDTLMT-SNDRVGYQVG 720 (953)
Q Consensus 642 ~~~~~~~~~~~~l~~~~~~~~~s~~~R~l~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~I~sl~dL~~-~~~~ig~~~~ 720 (953)
..+++++||.. .+.+||+..|
T Consensus 131 ----------------------------------------------------------~~i~~~~dl~~~~g~~Igv~~g 152 (275)
T TIGR02995 131 ----------------------------------------------------------KGLKSYKDIAKNPDAKIAAPGG 152 (275)
T ss_pred ----------------------------------------------------------CCCCCHHHhccCCCceEEEeCC
Confidence 35778888854 3689999999
Q ss_pred chHHHHHHHhhCCCccceEeCCCHHHHHHHHHcCCcEEEEccchhHHHHHhcCc--ceEEeCCc---cccCccEEEecCC
Q 002211 721 SFAENYLIEELSIPKSRLVALGSPEEYAIALENRTVAAVVDERPYIDLFLSDHC--QFSVRGQE---FTKSGWGFAFPRD 795 (953)
Q Consensus 721 s~~~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~g~~~a~~~~~~~~~~~~~~~~--~l~~~~~~---~~~~~~~~~~~k~ 795 (953)
+...+++.+ .+.+..+++.+++.++++++|.+|++|+++.+...+.+++++.. ++..+... .....++++++++
T Consensus 153 ~~~~~~l~~-~~~~~~~i~~~~~~~~~i~~L~~grvDa~i~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 231 (275)
T TIGR02995 153 GTEEKLARE-AGVKREQIIVVPDGQSGLKMVQDGRADAYSLTVLTINDLASKAGDPNVEVLAPFKDAPVRYYGGAAFRPE 231 (275)
T ss_pred cHHHHHHHH-cCCChhhEEEeCCHHHHHHHHHcCCCCEEecChHHHHHHHHhCCCCCceeecCccCCccccceeEEECCC
Confidence 998888854 44444577889999999999999999999999999888877532 44443321 1112337888887
Q ss_pred Cc-chHHHHHHHHhhhccccHHHHHHHhcc
Q 002211 796 SP-LAIDMSTAILTLSENGELQRIHDKWLR 824 (953)
Q Consensus 796 sp-l~~~~n~~i~~l~e~G~~~~~~~~w~~ 824 (953)
++ +++.||++|.++.++|.+++|.+||--
T Consensus 232 ~~~l~~~~n~~l~~~~~sG~~~~i~~ky~~ 261 (275)
T TIGR02995 232 DKELRDAFNVELAKLKESGEFAKIIAPYGF 261 (275)
T ss_pred CHHHHHHHHHHHHHHHhChHHHHHHHHhCC
Confidence 76 999999999999999999999999943
No 95
>PRK10859 membrane-bound lytic transglycosylase F; Provisional
Probab=99.78 E-value=3.8e-18 Score=196.40 Aligned_cols=221 Identities=18% Similarity=0.225 Sum_probs=179.5
Q ss_pred CCcceEEEecCcccccccEEeeCCcceEEEeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEe
Q 002211 483 NGRQLRIGVPNRVSYRDFVFKVNGTDIVHGYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVG 562 (953)
Q Consensus 483 ~g~~lri~v~~~~~~~p~~~~~~~~~~~~G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~ 562 (953)
..++|||++.. .|+.+.++ .+...||++|+++++++++|.+++++.. .+|++++..|.+|++|++++
T Consensus 41 ~~g~LrVg~~~----~P~~~~~~-~~~~~G~~~DLl~~ia~~LGv~~e~v~~--------~~~~~ll~aL~~G~iDi~~~ 107 (482)
T PRK10859 41 ERGELRVGTIN----SPLTYYIG-NDGPTGFEYELAKRFADYLGVKLEIKVR--------DNISQLFDALDKGKADLAAA 107 (482)
T ss_pred hCCEEEEEEec----CCCeeEec-CCCcccHHHHHHHHHHHHhCCcEEEEec--------CCHHHHHHHHhCCCCCEEec
Confidence 56789999974 34444443 2334999999999999999977555522 56999999999999999888
Q ss_pred cEEEecCccceeeccccceecceEEEEecccCCcCcceeeccCchhHHHHHHHHHHHHHHHhhhhhcccCCCCCCCCccc
Q 002211 563 DIAIVTNRTKAVDFTQPYIESGLVVVAPVRKLNSSAWAFLRPFTPLMWAVTGVFFLVVGTVVWILEHRLNDEFRGPPRKQ 642 (953)
Q Consensus 563 ~~~~t~~r~~~vdft~p~~~~~~~~~v~~~~~~~~~~~~l~PF~~~vW~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~ 642 (953)
++++|++|.+.++||.||.....++++++..
T Consensus 108 ~lt~T~eR~~~~~FS~Py~~~~~~lv~r~~~------------------------------------------------- 138 (482)
T PRK10859 108 GLTYTPERLKQFRFGPPYYSVSQQLVYRKGQ------------------------------------------------- 138 (482)
T ss_pred cCcCChhhhccCcccCCceeeeEEEEEeCCC-------------------------------------------------
Confidence 8999999999999999999999999998766
Q ss_pred chhhHHHHHHHhhccccCCcccchhHHHHHHHHHHHHHhhhhcccceeeeeeeccccCCCCChHHhhhCCCeEEEEeCch
Q 002211 643 IVTVLWFSFSTMFFAHRENTVSTLGRVVLIIWLFVVLIITSSYTASLTSILTVQQLSSPIKGIDTLMTSNDRVGYQVGSF 722 (953)
Q Consensus 643 ~~~~~~~~~~~l~~~~~~~~~s~~~R~l~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~I~sl~dL~~~~~~ig~~~~s~ 722 (953)
+.+++++||. |++|++..|+.
T Consensus 139 ---------------------------------------------------------~~i~~l~dL~--Gk~I~V~~gS~ 159 (482)
T PRK10859 139 ---------------------------------------------------------PRPRSLGDLK--GGTLTVAAGSS 159 (482)
T ss_pred ---------------------------------------------------------CCCCCHHHhC--CCeEEEECCCc
Confidence 5688999996 89999999998
Q ss_pred HHHHHHHhhC-CCccce--EeCCCHHHHHHHHHcCCcEEEEccchhHHHHHhcCcceEEeCCccccCccEEEecCC-Cc-
Q 002211 723 AENYLIEELS-IPKSRL--VALGSPEEYAIALENRTVAAVVDERPYIDLFLSDHCQFSVRGQEFTKSGWGFAFPRD-SP- 797 (953)
Q Consensus 723 ~~~~l~~~~~-~~~~~~--~~~~~~~~~~~~l~~g~~~a~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~k~-sp- 797 (953)
..+.+.+... .+..++ ..+.+.++++++|.+|++|+++.+...+.+......++.+........+++++++|+ ++
T Consensus 160 ~~~~L~~l~~~~p~i~~~~~~~~s~~e~l~aL~~G~iDa~v~d~~~~~~~~~~~p~l~v~~~l~~~~~~~~av~k~~~~~ 239 (482)
T PRK10859 160 HVETLQELKKKYPELSWEESDDKDSEELLEQVAEGKIDYTIADSVEISLNQRYHPELAVAFDLTDEQPVAWALPPSGDDS 239 (482)
T ss_pred HHHHHHHHHHhCCCceEEecCCCCHHHHHHHHHCCCCCEEEECcHHHHHHHHhCCCceeeeecCCCceeEEEEeCCCCHH
Confidence 8887753211 122333 346799999999999999999999887776555556666655444556789999994 56
Q ss_pred chHHHHHHHHhhhccccHHHHHHHhcc
Q 002211 798 LAIDMSTAILTLSENGELQRIHDKWLR 824 (953)
Q Consensus 798 l~~~~n~~i~~l~e~G~~~~~~~~w~~ 824 (953)
|+..+|++|.++.++|.++++.+||+.
T Consensus 240 L~~~ln~~L~~i~~~G~l~~L~~kyfg 266 (482)
T PRK10859 240 LYAALLDFFNQIKEDGTLARLEEKYFG 266 (482)
T ss_pred HHHHHHHHHHHhhcCCHHHHHHHHHhh
Confidence 999999999999999999999999998
No 96
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=99.76 E-value=2.4e-17 Score=213.98 Aligned_cols=216 Identities=16% Similarity=0.209 Sum_probs=179.4
Q ss_pred CcceEEEecCcccccccEEeeCCcceEEEeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEec
Q 002211 484 GRQLRIGVPNRVSYRDFVFKVNGTDIVHGYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGD 563 (953)
Q Consensus 484 g~~lri~v~~~~~~~p~~~~~~~~~~~~G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~ 563 (953)
.++|+|++.. +|+||.+.+. ++++.||.+|+++++++++|.+ +++++. .+|..++..+.+|++|++.+
T Consensus 301 ~~~l~v~~~~--~~pP~~~~d~-~g~~~G~~~Dll~~i~~~~g~~--~~~v~~------~~~~~~~~~l~~g~~D~i~~- 368 (1197)
T PRK09959 301 HPDLKVLENP--YSPPYSMTDE-NGSVRGVMGDILNIITLQTGLN--FSPITV------SHNIHAGTQLNPGGWDIIPG- 368 (1197)
T ss_pred CCceEEEcCC--CCCCeeEECC-CCcEeeehHHHHHHHHHHHCCe--EEEEec------CCHHHHHHHHHCCCceEeec-
Confidence 3579998876 8999999975 6899999999999999999955 555553 45888999999999998765
Q ss_pred EEEecCccceeeccccceecceEEEEecccCCcCcceeeccCchhHHHHHHHHHHHHHHHhhhhhcccCCCCCCCCcccc
Q 002211 564 IAIVTNRTKAVDFTQPYIESGLVVVAPVRKLNSSAWAFLRPFTPLMWAVTGVFFLVVGTVVWILEHRLNDEFRGPPRKQI 643 (953)
Q Consensus 564 ~~~t~~r~~~vdft~p~~~~~~~~~v~~~~~~~~~~~~l~PF~~~vW~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~ 643 (953)
+..+++|.+.++||.||+.+++++++++..
T Consensus 369 ~~~t~~r~~~~~fs~py~~~~~~~v~~~~~-------------------------------------------------- 398 (1197)
T PRK09959 369 AIYSEDRENNVLFAEAFITTPYVFVMQKAP-------------------------------------------------- 398 (1197)
T ss_pred ccCCccccccceeccccccCCEEEEEecCC--------------------------------------------------
Confidence 668999999999999999999999987554
Q ss_pred hhhHHHHHHHhhccccCCcccchhHHHHHHHHHHHHHhhhhcccceeeeeeeccccCCCCChHHhhhCCCeEEEEeCchH
Q 002211 644 VTVLWFSFSTMFFAHRENTVSTLGRVVLIIWLFVVLIITSSYTASLTSILTVQQLSSPIKGIDTLMTSNDRVGYQVGSFA 723 (953)
Q Consensus 644 ~~~~~~~~~~l~~~~~~~~~s~~~R~l~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~I~sl~dL~~~~~~ig~~~~s~~ 723 (953)
..+.+ +. .|++||+..|+..
T Consensus 399 --------------------------------------------------------~~~~~---~~-~g~~vav~~g~~~ 418 (1197)
T PRK09959 399 --------------------------------------------------------DSEQT---LK-KGMKVAIPYYYEL 418 (1197)
T ss_pred --------------------------------------------------------CCccc---cc-cCCEEEEeCCcch
Confidence 12222 22 5889999999988
Q ss_pred HHHHHHhhCCCccceEeCCCHHHHHHHHHcCCcEEEEccchhHHHHHhcCc--c-eEEeCCccccCccEEEecCCCc-ch
Q 002211 724 ENYLIEELSIPKSRLVALGSPEEYAIALENRTVAAVVDERPYIDLFLSDHC--Q-FSVRGQEFTKSGWGFAFPRDSP-LA 799 (953)
Q Consensus 724 ~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~g~~~a~~~~~~~~~~~~~~~~--~-l~~~~~~~~~~~~~~~~~k~sp-l~ 799 (953)
.+++.+.+ +..+++.+++.++++++|.+|++||++.+...+.|++++.. + +....+.+....++|+++|+.| |+
T Consensus 419 ~~~~~~~~--p~~~~~~~~~~~~~l~av~~G~~Da~i~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~av~k~~~~L~ 496 (1197)
T PRK09959 419 HSQLKEMY--PEVEWIKVDNASAAFHKVKEGELDALVATQLNSRYMIDHYYPNELYHFLIPGVPNASLSFAFPRGEPELK 496 (1197)
T ss_pred HHHHHHHC--CCcEEEEcCCHHHHHHHHHcCCCCEEehhhHHHHHHHHhcccccceeeecCCCCchheEEeeCCCCHHHH
Confidence 88886543 45688999999999999999999999999999999988742 2 2333344445678999999998 99
Q ss_pred HHHHHHHHhhhccccHHHHHHHhcc
Q 002211 800 IDMSTAILTLSENGELQRIHDKWLR 824 (953)
Q Consensus 800 ~~~n~~i~~l~e~G~~~~~~~~w~~ 824 (953)
..+|++|..+.++ .++++.+||+.
T Consensus 497 ~~lnk~l~~i~~~-~~~~i~~kW~~ 520 (1197)
T PRK09959 497 DIINKALNAIPPS-EVLRLTEKWIK 520 (1197)
T ss_pred HHHHHHHHhCCHH-HHHHHHhhccc
Confidence 9999999999998 78899999987
No 97
>PF00060 Lig_chan: Ligand-gated ion channel; InterPro: IPR001320 The ability of synapses to modify their synaptic strength in response to activity is a fundamental property of the nervous system and may be an essential component of learning and memory. There are three classes of ionotropic glutamate receptor, namely NMDA (N-methyl-D-aspartate), AMPA (alpha-amino-3-hydroxy-5-methyl-4-isoxazole-4-propionic acid) and kainate receptors. They are believed to play critical roles in synaptic plasticity. At many synapses in the brain, transient activation of NMDA receptors leads to a persistent modification in the strength of synaptic transmission mediated by AMPA receptors and kainate receptors can act as the induction trigger for long-term changes in synaptic transmission [].; GO: 0004970 ionotropic glutamate receptor activity, 0005234 extracellular-glutamate-gated ion channel activity, 0016020 membrane; PDB: 3FAT_A 3KFM_A 3KEI_A 3EN3_A 3EPE_B 3FAS_A 2F34_A 3C34_B 3S2V_A 3GBB_B ....
Probab=99.73 E-value=3.5e-19 Score=172.05 Aligned_cols=107 Identities=31% Similarity=0.545 Sum_probs=82.6
Q ss_pred chhHHHHHHHHHHHHHHHhhhhhcccCCCCCC-------CCcccchhhHHHHHHHhhccc-cCCcccchhHHHHHHHHHH
Q 002211 606 TPLMWAVTGVFFLVVGTVVWILEHRLNDEFRG-------PPRKQIVTVLWFSFSTMFFAH-RENTVSTLGRVVLIIWLFV 677 (953)
Q Consensus 606 ~~~vW~~i~~~~~~~~~~~~~l~~~~~~~~~~-------~~~~~~~~~~~~~~~~l~~~~-~~~~~s~~~R~l~~~w~~~ 677 (953)
++++|++++++++++++++|++++..+.+++. +...++.+++|+.++++++|+ ...|++.++|++.++|+++
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 57999999999999999999999987776655 234568899999999999775 4589999999999999999
Q ss_pred HHHhhhhcccceeeeeeeccccCCCCChHHhhhCC
Q 002211 678 VLIITSSYTASLTSILTVQQLSSPIKGIDTLMTSN 712 (953)
Q Consensus 678 ~lil~~~Yta~L~s~Lt~~~~~~~I~sl~dL~~~~ 712 (953)
+++++++|||+|+|+||.++.+++|+|++||.+++
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 99999999999999999999999999999999776
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=99.73 E-value=6.7e-17 Score=170.14 Aligned_cols=208 Identities=16% Similarity=0.188 Sum_probs=157.5
Q ss_pred ceEEEecCcccccccEEeeCCcceEEEeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHH---HHHHcCceeEEEe
Q 002211 486 QLRIGVPNRVSYRDFVFKVNGTDIVHGYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELI---NQITTGVFDAAVG 562 (953)
Q Consensus 486 ~lri~v~~~~~~~p~~~~~~~~~~~~G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i---~~l~~g~~Di~~~ 562 (953)
+|+||+.. +|+||.+.+. .||++|+++++++++|++++++ + ..|++++ ..|.+|++|++++
T Consensus 1 ~l~vg~~~--~~pPf~~~~~-----~Gfdvdl~~~ia~~lg~~~~~~--~-------~~~~~~~~~~~~L~~g~~Dii~~ 64 (246)
T TIGR03870 1 TLRVCAAT--KEAPYSTKDG-----SGFENKIAAALAAAMGRKVVFV--W-------LAKPAIYLVRDGLDKKLCDVVLG 64 (246)
T ss_pred CeEEEeCC--CCCCCccCCC-----CcchHHHHHHHHHHhCCCeEEE--E-------eccchhhHHHHHHhcCCccEEEe
Confidence 47899986 8999999642 6999999999999999765554 4 3477766 6999999999885
Q ss_pred cEEEecCccceeeccccceecceEEEEecccCCcCcceeeccCchhHHHHHHHHHHHHHHHhhhhhcccCCCCCCCCccc
Q 002211 563 DIAIVTNRTKAVDFTQPYIESGLVVVAPVRKLNSSAWAFLRPFTPLMWAVTGVFFLVVGTVVWILEHRLNDEFRGPPRKQ 642 (953)
Q Consensus 563 ~~~~t~~r~~~vdft~p~~~~~~~~~v~~~~~~~~~~~~l~PF~~~vW~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~ 642 (953)
++++++| ++||.||+.++.++++++.+.
T Consensus 65 -~~~t~~r---~~fS~PY~~~~~~~v~~k~~~------------------------------------------------ 92 (246)
T TIGR03870 65 -LDTGDPR---VLTTKPYYRSSYVFLTRKDRN------------------------------------------------ 92 (246)
T ss_pred -CCCChHH---HhcccCcEEeeeEEEEeCCCC------------------------------------------------
Confidence 8787776 689999999999999998761
Q ss_pred chhhHHHHHHHhhccccCCcccchhHHHHHHHHHHHHHhhhhcccceeeeeeeccccCCCCChHH--hhhCCC-eEEEEe
Q 002211 643 IVTVLWFSFSTMFFAHRENTVSTLGRVVLIIWLFVVLIITSSYTASLTSILTVQQLSSPIKGIDT--LMTSND-RVGYQV 719 (953)
Q Consensus 643 ~~~~~~~~~~~l~~~~~~~~~s~~~R~l~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~I~sl~d--L~~~~~-~ig~~~ 719 (953)
..+++++| |. |+ +||++.
T Consensus 93 ---------------------------------------------------------~~~~~~~d~~L~--g~~~vgv~~ 113 (246)
T TIGR03870 93 ---------------------------------------------------------LDIKSWNDPRLK--KVSKIGVIF 113 (246)
T ss_pred ---------------------------------------------------------CCCCCccchhhc--cCceEEEec
Confidence 35777765 64 87 999999
Q ss_pred CchHHHHHHHhhCCC-----ccceEeCC---------CHHHHHHHHHcCCcEEEEccchhHHHHHhcC-cceE--EeCCc
Q 002211 720 GSFAENYLIEELSIP-----KSRLVALG---------SPEEYAIALENRTVAAVVDERPYIDLFLSDH-CQFS--VRGQE 782 (953)
Q Consensus 720 ~s~~~~~l~~~~~~~-----~~~~~~~~---------~~~~~~~~l~~g~~~a~~~~~~~~~~~~~~~-~~l~--~~~~~ 782 (953)
|+..+.++.+..... ...+..++ +.++++++|..|++||++.+.+.+.+++.+. ..+. .+++.
T Consensus 114 gs~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~aL~~GrvDa~i~~~~~~~~~~~~~~~~~~~~~~~~~ 193 (246)
T TIGR03870 114 GSPAETMLKQIGRYEDNFAYLYSLVNFKSPRNQYTQIDPRKLVSEVATGKADLAVAFAPEVARYVKASPEPLRMTVIPDD 193 (246)
T ss_pred CChHHHHHHhcCccccccccccccccccCcccccccCCHHHHHHHHHcCCCCEEEeeHHhHHHHHHhCCCCceEEecccc
Confidence 999999885421110 01122221 4678999999999999999877776776643 2333 23322
Q ss_pred c-------c--cCccEEEecCCCc-chHHHHHHHHhhhccccHHHHHHHh
Q 002211 783 F-------T--KSGWGFAFPRDSP-LAIDMSTAILTLSENGELQRIHDKW 822 (953)
Q Consensus 783 ~-------~--~~~~~~~~~k~sp-l~~~~n~~i~~l~e~G~~~~~~~~w 822 (953)
. . ..+++++++|+.+ |++.||++|.+|. |.+++|..+|
T Consensus 194 ~~~~~~~~~~~~~~~~iav~k~~~~L~~~in~aL~~l~--~~~~~i~~~y 241 (246)
T TIGR03870 194 ATRSDGAKIPMQYDQSMGVRKDDTALLAEIDAALAKAK--PRIDAILKEE 241 (246)
T ss_pred ccccCCCCcceeeEEEEEEccCCHHHHHHHHHHHHHhH--HHHHHHHHHc
Confidence 1 0 1135899999998 9999999999999 4899999998
No 99
>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=99.72 E-value=1e-16 Score=171.46 Aligned_cols=230 Identities=12% Similarity=0.147 Sum_probs=167.2
Q ss_pred CCcceEEEecCcccccccEEeeCCcceEEEeeHHHHHHHHHhC-CCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEE
Q 002211 483 NGRQLRIGVPNRVSYRDFVFKVNGTDIVHGYCIDVFLAAVRLL-PYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAV 561 (953)
Q Consensus 483 ~g~~lri~v~~~~~~~p~~~~~~~~~~~~G~~~dll~~la~~l-~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~ 561 (953)
..++|++++. +|+||.+.+. ++...|+..++++++++++ ++.+++...| |++++..+ .|+.|+++
T Consensus 16 ~~~~l~~~~~---~~pPf~~~~~-~~~~~G~~~~i~~~i~~~~~~~~~~~~~~p---------w~r~l~~l-~~~~d~~~ 81 (268)
T TIGR02285 16 AKEAITWIVN---DFPPFFIFSG-PSKGRGVFDVILQEIRRALPQYEHRFVRVS---------FARSLKEL-QGKGGVCT 81 (268)
T ss_pred ccceeEEEec---ccCCeeEeCC-CCCCCChHHHHHHHHHHHcCCCceeEEECC---------HHHHHHHH-hcCCCeEE
Confidence 3578998876 6899998754 5778999999999999998 8776666544 99999999 77777777
Q ss_pred ecEEEecCccceeecccccee-cceEEEEecccCCcCcceeeccCchhHHHHHHHHHHHHHHHhhhhhcccCCCCCCCCc
Q 002211 562 GDIAIVTNRTKAVDFTQPYIE-SGLVVVAPVRKLNSSAWAFLRPFTPLMWAVTGVFFLVVGTVVWILEHRLNDEFRGPPR 640 (953)
Q Consensus 562 ~~~~~t~~r~~~vdft~p~~~-~~~~~~v~~~~~~~~~~~~l~PF~~~vW~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~ 640 (953)
.++++|++|.+.++||.||.. ...++++++......
T Consensus 82 ~~~~~t~eR~~~~~Fs~P~~~~~~~~~~~~~~~~~~~------------------------------------------- 118 (268)
T TIGR02285 82 VNLLRTPEREKFLIFSDPTLRALPVGLVLRKELTAGV------------------------------------------- 118 (268)
T ss_pred eeccCCcchhhceeecCCccccCCceEEEccchhhhc-------------------------------------------
Confidence 679999999999999999975 578888887651000
Q ss_pred ccchhhHHHHHHHhhccccCCcccchhHHHHHHHHHHHHHhhhhcccceeeeeeeccccCCCCChHHhhh-CCCeEEEEe
Q 002211 641 KQIVTVLWFSFSTMFFAHRENTVSTLGRVVLIIWLFVVLIITSSYTASLTSILTVQQLSSPIKGIDTLMT-SNDRVGYQV 719 (953)
Q Consensus 641 ~~~~~~~~~~~~~l~~~~~~~~~s~~~R~l~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~I~sl~dL~~-~~~~ig~~~ 719 (953)
..+.....++.+|.+ +++++|+..
T Consensus 119 -------------------------------------------------------~~~~d~~~~~~~l~~l~g~~vgv~~ 143 (268)
T TIGR02285 119 -------------------------------------------------------RDEQDGDVDLKKLLASKKKRLGVIA 143 (268)
T ss_pred -------------------------------------------------------cccCCCCccHHHHhcCCCeEEEEec
Confidence 000010112333321 377899998
Q ss_pred CchHHHHHHH---hhCC-CccceEeCCCHHHHHHHHHcCCcEEEEccchhHHHHHhcC----cceEEeCCcc--ccCccE
Q 002211 720 GSFAENYLIE---ELSI-PKSRLVALGSPEEYAIALENRTVAAVVDERPYIDLFLSDH----CQFSVRGQEF--TKSGWG 789 (953)
Q Consensus 720 ~s~~~~~l~~---~~~~-~~~~~~~~~~~~~~~~~l~~g~~~a~~~~~~~~~~~~~~~----~~l~~~~~~~--~~~~~~ 789 (953)
|+.....+.+ ..+. ...++..+.+.++.+++|.+|++|+++.+...+.+++.+. ..+....... ...+++
T Consensus 144 g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~GrvD~~v~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 223 (268)
T TIGR02285 144 SRSYGQQIDDILSDSGYQHNTRIIGNAAMGNLFKMLEKGRVNYTLAYPPEKTYYEELNNGALPPLKFLPVAGMPAHISVW 223 (268)
T ss_pred ceeccHHHHHHHHhCCcccceeeeccchHHHHHHHHHcCCccEEEeCcHHHHHHHHhccCCcCCeeEeecCCCccceEEE
Confidence 8765433322 1221 1124555778888999999999999999999998887642 2344443221 223578
Q ss_pred EEecCCC---cchHHHHHHHHhhhccccHHHHHHHhcc
Q 002211 790 FAFPRDS---PLAIDMSTAILTLSENGELQRIHDKWLR 824 (953)
Q Consensus 790 ~~~~k~s---pl~~~~n~~i~~l~e~G~~~~~~~~w~~ 824 (953)
++++|+. .+++.||++|.+|.++|.++++.+||+.
T Consensus 224 i~~~k~~~~~~l~~~in~~L~~l~~dG~~~~i~~k~~~ 261 (268)
T TIGR02285 224 VACPKTEWGRKVIADIDQALSELNVDPKYYKYFDRWLS 261 (268)
T ss_pred EEeCCCHHHHHHHHHHHHHHHHHhhCHHHHHHHHHhCC
Confidence 9999974 3999999999999999999999999997
No 100
>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=99.70 E-value=1e-15 Score=157.87 Aligned_cols=214 Identities=29% Similarity=0.514 Sum_probs=178.9
Q ss_pred eEEEecCcccccccEEeeCCcceEEEeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEecEEE
Q 002211 487 LRIGVPNRVSYRDFVFKVNGTDIVHGYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGDIAI 566 (953)
Q Consensus 487 lri~v~~~~~~~p~~~~~~~~~~~~G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~~~~ 566 (953)
|+|++.. .++||.+.+. ++.+.|++.++++.+.+++|.++++ ++ ..|.+++..|.+|++|++++....
T Consensus 1 l~i~~~~--~~~p~~~~~~-~g~~~G~~~~~~~~~~~~~g~~~~~--~~-------~~~~~~~~~l~~g~~D~~~~~~~~ 68 (218)
T cd00134 1 LTVGTAG--TYPPFSFRDA-NGELTGFDVDLAKAIAKELGVKVKF--VE-------VDWDGLITALKSGKVDLIAAGMTI 68 (218)
T ss_pred CEEecCC--CCCCeeEECC-CCCEEeeeHHHHHHHHHHhCCeEEE--Ee-------CCHHHHHHHHhcCCcCEEeecCcC
Confidence 5788876 7899998864 7899999999999999999966444 44 239999999999999999987777
Q ss_pred ecCccceeeccccceecceEEEEecccCCcCcceeeccCchhHHHHHHHHHHHHHHHhhhhhcccCCCCCCCCcccchhh
Q 002211 567 VTNRTKAVDFTQPYIESGLVVVAPVRKLNSSAWAFLRPFTPLMWAVTGVFFLVVGTVVWILEHRLNDEFRGPPRKQIVTV 646 (953)
Q Consensus 567 t~~r~~~vdft~p~~~~~~~~~v~~~~~~~~~~~~l~PF~~~vW~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~ 646 (953)
+.+|.+.+.|+.|+.....++++++..
T Consensus 69 ~~~~~~~~~~~~~~~~~~~~~~~~~~~----------------------------------------------------- 95 (218)
T cd00134 69 TPERAKQVDFSDPYYKSGQVILVKKGS----------------------------------------------------- 95 (218)
T ss_pred CHHHHhhccCcccceeccEEEEEECCC-----------------------------------------------------
Confidence 889988999999999999999998776
Q ss_pred HHHHHHHhhccccCCcccchhHHHHHHHHHHHHHhhhhcccceeeeeeeccccCCCCChHHhhhCCCeEEEEeCchHHHH
Q 002211 647 LWFSFSTMFFAHRENTVSTLGRVVLIIWLFVVLIITSSYTASLTSILTVQQLSSPIKGIDTLMTSNDRVGYQVGSFAENY 726 (953)
Q Consensus 647 ~~~~~~~l~~~~~~~~~s~~~R~l~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~I~sl~dL~~~~~~ig~~~~s~~~~~ 726 (953)
++.+++||. |+++++..|+....+
T Consensus 96 ------------------------------------------------------~~~~~~dl~--g~~i~~~~~~~~~~~ 119 (218)
T cd00134 96 ------------------------------------------------------PIKSVKDLK--GKKVAVQKGSTAEKY 119 (218)
T ss_pred ------------------------------------------------------CCCChHHhC--CCEEEEEcCchHHHH
Confidence 345889995 889999988877777
Q ss_pred HHHhhCCCccceEeCCCHHHHHHHHHcCCcEEEEccchhHHHHHhcC-cceEEeCCc--cccCccEEEecCCCc-chHHH
Q 002211 727 LIEELSIPKSRLVALGSPEEYAIALENRTVAAVVDERPYIDLFLSDH-CQFSVRGQE--FTKSGWGFAFPRDSP-LAIDM 802 (953)
Q Consensus 727 l~~~~~~~~~~~~~~~~~~~~~~~l~~g~~~a~~~~~~~~~~~~~~~-~~l~~~~~~--~~~~~~~~~~~k~sp-l~~~~ 802 (953)
+.+... ..++..+.+.++.++.|.+|++|+++.+.....+...+. +++.++... .....++++..++++ +...|
T Consensus 120 ~~~~~~--~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~l~~~~ 197 (218)
T cd00134 120 LKKALP--EAKVVSYDDNAEALAALENGRADAVIVDEIALAALLKKHPPELKIVGPSIDLEPLGFGVAVGKDNKELLDAV 197 (218)
T ss_pred HHHhCC--cccEEEeCCHHHHHHHHHcCCccEEEeccHHHHHHHHhcCCCcEEeccccCCCccceEEEEcCCCHHHHHHH
Confidence 755433 346778889999999999999999999999988887665 677777653 334456677777775 99999
Q ss_pred HHHHHhhhccccHHHHHHHhc
Q 002211 803 STAILTLSENGELQRIHDKWL 823 (953)
Q Consensus 803 n~~i~~l~e~G~~~~~~~~w~ 823 (953)
+++|..+.++|.++.+.+||+
T Consensus 198 ~~~l~~~~~~g~~~~i~~~~~ 218 (218)
T cd00134 198 NKALKELRADGELKKISKKWF 218 (218)
T ss_pred HHHHHHHHhCccHHHHHHhhC
Confidence 999999999999999999996
No 101
>COG0834 HisJ ABC-type amino acid transport/signal transduction systems, periplasmic component/domain [Amino acid transport and metabolism / Signal transduction mechanisms]
Probab=99.70 E-value=7.1e-16 Score=166.20 Aligned_cols=225 Identities=26% Similarity=0.383 Sum_probs=183.6
Q ss_pred CCcceEEEecCcccccccEEeeCCcceEEEeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEe
Q 002211 483 NGRQLRIGVPNRVSYRDFVFKVNGTDIVHGYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVG 562 (953)
Q Consensus 483 ~g~~lri~v~~~~~~~p~~~~~~~~~~~~G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~ 562 (953)
....+++++... ..+||.+.+.+.+.+.||++|+++++++.++......+++ ..|++++..+..|++|+.++
T Consensus 32 ~~~~~~v~~~~~-~~~p~~~~~~~~~~~~G~dvdl~~~ia~~l~~~~~~~~~~-------~~~~~~~~~l~~g~~D~~~~ 103 (275)
T COG0834 32 ARGKLRVGTEAT-YAPPFEFLDAKGGKLVGFDVDLAKAIAKRLGGDKKVEFVP-------VAWDGLIPALKAGKVDIIIA 103 (275)
T ss_pred hcCeEEEEecCC-CCCCcccccCCCCeEEeeeHHHHHHHHHHhCCcceeEEec-------cchhhhhHHHhcCCcCEEEe
Confidence 457788888852 4569999886336999999999999999998653344443 46999999999999999999
Q ss_pred cEEEecCccceeeccccceecceEEEEecccCCcCcceeeccCchhHHHHHHHHHHHHHHHhhhhhcccCCCCCCCCccc
Q 002211 563 DIAIVTNRTKAVDFTQPYIESGLVVVAPVRKLNSSAWAFLRPFTPLMWAVTGVFFLVVGTVVWILEHRLNDEFRGPPRKQ 642 (953)
Q Consensus 563 ~~~~t~~r~~~vdft~p~~~~~~~~~v~~~~~~~~~~~~l~PF~~~vW~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~ 642 (953)
.+++|++|.+.++||.||+..+..+++++...
T Consensus 104 ~~~~t~er~~~~~fs~py~~~~~~~~~~~~~~------------------------------------------------ 135 (275)
T COG0834 104 GMTITPERKKKVDFSDPYYYSGQVLLVKKDSD------------------------------------------------ 135 (275)
T ss_pred ccccCHHHhccccccccccccCeEEEEECCCC------------------------------------------------
Confidence 99999999999999999999999999998872
Q ss_pred chhhHHHHHHHhhccccCCcccchhHHHHHHHHHHHHHhhhhcccceeeeeeeccccCCCCChHHhhhCCCeEEEEeCch
Q 002211 643 IVTVLWFSFSTMFFAHRENTVSTLGRVVLIIWLFVVLIITSSYTASLTSILTVQQLSSPIKGIDTLMTSNDRVGYQVGSF 722 (953)
Q Consensus 643 ~~~~~~~~~~~l~~~~~~~~~s~~~R~l~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~I~sl~dL~~~~~~ig~~~~s~ 722 (953)
..+.+++||. +++||++.|+.
T Consensus 136 ---------------------------------------------------------~~~~~~~DL~--gk~v~v~~gt~ 156 (275)
T COG0834 136 ---------------------------------------------------------IGIKSLEDLK--GKKVGVQLGTT 156 (275)
T ss_pred ---------------------------------------------------------cCcCCHHHhC--CCEEEEEcCcc
Confidence 2378999996 89999999998
Q ss_pred --HHHHHHHhhCCCccceEeCCCHHHHHHHHHcCCcEEEEccchhHHHH--HhcCcc-eEEeCCcccc-CccEEEecCC-
Q 002211 723 --AENYLIEELSIPKSRLVALGSPEEYAIALENRTVAAVVDERPYIDLF--LSDHCQ-FSVRGQEFTK-SGWGFAFPRD- 795 (953)
Q Consensus 723 --~~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~g~~~a~~~~~~~~~~~--~~~~~~-l~~~~~~~~~-~~~~~~~~k~- 795 (953)
...+... ..+...++.+++..+.+.+|.+|++|+++.+.+.+.++ ..+... .......... .+++++++|+
T Consensus 157 ~~~~~~~~~--~~~~~~~~~~~~~~~~~~al~~Gr~Da~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 234 (275)
T COG0834 157 DEAEEKAKK--PGPNAKIVAYDSNAEALLALKNGRADAVVSDSAVLAGLKLLKKNPGLYVLLVFPGLSVEYLGIALRKGD 234 (275)
T ss_pred hhHHHHHhh--ccCCceEEeeCCHHHHHHHHHcCCccEEEcchHhhhhhhhhhcCCCCceeeeccCCCcceeEEEeccCC
Confidence 4444322 22346788999999999999999999999999998884 333332 2333333333 6899999999
Q ss_pred -CcchHHHHHHHHhhhccccHHHHHHHhcc
Q 002211 796 -SPLAIDMSTAILTLSENGELQRIHDKWLR 824 (953)
Q Consensus 796 -spl~~~~n~~i~~l~e~G~~~~~~~~w~~ 824 (953)
..+++.+|+.+.++.++|.++++.++|+.
T Consensus 235 ~~~l~~~in~~l~~l~~~G~~~~i~~kw~~ 264 (275)
T COG0834 235 DPELLEAVNKALKELKADGTLQKISDKWFG 264 (275)
T ss_pred cHHHHHHHHHHHHHHHhCccHHHHHHHhcC
Confidence 46999999999999999999999999997
No 102
>smart00062 PBPb Bacterial periplasmic substrate-binding proteins. bacterial proteins, eukaryotic ones are in PBPe
Probab=99.68 E-value=1.8e-15 Score=156.01 Aligned_cols=215 Identities=27% Similarity=0.530 Sum_probs=181.8
Q ss_pred ceEEEecCcccccccEEeeCCcceEEEeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEecEE
Q 002211 486 QLRIGVPNRVSYRDFVFKVNGTDIVHGYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGDIA 565 (953)
Q Consensus 486 ~lri~v~~~~~~~p~~~~~~~~~~~~G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~~~ 565 (953)
+|+|++.. .++||.+.+. ++...|+.+|+++.+.+++|.++ ++.+ ..|..++..+.+|++|++++...
T Consensus 1 ~l~v~~~~--~~~p~~~~~~-~g~~~G~~~~~~~~~~~~~g~~~--~~~~-------~~~~~~~~~l~~g~~D~~~~~~~ 68 (219)
T smart00062 1 TLRVGTNG--DYPPFSFADE-DGELTGFDVDLAKAIAKELGLKV--EFVE-------VSFDNLLTALKSGKIDVVAAGMT 68 (219)
T ss_pred CEEEEecC--CCCCcEEECC-CCCcccchHHHHHHHHHHhCCeE--EEEe-------ccHHHHHHHHHCCcccEEecccc
Confidence 47899874 7899988764 67799999999999999999664 4444 35999999999999999998777
Q ss_pred EecCccceeeccccceecceEEEEecccCCcCcceeeccCchhHHHHHHHHHHHHHHHhhhhhcccCCCCCCCCcccchh
Q 002211 566 IVTNRTKAVDFTQPYIESGLVVVAPVRKLNSSAWAFLRPFTPLMWAVTGVFFLVVGTVVWILEHRLNDEFRGPPRKQIVT 645 (953)
Q Consensus 566 ~t~~r~~~vdft~p~~~~~~~~~v~~~~~~~~~~~~l~PF~~~vW~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~ 645 (953)
.+.+|...+.++.|+...+.++++++..
T Consensus 69 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~---------------------------------------------------- 96 (219)
T smart00062 69 ITPERAKQVDFSDPYYKSGQVILVRKDS---------------------------------------------------- 96 (219)
T ss_pred CCHHHHhheeeccceeeceeEEEEecCC----------------------------------------------------
Confidence 7888888899999999999999888655
Q ss_pred hHHHHHHHhhccccCCcccchhHHHHHHHHHHHHHhhhhcccceeeeeeeccccCCCCChHHhhhCCCeEEEEeCchHHH
Q 002211 646 VLWFSFSTMFFAHRENTVSTLGRVVLIIWLFVVLIITSSYTASLTSILTVQQLSSPIKGIDTLMTSNDRVGYQVGSFAEN 725 (953)
Q Consensus 646 ~~~~~~~~l~~~~~~~~~s~~~R~l~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~I~sl~dL~~~~~~ig~~~~s~~~~ 725 (953)
++.+++||. |++|++..|+....
T Consensus 97 -------------------------------------------------------~~~~~~dL~--g~~i~~~~g~~~~~ 119 (219)
T smart00062 97 -------------------------------------------------------PIKSLEDLK--GKKVAVVAGTTGEE 119 (219)
T ss_pred -------------------------------------------------------CCCChHHhC--CCEEEEecCccHHH
Confidence 478999995 88999999988888
Q ss_pred HHHHhhCCCccceEeCCCHHHHHHHHHcCCcEEEEccchhHHHHHhcC--cceEEeCCcccc-CccEEEecCCCc-chHH
Q 002211 726 YLIEELSIPKSRLVALGSPEEYAIALENRTVAAVVDERPYIDLFLSDH--CQFSVRGQEFTK-SGWGFAFPRDSP-LAID 801 (953)
Q Consensus 726 ~l~~~~~~~~~~~~~~~~~~~~~~~l~~g~~~a~~~~~~~~~~~~~~~--~~l~~~~~~~~~-~~~~~~~~k~sp-l~~~ 801 (953)
++... ....++..+.+..+.+.+|.+|++|+++...+.+.+...+. +++.++...... ..++++++++++ +.+.
T Consensus 120 ~~~~~--~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 197 (219)
T smart00062 120 LLKKL--YPEAKIVSYDSQAEALAALKAGRADAAVADAPALAALVKQHGLPELKIVGDPLDTPEGYAFAVRKGDPELLDK 197 (219)
T ss_pred HHHHh--CCCceEEEcCCHHHHHHHhhcCcccEEEeccHHHHHHHHhcCCCceeeccCCCCCCcceEEEEECCCHHHHHH
Confidence 87543 23456777889999999999999999999999888887764 567777665544 788999999987 9999
Q ss_pred HHHHHHhhhccccHHHHHHHhc
Q 002211 802 MSTAILTLSENGELQRIHDKWL 823 (953)
Q Consensus 802 ~n~~i~~l~e~G~~~~~~~~w~ 823 (953)
++++|..+.++|.++++.++|+
T Consensus 198 ~~~~l~~~~~~~~~~~i~~~~~ 219 (219)
T smart00062 198 INKALKELKADGTLKKIYEKWF 219 (219)
T ss_pred HHHHHHHHHhCchHHHHHhccC
Confidence 9999999999999999999985
No 103
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=99.68 E-value=5.1e-16 Score=201.60 Aligned_cols=222 Identities=12% Similarity=0.156 Sum_probs=184.8
Q ss_pred CCCcceEEEecCcccccccEEeeCCcceEEEeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEE
Q 002211 482 NNGRQLRIGVPNRVSYRDFVFKVNGTDIVHGYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAV 561 (953)
Q Consensus 482 ~~g~~lri~v~~~~~~~p~~~~~~~~~~~~G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~ 561 (953)
.+.++|+||+.. +++|+.+..+.++++.||.+|+++.+++++|. +++++++ .+|++++.++.+|++|++.
T Consensus 53 ~~~~~l~vgv~~--~~~p~~~~~~~~g~~~G~~~D~l~~ia~~lG~--~~e~v~~------~~~~~~l~~l~~g~iDl~~ 122 (1197)
T PRK09959 53 ASKKNLVIAVHK--SQTATLLHTDSQQRVRGINADYLNLLKRALNI--KLTLREY------ADHQKAMDALEEGEVDIVL 122 (1197)
T ss_pred hhCCeEEEEecC--CCCCCceeecCCCccceecHHHHHHHHHhcCC--ceEEEeC------CCHHHHHHHHHcCCCcEec
Confidence 356789999986 56555554334789999999999999999995 5666653 4799999999999999998
Q ss_pred ecEEEecCccceeeccccceecceEEEEecccCCcCcceeeccCchhHHHHHHHHHHHHHHHhhhhhcccCCCCCCCCcc
Q 002211 562 GDIAIVTNRTKAVDFTQPYIESGLVVVAPVRKLNSSAWAFLRPFTPLMWAVTGVFFLVVGTVVWILEHRLNDEFRGPPRK 641 (953)
Q Consensus 562 ~~~~~t~~r~~~vdft~p~~~~~~~~~v~~~~~~~~~~~~l~PF~~~vW~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~ 641 (953)
+.++.+++|.+.++||.||+.+..++++++..
T Consensus 123 ~~~~~~~~r~~~~~fs~py~~~~~~~v~~~~~------------------------------------------------ 154 (1197)
T PRK09959 123 SHLVASPPLNDDIAATKPLIITFPALVTTLHD------------------------------------------------ 154 (1197)
T ss_pred CccccccccccchhcCCCccCCCceEEEeCCC------------------------------------------------
Confidence 88999999999999999999999999998755
Q ss_pred cchhhHHHHHHHhhccccCCcccchhHHHHHHHHHHHHHhhhhcccceeeeeeeccccCCCCChHHhhhCCCeEEEEeCc
Q 002211 642 QIVTVLWFSFSTMFFAHRENTVSTLGRVVLIIWLFVVLIITSSYTASLTSILTVQQLSSPIKGIDTLMTSNDRVGYQVGS 721 (953)
Q Consensus 642 ~~~~~~~~~~~~l~~~~~~~~~s~~~R~l~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~I~sl~dL~~~~~~ig~~~~s 721 (953)
.+++++++. +++++++.|+
T Consensus 155 -----------------------------------------------------------~~~~~~~l~--~~~i~~~~g~ 173 (1197)
T PRK09959 155 -----------------------------------------------------------SMRPLTSSK--PVNIARVANY 173 (1197)
T ss_pred -----------------------------------------------------------CCCCccccc--CeEEEEeCCC
Confidence 456677774 7889999999
Q ss_pred hHHHHHHHhhCCCccceEeCCCHHHHHHHHHcCCcEEEEccchhHHHHHhcCc--ceEEeCCc-cccCccEEEecCCCc-
Q 002211 722 FAENYLIEELSIPKSRLVALGSPEEYAIALENRTVAAVVDERPYIDLFLSDHC--QFSVRGQE-FTKSGWGFAFPRDSP- 797 (953)
Q Consensus 722 ~~~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~g~~~a~~~~~~~~~~~~~~~~--~l~~~~~~-~~~~~~~~~~~k~sp- 797 (953)
...+++++.+ +..+++.|++.++++++|.+|++||++++...+.|+++++. ++.+++.. .......++++|+.|
T Consensus 174 ~~~~~~~~~~--p~~~i~~~~s~~~al~av~~G~~Da~i~~~~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~ 251 (1197)
T PRK09959 174 PPDEVIHQSF--PKATIISFTNLYQALASVSAGQNDYFIGSNIITSSMISRYFTHSLNVVKYYNSPRQYNFFLTRKESVI 251 (1197)
T ss_pred CCHHHHHHhC--CCCEEEeCCCHHHHHHHHHcCCCCEEEccHHHHHHHHhcccccceEEEeeccCCCCceeEEEcCCcHH
Confidence 9888886644 56789999999999999999999999999999999988743 45555432 223346688899998
Q ss_pred chHHHHHHHHhhhccccHHHHHHHhccc
Q 002211 798 LAIDMSTAILTLSENGELQRIHDKWLRK 825 (953)
Q Consensus 798 l~~~~n~~i~~l~e~G~~~~~~~~w~~~ 825 (953)
|...+|++|..+.++|.. ++.+||+..
T Consensus 252 L~~~lnkal~~i~~~~~~-~i~~kW~~~ 278 (1197)
T PRK09959 252 LNEVLNRFVDALTNEVRY-EVSQNWLDT 278 (1197)
T ss_pred HHHHHHHHHHhCCHHHHH-HHHHhccCC
Confidence 999999999999999977 999999973
No 104
>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=99.67 E-value=7.7e-15 Score=156.74 Aligned_cols=257 Identities=19% Similarity=0.280 Sum_probs=200.6
Q ss_pred EEeEEEecC--CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEEccCChhhHH
Q 002211 51 NVGAIFSFG--TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIVGPQSAVMAH 128 (953)
Q Consensus 51 ~IG~l~~~~--~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aiiGp~~S~~a~ 128 (953)
+||+++|.+ ..++.....|++.|++++ |..+++++.|+++++....+.+.+++.+++.+|||+.++....
T Consensus 1 ~Ig~i~~~~~~~~~~~~~~~~~~~~~~~~--------g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~ii~~~~~~~~~ 72 (269)
T cd01391 1 KIGVLLPLSGSAPFGAQLLAGIELAAEEI--------GRGLEVILADSQSDPERALEALRDLIQQGVDGIIGPPSSSSAL 72 (269)
T ss_pred CceEEeecCCCcHHHHHHHHHHHHHHHHh--------CCceEEEEecCCCCHHHHHHHHHHHHHcCCCEEEecCCCHHHH
Confidence 589999987 566778889999999887 4678888999999998899999999999999999999987777
Q ss_pred HHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecC-ccccchHHHHHHHHH
Q 002211 129 VLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDD-DQGRNGVTALGDKLA 207 (953)
Q Consensus 129 av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~-~~g~~~~~~l~~~l~ 207 (953)
.+...+...++|+|++.+..+... .+++++++.+++..++..+++++.+.+|+++++++.+. .++....+.+++.++
T Consensus 73 ~~~~~~~~~~ip~v~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~i~~i~~~~~~~~~~~~~~~~~~~~ 150 (269)
T cd01391 73 AVVELAAAAGIPVVSLDATAPDLT--GYPYVFRVGPDNEQAGEAAAEYLAEKGWKRVALIYGDDGAYGRERLEGFKAALK 150 (269)
T ss_pred HHHHHHHHcCCcEEEecCCCCccC--CCceEEEEcCCcHHHHHHHHHHHHHhCCceEEEEecCCcchhhHHHHHHHHHHH
Confidence 688889999999999877765544 57899999999999999999999999999999999877 678888999999999
Q ss_pred hcCcEEEEEEecCCCCCCChHHHHHHHHHHhcC-CceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEEeCcccccccCC
Q 002211 208 EIRCKISYKSALPPDQSVTETDVRNELVKVRMM-EARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIATTWLSTFIDSK 286 (953)
Q Consensus 208 ~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~-~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~~~~~ 286 (953)
+.|.++......+.. ...++......+++. ++++|++++. ..+..+++++.+.|+.+.++.|++.+.+.....
T Consensus 151 ~~~~~~~~~~~~~~~---~~~~~~~~~~~l~~~~~~~~i~~~~~-~~a~~~~~~~~~~g~~~~~~~ii~~~~~~~~~~-- 224 (269)
T cd01391 151 KAGIEVVAIEYGDLD---TEKGFQALLQLLKAAPKPDAIFACND-EMAAGALKAAREAGLTPGDISIIGFDGSPAALL-- 224 (269)
T ss_pred hcCcEEEeccccCCC---ccccHHHHHHHHhcCCCCCEEEEcCc-hHHHHHHHHHHHcCCCCCCCEEEeccccccccc--
Confidence 999877654444433 235677777788776 7999999887 888999999999998755677777776543321
Q ss_pred CCCchhhhhhccceEEEEEecCCChhhHHHHHHHHhhcCCCCCCCchhhHHhhHHHH
Q 002211 287 SPLSLKTAKSILGALTLRQHTPDSKRRRDFVSRWNTLSNGSIGLNPYGLYAYDTVWM 343 (953)
Q Consensus 287 ~~~~~~~~~~~~g~~~~~~~~~~~~~~~~F~~~~~~~~~~~~~~~~~~~~~YDAv~~ 343 (953)
.......++..+....+..+. ..++.+...+|||+.+
T Consensus 225 -----~~~~~~~~~~ti~~~~~~~~~---------------~~~~~~~~~~~~a~~~ 261 (269)
T cd01391 225 -----AAGEAGPGLTTVAQPFPGDDP---------------DQPDYPAALGYDAVLL 261 (269)
T ss_pred -----ccccccceEEecccCCCCCCC---------------CCCCccccceeeeeee
Confidence 012233445555544433332 2445566778888766
No 105
>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=99.65 E-value=3.9e-15 Score=155.84 Aligned_cols=211 Identities=16% Similarity=0.191 Sum_probs=160.7
Q ss_pred ceEEEecCcccccccEEeeCCcceEEEeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEecEE
Q 002211 486 QLRIGVPNRVSYRDFVFKVNGTDIVHGYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGDIA 565 (953)
Q Consensus 486 ~lri~v~~~~~~~p~~~~~~~~~~~~G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~~~ 565 (953)
.|||++.. +|+||.+.+ ..|+++||++++++++|.+++++..+ ..+..++..+.+|++|++++
T Consensus 1 ~l~v~~~~--~~~P~~~~~-----~~G~~~el~~~i~~~~g~~i~~~~~~-------~~~~~~~~~l~~g~~Di~~~--- 63 (232)
T TIGR03871 1 ALRVCADP--NNLPFSNEK-----GEGFENKIAQLLADDLGLPLEYTWFP-------QRRGFVRNTLNAGRCDVVIG--- 63 (232)
T ss_pred CeEEEeCC--CCCCccCCC-----CCchHHHHHHHHHHHcCCceEEEecC-------cchhhHHHHHhcCCccEEEe---
Confidence 37888875 789987642 36999999999999999887776554 22444677899999999876
Q ss_pred EecCccceeeccccceecceEEEEecccCCcCcceeeccCchhHHHHHHHHHHHHHHHhhhhhcccCCCCCCCCcccchh
Q 002211 566 IVTNRTKAVDFTQPYIESGLVVVAPVRKLNSSAWAFLRPFTPLMWAVTGVFFLVVGTVVWILEHRLNDEFRGPPRKQIVT 645 (953)
Q Consensus 566 ~t~~r~~~vdft~p~~~~~~~~~v~~~~~~~~~~~~l~PF~~~vW~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~ 645 (953)
+++|.+.++||.||...+.++++++...
T Consensus 64 -~~~r~~~~~fs~py~~~~~~lv~~~~~~--------------------------------------------------- 91 (232)
T TIGR03871 64 -VPAGYEMVLTTRPYYRSTYVFVTRKDSL--------------------------------------------------- 91 (232)
T ss_pred -ccCccccccccCCcEeeeEEEEEeCCCc---------------------------------------------------
Confidence 4778889999999999999999988751
Q ss_pred hHHHHHHHhhccccCCcccchhHHHHHHHHHHHHHhhhhcccceeeeeeeccccCCCCChHHhhhCCCeEEEEeCchHHH
Q 002211 646 VLWFSFSTMFFAHRENTVSTLGRVVLIIWLFVVLIITSSYTASLTSILTVQQLSSPIKGIDTLMTSNDRVGYQVGSFAEN 725 (953)
Q Consensus 646 ~~~~~~~~l~~~~~~~~~s~~~R~l~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~I~sl~dL~~~~~~ig~~~~s~~~~ 725 (953)
..+++++|+.-.+.+||+..|+...+
T Consensus 92 ------------------------------------------------------~~~~~~~d~~l~g~~V~v~~g~~~~~ 117 (232)
T TIGR03871 92 ------------------------------------------------------LDVKSLDDPRLKKLRIGVFAGTPPAH 117 (232)
T ss_pred ------------------------------------------------------ccccchhhhhhcCCeEEEEcCChHHH
Confidence 36778888322478999999999888
Q ss_pred HHHHhhCCCccceE---------eCCCHHHHHHHHHcCCcEEEEccchhHHHHHhcC-cceEEeCCc------cccCccE
Q 002211 726 YLIEELSIPKSRLV---------ALGSPEEYAIALENRTVAAVVDERPYIDLFLSDH-CQFSVRGQE------FTKSGWG 789 (953)
Q Consensus 726 ~l~~~~~~~~~~~~---------~~~~~~~~~~~l~~g~~~a~~~~~~~~~~~~~~~-~~l~~~~~~------~~~~~~~ 789 (953)
++.+. +.. .++. ...+..+.+.+|.+|++|+++.+...+.+++++. .++.+.... ....+++
T Consensus 118 ~l~~~-~~~-~~~~~~~~~~~~~~~~~~~~~~~~l~~G~~Da~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 195 (232)
T TIGR03871 118 WLARH-GLV-ENVVGYSLFGDYRPESPPGRMVEDLAAGEIDVAIVWGPIAGYFAKQAGPPLVVVPLLPEDGGIPFDYRIA 195 (232)
T ss_pred HHHhc-Ccc-cccccccccccccccCCHHHHHHHHHcCCcCEEEeccHHHHHHHHhCCCCceeeccccCCCCCCccceEE
Confidence 88542 211 1211 1347899999999999999999988888877653 244443321 1234578
Q ss_pred EEecCCCc-chHHHHHHHHhhhccccHHHHHHHhc
Q 002211 790 FAFPRDSP-LAIDMSTAILTLSENGELQRIHDKWL 823 (953)
Q Consensus 790 ~~~~k~sp-l~~~~n~~i~~l~e~G~~~~~~~~w~ 823 (953)
++++++++ ++..||++|.++. |.+++|.+||.
T Consensus 196 ~~~~~~~~~l~~~~n~~l~~~~--~~~~~i~~kyg 228 (232)
T TIGR03871 196 MGVRKGDKAWKDELNAVLDRRQ--AEIDAILREYG 228 (232)
T ss_pred EEEecCCHHHHHHHHHHHHHHH--HHHHHHHHHcC
Confidence 88999877 9999999999985 47999999994
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=99.40 E-value=3.1e-11 Score=139.12 Aligned_cols=299 Identities=14% Similarity=0.139 Sum_probs=165.2
Q ss_pred CceEEEeEEEecCCCc---hhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEEccCC
Q 002211 47 PEVLNVGAIFSFGTVN---GQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIVGPQS 123 (953)
Q Consensus 47 ~~~i~IG~l~~~~~~~---g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aiiGp~~ 123 (953)
..+-+|++++|+++.+ |...+.|+..|. ++.+ +.+.++.++|+..++.. ....+.+.+|+..||||..
T Consensus 217 ~~~~~IavLLPlsG~~a~~~~aI~~G~~aA~---~~~~----~~~~~l~~~Dt~~~~~~--~~~~~a~~~ga~~ViGPL~ 287 (536)
T PF04348_consen 217 APPQRIAVLLPLSGRLARAGQAIRDGFLAAY---YADA----DSRPELRFYDTNADSAD--ALYQQAVADGADFVIGPLL 287 (536)
T ss_dssp -----EEEEE--SSTTHHHHHHHHHHHHHHH------T----T--S-EEEEETTTS-HH--HHHHHHHHTT--EEE---S
T ss_pred CCccCEEEEeCCCCchhHHHHHHHHHHHHhh---cccc----cCCCceEEecCCCCCHH--HHHHHHHHcCCCEEEcCCC
Confidence 3456899999999655 677888988888 2222 34677888999877433 3456677889999999998
Q ss_pred hhhHHHHHHhhhh--CCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecCccccchHHH
Q 002211 124 AVMAHVLSHLANE--LQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDDDQGRNGVTA 201 (953)
Q Consensus 124 S~~a~av~~v~~~--~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~~~g~~~~~~ 201 (953)
-+...+++..-.. ..||++.....+.. .. -+.+|...-+....+..+++.+..-|+++..||+.++++|+...++
T Consensus 288 k~~V~~l~~~~~~~~~~vp~LaLN~~~~~-~~--~~~l~~f~LspEdEA~q~A~~a~~~g~~~alvl~p~~~~g~R~~~a 364 (536)
T PF04348_consen 288 KSNVEALAQLPQLQAQPVPVLALNQPDNS-QA--PPNLYQFGLSPEDEARQAAQKAFQDGYRRALVLAPQNAWGQRMAEA 364 (536)
T ss_dssp HHHHHHHHH-GG-GGTT-EEEES---TT-------TTEEE----HHHHHHHHHHHHHHTT--S-EEEEESSHHHHHHHHH
T ss_pred HHHHHHHHhcCcccccCCceeeccCCCcc-cC--ccceEEEeCCcHHHHHHHHHHHHhcCCCCEEEEcCCChHHHHHHHH
Confidence 8877777665542 58999987665543 11 2455666666677899999999999999999999999999999999
Q ss_pred HHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEEeCcccc
Q 002211 202 LGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIATTWLST 281 (953)
Q Consensus 202 l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~ 281 (953)
|.+.+++.|+.++....+.. ..++...++.-...+.|.|++.+.+.++..+--...-. ...+-..+.++....
T Consensus 365 F~~~W~~~gg~~~~~~~~~~-----~~~~~~~i~~r~r~d~D~ifl~a~~~~ar~ikP~l~~~--~a~~lPvyatS~~~~ 437 (536)
T PF04348_consen 365 FNQQWQALGGQVAEVSYYGS-----PADLQAAIQPRRRQDIDAIFLVANPEQARLIKPQLDFH--FAGDLPVYATSRSYS 437 (536)
T ss_dssp HHHHHHHHHSS--EEEEESS-----TTHHHHHHHHS--TT--EEEE---HHHHHHHHHHHTT---T-TT-EEEE-GGG--
T ss_pred HHHHHHHcCCCceeeEecCC-----HHHHHHHHhhcCCCCCCEEEEeCCHHHHHHHhhhcccc--cCCCCCEEEeccccC
Confidence 99999999998876666653 46888888866667899999999999888777666432 122222334332211
Q ss_pred cccCCCCCchhhhhhccceEEEEEe---cCCChhhHHHHHHHHhhcCCCCCCCchhhHHhhHHHHHHHHHHHHHhcCCcc
Q 002211 282 FIDSKSPLSLKTAKSILGALTLRQH---TPDSKRRRDFVSRWNTLSNGSIGLNPYGLYAYDTVWMIARALKLFLDQGNTI 358 (953)
Q Consensus 282 ~~~~~~~~~~~~~~~~~g~~~~~~~---~~~~~~~~~F~~~~~~~~~~~~~~~~~~~~~YDAv~~la~Al~~~~~~~~~~ 358 (953)
.. .+......+.|+..+... .+..+..+.+...|.... ....-.-+.+|||..++.+
T Consensus 438 g~-----~~~~~~~dL~gv~f~d~Pwll~~~~~~~~~~~~~~~~~~---~~~~RL~AlG~DA~~L~~~------------ 497 (536)
T PF04348_consen 438 GS-----PNPSQDRDLNGVRFSDMPWLLDPNSPLRQQLAALWPNAS---NSLQRLYALGIDAYRLAPR------------ 497 (536)
T ss_dssp HH-----T-HHHHHHTTT-EEEE-GGGG---SHHHHHHH-HHTTT----HHHHHHHHHHHHHHHHHHT------------
T ss_pred CC-----CCcchhhhhcCCEEeccccccCCCchHHHHHHhhccCCc---cHHHHHHHHHHHHHHHHHH------------
Confidence 11 113445678998877543 223344444444443221 0111223456666554321
Q ss_pred cccCCCccCCCCCCcccCCCccccCchHHHHHHHHhcccCCcceeEEEccCCC
Q 002211 359 SFSNDTKLNGLGGGTLNLGALSIFDGGKKFLANILQTNMTGLSGPIHFNQDRS 411 (953)
Q Consensus 359 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~f~G~tG~v~Fd~~g~ 411 (953)
-.-++.+....+.|.||.+++|++|.
T Consensus 498 ---------------------------l~~l~~~~~~~~~G~TG~L~~~~~g~ 523 (536)
T PF04348_consen 498 ---------------------------LPQLRQFPGYRLDGLTGQLSLDEDGR 523 (536)
T ss_dssp ---------------------------HHHHHHSTT--EEETTEEEEE-TT-B
T ss_pred ---------------------------HHHHhhCCCCcccCCceeEEECCCCe
Confidence 11233344567899999999999885
No 107
>smart00079 PBPe Eukaryotic homologues of bacterial periplasmic substrate binding proteins. Prokaryotic homologues are represented by a separate alignment: PBPb
Probab=99.39 E-value=1.9e-12 Score=122.50 Aligned_cols=123 Identities=33% Similarity=0.517 Sum_probs=107.5
Q ss_pred CCCChHHhhhC-CCeEEEEeCchHHHHHHHhhCCC------c---cceEeCCCHHHHHHHHHcCCcEEEEccchhHHHHH
Q 002211 701 PIKGIDTLMTS-NDRVGYQVGSFAENYLIEELSIP------K---SRLVALGSPEEYAIALENRTVAAVVDERPYIDLFL 770 (953)
Q Consensus 701 ~I~sl~dL~~~-~~~ig~~~~s~~~~~l~~~~~~~------~---~~~~~~~~~~~~~~~l~~g~~~a~~~~~~~~~~~~ 770 (953)
+|++++||..+ +.+||++.|++.+.++++..... . .+++.+++..+++.+|++|+ ||++.+.+.+.+++
T Consensus 1 ~i~~~~dl~~~~~~~vgv~~gs~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~-da~v~d~~~~~~~~ 79 (134)
T smart00079 1 PITSVEDLAKQTKIEYGTIRGSSTLAFFKRSGNPEYSRMWNYMSASPSVFVKSYAEGVQRVRVSN-YAFLMESTYLDYEL 79 (134)
T ss_pred CCCChHHHhhCCCccceEecCchHHHHHHhCCChHHHHHHHHHHhCCCCCCCCHHHHHHHHHcCC-CEEEeehHhHHHHH
Confidence 47899999743 36899999999999996533210 0 25677899999999999999 99999999999998
Q ss_pred hcCcceEEeCCccccCccEEEecCCCcchHHHHHHHHhhhccccHHHHHHHhcc
Q 002211 771 SDHCQFSVRGQEFTKSGWGFAFPRDSPLAIDMSTAILTLSENGELQRIHDKWLR 824 (953)
Q Consensus 771 ~~~~~l~~~~~~~~~~~~~~~~~k~spl~~~~n~~i~~l~e~G~~~~~~~~w~~ 824 (953)
.+.|++.+++..+...+++++++|+++|++.+|.+|.++.++|.++++.++|+.
T Consensus 80 ~~~~~~~~~~~~~~~~~~~ia~~k~~~l~~~vn~~l~~l~~~G~~~~l~~kw~~ 133 (134)
T smart00079 80 SQNCDLMTVGENFGRKGYGIAFPKGSPLRDDLSRAILKLSESGELQKLENKWWK 133 (134)
T ss_pred hCCCCeEEcCcccCCCceEEEecCCCHHHHHHHHHHHHHHhcCcHHHHHHhhcc
Confidence 888999999988888899999999999999999999999999999999999985
No 108
>COG4623 Predicted soluble lytic transglycosylase fused to an ABC-type amino acid-binding protein [Cell envelope biogenesis, outer membrane]
Probab=99.29 E-value=3.7e-11 Score=123.46 Aligned_cols=220 Identities=17% Similarity=0.185 Sum_probs=176.5
Q ss_pred CCcceEEEecCcccccccEEeeCCcceEEEeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEe
Q 002211 483 NGRQLRIGVPNRVSYRDFVFKVNGTDIVHGYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVG 562 (953)
Q Consensus 483 ~g~~lri~v~~~~~~~p~~~~~~~~~~~~G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~ 562 (953)
..+.|||++.+ .|..+... ++...|+++++.+++++.||. +.+..+. .+-+++..+|.+|++|++.+
T Consensus 21 ~rGvLrV~tin----sp~sy~~~-~~~p~G~eYelak~Fa~yLgV--~Lki~~~------~n~dqLf~aL~ng~~DL~Aa 87 (473)
T COG4623 21 ARGVLRVSTIN----SPLSYFED-KGGPTGLEYELAKAFADYLGV--KLKIIPA------DNIDQLFDALDNGNADLAAA 87 (473)
T ss_pred hcCeEEEEeec----Cccceecc-CCCccchhHHHHHHHHHHhCC--eEEEEec------CCHHHHHHHHhCCCcceecc
Confidence 45789999986 34544433 556679999999999999994 4555553 45789999999999999999
Q ss_pred cEEEecCccceeeccccceecceEEEEecccCCcCcceeeccCchhHHHHHHHHHHHHHHHhhhhhcccCCCCCCCCccc
Q 002211 563 DIAIVTNRTKAVDFTQPYIESGLVVVAPVRKLNSSAWAFLRPFTPLMWAVTGVFFLVVGTVVWILEHRLNDEFRGPPRKQ 642 (953)
Q Consensus 563 ~~~~t~~r~~~vdft~p~~~~~~~~~v~~~~~~~~~~~~l~PF~~~vW~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~ 642 (953)
++...++|.+.+.....|+..+..++.++..
T Consensus 88 gl~~~~~~l~~~~~gP~y~svs~qlVyRkG~------------------------------------------------- 118 (473)
T COG4623 88 GLLYNSERLKNFQPGPTYYSVSQQLVYRKGQ------------------------------------------------- 118 (473)
T ss_pred cccCChhHhcccCCCCceecccHHHHhhcCC-------------------------------------------------
Confidence 9999999999998888899999999998888
Q ss_pred chhhHHHHHHHhhccccCCcccchhHHHHHHHHHHHHHhhhhcccceeeeeeeccccCCCCChHHhhhCCCeEEEEeCch
Q 002211 643 IVTVLWFSFSTMFFAHRENTVSTLGRVVLIIWLFVVLIITSSYTASLTSILTVQQLSSPIKGIDTLMTSNDRVGYQVGSF 722 (953)
Q Consensus 643 ~~~~~~~~~~~l~~~~~~~~~s~~~R~l~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~I~sl~dL~~~~~~ig~~~~s~ 722 (953)
...+++++|. +..|.+..|+.
T Consensus 119 ---------------------------------------------------------~Rp~~l~~L~--g~~i~v~~gs~ 139 (473)
T COG4623 119 ---------------------------------------------------------YRPRSLGQLK--GRQITVAKGSA 139 (473)
T ss_pred ---------------------------------------------------------CCCCCHHHcc--CceeeccCCcH
Confidence 4567899996 77888899987
Q ss_pred HHHHHHHhh--CCCccceEeC---CCHHHHHHHHHcCCcEEEEccchhHHHHHhcCcceEEeCCccccCccEEEecCCC-
Q 002211 723 AENYLIEEL--SIPKSRLVAL---GSPEEYAIALENRTVAAVVDERPYIDLFLSDHCQFSVRGQEFTKSGWGFAFPRDS- 796 (953)
Q Consensus 723 ~~~~l~~~~--~~~~~~~~~~---~~~~~~~~~l~~g~~~a~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~k~s- 796 (953)
..+.++... ..| ..+... .+.+|.++.+..|..+..+.+.+.+..+..-++++.+.-..-...+.++.+|.+.
T Consensus 140 ~~~~l~~lk~~kyP-~l~~k~d~~~~~~dLle~v~~Gkldytiads~~is~~q~i~P~laVafd~tde~~v~Wy~~~~dd 218 (473)
T COG4623 140 HVEDLKLLKETKYP-ELIWKVDDKLGVEDLLEMVAEGKLDYTIADSVEISLFQRVHPELAVAFDLTDEQPVAWYLPRDDD 218 (473)
T ss_pred HHHHHHHHHHhhcc-hhhhhhcccccHHHHHHHHhcCCcceeeeccHHHHHHHHhCccceeeeecccccCceeeccCCch
Confidence 655543211 122 222222 3788999999999999999999999888666787777665555678999999864
Q ss_pred -cchHHHHHHHHhhhccccHHHHHHHhcc
Q 002211 797 -PLAIDMSTAILTLSENGELQRIHDKWLR 824 (953)
Q Consensus 797 -pl~~~~n~~i~~l~e~G~~~~~~~~w~~ 824 (953)
.|...++.++..+.|.|.++++++||++
T Consensus 219 ~tL~a~ll~F~~~~~e~g~larleeky~g 247 (473)
T COG4623 219 STLSAALLDFLNEAKEDGLLARLEEKYLG 247 (473)
T ss_pred HHHHHHHHHHHHHhhcchHHHHHHHHHhc
Confidence 4999999999999999999999999997
No 109
>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=99.03 E-value=1.7e-08 Score=107.57 Aligned_cols=205 Identities=10% Similarity=0.045 Sum_probs=151.7
Q ss_pred EEeEEEecC-CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEEccCChhhHHH
Q 002211 51 NVGAIFSFG-TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIVGPQSAVMAHV 129 (953)
Q Consensus 51 ~IG~l~~~~-~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aiiGp~~S~~a~a 129 (953)
+||+++|.+ ..+......|++.++++. | +++.+.|+..++....+.+.+++.+++.+||+...+.....
T Consensus 1 ~ig~v~~~~~~~~~~~~~~g~~~~~~~~--------g--~~l~~~~~~~~~~~~~~~~~~~~~~~~d~ii~~~~~~~~~~ 70 (264)
T cd01537 1 TIGVLVPDLDNPFFAQVLKGIEEAAKAA--------G--YQVLLANSQNDAEKQLSALENLIARGVDGIIIAPSDLTAPT 70 (264)
T ss_pred CeEEEEcCCCChHHHHHHHHHHHHHHHc--------C--CeEEEEeCCCCHHHHHHHHHHHHHcCCCEEEEecCCCcchh
Confidence 589999985 556677788888888872 4 45567788888888888888999889999998666655544
Q ss_pred HHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecCc--cccchHHHHHHHHH
Q 002211 130 LSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDDD--QGRNGVTALGDKLA 207 (953)
Q Consensus 130 v~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~~--~g~~~~~~l~~~l~ 207 (953)
....+...++|+|.+....+. .++++++..++...+..+++++...|-++++++..+.. ++....+.|.+.++
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 578888899999998666542 24667788888899999999999889999999986544 66677899999998
Q ss_pred hcC-cEEEEEEecCCCCCCChHHHHHHHHHHhcCC--ceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEE
Q 002211 208 EIR-CKISYKSALPPDQSVTETDVRNELVKVRMME--ARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIA 275 (953)
Q Consensus 208 ~~g-~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~--~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~ 275 (953)
+.| ..+........ +.++....+.++.+.+ +++|+.... ..+..+++++.+.|+..++.+-+.
T Consensus 146 ~~~~~~~~~~~~~~~----~~~~~~~~~~~~l~~~~~~~~i~~~~~-~~a~~~~~~~~~~g~~i~~~i~i~ 211 (264)
T cd01537 146 EAGPIEIVLVQEGDW----DAEKGYQAAEELLTAHPDPTAIFAAND-DMALGALRALREAGLRVPDDISVI 211 (264)
T ss_pred HcCCcChhhhccCCC----CHHHHHHHHHHHHhcCCCCCEEEEcCc-HHHHHHHHHHHHhCCCCCCCeEEE
Confidence 887 44433222222 2566777788887766 566665544 456678899999998644444444
No 110
>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=98.97 E-value=6.9e-09 Score=110.18 Aligned_cols=199 Identities=20% Similarity=0.169 Sum_probs=142.5
Q ss_pred CcceEEEecCcccccccEEeeCCcceEEEeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEec
Q 002211 484 GRQLRIGVPNRVSYRDFVFKVNGTDIVHGYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGD 563 (953)
Q Consensus 484 g~~lri~v~~~~~~~p~~~~~~~~~~~~G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~ 563 (953)
..+|+||+.. .++|+.. .+...++.+.+++++|.++++... .+|++++..+.+|++|+++.+
T Consensus 31 ~~~l~vg~~~--~~~~~~~--------~~~~~~l~~~l~~~~g~~v~~~~~--------~~~~~~~~~l~~g~~Di~~~~ 92 (254)
T TIGR01098 31 PKELNFGILP--GENASNL--------TRRWEPLADYLEKKLGIKVQLFVA--------TDYSAVIEAMRFGRVDIAWFG 92 (254)
T ss_pred CCceEEEECC--CCCHHHH--------HHHHHHHHHHHHHHhCCcEEEEeC--------CCHHHHHHHHHcCCccEEEEC
Confidence 3579999975 4444322 244679999999999976555432 469999999999999999865
Q ss_pred EEEec---Cccceeeccccceec------ceEEEEecccCCcCcceeeccCchhHHHHHHHHHHHHHHHhhhhhcccCCC
Q 002211 564 IAIVT---NRTKAVDFTQPYIES------GLVVVAPVRKLNSSAWAFLRPFTPLMWAVTGVFFLVVGTVVWILEHRLNDE 634 (953)
Q Consensus 564 ~~~t~---~r~~~vdft~p~~~~------~~~~~v~~~~~~~~~~~~l~PF~~~vW~~i~~~~~~~~~~~~~l~~~~~~~ 634 (953)
..... +|....+|+.||... ...+++++..
T Consensus 93 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lvv~~d~----------------------------------------- 131 (254)
T TIGR01098 93 PSSYVLAHYRANAEVFALTAVSTDGSPGYYSVIIVKADS----------------------------------------- 131 (254)
T ss_pred cHHHHHHHHhcCCceEEeeccccCCCCceEEEEEEECCC-----------------------------------------
Confidence 54332 566667788876543 2456666543
Q ss_pred CCCCCcccchhhHHHHHHHhhccccCCcccchhHHHHHHHHHHHHHhhhhcccceeeeeeeccccCCCCChHHhhhCCCe
Q 002211 635 FRGPPRKQIVTVLWFSFSTMFFAHRENTVSTLGRVVLIIWLFVVLIITSSYTASLTSILTVQQLSSPIKGIDTLMTSNDR 714 (953)
Q Consensus 635 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~s~~~R~l~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~I~sl~dL~~~~~~ 714 (953)
+|++++||. |++
T Consensus 132 ------------------------------------------------------------------~i~~~~dL~--gk~ 143 (254)
T TIGR01098 132 ------------------------------------------------------------------PIKSLKDLK--GKT 143 (254)
T ss_pred ------------------------------------------------------------------CCCChHHhc--CCE
Confidence 688999995 889
Q ss_pred EEEEe-CchH-----HHHHHHhhCCCc----cceEeCCCHHHHHHHHHcCCcEEEEccchhHHHHHhcCc----ceEEeC
Q 002211 715 VGYQV-GSFA-----ENYLIEELSIPK----SRLVALGSPEEYAIALENRTVAAVVDERPYIDLFLSDHC----QFSVRG 780 (953)
Q Consensus 715 ig~~~-~s~~-----~~~l~~~~~~~~----~~~~~~~~~~~~~~~l~~g~~~a~~~~~~~~~~~~~~~~----~l~~~~ 780 (953)
|++.. ++.. ..++.+..+... .++....+..+.+++|.+|++|+.+.+.+.+..+..+.. +++++.
T Consensus 144 I~~~~~~s~~~~~~~~~~l~~~~~~~~~~~~~~i~~~~~~~~~~~al~~G~~Da~~~~~~~~~~~~~~~~~~~~~~~~~~ 223 (254)
T TIGR01098 144 FAFGDPASTSGYLVPRYQLKKEGGLDADGFFSEVVFSGSHDASALAVANGKVDAATNNSSAIGRLKKRGPSDMKKVRVIW 223 (254)
T ss_pred EEeeCCCCccchHhHHHHHHHhcCCChHHhhhheeecCchHHHHHHHHcCCCCeEEecHHHHHHHHHhCccchhheEEEE
Confidence 99874 3321 234444443221 345556678899999999999999999988877766532 578887
Q ss_pred CccccCccEEEecCC-Cc-chHHHHHHHHhh
Q 002211 781 QEFTKSGWGFAFPRD-SP-LAIDMSTAILTL 809 (953)
Q Consensus 781 ~~~~~~~~~~~~~k~-sp-l~~~~n~~i~~l 809 (953)
+.....+++++++|+ .+ +++.+|++|..+
T Consensus 224 ~~~~~~~~~~~~~~~~~~~l~~~i~~~l~~~ 254 (254)
T TIGR01098 224 KSPLIPNDPIAVRKDLPPELKEKIRDAFLTL 254 (254)
T ss_pred ecCCCCCCCEEEECCCCHHHHHHHHHHHhhC
Confidence 666666789999999 55 999999999764
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=98.94 E-value=1.7e-07 Score=100.20 Aligned_cols=205 Identities=12% Similarity=0.072 Sum_probs=143.8
Q ss_pred EEeEEEecC-CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEEccCC-hhhHH
Q 002211 51 NVGAIFSFG-TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIVGPQS-AVMAH 128 (953)
Q Consensus 51 ~IG~l~~~~-~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aiiGp~~-S~~a~ 128 (953)
+||++.|.. ..+......+++.|.++. | +++.+.|+..++........+++.+++.+||+... +....
T Consensus 1 ~ig~i~p~~~~~~~~~~~~~~~~~a~~~--------g--~~~~~~~~~~~~~~~~~~~~~l~~~~vdgvi~~~~~~~~~~ 70 (267)
T cd01536 1 KIGLVVPSLNNPFWQAMNKGAEAAAKEL--------G--VELIVLDAQNDVSKQIQQIEDLIAQGVDGIIISPVDSAALT 70 (267)
T ss_pred CEEEEeccccCHHHHHHHHHHHHHHHhc--------C--ceEEEECCCCCHHHHHHHHHHHHHcCCCEEEEeCCCchhHH
Confidence 589999874 566677888888888872 4 44456777778888888888899889998886433 33333
Q ss_pred HHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHc--CCcEEEEEEecC--ccccchHHHHHH
Q 002211 129 VLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYF--GWGEVIAIFNDD--DQGRNGVTALGD 204 (953)
Q Consensus 129 av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~--~w~~vaii~~d~--~~g~~~~~~l~~ 204 (953)
.....+.+.++|+|......+. .+.+..+.+++...+..+++++.+. |-+++++++.+. .++....+.|.+
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 4556677889999987654432 2345566777788888899998776 889999998654 477778899999
Q ss_pred HHHhcC-cEEEEEEecCCCCCCChHHHHHHHHHHhcCCc--eEEEEEcchhhHHHHHHHHHHcCCCCCceEEEEe
Q 002211 205 KLAEIR-CKISYKSALPPDQSVTETDVRNELVKVRMMEA--RVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIAT 276 (953)
Q Consensus 205 ~l~~~g-~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~--~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~ 276 (953)
.+++.| .++........ +..+....+.++.+..+ ++|++ +....+..+++++++.|+. .+...++.
T Consensus 146 ~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~i~~-~~d~~a~~~~~~l~~~g~~-~~i~ivg~ 214 (267)
T cd01536 146 ALKEYPDIEIVAVQDGNW----DREKALQAMEDLLQANPDIDAIFA-ANDSMALGAVAALKAAGRK-GDVKIVGV 214 (267)
T ss_pred HHHhCCCcEEEEEecCCC----cHHHHHHHHHHHHHhCCCccEEEE-ecCCchHHHHHHHHhcCCC-CCceEEec
Confidence 999984 66554322222 24566777788766554 44444 3446677799999999975 34434433
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=98.85 E-value=1.8e-07 Score=99.74 Aligned_cols=205 Identities=10% Similarity=0.005 Sum_probs=145.0
Q ss_pred EEeEEEecC-CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEEccCChhhHHH
Q 002211 51 NVGAIFSFG-TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIVGPQSAVMAHV 129 (953)
Q Consensus 51 ~IG~l~~~~-~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aiiGp~~S~~a~a 129 (953)
+||++.|.. ..+......+++.+.++. |+++ .+.|...++.+..+...+++++++.+||....+..+..
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 489999884 556666777777777662 4454 45687888888889999999999999887666655555
Q ss_pred HHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecC--ccccchHHHHHHHHH
Q 002211 130 LSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDD--DQGRNGVTALGDKLA 207 (953)
Q Consensus 130 v~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~--~~g~~~~~~l~~~l~ 207 (953)
...+...++|+|......+. +.+..+..++...+..+++++...|.+++++++.+. .++....+.+.+.++
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 67788999999998655432 345556677778888888998888999999998654 367777889999999
Q ss_pred hcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCC--ceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEE
Q 002211 208 EIRCKISYKSALPPDQSVTETDVRNELVKVRMME--ARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIA 275 (953)
Q Consensus 208 ~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~--~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~ 275 (953)
+.|..+......... .+..+....+.++.+.. +++|+.. ....+..+++++++.|+..++.+.|.
T Consensus 144 ~~~~~~~~~~~~~~~--~~~~~~~~~~~~~l~~~~~~~~i~~~-~~~~a~~~~~al~~~g~~~~~~i~i~ 210 (264)
T cd06267 144 EAGIPLDEELIVEGD--FSEESGYEAARELLASGERPTAIFAA-NDLMAIGALRALRELGLRVPEDVSVV 210 (264)
T ss_pred HcCCCCCcceEEecc--cchhhHHHHHHHHHhcCCCCcEEEEc-CcHHHHHHHHHHHHhCCCCCCceEEE
Confidence 888533222112222 12456667777777665 6666654 44566788899999998644444443
No 113
>PRK00489 hisG ATP phosphoribosyltransferase; Reviewed
Probab=98.85 E-value=1.4e-08 Score=108.82 Aligned_cols=164 Identities=17% Similarity=0.225 Sum_probs=134.2
Q ss_pred CChHHHHHHHHcCceeEEEecEEEecCccceeecccc--ceecceEEEEecccCCcCcceeeccCchhHHHHHHHHHHHH
Q 002211 543 PTYSELINQITTGVFDAAVGDIAIVTNRTKAVDFTQP--YIESGLVVVAPVRKLNSSAWAFLRPFTPLMWAVTGVFFLVV 620 (953)
Q Consensus 543 ~~~~~~i~~l~~g~~Di~~~~~~~t~~r~~~vdft~p--~~~~~~~~~v~~~~~~~~~~~~l~PF~~~vW~~i~~~~~~~ 620 (953)
.+|.+++..|.+|++|+++.+..++.+|.+.++|+.| |....+++++|...
T Consensus 51 ~~~~~i~~~L~sG~vDlgi~g~~~~~er~~~v~~~~~l~~~~~~lvvvvp~~~--------------------------- 103 (287)
T PRK00489 51 LRPDDIPGYVADGVVDLGITGEDLLEESGADVEELLDLGFGKCRLVLAVPEDS--------------------------- 103 (287)
T ss_pred ECcHHHHHHHHcCCCCEEEcchHHHHHCCCCceEeeeccCCceEEEEEEECCC---------------------------
Confidence 4589999999999999999999999999989999988 77778888888665
Q ss_pred HHHhhhhhcccCCCCCCCCcccchhhHHHHHHHhhccccCCcccchhHHHHHHHHHHHHHhhhhcccceeeeeeeccccC
Q 002211 621 GTVVWILEHRLNDEFRGPPRKQIVTVLWFSFSTMFFAHRENTVSTLGRVVLIIWLFVVLIITSSYTASLTSILTVQQLSS 700 (953)
Q Consensus 621 ~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~s~~~R~l~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~ 700 (953)
T Consensus 104 -------------------------------------------------------------------------------- 103 (287)
T PRK00489 104 -------------------------------------------------------------------------------- 103 (287)
T ss_pred --------------------------------------------------------------------------------
Confidence
Q ss_pred CCCChHHhhhCCCeEEEEeCchHHHHHHHhhCCCccceEeCCCHHHHHHHHHcCCcEEEEccchhHHHHHhcCcceEEeC
Q 002211 701 PIKGIDTLMTSNDRVGYQVGSFAENYLIEELSIPKSRLVALGSPEEYAIALENRTVAAVVDERPYIDLFLSDHCQFSVRG 780 (953)
Q Consensus 701 ~I~sl~dL~~~~~~ig~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~g~~~a~~~~~~~~~~~~~~~~~l~~~~ 780 (953)
+|++++||. |+++++..+.....+|.+ .+. ..+++.+.+..|. ++..|..|++++.......+.++ ++.++
T Consensus 104 ~i~sl~DL~--Gk~ia~~~~~~~~~~l~~-~gi-~~~iv~~~gs~ea--a~~~G~aDaivd~~~~~~~l~~~--~L~~v- 174 (287)
T PRK00489 104 DWQGVEDLA--GKRIATSYPNLTRRYLAE-KGI-DAEVVELSGAVEV--APRLGLADAIVDVVSTGTTLRAN--GLKIV- 174 (287)
T ss_pred CCCChHHhC--CCEEEEcCcHHHHHHHHH-cCC-ceEEEECCCchhh--hhcCCcccEEEeeHHHHHHHHHC--CCEEE-
Confidence 578899996 889999988888888854 343 3466677766665 56669999999888777776553 57777
Q ss_pred CccccCccEEEecC--CCc-chHHHHHHHHhhhccccHHHHHHHhcc
Q 002211 781 QEFTKSGWGFAFPR--DSP-LAIDMSTAILTLSENGELQRIHDKWLR 824 (953)
Q Consensus 781 ~~~~~~~~~~~~~k--~sp-l~~~~n~~i~~l~e~G~~~~~~~~w~~ 824 (953)
+.+.....+++.+| .+| ....+|..+.++ .|.+..+.+||+.
T Consensus 175 ~~~~~~~~~li~~k~~~~~~~~~~i~~~l~~l--~g~l~a~~~k~~~ 219 (287)
T PRK00489 175 EVILRSEAVLIARKGWLDPEKQEKIDQLLTRL--QGVLRARESKYLM 219 (287)
T ss_pred EeeeeeeEEEEEcccccChhHHHHHHHHHHHH--HHHHHhhceEEEE
Confidence 45556678999999 677 888999999999 5999999999997
No 114
>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=98.84 E-value=2.4e-07 Score=99.95 Aligned_cols=201 Identities=16% Similarity=0.139 Sum_probs=141.5
Q ss_pred EEeEEEecCCCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEEccCChhhHHHH
Q 002211 51 NVGAIFSFGTVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIVGPQSAVMAHVL 130 (953)
Q Consensus 51 ~IG~l~~~~~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aiiGp~~S~~a~av 130 (953)
+||++.+....+-.....+++ +++++.|..+ |.++++.+.|+..++........+++++++.+||+..++. ....
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 589999876555445555555 5666677665 7999999999999999999999999998999999865432 2222
Q ss_pred HHhhhhCCCcEEEeecCCCCCCC----CCCCcEEEccCChHHHHHHHHHHHHHc--CCcEEEEEEecC-ccccchHHHHH
Q 002211 131 SHLANELQVPLLSFTALDPTLSP----LQYPFFVQTAPNDLYLMSAIAEMVSYF--GWGEVIAIFNDD-DQGRNGVTALG 203 (953)
Q Consensus 131 ~~v~~~~~vP~Is~~at~~~ls~----~~~p~~fr~~p~d~~~~~ai~~~l~~~--~w~~vaii~~d~-~~g~~~~~~l~ 203 (953)
.+...++|+|.++..++.... ...+....+..++...+..+++++... |.+++++++.+. .++....+.++
T Consensus 76 --~~~~~~iPvV~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~g~~~i~~l~~~~~~~~~~r~~g~~ 153 (281)
T cd06325 76 --ANATKDIPIVFTAVTDPVGAGLVKSLEKPGGNVTGVSDLVPVETQLELLKKLLPDAKTVGVLYNPSEANSVVQVKELK 153 (281)
T ss_pred --HHcCCCCCEEEEecCCccccccccccccCCCceeCeecccchHHHHHHHHHHCCCCcEEEEEeCCCCccHHHHHHHHH
Confidence 256779999988755432111 111122223445666678888888776 999999998653 36777789999
Q ss_pred HHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHHHcCC
Q 002211 204 DKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQRLGM 266 (953)
Q Consensus 204 ~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~~~g~ 266 (953)
+.+++.|+++.... . .. ..++...++++.+ ++|+|++... ..+..+++++++.|+
T Consensus 154 ~~~~~~g~~~~~~~-~-~~----~~~~~~~~~~~~~-~~dai~~~~d-~~a~~~~~~~~~~~~ 208 (281)
T cd06325 154 KAAAKLGIEVVEAT-V-SS----SNDVQQAAQSLAG-KVDAIYVPTD-NTVASAMEAVVKVAN 208 (281)
T ss_pred HHHHhCCCEEEEEe-c-CC----HHHHHHHHHHhcc-cCCEEEEcCc-hhHHhHHHHHHHHHH
Confidence 99999998876532 1 22 5667777888764 4687776554 466678888888775
No 115
>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=98.83 E-value=6.8e-07 Score=95.95 Aligned_cols=202 Identities=13% Similarity=0.066 Sum_probs=141.6
Q ss_pred EEeEEEecC-CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEEccCChhh-HH
Q 002211 51 NVGAIFSFG-TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIVGPQSAVM-AH 128 (953)
Q Consensus 51 ~IG~l~~~~-~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aiiGp~~S~~-a~ 128 (953)
|||+++|.. ..+-.....+++.+.++. +. .|+++++.+.|+..++....+...+++++++.+||....+.. ..
T Consensus 1 ~Ig~i~~~~~~~~~~~~~~~i~~~~~~~----~~-~g~~~~l~i~~~~~~~~~~~~~~~~~~~~~vdgiIi~~~~~~~~~ 75 (272)
T cd06300 1 KIGLSNSYAGNTWRAQMLDEFKAQAKEL----KK-AGLISEFIVTSADGDVAQQIADIRNLIAQGVDAIIINPASPTALN 75 (272)
T ss_pred CeEEeccccCChHHHHHHHHHHHHHHhh----hc-cCCeeEEEEecCCCCHHHHHHHHHHHHHcCCCEEEEeCCChhhhH
Confidence 689999764 333344566666666552 11 267889999999999999889999999999999998544332 33
Q ss_pred HHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHc--CCcEEEEEEec--CccccchHHHHHH
Q 002211 129 VLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYF--GWGEVIAIFND--DDQGRNGVTALGD 204 (953)
Q Consensus 129 av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~--~w~~vaii~~d--~~~g~~~~~~l~~ 204 (953)
.....+.+.++|+|......+ . +.+.++.+++...+..+++++... |-++++++..+ ...+....+.+++
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 345667788999998754321 1 456778888888899999998776 88899999743 3445667788999
Q ss_pred HHHhcC-cEEEEEEecCCCCCCChHHHHHHHHHHhcCCc--eEEEEEcchhhHHHHHHHHHHcCCCCC
Q 002211 205 KLAEIR-CKISYKSALPPDQSVTETDVRNELVKVRMMEA--RVIVVHGYSRTGLMVFDVAQRLGMMDS 269 (953)
Q Consensus 205 ~l~~~g-~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~--~vii~~~~~~~~~~~~~~a~~~g~~~~ 269 (953)
.+++.| +++......+ .+.++....+.++.++++ ++|+..... +..+++.+++.|+..+
T Consensus 150 a~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~l~~~~~~~~i~~~~d~--A~g~~~al~~~g~~~p 211 (272)
T cd06300 150 VLKEYPGIKIVGEVYGD----WDQAVAQKAVADFLASNPDVDGIWTQGGD--AVGAVQAFEQAGRDIP 211 (272)
T ss_pred HHHHCCCcEEEeecCCC----CCHHHHHHHHHHHHHhCCCcCEEEecCCC--cHHHHHHHHHcCCCCc
Confidence 999887 7765322222 224566677778766555 544444333 8889999999998443
No 116
>PF10613 Lig_chan-Glu_bd: Ligated ion channel L-glutamate- and glycine-binding site; InterPro: IPR019594 This entry, sometimes called the S1 domain, is the luminal domain just upstream of the first, M1, transmembrane region of transmembrane ion-channel proteins, and binds L-glutamate and glycine [, ]. It is found in association with IPR001320 from INTERPRO. ; GO: 0004970 ionotropic glutamate receptor activity, 0005234 extracellular-glutamate-gated ion channel activity, 0016020 membrane; PDB: 4E0W_A 3S9E_A 3QXM_B 2F34_A 3C34_B 3S2V_A 3GBB_B 2F36_D 4E0X_A 1TXF_A ....
Probab=98.69 E-value=5.5e-09 Score=81.75 Aligned_cols=49 Identities=24% Similarity=0.548 Sum_probs=39.4
Q ss_pred CcceEEEeeHHHHHHHHHhCCCcccEEEeeCC---CCCCCCChHHHHHHHHc
Q 002211 506 GTDIVHGYCIDVFLAAVRLLPYAVPYKFIPYG---DGHKNPTYSELINQITT 554 (953)
Q Consensus 506 ~~~~~~G~~~dll~~la~~l~~~~~~~~~~~~---~~~~n~~~~~~i~~l~~ 554 (953)
++.++.|||+||+++|++.|||++++..++.+ .-+.|++|+||+++|.+
T Consensus 14 g~~~~eGyciDll~~la~~l~F~y~i~~~~Dg~yG~~~~~g~W~GmiGeli~ 65 (65)
T PF10613_consen 14 GNDRYEGYCIDLLEELAEELNFTYEIYLVPDGKYGSKNPNGSWNGMIGELIR 65 (65)
T ss_dssp GGGGEESHHHHHHHHHHHHHT-EEEEEE-TTS--EEBETTSEBEHHHHHHHT
T ss_pred CCccEEEEHHHHHHHHHHHcCCeEEEEECCCCCCcCcCCCCcCcCHHHHhcC
Confidence 47799999999999999999999777777643 23368999999999974
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=98.65 E-value=5.2e-06 Score=89.23 Aligned_cols=199 Identities=9% Similarity=0.024 Sum_probs=132.9
Q ss_pred EEeEEEec-CCCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEE-EccCChhhHH
Q 002211 51 NVGAIFSF-GTVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAI-VGPQSAVMAH 128 (953)
Q Consensus 51 ~IG~l~~~-~~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~ai-iGp~~S~~a~ 128 (953)
+||++.|- +..+-.....+++-|.++. |+++.+...|+..++....+....+++++|.+| +.|..+....
T Consensus 1 ~igvi~~~~~~~~~~~~~~gi~~~~~~~--------g~~~~~~~~~~~~~~~~~~~~i~~l~~~~vdgiIi~~~~~~~~~ 72 (275)
T cd06320 1 KYGVVLKTLSNEFWRSLKEGYENEAKKL--------GVSVDIQAAPSEGDQQGQLSIAENMINKGYKGLLFSPISDVNLV 72 (275)
T ss_pred CeeEEEecCCCHHHHHHHHHHHHHHHHh--------CCeEEEEccCCCCCHHHHHHHHHHHHHhCCCEEEECCCChHHhH
Confidence 58999984 4444455567777777762 678887777877788777788888888888874 5666555444
Q ss_pred HHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHc--CCcEEEEEEecC--ccccchHHHHHH
Q 002211 129 VLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYF--GWGEVIAIFNDD--DQGRNGVTALGD 204 (953)
Q Consensus 129 av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~--~w~~vaii~~d~--~~g~~~~~~l~~ 204 (953)
+....+.+.++|+|......+ ....+ .+..++...+..+++++... |.++++++.... .......+.+.+
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 556677889999998754321 11112 24666777788889987766 889999997532 233455688999
Q ss_pred HHHhc-CcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEc-chhhHHHHHHHHHHcCCC
Q 002211 205 KLAEI-RCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHG-YSRTGLMVFDVAQRLGMM 267 (953)
Q Consensus 205 ~l~~~-g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~-~~~~~~~~~~~a~~~g~~ 267 (953)
.+++. |+++....... .+..+....+.++.+..+++-.+.+ +...+..+++.+++.|+.
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 88875432111 2244555667776655444433333 445566788888998874
No 118
>PRK10653 D-ribose transporter subunit RbsB; Provisional
Probab=98.56 E-value=2.3e-05 Score=85.21 Aligned_cols=223 Identities=13% Similarity=0.096 Sum_probs=136.4
Q ss_pred HHHHHHHHHHHhhhhhcccccCCCCceEEEeEEEec-CCCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChH
Q 002211 23 TMNLWWLVSIFSFCIGTAIQGALKPEVLNVGAIFSF-GTVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGF 101 (953)
Q Consensus 23 ~m~~~~~l~~~~~~~~~~~~~~~~~~~i~IG~l~~~-~~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~ 101 (953)
.|++...|+.+.++.|. ........-+||++.|. +..+-.....+++.+.++. |+++. +.|+..++.
T Consensus 2 ~~~~~~~~~~~~~~~~~--~~~~~~~~~~I~vi~~~~~~~f~~~~~~~i~~~~~~~--------G~~~~--~~~~~~d~~ 69 (295)
T PRK10653 2 NMKKLATLVSAVALSAT--VSANAMAKDTIALVVSTLNNPFFVSLKDGAQKEADKL--------GYNLV--VLDSQNNPA 69 (295)
T ss_pred chHHHHHHHHHHHHHHh--cCCccccCCeEEEEecCCCChHHHHHHHHHHHHHHHc--------CCeEE--EecCCCCHH
Confidence 36666555444433321 12223345589999985 4455556777888877772 44554 467777888
Q ss_pred HHHHHHHHHHhcCcE-EEEccCChhhHHHHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHc
Q 002211 102 LSIMGALQFMETDTL-AIVGPQSAVMAHVLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYF 180 (953)
Q Consensus 102 ~a~~~a~~li~~~v~-aiiGp~~S~~a~av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~ 180 (953)
.......+++++++. +|++|..+.........+.+.++|+|.+....+ ..+.+..+.+++..-+..+++++...
T Consensus 70 ~~~~~~~~l~~~~~dgiii~~~~~~~~~~~l~~~~~~~ipvV~~~~~~~-----~~~~~~~V~~D~~~~g~~~~~~l~~~ 144 (295)
T PRK10653 70 KELANVQDLTVRGTKILLINPTDSDAVGNAVKMANQANIPVITLDRGAT-----KGEVVSHIASDNVAGGKMAGDFIAKK 144 (295)
T ss_pred HHHHHHHHHHHcCCCEEEEcCCChHHHHHHHHHHHHCCCCEEEEccCCC-----CCceeeEEccChHHHHHHHHHHHHHH
Confidence 787777888888876 455666555544556777788999998753321 11234455566666578888886654
Q ss_pred -CCc-EEEEEEec--CccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEE-EcchhhHH
Q 002211 181 -GWG-EVIAIFND--DDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVV-HGYSRTGL 255 (953)
Q Consensus 181 -~w~-~vaii~~d--~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~-~~~~~~~~ 255 (953)
|.+ +++++..+ ........+.|.+++++.|..+... .... .+..+....+.++.+..++.-.+ +.....+.
T Consensus 145 ~~~~~~i~~~~~~~~~~~~~~R~~gf~~al~~~g~~~~~~--~~~~--~~~~~~~~~~~~~l~~~~~~~ai~~~~d~~A~ 220 (295)
T PRK10653 145 LGEGAKVIQLEGIAGTSAARERGEGFKQAVAAHKFNVLAS--QPAD--FDRTKGLNVMQNLLTAHPDVQAVFAQNDEMAL 220 (295)
T ss_pred hCCCceEEEEEccCCCccHHHHHHHHHHHHhhCCCEEEEe--cCCC--CCHHHHHHHHHHHHHhCCCcCEEEECCChhHH
Confidence 543 56666533 2234566789999999999876432 1111 12334445566665554443233 33445566
Q ss_pred HHHHHHHHcCC
Q 002211 256 MVFDVAQRLGM 266 (953)
Q Consensus 256 ~~~~~a~~~g~ 266 (953)
.+++++++.|+
T Consensus 221 g~l~al~~~G~ 231 (295)
T PRK10653 221 GALRALQTAGK 231 (295)
T ss_pred HHHHHHHHcCC
Confidence 78999999997
No 119
>COG2984 ABC-type uncharacterized transport system, periplasmic component [General function prediction only]
Probab=98.56 E-value=2.6e-05 Score=80.85 Aligned_cols=204 Identities=15% Similarity=0.121 Sum_probs=145.5
Q ss_pred CCCceEEEeEEEecCCCchhHHHHHHHHHHHHHhcCCCCCCCc-EEEEEEecCCCChHHHHHHHHHHHhcCcEEEEccCC
Q 002211 45 LKPEVLNVGAIFSFGTVNGQVSRIAMKAAQDDINSDPRVLGGR-KLSITMHDAKFNGFLSIMGALQFMETDTLAIVGPQS 123 (953)
Q Consensus 45 ~~~~~i~IG~l~~~~~~~g~~~~~a~~lAve~iN~~g~il~g~-~l~l~~~D~~~~~~~a~~~a~~li~~~v~aiiGp~~ 123 (953)
..++.++||+....+.+.-.....|++-|+.+. |+ .+++.+...++|+..+...+++|..++.+.|++-.+
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 456778899999887665566778888777774 33 688888999999999999999999997777776443
Q ss_pred hhhHHHHHHhhhhCCCcEEEeecCCCCCCC--C--CCCcEEEccCChHHHHHHHHHHHHHc--CCcEEEEEEec-Ccccc
Q 002211 124 AVMAHVLSHLANELQVPLLSFTALDPTLSP--L--QYPFFVQTAPNDLYLMSAIAEMVSYF--GWGEVIAIFND-DDQGR 196 (953)
Q Consensus 124 S~~a~av~~v~~~~~vP~Is~~at~~~ls~--~--~~p~~fr~~p~d~~~~~ai~~~l~~~--~w~~vaii~~d-~~~g~ 196 (953)
..+.++..-.. ++|+|-.+.+||.-.. . .-|----|..||..-...-++++++. +.++++++|.. .+...
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 -PAAQALVSATK--TIPVVFAAVTDPVGAKLVKSLEQPGGNVTGVSDLLPVAQQIELIKALLPNAKSIGVLYNPGEANSV 174 (322)
T ss_pred -HHHHHHHHhcC--CCCEEEEccCchhhccCCccccCCCCceeecCCcchHHHHHHHHHHhCCCCeeEEEEeCCCCcccH
Confidence 44444333222 3999988887764332 1 12333445667776666667777764 78999999965 44788
Q ss_pred chHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcch---hhHHHHHHHHHHcCC
Q 002211 197 NGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYS---RTGLMVFDVAQRLGM 266 (953)
Q Consensus 197 ~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~---~~~~~~~~~a~~~g~ 266 (953)
...+.+++.+++.|++|+.. ..+. ..|....++.+. .++|+|+..++. .....+++.+.+.+.
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-AVTS-----VNDIPRAVQALL-GKVDVIYIPTDNLIVSAIESLLQVANKAKI 240 (322)
T ss_pred HHHHHHHHHHHHCCCEEEEE-ecCc-----ccccHHHHHHhc-CCCcEEEEecchHHHHHHHHHHHHHHHhCC
Confidence 89999999999999998743 3322 346666666665 789999998876 445566777777553
No 120
>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=98.56 E-value=6.8e-06 Score=87.74 Aligned_cols=201 Identities=10% Similarity=0.088 Sum_probs=131.4
Q ss_pred EEeEEEecC-CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEEccCChhhHHH
Q 002211 51 NVGAIFSFG-TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIVGPQSAVMAHV 129 (953)
Q Consensus 51 ~IG~l~~~~-~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aiiGp~~S~~a~a 129 (953)
.||++.|-. ..+-.....+++-+.++ .|+.+.+ .++..++....+...+++.+++.+||....+.....
T Consensus 1 ~igvv~~~~~~~~~~~~~~~i~~~~~~--------~g~~~~~--~~~~~~~~~~~~~~~~l~~~~vdgiii~~~~~~~~~ 70 (266)
T cd06282 1 TVGVVLPSLANPVFAECVQGIQEEARA--------AGYSLLL--ATTDYDAEREADAVETLLRQRVDGLILTVADAATSP 70 (266)
T ss_pred CeEEEeCCCCcchHHHHHHHHHHHHHH--------CCCEEEE--eeCCCCHHHHHHHHHHHHhcCCCEEEEecCCCCchH
Confidence 378888753 44444556666666655 1455554 566677777778888888889998886333322334
Q ss_pred HHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEec---CccccchHHHHHHHH
Q 002211 130 LSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFND---DDQGRNGVTALGDKL 206 (953)
Q Consensus 130 v~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d---~~~g~~~~~~l~~~l 206 (953)
....+.+.++|+|......+ ...+++ ..++...+..+++++...|.++++++..+ .+++....+.|.+.+
T Consensus 71 ~~~~~~~~~ipvV~~~~~~~----~~~~~v---~~d~~~~g~~~~~~l~~~g~~~i~~i~~~~~~~~~~~~r~~gf~~~l 143 (266)
T cd06282 71 ALDLLDAERVPYVLAYNDPQ----PGRPSV---SVDNRAAARDVAQALAALGHRRIAMLAGRLAASDRARQRYAGYRAAM 143 (266)
T ss_pred HHHHHhhCCCCEEEEeccCC----CCCCEE---eeCcHHHHHHHHHHHHHcCcccEEEeccccccCchHHHHHHHHHHHH
Confidence 55677888999988754322 223443 35667788889999888899999999742 345667789999999
Q ss_pred HhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcC--CceEEEEEcchhhHHHHHHHHHHcCCCCCceEE
Q 002211 207 AEIRCKISYKSALPPDQSVTETDVRNELVKVRMM--EARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVW 273 (953)
Q Consensus 207 ~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~--~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~w 273 (953)
++.|+.+......+.. ..+....+.++... .+++|+. ++...+..+++++++.|+..++.+-
T Consensus 144 ~~~~~~~~~~~~~~~~----~~~~~~~~~~~l~~~~~~~ai~~-~~d~~a~g~~~al~~~g~~~p~di~ 207 (266)
T cd06282 144 RAAGLAPLPPVEIPFN----TAALPSALLALLTAHPAPTAIFC-SNDLLALAVIRALRRLGLRVPDDLS 207 (266)
T ss_pred HHcCCCCCccccCCCc----HHHHHHHHHHHhcCCCCCCEEEE-CCcHHHHHHHHHHHHcCCCCCCceE
Confidence 9998764332222222 33334445544333 4676666 4566677899999999986544443
No 121
>COG3107 LppC Putative lipoprotein [General function prediction only]
Probab=98.47 E-value=1.1e-05 Score=87.81 Aligned_cols=301 Identities=11% Similarity=0.096 Sum_probs=182.5
Q ss_pred CCceEEEeEEEecC---CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEEccC
Q 002211 46 KPEVLNVGAIFSFG---TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIVGPQ 122 (953)
Q Consensus 46 ~~~~i~IG~l~~~~---~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aiiGp~ 122 (953)
...+=+|+.++|++ +..|...+.|+..|-. -|+.. ++-..++.++||...+..++- .+...+|+..|+||.
T Consensus 254 ~~~~skiALLLPLtG~~a~~a~~IqdGF~aA~~-~~~~~---~~~~~~~~i~dT~~~~l~~i~--aqaqq~G~~~VVGPL 327 (604)
T COG3107 254 QASPSKIALLLPLTGQAAVFARTIQDGFLAAKN-APATQ---TAQVAELKIYDTSAQPLDAIL--AQAQQDGADFVVGPL 327 (604)
T ss_pred cCCchheeEEeccCChhHHHHHHHHHHHHHhcc-CcccC---CccccceeeccCCcccHHHHH--HHHHhcCCcEEeccc
Confidence 34567899999998 4567888899888765 12221 333478889999987766543 233445999999999
Q ss_pred ChhhHHHHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecCccccchHHHH
Q 002211 123 SAVMAHVLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDDDQGRNGVTAL 202 (953)
Q Consensus 123 ~S~~a~av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~~~g~~~~~~l 202 (953)
.-....++..-.. ..+|++....++..- ..+......-+....++..++.+-.-|.+...++.+.+++|+...++|
T Consensus 328 lK~nVe~L~~~~q-~~i~vLALN~~~n~r---~~~~~cyfaLSPEDEa~~AA~~l~~qG~R~plvlvPr~~lG~Rv~~AF 403 (604)
T COG3107 328 LKPNVEALLASNQ-QPIPVLALNQPENSR---NPAQLCYFALSPEDEARDAANHLWDQGKRNPLVLVPRNDLGDRVANAF 403 (604)
T ss_pred cchhHHHHHhCcC-CCCceeeecCCcccc---CcccceeeecChhHHHHHHHHHHHHccccCceEEecchHHHHHHHHHH
Confidence 9887776654433 678888764443221 234444444455556889999999999999999999999999999999
Q ss_pred HHHHHhcCcEEEEEEecCCCC--------------CCChHHHHHHH----HHHhcCC-ceEEEEEcchhhHHHHHHHHHH
Q 002211 203 GDKLAEIRCKISYKSALPPDQ--------------SVTETDVRNEL----VKVRMME-ARVIVVHGYSRTGLMVFDVAQR 263 (953)
Q Consensus 203 ~~~l~~~g~~v~~~~~~~~~~--------------~~~~~d~~~~l----~~i~~~~-~~vii~~~~~~~~~~~~~~a~~ 263 (953)
.+++++.|+..+....|.... .....|..... .-+.+.. .|.|++...++++..+--...-
T Consensus 404 ~~~Wq~~gg~~v~~~~fg~~~~l~~~i~~~a~ir~~~~p~~~~~~~g~~~~p~~~~d~iDaVyivAtp~el~~IKP~ia~ 483 (604)
T COG3107 404 NQEWQKLGGGTVLQQKFGSTSELRQGINDGAGIRLTGLPADLTTTNGLQTPPLDDQDTIDAVYIVATPSELALIKPMIAM 483 (604)
T ss_pred HHHHHHhcCCchhHhhcCcHHHHHhhcccccceeecCCccchhcccCCCCCCcccccccceEEEEecchhHhHHhhHHHh
Confidence 999999988444333332110 00011111000 1122233 7889999888887766555443
Q ss_pred cCCCCCceEEEEeCcccccccCCCCCchhhhhhccceEEEEE---ecCCChhhHHHHHHHHhhcCCCCCCCchhhHHhhH
Q 002211 264 LGMMDSGYVWIATTWLSTFIDSKSPLSLKTAKSILGALTLRQ---HTPDSKRRRDFVSRWNTLSNGSIGLNPYGLYAYDT 340 (953)
Q Consensus 264 ~g~~~~~~~wi~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~---~~~~~~~~~~F~~~~~~~~~~~~~~~~~~~~~YDA 340 (953)
++.... -....++-... ... .++....++|+..... ..+..|.++....+|... |-.
T Consensus 484 ~~~~~~-~p~yaSSr~~~--gT~---~P~~~~~m~GiqysdiP~l~~~~~p~~qq~a~~~p~~--------------~sl 543 (604)
T COG3107 484 ANGSDS-PPLYASSRSSQ--GTN---GPDFRLEMEGIQYSDIPWLAQPNPPLMQQAAAAWPND--------------YSL 543 (604)
T ss_pred hcCCCC-cceeeeccccc--cCC---CccHHHhccCccccCCchhcCCCchHHHHHHHhcCCc--------------hHH
Confidence 332211 12223322111 111 1345566788654322 134456666666666532 345
Q ss_pred HHHHHHHHHHHHhcCCcccccCCCccCCCCCCcccCCCccccCchHHHHHH------HHhcccCCcceeEEEccCCC
Q 002211 341 VWMIARALKLFLDQGNTISFSNDTKLNGLGGGTLNLGALSIFDGGKKFLAN------ILQTNMTGLSGPIHFNQDRS 411 (953)
Q Consensus 341 v~~la~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~------l~~~~f~G~tG~v~Fd~~g~ 411 (953)
+.++|.+++. +.|..+ ..+-+++|+||.++.|+++.
T Consensus 544 ~RLyAmGvDA-----------------------------------wrLan~f~elrqV~G~~i~G~TG~Lsad~~c~ 585 (604)
T COG3107 544 ARLYAMGVDA-----------------------------------WRLANHFSELRQVPGYQIDGLTGTLSADPDCV 585 (604)
T ss_pred HHHHHhcchH-----------------------------------HHHHHHhHHhhcCCCcccccccceeecCCCce
Confidence 5666665553 222222 23335789999999998875
No 122
>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=98.47 E-value=2.6e-05 Score=83.34 Aligned_cols=205 Identities=13% Similarity=0.104 Sum_probs=132.3
Q ss_pred EEeEEEec-CCCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEE-EEccCChhhHH
Q 002211 51 NVGAIFSF-GTVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLA-IVGPQSAVMAH 128 (953)
Q Consensus 51 ~IG~l~~~-~~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~a-iiGp~~S~~a~ 128 (953)
.||+++|. +..+......+++.+.++. |+.+ .+.++..++....+...+++.+++.+ |++|..+....
T Consensus 1 ~I~vv~~~~~~~~~~~~~~~i~~~~~~~--------g~~v--~~~~~~~~~~~~~~~~~~~~~~~~dgii~~~~~~~~~~ 70 (268)
T cd06323 1 TIGLSVSTLNNPFFVTLKDGAQKEAKEL--------GYEL--TVLDAQNDAAKQLNDIEDLITRGVDAIIINPTDSDAVV 70 (268)
T ss_pred CeeEecccccCHHHHHHHHHHHHHHHHc--------CceE--EecCCCCCHHHHHHHHHHHHHcCCCEEEEcCCChHHHH
Confidence 37888874 4556667778888887772 4555 45677778887778888888888888 55666555444
Q ss_pred HHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHc--CCcEEEEEEec--CccccchHHHHHH
Q 002211 129 VLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYF--GWGEVIAIFND--DDQGRNGVTALGD 204 (953)
Q Consensus 129 av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~--~w~~vaii~~d--~~~g~~~~~~l~~ 204 (953)
.....+...++|+|......+ ..+.+-.+..++...+..+++++... |-+++++++.+ ..++....+.+.+
T Consensus 71 ~~l~~l~~~~ipvv~~~~~~~-----~~~~~~~v~~d~~~~~~~~~~~l~~~~~g~~~i~~l~~~~~~~~~~~r~~g~~~ 145 (268)
T cd06323 71 PAVKAANEAGIPVFTIDREAN-----GGEVVSQIASDNVAGGKMAAEYLVKLLGGKGKVVELQGIPGASAARERGKGFHE 145 (268)
T ss_pred HHHHHHHHCCCcEEEEccCCC-----CCceEEEEccCcHHHHHHHHHHHHHHhCCCceEEEEeCCCCCccHHHHHHHHHH
Confidence 555566778999998854332 11223345556666678888988776 78999999853 3456677889999
Q ss_pred HHHhc-CcEEEEEEecCCCCCCChHHHHHHHHHHhcCC--ceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEEeC
Q 002211 205 KLAEI-RCKISYKSALPPDQSVTETDVRNELVKVRMME--ARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIATT 277 (953)
Q Consensus 205 ~l~~~-g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~--~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~ 277 (953)
++++. |.++........ +..+....+.++.+.. +++| ++.+...+..+++++++.|+ ++...++.+
T Consensus 146 ~l~~~~~~~~~~~~~~~~----~~~~~~~~~~~~l~~~~~~~ai-~~~~d~~a~~~~~~l~~~g~--~di~iig~d 214 (268)
T cd06323 146 VVDKYPGLKVVASQPADF----DRAKGLNVMENILQAHPDIKGV-FAQNDEMALGAIEALKAAGK--DDVKVVGFD 214 (268)
T ss_pred HHHhCCCcEEEecccCCC----CHHHHHHHHHHHHHHCCCcCEE-EEcCCchHHHHHHHHHHcCC--CCcEEEEeC
Confidence 99984 777653221111 1333344555554443 4553 33444555568899999987 344444443
No 123
>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=98.40 E-value=3.8e-05 Score=82.45 Aligned_cols=208 Identities=14% Similarity=0.139 Sum_probs=130.4
Q ss_pred EEeEEEec--CCCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEE-ccCChhhH
Q 002211 51 NVGAIFSF--GTVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIV-GPQSAVMA 127 (953)
Q Consensus 51 ~IG~l~~~--~~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aii-Gp~~S~~a 127 (953)
.||++.|. +..+......+++.+.++. |+.+ .+.++..++....+....++.+++.+|| .|..+...
T Consensus 1 ~i~vi~p~~~~~~~~~~~~~g~~~~~~~~--------g~~~--~~~~~~~~~~~~~~~~~~l~~~~vdgiii~~~~~~~~ 70 (275)
T cd06317 1 TIGYTQNNVGSHSYQTTYNKAFQAAAEED--------GVEV--IVLDANGDVARQAAQVEDLIAQKVDGIILWPTDGQAY 70 (275)
T ss_pred CeEEEecccCCCHHHHHHHHHHHHHHHhc--------CCEE--EEEcCCcCHHHHHHHHHHHHHcCCCEEEEecCCcccc
Confidence 37888886 4566777788888888872 4444 4567888888888888888888888875 45444444
Q ss_pred HHHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEc-cCChHHHHHHHHHHHHHc--CCcEEEEEEecCcc--ccchHHHH
Q 002211 128 HVLSHLANELQVPLLSFTALDPTLSPLQYPFFVQT-APNDLYLMSAIAEMVSYF--GWGEVIAIFNDDDQ--GRNGVTAL 202 (953)
Q Consensus 128 ~av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~-~p~d~~~~~ai~~~l~~~--~w~~vaii~~d~~~--g~~~~~~l 202 (953)
......+.+.++|+|......+ ....++++.. .+++...+..+++.+.+. |-+++++++.+.++ +....+.|
T Consensus 71 ~~~l~~~~~~~iPvV~~~~~~~---~~~~~~v~~~v~~d~~~~g~~~~~~l~~~~~g~~~i~~l~~~~~~~~~~~r~~g~ 147 (275)
T cd06317 71 IPGLRKAKQAGIPVVITNSNIS---EKGFEFIKSFTGPDDISQGERSAEAMCKALGGKGQIVVIAGQPGNGTAIERQKGF 147 (275)
T ss_pred HHHHHHHHHCCCcEEEeCCCCC---CCccchhhhhccccHHHHHHHHHHHHHHHcCCCceEEEEecCCCCchHHHHHHHH
Confidence 4555667889999998754321 2233544333 344556677777776554 77899999754333 44456889
Q ss_pred HHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhc---CCceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEE
Q 002211 203 GDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRM---MEARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIA 275 (953)
Q Consensus 203 ~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~---~~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~ 275 (953)
++.+++.|..+......... .+..+....+.++-+ .++++|++. +...+..+++++++.|+. .+...++
T Consensus 148 ~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~l~~~~~~~~ai~~~-~d~~a~g~~~~l~~~g~~-~dv~v~g 219 (275)
T cd06317 148 EDELAEVCPGVEVLDTQPAD--WDREKAQVAMEALITKFGDDIDGVYAG-DDNMARGALNAAKEAGLA-GGIVIVG 219 (275)
T ss_pred HHHHHhhCCCCEEEeccCCC--CCHHHHHHHHHHHHHhCCCCccEEEEC-CCcHHHHHHHHHHhcCCc-CCcEEEE
Confidence 99999886433222212111 112333334444432 246777754 445578899999999985 3333343
No 124
>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=98.39 E-value=2.6e-05 Score=83.35 Aligned_cols=200 Identities=17% Similarity=0.164 Sum_probs=131.8
Q ss_pred EEeEEEec-CCCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEE--ccCChhhH
Q 002211 51 NVGAIFSF-GTVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIV--GPQSAVMA 127 (953)
Q Consensus 51 ~IG~l~~~-~~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aii--Gp~~S~~a 127 (953)
+||++.|. +..+-.....+++-++++. |+.+. +.|+..++.........+++++|.+|| ++..+.
T Consensus 1 ~i~vv~p~~~~~~~~~~~~~i~~~~~~~--------g~~~~--~~~~~~~~~~~~~~~~~l~~~~vdgiii~~~~~~~-- 68 (268)
T cd06273 1 TIGAIVPTLDNAIFARVIQAFQETLAAH--------GYTLL--VASSGYDLDREYAQARKLLERGVDGLALIGLDHSP-- 68 (268)
T ss_pred CeEEEeCCCCCchHHHHHHHHHHHHHHC--------CCEEE--EecCCCCHHHHHHHHHHHHhcCCCEEEEeCCCCCH--
Confidence 48999985 3445556667777766662 45554 478888888888888889988776655 433222
Q ss_pred HHHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEec---CccccchHHHHHH
Q 002211 128 HVLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFND---DDQGRNGVTALGD 204 (953)
Q Consensus 128 ~av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d---~~~g~~~~~~l~~ 204 (953)
.....+.+.++|+|......+ ....+| ...++...+..+++++...|.+++++|... ..++......|.+
T Consensus 69 -~~~~~l~~~~iPvv~~~~~~~---~~~~~~---v~~d~~~~~~~~~~~l~~~g~~~i~~i~~~~~~~~~~~~r~~gf~~ 141 (268)
T cd06273 69 -ALLDLLARRGVPYVATWNYSP---DSPYPC---VGFDNREAGRLAARHLIALGHRRIAMIFGPTQGNDRARARRAGVRA 141 (268)
T ss_pred -HHHHHHHhCCCCEEEEcCCCC---CCCCCE---EEeChHHHHHHHHHHHHHCCCCeEEEEeccccCCccHHHHHHHHHH
Confidence 334566778999998754322 122343 345677788889999888899999999743 2346677889999
Q ss_pred HHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhc--CCceEEEEEcchhhHHHHHHHHHHcCCCCCceE
Q 002211 205 KLAEIRCKISYKSALPPDQSVTETDVRNELVKVRM--MEARVIVVHGYSRTGLMVFDVAQRLGMMDSGYV 272 (953)
Q Consensus 205 ~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~--~~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~ 272 (953)
.+++.|+.+.....+... .+.++....+.++.+ ..+++|+. ++...+..+++++++.|+..++.+
T Consensus 142 ~l~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~l~~~~~~~ai~~-~~~~~a~~~~~~l~~~g~~~p~~i 208 (268)
T cd06273 142 ALAEAGLELPELWQVEAP--YSIADGRAALRQLLEQPPRPTAVIC-GNDVLALGALYEARRLGLSVPEDL 208 (268)
T ss_pred HHHHcCCCCCHHHeeeCC--CcHHHHHHHHHHHHcCCCCCCEEEE-cChHHHHHHHHHHHHcCCCCCCce
Confidence 999988654322222211 123344455666654 34777775 556667789999999998655444
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=98.34 E-value=7.3e-05 Score=80.35 Aligned_cols=208 Identities=11% Similarity=0.067 Sum_probs=130.1
Q ss_pred EEeEEEecC-CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEE-EccCChhhHH
Q 002211 51 NVGAIFSFG-TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAI-VGPQSAVMAH 128 (953)
Q Consensus 51 ~IG~l~~~~-~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~ai-iGp~~S~~a~ 128 (953)
+||++.|.. ..+-.....+++.+.++. |+++ .+.|+..++........+++.+++.+| ++|..+....
T Consensus 1 ~i~vi~~~~~~~~~~~~~~~i~~~~~~~--------g~~~--~~~~~~~~~~~~~~~i~~~~~~~~dgiii~~~~~~~~~ 70 (277)
T cd06319 1 QIAYIVSDLRIPFWQIMGRGVKSKAKAL--------GYDA--VELSAENSAKKELENLRTAIDKGVSGIIISPTNSSAAV 70 (277)
T ss_pred CeEEEeCCCCchHHHHHHHHHHHHHHhc--------CCeE--EEecCCCCHHHHHHHHHHHHhcCCCEEEEcCCchhhhH
Confidence 478888853 444445556666655552 4455 456888888888888888888888877 4776665455
Q ss_pred HHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHc------CCcEEEEEEec--CccccchHH
Q 002211 129 VLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYF------GWGEVIAIFND--DDQGRNGVT 200 (953)
Q Consensus 129 av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~------~w~~vaii~~d--~~~g~~~~~ 200 (953)
.....+.+.++|+|.+....+ + ..++..+.+++..-+..+++++.+. |-+++++++.. ...+....+
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 666778889999998643221 1 1233445556666566777765543 66899999743 345667788
Q ss_pred HHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEE-EEEcchhhHHHHHHHHHHcCCCCCceEEEEeC
Q 002211 201 ALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVI-VVHGYSRTGLMVFDVAQRLGMMDSGYVWIATT 277 (953)
Q Consensus 201 ~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vi-i~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~ 277 (953)
.|++.+++.|..+.... ...+ .+..+....+.++.++.++.. |++.....+..+++++++.|+. .+...++.+
T Consensus 146 gf~~~l~~~~~~~~~~~-~~~~--~~~~~~~~~~~~~l~~~~~~~ai~~~~d~~a~g~~~al~~~g~~-~di~vvg~d 219 (277)
T cd06319 146 GFKEAMKEAGCDLAGIR-QQKD--FSYQETFDYTNDLLTANPDIRAIWLQGSDRYQGALDAIATAGKT-GKVLLICFD 219 (277)
T ss_pred HHHHHHHhcCCceEeec-cCCC--CCHHHHHHHHHHHHHhCCCCCEEEECCCccchHHHHHHHHcCCC-CCEEEEEcC
Confidence 99999999988754221 1111 123344455666655545432 2333444567899999999985 333344433
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=98.29 E-value=0.00016 Score=77.55 Aligned_cols=200 Identities=12% Similarity=0.097 Sum_probs=132.7
Q ss_pred EEeEEEecC--CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEEc-cCChhhH
Q 002211 51 NVGAIFSFG--TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIVG-PQSAVMA 127 (953)
Q Consensus 51 ~IG~l~~~~--~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aiiG-p~~S~~a 127 (953)
|||++.|.. ..+-.....+++.|.++. |+.+.+...|. .++........+++++++.+||. |......
T Consensus 1 ~i~~i~~~~~~~~~~~~~~~g~~~~~~~~--------g~~v~~~~~~~-~~~~~~~~~i~~l~~~~vdgiii~~~~~~~~ 71 (271)
T cd06312 1 KIAFVTHGPAGDPFWTVVKNGAEDAAKDL--------GVDVEYRGPET-FDVADMARLIEAAIAAKPDGIVVTIPDPDAL 71 (271)
T ss_pred CEEEecCCCCCCcHHHHHHHHHHHHHHHh--------CCEEEEECCCC-CCHHHHHHHHHHHHHhCCCEEEEeCCChHHh
Confidence 588888864 455667778888888872 56665543333 37877778888888888888876 3333323
Q ss_pred HHHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHH-cCCcEEEEEEec--CccccchHHHHHH
Q 002211 128 HVLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSY-FGWGEVIAIFND--DDQGRNGVTALGD 204 (953)
Q Consensus 128 ~av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~-~~w~~vaii~~d--~~~g~~~~~~l~~ 204 (953)
......+.+.++|+|......+... ..+.+..+..++...+..+++++.+ .|-++++++..+ +..+....+.+.+
T Consensus 72 ~~~l~~~~~~~ipvV~~~~~~~~~~--~~~~~~~V~~d~~~~g~~~~~~l~~~~g~~~i~~i~g~~~~~~~~~r~~g~~~ 149 (271)
T cd06312 72 DPAIKRAVAAGIPVISFNAGDPKYK--ELGALAYVGQDEYAAGEAAGERLAELKGGKNVLCVIHEPGNVTLEDRCAGFAD 149 (271)
T ss_pred HHHHHHHHHCCCeEEEeCCCCCccc--cccceEEeccChHHHHHHHHHHHHHhcCCCeEEEEecCCCCccHHHHHHHHHH
Confidence 3444556778999998764332221 1245566778888999999999888 899999999743 3445667889999
Q ss_pred HHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcC--CceEEEEEcchhhHHHHHHHHHHcCCC
Q 002211 205 KLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMM--EARVIVVHGYSRTGLMVFDVAQRLGMM 267 (953)
Q Consensus 205 ~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~--~~~vii~~~~~~~~~~~~~~a~~~g~~ 267 (953)
++++.|+.+.. +... .+..+....++++.+. ++++|+... ...+..+++.+++.|+.
T Consensus 150 ~~~~~~~~~~~---~~~~--~~~~~~~~~~~~~l~~~~~~~aI~~~~-d~~a~g~~~al~~~g~~ 208 (271)
T cd06312 150 GLGGAGITEEV---IETG--ADPTEVASRIAAYLRANPDVDAVLTLG-APSAAPAAKALKQAGLK 208 (271)
T ss_pred HHHhcCceeeE---eecC--CCHHHHHHHHHHHHHhCCCccEEEEeC-CccchHHHHHHHhcCCC
Confidence 99988875432 1111 1233444555555433 356655544 44567788889999976
No 127
>TIGR03431 PhnD phosphonate ABC transporter, periplasmic phosphonate binding protein. Note that this model does not identify all phnD-subfamily genes with evident phosphonate context, but all sequences above the trusted context may be inferred to bind phosphonate compounds even in the absence of such context. Furthermore, there is ample evidence to suggest that many other members of the TIGR01098 subfamily have a different primary function.
Probab=98.26 E-value=1.6e-05 Score=85.97 Aligned_cols=117 Identities=20% Similarity=0.255 Sum_probs=77.2
Q ss_pred CCCCChHHhhhCCCeEEEEe-CchHH-----HHHHHhhCCCcc---ceEeCC-CHHHHHHHHHcCCcEEEEccchhHHHH
Q 002211 700 SPIKGIDTLMTSNDRVGYQV-GSFAE-----NYLIEELSIPKS---RLVALG-SPEEYAIALENRTVAAVVDERPYIDLF 769 (953)
Q Consensus 700 ~~I~sl~dL~~~~~~ig~~~-~s~~~-----~~l~~~~~~~~~---~~~~~~-~~~~~~~~l~~g~~~a~~~~~~~~~~~ 769 (953)
.+|++++||. |++|++.. ++... ..+.+..+.... +.+.+. +..+.+.+|.+|++|+.+.+.+.+..+
T Consensus 125 s~i~sl~DL~--Gk~v~~~~~~s~~~~~~~~~~l~~~~g~~~~~~~~~v~~~~~~~~~~~al~~G~vDa~~~~~~~~~~~ 202 (288)
T TIGR03431 125 SPIKSLEDLK--GKTFGFVDPNSTSGFLVPSYYLFKKNGIKPKEYFKKVTFSGSHEAAILAVANGTVDAATTNDENLDRM 202 (288)
T ss_pred CCCCcHHHhC--CCEEEeeCCCcchhhHHHHHHHHHhcCCChHHhHHhheecCchHHHHHHHHcCCCCeEeccHHHHHHH
Confidence 3689999995 88999863 33221 122233333211 223444 688999999999999999988877776
Q ss_pred Hhc-C----cceEEeCCccccCccEEEecCCC-c-chHHHHHHHHhhhccccHHHH
Q 002211 770 LSD-H----CQFSVRGQEFTKSGWGFAFPRDS-P-LAIDMSTAILTLSENGELQRI 818 (953)
Q Consensus 770 ~~~-~----~~l~~~~~~~~~~~~~~~~~k~s-p-l~~~~n~~i~~l~e~G~~~~~ 818 (953)
..+ . .++++..........+++++++- + +.+.+++++..+.+++..+++
T Consensus 203 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~l~~~~~~~~~~~~ 258 (288)
T TIGR03431 203 IRKGQPDAMEDLRIIWKSPLIPNGPIVYRKDLPADLKAKIRKAFLNYHKTDKACFE 258 (288)
T ss_pred HHcCCCCchhheEEEEEcCCCCCCcEEEeCCCCHHHHHHHHHHHHhcCCCcHHHHH
Confidence 653 2 13454432211224678889994 4 999999999999999665543
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=98.25 E-value=0.00019 Score=76.81 Aligned_cols=209 Identities=15% Similarity=0.118 Sum_probs=131.1
Q ss_pred EEeEEEecC-CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEE-ccCChhhHH
Q 002211 51 NVGAIFSFG-TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIV-GPQSAVMAH 128 (953)
Q Consensus 51 ~IG~l~~~~-~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aii-Gp~~S~~a~ 128 (953)
+||+++|-. ..+-.....|++-|.++. .| +.+++.++..++..-.+....+++.++.++| .|..+....
T Consensus 1 ~igvi~~~~~~~~~~~~~~gi~~~~~~~-------~~--~~~~~~~~~~~~~~~~~~i~~l~~~~vdgiii~~~~~~~~~ 71 (272)
T cd06301 1 KIGVSMANFDDNFLTLLRNAMKEHAKVL-------GG--VELQFEDAKNDVATQLSQVENFIAQGVDAIIVVPVDTAATA 71 (272)
T ss_pred CeeEeecccCCHHHHHHHHHHHHHHHHc-------CC--cEEEEeCCCCCHHHHHHHHHHHHHcCCCEEEEecCchhhhH
Confidence 589998753 444445556666665551 14 4444567778888888888888888888876 666555445
Q ss_pred HHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHc--CCcEEEEEEecC--ccccchHHHHHH
Q 002211 129 VLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYF--GWGEVIAIFNDD--DQGRNGVTALGD 204 (953)
Q Consensus 129 av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~--~w~~vaii~~d~--~~g~~~~~~l~~ 204 (953)
.+...+...++|+|......+.. .+.+..+..++...+..+++++... +-++++++.... .......+.|.+
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 1234456777778888888887665 456999997543 334555788999
Q ss_pred HHHhcC-cEEEEEEecCCCCCCChHHHHHHHHHHhcC--CceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEEeC
Q 002211 205 KLAEIR-CKISYKSALPPDQSVTETDVRNELVKVRMM--EARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIATT 277 (953)
Q Consensus 205 ~l~~~g-~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~--~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~ 277 (953)
++++.| ..+... .... .+.......+.++.+. ++++|+ +.+...+..+++.+++.|....+...++.+
T Consensus 148 ~l~~~~~~~~~~~--~~~~--~~~~~~~~~~~~~l~~~~~~~ai~-~~~d~~a~~~~~~l~~~g~~~~di~ivg~d 218 (272)
T cd06301 148 VLAKYPDIKVVEE--QTAN--WSRAEAMDLMENWLSSGGKIDAVV-ANNDEMALGAIMALKAAGKSDKDVPVAGID 218 (272)
T ss_pred HHHHCCCcEEEec--CCCC--ccHHHHHHHHHHHHHhCCCCCEEE-ECCCchHHHHHHHHHHcCCCCCCcEEEeeC
Confidence 999887 443321 1111 1222333455554433 456554 444456678899999999863354455544
No 129
>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=98.24 E-value=0.00018 Score=77.12 Aligned_cols=208 Identities=13% Similarity=0.007 Sum_probs=130.4
Q ss_pred EEeEEEec-CCCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEEcc-CChhhHH
Q 002211 51 NVGAIFSF-GTVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIVGP-QSAVMAH 128 (953)
Q Consensus 51 ~IG~l~~~-~~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aiiGp-~~S~~a~ 128 (953)
+||++.|. +..+-.....+++-|.++. |+++. +.++..++....+....++.+++.+||.. ..+....
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 48888885 3444456667777776663 45554 46788888888888888888899988874 3333334
Q ss_pred HHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHH--cCCcEEEEEEec-CccccchHHHHHHH
Q 002211 129 VLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSY--FGWGEVIAIFND-DDQGRNGVTALGDK 205 (953)
Q Consensus 129 av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~--~~w~~vaii~~d-~~~g~~~~~~l~~~ 205 (953)
.+...+.+.++|+|......+. +.+..+..++...++.+++++.. .|.++++++... ..........+.+.
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 4455677889999987543221 22334566777788888888766 588999999743 22334456678888
Q ss_pred HHhcC-cEEEEEEecCCCCCCChHHHHHHHHHHhcCCceE---EEEEcchhhHHHHHHHHHHcCCCCCceEEEEeC
Q 002211 206 LAEIR-CKISYKSALPPDQSVTETDVRNELVKVRMMEARV---IVVHGYSRTGLMVFDVAQRLGMMDSGYVWIATT 277 (953)
Q Consensus 206 l~~~g-~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~v---ii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~ 277 (953)
+++.+ ..+......... .+.++....++++....+++ .|++.+...+..+++.+++.|+.. +...++.+
T Consensus 145 ~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~l~~~~~~~~~ai~~~~d~~a~g~~~~l~~~g~~~-di~iig~d 217 (273)
T cd06305 145 LKAYPGIKEVAELGDVSN--NTAQDAAAQVEAVLKKYPKGGIDAIWAAWDEFAKGAKQALDEAGRTD-EIKIYGVD 217 (273)
T ss_pred HHHCCCcEEecccccccc--cchhHHHHHHHHHHHHCCCcccCeEEEcChhhhHHHHHHHHHcCCCC-CceEEEec
Confidence 88877 554432211111 12334445566665444443 233334556777888999999753 33344444
No 130
>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=98.23 E-value=0.00034 Score=74.96 Aligned_cols=209 Identities=10% Similarity=-0.027 Sum_probs=126.3
Q ss_pred EEeEEEecC-CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEEccCCh-hhHH
Q 002211 51 NVGAIFSFG-TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIVGPQSA-VMAH 128 (953)
Q Consensus 51 ~IG~l~~~~-~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aiiGp~~S-~~a~ 128 (953)
|||++.|.- ..+-.....+++-+.++ .|+++.+...++..++....+....++.+++.+||--.+. ....
T Consensus 1 ~Igvi~~~~~~~~~~~~~~g~~~~~~~--------~g~~~~~~~~~~~~~~~~~~~~i~~l~~~~vdgvii~~~~~~~~~ 72 (273)
T cd06310 1 KIALVPKGTTSDFWQAVKAGAEAAAKE--------LGVKVTFQGPASETDVAGQVNLLENAIARGPDAILLAPTDAKALV 72 (273)
T ss_pred CeEEEecCCCcHHHHHHHHHHHHHHHH--------cCCEEEEecCccCCCHHHHHHHHHHHHHhCCCEEEEcCCChhhhH
Confidence 689998763 33333445555555554 2567776654445677777777778888888888753232 2223
Q ss_pred HHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHc--CCcEEEEEEecCcc--ccchHHHHHH
Q 002211 129 VLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYF--GWGEVIAIFNDDDQ--GRNGVTALGD 204 (953)
Q Consensus 129 av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~--~w~~vaii~~d~~~--g~~~~~~l~~ 204 (953)
.....+...++|+|......+ + ..+ +-.+..++...+..+++++.+. |.++++++....++ .....+.|.+
T Consensus 73 ~~l~~~~~~~ipvV~~~~~~~---~-~~~-~~~v~~d~~~~~~~~~~~l~~~~~g~~~i~~i~~~~~~~~~~~r~~gf~~ 147 (273)
T cd06310 73 PPLKEAKDAGIPVVLIDSGLN---S-DIA-VSFVATDNVAAGKLAAEALAELLGKKGKVAVISFVPGSSTTDQREEGFLE 147 (273)
T ss_pred HHHHHHHHCCCCEEEecCCCC---C-Ccc-eEEEeeChHHHHHHHHHHHHHHcCCCceEEEEeCCCCCccHHHHHHHHHH
Confidence 445556678999998753221 1 011 2224455556678888887776 89999999744333 3445788999
Q ss_pred HHHhc-CcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceE-EEEEcchhhHHHHHHHHHHcCCCCCceEEEEeC
Q 002211 205 KLAEI-RCKISYKSALPPDQSVTETDVRNELVKVRMMEARV-IVVHGYSRTGLMVFDVAQRLGMMDSGYVWIATT 277 (953)
Q Consensus 205 ~l~~~-g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~v-ii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~ 277 (953)
++++. |+.+... .... .+..+-...+.++.+..+++ .|++.+...+..+++.+++.|+. ++...++.|
T Consensus 148 a~~~~~~~~~~~~--~~~~--~~~~~~~~~~~~~l~~~~~~~~i~~~~d~~a~g~~~~l~~~g~~-~di~vig~d 217 (273)
T cd06310 148 GLKEYPGIEIVAT--QYSD--SDYAKALDITEDLLTANPDLKGIFGANEGSAVGAARAVRQAGKA-GKVKVVGFD 217 (273)
T ss_pred HHHhCCCcEEEec--ccCC--cCHHHHHHHHHHHHHhCCCceEEEecCchhHHHHHHHHHhcCCC-CCeEEEEeC
Confidence 99988 8766431 1111 11233344555655444332 33344456677899999999985 444455544
No 131
>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=98.20 E-value=0.00024 Score=76.24 Aligned_cols=209 Identities=11% Similarity=0.062 Sum_probs=131.3
Q ss_pred EEeEEEec-CCCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEE-ccCChhhHH
Q 002211 51 NVGAIFSF-GTVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIV-GPQSAVMAH 128 (953)
Q Consensus 51 ~IG~l~~~-~~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aii-Gp~~S~~a~ 128 (953)
+||++.|- +..+-.....+++-+.++. |+++. +.++..+...-.+....++.+++.+|| .|..+....
T Consensus 1 ~~g~~~~~~~~~~~~~~~~~~~~~a~~~--------g~~~~--~~~~~~~~~~~~~~i~~l~~~~vdgiIi~~~~~~~~~ 70 (273)
T cd06309 1 TVGFSQVGAESPWRTAETKSIKDAAEKR--------GFDLK--FADAQQKQENQISAIRSFIAQGVDVIILAPVVETGWD 70 (273)
T ss_pred CeeeccCCCCCHHHHHHHHHHHHHHHhc--------CCEEE--EeCCCCCHHHHHHHHHHHHHcCCCEEEEcCCccccch
Confidence 48999884 4444445556666665552 55555 466666777777777888888888775 454444333
Q ss_pred HHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHc--CCcEEEEEEecCc--cccchHHHHHH
Q 002211 129 VLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYF--GWGEVIAIFNDDD--QGRNGVTALGD 204 (953)
Q Consensus 129 av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~--~w~~vaii~~d~~--~g~~~~~~l~~ 204 (953)
.....+.+.++|+|......+.. ...+++.++.+++...+..+++++... |-+++++++.+.. ......+.|.+
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 44566778899999876532211 112467778888888899999998776 8899999975432 23455788999
Q ss_pred HHHhc-CcEEEEEEecCCCCCCChHHHHHHHHHHhcC---CceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEEe
Q 002211 205 KLAEI-RCKISYKSALPPDQSVTETDVRNELVKVRMM---EARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIAT 276 (953)
Q Consensus 205 ~l~~~-g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~---~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~ 276 (953)
++++. +.++... .... .+..+....+.++.+. .+++|+. .+...+..+++++++.|+..++-+-|.+
T Consensus 149 ~l~~~~~~~~~~~--~~~~--~~~~~~~~~~~~~l~~~~~~~~aI~~-~~d~~a~g~~~a~~~~g~~ip~di~iig 219 (273)
T cd06309 149 VIKKYPNMKIVAS--QTGD--FTRAKGKEVMEALLKAHGDDIDAVYA-HNDEMALGAIQAIKAAGKKPGKDIKIVS 219 (273)
T ss_pred HHHHCCCCEEeec--cCCc--ccHHHHHHHHHHHHHhCCCCccEEEE-CCcHHHHHHHHHHHHcCCCCCCCeEEEe
Confidence 99987 4554421 1111 1233334445555433 3565543 3445566788999999987554444443
No 132
>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=98.19 E-value=0.00015 Score=76.94 Aligned_cols=201 Identities=16% Similarity=0.122 Sum_probs=141.3
Q ss_pred EeEEEecC-CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEE-ccCChhhHHH
Q 002211 52 VGAIFSFG-TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIV-GPQSAVMAHV 129 (953)
Q Consensus 52 IG~l~~~~-~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aii-Gp~~S~~a~a 129 (953)
||++.|.. ..+......+++-|.++. |..+.+. .|...|+..-.+...+++++++.+|| .|..+.....
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 78888886 446667889999999996 4566665 89999999999999999999988877 7777766667
Q ss_pred HHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHc-CC-cEEEEEEecCc--cccchHHHHHHH
Q 002211 130 LSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYF-GW-GEVIAIFNDDD--QGRNGVTALGDK 205 (953)
Q Consensus 130 v~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~-~w-~~vaii~~d~~--~g~~~~~~l~~~ 205 (953)
...-+...+||+|.+... .....+....+.+++...+..+++++... +- .+++++....+ ......+.+.+.
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 777788899999997554 11123445566778888899999997553 32 67887764433 334567888999
Q ss_pred HHh-cCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHHHcCCCC
Q 002211 206 LAE-IRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQRLGMMD 268 (953)
Q Consensus 206 l~~-~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~~~g~~~ 268 (953)
+++ .++++..... ... .+.++....+.++.+.++-..|+++....+..+++.+++.|+.+
T Consensus 148 l~~~~~~~~~~~~~-~~~--~~~~~a~~~~~~~l~~~~~~~i~~~~~~~~~g~~~al~~~g~~~ 208 (257)
T PF13407_consen 148 LKEYPGVEIVDEYE-YTD--WDPEDARQAIENLLQANPVDAIIACNDGMALGAAQALQQAGRAG 208 (257)
T ss_dssp HHHCTTEEEEEEEE-ECT--TSHHHHHHHHHHHHHHTTEEEEEESSHHHHHHHHHHHHHTTCTT
T ss_pred Hhhcceeeeeeeee-ccC--CCHHHHHHHHHHhhhcCCceEEEeCCChHHHHHHHHHHHcCCcc
Confidence 988 4666665322 212 23566666666665555422335566677777999999999843
No 133
>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=98.13 E-value=0.00024 Score=75.98 Aligned_cols=208 Identities=14% Similarity=0.077 Sum_probs=129.2
Q ss_pred EEeEEEecC-CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHH-HhcCcEEEEccCChhhHH
Q 002211 51 NVGAIFSFG-TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQF-METDTLAIVGPQSAVMAH 128 (953)
Q Consensus 51 ~IG~l~~~~-~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~l-i~~~v~aiiGp~~S~~a~ 128 (953)
.||++.|-. ..+......|++.++++. |+.+.+...|... ......+.++ ..+++.+||....+....
T Consensus 1 ~I~vi~~~~~~~~~~~~~~gi~~~~~~~--------g~~~~~~~~~~~~--~~~~~~~~~~l~~~~vdgiii~~~~~~~~ 70 (270)
T cd01545 1 LIGLLYDNPSPGYVSEIQLGALDACRDT--------GYQLVIEPCDSGS--PDLAERVRALLQRSRVDGVILTPPLSDNP 70 (270)
T ss_pred CEEEEEcCCCcccHHHHHHHHHHHHHhC--------CCeEEEEeCCCCc--hHHHHHHHHHHHHCCCCEEEEeCCCCCcc
Confidence 378999863 567778888888888752 5777766555432 2234445554 466899988754433234
Q ss_pred HHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecCccc--cchHHHHHHHH
Q 002211 129 VLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDDDQG--RNGVTALGDKL 206 (953)
Q Consensus 129 av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~~~g--~~~~~~l~~~l 206 (953)
...+.+...++|+|......+. ...++ +..++...+..+++++...|.++++++..+..+. ....+.|.+.+
T Consensus 71 ~~~~~~~~~~ipvv~i~~~~~~---~~~~~---V~~d~~~~g~~a~~~l~~~g~~~i~~i~~~~~~~~~~~R~~Gf~~~~ 144 (270)
T cd01545 71 ELLDLLDEAGVPYVRIAPGTPD---PDSPC---VRIDDRAAAREMTRHLIDLGHRRIAFIAGPPDHRASAERLEGYRDAL 144 (270)
T ss_pred HHHHHHHhcCCCEEEEecCCCC---CCCCe---EEeccHHHHHHHHHHHHHCCCceEEEEeCCCCchhHHHHHHHHHHHH
Confidence 4556777889999987654332 22233 2345666678888888888999999998654432 34467899999
Q ss_pred HhcCcEEEEEEecCCCCCCChHHHHHHHHHHhc--CCceEEEEEcchhhHHHHHHHHHHcCCCCCc-eEEEEeC
Q 002211 207 AEIRCKISYKSALPPDQSVTETDVRNELVKVRM--MEARVIVVHGYSRTGLMVFDVAQRLGMMDSG-YVWIATT 277 (953)
Q Consensus 207 ~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~--~~~~vii~~~~~~~~~~~~~~a~~~g~~~~~-~~wi~~~ 277 (953)
++.|+.+......... .+..+-...+.++.+ .++++|+. .+...+..+++.+++.|...++ ...++.+
T Consensus 145 ~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~l~~~~~~~~i~~-~~d~~a~~~~~~~~~~g~~~p~~i~vig~d 215 (270)
T cd01545 145 AEAGLPLDPELVAQGD--FTFESGLEAAEALLALPDRPTAIFA-SNDDMAAGVLAVAHRRGLRVPDDLSVVGFD 215 (270)
T ss_pred HHcCCCCChhhEEeCC--CChhhHHHHHHHHHhCCCCCCEEEE-cCcHHHHHHHHHHHHcCCCCCCceEEEEEC
Confidence 8888765210011111 112222234455543 35777774 4557778999999999986443 3344444
No 134
>PRK10936 TMAO reductase system periplasmic protein TorT; Provisional
Probab=98.03 E-value=0.002 Score=71.51 Aligned_cols=208 Identities=10% Similarity=0.012 Sum_probs=124.6
Q ss_pred CceEEEeEEEecC-CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEE-ccCCh
Q 002211 47 PEVLNVGAIFSFG-TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIV-GPQSA 124 (953)
Q Consensus 47 ~~~i~IG~l~~~~-~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aii-Gp~~S 124 (953)
...-+||++.|.. ..+-.....+++-+.++. |+++.+...+...+...-.+....++++++.+|| .|...
T Consensus 44 r~t~~Igvv~p~~~~~f~~~~~~gi~~aa~~~--------G~~l~i~~~~~~~~~~~q~~~i~~l~~~~vdgIIl~~~~~ 115 (343)
T PRK10936 44 KKAWKLCALYPHLKDSYWLSVNYGMVEEAKRL--------GVDLKVLEAGGYYNLAKQQQQLEQCVAWGADAILLGAVTP 115 (343)
T ss_pred CCCeEEEEEecCCCchHHHHHHHHHHHHHHHh--------CCEEEEEcCCCCCCHHHHHHHHHHHHHhCCCEEEEeCCCh
Confidence 4578999999874 334445566777766652 5565554332234555555666778888888776 45444
Q ss_pred hhHHHHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHc-----CCcEEEEEEec--Cccccc
Q 002211 125 VMAHVLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYF-----GWGEVIAIFND--DDQGRN 197 (953)
Q Consensus 125 ~~a~av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~-----~w~~vaii~~d--~~~g~~ 197 (953)
....... .+.+.++|+|.+..... ++. ....+..++...+...++++... |-++++++..+ ......
T Consensus 116 ~~~~~~l-~~~~~giPvV~~~~~~~--~~~---~~~~V~~D~~~~g~~aa~~L~~~~~~~~g~~~i~~i~g~~~~~~~~~ 189 (343)
T PRK10936 116 DGLNPDL-ELQAANIPVIALVNGID--SPQ---VTTRVGVSWYQMGYQAGRYLAQWHPKGSKPLNVALLPGPEGAGGSKA 189 (343)
T ss_pred HHhHHHH-HHHHCCCCEEEecCCCC--Ccc---ceEEEecChHHHHHHHHHHHHHHHHhcCCCceEEEEECCCCCchHHH
Confidence 3322233 45678999997632211 111 12335567777788888886655 47899999743 223344
Q ss_pred hHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhc--CCceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEE
Q 002211 198 GVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRM--MEARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIA 275 (953)
Q Consensus 198 ~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~--~~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~ 275 (953)
..+.|.+.+++.|+++.... .... +.+.-...++++.+ .++++|+ +....+..+++.+++.|+. +.+.|.
T Consensus 190 R~~Gf~~~l~~~~i~~~~~~-~~~~---~~~~~~~~~~~~l~~~~~~~ai~--~~d~~A~ga~~al~~~g~~--~di~Vv 261 (343)
T PRK10936 190 VEQGFRAAIAGSDVRIVDIA-YGDN---DKELQRNLLQELLERHPDIDYIA--GSAVAAEAAIGELRGRNLT--DKIKLV 261 (343)
T ss_pred HHHHHHHHHhcCCCEEEEee-cCCC---cHHHHHHHHHHHHHhCCCccEEE--eCCHHHHHHHHHHHhcCCC--CCeEEE
Confidence 57889999988898875421 1111 12333344555543 3468776 3456677788999999973 334444
Q ss_pred e
Q 002211 276 T 276 (953)
Q Consensus 276 ~ 276 (953)
+
T Consensus 262 g 262 (343)
T PRK10936 262 S 262 (343)
T ss_pred E
Confidence 3
No 135
>cd06298 PBP1_CcpA_like Ligand-binding domain of the catabolite control protein A (CcpA), which functions as the major transcriptional regulator of carbon catabolite repression/regulation. Ligand-binding domain of the catabolite control protein A (CcpA), which functions as the major transcriptional regulator of carbon catabolite repression/regulation (CCR), a process in which enzymes necessary for the metabolism of alternative sugars are inhibited in the presence of glucose. In gram-positive bacteria, CCR is controlled by HPr, a phosphoenolpyruvate:sugar phsophotrasnferase system (PTS) and a transcriptional regulator CcpA. Moreover, CcpA can regulate sporulation and antibiotic resistance as well as play a role in virulence development of certain pathogens such as the group A streptococcus. The ligand binding domain of CcpA is a member of the LacI-GalR family of bacterial transcription regulators.
Probab=97.99 E-value=0.00057 Score=72.96 Aligned_cols=207 Identities=10% Similarity=0.003 Sum_probs=127.8
Q ss_pred EEeEEEecC-CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEEccCChhhHHH
Q 002211 51 NVGAIFSFG-TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIVGPQSAVMAHV 129 (953)
Q Consensus 51 ~IG~l~~~~-~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aiiGp~~S~~a~a 129 (953)
+||+++|.. ..+-.....+++-+.++. |+.+.+. .+..++..-.+....+++.++++||=..+. ....
T Consensus 1 ~i~vi~~~~~~~~~~~~~~~~~~~~~~~--------g~~~~~~--~~~~~~~~~~~~i~~l~~~~vdgiii~~~~-~~~~ 69 (268)
T cd06298 1 TVGVIIPDITNSYFAELARGIDDIATMY--------KYNIILS--NSDNDKEKELKVLNNLLAKQVDGIIFMGGK-ISEE 69 (268)
T ss_pred CEEEEECCCcchHHHHHHHHHHHHHHHc--------CCeEEEE--eCCCCHHHHHHHHHHHHHhcCCEEEEeCCC-CcHH
Confidence 378888763 444445566666665552 5666654 345566666666777787788877732111 1223
Q ss_pred HHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecC---ccccchHHHHHHHH
Q 002211 130 LSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDD---DQGRNGVTALGDKL 206 (953)
Q Consensus 130 v~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~---~~g~~~~~~l~~~l 206 (953)
+...+...++|+|......+ ....++ +.+++...+..+++++...|-++++++..+. .++....+.|.+.+
T Consensus 70 ~~~~l~~~~ipvV~~~~~~~---~~~~~~---v~~d~~~~~~~~~~~l~~~g~~~i~~l~~~~~~~~~~~~r~~gf~~~~ 143 (268)
T cd06298 70 HREEFKRSPTPVVLAGSVDE---DNELPS---VNIDYKKAAFEATELLIKNGHKKIAFISGPLEDSINGDERLAGYKEAL 143 (268)
T ss_pred HHHHHhcCCCCEEEEccccC---CCCCCE---EEECcHHHHHHHHHHHHHcCCceEEEEeCCcccccchhHHHHHHHHHH
Confidence 45556677999998754322 122233 3556667778888988888999999997433 35677789999999
Q ss_pred HhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCC-ceEEEEEcchhhHHHHHHHHHHcCCCCCceE-EEEeC
Q 002211 207 AEIRCKISYKSALPPDQSVTETDVRNELVKVRMME-ARVIVVHGYSRTGLMVFDVAQRLGMMDSGYV-WIATT 277 (953)
Q Consensus 207 ~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~-~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~-wi~~~ 277 (953)
++.|+.+.....+... .+.......+.++.+.. +++|+.. +...+..+++.+++.|+..++.+ +++.+
T Consensus 144 ~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~l~~~~~~ai~~~-~d~~a~~~~~~l~~~g~~vp~di~vvg~d 213 (268)
T cd06298 144 SEANIEFDESLIFEGD--YTYESGYELAEELLEDGKPTAAFVT-DDELAIGILNAAQDAGLKVPEDFEIIGFN 213 (268)
T ss_pred HHcCCCCCHHHeEeCC--CChhHHHHHHHHHhcCCCCCEEEEc-CcHHHHHHHHHHHHcCCCCccceEEEeec
Confidence 9988654221111111 11223334556665544 7877764 44457789999999998655443 44444
No 136
>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=97.98 E-value=0.0016 Score=71.05 Aligned_cols=208 Identities=9% Similarity=0.056 Sum_probs=121.8
Q ss_pred EEeEEEecC-CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEE-ccCChhhHH
Q 002211 51 NVGAIFSFG-TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIV-GPQSAVMAH 128 (953)
Q Consensus 51 ~IG~l~~~~-~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aii-Gp~~S~~a~ 128 (953)
+||++.|.. ..+-.....+++-+.++.+ .| +.+.+.+...++..-.+....++.+++.+|| .|..+....
T Consensus 1 ~Igviv~~~~~~~~~~~~~gi~~~a~~~~------~g--~~~~~~~~~~~~~~q~~~i~~l~~~~vdgiii~~~~~~~~~ 72 (303)
T cd01539 1 KIGVFLYKFDDTFISLVRKNLEDIQKENG------GK--VEFTFYDAKNNQSTQNEQIDTALAKGVDLLAVNLVDPTAAQ 72 (303)
T ss_pred CeEEEeeCCCChHHHHHHHHHHHHHHhhC------CC--eeEEEecCCCCHHHHHHHHHHHHHcCCCEEEEecCchhhHH
Confidence 589998853 4444456677777776651 13 4455667777887777777788888888765 455544444
Q ss_pred HHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHc--CCc---------E--EEEEEecC--c
Q 002211 129 VLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYF--GWG---------E--VIAIFNDD--D 193 (953)
Q Consensus 129 av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~--~w~---------~--vaii~~d~--~ 193 (953)
.+...+...++|+|......+...-...+-+..+.+++...+..+++++... |-+ + ++++..+. .
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 5556667789999987643221110111223445667766777777877554 221 2 34454332 2
Q ss_pred cccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcC---CceEEEEEcchhhHHHHHHHHHHcCCCCC
Q 002211 194 QGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMM---EARVIVVHGYSRTGLMVFDVAQRLGMMDS 269 (953)
Q Consensus 194 ~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~---~~~vii~~~~~~~~~~~~~~a~~~g~~~~ 269 (953)
......+.+.+.+++.|..+......... .+.+.....++++... ++++|+. .+...+..+++++++.|...+
T Consensus 153 ~~~~R~~gf~~~l~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~L~~~~~~~~ai~~-~~d~~a~g~~~al~~~g~~~p 228 (303)
T cd01539 153 DAIARTKYSIETLNDAGIKTEELASDTAN--WDRAQAKDKMDALLLKYGDKIEAVIA-NNDAMALGAIEALQKYGYNKG 228 (303)
T ss_pred hhhhhhhhHHHHHHhcCCCeEEEEeecCC--CCHHHHHHHHHHHHHhcCCCccEEEE-CCchHHHHHHHHHHHcCCCcC
Confidence 23445778999999888765322222211 1233333445555433 2566554 444556678889999887654
No 137
>PRK09701 D-allose transporter subunit; Provisional
Probab=97.98 E-value=0.0045 Score=67.73 Aligned_cols=213 Identities=11% Similarity=0.045 Sum_probs=127.8
Q ss_pred EEeEEEec-CCCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEEc-cCChhhHH
Q 002211 51 NVGAIFSF-GTVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIVG-PQSAVMAH 128 (953)
Q Consensus 51 ~IG~l~~~-~~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aiiG-p~~S~~a~ 128 (953)
+||++.|. +..+-.....+++-+.++. |+++.+...+...++..-.+....++.+++.+||- |..+....
T Consensus 26 ~Igvi~~~~~~~f~~~~~~gi~~~a~~~--------g~~v~~~~~~~~~~~~~~~~~i~~l~~~~vDgiIi~~~~~~~~~ 97 (311)
T PRK09701 26 EYAVVLKTLSNPFWVDMKKGIEDEAKTL--------GVSVDIFASPSEGDFQSQLQLFEDLSNKNYKGIAFAPLSSVNLV 97 (311)
T ss_pred eEEEEeCCCCCHHHHHHHHHHHHHHHHc--------CCeEEEecCCCCCCHHHHHHHHHHHHHcCCCEEEEeCCChHHHH
Confidence 89999986 3444445566666665542 56777654455566666677777888888887763 33333222
Q ss_pred HHHHhhhhCCCcEEEeecCCCC--CCCCCCCcEEEccCChHHHHHHHHHHHHH-cCC--cEEEEEEec--CccccchHHH
Q 002211 129 VLSHLANELQVPLLSFTALDPT--LSPLQYPFFVQTAPNDLYLMSAIAEMVSY-FGW--GEVIAIFND--DDQGRNGVTA 201 (953)
Q Consensus 129 av~~v~~~~~vP~Is~~at~~~--ls~~~~p~~fr~~p~d~~~~~ai~~~l~~-~~w--~~vaii~~d--~~~g~~~~~~ 201 (953)
.....+.+.++|++.+....+. +....-....-+..++...+...++++.+ .|- ++++++..+ ........+.
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 2233446789999988643321 11111112334667777888889998755 464 799988643 2334566788
Q ss_pred HHHHHHhcC-cEEEEEEecCCCCCCChHHHHHHHHHHhcC--CceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEEeC
Q 002211 202 LGDKLAEIR-CKISYKSALPPDQSVTETDVRNELVKVRMM--EARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIATT 277 (953)
Q Consensus 202 l~~~l~~~g-~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~--~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~ 277 (953)
|.+.+++.| +++.... ... .+..+-...++++.+. ++++|+ +.+...+..+++.+++.|.. .+...++.|
T Consensus 178 f~~al~~~~~~~~~~~~--~~~--~~~~~~~~~~~~ll~~~~~~~~I~-~~~d~~A~g~~~al~~~G~~-~dv~vvg~d 250 (311)
T PRK09701 178 ATEAFKKASQIKLVASQ--PAD--WDRIKALDVATNVLQRNPNIKAIY-CANDTMAMGVAQAVANAGKT-GKVLVVGTD 250 (311)
T ss_pred HHHHHHhCCCcEEEEec--CCC--CCHHHHHHHHHHHHHhCCCCCEEE-ECCcchHHHHHHHHHHcCCC-CCEEEEEeC
Confidence 999998887 7654321 111 1123334455555433 456544 55566777899999999974 333344433
No 138
>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=97.96 E-value=0.00063 Score=72.60 Aligned_cols=203 Identities=10% Similarity=0.053 Sum_probs=126.5
Q ss_pred EEeEEEecC-CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEEccCChhhHHH
Q 002211 51 NVGAIFSFG-TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIVGPQSAVMAHV 129 (953)
Q Consensus 51 ~IG~l~~~~-~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aiiGp~~S~~a~a 129 (953)
.||++.|.. ..+-.....+++-+.++. |+++. +.++..++..-.+....++++++.+||...+......
T Consensus 1 ~I~vi~~~~~~~~~~~~~~g~~~~a~~~--------g~~~~--~~~~~~~~~~~~~~i~~~~~~~vdgiii~~~~~~~~~ 70 (268)
T cd06289 1 TIGLVINDLTNPFFAELAAGLEEVLEEA--------GYTVF--LANSGEDVERQEQLLSTMLEHGVAGIILCPAAGTSPD 70 (268)
T ss_pred CEEEEecCCCcchHHHHHHHHHHHHHHc--------CCeEE--EecCCCChHHHHHHHHHHHHcCCCEEEEeCCCCccHH
Confidence 378888763 445556777888777763 45553 4566667776667777888888988887544333333
Q ss_pred HHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecC--ccccchHHHHHHHHH
Q 002211 130 LSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDD--DQGRNGVTALGDKLA 207 (953)
Q Consensus 130 v~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~--~~g~~~~~~l~~~l~ 207 (953)
....+...++|+|......+. ...+| +..++...+..+++++...|-++|+++..+. .......+.|.+.++
T Consensus 71 ~~~~~~~~~ipvV~~~~~~~~---~~~~~---v~~d~~~~~~~~~~~l~~~g~~~i~~l~~~~~~~~~~~r~~gf~~~l~ 144 (268)
T cd06289 71 LLKRLAESGIPVVLVAREVAG---APFDY---VGPDNAAGARLATEHLISLGHRRIAFIGGLEDSSTRRERLAGYRAALA 144 (268)
T ss_pred HHHHHHhcCCCEEEEeccCCC---CCCCE---EeecchHHHHHHHHHHHHCCCCCEEEecCCccccchHHHHHHHHHHHH
Confidence 556677889999987543221 12222 4455666778888888888999999987432 345567789999998
Q ss_pred hcCcEEEEEEecCCCCCCChHHHHHHHHHHhcC--CceEEEEEcchhhHHHHHHHHHHcCCCCCceE
Q 002211 208 EIRCKISYKSALPPDQSVTETDVRNELVKVRMM--EARVIVVHGYSRTGLMVFDVAQRLGMMDSGYV 272 (953)
Q Consensus 208 ~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~--~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~ 272 (953)
+.|..+.....+... .+.+.....++++... ++++|+.. +...+..+++.+++.|+..++.+
T Consensus 145 ~~~~~~~~~~~~~~~--~~~~~~~~~~~~~l~~~~~~~~i~~~-~~~~a~~~~~al~~~g~~~p~di 208 (268)
T cd06289 145 EAGLPFDSELVVEGP--PSRQGGAEAVAQLLDLPPRPTAIVCF-NDLVAFGAMSGLRRAGLTPGRDI 208 (268)
T ss_pred HcCCCCCchhEEecC--cchhhHHHHHHHHHcCCCCCCEEEEc-CcHHHHHHHHHHHHcCCCCCcce
Confidence 887532211111111 1122333445555433 45665544 44456678999999998654333
No 139
>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=97.94 E-value=0.001 Score=70.89 Aligned_cols=198 Identities=8% Similarity=-0.008 Sum_probs=123.0
Q ss_pred EeEEEecC-CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEEccCChhhHHHH
Q 002211 52 VGAIFSFG-TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIVGPQSAVMAHVL 130 (953)
Q Consensus 52 IG~l~~~~-~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aiiGp~~S~~a~av 130 (953)
||++.|.. ..+-.....+++-|.++. |+++ .+.|+..++.........++.++|.+||......... .
T Consensus 2 i~~v~~~~~~~~~~~~~~~i~~~~~~~--------g~~~--~~~~~~~~~~~~~~~~~~~~~~~vdgiii~~~~~~~~-~ 70 (267)
T cd06284 2 ILVLVPDIANPFFSEILKGIEDEAREA--------GYGV--LLGDTRSDPEREQEYLDLLRRKQADGIILLDGSLPPT-A 70 (267)
T ss_pred EEEEECCCCCccHHHHHHHHHHHHHHc--------CCeE--EEecCCCChHHHHHHHHHHHHcCCCEEEEecCCCCHH-H
Confidence 78888864 444455667777666661 5555 4567777877776666777778899887632221211 2
Q ss_pred HHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEec--CccccchHHHHHHHHHh
Q 002211 131 SHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFND--DDQGRNGVTALGDKLAE 208 (953)
Q Consensus 131 ~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d--~~~g~~~~~~l~~~l~~ 208 (953)
.... ..++|+|......+ . +.+..+..++...+..+++++...|.+++++++.+ +..+....+.|.+.+++
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 45999997642211 1 22233556677778889999888899999999754 34566678899999999
Q ss_pred cCcEEEEEEecCCCCCCChHHHHHHHHHHhcC--CceEEEEEcchhhHHHHHHHHHHcCCCCCc
Q 002211 209 IRCKISYKSALPPDQSVTETDVRNELVKVRMM--EARVIVVHGYSRTGLMVFDVAQRLGMMDSG 270 (953)
Q Consensus 209 ~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~--~~~vii~~~~~~~~~~~~~~a~~~g~~~~~ 270 (953)
.|+++......... .+.++....+.++.+. .+++|+.. +...+..+++++++.|+..++
T Consensus 144 ~~~~~~~~~~~~~~--~~~~~~~~~~~~~l~~~~~~~ai~~~-~~~~a~g~~~al~~~g~~~p~ 204 (267)
T cd06284 144 AGLPADEELIQEGD--FSLESGYAAARRLLALPDRPTAIFCF-SDEMAIGAISALKELGLRVPE 204 (267)
T ss_pred cCCCCCcceEEeCC--CChHHHHHHHHHHHhCCCCCcEEEEc-CcHHHHHHHHHHHHcCCCCcc
Confidence 88543211111111 1133344455555433 46776665 444567889999999976443
No 140
>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=97.94 E-value=0.0022 Score=69.02 Aligned_cols=213 Identities=8% Similarity=-0.019 Sum_probs=120.6
Q ss_pred EEeEEEecC--CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCC--CChHHHHHHHHHHHhcCcEEEEccCChhh
Q 002211 51 NVGAIFSFG--TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAK--FNGFLSIMGALQFMETDTLAIVGPQSAVM 126 (953)
Q Consensus 51 ~IG~l~~~~--~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~--~~~~~a~~~a~~li~~~v~aiiGp~~S~~ 126 (953)
|||+++|.. ..+-.....+++-+.++ . |+++.+...++. .++..-......+++++|.+||=...+..
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 589999863 23323334444444433 2 566776654443 35555556666788888888774322222
Q ss_pred HHHHHHhhhhCCCcEEEeec-CCCCCCCCCCCcEEEccCChHHHHHHHHHHHHH--cCCcEEEEEEec-CccccchHHHH
Q 002211 127 AHVLSHLANELQVPLLSFTA-LDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSY--FGWGEVIAIFND-DDQGRNGVTAL 202 (953)
Q Consensus 127 a~av~~v~~~~~vP~Is~~a-t~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~--~~w~~vaii~~d-~~~g~~~~~~l 202 (953)
......-+.+.++|.|.... ..+.......+..-.+..++..-+..+++++.. .|.+++++|... ...+....+.|
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 22222334456777666522 222111000122334566777777888888777 789999999753 23344567889
Q ss_pred HHHHHhc-CcEEEEEEecCCCCCCChHHHHHHHHHHhcC--CceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEEeC
Q 002211 203 GDKLAEI-RCKISYKSALPPDQSVTETDVRNELVKVRMM--EARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIATT 277 (953)
Q Consensus 203 ~~~l~~~-g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~--~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~ 277 (953)
.+++++. |+.+... +... .+..+....+.++.+. ++++|+ +.+...+..+++.+++.|+. .+...++-+
T Consensus 153 ~~al~~~~~~~~~~~--~~~~--~~~~~~~~~~~~~l~~~~~~~ai~-~~nd~~A~g~l~al~~~G~~-~dv~vvg~d 224 (280)
T cd06303 153 IDCVHARNNWTLTSE--FYTD--ATRQKAYQATSDILSNNPDVDFIY-ACSTDIALGASDALKELGRE-DDILINGWG 224 (280)
T ss_pred HHHHHhCCCceEEEe--ecCC--CCHHHHHHHHHHHHHhCCCCcEEE-ECCcHHHHHHHHHHHHcCCC-CCcEEEecC
Confidence 9999988 7664322 2222 2233444455555444 356555 45556677899999999985 344444433
No 141
>COG1879 RbsB ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]
Probab=97.93 E-value=0.0033 Score=69.18 Aligned_cols=212 Identities=13% Similarity=0.104 Sum_probs=138.7
Q ss_pred CCceEEEeEEEecC-CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEE-ccCC
Q 002211 46 KPEVLNVGAIFSFG-TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIV-GPQS 123 (953)
Q Consensus 46 ~~~~i~IG~l~~~~-~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aii-Gp~~ 123 (953)
.....+||++.+.. ..+-.....+++-+.++. |....+...|.+.|+..-++...+++.+++.+|+ .|.+
T Consensus 30 ~~~~~~i~~~~~~~~~~f~~~~~~g~~~~a~~~--------g~~~~~~~~~~~~d~~~Q~~~i~~~ia~~~daIiv~~~d 101 (322)
T COG1879 30 AAAGKTIGVVVPTLGNPFFQAVRKGAEAAAKKL--------GVVVAVVIADAQNDVAKQIAQIEDLIAQGVDAIIINPVD 101 (322)
T ss_pred hccCceEEEEeccCCChHHHHHHHHHHHHHHHc--------CCcEEEEecccccChHHHHHHHHHHHHcCCCEEEEcCCC
Confidence 34448899998875 444455566666655554 2357777889999999999999999999987765 7888
Q ss_pred hhhHHHHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHH-cCC-cEEEEEEec--CccccchH
Q 002211 124 AVMAHVLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSY-FGW-GEVIAIFND--DDQGRNGV 199 (953)
Q Consensus 124 S~~a~av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~-~~w-~~vaii~~d--~~~g~~~~ 199 (953)
+.....+..-+...+||+|.+....+.- .........+....+...++++.+ ++- -+++++... ........
T Consensus 102 ~~~~~~~v~~a~~aGIpVv~~d~~~~~~----~~~~~~vg~dn~~~G~~~a~~l~~~~~~~g~v~~~~g~~~~~~~~~R~ 177 (322)
T COG1879 102 PDALTPAVKKAKAAGIPVVTVDSDIPGP----GDRVAYVGSDNYKAGRLAAEYLAKALGGKGKVVVLVGSPGNSSAEERV 177 (322)
T ss_pred hhhhHHHHHHHHHCCCcEEEEecCCCCC----CceeEEEecCcHHHHHHHHHHHHHHhCCCCeEEEEecCCCCchHHHHH
Confidence 9999999999999999999986554322 122233333555556666777544 432 346666533 44455678
Q ss_pred HHHHHHHHhcCc--EEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcch-hhHHHHHHHHHHcCCCCCceEEEE
Q 002211 200 TALGDKLAEIRC--KISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYS-RTGLMVFDVAQRLGMMDSGYVWIA 275 (953)
Q Consensus 200 ~~l~~~l~~~g~--~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~-~~~~~~~~~a~~~g~~~~~~~wi~ 275 (953)
+.+.+.+++.+. .++.. ...+ .+.+.-......+....||+-.+++.. ..+....+.+++.|... .+.+.
T Consensus 178 ~G~~~~l~~~~~~~~v~~~--~~~~--~~~~~a~~~~~~~L~~~pdi~~i~~~~d~~a~ga~~A~~~~g~~~--~v~v~ 250 (322)
T COG1879 178 KGFRDALKEHPPDIEVVDV--QTGD--WDRDKALEVMEDLLAANPDIDGIYAANDGMALGAIQALKAAGRKG--DVVVV 250 (322)
T ss_pred hhHHHHHHhCCCcEEEeec--cCCc--ccHHHHHHHHHHHHHhCCCceEEEECCchhHHHHHHHHHHcCCCC--ceEEE
Confidence 899999998875 33332 2222 224445566777777788876666554 34445556777778754 34444
No 142
>PRK15395 methyl-galactoside ABC transporter galactose-binding periplasmic protein MglB; Provisional
Probab=97.92 E-value=0.0043 Score=68.48 Aligned_cols=209 Identities=10% Similarity=0.029 Sum_probs=117.2
Q ss_pred CCCceEEEeEEEec-CCCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEEc-cC
Q 002211 45 LKPEVLNVGAIFSF-GTVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIVG-PQ 122 (953)
Q Consensus 45 ~~~~~i~IG~l~~~-~~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aiiG-p~ 122 (953)
....+.+||++.|- +..+-.....+++-+.++. | +. .+++.++..++.........++.++|.+||= |.
T Consensus 20 ~~~~~~~Igvv~~~~~~~f~~~~~~gi~~~a~~~---g----~~--~~~~~~~~~~~~~~~~~i~~l~~~~vdgiIi~~~ 90 (330)
T PRK15395 20 AAAADTRIGVTIYKYDDNFMSVVRKAIEKDAKAA---P----DV--QLLMNDSQNDQSKQNDQIDVLLAKGVKALAINLV 90 (330)
T ss_pred hhcCCceEEEEEecCcchHHHHHHHHHHHHHHhc---C----Ce--EEEEecCCCCHHHHHHHHHHHHHcCCCEEEEecc
Confidence 45667899999974 3434445556666555553 2 23 3344566666666666666788878887763 33
Q ss_pred ChhhHHHHHHhhhhCCCcEEEeecCCCCCCC-CCCCcEEEccCChHHHHHHHHHHHHHc------------CCcEEEEEE
Q 002211 123 SAVMAHVLSHLANELQVPLLSFTALDPTLSP-LQYPFFVQTAPNDLYLMSAIAEMVSYF------------GWGEVIAIF 189 (953)
Q Consensus 123 ~S~~a~av~~v~~~~~vP~Is~~at~~~ls~-~~~p~~fr~~p~d~~~~~ai~~~l~~~------------~w~~vaii~ 189 (953)
.+.........+...++|+|.+....+ ... ...+-...+..++...+..+++++.++ |-.++++|.
T Consensus 91 ~~~~~~~~l~~l~~~giPvV~vd~~~~-~~~~~~~~~~~~V~~D~~~ag~~a~~~l~~~~~~~~~~~~~~~g~~~i~~i~ 169 (330)
T PRK15395 91 DPAAAPTVIEKARGQDVPVVFFNKEPS-RKALDSYDKAYYVGTDSKESGIIQGDLIAKHWKANPAWDLNKDGKIQYVLLK 169 (330)
T ss_pred CHHHHHHHHHHHHHCCCcEEEEcCCcc-ccccccccceeEEccChHHHHHHHHHHHHHHHhhccccccCCCCceEEEEEe
Confidence 333334444556778999999865321 111 111212234556666666666654432 323345454
Q ss_pred ec--CccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcC----CceEEEEEcchhhHHHHHHHHHH
Q 002211 190 ND--DDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMM----EARVIVVHGYSRTGLMVFDVAQR 263 (953)
Q Consensus 190 ~d--~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~----~~~vii~~~~~~~~~~~~~~a~~ 263 (953)
.. ........+.+.+++++.|+.+.... ...+. .+.++-...+.++.+. ++++|+ +++...+..+++.+++
T Consensus 170 g~~~~~~~~~R~~G~~~al~~~g~~~~~~~-~~~~~-~~~~~a~~~~~~~l~~~~~~~~~ai~-~~~d~~A~gvl~al~~ 246 (330)
T PRK15395 170 GEPGHPDAEARTTYVIKELNDKGIKTEQLQ-LDTAM-WDTAQAKDKMDAWLSGPNANKIEVVI-ANNDAMAMGAVEALKA 246 (330)
T ss_pred cCCCCchHHHHHHHHHHHHHhcCCCeeeee-cccCC-cCHHHHHHHHHHHHhhCcCCCeeEEE-ECCchHHHHHHHHHHh
Confidence 32 22344567889999998887654321 21110 1123333455555433 356555 4455667789999999
Q ss_pred cCC
Q 002211 264 LGM 266 (953)
Q Consensus 264 ~g~ 266 (953)
.|+
T Consensus 247 ~Gl 249 (330)
T PRK15395 247 HNK 249 (330)
T ss_pred cCC
Confidence 987
No 143
>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=97.92 E-value=0.0011 Score=70.28 Aligned_cols=200 Identities=13% Similarity=0.055 Sum_probs=129.6
Q ss_pred EeEEEec-CCCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEEccCChhhHHHH
Q 002211 52 VGAIFSF-GTVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIVGPQSAVMAHVL 130 (953)
Q Consensus 52 IG~l~~~-~~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aiiGp~~S~~a~av 130 (953)
||++.|- +..+-.....+++.+.++. |+++.+ .++..++..-.....+++.+++.++|....... ..+
T Consensus 2 igvv~~~~~~~~~~~~~~gi~~~~~~~--------g~~~~~--~~~~~~~~~~~~~i~~l~~~~~dgii~~~~~~~-~~~ 70 (259)
T cd01542 2 IGVIVPRLDSFSTSRTVKGILAALYEN--------GYQMLL--MNTNFSIEKEIEALELLARQKVDGIILLATTIT-DEH 70 (259)
T ss_pred eEEEecCCccchHHHHHHHHHHHHHHC--------CCEEEE--EeCCCCHHHHHHHHHHHHhcCCCEEEEeCCCCC-HHH
Confidence 7888875 3445556778888777652 566654 456667777777788888888888886433222 344
Q ss_pred HHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEec-C--ccccchHHHHHHHHH
Q 002211 131 SHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFND-D--DQGRNGVTALGDKLA 207 (953)
Q Consensus 131 ~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d-~--~~g~~~~~~l~~~l~ 207 (953)
...+.+.++|+|......+ ..+ .+..+....+..+++++.+.|-++++++... + ..++...+.|++.++
T Consensus 71 ~~~~~~~~ipvv~~~~~~~-----~~~---~v~~d~~~~~~~~~~~l~~~g~~~i~~v~~~~~~~~~~~~r~~gf~~~~~ 142 (259)
T cd01542 71 REAIKKLNVPVVVVGQDYP-----GIS---SVVYDDYGAGYELGEYLAQQGHKNIAYLGVSESDIAVGILRKQGYLDALK 142 (259)
T ss_pred HHHHhcCCCCEEEEeccCC-----CCC---EEEECcHHHHHHHHHHHHHcCCCcEEEEcCCcccchhHHHHHHHHHHHHH
Confidence 4566777999998754221 122 2456677778889999888899999999643 2 233556788999999
Q ss_pred hcCc-EEEEEEecCCCCCCChHHHHHHHHHHhcCC-ceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEEe
Q 002211 208 EIRC-KISYKSALPPDQSVTETDVRNELVKVRMME-ARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIAT 276 (953)
Q Consensus 208 ~~g~-~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~-~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~ 276 (953)
+.|. .+.. ..-.. +.......+.++.+.. +++|+... ...+..+++.+++.|+..++.+.+.+
T Consensus 143 ~~~~~~~~~-~~~~~----~~~~~~~~~~~~l~~~~~~~i~~~~-d~~a~g~~~~l~~~g~~vp~di~v~g 207 (259)
T cd01542 143 EHGICPPNI-VETDF----SYESAYEAAQELLEPQPPDAIVCAT-DTIALGAMKYLQELGRRIPEDISVAG 207 (259)
T ss_pred HcCCChHHe-eeccC----chhhHHHHHHHHhcCCCCCEEEEcC-cHHHHHHHHHHHHcCCCCCCceEEEe
Confidence 8887 2111 11111 1233344555555444 67766665 45677899999999987655555554
No 144
>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=97.91 E-value=0.0023 Score=68.54 Aligned_cols=211 Identities=10% Similarity=0.005 Sum_probs=126.2
Q ss_pred EeEEEec-CCCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEE-ccCChhhHHH
Q 002211 52 VGAIFSF-GTVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIV-GPQSAVMAHV 129 (953)
Q Consensus 52 IG~l~~~-~~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aii-Gp~~S~~a~a 129 (953)
||++.|- +..+-.....+++-+.++....+ .| +.+.+.+...++.........++.+++.+|| .|........
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 7888764 34454566777777777765433 23 4555677777776666666668887777666 3444333333
Q ss_pred HHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHc--CCcEEEEEEecC-ccccchHHHHHHHH
Q 002211 130 LSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYF--GWGEVIAIFNDD-DQGRNGVTALGDKL 206 (953)
Q Consensus 130 v~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~--~w~~vaii~~d~-~~g~~~~~~l~~~l 206 (953)
....+.+.+||+|......+ +.. .....+.+++...+..+++++... |.++++++.... .......+.|.+.+
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 33456778999998754321 110 112235666677788888887765 789999997433 23344578899999
Q ss_pred HhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcC--CceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEEeC
Q 002211 207 AEIRCKISYKSALPPDQSVTETDVRNELVKVRMM--EARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIATT 277 (953)
Q Consensus 207 ~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~--~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~ 277 (953)
++.|+++... .... .+.......+.++.+. ++++|+.. +...+..+++++++.|.. .+...++.+
T Consensus 153 ~~~~~~~~~~--~~~~--~~~~~~~~~~~~~l~~~~~~~ai~~~-~d~~a~g~~~al~~~g~~-~~~~ivg~d 219 (274)
T cd06311 153 AKYPIKILDR--QYAN--WNRDDAFSVMQDLLTKFPKIDAVWAH-DDDMAVGVLAAIKQAGRT-DIKFVVGGA 219 (274)
T ss_pred hhCCcEEEec--cCCC--CcHHHHHHHHHHHHHhCCCcCEEEEC-CCcHHHHHHHHHHHcCCC-CCceEEEeC
Confidence 9888766532 2211 1223333445554333 35665544 344567788999998875 233344434
No 145
>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=97.88 E-value=0.0026 Score=68.05 Aligned_cols=208 Identities=11% Similarity=0.125 Sum_probs=125.7
Q ss_pred EEeEEEec-CCCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEE-ccCChhhHH
Q 002211 51 NVGAIFSF-GTVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIV-GPQSAVMAH 128 (953)
Q Consensus 51 ~IG~l~~~-~~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aii-Gp~~S~~a~ 128 (953)
+||++.|- ...+-.....+++-+.++- + |+++. +.++..++..-.+....++.+++.+|| .|.......
T Consensus 1 ~ig~~~~~~~~~~~~~~~~~i~~~~~~~---~----g~~~~--~~~~~~~~~~~~~~i~~~~~~~vdgiii~~~~~~~~~ 71 (270)
T cd06308 1 VIGFSQCNLADPWRAAMNDEIQREASNY---P----DVELI--IADAADDNSKQVADIENFIRQGVDLLIISPNEAAPLT 71 (270)
T ss_pred CEEEEeeCCCCHHHHHHHHHHHHHHHhc---C----CcEEE--EEcCCCCHHHHHHHHHHHHHhCCCEEEEecCchhhch
Confidence 58888874 3434444555555544442 1 45564 456666777667777778887777665 333332223
Q ss_pred HHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHc--CCcEEEEEEecCc--cccchHHHHHH
Q 002211 129 VLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYF--GWGEVIAIFNDDD--QGRNGVTALGD 204 (953)
Q Consensus 129 av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~--~w~~vaii~~d~~--~g~~~~~~l~~ 204 (953)
.....+.+.++|+|.+....+ +. .+...+..++...+..+++++.+. |-++++++..... ......+.+.+
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 334445678999998754221 11 233345667777888888887775 8899999974332 23445788999
Q ss_pred HHHhc-CcEEEEEEecCCCCCCChHHHHHHHHHHhc--CCceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEEeCc
Q 002211 205 KLAEI-RCKISYKSALPPDQSVTETDVRNELVKVRM--MEARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIATTW 278 (953)
Q Consensus 205 ~l~~~-g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~--~~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~ 278 (953)
.+++. |+++.... . .. .+..+....+.++.+ .++++|+. .+...+..+++.+++.|+. .+...++.|.
T Consensus 147 ~l~~~~~~~~~~~~-~-~~--~~~~~~~~~~~~~l~~~~~~~aI~~-~~d~~a~g~~~al~~~g~~-~dv~vvg~d~ 217 (270)
T cd06308 147 ALSKYPKIKIVAQQ-D-GD--WLKEKAEEKMEELLQANPDIDLVYA-HNDPMALGAYLAAKRAGRE-KEIKFIGIDG 217 (270)
T ss_pred HHHHCCCCEEEEec-C-CC--ccHHHHHHHHHHHHHhCCCCcEEEe-CCcHHHHHHHHHHHHcCCC-CCcEEEEecC
Confidence 99998 87765321 1 11 112233344455433 34676544 4556677899999999987 4555555543
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=97.83 E-value=0.004 Score=67.32 Aligned_cols=215 Identities=11% Similarity=0.037 Sum_probs=125.1
Q ss_pred EEeEEEecC-CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEEc-cCChhhHH
Q 002211 51 NVGAIFSFG-TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIVG-PQSAVMAH 128 (953)
Q Consensus 51 ~IG~l~~~~-~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aiiG-p~~S~~a~ 128 (953)
+||++.|.. ..+-.....+++.+.++. |+++. +.++. ++..-......++..++.+||= |..+....
T Consensus 1 ~Ig~v~~~~~~~~~~~~~~gi~~~~~~~--------g~~~~--~~~~~-~~~~~~~~i~~~~~~~~dgiii~~~~~~~~~ 69 (289)
T cd01540 1 KIGFIVKQPEEPWFQTEWKFAKKAAKEK--------GFTVV--KIDVP-DGEKVLSAIDNLGAQGAKGFVICVPDVKLGP 69 (289)
T ss_pred CeeeecCCCCCcHHHHHHHHHHHHHHHc--------CCEEE--EccCC-CHHHHHHHHHHHHHcCCCEEEEccCchhhhH
Confidence 588888853 445556677777777762 56655 45555 6666566667777778877663 33333445
Q ss_pred HHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHH----HcCC--cEEEEEE-e--cCccccchH
Q 002211 129 VLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVS----YFGW--GEVIAIF-N--DDDQGRNGV 199 (953)
Q Consensus 129 av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~----~~~w--~~vaii~-~--d~~~g~~~~ 199 (953)
.....+...++|+|......+.......+.+-.+..+....+..+++++. ..|+ +++++|. . +........
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 55667778999999875432211100112223345566666666666544 3566 6888875 2 223456678
Q ss_pred HHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCC--ceE-EEEEcchhhHHHHHHHHHHcCCCCCceEEEEe
Q 002211 200 TALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMME--ARV-IVVHGYSRTGLMVFDVAQRLGMMDSGYVWIAT 276 (953)
Q Consensus 200 ~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~--~~v-ii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~ 276 (953)
+.+.+.+++.|+........+... .+.+.....++++.... ++. .|++.+...+..+++.+++.|...++...++.
T Consensus 150 ~G~~~~l~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~l~~~~~~~~~~i~~~~d~~a~g~~~al~~~g~~~~di~vig~ 228 (289)
T cd01540 150 DGALEALKAPGFPEANIFQAPQKT-TDTEGAFDAAASTLTKNPNVKNWIIYGLNDETVLGAVRATEQSGIAAADVIGVGI 228 (289)
T ss_pred HHHHHHHhcCCCCcceEecccccC-cchhhHHHHHHHHHHhCCCcCeeEEEeCCcHHHHHHHHHHHHcCCCCcceEEEec
Confidence 899999998886532111111110 01122233445554433 453 45666667788899999999987434444444
Q ss_pred C
Q 002211 277 T 277 (953)
Q Consensus 277 ~ 277 (953)
+
T Consensus 229 d 229 (289)
T cd01540 229 N 229 (289)
T ss_pred C
Confidence 4
No 147
>PRK10355 xylF D-xylose transporter subunit XylF; Provisional
Probab=97.83 E-value=0.0047 Score=68.11 Aligned_cols=203 Identities=9% Similarity=-0.006 Sum_probs=125.2
Q ss_pred CCceEEEeEEEec-CCCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEEc-cCC
Q 002211 46 KPEVLNVGAIFSF-GTVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIVG-PQS 123 (953)
Q Consensus 46 ~~~~i~IG~l~~~-~~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aiiG-p~~ 123 (953)
.++..+||++.|- +..+......+++-+.++. |+.+.+ .++..++..-.+....++++++.+||= |..
T Consensus 22 ~~~~~~Ig~i~~~~~~~f~~~~~~gi~~~a~~~--------g~~l~i--~~~~~~~~~~~~~i~~l~~~~vDGiIi~~~~ 91 (330)
T PRK10355 22 HAKEVKIGMAIDDLRLERWQKDRDIFVKKAESL--------GAKVFV--QSANGNEETQMSQIENMINRGVDVLVIIPYN 91 (330)
T ss_pred cCCCceEEEEecCCCchHHHHHHHHHHHHHHHc--------CCEEEE--ECCCCCHHHHHHHHHHHHHcCCCEEEEeCCC
Confidence 3568999999985 4556666677777776653 455554 566677777667777788888887763 333
Q ss_pred hhhHHHHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEec---CccccchHH
Q 002211 124 AVMAHVLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFND---DDQGRNGVT 200 (953)
Q Consensus 124 S~~a~av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d---~~~g~~~~~ 200 (953)
..........+...++|+|......+ +. +....+..++...+..+++++...|-++++++... ...+....+
T Consensus 92 ~~~~~~~l~~~~~~~iPvV~id~~~~---~~--~~~~~V~~D~~~~g~~a~~~L~~~g~~~i~~i~~g~~~~~~~~~R~~ 166 (330)
T PRK10355 92 GQVLSNVIKEAKQEGIKVLAYDRMIN---NA--DIDFYISFDNEKVGELQAKALVDKVPQGNYFLMGGSPVDNNAKLFRA 166 (330)
T ss_pred hhhHHHHHHHHHHCCCeEEEECCCCC---CC--CccEEEecCHHHHHHHHHHHHHHhcCCCCEEEEeCCCCCccHHHHHH
Confidence 22223444566788999998754321 11 12234677888889999999888888887665432 223345577
Q ss_pred HHHHHHHhc---C-cEEEEEEecCCCCCCChHHHHHHHHHHhc---CCceEEEEEcchhhHHHHHHHHHHcCCC
Q 002211 201 ALGDKLAEI---R-CKISYKSALPPDQSVTETDVRNELVKVRM---MEARVIVVHGYSRTGLMVFDVAQRLGMM 267 (953)
Q Consensus 201 ~l~~~l~~~---g-~~v~~~~~~~~~~~~~~~d~~~~l~~i~~---~~~~vii~~~~~~~~~~~~~~a~~~g~~ 267 (953)
.+++.+++. | +.+....... . .+..+-...++++.+ ..+++|+. .+...+..+++.++++|+.
T Consensus 167 gf~~~l~~~~~~~~i~~~~~~~~~-~--~~~~~~~~~~~~lL~~~~~~~~aI~~-~nD~~A~g~l~al~~~g~~ 236 (330)
T PRK10355 167 GQMKVLKPYIDSGKIKVVGDQWVD-G--WLPENALKIMENALTANNNKIDAVVA-SNDATAGGAIQALSAQGLS 236 (330)
T ss_pred HHHHHHhhhccCCCeEEecccCCC-C--CCHHHHHHHHHHHHHhCCCCccEEEE-CCCchHHHHHHHHHHCCCC
Confidence 888888764 4 4442221111 1 112233344555432 34676554 4555667789999999975
No 148
>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=97.83 E-value=0.0019 Score=68.94 Aligned_cols=203 Identities=12% Similarity=0.057 Sum_probs=123.0
Q ss_pred EeEEEecC-----CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhc-CcEEEEccCChh
Q 002211 52 VGAIFSFG-----TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMET-DTLAIVGPQSAV 125 (953)
Q Consensus 52 IG~l~~~~-----~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~-~v~aiiGp~~S~ 125 (953)
||+++|.. ..+......+++.+.++ .|+.+.+...++. ....+.+.+++.+ ++.+||...+..
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 78888852 45555566677665555 2567766654433 2334556666654 688888643322
Q ss_pred hHHHHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecC--ccccchHHHHH
Q 002211 126 MAHVLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDD--DQGRNGVTALG 203 (953)
Q Consensus 126 ~a~av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~--~~g~~~~~~l~ 203 (953)
.. .....+.+.++|+|.+....+ ...+++ +..++...+..+++++...|-++++++.... ..+....+.|.
T Consensus 71 ~~-~~~~~~~~~~ipvV~~~~~~~---~~~~~~---V~~d~~~~~~~a~~~l~~~g~~~i~~i~~~~~~~~~~~R~~gf~ 143 (268)
T cd06271 71 DD-PRVALLLERGFPFVTHGRTEL---GDPHPW---VDFDNEAAAYQAVRRLIALGHRRIALLNPPEDLTFAQHRRAGYR 143 (268)
T ss_pred CC-hHHHHHHhcCCCEEEECCcCC---CCCCCe---EeeCcHHHHHHHHHHHHHcCCCcEEEecCccccchHHHHHHHHH
Confidence 22 223456678999998754322 123444 3356667778888888888999999997443 23455678899
Q ss_pred HHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcC--CceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEE
Q 002211 204 DKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMM--EARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIA 275 (953)
Q Consensus 204 ~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~--~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~ 275 (953)
+.+++.|..+.....+... .+.......+.++.+. .+++|+... ...+..+++++++.|+..++.+-+.
T Consensus 144 ~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~l~~~~~~~ai~~~~-d~~a~g~~~al~~~g~~vp~~i~ii 214 (268)
T cd06271 144 RALAEAGLPLDPALIVSGD--MTEEGGYAAAAELLALPDRPTAIVCSS-ELMALGVLAALAEAGLRPGRDVSVV 214 (268)
T ss_pred HHHHHhCCCCCCceEEeCC--CChHHHHHHHHHHHhCCCCCCEEEEcC-cHHHHHHHHHHHHhCCCCCcceeEE
Confidence 9999988754221112211 1233334455555433 367777654 4566789999999998765444333
No 149
>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=97.82 E-value=0.0021 Score=71.10 Aligned_cols=203 Identities=8% Similarity=0.023 Sum_probs=126.0
Q ss_pred ceEEEeEEEec-CCCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEE--ccCCh
Q 002211 48 EVLNVGAIFSF-GTVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIV--GPQSA 124 (953)
Q Consensus 48 ~~i~IG~l~~~-~~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aii--Gp~~S 124 (953)
..-.||+++|- +..+-.....+++-+.++ .|+++.+ .++..++..-......+.++++.+|| ++..+
T Consensus 58 ~~~~Igvv~~~~~~~f~~~l~~~i~~~~~~--------~g~~~~i--~~~~~~~~~~~~~~~~l~~~~vdGiIi~~~~~~ 127 (329)
T TIGR01481 58 RTTTVGVIIPDISNIYYAELARGIEDIATM--------YKYNIIL--SNSDEDPEKEVQVLNTLLSKQVDGIIFMGGTIT 127 (329)
T ss_pred CCCEEEEEeCCCCchhHHHHHHHHHHHHHH--------cCCEEEE--EeCCCCHHHHHHHHHHHHhCCCCEEEEeCCCCC
Confidence 45689999985 344444555666655554 2566654 34444555555556667777887766 43222
Q ss_pred hhHHHHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecC--c-cccchHHH
Q 002211 125 VMAHVLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDD--D-QGRNGVTA 201 (953)
Q Consensus 125 ~~a~av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~--~-~g~~~~~~ 201 (953)
..+...+.+.++|+|......+ ...+++ +..++...+..+++++...|.++++++..+. . .+....+.
T Consensus 128 ---~~~~~~l~~~~iPvV~~~~~~~---~~~~~~---V~~D~~~~~~~a~~~L~~~G~~~I~~i~g~~~~~~~~~~R~~G 198 (329)
T TIGR01481 128 ---EKLREEFSRSPVPVVLAGTVDK---ENELPS---VNIDYKQATKEAVGELIAKGHKSIAFVGGPLSDSINGEDRLEG 198 (329)
T ss_pred ---hHHHHHHHhcCCCEEEEecCCC---CCCCCE---EEECcHHHHHHHHHHHHHCCCCeEEEEecCcccccchHHHHHH
Confidence 2344556677999998754322 122332 4456666677788888888999999996432 2 24667889
Q ss_pred HHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHHHcCCCCCceE
Q 002211 202 LGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQRLGMMDSGYV 272 (953)
Q Consensus 202 l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~ 272 (953)
|.+++++.|+.+......... .+..+....+.++.+.+|++|+.. +...+..+++++++.|+..++-+
T Consensus 199 f~~~l~~~g~~~~~~~~~~~~--~~~~~~~~~~~~ll~~~p~ai~~~-~d~~A~g~~~al~~~g~~vP~dv 266 (329)
T TIGR01481 199 YKEALNKAGIQFGEDLVCEGK--YSYDAGYKAFAELKGSLPTAVFVA-SDEMAAGILNAAMDAGIKVPEDL 266 (329)
T ss_pred HHHHHHHcCCCCCcceEEecC--CChHHHHHHHHHHhCCCCCEEEEc-CcHHHHHHHHHHHHcCCCCCCce
Confidence 999999998764322111111 112333455666666678877764 44577889999999998655433
No 150
>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=97.81 E-value=0.0017 Score=69.48 Aligned_cols=201 Identities=9% Similarity=-0.014 Sum_probs=124.3
Q ss_pred EEeEEEec-CCCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEEccCChhhHHH
Q 002211 51 NVGAIFSF-GTVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIVGPQSAVMAHV 129 (953)
Q Consensus 51 ~IG~l~~~-~~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aiiGp~~S~~a~a 129 (953)
.||+++|. +..+-.....+++-++++. |+.+. +.++..++....+....+++++|.+||--.+......
T Consensus 1 ~Igvv~~~~~~~~~~~~~~~i~~~a~~~--------g~~~~--~~~~~~~~~~~~~~i~~l~~~~vdgii~~~~~~~~~~ 70 (269)
T cd06281 1 TIGCLVSDITNPLLAQLFSGAEDRLRAA--------GYSLL--IANSLNDPERELEILRSFEQRRMDGIIIAPGDERDPE 70 (269)
T ss_pred CEEEEecCCccccHHHHHHHHHHHHHHc--------CCEEE--EEeCCCChHHHHHHHHHHHHcCCCEEEEecCCCCcHH
Confidence 48999985 3555556677777777762 55644 5567777776667777777778888774222222344
Q ss_pred HHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecC--ccccchHHHHHHHHH
Q 002211 130 LSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDD--DQGRNGVTALGDKLA 207 (953)
Q Consensus 130 v~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~--~~g~~~~~~l~~~l~ 207 (953)
+...+.+.++|+|......+ . ..++ +..++..-+..+++.+...|-++++++.... ..+....+.|.+.++
T Consensus 71 ~~~~~~~~~ipvV~i~~~~~--~--~~~~---V~~d~~~~g~~a~~~l~~~G~~~i~~l~~~~~~~~~~~R~~Gf~~~~~ 143 (269)
T cd06281 71 LVDALASLDLPIVLLDRDMG--G--GADA---VLFDHAAGMRQAVEYLISLGHRRIALVGGGSNTRPGRERLEGYKAAFA 143 (269)
T ss_pred HHHHHHhCCCCEEEEecccC--C--CCCE---EEECcHHHHHHHHHHHHHCCCcEEEEecCccccccHHHHHHHHHHHHH
Confidence 55667778999998865433 1 2232 3444555557777887778999999997532 233455688999999
Q ss_pred hcCcEEEEEEecCCCCCCChHHHHHHHHHHhc--CCceEEEEEcchhhHHHHHHHHHHcCCCCCceE
Q 002211 208 EIRCKISYKSALPPDQSVTETDVRNELVKVRM--MEARVIVVHGYSRTGLMVFDVAQRLGMMDSGYV 272 (953)
Q Consensus 208 ~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~--~~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~ 272 (953)
+.|+.+.....+..+ . .......+.++.+ ..+++|+. .+...+..+++.+++.|+..++.+
T Consensus 144 ~~~~~~~~~~~~~~~--~-~~~~~~~~~~~l~~~~~~~ai~~-~~d~~a~g~~~~l~~~g~~ip~dv 206 (269)
T cd06281 144 AAGLPPDPALVRLST--P-AASGFDATRALLALPDRPTAIIA-GGTQVLVGVLRALREAGLRIPRDL 206 (269)
T ss_pred HcCCCCCHHHeecCc--H-HHHHHHHHHHHHcCCCCCcEEEE-cCcHHHHHHHHHHHHcCCCCCcce
Confidence 888754211111111 1 1222334545433 34788764 455566678999999998655444
No 151
>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=97.80 E-value=0.0016 Score=69.44 Aligned_cols=203 Identities=12% Similarity=0.044 Sum_probs=125.8
Q ss_pred EEeEEEecC--CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEEccCChhhHH
Q 002211 51 NVGAIFSFG--TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIVGPQSAVMAH 128 (953)
Q Consensus 51 ~IG~l~~~~--~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aiiGp~~S~~a~ 128 (953)
.||+++|.. ..+......+++-+.++. |+.+. +.++..++..-......+...++.+||-........
T Consensus 1 ~ig~v~~~~~~~~~~~~~~~~i~~~~~~~--------g~~~~--~~~~~~~~~~~~~~~~~l~~~~~dgiii~~~~~~~~ 70 (269)
T cd06288 1 TIGLISDEIATTPFAVEIILGAQDAAREH--------GYLLL--VVNTGGDDELEAEAVEALLDHRVDGIIYATMYHREV 70 (269)
T ss_pred CeEEEeCCCCCCccHHHHHHHHHHHHHHC--------CCEEE--EEeCCCCHHHHHHHHHHHHHcCCCEEEEecCCCChh
Confidence 489999874 455556677777777662 55554 345555555555566677777888877643322111
Q ss_pred HHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecCc--cccchHHHHHHHH
Q 002211 129 VLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDDD--QGRNGVTALGDKL 206 (953)
Q Consensus 129 av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~~--~g~~~~~~l~~~l 206 (953)
.......++|+|......+. ..++ .+.+++...+..+++++...|-++++++..+.. ......+.|.+.+
T Consensus 71 --~~~~~~~~ipvv~~~~~~~~---~~~~---~v~~d~~~~~~~a~~~l~~~g~~~i~~l~~~~~~~~~~~R~~gf~~~~ 142 (269)
T cd06288 71 --TLPPELLSVPTVLLNCYDAD---GALP---SVVPDEEQGGYDATRHLLAAGHRRIAFINGEPWMLAAKDRLKGYRQAL 142 (269)
T ss_pred --HHHHHhcCCCEEEEecccCC---CCCC---eEEEccHHHHHHHHHHHHHcCCceEEEEeCCccchhHHHHHHHHHHHH
Confidence 22335578999987543321 1223 355677777888999888889999999985432 3455678899999
Q ss_pred HhcCcEEEE--EEecCCCCCCChHHHHHHHHHHhcC--CceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEEe
Q 002211 207 AEIRCKISY--KSALPPDQSVTETDVRNELVKVRMM--EARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIAT 276 (953)
Q Consensus 207 ~~~g~~v~~--~~~~~~~~~~~~~d~~~~l~~i~~~--~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~ 276 (953)
++.|+.+.. ....... ..+....++++.+. ++++|+. .+...+..+++++++.|+..++-+.+.+
T Consensus 143 ~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~l~~~~~~~ai~~-~~d~~a~~~~~~l~~~g~~vp~di~v~g 211 (269)
T cd06288 143 AEAGIPFDPDLVVHGDWS----ADDGYEAAAALLDLDDRPTAIFC-GNDRMAMGAYQALLERGLRIPQDVSVVG 211 (269)
T ss_pred HHcCCCCCHHHeEeCCCC----hHHHHHHHHHHHhCCCCCCEEEE-eCcHHHHHHHHHHHHcCCCCcccceEEe
Confidence 988865321 1111211 23344455665444 4677755 4455677789999999986554454444
No 152
>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=97.80 E-value=0.0044 Score=66.24 Aligned_cols=206 Identities=9% Similarity=-0.013 Sum_probs=125.6
Q ss_pred EEeEEEecC-CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEE-ccCChhhHH
Q 002211 51 NVGAIFSFG-TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIV-GPQSAVMAH 128 (953)
Q Consensus 51 ~IG~l~~~~-~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aii-Gp~~S~~a~ 128 (953)
+||+++|-. ..+-.....+++-+.++. |..+.+++.++..++..-.+....++++++.+|| .|.......
T Consensus 1 ~Ig~v~~~~~~~~~~~~~~gi~~~~~~~--------~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~dgiIi~~~~~~~~~ 72 (271)
T cd06321 1 KIGVSVGDLGNPFFVALAKGAEAAAKKL--------NPGVKVTVVSADYDLNKQVSQIDNFIAAKVDLILLNAVDSKGIA 72 (271)
T ss_pred CeEEEecccCCHHHHHHHHHHHHHHHHh--------CCCeEEEEccCCCCHHHHHHHHHHHHHhCCCEEEEeCCChhHhH
Confidence 489999864 444445667777777764 2334555667777777666666777777777654 444333223
Q ss_pred HHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHc--CCcEEEEEEecC-ccccchHHHHHHH
Q 002211 129 VLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYF--GWGEVIAIFNDD-DQGRNGVTALGDK 205 (953)
Q Consensus 129 av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~--~w~~vaii~~d~-~~g~~~~~~l~~~ 205 (953)
.....+.+.++|+|......+ + . ...+..++...+..+++++... |.++++++.... .......+.+.+.
T Consensus 73 ~~i~~~~~~~ipvv~~~~~~~---~-~---~~~V~~d~~~~g~~~~~~l~~~~~g~~~i~~i~g~~~~~~~~R~~g~~~~ 145 (271)
T cd06321 73 PAVKRAQAAGIVVVAVDVAAE---G-A---DATVTTDNVQAGEISCQYLADRLGGKGNVAILNGPPVSAVLDRVAGCKAA 145 (271)
T ss_pred HHHHHHHHCCCeEEEecCCCC---C-c---cceeeechHHHHHHHHHHHHHHhCCCceEEEEeCCCCchHHHHHHHHHHH
Confidence 333455677999999865332 1 1 1235667777888888988777 999999997542 2344557888999
Q ss_pred HHhc-CcEEEEEEecCCCCCCChHHHHHHHHHHhcC--CceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEEeC
Q 002211 206 LAEI-RCKISYKSALPPDQSVTETDVRNELVKVRMM--EARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIATT 277 (953)
Q Consensus 206 l~~~-g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~--~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~ 277 (953)
+++. +++..... .... .+...-...+.++.+. ++++|+.. +...+..+++.+++.|+ .+..+++.+
T Consensus 146 ~~~~~~~~~~~~~-~~~~--~~~~~~~~~~~~~l~~~~~~~ai~~~-~d~~a~g~~~al~~~g~--~di~v~g~d 214 (271)
T cd06321 146 LAKYPGIKLLSDD-QNGK--GSRDGGLRVMQGLLTRFPKLDGVFAI-NDPTAIGADLAAKQAGR--NDIKITSVD 214 (271)
T ss_pred HHhCCCcEEEeee-cCCC--CChhhHHHHHHHHHHhCCCCCEEEEC-CchhHHHHHHHHHHcCC--CCcEEEEec
Confidence 9887 56533211 1111 1122223345555433 45765554 44566778899999997 344455444
No 153
>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=97.78 E-value=0.0062 Score=64.91 Aligned_cols=194 Identities=15% Similarity=0.084 Sum_probs=120.1
Q ss_pred EeEEEecC-CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEEc-cCChhhHHH
Q 002211 52 VGAIFSFG-TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIVG-PQSAVMAHV 129 (953)
Q Consensus 52 IG~l~~~~-~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aiiG-p~~S~~a~a 129 (953)
||++.|.. ..+-.....+++-+.++ .|+++. +.++..++....+....++++++.++|- |..+.....
T Consensus 2 i~~~~~~~~~~~~~~~~~~i~~~~~~--------~g~~~~--i~~~~~~~~~~~~~~~~~~~~~vdgiii~~~~~~~~~~ 71 (267)
T cd06322 2 IGASLLTQQHPFYIELANAMKEEAKK--------QKVNLI--VSIANQDLNKQLSDVEDFITKKVDAIVLSPVDSKGIRA 71 (267)
T ss_pred eeEeecCcccHHHHHHHHHHHHHHHh--------cCCEEE--EecCCCCHHHHHHHHHHHHHcCCCEEEEcCCChhhhHH
Confidence 78888864 23334455666655554 145554 5677778877777888888888888775 444333333
Q ss_pred HHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHc--CCcEEEEEEecC-ccccchHHHHHHHH
Q 002211 130 LSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYF--GWGEVIAIFNDD-DQGRNGVTALGDKL 206 (953)
Q Consensus 130 v~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~--~w~~vaii~~d~-~~g~~~~~~l~~~l 206 (953)
....+.+.++|+|.+....+ ..+.+..+.+++...+...++++... |-+++++++..+ .......+.|++++
T Consensus 72 ~~~~~~~~~ipvV~~~~~~~-----~~~~~~~v~~d~~~~g~~~~~~l~~~~~g~~~i~~i~~~~~~~~~~R~~gf~~~~ 146 (267)
T cd06322 72 AIAKAKKAGIPVITVDIAAE-----GVAVVSHVATDNYAGGVLAGELAAKVLNGKGQVAIIDYPTVQSVVDRVRGFKEAL 146 (267)
T ss_pred HHHHHHHCCCCEEEEcccCC-----CCceEEEEecChHHHHHHHHHHHHHHhCCCceEEEEecCCCccHHHHHHHHHHHH
Confidence 44556778999998753211 11223345666667777888887765 788999997432 23445678899999
Q ss_pred Hhc-CcEEEEEEecCCCCCCChHHHHHHHHHHhcC--CceEEEEEcchhhHHHHHHHHHHcCC
Q 002211 207 AEI-RCKISYKSALPPDQSVTETDVRNELVKVRMM--EARVIVVHGYSRTGLMVFDVAQRLGM 266 (953)
Q Consensus 207 ~~~-g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~--~~~vii~~~~~~~~~~~~~~a~~~g~ 266 (953)
++. |+++... ... .+.+.....+.++... ++++|+. .+...+..+++.+++.|.
T Consensus 147 ~~~~~~~~~~~---~~~--~~~~~~~~~~~~~l~~~~~~~ai~~-~~d~~a~~~~~al~~~g~ 203 (267)
T cd06322 147 ADYPNIKIVAV---QPG--ITRAEALTAAQNILQANPDLDGIFA-FGDDAALGAVSAIKAAGR 203 (267)
T ss_pred HhCCCcEEEEe---cCC--CChHHHHHHHHHHHHhCCCCCEEEE-cCCcHHHHHHHHHHHCCC
Confidence 988 8876422 111 1123333344554333 4665544 444556778899999997
No 154
>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=97.78 E-value=0.0055 Score=65.60 Aligned_cols=197 Identities=11% Similarity=0.082 Sum_probs=122.2
Q ss_pred CchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEEc-cCChhhHHHHHHhhhhCCC
Q 002211 61 VNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIVG-PQSAVMAHVLSHLANELQV 139 (953)
Q Consensus 61 ~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aiiG-p~~S~~a~av~~v~~~~~v 139 (953)
++-.....+++-+.++ .|+++. +.++..++..-.+....++.+++.+||= |..+........-+.+.++
T Consensus 12 ~f~~~~~~gi~~~~~~--------~G~~~~--~~~~~~d~~~~~~~i~~~~~~~vdgiii~~~~~~~~~~~i~~~~~~~i 81 (272)
T cd06313 12 TWCAQGKQAADEAGKL--------LGVDVT--WYGGALDAVKQVAAIENMASQGWDFIAVDPLGIGTLTEAVQKAIARGI 81 (272)
T ss_pred hHHHHHHHHHHHHHHH--------cCCEEE--EecCCCCHHHHHHHHHHHHHcCCCEEEEcCCChHHhHHHHHHHHHCCC
Confidence 3334445566655554 155555 4566678888888888888888877664 4444434444455667799
Q ss_pred cEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHc--CCcEEEEEEecC--ccccchHHHHHHHHHhcC-cEEE
Q 002211 140 PLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYF--GWGEVIAIFNDD--DQGRNGVTALGDKLAEIR-CKIS 214 (953)
Q Consensus 140 P~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~--~w~~vaii~~d~--~~g~~~~~~l~~~l~~~g-~~v~ 214 (953)
|+|......+ ....+.+..+.+++...+..+++++.+. |.++++++..+. .......+.|.+.+++.+ .++.
T Consensus 82 PvV~~~~~~~---~~~~~~~~~v~~d~~~~g~~~~~~l~~~~~g~~~i~~l~g~~~~~~~~~R~~gf~~~~~~~~~~~~~ 158 (272)
T cd06313 82 PVIDMGTLIA---PLQINVHSFLAPDNYFMGASVAQALCNAMGGKGKIAMLQGALGHTGAQGRAQGFNDVIKKYPDIEVV 158 (272)
T ss_pred cEEEeCCCCC---CCCCceEEEECCCcHHHHHHHHHHHHHHcCCCceEEEEECCCCCcchhHHHHHHHHHHHhCCCCEEE
Confidence 9998755332 1111223456677788889999998776 889999997543 233456889999998875 5554
Q ss_pred EEEecCCCCCCChHHHHHHHHHHhcCC--ceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEEeC
Q 002211 215 YKSALPPDQSVTETDVRNELVKVRMME--ARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIATT 277 (953)
Q Consensus 215 ~~~~~~~~~~~~~~d~~~~l~~i~~~~--~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~ 277 (953)
.. .... .+.......++++.+.+ +++|+. .+...+..+++.+++.|+ .+...++-+
T Consensus 159 ~~--~~~~--~~~~~~~~~~~~~l~~~~~~~ai~~-~nd~~a~g~~~al~~~g~--~di~vvgfd 216 (272)
T cd06313 159 DE--QPAN--WDVSKAARIWETWLTKYPQLDGAFC-HNDSMALAAYQIMKAAGR--TKIVIGGVD 216 (272)
T ss_pred ec--cCCC--CCHHHHHHHHHHHHHhCCCCCEEEE-CCCcHHHHHHHHHHHcCC--CceEEEeec
Confidence 31 1211 12334445566654433 565444 455667788999999997 344444433
No 155
>PRK15408 autoinducer 2-binding protein lsrB; Provisional
Probab=97.75 E-value=0.013 Score=64.71 Aligned_cols=199 Identities=12% Similarity=-0.014 Sum_probs=114.9
Q ss_pred EEEeEEEecC-CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEEc-cCChhhH
Q 002211 50 LNVGAIFSFG-TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIVG-PQSAVMA 127 (953)
Q Consensus 50 i~IG~l~~~~-~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aiiG-p~~S~~a 127 (953)
.+||++.... .++-.....|++-|.++. |+++.+. ..+..++..-++....+++++|.+|+= |..+...
T Consensus 24 ~~i~~v~k~~~~pf~~~~~~Gi~~aa~~~--------G~~v~~~-~~~~~d~~~q~~~i~~li~~~vdgIiv~~~d~~al 94 (336)
T PRK15408 24 ERIAFIPKLVGVGFFTSGGNGAKEAGKEL--------GVDVTYD-GPTEPSVSGQVQLINNFVNQGYNAIIVSAVSPDGL 94 (336)
T ss_pred cEEEEEECCCCCHHHHHHHHHHHHHHHHh--------CCEEEEE-CCCCCCHHHHHHHHHHHHHcCCCEEEEecCCHHHH
Confidence 3789887654 455556667777777653 5666542 334556666667778899998887764 5555544
Q ss_pred HHHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHH-c--CCcEEEEEEecCc--cccchHHHH
Q 002211 128 HVLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSY-F--GWGEVIAIFNDDD--QGRNGVTAL 202 (953)
Q Consensus 128 ~av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~-~--~w~~vaii~~d~~--~g~~~~~~l 202 (953)
.....-+...+||+|.+.+..+. +. ..++-...++...+..+++++.+ + +-.+++++..... ......+.+
T Consensus 95 ~~~l~~a~~~gIpVV~~d~~~~~--~~--~~~~V~~~~~~~~G~~~~~~l~~~l~~g~gki~il~g~~~~~~~~~r~~g~ 170 (336)
T PRK15408 95 CPALKRAMQRGVKVLTWDSDTKP--EC--RSYYINQGTPEQLGSMLVEMAAKQVGKDKAKVAFFYSSPTVTDQNQWVKEA 170 (336)
T ss_pred HHHHHHHHHCCCeEEEeCCCCCC--cc--ceEEEecCCHHHHHHHHHHHHHHhcCCCCCEEEEEECCCCCccHHHHHHHH
Confidence 56667778889999997654221 11 11121112334567666777654 2 4568888874322 223345667
Q ss_pred HHHHHhc--CcEEEEEEecCCCCCCChHHHHHHHHHHhcCCce--EEEEEcchhhHHHHHHHHHHcCC
Q 002211 203 GDKLAEI--RCKISYKSALPPDQSVTETDVRNELVKVRMMEAR--VIVVHGYSRTGLMVFDVAQRLGM 266 (953)
Q Consensus 203 ~~~l~~~--g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~--vii~~~~~~~~~~~~~~a~~~g~ 266 (953)
.+.+++. +++++... +. . .+...-....+++.++.|| +|+.. ....+...++++++.|.
T Consensus 171 ~~~l~~~~p~~~vv~~~-~~-~--~d~~~a~~~~~~lL~~~pdi~aI~~~-~~~~~~Ga~~Al~~~g~ 233 (336)
T PRK15408 171 KAKIAKEHPGWEIVTTQ-FG-Y--NDATKSLQTAEGILKAYPDLDAIIAP-DANALPAAAQAAENLKR 233 (336)
T ss_pred HHHHHhhCCCCEEEeec-CC-C--CcHHHHHHHHHHHHHHCCCCcEEEEC-CCccHHHHHHHHHhCCC
Confidence 7777543 56766432 11 1 1233334456666555554 55443 33333457888888886
No 156
>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=97.73 E-value=0.0028 Score=67.69 Aligned_cols=206 Identities=9% Similarity=-0.032 Sum_probs=124.7
Q ss_pred EEeEEEecC-CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEEccCChhhHHH
Q 002211 51 NVGAIFSFG-TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIVGPQSAVMAHV 129 (953)
Q Consensus 51 ~IG~l~~~~-~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aiiGp~~S~~a~a 129 (953)
.||++.|-. ..+......+++-+.++. |+++. +.++..++..-.+....+..+++.+||=.........
T Consensus 1 ~igvi~~~~~~~~~~~~~~gi~~~~~~~--------g~~~~--~~~~~~~~~~~~~~i~~l~~~~vdgiii~~~~~~~~~ 70 (269)
T cd06275 1 TIGMLVTTSTNPFFAEVVRGVEQYCYRQ--------GYNLI--LCNTEGDPERQRSYLRMLAQKRVDGLLVMCSEYDQPL 70 (269)
T ss_pred CEEEEeCCCCcchHHHHHHHHHHHHHHc--------CCEEE--EEeCCCChHHHHHHHHHHHHcCCCEEEEecCCCChHH
Confidence 378888853 455566677777777662 55554 4566667776667777888887776663222112222
Q ss_pred HHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEec--CccccchHHHHHHHHH
Q 002211 130 LSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFND--DDQGRNGVTALGDKLA 207 (953)
Q Consensus 130 v~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d--~~~g~~~~~~l~~~l~ 207 (953)
+..+....++|+|......+ +..+++ +..++...+..+++++...|-++++++... +.......+.|.+.++
T Consensus 71 ~~~l~~~~~ipvV~i~~~~~---~~~~~~---V~~d~~~~~~~~~~~l~~~G~~~i~~i~~~~~~~~~~~r~~gf~~~~~ 144 (269)
T cd06275 71 LAMLERYRHIPMVVMDWGPE---DDFADK---IQDNSEEGGYLATRHLIELGHRRIGCITGPLEKAPAQQRLAGFRRAMA 144 (269)
T ss_pred HHHHHhcCCCCEEEEecccC---CCCCCe---EeeCcHHHHHHHHHHHHHCCCceEEEEeCCCCCccHHHHHHHHHHHHH
Confidence 23333456999998754322 122333 445566677888888888899999999743 2334456788999999
Q ss_pred hcCcEEEEEEecCCCCCCChHHHHHHHHHHhcC--CceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEE
Q 002211 208 EIRCKISYKSALPPDQSVTETDVRNELVKVRMM--EARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIA 275 (953)
Q Consensus 208 ~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~--~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~ 275 (953)
+.|+++......... .+.......++++.+. .+++|+. .+...+..+++.+++.|...++.+-+.
T Consensus 145 ~~~~~~~~~~~~~~~--~~~~~~~~~~~~~l~~~~~~~ai~~-~~d~~a~g~~~~l~~~g~~vp~di~vv 211 (269)
T cd06275 145 EAGLPVNPGWIVEGD--FECEGGYEAMQRLLAQPKRPTAVFC-GNDLMAMGALCAAQEAGLRVPQDLSII 211 (269)
T ss_pred HcCCCCCHHHhccCC--CChHHHHHHHHHHHcCCCCCcEEEE-CChHHHHHHHHHHHHcCCCCCcceEEE
Confidence 888764321111111 1123344556666544 3565554 445566788899999997655444444
No 157
>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=97.72 E-value=0.007 Score=64.62 Aligned_cols=196 Identities=11% Similarity=-0.038 Sum_probs=121.3
Q ss_pred EEeEEEec-CCCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEEc-cCChhhHH
Q 002211 51 NVGAIFSF-GTVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIVG-PQSAVMAH 128 (953)
Q Consensus 51 ~IG~l~~~-~~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aiiG-p~~S~~a~ 128 (953)
+||++.|. +..+-.....+++-+.++. |+++.+...+...+...-.+....++++++.+||= |.......
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 58999985 3444456667777777753 45555432222234455556677788888887763 33332222
Q ss_pred HHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCC-----cEEEEEEecC--ccccchHHH
Q 002211 129 VLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGW-----GEVIAIFNDD--DQGRNGVTA 201 (953)
Q Consensus 129 av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w-----~~vaii~~d~--~~g~~~~~~ 201 (953)
....+...++|+|......+ +. .....+..++...+..+++++.+.+- ++++++.... .......+.
T Consensus 73 -~~~~~~~~giPvV~~~~~~~---~~--~~~~~V~~d~~~~g~~~~~~l~~~g~~~~~~~~i~~l~g~~~~~~~~~R~~g 146 (268)
T cd06306 73 -EILQQVAASIPVIALVNDIN---SP--DITAKVGVSWYEMGYQAGEYLAQRHPKGSKPAKVAWFPGPKGAGWVKAVEKG 146 (268)
T ss_pred -HHHHHHHCCCCEEEeccCCC---Cc--ceeEEecCChHHHHHHHHHHHHHHhhcCCCCceEEEEeCCCCCchHHHHHHH
Confidence 23446778999998743211 11 12234566777778888898877775 8999997532 345566788
Q ss_pred HHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhc--CCceEEEEEcchhhHHHHHHHHHHcCC
Q 002211 202 LGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRM--MEARVIVVHGYSRTGLMVFDVAQRLGM 266 (953)
Q Consensus 202 l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~--~~~~vii~~~~~~~~~~~~~~a~~~g~ 266 (953)
|.+++++.++++... .... .+...-...++++.+ .++++|+. . ...+..+++.+++.|+
T Consensus 147 ~~~~~~~~~~~~~~~--~~~~--~~~~~~~~~~~~~l~~~~~~~~i~~-~-d~~a~~~~~~l~~~g~ 207 (268)
T cd06306 147 FRDALAGSAIEISAI--KYGD--TGKEVQRKLVEEALEAHPDIDYIVG-S-AVAAEAAVGILRQRGL 207 (268)
T ss_pred HHHHHhhcCcEEeee--ccCC--ccHHHHHHHHHHHHHhCCCcCEEee-c-chhhhHHHHHHHhcCC
Confidence 999999999877542 1111 123334445555543 34677764 3 6777889999999996
No 158
>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=97.72 E-value=0.0082 Score=65.07 Aligned_cols=211 Identities=11% Similarity=0.052 Sum_probs=120.9
Q ss_pred EEeEEEecC-CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEE-ccCChhhHH
Q 002211 51 NVGAIFSFG-TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIV-GPQSAVMAH 128 (953)
Q Consensus 51 ~IG~l~~~~-~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aii-Gp~~S~~a~ 128 (953)
|||++.|-- ..+-.....+++-+.++ . |+++.++ .++..++..-.+....++.+++.+|| .|.......
T Consensus 1 ~i~~i~~~~~~~~~~~~~~gi~~~a~~---~-----g~~~~~~-~~~~~~~~~~~~~l~~~~~~~~dgiii~~~~~~~~~ 71 (294)
T cd06316 1 KAAIVMHTSGSDWSNAQVRGAKDEFAK---L-----GIEVVAT-TDAQFDPAKQVADIETTISQKPDIIISIPVDPVSTA 71 (294)
T ss_pred CeEEEecCCCChHHHHHHHHHHHHHHH---c-----CCEEEEe-cCCCCCHHHHHHHHHHHHHhCCCEEEEcCCCchhhh
Confidence 688888742 32323344444433333 1 5666433 45667777777777788888887665 443333233
Q ss_pred HHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHc--CCcEEEEEEecCc--cccchHHHHHH
Q 002211 129 VLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYF--GWGEVIAIFNDDD--QGRNGVTALGD 204 (953)
Q Consensus 129 av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~--~w~~vaii~~d~~--~g~~~~~~l~~ 204 (953)
.+...+.+.++|+|.+....+.... .-+++..+..++..-+..+++++... |-++++++..+.+ ......+.|.+
T Consensus 72 ~~i~~~~~~~iPvV~~~~~~~~~~~-~~~~~~~v~~d~~~~g~~~~~~l~~~~~g~~~i~~l~~~~~~~~~~~R~~gf~~ 150 (294)
T cd06316 72 AAYKKVAEAGIKLVFMDNVPSGLEH-GKDYAGIVTDDNYGNGQIAADALAKALPGKGKVGLIYHGADYFVTNQRDQGFKE 150 (294)
T ss_pred HHHHHHHHcCCcEEEecCCCccccc-CcceEEEEccCcHHHHHHHHHHHHHHhCCCceEEEEeCCCCcccHHHHHHHHHH
Confidence 4445667789999987654332221 11233445566666678888887766 7899999975433 33445788888
Q ss_pred HHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcC--CceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEEeC
Q 002211 205 KLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMM--EARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIATT 277 (953)
Q Consensus 205 ~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~--~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~ 277 (953)
.+++.+..+......... +.......++++... ++++|+.. +...+..+++.+++.|+ .+...++.+
T Consensus 151 ~l~~~~~~~~~~~~~~~~---~~~~~~~~~~~~l~~~~~~~ai~~~-~d~~a~g~~~~l~~~g~--~di~vvg~d 219 (294)
T cd06316 151 TIKKNYPDITIVAEKGID---GPSKAEDIANAMLTQNPDLKGIYAV-WDVPAEGVIAALRAAGR--DDIKVTTVD 219 (294)
T ss_pred HHHHhCCCcEEEeecCCc---chhHHHHHHHHHHHhCCCeeEEEeC-CCchhHHHHHHHHHcCC--CCceEEEeC
Confidence 888765332111111111 012223344554333 45665544 45568889999999987 343444444
No 159
>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=97.72 E-value=0.0042 Score=66.20 Aligned_cols=205 Identities=10% Similarity=0.027 Sum_probs=123.9
Q ss_pred EEeEEEecC-CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEEccCChhhHHH
Q 002211 51 NVGAIFSFG-TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIVGPQSAVMAHV 129 (953)
Q Consensus 51 ~IG~l~~~~-~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aiiGp~~S~~a~a 129 (953)
.||++.|.. ..+-.....+++-+.++. |+.+.+ .++..++..-.+....++.+++.+||--..... ..
T Consensus 1 ~Ig~i~~~~~~~~~~~~~~gi~~~~~~~--------g~~~~~--~~~~~~~~~~~~~~~~l~~~~vdgiii~~~~~~-~~ 69 (268)
T cd01575 1 LVAVLVPSLSNSVFADVLQGISDVLEAA--------GYQLLL--GNTGYSPEREEELLRTLLSRRPAGLILTGLEHT-ER 69 (268)
T ss_pred CEEEEeCCCcchhHHHHHHHHHHHHHHc--------CCEEEE--ecCCCCchhHHHHHHHHHHcCCCEEEEeCCCCC-HH
Confidence 378898863 333344556666666652 555544 555556666566777788888888774222111 23
Q ss_pred HHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecC--ccccchHHHHHHHHH
Q 002211 130 LSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDD--DQGRNGVTALGDKLA 207 (953)
Q Consensus 130 v~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~--~~g~~~~~~l~~~l~ 207 (953)
....+...++|+|......+ . +....+..+....+..+++++...|-++++++..+. .......+.|.+.++
T Consensus 70 ~~~~~~~~~ipvv~~~~~~~---~---~~~~~v~~d~~~~~~~~~~~l~~~g~~~i~~i~~~~~~~~~~~r~~gf~~~l~ 143 (268)
T cd01575 70 TRQLLRAAGIPVVEIMDLPP---D---PIDMAVGFSHAEAGRAMARHLLARGYRRIGFLGARMDDTRAQQRLEGFRAALR 143 (268)
T ss_pred HHHHHHhcCCCEEEEecCCC---C---CCCCeEEeCcHHHHHHHHHHHHHCCCCcEEEecCCCCcccHHHHHHHHHHHHH
Confidence 34456677999998743221 1 112234556677788888998888999999998653 344556788999999
Q ss_pred hcCcEEEEEEecCCCCCCChHHHHHHHHHHhcC--CceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEE
Q 002211 208 EIRCKISYKSALPPDQSVTETDVRNELVKVRMM--EARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIA 275 (953)
Q Consensus 208 ~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~--~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~ 275 (953)
+.|............ .+.......+.++.+. ++++|+. .+...+..+++.+++.|...++.+-+.
T Consensus 144 ~~~~~~~~~~~~~~~--~~~~~~~~~~~~~l~~~~~~~ai~~-~~d~~a~~~~~~l~~~g~~~p~di~vi 210 (268)
T cd01575 144 AAGLDPPLVVTTPEP--SSFALGRELLAELLARWPDLDAVFC-SNDDLALGALFECQRRGISVPEDIAIA 210 (268)
T ss_pred HcCCCCCceeEeccC--CCHHHHHHHHHHHHhCCCCCCEEEE-CCcHHHHHHHHHHHHhCCCCCcceEEE
Confidence 888632221111111 1133344555565433 4677665 444556788999999997655444333
No 160
>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=97.72 E-value=0.007 Score=65.39 Aligned_cols=199 Identities=10% Similarity=0.066 Sum_probs=121.4
Q ss_pred EEeEEEec-CCCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEE-ccCChhhHH
Q 002211 51 NVGAIFSF-GTVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIV-GPQSAVMAH 128 (953)
Q Consensus 51 ~IG~l~~~-~~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aii-Gp~~S~~a~ 128 (953)
+||+++|. +..+-.....+++-+.++. |+.+. +.++..++..-.+...+++.+++.+|| .|..+....
T Consensus 1 ~I~vi~~~~~~~~~~~~~~gi~~~a~~~--------g~~~~--~~~~~~~~~~~~~~i~~~~~~~vdgiii~~~~~~~~~ 70 (288)
T cd01538 1 KIGLSLPTKTEERWIRDRPNFEAALKEL--------GAEVI--VQNANGDPAKQISQIENMIAKGVDVLVIAPVDGEALA 70 (288)
T ss_pred CeEEEEeCCCcHHHHHHHHHHHHHHHHc--------CCEEE--EECCCCCHHHHHHHHHHHHHcCCCEEEEecCChhhHH
Confidence 48999985 3444455566777666652 45544 466777777777777788888888776 444333334
Q ss_pred HHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHc------CCcEEEEEEecCc--cccchHH
Q 002211 129 VLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYF------GWGEVIAIFNDDD--QGRNGVT 200 (953)
Q Consensus 129 av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~------~w~~vaii~~d~~--~g~~~~~ 200 (953)
.....+...++|+|......+. ...++ .+..++...+..+++++... |-++++++..+.. ......+
T Consensus 71 ~~l~~l~~~~ipvV~~~~~~~~---~~~~~--~v~~d~~~~g~~~~~~l~~~~~~~~~g~~~i~~l~g~~~~~~~~~R~~ 145 (288)
T cd01538 71 SAVEKAADAGIPVIAYDRLILN---SNVDY--YVSFDNEKVGELQGQALVDGLGAKGKPPGNIELIAGSPTDNNAKLFFN 145 (288)
T ss_pred HHHHHHHHCCCCEEEECCCCCC---CCcce--EEEeChHHHHHHHHHHHHHHHhhcCCCCceEEEEECCCCCchHHHHHH
Confidence 4555667789999987654321 11222 23455566677777776555 8899999975432 3334578
Q ss_pred HHHHHHHhcC----cEEEEEEecCCCCCCChHHHHHHHHHHhcC---CceEEEEEcchhhHHHHHHHHHHcCCCC
Q 002211 201 ALGDKLAEIR----CKISYKSALPPDQSVTETDVRNELVKVRMM---EARVIVVHGYSRTGLMVFDVAQRLGMMD 268 (953)
Q Consensus 201 ~l~~~l~~~g----~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~---~~~vii~~~~~~~~~~~~~~a~~~g~~~ 268 (953)
.|.+.+++.+ +++... ..... .+...-...+.++.+. ++++|+.. +...+..+++++++.|+..
T Consensus 146 gf~~~l~~~~~~~~~~~~~~-~~~~~--~~~~~~~~~~~~~l~~~~~~~~~I~~~-~d~~a~g~~~al~~~g~~~ 216 (288)
T cd01538 146 GAMSVLKPLIDSGKITIVGE-VATPD--WDPETAQKRMENALTANYNKVDGVLAA-NDGTAGGAIAALKAAGLAG 216 (288)
T ss_pred HHHHHHHhccccCCeeEEec-cccCC--CCHHHHHHHHHHHHHhCCCCccEEEeC-CcHHHHHHHHHHHHcCCCC
Confidence 8899999887 444322 11211 1122333445555433 35655554 3556777889999999764
No 161
>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=97.71 E-value=0.0081 Score=65.53 Aligned_cols=210 Identities=19% Similarity=0.136 Sum_probs=128.2
Q ss_pred EeEEEecC--CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhc--CcEEEEc-cCChhh
Q 002211 52 VGAIFSFG--TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMET--DTLAIVG-PQSAVM 126 (953)
Q Consensus 52 IG~l~~~~--~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~--~v~aiiG-p~~S~~ 126 (953)
||+++|-. ..+-.....+++-+.++. |+++.+ .++..++..-......++++ +|.+||= |... .
T Consensus 2 Igvi~~~~~~~~~~~~~~~gi~~~~~~~--------g~~v~~--~~~~~~~~~~~~~i~~~~~~~~~vdgiIi~~~~~-~ 70 (305)
T cd06324 2 VVFLNPGKSDEPFWNSVARFMQAAADDL--------GIELEV--LYAERDRFLMLQQARTILQRPDKPDALIFTNEKS-V 70 (305)
T ss_pred eEEecCCCCCCcHHHHHHHHHHHHHHhc--------CCeEEE--EeCCCCHHHHHHHHHHHHHhccCCCEEEEcCCcc-c
Confidence 78888764 334445566777666552 566654 35666777777778888988 8988663 3322 2
Q ss_pred HHHHHHhhhhCCCcEEEeecCCCCCC-----C--CCC-CcEEEccCChHHHHHHHHHHHHHcCCcE--------EEEEEe
Q 002211 127 AHVLSHLANELQVPLLSFTALDPTLS-----P--LQY-PFFVQTAPNDLYLMSAIAEMVSYFGWGE--------VIAIFN 190 (953)
Q Consensus 127 a~av~~v~~~~~vP~Is~~at~~~ls-----~--~~~-p~~fr~~p~d~~~~~ai~~~l~~~~w~~--------vaii~~ 190 (953)
.......+.+.++|+|.+....+... . ..+ +++-...+++...+..+++.+.+.|-++ ++++..
T Consensus 71 ~~~~~~~~~~~giPvV~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~d~~~~g~~~~~~l~~~g~~~~~~~g~~~i~~i~~ 150 (305)
T cd06324 71 APELLRLAEGAGVKLFLVNSGLTEAQARELGPPREKFPDWLGQLLPNDEEAGYLMAEALISQARSVQAPGGRIDLLAISG 150 (305)
T ss_pred hHHHHHHHHhCCCeEEEEecCCCcchhhcccccccccCceeeeeccCcHHHHHHHHHHHHHHhhcccCCCCceeEEEEeC
Confidence 33344567778999998865432211 0 111 2345566778888888999887777664 776763
Q ss_pred c--CccccchHHHHHHHHHhcC-cEEEEEEecCCCCCCChHHHHHHHHHHhcC--CceEEEEEcchhhHHHHHHHHHHcC
Q 002211 191 D--DDQGRNGVTALGDKLAEIR-CKISYKSALPPDQSVTETDVRNELVKVRMM--EARVIVVHGYSRTGLMVFDVAQRLG 265 (953)
Q Consensus 191 d--~~~g~~~~~~l~~~l~~~g-~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~--~~~vii~~~~~~~~~~~~~~a~~~g 265 (953)
+ ........+.|++.+++.| ..+.. .+... .+...-...+.++.+. ++++|+ +.+...+..+++++++.|
T Consensus 151 ~~~~~~~~~R~~Gf~~~~~~~g~~~~~~--~~~~~--~~~~~~~~~~~~~l~~~~~~~ai~-~~~d~~A~g~~~al~~~g 225 (305)
T cd06324 151 DPTTPAAILREAGLRRALAEHPDVRLRQ--VVYAG--WSEDEAYEQAENLLKRYPDVRLIW-AANDQMAFGALRAAKEAG 225 (305)
T ss_pred CCCChHHHHHHHHHHHHHHHCCCceEee--eecCC--CCHHHHHHHHHHHHHHCCCccEEE-ECCchHHHHHHHHHHHcC
Confidence 3 2334456788999999887 33322 12212 1233444455565433 467655 445666778999999999
Q ss_pred CCCCceE-EEEeC
Q 002211 266 MMDSGYV-WIATT 277 (953)
Q Consensus 266 ~~~~~~~-wi~~~ 277 (953)
+..++-+ .++-+
T Consensus 226 ~~vp~di~vig~D 238 (305)
T cd06324 226 RKPGRDVLFGGVN 238 (305)
T ss_pred CCcCCCEEEEecC
Confidence 8754433 44433
No 162
>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=97.70 E-value=0.0038 Score=66.94 Aligned_cols=204 Identities=11% Similarity=0.052 Sum_probs=117.5
Q ss_pred EEEeEEEec--------CCCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHH-hcCcEEEEc
Q 002211 50 LNVGAIFSF--------GTVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFM-ETDTLAIVG 120 (953)
Q Consensus 50 i~IG~l~~~--------~~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li-~~~v~aiiG 120 (953)
=.||++.|. +..+-.....+++-++++. |+++.+...+.. . ...+.+.+ .+++.+||=
T Consensus 4 ~~i~vi~p~~~~~~~~~~~~~~~~~~~gi~~~~~~~--------g~~~~v~~~~~~--~---~~~~~~~l~~~~~dgiii 70 (275)
T cd06295 4 DTIALVVPEPHERDQSFSDPFFLSLLGGIADALAER--------GYDLLLSFVSSP--D---RDWLARYLASGRADGVIL 70 (275)
T ss_pred eEEEEEecCccccccccCCchHHHHHHHHHHHHHHc--------CCEEEEEeCCch--h---HHHHHHHHHhCCCCEEEE
Confidence 468999985 2333344455555444432 567766544332 1 12334444 457777752
Q ss_pred -cCChhhHHHHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecC--ccccc
Q 002211 121 -PQSAVMAHVLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDD--DQGRN 197 (953)
Q Consensus 121 -p~~S~~a~av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~--~~g~~ 197 (953)
|.... . .....+...++|+|.++...+. ..++ .+.+++...+..+++++...|.++++++..+. ..+..
T Consensus 71 ~~~~~~-~-~~~~~~~~~~ipvV~~~~~~~~---~~~~---~V~~d~~~~g~~~a~~l~~~g~~~i~~i~~~~~~~~~~~ 142 (275)
T cd06295 71 IGQHDQ-D-PLPERLAETGLPFVVWGRPLPG---QPYC---YVGSDNVGGGRLATEHLLARGRRRIAFLGGPQDMPEGEE 142 (275)
T ss_pred eCCCCC-h-HHHHHHHhCCCCEEEECCccCC---CCCC---EEEECcHHHHHHHHHHHHHCCCCeEEEEcCCCCcchhHH
Confidence 22222 1 2245567789999987653322 2223 35566777788889998888999999997543 23445
Q ss_pred hHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcC--CceEEEEEcchhhHHHHHHHHHHcCCCCCceE-EE
Q 002211 198 GVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMM--EARVIVVHGYSRTGLMVFDVAQRLGMMDSGYV-WI 274 (953)
Q Consensus 198 ~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~--~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~-wi 274 (953)
..+.|.+.+++.|..+........+ .+.......+.++.+. ++++|+... ...+..+++.+++.|...++-+ .+
T Consensus 143 r~~gf~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~l~~~~~~~ai~~~~-~~~a~g~~~~l~~~g~~ip~~i~ii 219 (275)
T cd06295 143 RLEGYREALAEAGLPLDPRLVAPGD--FTEESGRAAMRALLERGPDFDAVFAAS-DLMALGALRALREAGRRVPEDVAVV 219 (275)
T ss_pred HHHHHHHHHHHcCCCCChhhEEecc--CCHHHHHHHHHHHHhCCCCCCEEEECC-cHHHHHHHHHHHHhCCCCccceEEE
Confidence 6788999999887543221111111 1133334455555443 457666654 4556678899999998544434 34
Q ss_pred EeC
Q 002211 275 ATT 277 (953)
Q Consensus 275 ~~~ 277 (953)
+.|
T Consensus 220 ~~d 222 (275)
T cd06295 220 GFD 222 (275)
T ss_pred eeC
Confidence 433
No 163
>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=97.68 E-value=0.0046 Score=65.83 Aligned_cols=205 Identities=12% Similarity=0.047 Sum_probs=122.6
Q ss_pred EEeEEEecC-CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEEccCChhhHHH
Q 002211 51 NVGAIFSFG-TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIVGPQSAVMAHV 129 (953)
Q Consensus 51 ~IG~l~~~~-~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aiiGp~~S~~a~a 129 (953)
+||+++|.. ..+-.....+++-+.++. |+.+.+ .++..++..-......++..++.+||=-.......
T Consensus 1 ~igvv~~~~~~~~~~~~~~gi~~~~~~~--------g~~~~~--~~~~~~~~~~~~~~~~l~~~~vdgiIi~~~~~~~~- 69 (265)
T cd06299 1 TIGVIVPDIRNPYFASLATAIQDAASAA--------GYSTII--GNSDENPETENRYLDNLLSQRVDGIIVVPHEQSAE- 69 (265)
T ss_pred CEEEEecCCCCccHHHHHHHHHHHHHHc--------CCEEEE--EeCCCCHHHHHHHHHHHHhcCCCEEEEcCCCCChH-
Confidence 489998853 445556677777777663 455553 45555666555666677777888777422222222
Q ss_pred HHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecC--ccccchHHHHHHHHH
Q 002211 130 LSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDD--DQGRNGVTALGDKLA 207 (953)
Q Consensus 130 v~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~--~~g~~~~~~l~~~l~ 207 (953)
...-+.+.++|+|......+ ....+++ ..++...+..+++++...|-++++++.... .......+.|.+.++
T Consensus 70 ~~~~l~~~~ipvV~~~~~~~---~~~~~~v---~~d~~~~~~~~~~~l~~~g~~~I~~i~~~~~~~~~~~R~~gf~~~~~ 143 (265)
T cd06299 70 QLEDLLKRGIPVVFVDREIT---GSPIPFV---TSDPQPGMTEAVSLLVALGHKKIGYISGPQDTSTGRERLEAFRQACA 143 (265)
T ss_pred HHHHHHhCCCCEEEEecccC---CCCCCEE---EECcHHHHHHHHHHHHHcCCCcEEEEeCCCCcccHHHHHHHHHHHHH
Confidence 34555678999998765432 2233443 234444455667777778999999996432 334455688999999
Q ss_pred hcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEE
Q 002211 208 EIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIA 275 (953)
Q Consensus 208 ~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~ 275 (953)
+.|..+......... ....+....+.++.+.++++|+. .+...+..+++.+++.|+..++-+.+.
T Consensus 144 ~~~~~~~~~~~~~~~--~~~~~~~~~~~~~l~~~~~av~~-~~d~~a~gv~~al~~~g~~vp~dv~v~ 208 (265)
T cd06299 144 SLGLEVNEDLVVLGG--YSQESGYAGATKLLDQGATAIIA-GDSMMTIGAIRAIHDAGLVIGEDISLI 208 (265)
T ss_pred HCCCCCChHhEEecC--cchHHHHHHHHHHHcCCCCEEEE-cCcHHHHHHHHHHHHhCCCCCcceeEE
Confidence 888542211111111 11233344566655555887555 445567788999999998655444444
No 164
>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=97.68 E-value=0.0059 Score=64.98 Aligned_cols=205 Identities=9% Similarity=0.019 Sum_probs=124.7
Q ss_pred EEeEEEecC-CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEEccCChhhHHH
Q 002211 51 NVGAIFSFG-TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIVGPQSAVMAHV 129 (953)
Q Consensus 51 ~IG~l~~~~-~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aiiGp~~S~~a~a 129 (953)
.||++.|.. ..+-.....+++-|.++. |+.+. +.++..++..-......++..++.+||=-........
T Consensus 1 ~igvi~~~~~~~~~~~~~~~i~~~a~~~--------g~~~~--~~~~~~~~~~~~~~~~~l~~~~~dgiii~~~~~~~~~ 70 (267)
T cd06283 1 LIGVIVADITNPFSSLVLKGIEDVCRAH--------GYQVL--VCNSDNDPEKEKEYLESLLAYQVDGLIVNPTGNNKEL 70 (267)
T ss_pred CEEEEecCCccccHHHHHHHHHHHHHHc--------CCEEE--EEcCCCCHHHHHHHHHHHHHcCcCEEEEeCCCCChHH
Confidence 378888864 444456677777777652 45554 4556666766666677788887777763222212222
Q ss_pred HHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecCc--c-ccchHHHHHHHH
Q 002211 130 LSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDDD--Q-GRNGVTALGDKL 206 (953)
Q Consensus 130 v~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~~--~-g~~~~~~l~~~l 206 (953)
...+...++|+|......+ ....++ +..++...+..+++++...|-++++++..... . .......+.+.+
T Consensus 71 -l~~~~~~~ipvV~~~~~~~---~~~~~~---v~~d~~~~g~~~~~~l~~~g~~~i~~l~~~~~~~~~~~~r~~g~~~~~ 143 (267)
T cd06283 71 -YQRLAKNGKPVVLVDRKIP---ELGVDT---VTLDNYEAAKEAVDHLIEKGYERILFVTEPLDEISPRMERYEGFKEAL 143 (267)
T ss_pred -HHHHhcCCCCEEEEcCCCC---CCCCCE---EEeccHHHHHHHHHHHHHcCCCcEEEEecCccccccHHHHHHHHHHHH
Confidence 3445678999998754322 112233 34556677888899988889999999975432 1 235678889999
Q ss_pred HhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCC--ceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEE
Q 002211 207 AEIRCKISYKSALPPDQSVTETDVRNELVKVRMME--ARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIA 275 (953)
Q Consensus 207 ~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~--~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~ 275 (953)
++.|............ .+..+....+.++.++. +++|+... ...+..+++.+++.|+..++-+-|.
T Consensus 144 ~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~l~~~~~~~ai~~~~-d~~a~g~~~~l~~~g~~vp~di~v~ 211 (267)
T cd06283 144 AEHGIGVNEELIEIDD--EDADELDERLRQLLNKPKKKTAIFAAN-GLILLEVLKALKELGIRIPEDVGLI 211 (267)
T ss_pred HHcCCCCCcceeEecc--cchHHHHHHHHHHHcCCCCCCEEEEcC-cHHHHHHHHHHHHcCCCCccceEEE
Confidence 8887432211111111 11344556666765443 56666654 4456678999999998655444433
No 165
>cd06278 PBP1_LacI_like_2 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=97.66 E-value=0.0046 Score=65.82 Aligned_cols=191 Identities=12% Similarity=0.042 Sum_probs=116.3
Q ss_pred EeEEEecC-CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEEccCChhhHHHH
Q 002211 52 VGAIFSFG-TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIVGPQSAVMAHVL 130 (953)
Q Consensus 52 IG~l~~~~-~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aiiGp~~S~~a~av 130 (953)
||++.|.. ..+-.....+++-+.++. |+++.+...|+ +. ...+...+++.+++.+||--.+.... ..
T Consensus 2 I~~i~~~~~~~~~~~~~~~i~~~~~~~--------g~~~~~~~~~~--~~-~~~~~i~~~~~~~vdgiii~~~~~~~-~~ 69 (266)
T cd06278 2 IGVVVADLDNPFYSELLEALSRALQAR--------GYQPLLINTDD--DE-DLDAALRQLLQYRVDGVIVTSGTLSS-EL 69 (266)
T ss_pred EEEEeCCCCCchHHHHHHHHHHHHHHC--------CCeEEEEcCCC--CH-HHHHHHHHHHHcCCCEEEEecCCCCH-HH
Confidence 78888863 444445556665444442 56776665543 32 33345566777788877753222222 33
Q ss_pred HHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecC--ccccchHHHHHHHHHh
Q 002211 131 SHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDD--DQGRNGVTALGDKLAE 208 (953)
Q Consensus 131 ~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~--~~g~~~~~~l~~~l~~ 208 (953)
...+...++|+|......+ + +.+..+..++...+..+++++...|-++++++..+. .......+.|.+.+++
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 5566778999998754322 1 123346677888888899998888999999998543 3445567889999998
Q ss_pred cCcEEEEEEecCCCCCCChHHHHHHHHHHhcC--CceEEEEEcchhhHHHHHHHHHHcC
Q 002211 209 IRCKISYKSALPPDQSVTETDVRNELVKVRMM--EARVIVVHGYSRTGLMVFDVAQRLG 265 (953)
Q Consensus 209 ~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~--~~~vii~~~~~~~~~~~~~~a~~~g 265 (953)
.|..+... ..... +..+....+.++.+. ++++|+... ...+..+++.+++.+
T Consensus 144 ~~~~~~~~-~~~~~---~~~~~~~~~~~~l~~~~~~~~i~~~~-~~~a~~~~~~l~~~~ 197 (266)
T cd06278 144 AGVPVVVE-EAGDY---SYEGGYEAARRLLASRPRPDAIFCAN-DLLAIGVMDAARQEG 197 (266)
T ss_pred cCCChhhh-ccCCC---CHHHHHHHHHHHHhcCCCCCEEEEcC-cHHHHHHHHHHHHhc
Confidence 88764321 11111 133334455555443 456666553 444666777777753
No 166
>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=97.65 E-value=0.0069 Score=64.43 Aligned_cols=206 Identities=11% Similarity=0.023 Sum_probs=121.0
Q ss_pred EEeEEEecC-CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEEccCChhhHHH
Q 002211 51 NVGAIFSFG-TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIVGPQSAVMAHV 129 (953)
Q Consensus 51 ~IG~l~~~~-~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aiiGp~~S~~a~a 129 (953)
.||+++|.. ..+-.....+++-+.++ .|+.+.+ .++..++..-.+....++.+++.+||=.........
T Consensus 1 ~igvi~~~~~~~~~~~~~~~~~~~~~~--------~g~~~~~--~~~~~~~~~~~~~i~~l~~~~vdgiii~~~~~~~~~ 70 (264)
T cd06274 1 TIGLIIPDLENRSFARIAKRLEALARE--------RGYQLLI--ACSDDDPETERETVETLIARQVDALIVAGSLPPDDP 70 (264)
T ss_pred CEEEEeccccCchHHHHHHHHHHHHHH--------CCCEEEE--EeCCCCHHHHHHHHHHHHHcCCCEEEEcCCCCchHH
Confidence 378998863 33333334444433333 1555544 455567766666777788888887773222222222
Q ss_pred HHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecC--ccccchHHHHHHHHH
Q 002211 130 LSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDD--DQGRNGVTALGDKLA 207 (953)
Q Consensus 130 v~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~--~~g~~~~~~l~~~l~ 207 (953)
+ ..+...++|+|.+....+ +...++ +..++...+..+++++...|-++++++..+. .......+.+.+.++
T Consensus 71 ~-~~~~~~~ipvV~~~~~~~---~~~~~~---V~~d~~~~g~~~~~~l~~~g~~~i~~i~~~~~~~~~~~R~~gf~~~~~ 143 (264)
T cd06274 71 Y-YLCQKAGLPVVALDRPGD---PSRFPS---VVSDNRDGAAELTRELLAAPPEEVLFLGGLPELSPSRERLAGFRQALA 143 (264)
T ss_pred H-HHHHhcCCCEEEecCccC---CCCCCE---EEEccHHHHHHHHHHHHHCCCCcEEEEeCCCcccchHHHHHHHHHHHH
Confidence 3 345678999998754332 122333 3445555667788888888999999997543 234556789999999
Q ss_pred hcCcEEEEEEecCCCCCCChHHHHHHHHHHhcC---CceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEEe
Q 002211 208 EIRCKISYKSALPPDQSVTETDVRNELVKVRMM---EARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIAT 276 (953)
Q Consensus 208 ~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~---~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~ 276 (953)
+.|..+......... .+...-...+.++.+. .+++|+.. +...+..+++++++.|+..++-+-|.+
T Consensus 144 ~~~~~~~~~~~~~~~--~~~~~~~~~~~~~l~~~~~~~~ai~~~-~d~~A~g~~~al~~~g~~ip~dv~v~g 212 (264)
T cd06274 144 DAGLPVQPDWIYAEG--YSPESGYQLMAELLARLGRLPRALFTT-SYTLLEGVLRFLRERPGLAPSDLRIAT 212 (264)
T ss_pred HcCCCCCcceeecCC--CChHHHHHHHHHHHccCCCCCcEEEEc-ChHHHHHHHHHHHHcCCCCCcceEEEE
Confidence 888543211111111 1123333445555433 36776655 455677899999999987555454443
No 167
>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=97.64 E-value=0.0076 Score=64.27 Aligned_cols=202 Identities=13% Similarity=0.008 Sum_probs=123.9
Q ss_pred EEeEEEecC-CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEEccCChhhHHH
Q 002211 51 NVGAIFSFG-TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIVGPQSAVMAHV 129 (953)
Q Consensus 51 ~IG~l~~~~-~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aiiGp~~S~~a~a 129 (953)
.||+++|.. ..+-.....|++-+.++. |+++.+. ++..++..-.+....++++++.+||--.+.... .
T Consensus 1 ~igvi~p~~~~~~~~~~~~g~~~~a~~~--------g~~~~~~--~~~~~~~~~~~~i~~~~~~~vdgii~~~~~~~~-~ 69 (268)
T cd06270 1 TIGLVVSDLDGPFFGPLLSGVESVARKA--------GKHLIIT--AGHHSAEKEREAIEFLLERRCDALILHSKALSD-D 69 (268)
T ss_pred CEEEEEccccCcchHHHHHHHHHHHHHC--------CCEEEEE--eCCCchHHHHHHHHHHHHcCCCEEEEecCCCCH-H
Confidence 388999863 445556677777777662 5666653 444556555666667888888877742221111 2
Q ss_pred HHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecCc--cccchHHHHHHHHH
Q 002211 130 LSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDDD--QGRNGVTALGDKLA 207 (953)
Q Consensus 130 v~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~~--~g~~~~~~l~~~l~ 207 (953)
....+...++|+|......+ ...+++ +..++...+..+++++...|-+++++|..+.. ......+.|.+.++
T Consensus 70 ~~~~~~~~~ipvV~~~~~~~---~~~~~~---v~~d~~~~~~~~~~~l~~~g~~~i~~i~~~~~~~~~~~R~~gf~~~~~ 143 (268)
T cd06270 70 ELIELAAQVPPLVLINRHIP---GLADRC---IWLDNEQGGYLATEHLIELGHRKIACITGPLTKEDARLRLQGYRDALA 143 (268)
T ss_pred HHHHHhhCCCCEEEEeccCC---CCCCCe---EEECcHHHHHHHHHHHHHCCCceEEEEeCCcccccHHHHHHHHHHHHH
Confidence 13445678999998754332 112232 44667777888999988889999999975432 23345678899999
Q ss_pred hcCcEEEEEEecCCCCCCChHHHHHHHHHHhcC--CceEEEEEcchhhHHHHHHHHHHcCCCCCceE
Q 002211 208 EIRCKISYKSALPPDQSVTETDVRNELVKVRMM--EARVIVVHGYSRTGLMVFDVAQRLGMMDSGYV 272 (953)
Q Consensus 208 ~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~--~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~ 272 (953)
+.|.++.....+... .+..+....+.++.+. .+++|+.. ....+..+++.+++.|+..++-+
T Consensus 144 ~~~~~~~~~~~~~~~--~~~~~~~~~~~~~l~~~~~~~ai~~~-~d~~a~g~~~~l~~~g~~ip~di 207 (268)
T cd06270 144 EAGIALDESLIIEGD--FTEEGGYAAMQELLARGAPFTAVFCA-NDEMAAGAISALREHGISVPQDV 207 (268)
T ss_pred HcCCCCCcceEEECC--CCHHHHHHHHHHHHhCCCCCCEEEEc-CcHHHHHHHHHHHHcCCCCCCce
Confidence 888654211111111 1234445556666544 35665544 34566778999999998654433
No 168
>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=97.62 E-value=0.0098 Score=63.20 Aligned_cols=202 Identities=9% Similarity=0.030 Sum_probs=121.5
Q ss_pred EEeEEEecC-CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEEc-cCChhhHH
Q 002211 51 NVGAIFSFG-TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIVG-PQSAVMAH 128 (953)
Q Consensus 51 ~IG~l~~~~-~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aiiG-p~~S~~a~ 128 (953)
.||+++|-. ..+-.....+++-+.++. |+.+.+...+. .++..-.+....++++++.++|- +..... .
T Consensus 1 ~i~vi~~~~~~~~~~~~~~gi~~~~~~~--------~~~~~~~~~~~-~~~~~~~~~~~~l~~~~vdgiii~~~~~~~-~ 70 (264)
T cd01574 1 TIGVVTTDLALHGPSSTLAAIESAAREA--------GYAVTLSMLAE-ADEEALRAAVRRLLAQRVDGVIVNAPLDDA-D 70 (264)
T ss_pred CEEEEeCCCCcccHHHHHHHHHHHHHHC--------CCeEEEEeCCC-CchHHHHHHHHHHHhcCCCEEEEeCCCCCh-H
Confidence 388999853 344455666666666662 56776553322 23455555566677778888873 332222 2
Q ss_pred HHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecCcc--ccchHHHHHHHH
Q 002211 129 VLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDDDQ--GRNGVTALGDKL 206 (953)
Q Consensus 129 av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~~~--g~~~~~~l~~~l 206 (953)
.+.. ..+.++|+|......+ ...+ .+..++...+..+++++...|-++|+++..+... .....+.|.+.+
T Consensus 71 ~~~~-~~~~~ipvv~~~~~~~----~~~~---~v~~d~~~~g~~~~~~l~~~g~~~i~~i~~~~~~~~~~~r~~gf~~~l 142 (264)
T cd01574 71 AALA-AAPADVPVVFVDGSPS----PRVS---TVSVDQEGGARLATEHLLELGHRTIAHVAGPEEWLSARARLAGWRAAL 142 (264)
T ss_pred HHHH-HHhcCCCEEEEeccCC----CCCC---EEEeCcHHHHHHHHHHHHHCCCCEEEEEecCCccchHHHHHHHHHHHH
Confidence 3333 3567899999865321 1223 3556667778889999888899999999754332 234567889999
Q ss_pred HhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCC-ceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEE
Q 002211 207 AEIRCKISYKSALPPDQSVTETDVRNELVKVRMME-ARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIA 275 (953)
Q Consensus 207 ~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~-~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~ 275 (953)
++.|+.+.... ..+ .+.+.....+.++.+.. +++|+.. +...+..+++.+++.|...++.+-|.
T Consensus 143 ~~~~~~~~~~~--~~~--~~~~~~~~~~~~~l~~~~~~ai~~~-~d~~a~g~~~~~~~~g~~ip~~i~ii 207 (264)
T cd01574 143 EAAGIAPPPVL--EGD--WSAESGYRAGRELLREGDPTAVFAA-NDQMALGVLRALHELGLRVPDDVSVV 207 (264)
T ss_pred HHCCCCcceee--ecC--CCHHHHHHHHHHHHhCCCCcEEEEc-CcHHHHHHHHHHHHcCCCCccceEEe
Confidence 88887654321 111 11333344555554433 6765554 55567788999999997544433333
No 169
>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=97.60 E-value=0.0035 Score=67.26 Aligned_cols=208 Identities=10% Similarity=0.008 Sum_probs=135.7
Q ss_pred EEeEEEecC-CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEEccCChhhHHH
Q 002211 51 NVGAIFSFG-TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIVGPQSAVMAHV 129 (953)
Q Consensus 51 ~IG~l~~~~-~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aiiGp~~S~~a~a 129 (953)
+||++.|-- .++-.....|++-+.++ .|+.+-+ .++..++..- +....|.+++|+++|=.........
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 699999985 44445566777766666 2677655 4556666655 6666777778888774322222345
Q ss_pred HHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCCcE-EEEEEecCcc--ccchHHHHHHHH
Q 002211 130 LSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGWGE-VIAIFNDDDQ--GRNGVTALGDKL 206 (953)
Q Consensus 130 v~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~-vaii~~d~~~--g~~~~~~l~~~l 206 (953)
+..+.+. ++|+|......... ...|++. .++..-+..+++++.+.|-++ ++++..+... .....+.+.+++
T Consensus 72 l~~~~~~-~iPvV~~~~~~~~~--~~~~~V~---~D~~~a~~~a~~~Li~~Gh~~~I~~i~~~~~~~~~~~R~~Gy~~Al 145 (279)
T PF00532_consen 72 LRRLIKS-GIPVVLIDRYIDNP--EGVPSVY---IDNYEAGYEATEYLIKKGHRRPIAFIGGPEDSSTSRERLQGYRDAL 145 (279)
T ss_dssp HHHHHHT-TSEEEEESS-SCTT--CTSCEEE---EEHHHHHHHHHHHHHHTTCCSTEEEEEESTTTHHHHHHHHHHHHHH
T ss_pred HHHHHHc-CCCEEEEEeccCCc--ccCCEEE---EcchHHHHHHHHHHHhcccCCeEEEEecCcchHHHHHHHHHHHHHH
Confidence 5666666 99999865442111 1344443 346666778888899999999 9999976443 455678899999
Q ss_pred HhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceE-EEEEcchhhHHHHHHHHHHcC-CCCCceEEEEeC
Q 002211 207 AEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARV-IVVHGYSRTGLMVFDVAQRLG-MMDSGYVWIATT 277 (953)
Q Consensus 207 ~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~v-ii~~~~~~~~~~~~~~a~~~g-~~~~~~~wi~~~ 277 (953)
++.|+++......... .+..+-...++++.+.+|++ .|++++...+...++.+++.| ...++-+-+..+
T Consensus 146 ~~~Gl~~~~~~i~~~~--~~~~~g~~~~~~ll~~~p~idai~~~nd~~A~ga~~~l~~~gr~~ip~di~~~~~ 216 (279)
T PF00532_consen 146 KEAGLPIDEEWIFEGD--FDYESGYEAARELLESHPDIDAIFCANDMMAIGAIRALRERGRLKIPEDIVSGFD 216 (279)
T ss_dssp HHTTSCEEEEEEEESS--SSHHHHHHHHHHHHHTSTT-SEEEESSHHHHHHHHHHHHHTT-TCTTTEEEECSC
T ss_pred HHcCCCCCcccccccC--CCHHHHHHHHHHHHhhCCCCEEEEEeCHHHHHHHHHHHHHcCCcccChhheeeec
Confidence 9999965544433322 23455556677777777772 344556667888999999999 777665543333
No 170
>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=97.60 E-value=0.0077 Score=64.11 Aligned_cols=203 Identities=11% Similarity=0.066 Sum_probs=124.5
Q ss_pred EEeEEEecC-CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEE-ccCChhhHH
Q 002211 51 NVGAIFSFG-TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIV-GPQSAVMAH 128 (953)
Q Consensus 51 ~IG~l~~~~-~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aii-Gp~~S~~a~ 128 (953)
.||+++|-. ..+-.....+++-+.++. |+++. +.++..++..-.+....+..+++.+|| .|... ...
T Consensus 1 ~igvi~p~~~~~~~~~~~~gi~~~~~~~--------~~~~~--~~~~~~~~~~~~~~i~~l~~~~~dgiii~~~~~-~~~ 69 (265)
T cd06285 1 TIGVLVPRLTDTVMATMYEGIEEAAAER--------GYSTF--VANTGDNPDAQRRAIEMLLDRRVDGLILGDARS-DDH 69 (265)
T ss_pred CEEEEeCCCCCccHHHHHHHHHHHHHHC--------CCEEE--EEeCCCCHHHHHHHHHHHHHcCCCEEEEecCCC-ChH
Confidence 389999863 444455566666666652 45653 455556666666666677778888766 44332 222
Q ss_pred HHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecC--ccccchHHHHHHHH
Q 002211 129 VLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDD--DQGRNGVTALGDKL 206 (953)
Q Consensus 129 av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~--~~g~~~~~~l~~~l 206 (953)
. ...+...++|+|......+ ..++ +..++..-+..+++++...|-++++++..+. ..+....+.|.+.+
T Consensus 70 ~-~~~~~~~~iPvv~~~~~~~-----~~~~---V~~d~~~ag~~a~~~L~~~g~~~i~~i~~~~~~~~~~~R~~Gf~~~~ 140 (265)
T cd06285 70 F-LDELTRRGVPFVLVLRHAG-----TSPA---VTGDDVLGGRLATRHLLDLGHRRIAVLAGPDYASTARDRLAGFRAAL 140 (265)
T ss_pred H-HHHHHHcCCCEEEEccCCC-----CCCE---EEeCcHHHHHHHHHHHHHCCCccEEEEeCCcccccHHHHHHHHHHHH
Confidence 3 3445678999998754321 2333 3456667778888888888999999997543 34556678899999
Q ss_pred HhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcC--CceEEEEEcchhhHHHHHHHHHHcCCCCCceE-EEEe
Q 002211 207 AEIRCKISYKSALPPDQSVTETDVRNELVKVRMM--EARVIVVHGYSRTGLMVFDVAQRLGMMDSGYV-WIAT 276 (953)
Q Consensus 207 ~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~--~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~-wi~~ 276 (953)
++.|..+.....+... .+.......+.++.+. .+++|+.. +...+..+++.+++.|+..++-+ .++-
T Consensus 141 ~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~l~~~~~~~ai~~~-~d~~a~g~~~~l~~~g~~~p~di~iig~ 210 (265)
T cd06285 141 AEAGIEVPPERIVYSG--FDIEGGEAAAEKLLRSDSPPTAIFAV-NDFAAIGVMGAARDRGLRVPDDVALVGY 210 (265)
T ss_pred HHcCCCCChhhEEeCC--CCHHHHHHHHHHHHcCCCCCCEEEEc-CcHHHHHHHHHHHHcCCCCCcceEEEee
Confidence 9888764321111111 1133334455565433 45665544 55567789999999998644333 3443
No 171
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=97.59 E-value=0.0063 Score=67.60 Aligned_cols=209 Identities=10% Similarity=0.007 Sum_probs=125.3
Q ss_pred ceEEEeEEEecC-CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEEccCChhh
Q 002211 48 EVLNVGAIFSFG-TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIVGPQSAVM 126 (953)
Q Consensus 48 ~~i~IG~l~~~~-~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aiiGp~~S~~ 126 (953)
..-+||+++|.. ..+-.....+++-+.++. |+++. +.++..++..-......++.+++.+||--.....
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 345899999864 444455566766666652 44544 4455666766666667777778887763111111
Q ss_pred HHHHHHhhhh-CCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEec--CccccchHHHHH
Q 002211 127 AHVLSHLANE-LQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFND--DDQGRNGVTALG 203 (953)
Q Consensus 127 a~av~~v~~~-~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d--~~~g~~~~~~l~ 203 (953)
. .....+.. .++|+|......+ +..++.+ ..+++...+..+++.+...|-+++++|..+ +..++...+.|.
T Consensus 128 ~-~~~~~l~~~~~iPvV~~d~~~~---~~~~~~~--v~~d~~~~g~~a~~~L~~~G~~~i~~i~~~~~~~~~~~R~~Gf~ 201 (341)
T PRK10703 128 E-PLLAMLEEYRHIPMVVMDWGEA---KADFTDA--IIDNAFEGGYLAGRYLIERGHRDIGVIPGPLERNTGAGRLAGFM 201 (341)
T ss_pred H-HHHHHHHhcCCCCEEEEecccC---CcCCCCe--EEECcHHHHHHHHHHHHHCCCCcEEEEeCCccccchHHHHHHHH
Confidence 2 23344445 6999998754322 1111222 344445567888888877899999999643 334556678999
Q ss_pred HHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcC--CceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEE
Q 002211 204 DKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMM--EARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIA 275 (953)
Q Consensus 204 ~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~--~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~ 275 (953)
+.+++.|+++........+ ....+....+.++.+. .+++|+. .+...+..+++++++.|...++-+.+.
T Consensus 202 ~~l~~~gi~~~~~~~~~~~--~~~~~~~~~~~~~l~~~~~~~ai~~-~nd~~a~g~~~al~~~g~~ip~dv~vv 272 (341)
T PRK10703 202 KAMEEANIKVPEEWIVQGD--FEPESGYEAMQQILSQKHRPTAVFC-GGDIMAMGAICAADEMGLRVPQDISVI 272 (341)
T ss_pred HHHHHcCCCCChHHeEeCC--CCHHHHHHHHHHHHhCCCCCCEEEE-CCcHHHHHHHHHHHHcCCCCCCceEEE
Confidence 9999999765421111111 1133444556565443 4676665 445567789999999997655444443
No 172
>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=97.58 E-value=0.01 Score=63.39 Aligned_cols=205 Identities=11% Similarity=0.007 Sum_probs=123.3
Q ss_pred EEeEEEec-CCCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEEccCChhhHHH
Q 002211 51 NVGAIFSF-GTVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIVGPQSAVMAHV 129 (953)
Q Consensus 51 ~IG~l~~~-~~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aiiGp~~S~~a~a 129 (953)
+||++.|- +..+-.....+++-+.++. |+++.+. ++..++..-......+...++.+||--.+......
T Consensus 1 ~Ig~i~~~~~~~~~~~~~~gi~~~~~~~--------gy~v~~~--~~~~~~~~~~~~i~~~~~~~~dgiii~~~~~~~~~ 70 (269)
T cd06293 1 TIGLVVPDIANPFFAELADAVEEEADAR--------GLSLVLC--ATRNRPERELTYLRWLDTNHVDGLIFVTNRPDDGA 70 (269)
T ss_pred CEEEEeCCCCCCcHHHHHHHHHHHHHHC--------CCEEEEE--eCCCCHHHHHHHHHHHHHCCCCEEEEeCCCCCHHH
Confidence 47889875 3444455666666666542 5677544 44446665555666677778888885322211222
Q ss_pred HHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecCc--cccchHHHHHHHHH
Q 002211 130 LSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDDD--QGRNGVTALGDKLA 207 (953)
Q Consensus 130 v~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~~--~g~~~~~~l~~~l~ 207 (953)
+..+. ..++|+|......+. ...+ .+.+++...+..+++++...|-++++++..+.. ......+.|.++++
T Consensus 71 ~~~~~-~~~~pvV~i~~~~~~---~~~~---~V~~d~~~~~~~~~~~L~~~G~~~i~~i~~~~~~~~~~~R~~Gf~~a~~ 143 (269)
T cd06293 71 LAKLI-NSYGNIVLVDEDVPG---AKVP---KVFCDNEQGGRLATRHLARAGHRRIAFVGGPDALISARERYAGYREALA 143 (269)
T ss_pred HHHHH-hcCCCEEEECCCCCC---CCCC---EEEECCHHHHHHHHHHHHHCCCceEEEEecCcccccHHHHHHHHHHHHH
Confidence 33333 357999987654321 1122 345677888888999988889999999974433 23355788999999
Q ss_pred hcCcEEEEEEecCCCCCCChHHHHHHHHHHhc--CCceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEE
Q 002211 208 EIRCKISYKSALPPDQSVTETDVRNELVKVRM--MEARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIA 275 (953)
Q Consensus 208 ~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~--~~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~ 275 (953)
+.|..+.....+... .+..+....+.++.+ ..+++|+.. +...+..+++.+++.|...++-+-|.
T Consensus 144 ~~~~~~~~~~~~~~~--~~~~~~~~~~~~~l~~~~~~~ai~~~-~d~~a~g~~~al~~~g~~vp~di~i~ 210 (269)
T cd06293 144 EAHIPEVPEYVCFGD--YTREFGRAAAAQLLARGDPPTAIFAA-SDEIAIGLLEVLRERGLSIPGDMSLV 210 (269)
T ss_pred HcCCCCChheEEecC--CCHHHHHHHHHHHHcCCCCCCEEEEc-CcHHHHHHHHHHHHcCCCCccceEEE
Confidence 888653211111111 112333445555543 346766655 45567788999999998655544444
No 173
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=97.57 E-value=0.013 Score=64.53 Aligned_cols=206 Identities=10% Similarity=-0.021 Sum_probs=124.3
Q ss_pred ceEEEeEEEec-CCCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEEc-cCChh
Q 002211 48 EVLNVGAIFSF-GTVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIVG-PQSAV 125 (953)
Q Consensus 48 ~~i~IG~l~~~-~~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aiiG-p~~S~ 125 (953)
..-.||+++|. +..+-.....+++-+.++ .|+++.+. ++..++..-.+....++.+++.+||= |....
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 45689999985 344434455666666654 25666553 44445555555566677778888763 22222
Q ss_pred hHHHHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecC--ccccchHHHHH
Q 002211 126 MAHVLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDD--DQGRNGVTALG 203 (953)
Q Consensus 126 ~a~av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~--~~g~~~~~~l~ 203 (953)
.... ...+.+.++|+|......+ ...+++ +..++...+..+++++...|-++++++.... ..+....+.|.
T Consensus 130 ~~~~-~~~l~~~~iPvV~v~~~~~---~~~~~~---V~~d~~~~~~~a~~~L~~~G~r~I~~i~~~~~~~~~~~R~~Gf~ 202 (328)
T PRK11303 130 EHPF-YQRLQNDGLPIIALDRALD---REHFTS---VVSDDQDDAEMLAESLLKFPAESILLLGALPELSVSFEREQGFR 202 (328)
T ss_pred ChHH-HHHHHhcCCCEEEECCCCC---CCCCCE---EEeCCHHHHHHHHHHHHHCCCCeEEEEeCccccccHHHHHHHHH
Confidence 2222 3344567999998754321 122333 3456667778888888888999999997543 23455678999
Q ss_pred HHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcC--CceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEE
Q 002211 204 DKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMM--EARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIA 275 (953)
Q Consensus 204 ~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~--~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~ 275 (953)
+++++.|+.+.... ... .+.++-...+.++.+. .+++|+... ...+..+++++++.|+..++-+-|+
T Consensus 203 ~al~~~g~~~~~~~--~~~--~~~~~~~~~~~~~l~~~~~~~ai~~~~-d~~A~g~~~al~~~g~~vP~disv~ 271 (328)
T PRK11303 203 QALKDDPREVHYLY--ANS--FEREAGAQLFEKWLETHPMPDALFTTS-YTLLQGVLDVLLERPGELPSDLAIA 271 (328)
T ss_pred HHHHHcCCCceEEE--eCC--CChHHHHHHHHHHHcCCCCCCEEEEcC-cHHHHHHHHHHHHcCCCCCCceEEE
Confidence 99999987543221 111 1122333455555443 477766654 4556778899999998665544443
No 174
>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=97.55 E-value=0.018 Score=61.89 Aligned_cols=198 Identities=14% Similarity=0.052 Sum_probs=120.5
Q ss_pred EEeEEEecC-CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEE-ccCChhhHH
Q 002211 51 NVGAIFSFG-TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIV-GPQSAVMAH 128 (953)
Q Consensus 51 ~IG~l~~~~-~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aii-Gp~~S~~a~ 128 (953)
+||++.|.. ..+-.....+++-+.++. |+.+. +.++..++..-.+....++++++.+|| .+..+....
T Consensus 1 ~igv~~~~~~~~~~~~~~~~i~~~~~~~--------g~~v~--~~~~~~~~~~~~~~i~~~~~~~~Dgiii~~~~~~~~~ 70 (282)
T cd06318 1 KIGFSQYTLNSPFFAALTEAAKAHAKAL--------GYELI--STDAQGDLTKQIADVEDLLTRGVNVLIINPVDPEGLV 70 (282)
T ss_pred CeeEEeccccCHHHHHHHHHHHHHHHHc--------CCEEE--EEcCCCCHHHHHHHHHHHHHcCCCEEEEecCCccchH
Confidence 588888863 334445566666666652 45554 456666777666777778888887766 343333223
Q ss_pred HHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHH-cCCc--EEEEEEec--CccccchHHHHH
Q 002211 129 VLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSY-FGWG--EVIAIFND--DDQGRNGVTALG 203 (953)
Q Consensus 129 av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~-~~w~--~vaii~~d--~~~g~~~~~~l~ 203 (953)
.....+.+.++|+|......+ + ..+.+..+..++...+..+++++.+ .|-+ +++++..+ ...+....+.|+
T Consensus 71 ~~i~~~~~~~iPvV~~~~~~~---~-~~~~~~~v~~d~~~~g~~~~~~l~~~~g~~~~~i~~i~~~~~~~~~~~R~~gf~ 146 (282)
T cd06318 71 PAVAAAKAAGVPVVVVDSSIN---L-EAGVVTQVQSSNAKNGNLVGEWVVGELGDKPMKIILLSGDAGNLVGQARRDGFL 146 (282)
T ss_pred HHHHHHHHCCCCEEEecCCCC---C-CcCeEEEEecCcHHHHHHHHHHHHHHhCCCCceEEEEECCCCCchHhHHHHhHH
Confidence 344556778999998764321 1 0123445667777788889988755 6754 88888743 344667778899
Q ss_pred HHHHhcCcE--------EEEEEecCCCCCCChHHHHHHHHHHhcC--CceEEEEEcchhhHHHHHHHHHHcCCC
Q 002211 204 DKLAEIRCK--------ISYKSALPPDQSVTETDVRNELVKVRMM--EARVIVVHGYSRTGLMVFDVAQRLGMM 267 (953)
Q Consensus 204 ~~l~~~g~~--------v~~~~~~~~~~~~~~~d~~~~l~~i~~~--~~~vii~~~~~~~~~~~~~~a~~~g~~ 267 (953)
+.+++.|.. +.. ..... .+..+....+.++... ++++|+.. +...+..+++.+++.|+.
T Consensus 147 ~~l~~~~~~~~~~~~~~~~~-~~~~~---~~~~~~~~~~~~~l~~~~~~~ai~~~-~d~~a~g~~~al~~~g~~ 215 (282)
T cd06318 147 LGVSEAQLRKYGKTNFTIVA-QGYGD---WTREGGLKAMEDLLVAHPDINVVYSE-NDDMALGAMRVLAEAGKT 215 (282)
T ss_pred HHHhhCcccccccCCeEEEe-cCCCC---CCHHHHHHHHHHHHHhCCCcCEEEEC-CcchHHHHHHHHHHcCCC
Confidence 999988642 211 01111 1123333445554333 45655554 444567789999999974
No 175
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=97.52 E-value=0.013 Score=65.01 Aligned_cols=203 Identities=10% Similarity=0.038 Sum_probs=123.5
Q ss_pred ceEEEeEEEec-CCCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEEccCChhh
Q 002211 48 EVLNVGAIFSF-GTVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIVGPQSAVM 126 (953)
Q Consensus 48 ~~i~IG~l~~~-~~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aiiGp~~S~~ 126 (953)
..-.||+++|- +..+-.....+++-+.++ . |+.+-+ .++..++..-......++.+++.+||=-.....
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 45689999985 344545556666666554 2 455543 455556665556666777778887773211222
Q ss_pred HHHHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecCc--cccchHHHHHH
Q 002211 127 AHVLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDDD--QGRNGVTALGD 204 (953)
Q Consensus 127 a~av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~~--~g~~~~~~l~~ 204 (953)
.......+...++|+|...... ....+++ +..++...+..++++|...|.++++++..+.. ......+.|.+
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 2344566677899999875321 1122332 45566777888889988899999999974432 23446678999
Q ss_pred HHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcC--CceEEEEEcchhhHHHHHHHHHHcCCCCC
Q 002211 205 KLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMM--EARVIVVHGYSRTGLMVFDVAQRLGMMDS 269 (953)
Q Consensus 205 ~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~--~~~vii~~~~~~~~~~~~~~a~~~g~~~~ 269 (953)
++++.|+.+.....+... .........+.++.+. .+++|+ +.+...+..+++.+.+.|+..+
T Consensus 207 al~~~g~~~~~~~~~~~~--~~~~~~~~~~~~~l~~~~~~~ai~-~~nd~~A~g~~~~l~~~g~~vp 270 (342)
T PRK10014 207 TLLKFGLPFHSEWVLECT--SSQKQAAEAITALLRHNPTISAVV-CYNETIAMGAWFGLLRAGRQSG 270 (342)
T ss_pred HHHHcCCCCCcceEecCC--CChHHHHHHHHHHHcCCCCCCEEE-ECCcHHHHHHHHHHHHcCCCCC
Confidence 999988754322111111 1123333445555443 456665 4455667788899999998654
No 176
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=97.49 E-value=0.022 Score=62.66 Aligned_cols=202 Identities=10% Similarity=0.025 Sum_probs=135.4
Q ss_pred CceEEEeEEEecC-CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEEccCChh
Q 002211 47 PEVLNVGAIFSFG-TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIVGPQSAV 125 (953)
Q Consensus 47 ~~~i~IG~l~~~~-~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aiiGp~~S~ 125 (953)
...-.||++.|-- ..+-.....|++-+.++ .|+.+-+. .+..++..-......+.+++|++||=-. ..
T Consensus 56 ~~s~~Ig~i~p~~~~~~~~~i~~gi~~~~~~--------~gy~~~l~--~~~~~~~~e~~~~~~l~~~~vdGiIi~~-~~ 124 (333)
T COG1609 56 GRTKTIGLVVPDITNPFFAEILKGIEEAARE--------AGYSLLLA--NTDDDPEKEREYLETLLQKRVDGLILLG-ER 124 (333)
T ss_pred CCCCEEEEEeCCCCCchHHHHHHHHHHHHHH--------cCCEEEEE--CCCCCHHHHHHHHHHHHHcCCCEEEEec-CC
Confidence 3567899999942 33444556677666665 25666554 4444777766677777788888887433 23
Q ss_pred hHHHHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEec--CccccchHHHHH
Q 002211 126 MAHVLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFND--DDQGRNGVTALG 203 (953)
Q Consensus 126 ~a~av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d--~~~g~~~~~~l~ 203 (953)
........+.+.++|+|......+ +..+ -.+..++..-+..+++++...|-+++++|... ...+....+.+.
T Consensus 125 ~~~~~~~~l~~~~~P~V~i~~~~~---~~~~---~~V~~Dn~~~~~~a~~~L~~~G~~~i~~i~~~~~~~~~~~R~~Gf~ 198 (333)
T COG1609 125 PNDSLLELLAAAGIPVVVIDRSPP---GLGV---PSVGIDNFAGAYLATEHLIELGHRRIAFIGGPLDSSASRERLEGYR 198 (333)
T ss_pred CCHHHHHHHHhcCCCEEEEeCCCc---cCCC---CEEEEChHHHHHHHHHHHHHCCCceEEEEeCCCccccHhHHHHHHH
Confidence 334456677777999998765544 2222 33456777888889999999999999999965 455677789999
Q ss_pred HHHHhcCcEE--EEEEecCCCCCCChHHHHHHHHHHhcCC---ceEEEEEcchhhHHHHHHHHHHcCCCCCc
Q 002211 204 DKLAEIRCKI--SYKSALPPDQSVTETDVRNELVKVRMME---ARVIVVHGYSRTGLMVFDVAQRLGMMDSG 270 (953)
Q Consensus 204 ~~l~~~g~~v--~~~~~~~~~~~~~~~d~~~~l~~i~~~~---~~vii~~~~~~~~~~~~~~a~~~g~~~~~ 270 (953)
+++++.|+.. .....-.. +..+-...+.++.... |++|+. ++...+..+++.+++.|...++
T Consensus 199 ~al~~~~~~~~~~~i~~~~~----~~~~g~~~~~~ll~~~~~~ptAif~-~nD~~Alg~l~~~~~~g~~vP~ 265 (333)
T COG1609 199 AALREAGLPINPEWIVEGDF----SEESGYEAAERLLARGEPRPTAIFC-ANDLMALGALRALRELGLRVPE 265 (333)
T ss_pred HHHHHCCCCCCcceEEecCC----ChHHHHHHHHHHHhcCCCCCcEEEE-cCcHHHHHHHHHHHHcCCCCCC
Confidence 9999999875 22111111 2344455555555432 666654 4556788899999999987654
No 177
>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=97.49 E-value=0.015 Score=62.27 Aligned_cols=206 Identities=15% Similarity=0.079 Sum_probs=125.4
Q ss_pred EeEEEecC-CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEE--ccCChh--h
Q 002211 52 VGAIFSFG-TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIV--GPQSAV--M 126 (953)
Q Consensus 52 IG~l~~~~-~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aii--Gp~~S~--~ 126 (953)
||++.|-. ..+-.....+++-+.++ .|+.+. +.++..++..-.+....++++++.++| ++.... .
T Consensus 2 Igvi~~~~~~~~~~~~~~gi~~~~~~--------~g~~~~--~~~~~~~~~~~~~~i~~l~~~~vdgiIi~~~~~~~~~~ 71 (273)
T cd06292 2 VGLLVPELSNPIFPAFAEAIEAALAQ--------YGYTVL--LCNTYRGGVSEADYVEDLLARGVRGVVFISSLHADTHA 71 (273)
T ss_pred EEEEeCCCcCchHHHHHHHHHHHHHH--------CCCEEE--EEeCCCChHHHHHHHHHHHHcCCCEEEEeCCCCCcccc
Confidence 78998863 44445566677766666 156664 455666666666777888888888766 322221 1
Q ss_pred HHHHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecC--ccccchHHHHHH
Q 002211 127 AHVLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDD--DQGRNGVTALGD 204 (953)
Q Consensus 127 a~av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~--~~g~~~~~~l~~ 204 (953)
......-+...++|+|......+. ...+++ +..++...+..+++.+...|-++++++.... .......+.|.+
T Consensus 72 ~~~~i~~~~~~~ipvV~i~~~~~~--~~~~~~---V~~d~~~~~~~~~~~l~~~g~~~i~~i~~~~~~~~~~~R~~gf~~ 146 (273)
T cd06292 72 DHSHYERLAERGLPVVLVNGRAPP--PLKVPH---VSTDDALAMRLAVRHLVALGHRRIGFASGPGRTVPRRRKIAGFRA 146 (273)
T ss_pred hhHHHHHHHhCCCCEEEEcCCCCC--CCCCCE---EEECcHHHHHHHHHHHHHCCCceEEEEeCCcccccHHHHHHHHHH
Confidence 122234456789999988654322 012332 4556777788888998888999999997432 234456788999
Q ss_pred HHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEE
Q 002211 205 KLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIA 275 (953)
Q Consensus 205 ~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~ 275 (953)
.+++.|+.......+... .+.......+.++...++++|+.. +...+..+++.+++.|+..++-+-+.
T Consensus 147 ~~~~~~~~~~~~~i~~~~--~~~~~~~~~~~~~l~~~~~ai~~~-~d~~a~g~~~~l~~~g~~ip~di~ii 214 (273)
T cd06292 147 ALEEAGLEPPEALVARGM--FSVEGGQAAAVELLGSGPTAIVAA-SDLMALGAIRAARRRGLRVPEDVSVV 214 (273)
T ss_pred HHHHcCCCCChhheEeCC--CCHHHHHHHHHHHhcCCCCEEEEc-CcHHHHHHHHHHHHcCCCCCcceEEE
Confidence 999888532110011111 112233344555544458876654 45566778899999998655444444
No 178
>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=97.48 E-value=0.0091 Score=63.67 Aligned_cols=202 Identities=12% Similarity=0.080 Sum_probs=117.6
Q ss_pred EEeEEEec------CCCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhc-CcEEEEccCC
Q 002211 51 NVGAIFSF------GTVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMET-DTLAIVGPQS 123 (953)
Q Consensus 51 ~IG~l~~~------~~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~-~v~aiiGp~~ 123 (953)
.||+++|. +..+-.....+++-+.++. |+++.+. +... +..-.....+++.. ++.+||-...
T Consensus 1 ~igli~p~~~~~~~~~~~~~~~~~~~~~~~~~~--------g~~~~~~--~~~~-~~~~~~~~~~~~~~~~~dgiii~~~ 69 (270)
T cd06294 1 TIGVVLPPSADEAFQNPFFIEVLRGISAVANEN--------GYDISLA--TGKN-EEELLEEVKKMIQQKRVDGFILLYS 69 (270)
T ss_pred CEEEEeCCccccCcCCCCHHHHHHHHHHHHHHC--------CCEEEEe--cCCC-cHHHHHHHHHHHHHcCcCEEEEecC
Confidence 37888884 3444455667777666652 5666543 3332 33344556666654 5777664221
Q ss_pred hhhHHHHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecCcc--ccchHHH
Q 002211 124 AVMAHVLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDDDQ--GRNGVTA 201 (953)
Q Consensus 124 S~~a~av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~~~--g~~~~~~ 201 (953)
... ......+.+.++|+|......+. ....+| +..++...+..+++.+...|-++++++.....+ .....+.
T Consensus 70 ~~~-~~~~~~~~~~~ipvV~~~~~~~~--~~~~~~---v~~d~~~~g~~~~~~l~~~g~~~i~~i~~~~~~~~~~~r~~g 143 (270)
T cd06294 70 RED-DPIIDYLKEEKFPFVVIGKPEDD--KENITY---VDNDNIQAGYDATEYLIKLGHKKIAFVGGDLDLEVTQDRLQG 143 (270)
T ss_pred cCC-cHHHHHHHhcCCCEEEECCCCCC--CCCCCe---EEECcHHHHHHHHHHHHHcCCccEEEecCCcccHHHHHHHHH
Confidence 111 23344557789999987543221 012222 344566677788888888899999999754332 3445788
Q ss_pred HHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcC--CceEEEEEcchhhHHHHHHHHHHcCCCCCceE
Q 002211 202 LGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMM--EARVIVVHGYSRTGLMVFDVAQRLGMMDSGYV 272 (953)
Q Consensus 202 l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~--~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~ 272 (953)
|.+.+++.|..+......... .+..+....+.++.+. ++++|+. .+...+..+++.+++.|+..++-+
T Consensus 144 f~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~l~~~~~~~ai~~-~~d~~a~g~~~al~~~g~~iP~dv 213 (270)
T cd06294 144 YKQALEDHGIPDRNEVIISLD--FSEEGGYKALKKLLEQHPRPTAIVA-TDDLLALGVLKVLNELGLKVPEDL 213 (270)
T ss_pred HHHHHHHcCCCCCcceEEecC--CchHHHHHHHHHHHhCCCCCCEEEE-CChHHHHHHHHHHHHcCCCCCcce
Confidence 999999888532111111111 1123344555555443 4676666 455677889999999998655443
No 179
>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=97.48 E-value=0.028 Score=61.00 Aligned_cols=207 Identities=9% Similarity=-0.031 Sum_probs=121.5
Q ss_pred EEeEEEec-CCCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEEc-cCChhhHH
Q 002211 51 NVGAIFSF-GTVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIVG-PQSAVMAH 128 (953)
Q Consensus 51 ~IG~l~~~-~~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aiiG-p~~S~~a~ 128 (953)
+||++.|. +..+-.....+++-+.++. |+++.+. .++..++....+....++++++.+||= +..+....
T Consensus 1 ~I~vi~~~~~~~f~~~i~~gi~~~a~~~--------g~~v~~~-~~~~~d~~~~~~~i~~~~~~~~DgiIi~~~~~~~~~ 71 (298)
T cd06302 1 TIAFVPKVTGIPYFNRMEEGAKEAAKEL--------GVDAIYV-GPTTADAAGQVQIIEDLIAQGVDAIAVVPNDPDALE 71 (298)
T ss_pred CEEEEEcCCCChHHHHHHHHHHHHHHHh--------CCeEEEE-CCCCCCHHHHHHHHHHHHhcCCCEEEEecCCHHHHH
Confidence 48888874 3444445566777666661 5555532 244467777777777788888887774 33333233
Q ss_pred HHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHc-CC-cEEEEEEecCc--cccchHHHHHH
Q 002211 129 VLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYF-GW-GEVIAIFNDDD--QGRNGVTALGD 204 (953)
Q Consensus 129 av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~-~w-~~vaii~~d~~--~g~~~~~~l~~ 204 (953)
.....+...++|+|......+. .. ..+.....++...+..+++++.+. +- ++++++..+.. ......+.|.+
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 01 123344567777788888887766 43 69999975332 33445688999
Q ss_pred HHHhcC---cEEEEEEecCCCCCCChHHHHHHHHHHhcC--CceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEEe
Q 002211 205 KLAEIR---CKISYKSALPPDQSVTETDVRNELVKVRMM--EARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIAT 276 (953)
Q Consensus 205 ~l~~~g---~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~--~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~ 276 (953)
+++++| .++.. ..... .+...-...++++.+. ++++|+.. +...+..+++.++++|+. .+...++-
T Consensus 148 ~l~~~g~~~~~~~~--~~~~~--~~~~~~~~~~~~~l~~~~~~~ai~~~-~D~~A~g~~~al~~~g~~-~dv~vvG~ 218 (298)
T cd06302 148 YQKEKYYPMLELVD--RQYGD--DDADKSYQTAQELLKAYPDLKGIIGP-TSVGIPGAARAVEEAGLK-GKVAVTGL 218 (298)
T ss_pred HHhhcCCCCeEEeC--cccCC--CCHHHHHHHHHHHHHhCCCceEEEEC-CCcchhHHHHHHHhcCCC-CCEEEEEe
Confidence 999887 23221 11111 1223333344454333 35555544 456678899999999975 33333333
No 180
>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=97.46 E-value=0.011 Score=63.14 Aligned_cols=207 Identities=10% Similarity=0.028 Sum_probs=124.9
Q ss_pred EEeEEEec-CCCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEE-ccCChhhHH
Q 002211 51 NVGAIFSF-GTVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIV-GPQSAVMAH 128 (953)
Q Consensus 51 ~IG~l~~~-~~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aii-Gp~~S~~a~ 128 (953)
.||++.|. +..+-.....+++-+.++. |+++. +.++..++..-.+....++++++.+|| .|.....
T Consensus 1 ~i~vi~~~~~~~~~~~~~~gi~~~~~~~--------g~~~~--~~~~~~~~~~~~~~i~~l~~~~~dgiii~~~~~~~-- 68 (270)
T cd06296 1 LIGLVFPDLDSPWASEVLRGVEEAAAAA--------GYDVV--LSESGRRTSPERQWVERLSARRTDGVILVTPELTS-- 68 (270)
T ss_pred CeEEEECCCCCccHHHHHHHHHHHHHHc--------CCeEE--EecCCCchHHHHHHHHHHHHcCCCEEEEecCCCCh--
Confidence 37888875 3555566677777666651 55654 445555555555566677788888776 3333222
Q ss_pred HHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEec--CccccchHHHHHHHH
Q 002211 129 VLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFND--DDQGRNGVTALGDKL 206 (953)
Q Consensus 129 av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d--~~~g~~~~~~l~~~l 206 (953)
.....+...++|+|........ ...+++ ..+++...+..+++.+...|.++++++..+ +.......+.|.+.+
T Consensus 69 ~~~~~~~~~~ipvV~i~~~~~~--~~~~~~---v~~d~~~~~~~a~~~l~~~g~~~i~~i~~~~~~~~~~~r~~gf~~~~ 143 (270)
T cd06296 69 AQRAALRRTGIPFVVVDPAGDP--DADVPS---VGATNWAGGLAATEHLLELGHRRIGFITGPPDLLCSRARLDGYRAAL 143 (270)
T ss_pred HHHHHHhcCCCCEEEEecccCC--CCCCCE---EEeCcHHHHHHHHHHHHHcCCCcEEEEcCCCcchhHHHHHHHHHHHH
Confidence 2345567789999988654211 122333 456667778888888888899999999743 233455678899999
Q ss_pred HhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcC--CceEEEEEcchhhHHHHHHHHHHcCCCCCceE-EEEeC
Q 002211 207 AEIRCKISYKSALPPDQSVTETDVRNELVKVRMM--EARVIVVHGYSRTGLMVFDVAQRLGMMDSGYV-WIATT 277 (953)
Q Consensus 207 ~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~--~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~-wi~~~ 277 (953)
++.|+.+......... .+.+.....+.++.+. .+++|+.. +...+..+++.+++.|+..++-+ .++.+
T Consensus 144 ~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~l~~~~~~~ai~~~-~d~~a~~~~~~l~~~g~~~p~~i~v~~~d 214 (270)
T cd06296 144 AEAGIPVDPALVREGD--FSTESGFRAAAELLALPERPTAIFAG-NDLMALGVYEAARERGLRIPEDLSVVGFD 214 (270)
T ss_pred HHcCCCCChHHheeCC--CCHHHHHHHHHHHHhCCCCCcEEEEc-CcHHHHHHHHHHHHhCCCCCCceEEEEEC
Confidence 8887654221111111 1123334445555433 45665544 45567788999999998644433 44443
No 181
>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=97.45 E-value=0.039 Score=58.91 Aligned_cols=206 Identities=10% Similarity=0.114 Sum_probs=117.2
Q ss_pred EEeEEEecCCCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEE-ccCChhhHHH
Q 002211 51 NVGAIFSFGTVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIV-GPQSAVMAHV 129 (953)
Q Consensus 51 ~IG~l~~~~~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aii-Gp~~S~~a~a 129 (953)
+||++...+..+-.....+++-+.++. |+.+.+. .++..++..-.+....+++++|.++| .|........
T Consensus 1 ~i~~v~~~~~~~~~~~~~gi~~~~~~~--------g~~~~~~-~~~~~~~~~~~~~i~~l~~~~vDgiIi~~~~~~~~~~ 71 (271)
T cd06314 1 TIAVVTNGASPFWKIAEAGVKAAGKEL--------GVDVEFV-VPQQGTVNAQLRMLEDLIAEGVDGIAISPIDPKAVIP 71 (271)
T ss_pred CeEEEcCCCcHHHHHHHHHHHHHHHHc--------CCeEEEe-CCCCCCHHHHHHHHHHHHhcCCCEEEEecCChhHhHH
Confidence 478887655544445556666555552 4565544 23444666666667778888888776 4443332223
Q ss_pred HHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHc--CCcEEEEEEecC--ccccchHHHHHHH
Q 002211 130 LSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYF--GWGEVIAIFNDD--DQGRNGVTALGDK 205 (953)
Q Consensus 130 v~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~--~w~~vaii~~d~--~~g~~~~~~l~~~ 205 (953)
...-+.+ ++|+|......+. ... +--+..++...+..+++++.+. +-.+++++.... .......+.++++
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 3333345 9999987543211 111 2224456666678888887664 335666665432 3345667889999
Q ss_pred HHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcC--CceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEEeC
Q 002211 206 LAEIRCKISYKSALPPDQSVTETDVRNELVKVRMM--EARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIATT 277 (953)
Q Consensus 206 l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~--~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~ 277 (953)
+++.|+++.... .. . .+..+....+.++.+. .+++|+.. +...+..+++.+++.|.. .+...++.+
T Consensus 146 ~~~~~~~~~~~~-~~-~--~~~~~~~~~~~~~l~~~~~~~~i~~~-~d~~a~~~~~al~~~g~~-~di~vig~d 213 (271)
T cd06314 146 IKDSKIEIVDTR-GD-E--EDFAKAKSNAEDALNAHPDLKCMFGL-YAYNGPAIAEAVKAAGKL-GKVKIVGFD 213 (271)
T ss_pred HhcCCcEEEEEe-cC-c--cCHHHHHHHHHHHHHhCCCccEEEec-CCccHHHHHHHHHHcCCC-CceEEEEeC
Confidence 999998765421 11 1 1233444556666443 35666544 334455678888888875 343444433
No 182
>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=97.43 E-value=0.011 Score=63.30 Aligned_cols=206 Identities=14% Similarity=0.112 Sum_probs=125.0
Q ss_pred EeEEEecC-CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEE-ccCChh---h
Q 002211 52 VGAIFSFG-TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIV-GPQSAV---M 126 (953)
Q Consensus 52 IG~l~~~~-~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aii-Gp~~S~---~ 126 (953)
||++.|-. +.+-.....+++-+.++ . |+++. +.++..++....+..+.+++.+|.+|| -|..+. .
T Consensus 2 igvv~~~~~~~~~~~~~~gi~~~~~~----~----g~~~~--~~~~~~~~~~~~~~i~~l~~~~vdgii~~~~~~~~~~~ 71 (273)
T cd01541 2 IGVITTYISDYIFPSIIRGIESVLSE----K----GYSLL--LASTNNDPERERKCLENMLSQGIDGLIIEPTKSALPNP 71 (273)
T ss_pred eEEEeCCccchhHHHHHHHHHHHHHH----c----CCEEE--EEeCCCCHHHHHHHHHHHHHcCCCEEEEeccccccccc
Confidence 78888753 44334455555544444 1 45554 466677887777888888888888886 333221 1
Q ss_pred HHHHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEec-CccccchHHHHHHH
Q 002211 127 AHVLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFND-DDQGRNGVTALGDK 205 (953)
Q Consensus 127 a~av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d-~~~g~~~~~~l~~~ 205 (953)
.......+...++|+|......+. .. +..+..++...+..+++++...|.++++++... +..+....+.+.+.
T Consensus 72 ~~~~~~~~~~~~ipvV~~~~~~~~---~~---~~~V~~D~~~~g~~~~~~l~~~G~~~i~~l~~~~~~~~~~r~~g~~~~ 145 (273)
T cd01541 72 NIDLYLKLEKLGIPYVFINASYEE---LN---FPSLVLDDEKGGYKATEYLIELGHRKIAGIFKADDLQGVKRMKGFIKA 145 (273)
T ss_pred cHHHHHHHHHCCCCEEEEecCCCC---CC---CCEEEECcHHHHHHHHHHHHHcCCcCEEEecCCCcccHHHHHHHHHHH
Confidence 213334457779999987643221 11 223556677778888999888899999988743 22344556788999
Q ss_pred HHhcCcEEEEE--EecCCCCCCChHHHHHHHHHHhcC--CceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEEe
Q 002211 206 LAEIRCKISYK--SALPPDQSVTETDVRNELVKVRMM--EARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIAT 276 (953)
Q Consensus 206 l~~~g~~v~~~--~~~~~~~~~~~~d~~~~l~~i~~~--~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~ 276 (953)
+++.|..+... ..+... .........++++.+. .+++|+. .+...+..+++.+++.|+..++-+-|.+
T Consensus 146 l~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~l~~~~~~~av~~-~~d~~a~g~~~al~~~g~~~p~dv~vvg 217 (273)
T cd01541 146 YREHGIPFNPSNVITYTTE--EKEEKLFEKIKEILKRPERPTAIVC-YNDEIALRVIDLLKELGLKIPEDISVVG 217 (273)
T ss_pred HHHcCCCCChHHEEecccc--chhhHHHHHHHHHHcCCCCCCEEEE-cCcHHHHHHHHHHHHcCCCCCCcEEEEE
Confidence 98888643211 111111 1112344555555433 4676644 4555677789999999986655444443
No 183
>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=97.42 E-value=0.031 Score=60.56 Aligned_cols=195 Identities=13% Similarity=0.004 Sum_probs=113.1
Q ss_pred EEeEEEecC-CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEE-ccCChhh-H
Q 002211 51 NVGAIFSFG-TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIV-GPQSAVM-A 127 (953)
Q Consensus 51 ~IG~l~~~~-~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aii-Gp~~S~~-a 127 (953)
+||++.|-. ..+-.....+++-+.++ .|+.+.+...+...++..-......++++++.+|| .|..... .
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 589998853 33333444555555554 15667664444334665666677778888888876 3332222 2
Q ss_pred HHHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcC-----CcEEEEEEecC--ccccchHH
Q 002211 128 HVLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFG-----WGEVIAIFNDD--DQGRNGVT 200 (953)
Q Consensus 128 ~av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~-----w~~vaii~~d~--~~g~~~~~ 200 (953)
..+.. +. .++|+|......+ +. ..+-.+..++..-+..+++++.... -+++++++... .......+
T Consensus 73 ~~l~~-~~-~~iPvV~~~~~~~---~~--~~~~~V~~D~~~~g~~~~~~L~~~~~~~~g~~~I~~i~g~~~~~~~~~R~~ 145 (295)
T TIGR02955 73 HDLAQ-LT-KSIPVFALVNQID---SN--QVKGRVGVDWYQMGYQAGEYLAQRHPKGSGPTTLAWLPGPKNRGGTKPVTQ 145 (295)
T ss_pred HHHHH-Hh-cCCCEEEEecCCC---cc--ceeEEEeecHHHHHHHHHHHHHHhcccCCCCeeEEEEeCCCcCCchhHHHH
Confidence 22333 33 4899987632211 11 1223455566666777888876621 24699997543 34556688
Q ss_pred HHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcC--CceEEEEEcchhhHHHHHHHHHHcCC
Q 002211 201 ALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMM--EARVIVVHGYSRTGLMVFDVAQRLGM 266 (953)
Q Consensus 201 ~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~--~~~vii~~~~~~~~~~~~~~a~~~g~ 266 (953)
.|.+.+++.|+++... .... .+..+-...++++.+. ++++| ++....+..+++.+++.|.
T Consensus 146 Gf~~al~~~g~~~~~~--~~~~--~~~~~~~~~~~~~L~~~~~~d~i--~~~d~~a~g~l~al~~~g~ 207 (295)
T TIGR02955 146 GFRAALEGSDVEISAI--LWAD--NDKELQRNLLQDLLKKHPDIDYL--VGSAVAAEAAISELRSLHM 207 (295)
T ss_pred HHHHHHhcCCcEEEEE--ecCC--CcHHHHHHHHHHHHHhCCCcCEE--EeccHHHHHHHHHHHhhCc
Confidence 9999999989876532 2211 1233334455555433 45754 4555667788899888876
No 184
>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=97.42 E-value=0.022 Score=62.73 Aligned_cols=205 Identities=8% Similarity=0.008 Sum_probs=122.7
Q ss_pred ceEEEeEEEec-CCCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEE-ccCChh
Q 002211 48 EVLNVGAIFSF-GTVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIV-GPQSAV 125 (953)
Q Consensus 48 ~~i~IG~l~~~-~~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aii-Gp~~S~ 125 (953)
..-.||+++|. +..+-.....+++-+.++ .|+.+.+. ++..++..-......+.++++.+|| -|....
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 45689999985 344444555666655554 26676544 4444565555566667777888766 333221
Q ss_pred hHHHHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecCc--cccchHHHHH
Q 002211 126 MAHVLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDDD--QGRNGVTALG 203 (953)
Q Consensus 126 ~a~av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~~--~g~~~~~~l~ 203 (953)
.. .....+...++|+|......+ +..+++ +..++..-+..+++++...|.++++++..... ......+.|.
T Consensus 129 ~~-~~~~~l~~~~iPvV~~~~~~~---~~~~~~---V~~dn~~~~~~~~~~L~~~G~~~I~~i~~~~~~~~~~~R~~Gf~ 201 (327)
T TIGR02417 129 ED-AYYQKLQNEGLPVVALDRSLD---DEHFCS---VISDDVDAAAELIERLLSQHADEFWYLGAQPELSVSRDRLAGFR 201 (327)
T ss_pred Ch-HHHHHHHhcCCCEEEEccccC---CCCCCE---EEeCcHHHHHHHHHHHHHCCCCeEEEEeCcccchhHHHHHHHHH
Confidence 22 223445567999998754322 122333 34455666777788888889999999974432 3455678899
Q ss_pred HHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcC---CceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEE
Q 002211 204 DKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMM---EARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIA 275 (953)
Q Consensus 204 ~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~---~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~ 275 (953)
+++++.|+.+.... ... .+.++-...+.++.+. .+++|+.. +...+..+++.+++.| ..++-+-|.
T Consensus 202 ~al~~~~~~~~~~~--~~~--~~~~~~~~~~~~ll~~~~~~~~Ai~~~-~D~~A~g~~~al~~~g-~vP~dvsvi 270 (327)
T TIGR02417 202 QALKQATLEVEWVY--GGN--YSRESGYQMFAKLCARLGRLPQALFTT-SYTLLEGVLDYMLERP-LLDSQLHLA 270 (327)
T ss_pred HHHHHcCCChHhEE--eCC--CChHHHHHHHHHHHhcCCCCCcEEEEc-CcHHHHHHHHHHHHcC-CCCCcceEE
Confidence 99999887532111 111 1123333455565443 36776665 4456778999999999 655444333
No 185
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=97.41 E-value=0.021 Score=62.88 Aligned_cols=208 Identities=7% Similarity=0.004 Sum_probs=122.2
Q ss_pred CceEEEeEEEecC-CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEEc-cCCh
Q 002211 47 PEVLNVGAIFSFG-TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIVG-PQSA 124 (953)
Q Consensus 47 ~~~i~IG~l~~~~-~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aiiG-p~~S 124 (953)
...-.||+++|.. ..+-.....+++-+.++ .|+++.+ .++..++..-.+....+.+++|.+||= |...
T Consensus 54 ~~~~~Igvi~~~~~~~~~~~~~~gi~~~~~~--------~g~~~~~--~~~~~~~~~~~~~~~~l~~~~vdGiI~~~~~~ 123 (327)
T PRK10423 54 NQTRTIGMLITASTNPFYSELVRGVERSCFE--------RGYSLVL--CNTEGDEQRMNRNLETLMQKRVDGLLLLCTET 123 (327)
T ss_pred CCCCeEEEEeCCCCCCcHHHHHHHHHHHHHH--------cCCEEEE--EeCCCCHHHHHHHHHHHHHcCCCEEEEeCCCc
Confidence 3456899999863 34444566677666665 1566554 455556665556666777777777662 2221
Q ss_pred hhHHHHHHhhhh-CCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEec--CccccchHHH
Q 002211 125 VMAHVLSHLANE-LQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFND--DDQGRNGVTA 201 (953)
Q Consensus 125 ~~a~av~~v~~~-~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d--~~~g~~~~~~ 201 (953)
.. ........ .++|+|....... ...++ ....++..-+..+++++...|-+++++|..+ ........+.
T Consensus 124 ~~--~~~~~l~~~~~iPvV~i~~~~~---~~~~~---~v~~d~~~~~~~a~~~L~~~G~~~I~~i~~~~~~~~~~~R~~G 195 (327)
T PRK10423 124 HQ--PSREIMQRYPSVPTVMMDWAPF---DGDSD---LIQDNSLLGGDLATQYLIDKGYTRIACITGPLDKTPARLRLEG 195 (327)
T ss_pred ch--hhHHHHHhcCCCCEEEECCccC---CCCCC---EEEEChHHHHHHHHHHHHHcCCCeEEEEeCCccccchHHHHHH
Confidence 11 11222333 4899998753211 11111 2334444557888888888999999999643 3344566789
Q ss_pred HHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcC--CceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEE
Q 002211 202 LGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMM--EARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIA 275 (953)
Q Consensus 202 l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~--~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~ 275 (953)
|.+++++.|+.+.....+..+ .+.......+.++.+. .+++|+.. +...+..+++.+++.|+..++-+-+.
T Consensus 196 f~~al~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~l~~~~~~~ai~~~-~d~~A~g~~~~l~~~g~~vP~dvsvi 268 (327)
T PRK10423 196 YRAAMKRAGLNIPDGYEVTGD--FEFNGGFDAMQQLLALPLRPQAVFTG-NDAMAVGVYQALYQAGLSVPQDIAVI 268 (327)
T ss_pred HHHHHHHcCCCCCcceEEeCC--CChHHHHHHHHHHhcCCCCCCEEEEc-CcHHHHHHHHHHHHcCCCCCCceEEE
Confidence 999999998764321111111 1122333445555433 46765554 45567789999999998765544444
No 186
>PF12974 Phosphonate-bd: ABC transporter, phosphonate, periplasmic substrate-binding protein ; PDB: 3N5L_B 3QUJ_C 3P7I_A 3QK6_A 3S4U_A.
Probab=97.41 E-value=0.0012 Score=69.39 Aligned_cols=121 Identities=24% Similarity=0.286 Sum_probs=77.1
Q ss_pred CCCCChHHhhhCCCeEEEEeCch-----HHHHHH-HhhCCCc---cceEeCCCHHHHHHHHHcCCcEEEEccchhHHHHH
Q 002211 700 SPIKGIDTLMTSNDRVGYQVGSF-----AENYLI-EELSIPK---SRLVALGSPEEYAIALENRTVAAVVDERPYIDLFL 770 (953)
Q Consensus 700 ~~I~sl~dL~~~~~~ig~~~~s~-----~~~~l~-~~~~~~~---~~~~~~~~~~~~~~~l~~g~~~a~~~~~~~~~~~~ 770 (953)
.+|++++||. |++|++...+. ....+. ++.++.. .+.+...+.+..+.+|.+|++|+.+.....++-+.
T Consensus 95 s~i~~l~dL~--Gk~v~~~~~~s~sg~l~~~~~L~~~~Gl~~~~~~~~~~~~~~~~~~~~l~~G~~Da~~~~~~~~~~~~ 172 (243)
T PF12974_consen 95 SPITSLADLK--GKRVAFPDPSSTSGYLIPRYELLREAGLDPGDDFKQVFVGSHDAVLEALLNGKADAAAIPSDAFERLE 172 (243)
T ss_dssp SS--SHHHHG--GSEEEEE-TT-TTTTHHHHHHTCCCCT--HHHHSSEEEEE-HHHHHHHHHTTSSSEEEEEHHHHHHHH
T ss_pred CCCCChhhcC--CCEEEEecCCccHHHHHHHHHHHHHcCCChhHceeEEEeCCHHHHHHHHHcCCccEEEEechhHHHHH
Confidence 4699999996 99999975442 222222 2334332 13345668899999999999999998887777766
Q ss_pred hcC----cceEEeCCccccCccEEEecCCCc--chHHHHHHHHhhhccccHHHHHHHh
Q 002211 771 SDH----CQFSVRGQEFTKSGWGFAFPRDSP--LAIDMSTAILTLSENGELQRIHDKW 822 (953)
Q Consensus 771 ~~~----~~l~~~~~~~~~~~~~~~~~k~sp--l~~~~n~~i~~l~e~G~~~~~~~~w 822 (953)
... .+++++...-....+.++.+++-| .++.+-.+++.+..+-.-.++.+.+
T Consensus 173 ~~~~~~~~~~rvl~~s~~~p~~~~~~~~~~~~~~~~~l~~al~~~~~~~~~~~~l~~~ 230 (243)
T PF12974_consen 173 AEGPDIPSQLRVLWTSPPYPNWPLVASPDLPPELRQRLRDALLSLSKDPEGKAILDAF 230 (243)
T ss_dssp HH-HHHHTTEEEEEEEEEEE--EEEEETTS-HHHHHHHHHHHHHTTSSHHHHHHHHHT
T ss_pred HccCcccccEEEEEEeCCCCCcEEEEeCCCCHHHHHHHHHHHHcCCCChhhHHHHHhc
Confidence 542 357777654333456787888755 8999999999999865444555544
No 187
>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=97.41 E-value=0.018 Score=61.38 Aligned_cols=196 Identities=15% Similarity=0.037 Sum_probs=110.0
Q ss_pred EEeEEEec----CCCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEEccCChhh
Q 002211 51 NVGAIFSF----GTVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIVGPQSAVM 126 (953)
Q Consensus 51 ~IG~l~~~----~~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aiiGp~~S~~ 126 (953)
|||++.|. +..+-.....|++-+.++ .|+++.+. +.. ++..-.+....+.+++|.+||--. +..
T Consensus 1 ~I~~i~~~~~~~~~~f~~~~~~gi~~~~~~--------~gy~~~i~--~~~-~~~~~~~~i~~l~~~~vdgiI~~~-~~~ 68 (265)
T cd06354 1 KVALVTDVGGLGDKSFNQSAWEGLERAAKE--------LGIEYKYV--ESK-SDADYEPNLEQLADAGYDLIVGVG-FLL 68 (265)
T ss_pred CEEEEeCCCCcCchhHHHHHHHHHHHHHHH--------cCCeEEEE--ecC-CHHHHHHHHHHHHhCCCCEEEEcC-cch
Confidence 58999985 233444556666666665 25666654 333 333334556667777888888522 122
Q ss_pred HHHHHHhhhhC-CCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHc-CCcEEEEEEecCc-cccchHHHHH
Q 002211 127 AHVLSHLANEL-QVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYF-GWGEVIAIFNDDD-QGRNGVTALG 203 (953)
Q Consensus 127 a~av~~v~~~~-~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~-~w~~vaii~~d~~-~g~~~~~~l~ 203 (953)
.........++ ++|++..+...+.. +.+-+...++..-+..++.++... |-++++++..+.. ......+.|.
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 23455566665 89999875432110 112223334444444445555543 8999999975322 1122236889
Q ss_pred HHHHhcC---cEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHHHcC
Q 002211 204 DKLAEIR---CKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQRLG 265 (953)
Q Consensus 204 ~~l~~~g---~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~~~g 265 (953)
+.+++.| ..+......... ..+..+-...++++.+.+||+|+.. ....+..+++.+++.|
T Consensus 144 ~~~~~~g~~~~~~~~~~~~~~~-~~~~~~~~~~~~~ll~~~pdaI~~~-nd~~A~gv~~al~~~g 206 (265)
T cd06354 144 AGVKYVNPGVPDIEVLVQYAGS-FNDPAKGKEIAQAMYDQGADVIFAA-AGGTGNGVFQAAKEAG 206 (265)
T ss_pred HHHHHHhccCCCceEEEEEcCc-ccCHHHHHHHHHHHHHCCCcEEEEC-CCCCchHHHHHHHhcC
Confidence 9998888 643322111111 0112333445666655568875554 5566778899999988
No 188
>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=97.39 E-value=0.019 Score=60.99 Aligned_cols=198 Identities=14% Similarity=0.099 Sum_probs=118.4
Q ss_pred EEeEEEec-CCCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEE-ccCChhhHH
Q 002211 51 NVGAIFSF-GTVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIV-GPQSAVMAH 128 (953)
Q Consensus 51 ~IG~l~~~-~~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aii-Gp~~S~~a~ 128 (953)
.||++.|. +..+-.....+++-+.++. |+++. +.++..++..-.+....+..+++.+|| .|..+.
T Consensus 1 ~I~vi~~~~~~~~~~~~~~gi~~~~~~~--------g~~~~--~~~~~~~~~~~~~~i~~~~~~~~dgiii~~~~~~--- 67 (265)
T cd06291 1 LIGLIVPTISNPFFSELARAVEKELYKK--------GYKLI--LCNSDNDPEKEREYLEMLRQNQVDGIIAGTHNLG--- 67 (265)
T ss_pred CEEEEECCCCChhHHHHHHHHHHHHHHC--------CCeEE--EecCCccHHHHHHHHHHHHHcCCCEEEEecCCcC---
Confidence 37888874 4444445566665555552 55654 455555666555666667777777766 333222
Q ss_pred HHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecC---ccccchHHHHHHH
Q 002211 129 VLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDD---DQGRNGVTALGDK 205 (953)
Q Consensus 129 av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~---~~g~~~~~~l~~~ 205 (953)
. .-+...++|+|......+ ...+| +..++...+..+++++...|.++++++.... .......+.|.+.
T Consensus 68 -~-~~~~~~gipvv~~~~~~~----~~~~~---V~~d~~~~g~~~~~~l~~~g~~~i~~i~~~~~~~~~~~~r~~gf~~~ 138 (265)
T cd06291 68 -I-EEYENIDLPIVSFDRYLS----ENIPI---VSSDNYEGGRLAAEELIERGCKHIAHIGGPNNTVSPTNLRYEGFLDV 138 (265)
T ss_pred -H-HHHhcCCCCEEEEeCCCC----CCCCe---EeechHHHHHHHHHHHHHcCCcEEEEEccCcccccchHHHHHHHHHH
Confidence 1 244567999998865432 12333 4455566778888888888999999997433 3345567889999
Q ss_pred HHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcC--CceEEEEEcchhhHHHHHHHHHHcCCCCCceEEE
Q 002211 206 LAEIRCKISYKSALPPDQSVTETDVRNELVKVRMM--EARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWI 274 (953)
Q Consensus 206 l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~--~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi 274 (953)
+++.|+.+.... .... .+..+....+.++.+. .+++|+... ...+..+++.+++.|...++-+-+
T Consensus 139 l~~~~~~~~~~~-~~~~--~~~~~~~~~~~~~l~~~~~~~ai~~~~-d~~a~~~~~al~~~g~~vp~di~v 205 (265)
T cd06291 139 LKENGLEVRIIE-IQEN--FDDAEKKEEIKELLEEYPDIDGIFASN-DLTAILVLKEAQQRGIRVPEDLQI 205 (265)
T ss_pred HHHcCCCCChhe-eecc--ccchHHHHHHHHHHhCCCCCCEEEECC-hHHHHHHHHHHHHcCCCCCcceEE
Confidence 998887542211 1111 1122233445555443 346555543 446778899999999764443333
No 189
>PRK11553 alkanesulfonate transporter substrate-binding subunit; Provisional
Probab=97.37 E-value=0.0015 Score=71.72 Aligned_cols=110 Identities=21% Similarity=0.283 Sum_probs=65.3
Q ss_pred CCCChHHhhhCCCeEEEEeCchHHHHHHH---hhCCCccce-EeCCCHHHHHHHHHcCCcEEEEccchhHHHHHhcCc-c
Q 002211 701 PIKGIDTLMTSNDRVGYQVGSFAENYLIE---ELSIPKSRL-VALGSPEEYAIALENRTVAAVVDERPYIDLFLSDHC-Q 775 (953)
Q Consensus 701 ~I~sl~dL~~~~~~ig~~~~s~~~~~l~~---~~~~~~~~~-~~~~~~~~~~~~l~~g~~~a~~~~~~~~~~~~~~~~-~ 775 (953)
+|.+++||. |++|++..|+..+.++.+ ..+.....+ ..+.+..+...++.+|++|+++...++......+.. +
T Consensus 120 ~i~s~~dL~--Gk~I~~~~gs~~~~~l~~~l~~~g~~~~dv~~v~~~~~~~~~al~~G~vDa~~~~ep~~~~~~~~~~~~ 197 (314)
T PRK11553 120 PIKTVADLK--GHKVAFQKGSSSHNLLLRALRKAGLKFTDIQPTYLTPADARAAFQQGNVDAWAIWDPYYSAALLQGGVR 197 (314)
T ss_pred CCCCHHHhC--CCEEeecCCCcHHHHHHHHHHHcCCCHHHeEEEecChHHHHHHHHcCCCCEEEEcCcHHHHHHhcCCcE
Confidence 678999996 889999888766665543 233332222 234577788999999999999988777766554432 2
Q ss_pred eEEeCCccccCccEEEecCC--CcchHHHHHHHHhhhcc
Q 002211 776 FSVRGQEFTKSGWGFAFPRD--SPLAIDMSTAILTLSEN 812 (953)
Q Consensus 776 l~~~~~~~~~~~~~~~~~k~--spl~~~~n~~i~~l~e~ 812 (953)
+...+..+...+..+++.+. ....+.+++.+..+.+.
T Consensus 198 ~~~~~~~~~~~~~~~~~~~~~~~~~p~~v~~~l~a~~~A 236 (314)
T PRK11553 198 VLKDGTDLNQTGSFYLAARPYAEKNGAFIQQVLATLTEA 236 (314)
T ss_pred EeecCcccCcCceEEEEcHHHHHHCHHHHHHHHHHHHHH
Confidence 33333333223323333322 12445555555555554
No 190
>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=97.36 E-value=0.045 Score=58.58 Aligned_cols=210 Identities=12% Similarity=0.047 Sum_probs=118.3
Q ss_pred EEeEEEecC-CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEE-ccCChhhHH
Q 002211 51 NVGAIFSFG-TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIV-GPQSAVMAH 128 (953)
Q Consensus 51 ~IG~l~~~~-~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aii-Gp~~S~~a~ 128 (953)
+||++.|-. ..+-.....+++-+.++.+-. ...+.... ....++..-.+....+.. ++.+|| .|..+....
T Consensus 1 ~ig~v~~~~~~~~~~~~~~~i~~~~~~~g~~-----~~~~~~~~-~~~~~~~~~~~~i~~~~~-~vdgiii~~~~~~~~~ 73 (275)
T cd06307 1 RLGFLLPKGSNAFYRELAAALEAAAAAFPDA-----RIRVRIHF-VESFDPAALAAALLRLGA-RSDGVALVAPDHPQVR 73 (275)
T ss_pred CeEEEeCCCCChHHHHHHHHHHHHHhhhhcc-----CceEEEEE-ccCCCHHHHHHHHHHHHh-cCCEEEEeCCCcHHHH
Confidence 588888763 344445566666666663211 12233222 233455554555555666 777765 444433333
Q ss_pred HHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHc-C--CcEEEEEEecCc--cccchHHHHH
Q 002211 129 VLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYF-G--WGEVIAIFNDDD--QGRNGVTALG 203 (953)
Q Consensus 129 av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~-~--w~~vaii~~d~~--~g~~~~~~l~ 203 (953)
.....+.+.++|+|.+....+. ... +..+..++...+..+++++.+. | -++++++..+.. ......+.|.
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 4446666789999987543221 111 2224555566667777776665 5 369999975432 3345578899
Q ss_pred HHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhc--CCceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEEeC
Q 002211 204 DKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRM--MEARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIATT 277 (953)
Q Consensus 204 ~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~--~~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~ 277 (953)
+++++.+..+......... .+..+....++++.+ .++++|+..... +..+++.+++.|+. .+...++.|
T Consensus 149 ~a~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~l~~~~~~~ai~~~~d~--~~g~~~al~~~g~~-~di~Ivg~d 219 (275)
T cd06307 149 SVLREEFPGLRVLETLEGL--DDPARAYEATRKLLARHPDLVGIYNAGGG--NRGVIRALREAGRA-GKVVFVGHE 219 (275)
T ss_pred HHHHhhCCCcEEEeeccCC--CChHHHHHHHHHHHHhCCCceEEEECCCC--hHHHHHHHHHcCCC-CCcEEEEec
Confidence 9998877544322222211 123334455556543 357787777653 36899999999975 344444443
No 191
>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=97.36 E-value=0.024 Score=60.44 Aligned_cols=198 Identities=10% Similarity=0.021 Sum_probs=114.1
Q ss_pred EeEEEec----CCCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEEccCChhhH
Q 002211 52 VGAIFSF----GTVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIVGPQSAVMA 127 (953)
Q Consensus 52 IG~l~~~----~~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aiiGp~~S~~a 127 (953)
||+++|. +..+-.....+++-+.++. |+++.+...|.. ...-......+.++++.+||-......
T Consensus 2 vgv~~~~~~~~~~~~~~~~~~~i~~~~~~~--------g~~~~~~~~~~~--~~~~~~~~~~l~~~~vdgiii~~~~~~- 70 (268)
T cd06277 2 IGLIASKRILNSPAFYSEIYRAIEEEAKKY--------GYNLILKFVSDE--DEEEFELPSFLEDGKVDGIILLGGIST- 70 (268)
T ss_pred eEEEEeccccccCCcHHHHHHHHHHHHHHc--------CCEEEEEeCCCC--hHHHHHHHHHHHHCCCCEEEEeCCCCh-
Confidence 7888886 2444445556665555541 677777665533 222223333466678888885222222
Q ss_pred HHHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecCc--cccchHHHHHHH
Q 002211 128 HVLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDDD--QGRNGVTALGDK 205 (953)
Q Consensus 128 ~av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~~--~g~~~~~~l~~~ 205 (953)
.....+...++|+|......+ ....++ +..++...+..+++++...|.++++++..+.. ......+.|.+.
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 225556778999998754332 122333 33455556677778887889999999975543 234456789999
Q ss_pred HHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHHHcCCCCCc
Q 002211 206 LAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQRLGMMDSG 270 (953)
Q Consensus 206 l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~~~g~~~~~ 270 (953)
+++.|+++.....+... ......+...+.+.. ..+++|+.. ....+..+++.+++.|+..++
T Consensus 144 ~~~~~~~~~~~~~~~~~-~~~~~~~~~~l~~~~-~~~~ai~~~-~d~~a~g~~~a~~~~g~~~p~ 205 (268)
T cd06277 144 LLDHGIPFNEDYDITEK-EEDEEDIGKFIDELK-PLPTAFFCS-NDGVAFLLIKVLKEMGIRVPE 205 (268)
T ss_pred HHHcCCCCCcceEEEcc-hhHHHHHHHHHhcCC-CCCCEEEEC-CcHHHHHHHHHHHHcCCCCCC
Confidence 99988764321111110 011233344343322 247765555 445567788888999986443
No 192
>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=97.36 E-value=0.017 Score=61.13 Aligned_cols=199 Identities=9% Similarity=0.034 Sum_probs=122.1
Q ss_pred EEeEEEec-CCCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEEc-cCChhhHH
Q 002211 51 NVGAIFSF-GTVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIVG-PQSAVMAH 128 (953)
Q Consensus 51 ~IG~l~~~-~~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aiiG-p~~S~~a~ 128 (953)
.||++.|. +..+-.....+++.+.++. |+.+.+ .++..++..-.+....++..++.+||= |.... ..
T Consensus 1 ~i~~i~~~~~~~~~~~i~~gi~~~~~~~--------g~~~~~--~~~~~~~~~~~~~i~~l~~~~vdgiii~~~~~~-~~ 69 (260)
T cd06286 1 TIGVVLPYINHPYFSQLVDGIEKAALKH--------GYKVVL--LQTNYDKEKELEYLELLKTKQVDGLILCSREND-WE 69 (260)
T ss_pred CEEEEeCCCCCchHHHHHHHHHHHHHHc--------CCEEEE--EeCCCChHHHHHHHHHHHHcCCCEEEEeCCCCC-HH
Confidence 37888886 3555566777888777752 566654 455666666666666777778887663 33222 23
Q ss_pred HHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEec--CccccchHHHHHHHH
Q 002211 129 VLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFND--DDQGRNGVTALGDKL 206 (953)
Q Consensus 129 av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d--~~~g~~~~~~l~~~l 206 (953)
.+..+.+ .+ |+|......+ ...++ +.+++...+..+++++...|-++++++..+ +.......+.|.+.+
T Consensus 70 ~~~~~~~-~~-pvv~~~~~~~----~~~~~---v~~d~~~~~~~~~~~l~~~g~~~i~~i~~~~~~~~~~~R~~Gf~~~l 140 (260)
T cd06286 70 VIEPYTK-YG-PIVLCEEYDS----KNISS---VYIDHYEAFYEALKYLIQKGYRKIAYCIGRKKSLNSQSRKKAYKDAL 140 (260)
T ss_pred HHHHHhc-CC-CEEEEecccC----CCCCE---EEECChHHHHHHHHHHHHCCCceEEEEcCCcccchhHHHHHHHHHHH
Confidence 3334333 34 8887643221 12232 455667778888899888899999999754 334455678999999
Q ss_pred HhcCcEEEEEEecCCCCCCChHHHHHHHHHHhc--CCceEEEEEcchhhHHHHHHHHHHcCCCCCceE
Q 002211 207 AEIRCKISYKSALPPDQSVTETDVRNELVKVRM--MEARVIVVHGYSRTGLMVFDVAQRLGMMDSGYV 272 (953)
Q Consensus 207 ~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~--~~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~ 272 (953)
++.|+.+.....+... .+..+-...+.++.+ ..+++|+ +++...+..+++.++++|+..++-+
T Consensus 141 ~~~~~~~~~~~i~~~~--~~~~~~~~~~~~~l~~~~~~~ai~-~~~d~~a~~~~~~l~~~g~~ip~di 205 (260)
T cd06286 141 EEYGLTPDEEWIFEGC--FTIEDGERIGHQLLKMKDRPDAIF-TGSDEVAAGIITEAKKQGIRVPEDL 205 (260)
T ss_pred HHcCCCCChHheEeCC--CCHHHHHHHHHHHHcCCCCCCEEE-EcchHHHHHHHHHHHHcCCCCCcce
Confidence 9988654221111111 112333445555544 3567655 5555667789999999998654433
No 193
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=97.32 E-value=0.026 Score=62.67 Aligned_cols=208 Identities=13% Similarity=0.067 Sum_probs=120.3
Q ss_pred CceEEEeEEEec-CCCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEEccCChh
Q 002211 47 PEVLNVGAIFSF-GTVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIVGPQSAV 125 (953)
Q Consensus 47 ~~~i~IG~l~~~-~~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aiiGp~~S~ 125 (953)
...-.||+++|- +..+-.....+++-+.++- |+.+ .+.++..++..-.+....++++++.+||=-....
T Consensus 57 ~~~~~Igvi~~~~~~~f~~~~~~gi~~~~~~~--------g~~~--~~~~~~~~~~~~~~~i~~l~~~~vdgiIi~~~~~ 126 (343)
T PRK10727 57 QSTETVGLVVGDVSDPFFGAMVKAVEQVAYHT--------GNFL--LIGNGYHNEQKERQAIEQLIRHRCAALVVHAKMI 126 (343)
T ss_pred CCCCeEEEEeCCCCcchHHHHHHHHHHHHHHc--------CCEE--EEEeCCCCHHHHHHHHHHHHhcCCCEEEEecCCC
Confidence 345789999874 3444445556666555542 4554 3455556666555666677777887776321111
Q ss_pred hHHHHHHhhhhCCCc-EEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecC--ccccchHHHH
Q 002211 126 MAHVLSHLANELQVP-LLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDD--DQGRNGVTAL 202 (953)
Q Consensus 126 ~a~av~~v~~~~~vP-~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~--~~g~~~~~~l 202 (953)
....+..+.. ++| +|......+ +...++ +..++...+..+++++...|.+++++|.... .......+.|
T Consensus 127 ~~~~~~~~~~--~~p~vV~i~~~~~---~~~~~~---V~~Dn~~~~~~a~~~L~~~G~~~I~~i~~~~~~~~~~~R~~Gf 198 (343)
T PRK10727 127 PDAELASLMK--QIPGMVLINRILP---GFENRC---IALDDRYGAWLATRHLIQQGHTRIGYLCSNHSISDAEDRLQGY 198 (343)
T ss_pred ChHHHHHHHh--cCCCEEEEecCCC---CCCCCE---EEECcHHHHHHHHHHHHHCCCccEEEEeCCccccchHHHHHHH
Confidence 1122333333 677 776543221 112232 3455666677788888888999999997543 2345567899
Q ss_pred HHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcC--CceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEE
Q 002211 203 GDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMM--EARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIA 275 (953)
Q Consensus 203 ~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~--~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~ 275 (953)
.+++++.|+.+......... .+...-...+.++.+. .+++|+. .+...+..+++.++++|+..++-+-|.
T Consensus 199 ~~al~~~gi~~~~~~~~~~~--~~~~~~~~~~~~~l~~~~~~~ai~~-~nD~~A~g~~~al~~~G~~vP~disVi 270 (343)
T PRK10727 199 YDALAESGIPANDRLVTFGE--PDESGGEQAMTELLGRGRNFTAVAC-YNDSMAAGAMGVLNDNGIDVPGEISLI 270 (343)
T ss_pred HHHHHHCCCCCChhhEEeCC--CChhHHHHHHHHHHhCCCCCCEEEE-cCcHHHHHHHHHHHHcCCCCCcceeEE
Confidence 99999998754221111111 1122223345555443 3676654 455667789999999998765444333
No 194
>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=97.32 E-value=0.022 Score=60.57 Aligned_cols=200 Identities=12% Similarity=0.036 Sum_probs=117.0
Q ss_pred EEeEEEec-CCCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEE-ccCChhhHH
Q 002211 51 NVGAIFSF-GTVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIV-GPQSAVMAH 128 (953)
Q Consensus 51 ~IG~l~~~-~~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aii-Gp~~S~~a~ 128 (953)
.||+++|- +..+-.....+++-+.++ .|+++.+ .++..++..-......+.++++.++| -|.... ..
T Consensus 1 ~i~vi~~~~~~~~~~~~~~gi~~~~~~--------~gy~~~~--~~~~~~~~~~~~~i~~l~~~~~dgiii~~~~~~-~~ 69 (265)
T cd06290 1 TIGVLTQDFASPFYGRILKGMERGLNG--------SGYSPII--ATGHWNQSRELEALELLKSRRVDALILLGGDLP-EE 69 (265)
T ss_pred CEEEEECCCCCchHHHHHHHHHHHHHH--------CCCEEEE--EeCCCCHHHHHHHHHHHHHCCCCEEEEeCCCCC-hH
Confidence 37888875 344444445555544443 2556654 44556666555566677777888876 332211 12
Q ss_pred HHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEec--CccccchHHHHHHHH
Q 002211 129 VLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFND--DDQGRNGVTALGDKL 206 (953)
Q Consensus 129 av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d--~~~g~~~~~~l~~~l 206 (953)
.+..+ . .++|+|......+ +...++ +..++...+..+++++...|-++++++..+ ........+.|.+.+
T Consensus 70 ~~~~~-~-~~iPvV~i~~~~~---~~~~~~---V~~d~~~a~~~~~~~l~~~g~~~i~~i~~~~~~~~~~~r~~gf~~~~ 141 (265)
T cd06290 70 EILAL-A-EEIPVLAVGRRVP---GPGAAS---IAVDNFQGGYLATQHLIDLGHRRIAHITGPRGHIDARDRLAGYRKAL 141 (265)
T ss_pred HHHHH-h-cCCCEEEECCCcC---CCCCCE---EEECcHHHHHHHHHHHHHCCCCeEEEEeCccccchhhHHHHHHHHHH
Confidence 22222 3 4899998765422 122233 345667777888888887899999999754 333445678889999
Q ss_pred HhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcC--CceEEEEEcchhhHHHHHHHHHHcCCCCCceE
Q 002211 207 AEIRCKISYKSALPPDQSVTETDVRNELVKVRMM--EARVIVVHGYSRTGLMVFDVAQRLGMMDSGYV 272 (953)
Q Consensus 207 ~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~--~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~ 272 (953)
.+.|..+.....+... .+.......+.++.+. .+++|+. ++...+..+++.+++.|+..++.+
T Consensus 142 ~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~l~~~~~~~aii~-~~~~~a~~~~~~l~~~g~~ip~di 206 (265)
T cd06290 142 EEAGLEVQPDLIVQGD--FEEESGLEAVEELLQRGPDFTAIFA-ANDQTAYGARLALYRRGLRVPEDV 206 (265)
T ss_pred HHcCCCCCHHHEEecC--CCHHHHHHHHHHHHcCCCCCCEEEE-cCcHHHHHHHHHHHHcCCCCCcce
Confidence 8887654211111111 1122333455565543 3676654 455667788999999998654433
No 195
>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=97.30 E-value=0.024 Score=60.11 Aligned_cols=196 Identities=11% Similarity=0.042 Sum_probs=108.5
Q ss_pred EEeEEEec---CCCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEEccCChhhH
Q 002211 51 NVGAIFSF---GTVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIVGPQSAVMA 127 (953)
Q Consensus 51 ~IG~l~~~---~~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aiiGp~~S~~a 127 (953)
|||+++|. +..+-.....+++-+.++ .|+.+.+ .++. ++....+....+..+++.+||=...+ ..
T Consensus 1 ~Igvi~~~~~~~~~f~~~l~~gi~~~~~~--------~gy~~~~--~~~~-~~~~~~~~~~~l~~~~vdgiii~~~~-~~ 68 (260)
T cd06304 1 KVALVYDGGGGDKSFNQSAYEGLEKAEKE--------LGVEVKY--VESV-EDADYEPNLRQLAAQGYDLIFGVGFG-FM 68 (260)
T ss_pred CEEEEecCCCCcchHHHHHHHHHHHHHHh--------cCceEEE--EecC-CHHHHHHHHHHHHHcCCCEEEECCcc-hh
Confidence 58999984 233333334444444443 1555554 4444 55555556666777788877642222 22
Q ss_pred HHHHHhhhhC-CCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHc-CCcEEEEEEecC-ccccchHHHHHH
Q 002211 128 HVLSHLANEL-QVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYF-GWGEVIAIFNDD-DQGRNGVTALGD 204 (953)
Q Consensus 128 ~av~~v~~~~-~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~-~w~~vaii~~d~-~~g~~~~~~l~~ 204 (953)
..+....++. ++|++......+. ....+ ....++..-+..++.++..+ |-+++++|..+. .......+.|.+
T Consensus 69 ~~~~~~~~~~~~ipvv~~~~~~~~--~~~~~---~v~~d~~~~~~~a~~l~~~~~g~~~I~~i~~~~~~~~~~R~~Gf~~ 143 (260)
T cd06304 69 DAVEKVAKEYPDVKFAIIDGVVDA--PPNVA---SYVFREYEGSYLAGVLAALMTKTGKVGFVGGMPIPEVNRFINGFAA 143 (260)
T ss_pred HHHHHHHHHCCCCEEEEecCccCC--CCCee---eeecchHHHHHHHHHHHHHhccCCceEEEeccccHHHHHHHHHHHH
Confidence 3444555544 7898876543211 01112 22333444444455555555 889999997532 233445778999
Q ss_pred HHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHHHcC
Q 002211 205 KLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQRLG 265 (953)
Q Consensus 205 ~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~~~g 265 (953)
.+++.|..+.......... .+.++-...++++.+.++++| ++.+...+..++++++++|
T Consensus 144 ~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~l~~~~~ai-~~~~d~~A~gv~~al~~~g 202 (260)
T cd06304 144 GAKSVNPDITVLVIYTGSF-FDPAKGKEAALALIDQGADVI-FAAAGGTGPGVIQAAKEAG 202 (260)
T ss_pred HHHHhCCCcEEEEEEecCc-cCcHHHHHHHHHHHhCCCCEE-EEcCCCCchHHHHHHHHcC
Confidence 9999886433211111110 112233445666665668876 5566667778999999988
No 196
>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=97.29 E-value=0.019 Score=60.89 Aligned_cols=200 Identities=14% Similarity=0.084 Sum_probs=117.0
Q ss_pred EEeEEEecC-CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEEccCChhhHHH
Q 002211 51 NVGAIFSFG-TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIVGPQSAVMAHV 129 (953)
Q Consensus 51 ~IG~l~~~~-~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aiiGp~~S~~a~a 129 (953)
.||++.|.. ..+-.....+++-+.++ .|+.+.+...+ +.. .....+..+++.+||=........
T Consensus 1 ~igvv~~~~~~~~~~~~~~gi~~~~~~--------~g~~~~~~~~~---~~~---~~~~~l~~~~vdgii~~~~~~~~~- 65 (261)
T cd06272 1 TIGLIWPSVSRVALTELVTGINQAISK--------NGYNMNVSITP---SLA---EAEDLFKENRFDGVIIFGESASDV- 65 (261)
T ss_pred CEEEEecCCCchhHHHHHHHHHHHHHH--------cCCEEEEEecc---cHH---HHHHHHHHcCcCEEEEeCCCCChH-
Confidence 378888863 44445556666666654 25666665544 222 233446666777766322222222
Q ss_pred HHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecCc--cccchHHHHHHHHH
Q 002211 130 LSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDDD--QGRNGVTALGDKLA 207 (953)
Q Consensus 130 v~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~~--~g~~~~~~l~~~l~ 207 (953)
....+...++|+|......+ ..+++ +..++...+..+++++...|-++++++..... ........|.+.++
T Consensus 66 ~~~~~~~~~ipvV~~~~~~~----~~~~~---V~~d~~~~~~~~~~~l~~~g~~~i~~i~~~~~~~~~~~R~~gf~~~~~ 138 (261)
T cd06272 66 EYLYKIKLAIPVVSYGVDYD----LKYPI---VNVDNEKAMELAVLYLAEKGHKKIAYIGDLSLDRRQRKRFKGFLETCD 138 (261)
T ss_pred HHHHHHHcCCCEEEEcccCC----CCCCE---EEEChHHHHHHHHHHHHHcCchhEEEeecccccccHHHHHHHHHHHHH
Confidence 23445678999998754322 12233 45567777888999988889999999975432 33445678999999
Q ss_pred hcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCC--ceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEE
Q 002211 208 EIRCKISYKSALPPDQSVTETDVRNELVKVRMME--ARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIA 275 (953)
Q Consensus 208 ~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~--~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~ 275 (953)
+.|+.+......... .+.......+.++.+.. +++|+ +++...+..+++.+++.|+..++-+-+.
T Consensus 139 ~~~~~~~~~~~~~~~--~~~~~~~~~~~~~l~~~~~~~ai~-~~~d~~a~~~~~~l~~~g~~vp~dv~vv 205 (261)
T cd06272 139 ENGISISDSHIDVDG--LSAEGGDNAAKKLLKESDLPTAII-CGSYDIALGVLSALNKQGISIPEDIEII 205 (261)
T ss_pred HcCCCCCHHHeeeCC--CCHHHHHHHHHHHHcCCCCCCEEE-ECCcHHHHHHHHHHHHhCCCCCCceEEE
Confidence 988643211111111 11233344555654443 56644 4445567788999999998655444333
No 197
>PRK09492 treR trehalose repressor; Provisional
Probab=97.25 E-value=0.038 Score=60.54 Aligned_cols=193 Identities=11% Similarity=-0.008 Sum_probs=117.9
Q ss_pred CceEEEeEEEec-CCCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEEccCChh
Q 002211 47 PEVLNVGAIFSF-GTVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIVGPQSAV 125 (953)
Q Consensus 47 ~~~i~IG~l~~~-~~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aiiGp~~S~ 125 (953)
...-+||++.|. +..+-.....+++- ++++. |+++ .+.++..++.........+.+++|.++|--..+.
T Consensus 60 ~~~~~Ig~i~~~~~~~~~~~~~~~i~~---~~~~~-----gy~~--~~~~~~~~~~~~~~~~~~l~~~~vdgiIi~~~~~ 129 (315)
T PRK09492 60 QSDKVVGIIVSRLDSLSENQAVRTMLP---AFYEQ-----GYDP--IIMESQFSPEKVNEHLGVLKRRNVDGVILFGFTG 129 (315)
T ss_pred CCCCeEEEEecCCcCcccHHHHHHHHH---HHHHc-----CCeE--EEEecCCChHHHHHHHHHHHhcCCCEEEEeCCCc
Confidence 344679999985 33333344455544 34433 4555 4456666776666666667777888888532221
Q ss_pred hHHHHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEec---CccccchHHHH
Q 002211 126 MAHVLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFND---DDQGRNGVTAL 202 (953)
Q Consensus 126 ~a~av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d---~~~g~~~~~~l 202 (953)
.. .......++|++...... ..++ .+..++...+..+++++...|-++++++... ...+....+.|
T Consensus 130 ~~---~~~l~~~~~pvv~i~~~~-----~~~~---~V~~D~~~~~~~a~~~L~~~G~~~I~~i~~~~~~~~~~~~R~~Gf 198 (315)
T PRK09492 130 IT---EEMLAPWQDKLVLLARDA-----KGFS---SVCYDDEGAIKLLMQRLYDQGHRHISYLGVDHSDVTTGKRRHQAY 198 (315)
T ss_pred cc---HHHHHhcCCCEEEEeccC-----CCCc---EEEECcHHHHHHHHHHHHHcCCCeEEEEcCCcccchhHHHHHHHH
Confidence 11 123344567877654321 1122 3445666677778888888899999999632 22345678899
Q ss_pred HHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHHHcCC
Q 002211 203 GDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQRLGM 266 (953)
Q Consensus 203 ~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~~~g~ 266 (953)
.+++++.|+.+... .... +...-...+.++.+.++++|+... ...+..+++.+++.|+
T Consensus 199 ~~al~~~g~~~~~~--~~~~---~~~~~~~~~~~~l~~~~~ai~~~~-D~~A~g~~~al~~~g~ 256 (315)
T PRK09492 199 LAFCKQHKLTPVAA--LGGL---SMQSGYELVAKVLTPETTALVCAT-DTLALGASKYLQEQGR 256 (315)
T ss_pred HHHHHHcCCCceee--cCCC---CchHHHHHHHHHhhcCCCEEEEcC-cHHHHHHHHHHHHcCC
Confidence 99999999875421 1111 122223345555556788887555 5667789999999997
No 198
>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=97.24 E-value=0.019 Score=62.06 Aligned_cols=185 Identities=10% Similarity=0.096 Sum_probs=111.6
Q ss_pred EEeEEEecCCCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEEccCChhhHHHH
Q 002211 51 NVGAIFSFGTVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIVGPQSAVMAHVL 130 (953)
Q Consensus 51 ~IG~l~~~~~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aiiGp~~S~~a~av 130 (953)
+||++...+...-.....|++-++++. |+.. ..+++.+.+.++|+....+.+.++.+++++.|+-- .+..+.++
T Consensus 1 ~v~i~~~~~~~~~~~~~~gf~~~L~~~----g~~~-~~~~~~~~~a~~d~~~~~~~~~~l~~~~~DlIi~~-gt~aa~~~ 74 (294)
T PF04392_consen 1 KVGILQFISHPALDDIVRGFKDGLKEL----GYDE-KNVEIEYKNAEGDPEKLRQIARKLKAQKPDLIIAI-GTPAAQAL 74 (294)
T ss_dssp EEEEEESS--HHHHHHHHHHHHHHHHT----T--C-CCEEEEEEE-TT-HHHHHHHHHHHCCTS-SEEEEE-SHHHHHHH
T ss_pred CeEEEEEeccHHHHHHHHHHHHHHHHc----CCcc-ccEEEEEecCCCCHHHHHHHHHHHhcCCCCEEEEe-CcHHHHHH
Confidence 688888877654456677777666664 2323 56888999999999999888888887777766642 34445555
Q ss_pred HHhhhhCCCcEEEeecCCCCCCC----CCCC--cEEEccCChHHHHHHHHHHHHHc--CCcEEEEEEecCcc-ccchHHH
Q 002211 131 SHLANELQVPLLSFTALDPTLSP----LQYP--FFVQTAPNDLYLMSAIAEMVSYF--GWGEVIAIFNDDDQ-GRNGVTA 201 (953)
Q Consensus 131 ~~v~~~~~vP~Is~~at~~~ls~----~~~p--~~fr~~p~d~~~~~ai~~~l~~~--~w~~vaii~~d~~~-g~~~~~~ 201 (953)
....... +|+|-.+.++|.-.. ...| ++.-+. +......-.++++++ +.++++++|.++.- +....+.
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 5544433 999987777775433 2222 444333 444455666666665 47999999976543 4567788
Q ss_pred HHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcch
Q 002211 202 LGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYS 251 (953)
Q Consensus 202 l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~ 251 (953)
+++.+++.|+++.... ++ + ..++...+..+. .+.|++++..+.
T Consensus 152 ~~~~a~~~g~~l~~~~-v~-~----~~~~~~~~~~l~-~~~da~~~~~~~ 194 (294)
T PF04392_consen 152 LRKAAKKLGIELVEIP-VP-S----SEDLEQALEALA-EKVDALYLLPDN 194 (294)
T ss_dssp HHHHHHHTT-EEEEEE-ES-S----GGGHHHHHHHHC-TT-SEEEE-S-H
T ss_pred HHHHHHHcCCEEEEEe-cC-c----HhHHHHHHHHhh-ccCCEEEEECCc
Confidence 8888899999876532 32 2 567888888875 467888887654
No 199
>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=97.24 E-value=0.037 Score=58.77 Aligned_cols=200 Identities=12% Similarity=0.092 Sum_probs=121.6
Q ss_pred EEeEEEecC-CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEE-ccCChhhHH
Q 002211 51 NVGAIFSFG-TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIV-GPQSAVMAH 128 (953)
Q Consensus 51 ~IG~l~~~~-~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aii-Gp~~S~~a~ 128 (953)
.||+++|.. ..+-.....+++-++++ .|+++.+ .++..++..-......+..+++.+|| .|......
T Consensus 1 ~Ig~i~p~~~~~~~~~~~~~i~~~~~~--------~g~~~~~--~~~~~~~~~~~~~i~~l~~~~~dgiii~~~~~~~~- 69 (263)
T cd06280 1 TVGLIVADIRNPFFTAVSRAVEDAAYR--------AGLRVIL--CNTDEDPEKEAMYLELMEEERVTGVIFAPTRATLR- 69 (263)
T ss_pred CEEEEecccccccHHHHHHHHHHHHHH--------CCCEEEE--EeCCCCHHHHHHHHHHHHhCCCCEEEEeCCCCCch-
Confidence 388998874 33445566777777776 2567654 45555665555555667776676655 33322222
Q ss_pred HHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEec-CccccchHHHHHHHHH
Q 002211 129 VLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFND-DDQGRNGVTALGDKLA 207 (953)
Q Consensus 129 av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d-~~~g~~~~~~l~~~l~ 207 (953)
.. -+...++|+|......+ ...++++ ..++..-+..+++++...|-++++++..+ ..........|.+.++
T Consensus 70 -~~-~~~~~~iPvV~~~~~~~---~~~~~~v---~~d~~~~g~~a~~~L~~~g~~~i~~~~~~~~~~~~~R~~gf~~~~~ 141 (263)
T cd06280 70 -RL-AELRLSFPVVLIDRAGP---AGRVDAV---VLDNRAAARTLVEHLVAQGYRRIGGLFGNASTTGAERRAGYEDAMR 141 (263)
T ss_pred -HH-HHHhcCCCEEEECCCCC---CCCCCEE---EECcHHHHHHHHHHHHHCCCceEEEEeCCCCCCHHHHHHHHHHHHH
Confidence 22 23566899998765432 2234443 34566677888888888899999998753 2233455788999999
Q ss_pred hcCcEEEEEEecCCCCCCChHHHHHHHHHHhcC--CceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEE
Q 002211 208 EIRCKISYKSALPPDQSVTETDVRNELVKVRMM--EARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIA 275 (953)
Q Consensus 208 ~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~--~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~ 275 (953)
+.|+..... ..... ..+....+.++... .+++|+. .+...+..+++.+++.|+..++-+.+.
T Consensus 142 ~~~~~~~~~-~~~~~----~~~~~~~~~~~l~~~~~~~ai~~-~~d~~a~g~~~~l~~~g~~~p~di~ii 205 (263)
T cd06280 142 RHGLAPDAR-FVAPT----AEAAEAALAAWLAAPERPEALVA-SNGLLLLGALRAVRAAGLRIPQDLALA 205 (263)
T ss_pred HcCCCCChh-hcccC----HHHHHHHHHHHhcCCCCCcEEEE-CCcHHHHHHHHHHHHcCCCCCCcEEEE
Confidence 888764321 11212 33333445555433 4666544 555667789999999998655444443
No 200
>PRK09526 lacI lac repressor; Reviewed
Probab=97.23 E-value=0.052 Score=60.23 Aligned_cols=204 Identities=12% Similarity=0.075 Sum_probs=120.1
Q ss_pred ceEEEeEEEecC-CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEEc--cCCh
Q 002211 48 EVLNVGAIFSFG-TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIVG--PQSA 124 (953)
Q Consensus 48 ~~i~IG~l~~~~-~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aiiG--p~~S 124 (953)
..-.||+++|.. ..+-.....+++-+.++ .|+.+.+...+. .++..-......+.++++++||- |..+
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 346799999853 23333455666655554 267776654332 23333344556677778888763 4433
Q ss_pred hhHHHHHHhh-hhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecC--ccccchHHH
Q 002211 125 VMAHVLSHLA-NELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDD--DQGRNGVTA 201 (953)
Q Consensus 125 ~~a~av~~v~-~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~--~~g~~~~~~ 201 (953)
... ..+. ...++|+|..... + +...+ .+..++..-+..+++++...|-++++++.... .......+.
T Consensus 133 ~~~---~~~~~~~~~iPvV~~d~~-~---~~~~~---~V~~d~~~~~~~a~~~L~~~G~~~I~~l~g~~~~~~~~~R~~G 202 (342)
T PRK09526 133 ADA---EKIVADCADVPCLFLDVS-P---QSPVN---SVSFDPEDGTRLGVEHLVELGHQRIALLAGPESSVSARLRLAG 202 (342)
T ss_pred chH---HHHHhhcCCCCEEEEecc-C---CCCCC---EEEECcHHHHHHHHHHHHHCCCCeEEEEeCCCccccHHHHHHH
Confidence 222 2222 2358999987532 1 11222 34556666678888998888999999997432 233456788
Q ss_pred HHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcC--CceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEE
Q 002211 202 LGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMM--EARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIA 275 (953)
Q Consensus 202 l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~--~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~ 275 (953)
|.+++++.|+.+.... ... .+..+-...+.++... .+++|+. .+...+..+++.+++.|+..++-+-|.
T Consensus 203 f~~al~~~gi~~~~~~--~~~--~~~~~~~~~~~~~l~~~~~~~ai~~-~~d~~A~g~~~al~~~g~~vP~disvi 273 (342)
T PRK09526 203 WLEYLTDYQLQPIAVR--EGD--WSAMSGYQQTLQMLREGPVPSAILV-ANDQMALGVLRALHESGLRVPGQISVI 273 (342)
T ss_pred HHHHHHHcCCCcceEE--eCC--CchHHHHHHHHHHhcCCCCCcEEEE-cCcHHHHHHHHHHHHcCCCCCCceEEE
Confidence 9999999988643221 111 1122223344555433 4676654 455667789999999998765544333
No 201
>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=97.21 E-value=0.031 Score=60.14 Aligned_cols=197 Identities=11% Similarity=0.000 Sum_probs=116.5
Q ss_pred EeEEEec------CCCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEEccCChh
Q 002211 52 VGAIFSF------GTVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIVGPQSAV 125 (953)
Q Consensus 52 IG~l~~~------~~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aiiGp~~S~ 125 (953)
||++.|. +.++-.....+++-+.++ .|+++.+...+. . .+....+...++.+||--....
T Consensus 2 igvi~p~~~~~~~~~~~~~~~~~gi~~~a~~--------~g~~~~~~~~~~---~---~~~~~~~~~~~~dgiii~~~~~ 67 (283)
T cd06279 2 VGVVLTDSLSYAFSDPVASQFLAGVAEVLDA--------AGVNLLLLPASS---E---DSDSALVVSALVDGFIVYGVPR 67 (283)
T ss_pred EEEEeCCcccccccCccHHHHHHHHHHHHHH--------CCCEEEEecCcc---H---HHHHHHHHhcCCCEEEEeCCCC
Confidence 8899886 233444556666655555 256776654332 1 1233456667888877533222
Q ss_pred hHHHHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecC-------------
Q 002211 126 MAHVLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDD------------- 192 (953)
Q Consensus 126 ~a~av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~------------- 192 (953)
. ......+...++|+|......+ .. +-.+..++...+..+++++...|-++++++..+.
T Consensus 68 ~-~~~~~~~~~~~ipvV~~~~~~~----~~---~~~v~~d~~~~g~~~~~~L~~~g~~~i~~i~~~~~~~~~~~~~~~~~ 139 (283)
T cd06279 68 D-DPLVAALLRRGLPVVVVDQPLP----PG---VPSVGIDDRAAAREAARHLLDLGHRRIGILGLRLGRDRNTGRVTDER 139 (283)
T ss_pred C-hHHHHHHHHcCCCEEEEecCCC----CC---CCEEeeCcHHHHHHHHHHHHHcCCCcEEEecCccccccccccccccc
Confidence 2 2344556778999998754321 11 2234566777788888999889999999997532
Q ss_pred ------ccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcC--CceEEEEEcchhhHHHHHHHHHHc
Q 002211 193 ------DQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMM--EARVIVVHGYSRTGLMVFDVAQRL 264 (953)
Q Consensus 193 ------~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~--~~~vii~~~~~~~~~~~~~~a~~~ 264 (953)
.......+.+.+++++.|++......+... ..+.......+.++.++ .+++|+ +++...+..+++.+++.
T Consensus 140 ~~~~~~~~~~~R~~gf~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~l~~~~~~~ai~-~~~d~~a~gv~~al~~~ 217 (283)
T cd06279 140 LASATFSVARERLEGYLEALEEAGIDISDVPIWEIP-ENDRASGEEAARELLDASPRPTAIL-CMSDVLALGALQVAREL 217 (283)
T ss_pred ccccccccHHHHHHHHHHHHHHcCCCCChheEEecC-CCchHHHHHHHHHHHcCCCCCcEEE-ECCcHHHHHHHHHHHHc
Confidence 223345788899998888543111111111 01134445556666444 356655 44556677889999999
Q ss_pred CCCCCceE
Q 002211 265 GMMDSGYV 272 (953)
Q Consensus 265 g~~~~~~~ 272 (953)
|+..++-+
T Consensus 218 g~~ip~di 225 (283)
T cd06279 218 GLRVPEDL 225 (283)
T ss_pred CCCCCCce
Confidence 98654433
No 202
>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=97.19 E-value=0.022 Score=60.57 Aligned_cols=203 Identities=9% Similarity=0.020 Sum_probs=118.3
Q ss_pred EEeEEEecCCCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEEccCChhhHHHH
Q 002211 51 NVGAIFSFGTVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIVGPQSAVMAHVL 130 (953)
Q Consensus 51 ~IG~l~~~~~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aiiGp~~S~~a~av 130 (953)
+||++.|.+..+......+++-+.++. + |+.+-+. ++ +. .+....|...+|.+||=...+. ..
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 489999966555555666666665553 2 4565543 22 11 3334445566888888532222 22
Q ss_pred HHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecCc-cccchHHHHHHHHHhc
Q 002211 131 SHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDDD-QGRNGVTALGDKLAEI 209 (953)
Q Consensus 131 ~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~~-~g~~~~~~l~~~l~~~ 209 (953)
...+...++|+|......+. +.+-++..++...+..+++++...|-++++++..... ......+.|++++++.
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 34456679999988653321 1233466777778888889888889999999874433 2234467899999999
Q ss_pred CcEEEEEEecCCCCCCChHHHHHHHHHHhcC--CceEEEEEcchhhHHHHHHHHHHcCCCCC-ceEEEEeC
Q 002211 210 RCKISYKSALPPDQSVTETDVRNELVKVRMM--EARVIVVHGYSRTGLMVFDVAQRLGMMDS-GYVWIATT 277 (953)
Q Consensus 210 g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~--~~~vii~~~~~~~~~~~~~~a~~~g~~~~-~~~wi~~~ 277 (953)
|..+............+..+-...+.++.+. ++++|+.. +...+..+++.+++.|+..+ +...++-|
T Consensus 138 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~-~d~~a~g~~~~l~~~g~~vp~di~vigfd 207 (265)
T cd01543 138 GYECSFFYRGLSTDAQSWEEEQEELAQWLQSLPKPVGIFAC-TDARARQLLEACRRAGIAVPEEVAVLGVD 207 (265)
T ss_pred CCccccccCccccccccHHHHHHHHHHHHhcCCCCcEEEec-ChHHHHHHHHHHHHhCCCCCCceEEEeeC
Confidence 8765211111000001112223445554333 46655544 55667778899999998644 34444444
No 203
>TIGR01729 taurine_ABC_bnd taurine ABC transporter, periplasmic binding protein. This model identifies a cluster of ABC transporter periplasmic substrate binding proteins, apparently specific for taurine. Transport systems for taurine (NH2-CH2-CH2-SO3H), sulfonates, and sulfate esters import sulfur when sulfate levels are low. The most closely related proteins outside this family are putative aliphatic sulfonate binding proteins (TIGR01728).
Probab=97.19 E-value=0.002 Score=70.15 Aligned_cols=71 Identities=15% Similarity=0.104 Sum_probs=48.9
Q ss_pred CCCCChHHhhhCCCeEEEEeCchHHHHHH---HhhCCCccceE-eCCCHHHHHHHHHcCCcEEEEccchhHHHHHhc
Q 002211 700 SPIKGIDTLMTSNDRVGYQVGSFAENYLI---EELSIPKSRLV-ALGSPEEYAIALENRTVAAVVDERPYIDLFLSD 772 (953)
Q Consensus 700 ~~I~sl~dL~~~~~~ig~~~~s~~~~~l~---~~~~~~~~~~~-~~~~~~~~~~~l~~g~~~a~~~~~~~~~~~~~~ 772 (953)
..|++++||. |++||+..++..+.++. +..++....+. ..-+..+...++.+|++||++...++......+
T Consensus 90 s~I~s~~DLk--GK~Igv~~~s~~~~~l~~~L~~~Gl~~~dv~~v~~~~~~~~~al~~G~vDa~~~~~p~~~~~~~~ 164 (300)
T TIGR01729 90 SGIEKPEDLK--GKNVAVPFVSTTHYSLLAALKHWKTDPREVNILNLKPPQIVAAWQRGDIDAAYVWPPALSELLKS 164 (300)
T ss_pred CCCCChhHcC--CCEEEeCCCCcHHHHHHHHHHHcCCChhheEEEecCcHHHHHHHHcCCcCEEEEecHHHHHHHhc
Confidence 4689999997 99999987765444332 22344332232 123567899999999999999988877655544
No 204
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=97.12 E-value=0.062 Score=59.35 Aligned_cols=207 Identities=6% Similarity=-0.002 Sum_probs=122.1
Q ss_pred ceEEEeEEEec-CCCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEEccCChhh
Q 002211 48 EVLNVGAIFSF-GTVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIVGPQSAVM 126 (953)
Q Consensus 48 ~~i~IG~l~~~-~~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aiiGp~~S~~ 126 (953)
..-.||++.|- +..+-.....+++-+.++ .|+++.+ .++..++..-......++++++.+||=-.....
T Consensus 62 ~~~~Igvi~~~~~~~~~~~~~~gi~~~~~~--------~g~~~~~--~~~~~~~~~~~~~~~~~~~~~vdgiI~~~~~~~ 131 (331)
T PRK14987 62 TSRAIGVLLPSLTNQVFAEVLRGIESVTDA--------HGYQTML--AHYGYKPEMEQERLESMLSWNIDGLILTERTHT 131 (331)
T ss_pred CCCEEEEEeCCCcchhHHHHHHHHHHHHHH--------CCCEEEE--ecCCCCHHHHHHHHHHHHhcCCCEEEEcCCCCC
Confidence 34579999984 344444556666666554 2566654 455555555455555677778888774211111
Q ss_pred HHHHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecC-ccccchHHHHHHH
Q 002211 127 AHVLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDD-DQGRNGVTALGDK 205 (953)
Q Consensus 127 a~av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~-~~g~~~~~~l~~~ 205 (953)
......+.+.++|+|....... + .... .+..++..-+..+++++...|-++++++.... .......+.|.++
T Consensus 132 -~~~~~~l~~~~iPvV~~~~~~~---~-~~~~--~V~~Dn~~~~~~a~~~L~~~Gh~~I~~i~~~~~~~~~~R~~Gf~~a 204 (331)
T PRK14987 132 -PRTLKMIEVAGIPVVELMDSQS---P-CLDI--AVGFDNFEAARQMTTAIIARGHRHIAYLGARLDERTIIKQKGYEQA 204 (331)
T ss_pred -HHHHHHHHhCCCCEEEEecCCC---C-CCCc--eEEeCcHHHHHHHHHHHHHCCCceEEEEcCCCcccHHHHHHHHHHH
Confidence 2333456778999997532111 1 1111 25566777778888988889999999996432 2233457889999
Q ss_pred HHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcC--CceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEE
Q 002211 206 LAEIRCKISYKSALPPDQSVTETDVRNELVKVRMM--EARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIA 275 (953)
Q Consensus 206 l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~--~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~ 275 (953)
+++.|+... ...+... .+...-...++++.+. ++++|+. .+...+..+++++++.|+..|+-+-|.
T Consensus 205 l~~~g~~~~-~~~~~~~--~~~~~~~~~~~~~l~~~~~~~ai~~-~nD~~A~g~~~al~~~g~~vP~disvi 272 (331)
T PRK14987 205 MLDAGLVPY-SVMVEQS--SSYSSGIELIRQARREYPQLDGVFC-TNDDLAVGAAFECQRLGLKVPDDMAIA 272 (331)
T ss_pred HHHcCCCcc-ceeecCC--CChhhHHHHHHHHHhcCCCCCEEEE-CCcHHHHHHHHHHHHcCCCCCCccEEE
Confidence 999886311 1111111 1122223345555443 4676665 455667788999999998766555444
No 205
>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=97.06 E-value=0.051 Score=57.97 Aligned_cols=200 Identities=12% Similarity=0.007 Sum_probs=118.6
Q ss_pred EeEEEecC-CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHH-HHhcCcEEEEccCChhhHHH
Q 002211 52 VGAIFSFG-TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQ-FMETDTLAIVGPQSAVMAHV 129 (953)
Q Consensus 52 IG~l~~~~-~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~-li~~~v~aiiGp~~S~~a~a 129 (953)
||++.|.. ..+-.....+++-+.++. |+++.+...|. + ....+...+ +..++|.+||=-..... ..
T Consensus 2 Igvi~p~~~~~~~~~~~~~i~~~~~~~--------gy~~~~~~~~~--~-~~~~~~~~~~l~~~~vdgvi~~~~~~~-~~ 69 (269)
T cd06297 2 ISVLLPVVATEFYRRLLEGIEGALLEQ--------RYDLALFPLLS--L-ARLKRYLESTTLAYLTDGLLLASYDLT-ER 69 (269)
T ss_pred EEEEeCCCcChhHHHHHHHHHHHHHHC--------CCEEEEEeCCC--c-HHHHHHHHHHHHhcCCCEEEEecCccC-hH
Confidence 78888863 444455566777666662 56777654442 2 222233333 55556776663222111 23
Q ss_pred HHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecC--c------cccchHHH
Q 002211 130 LSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDD--D------QGRNGVTA 201 (953)
Q Consensus 130 v~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~--~------~g~~~~~~ 201 (953)
....+.+.++|+|......+ ..+++ .+++..-+..+++.|... .++++++..+. . .+....+.
T Consensus 70 ~~~~l~~~~iPvv~~~~~~~-----~~~~v---~~d~~~~g~~a~~~L~~~-~~~i~~i~~~~~~~~~~~~~~~~~R~~g 140 (269)
T cd06297 70 LAERRLPTERPVVLVDAENP-----RFDSF---YLDNRLGGRLAGAYLADF-PGRIGAITVEEEPDRAFRRTVFAERRAG 140 (269)
T ss_pred HHHHHhhcCCCEEEEccCCC-----CCCEE---EECcHHHHHHHHHHHHHh-CCceEEEeCccccccccccccHHHHHHH
Confidence 44556678999998754321 22333 356777778888887777 79999986432 2 34556889
Q ss_pred HHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcC--CceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEE
Q 002211 202 LGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMM--EARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIA 275 (953)
Q Consensus 202 l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~--~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~ 275 (953)
|++.+++.|+++.....+... .+..+....+.++.+. ++++|+.. +...+..+++.+++.|...++-+-+.
T Consensus 141 f~~~~~~~g~~~~~~~~~~~~--~~~~~~~~~~~~~l~~~~~~~ai~~~-~d~~a~g~~~~l~~~g~~vP~di~vv 213 (269)
T cd06297 141 FQQALKDAGRPFSPDLLAITD--HSEEGGRLAMRHLLEKASPPLAVFAS-ADQQALGALQEAVELGLTVGEDVRVV 213 (269)
T ss_pred HHHHHHHcCCCCChhhEEeCC--CChhhHHHHHHHHHcCCCCCcEEEEc-CcHHHHHHHHHHHHcCCCCCCceEEE
Confidence 999999988764321111111 1133444566666543 35666655 44567789999999998665554444
No 206
>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=97.00 E-value=0.26 Score=53.59 Aligned_cols=198 Identities=8% Similarity=-0.009 Sum_probs=106.2
Q ss_pred EeEEEec-CCCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEE-ccCChhhHHH
Q 002211 52 VGAIFSF-GTVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIV-GPQSAVMAHV 129 (953)
Q Consensus 52 IG~l~~~-~~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aii-Gp~~S~~a~a 129 (953)
||++.|- +..+-.....+++-+.++. |+..-+...++..++..-.+....++++++.+|| -|..+.....
T Consensus 1 Igvi~~~~~~~f~~~~~~gi~~~a~~~--------g~~~~i~~~~~~~d~~~q~~~i~~l~~~~vdgiIi~~~~~~~~~~ 72 (302)
T TIGR02637 1 IGLVVKSLGNPFFEAANKGAEEAAKEL--------GSVYIIYTGPTGTTAEGQIEVVNSLIAQKVDAIAISANDPDALVP 72 (302)
T ss_pred CEEEeccCCCHHHHHHHHHHHHHHHHh--------CCeeEEEECCCCCCHHHHHHHHHHHHHcCCCEEEEeCCChHHHHH
Confidence 5667664 3334445566666666653 3222222234556777777777888888777655 3444443344
Q ss_pred HHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCCh-HHHHHHHHHHH-HHc-CCcEEEEEEecCcc--ccchHHHHHH
Q 002211 130 LSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPND-LYLMSAIAEMV-SYF-GWGEVIAIFNDDDQ--GRNGVTALGD 204 (953)
Q Consensus 130 v~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d-~~~~~ai~~~l-~~~-~w~~vaii~~d~~~--g~~~~~~l~~ 204 (953)
...-+.+.+||+|......+. + +....+...| ...+...++.+ +++ +-.++++|..+... .....+.+.+
T Consensus 73 ~l~~~~~~giPvV~~~~~~~~--~---~~~~~v~~~Dn~~~g~~aa~~l~~~l~~~~~I~~i~g~~~~~~~~~r~~g~~~ 147 (302)
T TIGR02637 73 ALKKAMKRGIKVVTWDSGVAP--E---GRNLFLNQASADLIGRTQVQLAAEQIGNGGEIAILSAASTATNQNAWIEIMKK 147 (302)
T ss_pred HHHHHHHCCCEEEEeCCCCCC--C---ceeEEEecCCHHHHHHHHHHHHHHHcCCCcEEEEEECCCCCccHHHHHHHHHH
Confidence 445567789999987543221 1 1223333333 33344455554 332 23689999754322 2234577777
Q ss_pred HHHhcC---cEEEEEEecCCCCCCChHHHHHHHHHHhcCC--ceEEEEEcchhhHHHHHHHHHHcCCC
Q 002211 205 KLAEIR---CKISYKSALPPDQSVTETDVRNELVKVRMME--ARVIVVHGYSRTGLMVFDVAQRLGMM 267 (953)
Q Consensus 205 ~l~~~g---~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~--~~vii~~~~~~~~~~~~~~a~~~g~~ 267 (953)
.+++.| .+++... ... .+.++-...++++.+.. +++|+.. ....+...++.+++.|..
T Consensus 148 ~~~~~~~~~~~~~~~~--~~~--~~~~~~~~~~~~~L~~~~~~~ai~~~-~d~~a~ga~~al~~~g~~ 210 (302)
T TIGR02637 148 ELKDPKYPKVKLVATV--YGD--DDAQKSYQEAQGLLKSYPNLKGIIAP-TTVGIKAAAQAVSDAKLI 210 (302)
T ss_pred HHhhccCCCCEEEeee--cCC--chHHHHHHHHHHHHHhCCCccEEEeC-CCchHHHHHHHHHhcCCC
Confidence 777643 3443221 111 11333344455554444 4555553 345666778888888864
No 207
>PRK11041 DNA-binding transcriptional regulator CytR; Provisional
Probab=96.89 E-value=0.13 Score=56.04 Aligned_cols=208 Identities=11% Similarity=0.034 Sum_probs=122.6
Q ss_pred CceEEEeEEEec-CCCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEEc-cCCh
Q 002211 47 PEVLNVGAIFSF-GTVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIVG-PQSA 124 (953)
Q Consensus 47 ~~~i~IG~l~~~-~~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aiiG-p~~S 124 (953)
...-+||++.|- +..+-.....+++-+.++. |+.+.+ .+...+...-......+..+++++||= |...
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 345789999985 3555566677777777763 455543 455555555555666677778877763 2221
Q ss_pred hhHHHHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecCc--cccchHHHH
Q 002211 125 VMAHVLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDDD--QGRNGVTAL 202 (953)
Q Consensus 125 ~~a~av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~~--~g~~~~~~l 202 (953)
. ..... .......|++..+...+. ..+++ +..++...+..+++++...|-+++++|..... ......+.|
T Consensus 103 ~-~~~~~-~~~~~~~pvv~~~~~~~~---~~~~~---V~~Dn~~~g~~a~~~l~~~G~~~I~~l~~~~~~~~~~~R~~Gf 174 (309)
T PRK11041 103 P-FDASK-EEQRNLPPMVMANEFAPE---LELPT---VHIDNLTAAFEAVNYLHELGHKRIACIAGPEEMPLCHYRLQGY 174 (309)
T ss_pred C-hHHHH-HHHhcCCCEEEEccccCC---CCCCE---EEECcHHHHHHHHHHHHHcCCceEEEEeCCccccchHHHHHHH
Confidence 1 11111 122222467765433221 12333 44566677788888888889999999975433 234567889
Q ss_pred HHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcC--CceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEE
Q 002211 203 GDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMM--EARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIA 275 (953)
Q Consensus 203 ~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~--~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~ 275 (953)
++.+++.|+++.....+..+ .+.......+.++.+. .+++|+.. ....+..+++.+++.|+..++-+.|.
T Consensus 175 ~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~l~~~~~~~ai~~~-~d~~a~gv~~al~~~g~~ip~di~vv 246 (309)
T PRK11041 175 VQALRRCGITVDPQYIARGD--FTFEAGAKALKQLLDLPQPPTAVFCH-SDVMALGALSQAKRMGLRVPQDLSII 246 (309)
T ss_pred HHHHHHcCCCCCHHHeEeCC--CCHHHHHHHHHHHHcCCCCCCEEEEc-CcHHHHHHHHHHHHcCCCCCcceEEE
Confidence 99999988764321111111 1233344566666543 36777754 55566678999999998654444444
No 208
>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=96.87 E-value=0.2 Score=54.40 Aligned_cols=197 Identities=12% Similarity=0.010 Sum_probs=116.1
Q ss_pred EeEEEec-CCCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEE-ccCChhhHHH
Q 002211 52 VGAIFSF-GTVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIV-GPQSAVMAHV 129 (953)
Q Consensus 52 IG~l~~~-~~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aii-Gp~~S~~a~a 129 (953)
||++.|- ...+-.....+++-+.++. |+++. +.++..++..-.+....++.+++.+|| .|..+.....
T Consensus 1 ig~~~~~~~~~~~~~~~~~i~~~a~~~--------g~~v~--~~~~~~~~~~q~~~i~~l~~~~vDgIIi~~~~~~~~~~ 70 (302)
T TIGR02634 1 IGVSIDDLRLERWQKDRDIFVAAAESL--------GAKVF--VQSANGNEAKQISQIENLIARGVDVLVIIPQNGQVLSN 70 (302)
T ss_pred CeeecCccchhhHHHHHHHHHHHHHhc--------CCEEE--EEeCCCCHHHHHHHHHHHHHcCCCEEEEeCCChhHHHH
Confidence 4666653 2444444555665555552 55554 467777777777777788888777665 3433333344
Q ss_pred HHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCCc-EEEEEEec--CccccchHHHHHHHH
Q 002211 130 LSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGWG-EVIAIFND--DDQGRNGVTALGDKL 206 (953)
Q Consensus 130 v~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~-~vaii~~d--~~~g~~~~~~l~~~l 206 (953)
....+.+.++|+|.+....+ ..+....+..++...+..+++++...+-+ +++++..+ ........+.+++.+
T Consensus 71 ~l~~~~~~~iPvV~~d~~~~-----~~~~~~~V~~d~~~~g~~~~~~L~~~g~~~~i~~i~g~~~~~~~~~R~~g~~~~~ 145 (302)
T TIGR02634 71 AVQEAKDEGIKVVAYDRLIN-----DADIDFYLSFDNEKVGEMQARAVLEAAPKGNYFLMGGSPTDNNAKLLRGGQMKVL 145 (302)
T ss_pred HHHHHHHCCCeEEEecCcCC-----CCCccEEEecCHHHHHHHHHHHHHhhCCCCCEEEEeCCCCCcchHHHHHHHHHHH
Confidence 55566788999998754321 11222345567777788889988777655 78887643 222334467778888
Q ss_pred Hhc----CcEEEEEEecCCCCCCChHHHHHHHHHHhc---CCceEEEEEcchhhHHHHHHHHHHcCCC
Q 002211 207 AEI----RCKISYKSALPPDQSVTETDVRNELVKVRM---MEARVIVVHGYSRTGLMVFDVAQRLGMM 267 (953)
Q Consensus 207 ~~~----g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~---~~~~vii~~~~~~~~~~~~~~a~~~g~~ 267 (953)
++. ++.+.... +... ....+....+.++.. ..+++|+.. ....+..+++.+++.|+.
T Consensus 146 ~~~~~~~~~~~~~~~-~~~~--~~~~~~~~~~~~ll~~~~~~~~aI~~~-~D~~A~g~~~al~~~g~~ 209 (302)
T TIGR02634 146 QPAIDSGDIKIVGDQ-WVDG--WLPENALRIMENALTANDNKVDAVVAS-NDATAGGAIQALTAQGLA 209 (302)
T ss_pred hhhccCCCeEEecCc-CCCC--CCHHHHHHHHHHHHHhCCCCccEEEEC-CCchHHHHHHHHHHCCCC
Confidence 764 35543221 1111 123344455666543 246766554 444566788999998874
No 209
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=96.84 E-value=0.15 Score=56.70 Aligned_cols=207 Identities=7% Similarity=-0.034 Sum_probs=119.3
Q ss_pred ceEEEeEEEecC-CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEEccCChhh
Q 002211 48 EVLNVGAIFSFG-TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIVGPQSAVM 126 (953)
Q Consensus 48 ~~i~IG~l~~~~-~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aiiGp~~S~~ 126 (953)
..-.||+++|-. ..+-.....+++-+.++. |+.+. +.++..++..-......+.++++.+||=-.....
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 456799999853 444445566666665552 45543 4455556655555566677777777663211111
Q ss_pred HHHHHHhhhhCCCc-EEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecC--ccccchHHHHH
Q 002211 127 AHVLSHLANELQVP-LLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDD--DQGRNGVTALG 203 (953)
Q Consensus 127 a~av~~v~~~~~vP-~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~--~~g~~~~~~l~ 203 (953)
...+..+.. ++| ++......+. ..+++ +..++..-+..+++++...|-+++++|.... ..+....+.|.
T Consensus 128 ~~~~~~~~~--~~p~vV~i~~~~~~---~~~~~---V~~D~~~~~~~a~~~L~~~G~~~I~~i~~~~~~~~~~~R~~Gf~ 199 (346)
T PRK10401 128 DDELAQFMD--QIPGMVLINRVVPG---YAHRC---VCLDNVSGARMATRMLLNNGHQRIGYLSSSHGIEDDAMRRAGWM 199 (346)
T ss_pred hHHHHHHHh--cCCCEEEEecccCC---CCCCE---EEECcHHHHHHHHHHHHHCCCCeEEEEeCCCcCcchHHHHHHHH
Confidence 122333433 355 6765433221 12232 3345555667778888888999999997433 34556788999
Q ss_pred HHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcC--CceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEE
Q 002211 204 DKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMM--EARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIA 275 (953)
Q Consensus 204 ~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~--~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~ 275 (953)
+++++.|+.+......... .+...-...+.++.+. .+++|+. .+...+..+++.+++.|+..|+-+-+.
T Consensus 200 ~al~~~gi~~~~~~~~~~~--~~~~~~~~~~~~~l~~~~~~~ai~~-~nd~~A~g~~~al~~~G~~vP~disvi 270 (346)
T PRK10401 200 SALKEQGIIPPESWIGTGT--PDMQGGEAAMVELLGRNLQLTAVFA-YNDNMAAGALTALKDNGIAIPLHLSII 270 (346)
T ss_pred HHHHHcCCCCChhheecCC--CChHHHHHHHHHHHcCCCCCcEEEE-CCcHHHHHHHHHHHHcCCCCCCceEEE
Confidence 9999998754321111111 1122223345555433 4677665 456677789999999998765444433
No 210
>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=96.62 E-value=0.32 Score=53.10 Aligned_cols=191 Identities=11% Similarity=-0.008 Sum_probs=113.4
Q ss_pred ceEEEeEEEec-CCCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEEc-cCChh
Q 002211 48 EVLNVGAIFSF-GTVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIVG-PQSAV 125 (953)
Q Consensus 48 ~~i~IG~l~~~-~~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aiiG-p~~S~ 125 (953)
..-.||+++|- +..+-.....+++-+.++ . |+.+-+ .++..++..-......+...++.++|= |....
T Consensus 58 ~~~~Ig~i~~~~~~~~~~~~~~~i~~~~~~---~-----gy~~~i--~~~~~~~~~~~~~~~~l~~~~vdGvIi~~~~~~ 127 (311)
T TIGR02405 58 SDKVVAVIVSRLDSPSENLAVSGMLPVFYT---A-----GYDPII--MESQFSPQLTNEHLSVLQKRNVDGVILFGFTGC 127 (311)
T ss_pred CCCEEEEEeCCcccccHHHHHHHHHHHHHH---C-----CCeEEE--ecCCCChHHHHHHHHHHHhcCCCEEEEeCCCCC
Confidence 34579999985 233323334444444433 2 566543 455556655555555566667887773 22211
Q ss_pred hHHHHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEec---CccccchHHHH
Q 002211 126 MAHVLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFND---DDQGRNGVTAL 202 (953)
Q Consensus 126 ~a~av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d---~~~g~~~~~~l 202 (953)
... .....++|+|..+... ..++ .+..++..-+..+++++...|-+++++|..+ ...+....+.|
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 2345678988765421 1122 3445666677788888888999999999732 23456678899
Q ss_pred HHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHHHcCC
Q 002211 203 GDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQRLGM 266 (953)
Q Consensus 203 ~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~~~g~ 266 (953)
.+++++.|+.... .... .+..+....+.++.+.++++|| +.+...+..+++.+++.|.
T Consensus 196 ~~a~~~~gi~~~~---~~~~--~~~~~~~~~~~~~l~~~~tAi~-~~~D~~A~g~~~~l~~~g~ 253 (311)
T TIGR02405 196 LAYCESANLEPIY---QTGQ--LSHESGYVLTDKVLKPETTALV-CATDTLALGAAKYLQELDR 253 (311)
T ss_pred HHHHHHcCCCcee---eeCC--CCHHHHHHHHHHHHhcCCCEEE-ECCcHHHHHHHHHHHHcCC
Confidence 9999999986321 1111 1123333445555445688775 5556677888999999886
No 211
>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=96.60 E-value=0.2 Score=53.32 Aligned_cols=194 Identities=10% Similarity=0.012 Sum_probs=110.4
Q ss_pred EEeEEEecC------CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEE-ccCC
Q 002211 51 NVGAIFSFG------TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIV-GPQS 123 (953)
Q Consensus 51 ~IG~l~~~~------~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aii-Gp~~ 123 (953)
+||++.+.+ ..+-.....+++-+.++ . |+.+.+...+ .+. .+..+++.++| .+..
T Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~gi~~~~~~----~----g~~~~~~~~~--~~~--------~~~~~~vdgii~~~~~ 62 (270)
T cd01544 1 RIAIVQWYSEEEELDDPYYLSIRLGIEKRAQE----L----GIELTKFFRD--DDL--------LEILEDVDGIIAIGKF 62 (270)
T ss_pred CeEEEEeccccccccCccHHHHHHHHHHHHHH----c----CCEEEEEecc--chh--------HHhccCcCEEEEecCC
Confidence 589998854 23333444555554444 2 5666654332 211 12345666655 2222
Q ss_pred hhhHHHHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecCc-------ccc
Q 002211 124 AVMAHVLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDDD-------QGR 196 (953)
Q Consensus 124 S~~a~av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~~-------~g~ 196 (953)
+. .....+.+.++|+|...... .+..+++ +..++...+..+++++...|-++++++..... +.+
T Consensus 63 ~~---~~~~~~~~~~~pvV~~~~~~---~~~~~~~---v~~D~~~a~~~~~~~l~~~g~~~i~~i~~~~~~~~~~~~~~~ 133 (270)
T cd01544 63 SQ---EQLAKLAKLNPNLVFVDSNP---APDGFDS---VVPDFEQAVEKALDYLLELGHTRIGFIGGEEKTTDGHEYIED 133 (270)
T ss_pred CH---HHHHHHHhhCCCEEEECCCC---CCCCCCE---EEECHHHHHHHHHHHHHHcCCCcEEEECCCcccccccchhhh
Confidence 22 33445566789999875432 2223343 45567777888888888889999999985432 344
Q ss_pred chHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcC----CceEEEEEcchhhHHHHHHHHHHcCCCCCceE
Q 002211 197 NGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMM----EARVIVVHGYSRTGLMVFDVAQRLGMMDSGYV 272 (953)
Q Consensus 197 ~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~----~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~ 272 (953)
...+.|.+++.+.|.. .....+... .+..+....++++.+. .+++|+. +....+..+++.+++.|+..++-+
T Consensus 134 ~R~~gf~~~~~~~~~~-~~~~~~~~~--~~~~~~~~~~~~~l~~~~~~~~~ai~~-~~d~~a~g~~~~l~~~g~~vp~di 209 (270)
T cd01544 134 PRETAFREYMKEKGLY-DPELIYIGD--FTVESGYQLMKEALKSLGDNLPTAFFI-ASDPMAIGALRALQEAGIKVPEDV 209 (270)
T ss_pred HHHHHHHHHHHHcCCC-ChheEeeCC--CCHHHHHHHHHHHHhccCCCCCCEEEE-cCcHHHHHHHHHHHHcCCCCCCce
Confidence 5578899999988841 100111111 1123333444454332 3565555 466778889999999998755444
Q ss_pred EEE
Q 002211 273 WIA 275 (953)
Q Consensus 273 wi~ 275 (953)
-|.
T Consensus 210 ~v~ 212 (270)
T cd01544 210 SVI 212 (270)
T ss_pred EEE
Confidence 333
No 212
>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=96.43 E-value=0.19 Score=53.11 Aligned_cols=196 Identities=13% Similarity=0.056 Sum_probs=104.8
Q ss_pred EEeEEEecC---CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEEccCChhhH
Q 002211 51 NVGAIFSFG---TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIVGPQSAVMA 127 (953)
Q Consensus 51 ~IG~l~~~~---~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aiiGp~~S~~a 127 (953)
|||+++|-. ..+......|++ ++.++. |.++. +.+...++.......++++++++..||+ .+....
T Consensus 1 kva~l~~g~~~D~~~n~~~~~G~~----~~~~~~----gv~~~--~~e~~~~~~~~~~~i~~~~~~g~dlIi~-~g~~~~ 69 (258)
T cd06353 1 KVAFVYVGPIGDQGWNYAHDEGRK----AAEKAL----GVEVT--YVENVPEGADAERVLRELAAQGYDLIFG-TSFGFM 69 (258)
T ss_pred CEEEEEeCCCCccchhHHHHHHHH----HHHHhc----CCeEE--EEecCCchHhHHHHHHHHHHcCCCEEEE-Cchhhh
Confidence 578888732 223333344444 443332 44444 4555556777888888999999999998 445556
Q ss_pred HHHHHhhhhC-CCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecC-ccccchHHHHHHH
Q 002211 128 HVLSHLANEL-QVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDD-DQGRNGVTALGDK 205 (953)
Q Consensus 128 ~av~~v~~~~-~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~-~~g~~~~~~l~~~ 205 (953)
.++..++.++ ++.++...+..+ - +.-..+.|+... ..+.+-.+|..+.+ -.+|++|..-. +.-......|.+-
T Consensus 70 ~~~~~vA~~~p~~~F~~~d~~~~-~-~Nv~~~~~~~~e-~~ylaG~~Aa~~t~--t~kVG~I~g~~~~~~~~~~~gF~~G 144 (258)
T cd06353 70 DAALKVAKEYPDVKFEHCSGYKT-A-PNVGSYFARIYE-GRYLAGVVAGKMTK--TNKVGYVAAFPIPEVVRGINAFALG 144 (258)
T ss_pred HHHHHHHHHCCCCEEEECCCCCC-C-CCeeeEechhhH-HHHHHHHHHHHhhc--CCcEEEEcCcccHHHHHHHHHHHHH
Confidence 6677777766 333333222111 0 111123333321 12333334444433 35899997532 3333455667766
Q ss_pred HHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHHHcCC
Q 002211 206 LAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQRLGM 266 (953)
Q Consensus 206 l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~~~g~ 266 (953)
++..+-.+.....+... -.+...-......+.+.++|+|+..+. ....++++++.|.
T Consensus 145 ~~~~~p~~~v~~~~~g~-~~D~~~a~~~a~~l~~~G~DvI~~~~~---~~g~~~aa~~~g~ 201 (258)
T cd06353 145 ARSVNPDATVKVIWTGS-WFDPAKEKEAALALIDQGADVIYQHTD---SPGVIQAAEEKGV 201 (258)
T ss_pred HHHHCCCcEEEEEEecC-CCCcHHHHHHHHHHHHCCCcEEEecCC---ChHHHHHHHHhCC
Confidence 65443332222222211 011233355556667789998888872 3457888888763
No 213
>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=96.42 E-value=0.54 Score=50.40 Aligned_cols=203 Identities=13% Similarity=0.035 Sum_probs=108.6
Q ss_pred EEeEEEecC-CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEEcc-CChhhHH
Q 002211 51 NVGAIFSFG-TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIVGP-QSAVMAH 128 (953)
Q Consensus 51 ~IG~l~~~~-~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aiiGp-~~S~~a~ 128 (953)
+||++.|.. ..+-.....+++-+.++. |+++- +.++..++..-.+....++.+++.+||=- .......
T Consensus 2 ~ig~i~~~~~~~~~~~~~~gi~~~a~~~--------gy~~~--~~~~~~~~~~~~~~i~~l~~~~vdgiil~~~~~~~~~ 71 (280)
T cd06315 2 NIIFVASDLKNGGILGVGEGVREAAKAI--------GWNLR--ILDGRGSEAGQAAALNQAIALKPDGIVLGGVDAAELQ 71 (280)
T ss_pred eEEEEecccCCcHHHHHHHHHHHHHHHc--------CcEEE--EECCCCCHHHHHHHHHHHHHcCCCEEEEcCCCHHHHH
Confidence 588888753 333334556666555542 45544 45666677666666677777777776642 2212122
Q ss_pred HHHHhhhhCCCcEEEeecCCCCCCCCCCC-cEEEccCChHHHHHHHHHHHHHc--CCcEEEEEEecC-cccc---chHHH
Q 002211 129 VLSHLANELQVPLLSFTALDPTLSPLQYP-FFVQTAPNDLYLMSAIAEMVSYF--GWGEVIAIFNDD-DQGR---NGVTA 201 (953)
Q Consensus 129 av~~v~~~~~vP~Is~~at~~~ls~~~~p-~~fr~~p~d~~~~~ai~~~l~~~--~w~~vaii~~d~-~~g~---~~~~~ 201 (953)
.....+.+.++|+|......+. .....+ .+-.+..++...+..++++|... |-++++++.... .... ...+.
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 3334456789999987543211 000011 13345666777778899988776 889999886432 1121 23334
Q ss_pred HHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcC---CceEEEEEcchhhHHHHHHHHHHcCCCCC
Q 002211 202 LGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMM---EARVIVVHGYSRTGLMVFDVAQRLGMMDS 269 (953)
Q Consensus 202 l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~---~~~vii~~~~~~~~~~~~~~a~~~g~~~~ 269 (953)
+.+++++.+ +......... .........++++.+. .+++|+. .+...+..+++.+++.|+..+
T Consensus 151 ~~~a~~~~~--~~~~~~~~~~--~~~~~~~~~~~~~l~~~~~~~~ai~~-~~D~~A~g~~~~l~~~g~~~p 216 (280)
T cd06315 151 IIEACKGCT--VLSIEDVPIS--RTATRMPALTARLLQRYGDKWTHSLA-INDLYFDYMAPPLASAGRKAD 216 (280)
T ss_pred HHHhCCCCE--EEEecccCcc--hhhhhhHHHHHHHHHhcCcccceecc-cchhhhHHhHHHHHHhcccCC
Confidence 444433333 3211111111 1011111334444332 3675544 455567788899999998654
No 214
>PF13379 NMT1_2: NMT1-like family; PDB: 2G29_A 3UN6_A 2I4C_A 2I49_A 2I4B_A 2I48_A 3QSL_A.
Probab=96.35 E-value=0.014 Score=61.57 Aligned_cols=74 Identities=20% Similarity=0.230 Sum_probs=49.8
Q ss_pred CCCCChHHhhh-----CCCeEEE-EeCchHHHHHH---HhhCCCc---cceEeCCCHHHHHHHHHcCCcEEEEccchhHH
Q 002211 700 SPIKGIDTLMT-----SNDRVGY-QVGSFAENYLI---EELSIPK---SRLVALGSPEEYAIALENRTVAAVVDERPYID 767 (953)
Q Consensus 700 ~~I~sl~dL~~-----~~~~ig~-~~~s~~~~~l~---~~~~~~~---~~~~~~~~~~~~~~~l~~g~~~a~~~~~~~~~ 767 (953)
+.+++++||.+ .|++|++ ..|+.....+. ++.++.. .+++.++. .+...++++|++|+++...|+..
T Consensus 104 ~~~~~~~dl~~~~~~~kGk~i~~~~~gs~~~~~l~~~l~~~Gl~~~~dv~~~~~~~-~~~~~al~~g~iDa~~~~eP~~~ 182 (252)
T PF13379_consen 104 SDIKSLADLIKKRKAQKGKKIAVPFPGSTHDMLLRYLLKKAGLDPKDDVTLVNVPP-PEMVAALRAGEIDAAVLWEPFAS 182 (252)
T ss_dssp STTCCGHHHHHTCCSCSTEEEEESSTTSHHHHHHHHHHHHTT--TTTSSEEEE--G-HHHHHHHHTTS-SEEEEETTHHH
T ss_pred CCccCHHHHHhhhcccCCcEEEEcCCCCHHHHHHHHHHHhCCCCcccceEEEecCH-HHHHHHHhCCCcCEEEecCCHHH
Confidence 57899999943 4888999 45554433332 3444443 45566666 99999999999999999999988
Q ss_pred HHHhcCc
Q 002211 768 LFLSDHC 774 (953)
Q Consensus 768 ~~~~~~~ 774 (953)
....+..
T Consensus 183 ~~~~~g~ 189 (252)
T PF13379_consen 183 QAEAKGI 189 (252)
T ss_dssp HHHHTTS
T ss_pred HHHhccC
Confidence 7776643
No 215
>COG3221 PhnD ABC-type phosphate/phosphonate transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=96.05 E-value=0.12 Score=55.07 Aligned_cols=110 Identities=21% Similarity=0.200 Sum_probs=77.7
Q ss_pred CCCCChHHhhhCCCeEEEEeCchH------HHHHHHhhCCCc---cceEeCCC-HHHHHHHHHcCCcEEEEccchhHHHH
Q 002211 700 SPIKGIDTLMTSNDRVGYQVGSFA------ENYLIEELSIPK---SRLVALGS-PEEYAIALENRTVAAVVDERPYIDLF 769 (953)
Q Consensus 700 ~~I~sl~dL~~~~~~ig~~~~s~~------~~~l~~~~~~~~---~~~~~~~~-~~~~~~~l~~g~~~a~~~~~~~~~~~ 769 (953)
++|++++||. |+++++..-+.. ..+|.++.+.+. ..-+.+.. .+..+.+|.+|++|+..........+
T Consensus 134 s~i~sl~dlk--gk~~af~d~~StSG~l~P~~~L~~~g~~d~~~~f~~v~~~G~H~~a~~aV~nG~vDva~~~~~~~~~~ 211 (299)
T COG3221 134 SPIKSLEDLK--GKRFAFGDPDSTSGYLFPLYYLAKEGGIDPDKFFGEVIFSGGHDAAVLAVANGQVDVAAVNSSARGLL 211 (299)
T ss_pred CCcchHHHhc--CCeEeccCCCcchhhHhHHHHHHHhcCCChhhhhceeeccChHHHHHHHHHcCCceEEeccHHHHhhh
Confidence 6899999997 999999753322 223333332221 12234554 88999999999999998887766665
Q ss_pred Hhc--C---cceEEeCCccccCccEEEecCCCc--chHHHHHHHHhhhc
Q 002211 770 LSD--H---CQFSVRGQEFTKSGWGFAFPRDSP--LAIDMSTAILTLSE 811 (953)
Q Consensus 770 ~~~--~---~~l~~~~~~~~~~~~~~~~~k~sp--l~~~~n~~i~~l~e 811 (953)
... . .+++++...-...+..++++++-| +++.+..+++.+.+
T Consensus 212 ~~~~~~~~~~~l~vi~~S~~iP~~pi~vr~~L~~~~k~kl~~af~~l~~ 260 (299)
T COG3221 212 KKAAPEGVAEKLRVIWKSPLIPNDPIAVRSDLPADLKEKLRDAFLDLAK 260 (299)
T ss_pred hhcccccchhhceEEEecCCCCCCCEEEeCCCCHHHHHHHHHHHHhcCc
Confidence 543 2 367777765445567788888866 99999999999987
No 216
>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=95.99 E-value=0.033 Score=60.77 Aligned_cols=68 Identities=19% Similarity=0.230 Sum_probs=50.2
Q ss_pred CCChHHhhhCCCeEEEEeCchHHHHHHH---hhCCCc--cceEeCCCHHHHHHHHHcCCcEEEEccchhHHHHHhc
Q 002211 702 IKGIDTLMTSNDRVGYQVGSFAENYLIE---ELSIPK--SRLVALGSPEEYAIALENRTVAAVVDERPYIDLFLSD 772 (953)
Q Consensus 702 I~sl~dL~~~~~~ig~~~~s~~~~~l~~---~~~~~~--~~~~~~~~~~~~~~~l~~g~~~a~~~~~~~~~~~~~~ 772 (953)
|++++||+ |++|++..|+..+.++.. ..+... .+++.. ++.+...++.+|++||.+...|+......+
T Consensus 98 i~svaDLK--GKkIav~~gs~~~~ll~~aL~~aGL~~~DV~~v~~-~~~d~~aAl~~G~VDAa~~~eP~~s~~~~~ 170 (328)
T TIGR03427 98 GKSLADLK--GQKVNLVELSVSHYLLARALESVGLSEKDVKVVNT-SDADIVAAFITKDVTAVVTWNPQLSEIKAQ 170 (328)
T ss_pred CCCHHHcC--CCEEeccCCChHHHHHHHHHHHcCCCHHHeEEEeC-ChHHHHHHHhcCCCcEEEEcCchHHHHHhC
Confidence 89999997 999999999876655543 233332 334444 557889999999999999988887655443
No 217
>COG4213 XylF ABC-type xylose transport system, periplasmic component [Carbohydrate transport and metabolism]
Probab=95.96 E-value=0.89 Score=47.38 Aligned_cols=208 Identities=10% Similarity=0.044 Sum_probs=120.1
Q ss_pred CCCCceEEEeEEEecC-CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEE-EEcc
Q 002211 44 ALKPEVLNVGAIFSFG-TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLA-IVGP 121 (953)
Q Consensus 44 ~~~~~~i~IG~l~~~~-~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~a-iiGp 121 (953)
++..++..||+..|-- ...-..-+.++.-+.|.+ |.+.- +.+-+++...-......++++++.+ ||+|
T Consensus 20 aa~~~d~~IGis~~d~~~eRW~~D~~~~~~~~e~~--------g~k~~--~q~A~~~~~~Q~~qien~i~qg~~vlvi~a 89 (341)
T COG4213 20 AAAAKDGVIGISMPDLRSERWIKDRDAFVKKAEAL--------GAKVD--VQSADGDEEKQLAQIENMINQGVKVLVIGA 89 (341)
T ss_pred hhhccCCeEEEEcCChhHhhhhhhhHHHHHHHHhc--------cchhh--hhhhccChhHHHHHHHHHHhcCCCEEEEEe
Confidence 4566788999988863 211123344454444443 44444 4555666777788889999997654 6699
Q ss_pred CChhhHHHHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEcc--CChHHHHHHHHHHHHHcC---CcEEEEEE--ecCc-
Q 002211 122 QSAVMAHVLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTA--PNDLYLMSAIAEMVSYFG---WGEVIAIF--NDDD- 193 (953)
Q Consensus 122 ~~S~~a~av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~--p~d~~~~~ai~~~l~~~~---w~~vaii~--~d~~- 193 (953)
..|.+...+.+.+...+||+|+|. ....+..+.|....- .--..|+.++.+.++... -..+.++. ++|.
T Consensus 90 ~d~~~l~~~i~~A~~~gikViaYD---RlI~n~dvd~YvsFDN~~VG~lQa~~l~~~lk~k~~~~~gn~~l~~GSp~DnN 166 (341)
T COG4213 90 IDGGVLSNAVEKAKSEGIKVIAYD---RLINNADVDFYVSFDNEKVGELQAKALVKGLKLKPLTSEGNYVLLGGSPDDNN 166 (341)
T ss_pred ccchhHHHHHHHHHHcCCeEEEee---cccccCCccEEEEecchhHHHHHHHHHHHHhccCCCCCCCCEEEecCCCCCcc
Confidence 999999999999999999999873 333333333332221 112346666655554433 34455554 2232
Q ss_pred ---cccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhc---CCceEEEEEcchhhHHHHHHHHHHcCCC
Q 002211 194 ---QGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRM---MEARVIVVHGYSRTGLMVFDVAQRLGMM 267 (953)
Q Consensus 194 ---~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~---~~~~vii~~~~~~~~~~~~~~a~~~g~~ 267 (953)
+-.+..+.|+..+..-.+.++.....+.- ..+.-...+..+.. .+.|.|+..-. ..+...+..+...|+.
T Consensus 167 A~lf~~G~m~VLkp~idsGkik~~Ge~~~d~W---~ps~Aq~~men~lta~~~~vdaVvA~nD-gtagGaI~aL~a~Gl~ 242 (341)
T COG4213 167 AKLFFAGAMKVLKPLIDSGKIKVVGEQWTDGW---LPSNAQQIMENLLTANYNDIDAVVAPND-GTAGGAIAALKAQGLA 242 (341)
T ss_pred hHHHHhcHHHHHHHHhhCCceEEeeecccccc---CHHHHHHHHHHHHhcccCceeEEEcCCC-chhHHHHHHHHhcccC
Confidence 22233455555555555666555555432 12233333333322 34555555544 4566778888888986
Q ss_pred C
Q 002211 268 D 268 (953)
Q Consensus 268 ~ 268 (953)
+
T Consensus 243 g 243 (341)
T COG4213 243 G 243 (341)
T ss_pred C
Confidence 3
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=95.26 E-value=0.11 Score=53.37 Aligned_cols=62 Identities=27% Similarity=0.257 Sum_probs=40.8
Q ss_pred CCCCChHHhhhCCCeEEEEeCchHHHHHH---HhhCCCccceEeC-CCHHHHHHHHHcCCcEEEEccc
Q 002211 700 SPIKGIDTLMTSNDRVGYQVGSFAENYLI---EELSIPKSRLVAL-GSPEEYAIALENRTVAAVVDER 763 (953)
Q Consensus 700 ~~I~sl~dL~~~~~~ig~~~~s~~~~~l~---~~~~~~~~~~~~~-~~~~~~~~~l~~g~~~a~~~~~ 763 (953)
+.|++++||. |++||+..++....++. +..++....+... .+..+...+|.+|++|+.+...
T Consensus 83 s~i~~~~DLk--GK~i~v~~~s~~~~~~~~~l~~~g~~~~~v~~v~~~~~~~~~al~~g~vDa~~~~~ 148 (216)
T PF09084_consen 83 SGIKSPADLK--GKKIGVSRGSSSEYFLRALLKKNGIDPDDVKIVNLGPPELAQALLSGQVDAAILWY 148 (216)
T ss_dssp TS-SSGGGGT--TSEEEESTTSHHHHHHHHHHHHTTT-GGGSEEEES-HHHHHHHHHTTSSSEEEEEE
T ss_pred CCCCCHHHhC--CCEEEEecCcchhHHHHHHHHHhccccccceeeeeehhhhhhhhhcCCCCEEEEcc
Confidence 4699999997 99999998765444332 3445544444332 2466777799999999999433
No 219
>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=94.95 E-value=0.087 Score=57.84 Aligned_cols=60 Identities=27% Similarity=0.207 Sum_probs=41.0
Q ss_pred CCCCChHHhhhCCCeEEEEe-CchHH----HHHHHhhCCCccc--eEeCCCHHHHHHHHHcCCcEEEEcc
Q 002211 700 SPIKGIDTLMTSNDRVGYQV-GSFAE----NYLIEELSIPKSR--LVALGSPEEYAIALENRTVAAVVDE 762 (953)
Q Consensus 700 ~~I~sl~dL~~~~~~ig~~~-~s~~~----~~l~~~~~~~~~~--~~~~~~~~~~~~~l~~g~~~a~~~~ 762 (953)
.++++++||. ++++++.. ++... .++ +..+..... .+.+.+..+...+|.+|++|+++..
T Consensus 131 ~~i~sl~dL~--gk~v~~~~~~s~~~~~~~~~l-~~~G~~~~~~~~v~~~~~~~~~~al~~G~vDa~~~~ 197 (320)
T TIGR02122 131 SGIKTVADLK--GKRVAVGAPGSGTELNARAVL-KAAGLTYDDVKKVEYLGYAEAADALKDGKIDAAFYT 197 (320)
T ss_pred CCCCcHHHcC--CCEEecCCCCcchHHHHHHHH-HHcCCCHHHccchhcCCHHHHHHHHHCCCccEEEEe
Confidence 3678999997 77887754 33222 233 334443222 3567788999999999999999987
No 220
>PF03466 LysR_substrate: LysR substrate binding domain; InterPro: IPR005119 The structure of this domain is known and is similar to the periplasmic binding proteins []. This domain is found in members of the LysR family of prokaryotic transcriptional regulatory proteins IPR000847 from INTERPRO which share sequence similarities over approximately 280 residues including a putative helix-turn-helix DNA-binding motif at their N terminus.; PDB: 3ONM_B 3FZJ_J 3FXR_B 3N6T_A 3FXQ_A 3FXU_A 3N6U_A 2QSX_B 3HO7_B 1IZ1_B ....
Probab=94.88 E-value=0.77 Score=46.09 Aligned_cols=196 Identities=18% Similarity=0.158 Sum_probs=121.6
Q ss_pred cceEEEecCcccccccEEeeCCcceEEEeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEecE
Q 002211 485 RQLRIGVPNRVSYRDFVFKVNGTDIVHGYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGDI 564 (953)
Q Consensus 485 ~~lri~v~~~~~~~p~~~~~~~~~~~~G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~~ 564 (953)
++||||+.. .+. ..+..+++..+.++.+- ++++... ++..++++.|.+|++|+++...
T Consensus 6 ~~l~Ig~~~--~~~------------~~~l~~~l~~~~~~~P~-i~i~~~~-------~~~~~~~~~l~~g~~Dl~i~~~ 63 (209)
T PF03466_consen 6 GTLRIGASP--SFA------------SSLLPPLLAEFRERHPN-IRIEIRE-------GDSDELIEALRSGELDLAITFG 63 (209)
T ss_dssp EEEEEEEEH--HHH------------HHTHHHHHHHHHHHSTT-EEEEEEE-------ESHHHHHHHHHTTSSSEEEESS
T ss_pred eEEEEEEEh--HHH------------HHHHHHHHHHHHHHCCC-cEEEEEe-------ccchhhhHHHhcccccEEEEEe
Confidence 568888864 111 23456788888888763 5566654 5578999999999999998744
Q ss_pred EEecCccceeeccccceecceEEEEecccCCcCcceeeccCchhHHHHHHHHHHHHHHHhhhhhcccCCCCCCCCcccch
Q 002211 565 AIVTNRTKAVDFTQPYIESGLVVVAPVRKLNSSAWAFLRPFTPLMWAVTGVFFLVVGTVVWILEHRLNDEFRGPPRKQIV 644 (953)
Q Consensus 565 ~~t~~r~~~vdft~p~~~~~~~~~v~~~~~~~~~~~~l~PF~~~vW~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~ 644 (953)
.. ....+. ..++....+++++++..+...
T Consensus 64 ~~---~~~~~~-~~~l~~~~~~~~~~~~~pl~~----------------------------------------------- 92 (209)
T PF03466_consen 64 PP---PPPGLE-SEPLGEEPLVLVVSPDHPLAQ----------------------------------------------- 92 (209)
T ss_dssp SS---SSTTEE-EEEEEEEEEEEEEETTSGGGT-----------------------------------------------
T ss_pred ec---cccccc-cccccceeeeeeeeccccccc-----------------------------------------------
Confidence 33 222233 567778889999887762110
Q ss_pred hhHHHHHHHhhccccCCcccchhHHHHHHHHHHHHHhhhhcccceeeeeeeccccCCCCChHHhhhCCCeEEEE-eCchH
Q 002211 645 TVLWFSFSTMFFAHRENTVSTLGRVVLIIWLFVVLIITSSYTASLTSILTVQQLSSPIKGIDTLMTSNDRVGYQ-VGSFA 723 (953)
Q Consensus 645 ~~~~~~~~~l~~~~~~~~~s~~~R~l~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~I~sl~dL~~~~~~ig~~-~~s~~ 723 (953)
...+ +++||. +.++... .+...
T Consensus 93 ------------------------------------------------------~~~i-~~~dL~--~~~~i~~~~~~~~ 115 (209)
T PF03466_consen 93 ------------------------------------------------------KKPI-TLEDLA--DYPLILLSPGSPY 115 (209)
T ss_dssp ------------------------------------------------------TSSS-SGGGGT--TSEEEEESTTTSH
T ss_pred ------------------------------------------------------cccc-hhhhhh--hcccccccccccc
Confidence 0344 889997 5665443 34444
Q ss_pred HHHHHHh---hCCCccceEeCCCHHHHHHHHHcCCcEEEEccchhHHHHHhcCcceEEeCC-ccccCccEEEecCCCcch
Q 002211 724 ENYLIEE---LSIPKSRLVALGSPEEYAIALENRTVAAVVDERPYIDLFLSDHCQFSVRGQ-EFTKSGWGFAFPRDSPLA 799 (953)
Q Consensus 724 ~~~l~~~---~~~~~~~~~~~~~~~~~~~~l~~g~~~a~~~~~~~~~~~~~~~~~l~~~~~-~~~~~~~~~~~~k~spl~ 799 (953)
...+.+. .+.........++.+.....+..|..-+++-+.....+.....-....+.+ .+. ..++++.+++.+..
T Consensus 116 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~~~~~~l~~~~~~~~~~~-~~~~l~~~~~~~~~ 194 (209)
T PF03466_consen 116 RDQLDRWLREHGFSPNIVIEVDSFESILSLVASGDGIAILPDSLAQDELESGELVFLPLPDPPLP-RPIYLVWRKDRPLS 194 (209)
T ss_dssp HHHHHHHHHHTTEEEEEEEEESSHHHHHHHHHTTSEBEEEEHHHHHHHHHCTTEEEEEESSSTEE-EEEEEEEETTGTTH
T ss_pred ccccccccccccccccccccccchhhhccccccccceeecCcccccccccCCCEEEEECCCCCCc-eEEEEEEECCCCCC
Confidence 4444332 233333445678999999999988776776654444444222223223344 443 77888888887766
Q ss_pred HHHHHHHHhhhc
Q 002211 800 IDMSTAILTLSE 811 (953)
Q Consensus 800 ~~~n~~i~~l~e 811 (953)
..+...+..+.+
T Consensus 195 ~~~~~~~~~l~~ 206 (209)
T PF03466_consen 195 PAIQWFIDLLRE 206 (209)
T ss_dssp HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHH
Confidence 666666555443
No 221
>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=94.81 E-value=0.53 Score=48.62 Aligned_cols=92 Identities=8% Similarity=0.002 Sum_probs=73.6
Q ss_pred HHHHHHHHHHHcCCcEEEEEEecCccccchHHHHHHHHHhcCcEEEEEEecCCCC-----CCChHHHHHHHHHHhcCCce
Q 002211 169 LMSAIAEMVSYFGWGEVIAIFNDDDQGRNGVTALGDKLAEIRCKISYKSALPPDQ-----SVTETDVRNELVKVRMMEAR 243 (953)
Q Consensus 169 ~~~ai~~~l~~~~w~~vaii~~d~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~-----~~~~~d~~~~l~~i~~~~~~ 243 (953)
-+.|+.+-++++|.+|++++. +|-....+.+.+.+++.|++|+....+.... ..+.+++...+.++...++|
T Consensus 107 ~~~A~~~AL~alg~~RIalvT---PY~~~v~~~~~~~l~~~G~eV~~~~~~~~~~~~~ia~i~p~~i~~~~~~~~~~~aD 183 (239)
T TIGR02990 107 PSSAAVDGLAALGVRRISLLT---PYTPETSRPMAQYFAVRGFEIVNFTCLGLTDDREMARISPDCIVEAALAAFDPDAD 183 (239)
T ss_pred HHHHHHHHHHHcCCCEEEEEC---CCcHHHHHHHHHHHHhCCcEEeeeeccCCCCCceeeecCHHHHHHHHHHhcCCCCC
Confidence 357888899999999999997 5888899999999999999998765554321 12355666667777678999
Q ss_pred EEEEEcchhhHHHHHHHHHH
Q 002211 244 VIVVHGYSRTGLMVFDVAQR 263 (953)
Q Consensus 244 vii~~~~~~~~~~~~~~a~~ 263 (953)
+|++.|..-....++.++.+
T Consensus 184 AifisCTnLrt~~vi~~lE~ 203 (239)
T TIGR02990 184 ALFLSCTALRAATCAQRIEQ 203 (239)
T ss_pred EEEEeCCCchhHHHHHHHHH
Confidence 99999998888888888855
No 222
>cd05466 PBP2_LTTR_substrate The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily. This model and hierarchy represent the the substrate-binding domain of the LysR-type transcriptional regulators that form the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA bin
Probab=94.72 E-value=1.5 Score=42.73 Aligned_cols=70 Identities=21% Similarity=0.345 Sum_probs=46.6
Q ss_pred EeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEecEEEecCccceeeccccceecceEEEEec
Q 002211 512 GYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGDIAIVTNRTKAVDFTQPYIESGLVVVAPV 591 (953)
Q Consensus 512 G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~~~~t~~r~~~vdft~p~~~~~~~~~v~~ 591 (953)
.+..++++.+.++.+ .+++++.. ....+++..+.+|++|+++..... ....++ ..++....+++++++
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 455677777877764 25565554 446789999999999999874433 222333 446667778888776
Q ss_pred cc
Q 002211 592 RK 593 (953)
Q Consensus 592 ~~ 593 (953)
..
T Consensus 81 ~~ 82 (197)
T cd05466 81 DH 82 (197)
T ss_pred CC
Confidence 65
No 223
>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=94.65 E-value=0.29 Score=52.56 Aligned_cols=71 Identities=17% Similarity=0.295 Sum_probs=49.2
Q ss_pred CCCCChHHhhhCCCeEEEEeCchHHHHHHH---hhCCCccce-EeCCCHHHHHHHHHcCCcEEEEccchhHHHHHhc
Q 002211 700 SPIKGIDTLMTSNDRVGYQVGSFAENYLIE---ELSIPKSRL-VALGSPEEYAIALENRTVAAVVDERPYIDLFLSD 772 (953)
Q Consensus 700 ~~I~sl~dL~~~~~~ig~~~~s~~~~~l~~---~~~~~~~~~-~~~~~~~~~~~~l~~g~~~a~~~~~~~~~~~~~~ 772 (953)
.+|++++||. |++|++..++.....+.. ..+.+...+ ..+.+..+...++.+|++|+++...++......+
T Consensus 91 ~~i~s~~dL~--Gk~i~~~~~~~~~~~~~~~l~~~G~~~~~v~~~~~~~~~~~~al~~g~vda~~~~~p~~~~~~~~ 165 (288)
T TIGR01728 91 SPIRTVADLK--GKRIAVPKGGSGHDLLLRALLKAGLSGDDVTILYLGPSDARAAFAAGQVDAWAIWEPWGSALVEE 165 (288)
T ss_pred CCCCCHHHcC--CCEEEecCCccHHHHHHHHHHHcCCCccceeEEecCcHHHHHHHHCCCCCEEEeccchHhHHhhc
Confidence 4788999997 889998877644443322 234433222 2334677889999999999999988877665544
No 224
>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=94.63 E-value=2.7 Score=44.71 Aligned_cols=183 Identities=10% Similarity=-0.006 Sum_probs=105.4
Q ss_pred HHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEEc-cCChhhHHHHHHhhhhCCCcEEE
Q 002211 65 VSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIVG-PQSAVMAHVLSHLANELQVPLLS 143 (953)
Q Consensus 65 ~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aiiG-p~~S~~a~av~~v~~~~~vP~Is 143 (953)
....+++-++++ .|+++.+...+. .. ..+...+|+++|- +... .. .....+.+.++|+|.
T Consensus 24 ~~~~~i~~~~~~--------~gy~~~~~~~~~---~~------~~l~~~~vdgiIi~~~~~-~~-~~~~~l~~~~iPvV~ 84 (269)
T cd06287 24 EVAAAAAESALE--------RGLALCLVPPHE---AD------SPLDALDIDGAILVEPMA-DD-PQVARLRQRGIPVVS 84 (269)
T ss_pred HHHHHHHHHHHH--------CCCEEEEEeCCC---ch------hhhhccCcCeEEEecCCC-CC-HHHHHHHHcCCCEEE
Confidence 445555555444 256676654441 11 1233557777653 2211 11 223344567999998
Q ss_pred eecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEec--CccccchHHHHHHHHHhcCcEEEEEEecCC
Q 002211 144 FTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFND--DDQGRNGVTALGDKLAEIRCKISYKSALPP 221 (953)
Q Consensus 144 ~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d--~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~ 221 (953)
.....+. ...+++ +..++...+..+++.+...|-+++++|... ..........|.+++++.|...... ....
T Consensus 85 i~~~~~~--~~~~~~---V~~d~~~~~~~a~~~L~~~G~~~I~~i~~~~~~~~~~~R~~gf~~a~~~~g~~~~~~-~~~~ 158 (269)
T cd06287 85 IGRPPGD--RTDVPY---VDLQSAATARMLLEHLRAQGARQIALIVGSARRNSYLEAEAAYRAFAAEHGMPPVVL-RVDE 158 (269)
T ss_pred eCCCCCC--CCCCCe---EeeCcHHHHHHHHHHHHHcCCCcEEEEeCCcccccHHHHHHHHHHHHHHcCCCccee-EecC
Confidence 7543210 122333 334566667888888888899999999643 2334456788999999988753211 1111
Q ss_pred CCCCChHHHHHHHHHHhcC--CceEEEEEcchhhHHHHHHHHHHcCCCCCceEEEE
Q 002211 222 DQSVTETDVRNELVKVRMM--EARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVWIA 275 (953)
Q Consensus 222 ~~~~~~~d~~~~l~~i~~~--~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~ 275 (953)
. .+.++-...++++.+. ++++|+.. +...+..+++.+++.|+..++-+-|.
T Consensus 159 ~--~~~~~~~~~~~~~l~~~~~~~ai~~~-~d~~A~gvl~al~~~gl~vP~dvsvi 211 (269)
T cd06287 159 A--GGEEAGYAACAQLLAQHPDLDALCVP-VDAFAVGAVRAATELGRAVPDQLRVV 211 (269)
T ss_pred C--CChHHHHHHHHHHHhCCCCCCEEEEc-CcHHHHHHHHHHHHcCCCCCCceEEE
Confidence 1 1123334455565433 46766644 56678889999999998766555444
No 225
>cd08440 PBP2_LTTR_like_4 TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold. LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse funct
Probab=94.41 E-value=2.4 Score=41.60 Aligned_cols=70 Identities=17% Similarity=0.305 Sum_probs=47.3
Q ss_pred EeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEecEEEecCccceeeccccceecceEEEEec
Q 002211 512 GYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGDIAIVTNRTKAVDFTQPYIESGLVVVAPV 591 (953)
Q Consensus 512 G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~~~~t~~r~~~vdft~p~~~~~~~~~v~~ 591 (953)
.+..+++..+.++.+ .++++... ++..++.+.+.+|++|+++... +.....+. +.++.+..+++++++
T Consensus 13 ~~l~~~l~~~~~~~p-~v~i~i~~-------~~~~~~~~~l~~g~~D~~i~~~---~~~~~~~~-~~~l~~~~~~~~~~~ 80 (197)
T cd08440 13 TLLPPVLAAFRRRHP-GIRVRLRD-------VSAEQVIEAVRSGEVDFGIGSE---PEADPDLE-FEPLLRDPFVLVCPK 80 (197)
T ss_pred hHHHHHHHHHHHhCC-CcEEEEEe-------CChHHHHHHHHcCCccEEEEeC---CCCCCCee-EEEeecccEEEEecC
Confidence 556788888888775 34555553 4578999999999999988632 22222232 356777788888876
Q ss_pred cc
Q 002211 592 RK 593 (953)
Q Consensus 592 ~~ 593 (953)
..
T Consensus 81 ~~ 82 (197)
T cd08440 81 DH 82 (197)
T ss_pred CC
Confidence 54
No 226
>cd08442 PBP2_YofA_SoxR_like The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, contains the type 2 periplasmic binding fold. YofA is a LysR-like transcriptional regulator of cell growth in Bacillus subtillis. YofA controls cell viability and the formation of constrictions during cell division. YofaA positively regulates expression of the cell division gene ftsW, and thus is essential for cell viability during stationary-phase growth of Bacillus substilis. YofA shows significant homology to SoxR from Arthrobacter sp. TE1826. SoxR is a negative regulator for the sarcosine oxidase gene soxA. Sarcosine oxidase catalyzes the oxidative demethylation of sarcosine, which is involved in the metabolism of creatine and choline. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides
Probab=94.29 E-value=2.3 Score=41.75 Aligned_cols=70 Identities=20% Similarity=0.214 Sum_probs=46.7
Q ss_pred EeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEecEEEecCccceeeccccceecceEEEEec
Q 002211 512 GYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGDIAIVTNRTKAVDFTQPYIESGLVVVAPV 591 (953)
Q Consensus 512 G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~~~~t~~r~~~vdft~p~~~~~~~~~v~~ 591 (953)
.+..+++..+.++.+- ++++... ++..+++..+.+|++|+++.. .......+. ..+.....++++++.
T Consensus 13 ~~l~~~l~~~~~~~P~-i~l~i~~-------~~~~~~~~~l~~g~~Dl~i~~---~~~~~~~~~-~~~l~~~~~~~v~~~ 80 (193)
T cd08442 13 VRLPPLLAAYHARYPK-VDLSLST-------GTTGALIQAVLEGRLDGAFVA---GPVEHPRLE-QEPVFQEELVLVSPK 80 (193)
T ss_pred hhhHHHHHHHHHHCCC-ceEEEEe-------CCcHHHHHHHHCCCccEEEEe---CCCCCCCcE-EEEeecCcEEEEecC
Confidence 5567888899888752 4555554 557789999999999998753 222222222 455667777777776
Q ss_pred cc
Q 002211 592 RK 593 (953)
Q Consensus 592 ~~ 593 (953)
..
T Consensus 81 ~~ 82 (193)
T cd08442 81 GH 82 (193)
T ss_pred CC
Confidence 54
No 227
>COG1744 Med Uncharacterized ABC-type transport system, periplasmic component/surface lipoprotein [General function prediction only]
Probab=94.13 E-value=5.5 Score=43.87 Aligned_cols=205 Identities=15% Similarity=0.054 Sum_probs=108.6
Q ss_pred CCceEEEeEEEecC---CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEec-CCC-ChHHHHHHHHHHHhcCcEEEEc
Q 002211 46 KPEVLNVGAIFSFG---TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHD-AKF-NGFLSIMGALQFMETDTLAIVG 120 (953)
Q Consensus 46 ~~~~i~IG~l~~~~---~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D-~~~-~~~~a~~~a~~li~~~v~aiiG 120 (953)
.....+++++.+-. ..+.+....|.+.+-++. |.+++....+ .+. +.....+..+++.+++...|+|
T Consensus 32 ~~~~~~~~~~~~g~~~D~s~n~~~~~g~~~~~~~~--------g~~~~~~~~~~~~~~~~~~~~~~~~~~a~~g~~lI~~ 103 (345)
T COG1744 32 AGKKKKVAVIDVGGIDDKSFNQSAYEGLLKAKKEL--------GLKVETYYWEYVQSDSEADYERALRALAEDGYDLIFG 103 (345)
T ss_pred cccceEEEEEecCCCCccchhHHHHHHHHHHHHHh--------CCceEeeeeeecCCcchhHHHHHHHHHHhcCCCEEEE
Confidence 34456666665432 334556667776555554 3445543333 222 3455566666788888888887
Q ss_pred cCChhhHHHHHHhhhhC-CCcEEEeecCCCCCCC--CCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEE-ecCcccc
Q 002211 121 PQSAVMAHVLSHLANEL-QVPLLSFTALDPTLSP--LQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIF-NDDDQGR 196 (953)
Q Consensus 121 p~~S~~a~av~~v~~~~-~vP~Is~~at~~~ls~--~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~-~d~~~g~ 196 (953)
. +-....++..++.++ ++.++- .+..... +-..|.||..-..... -.+|..+.+ -.+++.+. .+-+--.
T Consensus 104 ~-gf~~~d~~~~va~~~Pd~~F~i---id~~~~~~~Nv~s~~f~~~egayL~-G~~AA~~sk--~~~vG~vgg~~~p~v~ 176 (345)
T COG1744 104 T-GFAFSDALEKVAAEYPDVKFVI---IDGVVKKEDNVASYVFREYEGAYLA-GVAAAKMSK--SGKVGFVGGMDIPEVN 176 (345)
T ss_pred e-ccchhhHHHHHHHHCCCCEEEE---ecCccCCCCceEEEEeccccHHHHH-HHHHHHhhc--CCceeEEecccchhhH
Confidence 4 345566777777776 333332 2222221 2335777775443333 333333332 34555554 2444444
Q ss_pred chHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHHHcCCC
Q 002211 197 NGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQRLGMM 267 (953)
Q Consensus 197 ~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~~~g~~ 267 (953)
.....|..-.+..+-.+.....+...- .+...-......+.++++|||+-++.+.... .+.+|++.|..
T Consensus 177 ~f~~gF~~Gak~~np~i~v~v~~~gsf-~D~~k~k~~a~~li~~GaDVI~~~ag~~~~g-v~~~A~~~~~~ 245 (345)
T COG1744 177 RFINGFLAGAKSVNPDIKVKVVYVGSF-SDPAKGKEAANALIDQGADVIYPAAGGTGVG-VFQAAKELGAY 245 (345)
T ss_pred HHHHHHHHHHHhhCCCccEEEEEecCc-cChHHHHHHHHHHHhcCCCEEEecCCCCcch-HHHHHHHhCCC
Confidence 556666666665543322222222110 1122334477788889999999888765443 33377777743
No 228
>cd08468 PBP2_Pa0477 The C-terminal substrate biniding domain of an uncharacterized LysR-like transcriptional regulator Pa0477 related to DntR, contains the type 2 periplasmic binding fold. LysR-type transcriptional regulator Pa0477 is related to DntR, which controls genes encoding enzymes for oxidative degradation of the nitro-aromatic compound 2,4-dinitrotoluene. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their spec
Probab=94.02 E-value=2.6 Score=42.03 Aligned_cols=73 Identities=15% Similarity=0.202 Sum_probs=48.6
Q ss_pred EeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEecEEEecCccceeeccccceecceEEEEec
Q 002211 512 GYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGDIAIVTNRTKAVDFTQPYIESGLVVVAPV 591 (953)
Q Consensus 512 G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~~~~t~~r~~~vdft~p~~~~~~~~~v~~ 591 (953)
.+..+++..+.++.+ .+++.... ++.+++++.|.+|++|+++........-...+. +.+..+..++++++.
T Consensus 13 ~~l~~~l~~~~~~~P-~v~i~~~~-------~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~~~-~~~l~~~~~~~~~~~ 83 (202)
T cd08468 13 AVMPRLMARLEELAP-SVRLNLVH-------AEQKLPLDALLAGEIDFALGYSHDDGAEPRLIE-ERDWWEDTYVVIASR 83 (202)
T ss_pred HHhHHHHHHHHhhCC-CCEEEEEE-------CChHhHHHHHHCCCccEEEecccccccCCCCEE-EEEEecCcEEEEEeC
Confidence 456788899988874 24566554 568899999999999998863321100012333 356777788888876
Q ss_pred cc
Q 002211 592 RK 593 (953)
Q Consensus 592 ~~ 593 (953)
..
T Consensus 84 ~h 85 (202)
T cd08468 84 DH 85 (202)
T ss_pred CC
Confidence 55
No 229
>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=93.89 E-value=3 Score=41.05 Aligned_cols=70 Identities=16% Similarity=0.224 Sum_probs=46.1
Q ss_pred EeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEecEEEecCccceeeccccceecceEEEEec
Q 002211 512 GYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGDIAIVTNRTKAVDFTQPYIESGLVVVAPV 591 (953)
Q Consensus 512 G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~~~~t~~r~~~vdft~p~~~~~~~~~v~~ 591 (953)
.+-.+++..+.++.+ .+++.... ++..+++.+|.+|++|+++..... ....+. +.+.....++++++.
T Consensus 13 ~~l~~~l~~~~~~~P-~~~l~~~~-------~~~~~~~~~l~~g~~D~~i~~~~~---~~~~~~-~~~l~~~~~~~v~~~ 80 (201)
T cd08420 13 YLLPRLLARFRKRYP-EVRVSLTI-------GNTEEIAERVLDGEIDLGLVEGPV---DHPDLI-VEPFAEDELVLVVPP 80 (201)
T ss_pred hhhHHHHHHHHHHCC-CceEEEEe-------CCcHHHHHHHHCCCccEEEecCCC---CCcceE-EEeecCccEEEEecC
Confidence 456678888888864 24455543 446789999999999998863322 122232 356777778887765
Q ss_pred cc
Q 002211 592 RK 593 (953)
Q Consensus 592 ~~ 593 (953)
..
T Consensus 81 ~~ 82 (201)
T cd08420 81 DH 82 (201)
T ss_pred CC
Confidence 54
No 230
>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=93.83 E-value=4.4 Score=39.94 Aligned_cols=70 Identities=17% Similarity=0.271 Sum_probs=47.2
Q ss_pred EeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEecEEEecCccceeeccccceecceEEEEec
Q 002211 512 GYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGDIAIVTNRTKAVDFTQPYIESGLVVVAPV 591 (953)
Q Consensus 512 G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~~~~t~~r~~~vdft~p~~~~~~~~~v~~ 591 (953)
.+-.+++..+.++.+ .++++... ++..++++.+.+|++|+++... +.....+. ..+.....+++++++
T Consensus 13 ~~l~~~l~~~~~~~P-~i~i~~~~-------~~~~~~~~~l~~~~~D~~i~~~---~~~~~~~~-~~~l~~~~~~~v~~~ 80 (198)
T cd08421 13 EFLPEDLASFLAAHP-DVRIDLEE-------RLSADIVRAVAEGRADLGIVAG---NVDAAGLE-TRPYRTDRLVVVVPR 80 (198)
T ss_pred hhhHHHHHHHHHHCC-CceEEEEe-------cCcHHHHHHHhcCCceEEEEec---CCCCCCcE-EEEeecCcEEEEeCC
Confidence 345678888888764 24555554 4578899999999999988632 22223333 456777888888776
Q ss_pred cc
Q 002211 592 RK 593 (953)
Q Consensus 592 ~~ 593 (953)
..
T Consensus 81 ~~ 82 (198)
T cd08421 81 DH 82 (198)
T ss_pred CC
Confidence 54
No 231
>cd08438 PBP2_CidR The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains the type 2 periplasmic binding fold. This CD includes the substrate binding domain of CidR which positively up-regulates the expression of cidABC operon in the presence of acetic acid produced by the metabolism of excess glucose. The CidR affects the control of murein hydrolase activity by enhancing cidABC expression in the presence of acetic acid. Thus, up-regulation of cidABC expression results in increased murein hydrolase activity. This substrate binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate
Probab=93.76 E-value=4.4 Score=39.81 Aligned_cols=70 Identities=16% Similarity=0.249 Sum_probs=47.6
Q ss_pred EeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEecEEEecCccceeeccccceecceEEEEec
Q 002211 512 GYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGDIAIVTNRTKAVDFTQPYIESGLVVVAPV 591 (953)
Q Consensus 512 G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~~~~t~~r~~~vdft~p~~~~~~~~~v~~ 591 (953)
.+..++++.+.++.+ .++++... ++..+++..|.+|++|+++..... ....+. ..++.+..++++++.
T Consensus 13 ~~l~~~l~~~~~~~p-~v~i~i~~-------~~~~~~~~~L~~~~~Dl~i~~~~~---~~~~~~-~~~l~~~~~~~v~~~ 80 (197)
T cd08438 13 LLFAPLLAAFRQRYP-NIELELVE-------YGGKKVEQAVLNGELDVGITVLPV---DEEEFD-SQPLCNEPLVAVLPR 80 (197)
T ss_pred hhcHHHHHHHHHHCc-CeEEEEEE-------cCcHHHHHHHHcCCCCEEEEeccc---ccCCce-eEEeccccEEEEecC
Confidence 466788899988875 35565554 457889999999999998863222 112232 346677788888776
Q ss_pred cc
Q 002211 592 RK 593 (953)
Q Consensus 592 ~~ 593 (953)
..
T Consensus 81 ~~ 82 (197)
T cd08438 81 GH 82 (197)
T ss_pred CC
Confidence 55
No 232
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=93.69 E-value=5.7 Score=43.54 Aligned_cols=194 Identities=9% Similarity=-0.047 Sum_probs=107.2
Q ss_pred ceEEEeEEEec-----CCCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEEc-c
Q 002211 48 EVLNVGAIFSF-----GTVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIVG-P 121 (953)
Q Consensus 48 ~~i~IG~l~~~-----~~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aiiG-p 121 (953)
..-.||++.+. +..+-.....+++-+.++ .|+.+.+. .|...+ ...++|+++|- |
T Consensus 62 ~~~~i~v~~~~~~~~~~~~f~~~l~~~i~~~~~~--------~g~~~~~~-~~~~~~----------~~~~~vDgiI~~~ 122 (327)
T PRK10339 62 QHHILAIYSYQQELEINDPYYLAIRHGIETQCEK--------LGIELTNC-YEHSGL----------PDIKNVTGILIVG 122 (327)
T ss_pred cccEEEEEEccccccccCchHHHHHHHHHHHHHH--------CCCEEEEe-eccccc----------cccccCCEEEEeC
Confidence 34567777642 333333455666655554 25666543 232211 01346766653 2
Q ss_pred CChhhHHHHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecC--ccccchH
Q 002211 122 QSAVMAHVLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDD--DQGRNGV 199 (953)
Q Consensus 122 ~~S~~a~av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~--~~g~~~~ 199 (953)
..+. .....+.+.++|+|......+ ...+++ +..++..-+..+++++...|.++++++..+. .......
T Consensus 123 ~~~~---~~~~~l~~~~~pvV~~~~~~~---~~~~~~---V~~D~~~~~~~a~~~l~~~G~~~i~~i~~~~~~~~~~~R~ 193 (327)
T PRK10339 123 KPTP---ALRAAASALTDNICFIDFHEP---GSGYDA---VDIDLARISKEIIDFYINQGVNRIGFIGGEDEPGKADIRE 193 (327)
T ss_pred CCCH---HHHHHHHhcCCCEEEEeCCCC---CCCCCE---EEECHHHHHHHHHHHHHHCCCCeEEEeCCccccchhhHHH
Confidence 2222 233455677899997643221 122332 4456666678888888888999999996433 2334456
Q ss_pred HHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhc--CCceEEEEEcchhhHHHHHHHHHHcCCCCCceEE
Q 002211 200 TALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRM--MEARVIVVHGYSRTGLMVFDVAQRLGMMDSGYVW 273 (953)
Q Consensus 200 ~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~--~~~~vii~~~~~~~~~~~~~~a~~~g~~~~~~~w 273 (953)
..|.+.+++.|+. .....+..+ .+.++....++++.+ ..+++|+.. +...+..++++++++|...++-+-
T Consensus 194 ~gf~~~~~~~g~~-~~~~~~~~~--~~~~~~~~~~~~~l~~~~~~~ai~~~-~D~~A~g~~~al~~~g~~vP~di~ 265 (327)
T PRK10339 194 VAFAEYGRLKQVV-REEDIWRGG--FSSSSGYELAKQMLAREDYPKALFVA-SDSIAIGVLRAIHERGLNIPQDIS 265 (327)
T ss_pred HHHHHHHHHcCCC-ChhheeecC--cChhHHHHHHHHHHhCCCCCCEEEEC-CcHHHHHHHHHHHHcCCCCCCceE
Confidence 7888888888761 111111111 112233344555543 246765554 556678899999999986554443
No 233
>CHL00180 rbcR LysR transcriptional regulator; Provisional
Probab=93.68 E-value=3.4 Score=44.87 Aligned_cols=86 Identities=16% Similarity=0.181 Sum_probs=54.8
Q ss_pred cceEEEecCcccccccEEeeCCcceEEEeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEecE
Q 002211 485 RQLRIGVPNRVSYRDFVFKVNGTDIVHGYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGDI 564 (953)
Q Consensus 485 ~~lri~v~~~~~~~p~~~~~~~~~~~~G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~~ 564 (953)
+++|||+... . ...+..+++..+.+..+- +++.+.. ++...++..|.+|++|+++..-
T Consensus 95 g~l~ig~~~~--~------------~~~~~~~~l~~~~~~~P~-v~i~~~~-------~~~~~~~~~l~~g~~Dl~i~~~ 152 (305)
T CHL00180 95 GTLIIGASQT--T------------GTYLMPRLIGLFRQRYPQ-INVQLQV-------HSTRRIAWNVANGQIDIAIVGG 152 (305)
T ss_pred ceEEEEEcCc--c------------hHhHHHHHHHHHHHHCCC-ceEEEEe-------CCHHHHHHHHHcCCccEEEEcC
Confidence 5799988741 1 123456777888877642 4455543 4578999999999999998632
Q ss_pred EEecCccceeeccccceecceEEEEeccc
Q 002211 565 AIVTNRTKAVDFTQPYIESGLVVVAPVRK 593 (953)
Q Consensus 565 ~~t~~r~~~vdft~p~~~~~~~~~v~~~~ 593 (953)
....+....+ ...++....++++++...
T Consensus 153 ~~~~~~~~~~-~~~~l~~~~~~~v~~~~~ 180 (305)
T CHL00180 153 EVPTELKKIL-EITPYVEDELALIIPKSH 180 (305)
T ss_pred ccCcccccce-eEEEeccCcEEEEECCCC
Confidence 1111111122 356777888888887765
No 234
>cd08433 PBP2_Nac The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) protein, contains the type 2 periplasmic binding fold. The NAC is a LysR-type transcription regulator that activates expression of operons such as hut (histidine utilization) and ure (urea utilization), allowing use of non-preferred (poor) nitrogen sources, and represses expression of operons, such as glutamate dehydrogenase (gdh), allowing assimilation of the preferred nitrogen source. The expression of the nac gene is fully dependent on the nitrogen regulatory system (NTR) and the sigma54-containing RNA polymerase (sigma54-RNAP). In response to nitrogen starvation, NTR system activates the expression of nac, and NAC activates the expression of hut, ure, and put (proline utilization). NAC is not involved in the transcription of Sigma70-RNAP operons such as glnA, which directly respond by the NTR system, but activates the transcription of sigma70-RNAP dependent operons such as hut.
Probab=93.66 E-value=4.5 Score=39.92 Aligned_cols=70 Identities=19% Similarity=0.279 Sum_probs=46.2
Q ss_pred EeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEecEEEecCccceeeccccceecceEEEEec
Q 002211 512 GYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGDIAIVTNRTKAVDFTQPYIESGLVVVAPV 591 (953)
Q Consensus 512 G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~~~~t~~r~~~vdft~p~~~~~~~~~v~~ 591 (953)
.+-.+++..+.++.+ .+++.... .+-.++...|.+|++|+++... +.....+ -+.++....++++++.
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 455678888888875 34555553 3457899999999999988522 2222222 2456777788888765
Q ss_pred cc
Q 002211 592 RK 593 (953)
Q Consensus 592 ~~ 593 (953)
..
T Consensus 81 ~~ 82 (198)
T cd08433 81 DA 82 (198)
T ss_pred CC
Confidence 54
No 235
>PRK11151 DNA-binding transcriptional regulator OxyR; Provisional
Probab=93.51 E-value=3.5 Score=44.73 Aligned_cols=194 Identities=10% Similarity=0.079 Sum_probs=114.0
Q ss_pred cceEEEecCcccccccEEeeCCcceEEEeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEecE
Q 002211 485 RQLRIGVPNRVSYRDFVFKVNGTDIVHGYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGDI 564 (953)
Q Consensus 485 ~~lri~v~~~~~~~p~~~~~~~~~~~~G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~~ 564 (953)
+.++|++... -..++-..++..+.+..+- +++.... .+-+++++.|.+|++|+++...
T Consensus 91 g~l~i~~~~~--------------~~~~~~~~~l~~~~~~~P~-v~i~~~~-------~~~~~~~~~l~~g~~Dl~i~~~ 148 (305)
T PRK11151 91 GPLHIGLIPT--------------VGPYLLPHIIPMLHQTFPK-LEMYLHE-------AQTHQLLAQLDSGKLDCAILAL 148 (305)
T ss_pred ceEEEEecch--------------hHHHHHHHHHHHHHHHCCC-cEEEEEe-------CCHHHHHHHHHcCCccEEEEec
Confidence 5788888741 1124455677777776653 5666654 4578999999999999998633
Q ss_pred EEecCccceeeccccceecceEEEEecccCCcCcceeeccCchhHHHHHHHHHHHHHHHhhhhhcccCCCCCCCCcccch
Q 002211 565 AIVTNRTKAVDFTQPYIESGLVVVAPVRKLNSSAWAFLRPFTPLMWAVTGVFFLVVGTVVWILEHRLNDEFRGPPRKQIV 644 (953)
Q Consensus 565 ~~t~~r~~~vdft~p~~~~~~~~~v~~~~~~~~~~~~l~PF~~~vW~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~ 644 (953)
... ...+ .+.|+....+++++++..+..
T Consensus 149 ~~~---~~~l-~~~~l~~~~~~~~~~~~hpl~------------------------------------------------ 176 (305)
T PRK11151 149 VKE---SEAF-IEVPLFDEPMLLAVYEDHPWA------------------------------------------------ 176 (305)
T ss_pred CCC---CCCe-EEEEeccCcEEEEecCCCCcc------------------------------------------------
Confidence 221 1222 357888889999887655210
Q ss_pred hhHHHHHHHhhccccCCcccchhHHHHHHHHHHHHHhhhhcccceeeeeeeccccCCCCChHHhhhCCCeEEEEeCchHH
Q 002211 645 TVLWFSFSTMFFAHRENTVSTLGRVVLIIWLFVVLIITSSYTASLTSILTVQQLSSPIKGIDTLMTSNDRVGYQVGSFAE 724 (953)
Q Consensus 645 ~~~~~~~~~l~~~~~~~~~s~~~R~l~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~I~sl~dL~~~~~~ig~~~~s~~~ 724 (953)
....-+++||.+... |....++...
T Consensus 177 ------------------------------------------------------~~~~i~~~~L~~~~~-i~~~~~~~~~ 201 (305)
T PRK11151 177 ------------------------------------------------------NRDRVPMSDLAGEKL-LMLEDGHCLR 201 (305)
T ss_pred ------------------------------------------------------cCCccCHHHhcCCCe-EeecCCccHH
Confidence 023346788873332 4444443222
Q ss_pred H----HHHHhhCCCccceEeCCCHHHHHHHHHcCCcEEEEccchhHHHHHhcCcceEEeCC--ccccCccEEEecCCCcc
Q 002211 725 N----YLIEELSIPKSRLVALGSPEEYAIALENRTVAAVVDERPYIDLFLSDHCQFSVRGQ--EFTKSGWGFAFPRDSPL 798 (953)
Q Consensus 725 ~----~l~~~~~~~~~~~~~~~~~~~~~~~l~~g~~~a~~~~~~~~~~~~~~~~~l~~~~~--~~~~~~~~~~~~k~spl 798 (953)
. ++. ..+.........++.+...+.+..|...+++-......+. . ..++..++. ......+.++.+++.++
T Consensus 202 ~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~v~~g~gi~ilp~~~~~~~~-~-~~~l~~~~~~~~~~~~~~~l~~~~~~~~ 278 (305)
T PRK11151 202 DQAMGFCF-EAGADEDTHFRATSLETLRNMVAAGSGITLLPALAVPNER-K-RDGVCYLPCIKPEPRRTIGLVYRPGSPL 278 (305)
T ss_pred HHHHHHHH-HCCCCCCceEEeccHHHHHHHHHcCCCEEEeeHHhhhhhc-c-cCCEEEEECcCCccceEEEEEEcCCCcc
Confidence 2 221 2233323334678888888888887776666554332222 1 233444432 22234688888998877
Q ss_pred hHHHHHHHHhhh
Q 002211 799 AIDMSTAILTLS 810 (953)
Q Consensus 799 ~~~~n~~i~~l~ 810 (953)
.......+..+.
T Consensus 279 ~~~~~~~~~~~~ 290 (305)
T PRK11151 279 RSRYEQLAEAIR 290 (305)
T ss_pred hHHHHHHHHHHH
Confidence 777666665553
No 236
>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=93.37 E-value=0.16 Score=42.47 Aligned_cols=55 Identities=24% Similarity=0.449 Sum_probs=46.0
Q ss_pred cccchhhHHHHHHHhhccccC--CcccchhHHHHHHHHHHHHHhhhhcccceeeeee
Q 002211 640 RKQIVTVLWFSFSTMFFAHRE--NTVSTLGRVVLIIWLFVVLIITSSYTASLTSILT 694 (953)
Q Consensus 640 ~~~~~~~~~~~~~~l~~~~~~--~~~s~~~R~l~~~w~~~~lil~~~Yta~L~s~Lt 694 (953)
..+..+++|+++.++...|.. .|.+..+|++.+++.++++.+.....+.+++.++
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 457899999999999988744 7889999999999999999999999988877654
No 237
>cd08412 PBP2_PAO1_like The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator PAO1-like, a member of the type 2 periplasmic binding fold protein superfamily. This family includes the C-terminal substrate domain of a putative LysR-type transcriptional regulator from the plant pathogen Pseudomonas aeruginosa PAO1and its closely related homologs. The LysR-type transcriptional regulators (LTTRs) are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controll
Probab=93.36 E-value=5.6 Score=39.13 Aligned_cols=71 Identities=15% Similarity=0.146 Sum_probs=48.4
Q ss_pred EEeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEecEEEecCccceeeccccceecceEEEEe
Q 002211 511 HGYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGDIAIVTNRTKAVDFTQPYIESGLVVVAP 590 (953)
Q Consensus 511 ~G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~~~~t~~r~~~vdft~p~~~~~~~~~v~ 590 (953)
..+..+++..+.++.+ .++++... ++..+++..|.+|++|+++... ......+ ...|+....++++++
T Consensus 12 ~~~l~~~l~~~~~~~P-~i~l~i~~-------~~~~~~~~~l~~~~~D~~i~~~---~~~~~~~-~~~~l~~~~~~~~~~ 79 (198)
T cd08412 12 PYYLPGLLRRFREAYP-GVEVRVVE-------GNQEELEEGLRSGELDLALTYD---LDLPEDI-AFEPLARLPPYVWLP 79 (198)
T ss_pred hhhhHHHHHHHHHHCC-CcEEEEEE-------CCHHHHHHHHHcCCCcEEEEcC---CCCCccc-ceeeeeccceEEEec
Confidence 4566788889988875 24555554 5578899999999999988622 1112223 246777788888876
Q ss_pred ccc
Q 002211 591 VRK 593 (953)
Q Consensus 591 ~~~ 593 (953)
...
T Consensus 80 ~~~ 82 (198)
T cd08412 80 ADH 82 (198)
T ss_pred CCC
Confidence 654
No 238
>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=93.32 E-value=2.8 Score=41.57 Aligned_cols=70 Identities=16% Similarity=0.139 Sum_probs=47.6
Q ss_pred EeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEecEEEecCccceeeccccceecceEEEEec
Q 002211 512 GYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGDIAIVTNRTKAVDFTQPYIESGLVVVAPV 591 (953)
Q Consensus 512 G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~~~~t~~r~~~vdft~p~~~~~~~~~v~~ 591 (953)
.+-.+++..+.++.+- ++++... ++.+++...|.+|++|+++..... ....+. +.|.....++++++.
T Consensus 13 ~~l~~~l~~~~~~~P~-v~v~i~~-------~~~~~~~~~l~~g~~D~~i~~~~~---~~~~l~-~~~l~~~~~~~v~~~ 80 (201)
T cd08459 13 YFLPRLLAALREVAPG-VRIETVR-------LPVDELEEALESGEIDLAIGYLPD---LGAGFF-QQRLFRERYVCLVRK 80 (201)
T ss_pred HHHHHHHHHHHHHCCC-CeEEEEe-------cCccCHHHHhhCCCceEEEEcCCC---Ccccce-EEEeecCceEEEEcC
Confidence 4456788888888752 4555554 456789999999999999863221 122233 467888888888876
Q ss_pred cc
Q 002211 592 RK 593 (953)
Q Consensus 592 ~~ 593 (953)
..
T Consensus 81 ~~ 82 (201)
T cd08459 81 DH 82 (201)
T ss_pred CC
Confidence 54
No 239
>PRK12684 transcriptional regulator CysB-like protein; Reviewed
Probab=93.30 E-value=3 Score=45.44 Aligned_cols=197 Identities=13% Similarity=0.057 Sum_probs=115.2
Q ss_pred CcceEEEecCcccccccEEeeCCcceEEEeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEec
Q 002211 484 GRQLRIGVPNRVSYRDFVFKVNGTDIVHGYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGD 563 (953)
Q Consensus 484 g~~lri~v~~~~~~~p~~~~~~~~~~~~G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~ 563 (953)
.++|+||+.. .. ...+..+++..+.++.+- +.+.... ++..+++..|.+|++|+++..
T Consensus 92 ~g~l~Ig~~~--~~------------~~~~l~~~l~~~~~~~p~-i~l~~~~-------~~~~~~~~~L~~g~~D~~i~~ 149 (313)
T PRK12684 92 QGNLTIATTH--TQ------------ARYALPAAIKEFKKRYPK-VRLSILQ-------GSPTQIAEMVLHGQADLAIAT 149 (313)
T ss_pred CCeEEEEech--HH------------HHHHhHHHHHHHHHHCCC-ceEEEEe-------CChHHHHHHHHCCCcCEEEee
Confidence 4679999864 11 123456788888877642 4555543 457899999999999998753
Q ss_pred EEEecCccceeeccccceecceEEEEecccCCcCcceeeccCchhHHHHHHHHHHHHHHHhhhhhcccCCCCCCCCcccc
Q 002211 564 IAIVTNRTKAVDFTQPYIESGLVVVAPVRKLNSSAWAFLRPFTPLMWAVTGVFFLVVGTVVWILEHRLNDEFRGPPRKQI 643 (953)
Q Consensus 564 ~~~t~~r~~~vdft~p~~~~~~~~~v~~~~~~~~~~~~l~PF~~~vW~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~ 643 (953)
-.... . ..++ ..|+....++++++...+..
T Consensus 150 ~~~~~-~-~~l~-~~~l~~~~~~~v~~~~~pl~----------------------------------------------- 179 (313)
T PRK12684 150 EAIAD-Y-KELV-SLPCYQWNHCVVVPPDHPLL----------------------------------------------- 179 (313)
T ss_pred cCCCC-C-CCce-EEEeccceEEEEeCCCCccc-----------------------------------------------
Confidence 11111 1 1222 46677777888877655210
Q ss_pred hhhHHHHHHHhhccccCCcccchhHHHHHHHHHHHHHhhhhcccceeeeeeeccccCCCCChHHhhhCCCeEEEEeCchH
Q 002211 644 VTVLWFSFSTMFFAHRENTVSTLGRVVLIIWLFVVLIITSSYTASLTSILTVQQLSSPIKGIDTLMTSNDRVGYQVGSFA 723 (953)
Q Consensus 644 ~~~~~~~~~~l~~~~~~~~~s~~~R~l~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~I~sl~dL~~~~~~ig~~~~s~~ 723 (953)
....-+++||.+.. -|.+..++..
T Consensus 180 -------------------------------------------------------~~~~i~~~dL~~~~-~i~~~~~~~~ 203 (313)
T PRK12684 180 -------------------------------------------------------ERKPLTLEDLAQYP-LITYDFAFAG 203 (313)
T ss_pred -------------------------------------------------------cCCCcCHHHHhcCC-cEecCCCCcH
Confidence 01224678887333 2555555533
Q ss_pred HHHHH---HhhCCCccceEeCCCHHHHHHHHHcCCcEEEEccchhHHHHHhcCcceEEeC--CccccCccEEEecCCCcc
Q 002211 724 ENYLI---EELSIPKSRLVALGSPEEYAIALENRTVAAVVDERPYIDLFLSDHCQFSVRG--QEFTKSGWGFAFPRDSPL 798 (953)
Q Consensus 724 ~~~l~---~~~~~~~~~~~~~~~~~~~~~~l~~g~~~a~~~~~~~~~~~~~~~~~l~~~~--~~~~~~~~~~~~~k~spl 798 (953)
...+. +..+.........++.+...+.+.+|.--+++.+. ..+... ..++..+. .......++++.+|+.++
T Consensus 204 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~Gv~~lp~~-~~~~~~--~~~l~~~~i~~~~~~~~~~l~~~~~~~~ 280 (313)
T PRK12684 204 RSKINKAFALRGLKPDIVLEAIDADVIKTYVELGLGVGIVADM-AFDPER--DRNLRAIDAGHLFGSSTTRLGLRRGAYL 280 (313)
T ss_pred HHHHHHHHHHcCCCCCeEEEeCCHHHHHHHHHhCCceEEeehh-hccccc--cCCeEEEECCCCCcceeEEEEEECCCcC
Confidence 33332 22344434446678899999999988665666543 232221 22444443 222334678899999877
Q ss_pred hHHHHHHHHhhhc
Q 002211 799 AIDMSTAILTLSE 811 (953)
Q Consensus 799 ~~~~n~~i~~l~e 811 (953)
...+...+..+.+
T Consensus 281 ~~~~~~f~~~l~~ 293 (313)
T PRK12684 281 RGYVYTFIELFAP 293 (313)
T ss_pred CHHHHHHHHHHHH
Confidence 7766666655443
No 240
>cd08418 PBP2_TdcA The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is involved in the degradation of L-serine and L-threonine, contains the type 2 periplasmic binding fold. TdcA, a member of the LysR family, activates the expression of the anaerobically-regulated tdcABCDEFG operon which is involved in the degradation of L-serine and L-threonine to acetate and propionate, respectively. The tdc operon is comprised of one regulatory gene tdcA and six structural genes, tdcB to tdcG. The expression of the tdc operon is affected by several transcription factors including the cAMP receptor protein (CRP), integration host factor (IHF), histone-like protein (HU), and the operon specific regulators TdcA and TcdR. TcdR is divergently transcribed from the operon and encodes a small protein that is required for efficient expression of the Escherichia coli tdc operon. This substrate-binding domain shows significant homology to the type 2 periplasmic binding
Probab=93.19 E-value=5.6 Score=39.24 Aligned_cols=72 Identities=24% Similarity=0.269 Sum_probs=46.8
Q ss_pred EeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEecEEEecCccceeeccccceecceEEEEec
Q 002211 512 GYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGDIAIVTNRTKAVDFTQPYIESGLVVVAPV 591 (953)
Q Consensus 512 G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~~~~t~~r~~~vdft~p~~~~~~~~~v~~ 591 (953)
.+-.+++..+.++.+ .++++... .+..++...|.+|++|+++...... .....+. ..+.....++++++.
T Consensus 13 ~~l~~~l~~~~~~~P-~i~l~i~~-------~~~~~~~~~l~~g~~Dl~i~~~~~~-~~~~~~~-~~~l~~~~~~~v~~~ 82 (201)
T cd08418 13 TLMPAVINRFKEQFP-DVQISIYE-------GQLSSLLPELRDGRLDFAIGTLPDE-MYLKELI-SEPLFESDFVVVARK 82 (201)
T ss_pred hhhHHHHHHHHHHCC-CceEEEEe-------CcHHHHHHHHHcCCCcEEEEecCCC-CCCccee-EEeecCCceEEEeCC
Confidence 455677888888775 35566554 5578999999999999998632111 1112233 356667778888765
Q ss_pred cc
Q 002211 592 RK 593 (953)
Q Consensus 592 ~~ 593 (953)
..
T Consensus 83 ~~ 84 (201)
T cd08418 83 DH 84 (201)
T ss_pred CC
Confidence 54
No 241
>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=93.14 E-value=3.6 Score=40.69 Aligned_cols=70 Identities=13% Similarity=0.243 Sum_probs=45.6
Q ss_pred EeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEecEEEecCccceeeccccceecceEEEEec
Q 002211 512 GYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGDIAIVTNRTKAVDFTQPYIESGLVVVAPV 591 (953)
Q Consensus 512 G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~~~~t~~r~~~vdft~p~~~~~~~~~v~~ 591 (953)
.+..+++..+.++.+ .++++... ++..++++.+.+|++|+++.... .....+. ..++.+..++++++.
T Consensus 14 ~~l~~~l~~~~~~~P-~i~i~i~~-------~~~~~~~~~l~~~~~Dl~i~~~~---~~~~~~~-~~~l~~~~~~~v~~~ 81 (200)
T cd08411 14 YLLPRLLPALRQAYP-KLRLYLRE-------DQTERLLEKLRSGELDAALLALP---VDEPGLE-EEPLFDEPFLLAVPK 81 (200)
T ss_pred hhhHHHHHHHHHHCC-CcEEEEEe-------CcHHHHHHHHHcCCccEEEEecc---CCCCCce-EEEeeccceEEEecC
Confidence 356678888888764 24555553 55789999999999999985221 1112222 345667777777765
Q ss_pred cc
Q 002211 592 RK 593 (953)
Q Consensus 592 ~~ 593 (953)
..
T Consensus 82 ~~ 83 (200)
T cd08411 82 DH 83 (200)
T ss_pred CC
Confidence 54
No 242
>PRK11242 DNA-binding transcriptional regulator CynR; Provisional
Probab=93.01 E-value=4.3 Score=43.70 Aligned_cols=83 Identities=11% Similarity=0.110 Sum_probs=56.1
Q ss_pred cceEEEecCcccccccEEeeCCcceEEEeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEecE
Q 002211 485 RQLRIGVPNRVSYRDFVFKVNGTDIVHGYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGDI 564 (953)
Q Consensus 485 ~~lri~v~~~~~~~p~~~~~~~~~~~~G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~~ 564 (953)
++++|+++. . ....+..+++..+.++.+ .+.+.... +...+++..|.+|++|+++...
T Consensus 91 ~~i~I~~~~--~------------~~~~~l~~~l~~~~~~~p-~~~i~~~~-------~~~~~~~~~l~~g~~Dl~i~~~ 148 (296)
T PRK11242 91 GSLRLAMTP--T------------FTAYLIGPLIDAFHARYP-GITLTIRE-------MSQERIEALLADDELDVGIAFA 148 (296)
T ss_pred eEEEEEecc--c------------hhhhhhHHHHHHHHHHCC-CCEEEEEe-------CCHHHHHHHHHCCCCcEEEEec
Confidence 468998864 1 113456678888888764 45566554 4578899999999999998522
Q ss_pred EEecCccceeeccccceecceEEEEeccc
Q 002211 565 AIVTNRTKAVDFTQPYIESGLVVVAPVRK 593 (953)
Q Consensus 565 ~~t~~r~~~vdft~p~~~~~~~~~v~~~~ 593 (953)
+.+...+ .+.++....+++++++..
T Consensus 149 ---~~~~~~l-~~~~l~~~~~~~~~~~~~ 173 (296)
T PRK11242 149 ---PVHSPEI-EAQPLFTETLALVVGRHH 173 (296)
T ss_pred ---CCCCcce-eEEEeeeccEEEEEcCCC
Confidence 2222233 357777888888887765
No 243
>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=92.87 E-value=5.2 Score=39.30 Aligned_cols=71 Identities=13% Similarity=0.161 Sum_probs=48.5
Q ss_pred EEeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEecEEEecCccceeeccccceecceEEEEe
Q 002211 511 HGYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGDIAIVTNRTKAVDFTQPYIESGLVVVAP 590 (953)
Q Consensus 511 ~G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~~~~t~~r~~~vdft~p~~~~~~~~~v~ 590 (953)
..+..+++..+.+..+ .+++.... +...++...+.+|++|+++..... ....+ .+.|+....++++++
T Consensus 12 ~~~l~~~l~~~~~~~P-~i~l~i~~-------~~~~~~~~~l~~~~~Dl~i~~~~~---~~~~~-~~~~l~~~~~~~v~~ 79 (196)
T cd08415 12 LSLLPRAIARFRARHP-DVRISLHT-------LSSSTVVEAVLSGQADLGLASLPL---DHPGL-ESEPLASGRAVCVLP 79 (196)
T ss_pred ccccHHHHHHHHHHCC-CcEEEEEe-------cchHHHHHHHHcCCccEEEEeCCC---CCCcc-eeeeecccceEEEEc
Confidence 3566788999988774 24565554 557889999999999999863211 11222 356777788888887
Q ss_pred ccc
Q 002211 591 VRK 593 (953)
Q Consensus 591 ~~~ 593 (953)
+..
T Consensus 80 ~~~ 82 (196)
T cd08415 80 PGH 82 (196)
T ss_pred CCC
Confidence 554
No 244
>PRK12679 cbl transcriptional regulator Cbl; Reviewed
Probab=92.81 E-value=6.9 Score=42.70 Aligned_cols=208 Identities=11% Similarity=0.091 Sum_probs=127.2
Q ss_pred CcceEEEecCcccccccEEeeCCcceEEEeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEec
Q 002211 484 GRQLRIGVPNRVSYRDFVFKVNGTDIVHGYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGD 563 (953)
Q Consensus 484 g~~lri~v~~~~~~~p~~~~~~~~~~~~G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~ 563 (953)
.++||||++. .+ ...+-.+++..+.++.+- +.+.... ++.+++++.|.+|++|+++..
T Consensus 92 ~g~lrIg~~~--~~------------~~~~l~~~l~~f~~~~P~-i~l~l~~-------~~~~~~~~~L~~g~~Dl~i~~ 149 (316)
T PRK12679 92 SGVLTIATTH--TQ------------ARYSLPEVIKAFRELFPE-VRLELIQ-------GTPQEIATLLQNGEADIGIAS 149 (316)
T ss_pred CceEEEEech--Hh------------hhcchHHHHHHHHHHCCC-eEEEEec-------CCHHHHHHHHHcCCCCEEEec
Confidence 3579999874 11 235566788888887652 4455543 457789999999999998853
Q ss_pred EEEecCccceeeccccceecceEEEEecccCCcCcceeeccCchhHHHHHHHHHHHHHHHhhhhhcccCCCCCCCCcccc
Q 002211 564 IAIVTNRTKAVDFTQPYIESGLVVVAPVRKLNSSAWAFLRPFTPLMWAVTGVFFLVVGTVVWILEHRLNDEFRGPPRKQI 643 (953)
Q Consensus 564 ~~~t~~r~~~vdft~p~~~~~~~~~v~~~~~~~~~~~~l~PF~~~vW~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~ 643 (953)
... .. ...+. +.++.....++++++..+...
T Consensus 150 ~~~-~~-~~~l~-~~~l~~~~~~~v~~~~hpl~~---------------------------------------------- 180 (316)
T PRK12679 150 ERL-SN-DPQLV-AFPWFRWHHSLLVPHDHPLTQ---------------------------------------------- 180 (316)
T ss_pred ccC-CC-CCCce-EEEccCCcEEEEecCCCcccc----------------------------------------------
Confidence 211 11 12233 357778888888876652110
Q ss_pred hhhHHHHHHHhhccccCCcccchhHHHHHHHHHHHHHhhhhcccceeeeeeeccccCCCCChHHhhhCCCe-EEEEeCch
Q 002211 644 VTVLWFSFSTMFFAHRENTVSTLGRVVLIIWLFVVLIITSSYTASLTSILTVQQLSSPIKGIDTLMTSNDR-VGYQVGSF 722 (953)
Q Consensus 644 ~~~~~~~~~~l~~~~~~~~~s~~~R~l~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~I~sl~dL~~~~~~-ig~~~~s~ 722 (953)
...-+++||. +.+ |....+..
T Consensus 181 --------------------------------------------------------~~~i~~~~L~--~~~~i~~~~~~~ 202 (316)
T PRK12679 181 --------------------------------------------------------ITPLTLESIA--KWPLITYRQGIT 202 (316)
T ss_pred --------------------------------------------------------CCCCCHHHHh--CCCeEEecCCCc
Confidence 1224788886 333 44444433
Q ss_pred H----HHHHHHhhCCCccceEeCCCHHHHHHHHHcCCcEEEEccchhHHHHHhcCcceEEeC--CccccCccEEEecCCC
Q 002211 723 A----ENYLIEELSIPKSRLVALGSPEEYAIALENRTVAAVVDERPYIDLFLSDHCQFSVRG--QEFTKSGWGFAFPRDS 796 (953)
Q Consensus 723 ~----~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~g~~~a~~~~~~~~~~~~~~~~~l~~~~--~~~~~~~~~~~~~k~s 796 (953)
. ..++. ..+.........++.+...+.+..|.--+++-... ... . +..++..+. .......++++.+|+.
T Consensus 203 ~~~~~~~~~~-~~~~~~~~~~~~~s~~~~~~~v~~g~Gi~~lp~~~-~~~-~-~~~~L~~~~~~~~~~~~~~~l~~~~~~ 278 (316)
T PRK12679 203 GRSRIDDAFA-RKGLLADIVLSAQDSDVIKTYVALGLGIGLVAEQS-SGE-Q-EESNLIRLDTRHLFDANTVWLGLKRGQ 278 (316)
T ss_pred HHHHHHHHHH-HcCCCceEEEEeccHHHHHHHHHcCCcEEEecccc-ccc-c-cCCcEEEEECcccCCCceEEEEEeCCc
Confidence 2 33342 33443334456778888889999886666665443 332 1 334455443 2223456888999998
Q ss_pred cchHHHHHHHHhhhccccHHHHHHHhcc
Q 002211 797 PLAIDMSTAILTLSENGELQRIHDKWLR 824 (953)
Q Consensus 797 pl~~~~n~~i~~l~e~G~~~~~~~~w~~ 824 (953)
+....+...+..+.+.--.+.++++-+.
T Consensus 279 ~~~~~~~~f~~~~~~~~~~~~~~~~~~~ 306 (316)
T PRK12679 279 LQRNYVWRFLELCNAGLSVEDIKRQVME 306 (316)
T ss_pred hhhHHHHHHHHHHhcccCHHHHHHHHhh
Confidence 8888888888777666556777776654
No 245
>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=92.63 E-value=7.7 Score=38.74 Aligned_cols=71 Identities=11% Similarity=0.181 Sum_probs=47.7
Q ss_pred EeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEecEEEecCccceeeccccceecceEEEEec
Q 002211 512 GYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGDIAIVTNRTKAVDFTQPYIESGLVVVAPV 591 (953)
Q Consensus 512 G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~~~~t~~r~~~vdft~p~~~~~~~~~v~~ 591 (953)
.+-.+++..+.++.+- +++++... ++.+++++.|.+|++|+++..... ....++ ..++.+..+++++++
T Consensus 13 ~~~~~~l~~~~~~~P~-~~v~~~~~------~~~~~l~~~L~~g~lDl~i~~~~~---~~~~l~-~~~l~~~~~~lv~~~ 81 (203)
T cd08463 13 LFLPELVARFRREAPG-ARLEIHPL------GPDFDYERALASGELDLVIGNWPE---PPEHLH-LSPLFSDEIVCLMRA 81 (203)
T ss_pred HHhHHHHHHHHHHCCC-CEEEEEeC------CcchhHHHHHhcCCeeEEEecccc---CCCCcE-EeEeecCceEEEEeC
Confidence 5667888999888752 44555431 246789999999999999863211 112233 356777888888876
Q ss_pred cc
Q 002211 592 RK 593 (953)
Q Consensus 592 ~~ 593 (953)
..
T Consensus 82 ~h 83 (203)
T cd08463 82 DH 83 (203)
T ss_pred CC
Confidence 65
No 246
>PRK11480 tauA taurine transporter substrate binding subunit; Provisional
Probab=92.52 E-value=0.47 Score=51.99 Aligned_cols=67 Identities=16% Similarity=0.233 Sum_probs=46.4
Q ss_pred CCCCChHHhhhCCCeEEEEeCchHHHHHH---HhhCCCccce--EeCCCHHHHHHHHHcCCcEEEEccchhHHHH
Q 002211 700 SPIKGIDTLMTSNDRVGYQVGSFAENYLI---EELSIPKSRL--VALGSPEEYAIALENRTVAAVVDERPYIDLF 769 (953)
Q Consensus 700 ~~I~sl~dL~~~~~~ig~~~~s~~~~~l~---~~~~~~~~~~--~~~~~~~~~~~~l~~g~~~a~~~~~~~~~~~ 769 (953)
++|++++||. |++||+..++.....+. +..+.....+ +.. ...+...++.+|.+||++...++..-.
T Consensus 112 ~~I~s~~DLk--GK~Iav~~~s~~~~~l~~~L~~~Gl~~~dv~~v~~-~~~~~~~Al~~G~VDAa~~~~p~~~~~ 183 (320)
T PRK11480 112 KTISKPEDLI--GKRIAVPFISTTHYSLLAALKHWGIKPGQVEIVNL-QPPAIIAAWQRGDIDGAYVWAPAVNAL 183 (320)
T ss_pred CCCCChHHcC--CCEEecCCCCchHHHHHHHHHHcCCCHhheEEEEC-CcHHHHHHHHcCCcCEEEEcchHHHHH
Confidence 3699999997 99999987664433221 3445544333 333 467889999999999998877765433
No 247
>cd08434 PBP2_GltC_like The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA expression of glutamate synthase operon, contains type 2 periplasmic binding fold. GltC, a member of the LysR family of bacterial transcriptional factors, activates the expression of gltA gene of glutamate synthase operon and is essential for cell growth in the absence of glutamate. Glutamate synthase is a heterodimeric protein that encoded by gltA and gltB, whose expression is subject to nutritional regulation. GltC also negatively auto-regulates its own expression. This substrate-binding domain has strong homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity,
Probab=92.45 E-value=7.2 Score=38.11 Aligned_cols=70 Identities=20% Similarity=0.322 Sum_probs=46.1
Q ss_pred EeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEecEEEecCccceeeccccceecceEEEEec
Q 002211 512 GYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGDIAIVTNRTKAVDFTQPYIESGLVVVAPV 591 (953)
Q Consensus 512 G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~~~~t~~r~~~vdft~p~~~~~~~~~v~~ 591 (953)
.+...++..+.++.+- ++++... +...+++.++.+|++|+++... ......+. ..++.+..+++++++
T Consensus 13 ~~l~~~l~~~~~~~P~-i~i~i~~-------~~~~~~~~~l~~~~~Dl~i~~~---~~~~~~l~-~~~l~~~~~~~v~~~ 80 (195)
T cd08434 13 SLVPDLIRAFRKEYPN-VTFELHQ-------GSTDELLDDLKNGELDLALCSP---VPDEPDIE-WIPLFTEELVLVVPK 80 (195)
T ss_pred hhhHHHHHHHHHhCCC-eEEEEec-------CcHHHHHHHHHcCCccEEEEcc---CCCCCCee-EEEeecceEEEEecC
Confidence 4556778888887632 4455543 4567889999999999987632 22223333 356777788888766
Q ss_pred cc
Q 002211 592 RK 593 (953)
Q Consensus 592 ~~ 593 (953)
..
T Consensus 81 ~~ 82 (195)
T cd08434 81 DH 82 (195)
T ss_pred CC
Confidence 54
No 248
>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=92.44 E-value=9.8 Score=41.28 Aligned_cols=202 Identities=14% Similarity=0.079 Sum_probs=108.5
Q ss_pred EEEeEEEecC---CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCC-ChHHHHHHHHHHHhcCcEEEEccCChh
Q 002211 50 LNVGAIFSFG---TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKF-NGFLSIMGALQFMETDTLAIVGPQSAV 125 (953)
Q Consensus 50 i~IG~l~~~~---~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~-~~~~a~~~a~~li~~~v~aiiGp~~S~ 125 (953)
.+|+++.|-. ..+.+....|++-+.++. +| +++...+... ++.......+++.+++...||++ +..
T Consensus 2 ~~v~~~~~g~~~D~g~n~~~~~G~~~~~~~~-------~~--i~~~~~e~~~~~~~~~~~~~~~~~~~g~dlIi~~-g~~ 71 (306)
T PF02608_consen 2 KKVALLDPGGINDKGFNQSAYEGLKRAEKEL-------DG--IEIIYVENVPETDADYEEAIRQLADQGYDLIIGH-GFE 71 (306)
T ss_dssp EEEEEESSS-CCCSSHHHHHHHHHHHHHHHC-------TT--EEEEEEES-S-TCHHHHHHHHHHHHTT-SEEEEE-SGG
T ss_pred eEEEEEECCCCCCccHHHHHHHHHHHHHHHc-------CC--ceEEEEecCCccHHHHHHHHHHHHHcCCCEEEEc-cHH
Confidence 4677777654 344455566666666663 23 4444555554 56677777788888898888884 445
Q ss_pred hHHHHHHhhhhC-CCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEE---e-cCccccchHH
Q 002211 126 MAHVLSHLANEL-QVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIF---N-DDDQGRNGVT 200 (953)
Q Consensus 126 ~a~av~~v~~~~-~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~---~-d~~~g~~~~~ 200 (953)
...++..++.++ ++-++...+..+.-...-..+.||... ....+-.+|.++.+- .+++++. . +.+.-.....
T Consensus 72 ~~~~~~~vA~~yPd~~F~~~d~~~~~~~~Nv~~~~f~~~e-~~fLaG~~Aa~~tkt--~~vg~ig~i~G~~~p~~~~~~~ 148 (306)
T PF02608_consen 72 YSDALQEVAKEYPDTKFIIIDGYIDAPEPNVISITFREEE-ASFLAGYLAALMTKT--GKVGFIGDIGGMDIPPVNRFIN 148 (306)
T ss_dssp GHHHHHHHHTC-TTSEEEEESS---ST-TTEEEEEE-HHH-HHHHHHHHHHHHHSS--TEEEEEEEEES--SCTTHHHHH
T ss_pred HHHHHHHHHHHCCCCEEEEEecCcCCCCCcEEEEEccccc-hhHHHHHHHHHHhcc--CcccccccccCCCcHhHHHHHH
Confidence 566777888877 555555433322211112234454432 223334444444443 4788887 3 3444445666
Q ss_pred HHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHHHcCC
Q 002211 201 ALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQRLGM 266 (953)
Q Consensus 201 ~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~~~g~ 266 (953)
.|..-.+..+-.+.....+..+ -.+...-...-..+...++|||+-.+.. ....++++|++.|.
T Consensus 149 gF~~Ga~~~np~i~v~~~~~gs-~~D~~~~~~~a~~li~~GaDvI~~~ag~-~~~gv~~aa~e~g~ 212 (306)
T PF02608_consen 149 GFIAGAKYVNPDIKVNVSYTGS-FNDPAKAKEAAEALIDQGADVIFPVAGG-SGQGVIQAAKEAGV 212 (306)
T ss_dssp HHHHHHHHTTTT-EEEEEE-SS-SS-HHHHHHHHHHHHHTT-SEEEEE-CC-CHHHHHHHHHHHTH
T ss_pred HHHHHHHHhCcCceEEEEEcCC-cCchHHHHHHHHHHhhcCCeEEEECCCC-CchHHHHHHHHcCC
Confidence 7777776654333222222222 0123344555566667999999986654 45568889999774
No 249
>PRK09791 putative DNA-binding transcriptional regulator; Provisional
Probab=92.33 E-value=3.9 Score=44.30 Aligned_cols=86 Identities=14% Similarity=0.177 Sum_probs=56.8
Q ss_pred CcceEEEecCcccccccEEeeCCcceEEEeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEec
Q 002211 484 GRQLRIGVPNRVSYRDFVFKVNGTDIVHGYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGD 563 (953)
Q Consensus 484 g~~lri~v~~~~~~~p~~~~~~~~~~~~G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~ 563 (953)
.++|+|+++.. . ...+-.+++..+.++.+ .+++.... ++..+++..|.+|++|+++..
T Consensus 94 ~g~l~I~~~~~--~------------~~~~l~~~l~~~~~~~p-~i~~~~~~-------~~~~~~~~~l~~g~~Di~i~~ 151 (302)
T PRK09791 94 AGQINIGMGAS--I------------ARSLMPAVISRFHQQHP-QVKVRIME-------GQLVSMINELRQGELDFTINT 151 (302)
T ss_pred ceEEEEEechH--H------------HHhhhHHHHHHHHHHCC-CeEEEEEe-------CChHHHHHHHHCCCccEEEEe
Confidence 36799998741 1 13455677888888776 34555543 457899999999999998862
Q ss_pred EEEecCccceeeccccceecceEEEEeccc
Q 002211 564 IAIVTNRTKAVDFTQPYIESGLVVVAPVRK 593 (953)
Q Consensus 564 ~~~t~~r~~~vdft~p~~~~~~~~~v~~~~ 593 (953)
.... .....+. ..|+....+++++++..
T Consensus 152 ~~~~-~~~~~~~-~~~l~~~~~~l~~~~~~ 179 (302)
T PRK09791 152 YYQG-PYDHEFT-FEKLLEKQFAVFCRPGH 179 (302)
T ss_pred cCCc-cccccee-EEEeccceEEEEEcCCC
Confidence 1111 1112243 36788888888887665
No 250
>cd08462 PBP2_NodD The C-terminal substsrate binding domain of NodD family of LysR-type transcriptional regulators that regulates the expression of nodulation (nod) genes; contains the type 2 periplasmic binding fold. The nodulation (nod) genes in soil bacteria play important roles in the development of nodules. nod genes are involved in synthesis of Nod factors that are required for bacterial entry into root hairs. Thirteen nod genes have been identified and are classified into five transcription units: nodD, nodABCIJ, nodFEL, nodMNT, and nodO. NodD is negatively auto-regulates its own expression of nodD gene, while other nod genes are inducible and positively regulated by NodD in the presence of flavonoids released by plant roots. This substrate-binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. T
Probab=92.23 E-value=5.7 Score=39.44 Aligned_cols=68 Identities=18% Similarity=0.273 Sum_probs=44.0
Q ss_pred eeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEecEEEecCccceeeccccceecceEEEEecc
Q 002211 513 YCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGDIAIVTNRTKAVDFTQPYIESGLVVVAPVR 592 (953)
Q Consensus 513 ~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~~~~t~~r~~~vdft~p~~~~~~~~~v~~~ 592 (953)
+-..++..+.++.+ .++++... ++. ++++.|.+|++|+++..-.. ....+. ..|+....++++++..
T Consensus 14 ~l~~~i~~~~~~~P-~i~l~i~~-------~~~-~~~~~l~~g~~D~~i~~~~~---~~~~~~-~~~l~~~~~~~v~~~~ 80 (200)
T cd08462 14 LLPPVIERVAREAP-GVRFELLP-------PDD-QPHELLERGEVDLLIAPERF---MSDGHP-SEPLFEEEFVCVVWAD 80 (200)
T ss_pred HHHHHHHHHHHHCC-CCEEEEec-------CCh-hHHHHHhcCCeeEEEecCCC---CCCCce-eeeeeccceEEEEcCC
Confidence 44567777777764 24555543 344 89999999999999863211 112233 4467778888888766
Q ss_pred c
Q 002211 593 K 593 (953)
Q Consensus 593 ~ 593 (953)
.
T Consensus 81 h 81 (200)
T cd08462 81 N 81 (200)
T ss_pred C
Confidence 5
No 251
>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=92.18 E-value=3.8 Score=40.69 Aligned_cols=70 Identities=16% Similarity=0.288 Sum_probs=47.2
Q ss_pred EEeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEecEEEecCccceeeccccceecceEEEEe
Q 002211 511 HGYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGDIAIVTNRTKAVDFTQPYIESGLVVVAP 590 (953)
Q Consensus 511 ~G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~~~~t~~r~~~vdft~p~~~~~~~~~v~ 590 (953)
..+..+++..+.++.+ .++++... ++. ++++.+.+|++|++++.... ....+. ..|+.+..++++++
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 3566788888888875 35565553 345 78899999999998863211 112233 46777888888887
Q ss_pred ccc
Q 002211 591 VRK 593 (953)
Q Consensus 591 ~~~ 593 (953)
...
T Consensus 79 ~~h 81 (200)
T cd08460 79 AGH 81 (200)
T ss_pred CCC
Confidence 655
No 252
>PRK12681 cysB transcriptional regulator CysB; Reviewed
Probab=92.15 E-value=4.8 Score=44.15 Aligned_cols=85 Identities=15% Similarity=0.103 Sum_probs=54.5
Q ss_pred CcceEEEecCcccccccEEeeCCcceEEEeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEec
Q 002211 484 GRQLRIGVPNRVSYRDFVFKVNGTDIVHGYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGD 563 (953)
Q Consensus 484 g~~lri~v~~~~~~~p~~~~~~~~~~~~G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~ 563 (953)
.++|+||++. .+. ..+-.+++..+.++.+ .+++.... ++.+++++.+.+|++|+++..
T Consensus 92 ~g~l~Ig~~~--~~~------------~~~l~~~l~~f~~~~P-~i~i~i~~-------~~~~~~~~~L~~g~iDl~i~~ 149 (324)
T PRK12681 92 KGSLYIATTH--TQA------------RYALPPVIKGFIERYP-RVSLHMHQ-------GSPTQIAEAAAKGNADFAIAT 149 (324)
T ss_pred CCeEEEEech--hHH------------HHhhHHHHHHHHHHCC-CcEEEEEe-------CCHHHHHHHHHcCCCCEEEec
Confidence 3679999874 111 2355677788887765 35566554 568899999999999999863
Q ss_pred EEEecCccceeeccccceecceEEEEeccc
Q 002211 564 IAIVTNRTKAVDFTQPYIESGLVVVAPVRK 593 (953)
Q Consensus 564 ~~~t~~r~~~vdft~p~~~~~~~~~v~~~~ 593 (953)
-. ......+. ..|+.....+++++...
T Consensus 150 ~~--~~~~~~l~-~~~l~~~~~~~v~~~~h 176 (324)
T PRK12681 150 EA--LHLYDDLI-MLPCYHWNRSVVVPPDH 176 (324)
T ss_pred Cc--ccCCCCeE-EEEeccceeEEEeCCCC
Confidence 11 11122233 34666677777776554
No 253
>cd08426 PBP2_LTTR_like_5 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold. LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functi
Probab=92.13 E-value=8.7 Score=37.79 Aligned_cols=70 Identities=9% Similarity=0.092 Sum_probs=46.5
Q ss_pred EeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEecEEEecCccceeeccccceecceEEEEec
Q 002211 512 GYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGDIAIVTNRTKAVDFTQPYIESGLVVVAPV 591 (953)
Q Consensus 512 G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~~~~t~~r~~~vdft~p~~~~~~~~~v~~ 591 (953)
.+..+++..+.++.+ .++++... ++..+++..+.+|++|+++..... ....+. +.++....++++++.
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 445677888888764 24555543 456889999999999999863211 112232 466777888888876
Q ss_pred cc
Q 002211 592 RK 593 (953)
Q Consensus 592 ~~ 593 (953)
..
T Consensus 81 ~h 82 (199)
T cd08426 81 GH 82 (199)
T ss_pred CC
Confidence 54
No 254
>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=92.04 E-value=2.5 Score=43.23 Aligned_cols=73 Identities=8% Similarity=-0.065 Sum_probs=42.4
Q ss_pred eEeCCCHHHHHHHHHcCCcEEEEccchhHHHHHhcCcceEEeCCc-cccCccEEEecCCCcchHHHHHHHHhhhc
Q 002211 738 LVALGSPEEYAIALENRTVAAVVDERPYIDLFLSDHCQFSVRGQE-FTKSGWGFAFPRDSPLAIDMSTAILTLSE 811 (953)
Q Consensus 738 ~~~~~~~~~~~~~l~~g~~~a~~~~~~~~~~~~~~~~~l~~~~~~-~~~~~~~~~~~k~spl~~~~n~~i~~l~e 811 (953)
+....+..+..+.+.+|++++.+......... ........++.. .....+++++.|+++-.+.-.+.|..+..
T Consensus 132 ~~~~~~~~~~~~~~~~Ge~~~~~~~~~~~~~~-~~~~~~~~~P~~~~~~~~~~~ai~k~a~~~~~A~~fi~fl~s 205 (216)
T TIGR01256 132 LVYGEDVRQALQFVETGNAPAGIVALSDVIPS-KKVGSVATFPEDLYKPIRYPAVIVKGGKNNAAAKAFIDYLKS 205 (216)
T ss_pred eeecCcHHHHHHHHHcCCCCEEeeehhhhccc-CCccEEEEeCccccCCccccEEEEECCCChHHHHHHHHHHcC
Confidence 34445777888999999999987654332211 122223333332 22345688999998765555555554443
No 255
>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=91.98 E-value=13 Score=38.45 Aligned_cols=208 Identities=9% Similarity=0.026 Sum_probs=116.4
Q ss_pred eEEEeEEEecCCCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCC--CChHHHHHHHHHHHhc-CcEEEEcc-CCh
Q 002211 49 VLNVGAIFSFGTVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAK--FNGFLSIMGALQFMET-DTLAIVGP-QSA 124 (953)
Q Consensus 49 ~i~IG~l~~~~~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~--~~~~~a~~~a~~li~~-~v~aiiGp-~~S 124 (953)
.++||++.+. ...+....+|++..+++--.. .+.-+++-+. ..-.+.+.....|.++ .+-|||=. .-+
T Consensus 2 ~~kIGivTgt-vSq~ed~~r~Ae~l~~~Yg~~-------~I~h~tyPdnf~~e~EttIskI~~lAdDp~mKaIVv~q~vp 73 (275)
T PF12683_consen 2 DYKIGIVTGT-VSQSEDEYRGAEELIKKYGDV-------MIKHVTYPDNFMSEQETTISKIVSLADDPDMKAIVVSQAVP 73 (275)
T ss_dssp -EEEEEEE---TTT-HHHHHHHHHHHHHHHHH-------EEEEEE--TTGGGCHHHHHHHHHGGGG-TTEEEEEEE-SS-
T ss_pred ceEEEEEeCC-cccChHHHHHHHHHHHHhCcc-------eEEEEeCCCcccchHHHHHHHHHHhccCCCccEEEEeCCCc
Confidence 5899999775 334567778888888865322 5666666333 3566777777777777 56666632 345
Q ss_pred hhHHHHHHhhhhC-CCcEEEeecCC-CCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecCccccch----
Q 002211 125 VMAHVLSHLANEL-QVPLLSFTALD-PTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDDDQGRNG---- 198 (953)
Q Consensus 125 ~~a~av~~v~~~~-~vP~Is~~at~-~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~~~g~~~---- 198 (953)
+++.+.-.+=++. .|.+|+-.... |..-..... +-..+.....+..++...+++|.+.++-+.....-+...
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 6666666666543 56666532221 111111112 334467778899999999999999999886544333333
Q ss_pred HHHHHHHHHhcCcEEEEEEecCCCCCCCh---HHH--HHHHHHHhcCCceEEEEEcchhhHHHHHHHHHHcCC
Q 002211 199 VTALGDKLAEIRCKISYKSALPPDQSVTE---TDV--RNELVKVRMMEARVIVVHGYSRTGLMVFDVAQRLGM 266 (953)
Q Consensus 199 ~~~l~~~l~~~g~~v~~~~~~~~~~~~~~---~d~--~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~~~g~ 266 (953)
.+.++++.++.|++.+....-.+....+. .+| ...-+.+++-+.|+-+.+++......+++++.+.|.
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 46677788889999886554433311111 111 222345566799999999999999999999999774
No 256
>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=91.96 E-value=6.1 Score=38.97 Aligned_cols=70 Identities=21% Similarity=0.325 Sum_probs=46.6
Q ss_pred EeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEecEEEecCccceeeccccceecceEEEEec
Q 002211 512 GYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGDIAIVTNRTKAVDFTQPYIESGLVVVAPV 591 (953)
Q Consensus 512 G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~~~~t~~r~~~vdft~p~~~~~~~~~v~~ 591 (953)
.+..+++..+.++.+ .+++.... .+...+...+.+|++|+++... +.....+. ..++....++++++.
T Consensus 13 ~~~~~~i~~~~~~~P-~i~l~~~~-------~~~~~~~~~l~~g~~D~~i~~~---~~~~~~~~-~~~l~~~~~~~v~~~ 80 (200)
T cd08417 13 LLLPPLLARLRQEAP-GVRLRFVP-------LDRDDLEEALESGEIDLAIGVF---PELPPGLR-SQPLFEDRFVCVARK 80 (200)
T ss_pred HHHHHHHHHHHhhCC-CeEEEecc-------CCHHHHHHHHHcCCCCEEEeec---ccCCCccc-hhhhhcCceEEEecC
Confidence 445677788887764 23454443 5578999999999999998632 22222232 467778888888876
Q ss_pred cc
Q 002211 592 RK 593 (953)
Q Consensus 592 ~~ 593 (953)
..
T Consensus 81 ~~ 82 (200)
T cd08417 81 DH 82 (200)
T ss_pred CC
Confidence 55
No 257
>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=91.93 E-value=0.75 Score=48.57 Aligned_cols=103 Identities=12% Similarity=0.079 Sum_probs=64.1
Q ss_pred CCCCChHHhhhCCCeEEEEeCchHHHHHHHhhCCCccceEeCCCHHHHHHHHHcCCcEEEEccchhHHHH-HhcCcceEE
Q 002211 700 SPIKGIDTLMTSNDRVGYQVGSFAENYLIEELSIPKSRLVALGSPEEYAIALENRTVAAVVDERPYIDLF-LSDHCQFSV 778 (953)
Q Consensus 700 ~~I~sl~dL~~~~~~ig~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~g~~~a~~~~~~~~~~~-~~~~~~l~~ 778 (953)
.+|++++||. |+++++..++...+.++ .++ ...+ ..+..|...+|++|.+|+.+........+ +.+..++..
T Consensus 126 ~~i~s~~Dl~--G~kir~~~~~~~~~~~~-~~G---a~~v-~~~~~e~~~aL~~G~vDg~~~~~~~~~~~~~~ev~~y~~ 198 (257)
T TIGR00787 126 KPITKPEDLK--GLKIRIPNSPMNEAQFK-ALG---ANPE-PMAFSEVYTALQTGVVDGQENPLSNVYSSKFYEVQKYLS 198 (257)
T ss_pred CccCChHHhC--CCEEecCCCHHHHHHHH-HcC---Cccc-ccCHHHHHHHHHcCCcccccCCHHHHhhcchhhhcchhe
Confidence 5799999996 99999988777777774 444 2333 56888999999999999998764433211 111122222
Q ss_pred eCCccccCccEEEecCC--CcchHHHHHHHHhhh
Q 002211 779 RGQEFTKSGWGFAFPRD--SPLAIDMSTAILTLS 810 (953)
Q Consensus 779 ~~~~~~~~~~~~~~~k~--spl~~~~n~~i~~l~ 810 (953)
... .......+.+.++ ..|-+....+|.+..
T Consensus 199 ~~~-~~~~~~~~~~n~~~~~~L~~e~q~~i~~a~ 231 (257)
T TIGR00787 199 MTN-HGYLGYLVVVNKAFWKSLPPDLQAVVKEAA 231 (257)
T ss_pred ecC-CcccceEEEEeHHHHhcCCHHHHHHHHHHH
Confidence 222 2234556777776 225555555555443
No 258
>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=91.92 E-value=12 Score=39.21 Aligned_cols=144 Identities=9% Similarity=-0.012 Sum_probs=87.4
Q ss_pred HHHHHhcCcEEEE--ccCChhhHHHHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHH--cCC
Q 002211 107 ALQFMETDTLAIV--GPQSAVMAHVLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSY--FGW 182 (953)
Q Consensus 107 a~~li~~~v~aii--Gp~~S~~a~av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~--~~w 182 (953)
..+.++.+|.++| ++..+. ........+.++|++......+. ...+++ ...++..-+..+++.+.. .|-
T Consensus 45 ~~~~~~~~vdGvIi~~~~~~~--~~~~~~~~~~~~PvV~i~~~~~~--~~~~~~---V~~D~~~~~~~a~~~L~~~~~G~ 117 (247)
T cd06276 45 IISNTKGKYSGYVVMPHFKNE--IQYFLLKKIPKEKLLILDHSIPE--GGEYSS---VAQDFEKAIYNALQEGLEKLKKY 117 (247)
T ss_pred HHHHHhcCCCEEEEecCCCCc--HHHHHHhccCCCCEEEEcCcCCC--CCCCCe---EEEccHHHHHHHHHHHHHHhcCC
Confidence 3344456666655 432222 11344555578999987543221 112332 445666677778888888 899
Q ss_pred cEEEEEEecC-ccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHH
Q 002211 183 GEVIAIFNDD-DQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVA 261 (953)
Q Consensus 183 ~~vaii~~d~-~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a 261 (953)
+++++|.... ..++...+.+.+.+++.|+.... .. . ..+. .+ .++++ |++.+...+..+++.+
T Consensus 118 ~~Ia~i~~~~~~~~~~R~~gf~~~l~~~g~~~~~---~~-~----~~~~--~~-----~~~~a-i~~~~d~~A~g~~~~l 181 (247)
T cd06276 118 KKLILVFPNKTAIPKEIKRGFERFCKDYNIETEI---IN-D----YENR--EI-----EKGDL-YIILSDTDLVFLIKKA 181 (247)
T ss_pred CEEEEEecCccHhHHHHHHHHHHHHHHcCCCccc---cc-c----cchh--hc-----cCCcE-EEEeCHHHHHHHHHHH
Confidence 9999997533 34566788999999999976431 11 1 0110 00 13465 5555677788899999
Q ss_pred HHcCCCCCceEE
Q 002211 262 QRLGMMDSGYVW 273 (953)
Q Consensus 262 ~~~g~~~~~~~w 273 (953)
++.|+..++-+=
T Consensus 182 ~~~g~~iP~dis 193 (247)
T cd06276 182 RESGLLLGKDIG 193 (247)
T ss_pred HHcCCcCCceeE
Confidence 999987654443
No 259
>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=91.73 E-value=4.7 Score=42.32 Aligned_cols=120 Identities=13% Similarity=0.060 Sum_probs=68.8
Q ss_pred CCCCChHHhhhCCCeEEEEeCchHHHH----HHHhhCCC------------------c--cceEeCCCHHHHHHHHHcCC
Q 002211 700 SPIKGIDTLMTSNDRVGYQVGSFAENY----LIEELSIP------------------K--SRLVALGSPEEYAIALENRT 755 (953)
Q Consensus 700 ~~I~sl~dL~~~~~~ig~~~~s~~~~~----l~~~~~~~------------------~--~~~~~~~~~~~~~~~l~~g~ 755 (953)
..+++++||. .|.+|++.++...+.. | ++.+.. . .+++.+ ...+...++.+|+
T Consensus 106 ~~~~sl~dlk-~G~~IAip~d~~n~~raL~~L-~~aGLi~l~~~~~~~~t~~DI~~n~~~v~~vel-~~~~~~~al~~g~ 182 (258)
T TIGR00363 106 KKIKNVNELQ-DGAKVAVPNDPTNLGRALLLL-QKQGLIKLKDGNGLLPTVLDIVENPKKLNITEL-ETSQLPRALDDPK 182 (258)
T ss_pred cCCCCHHHcC-CCCEEEEeCCcchHHHHHHHH-HHcCCceecCCCCCcCChhhhhcCCCCCEEEEc-CHHHHHHHhhccc
Confidence 6899999995 4889999876543332 4 333321 1 233444 5566778899999
Q ss_pred cEEEEccchhHHHHHhcCc-ceEEeCCccccCccEEEecCCCcchHHHHHHHHhhhccccHHHHHHHh
Q 002211 756 VAAVVDERPYIDLFLSDHC-QFSVRGQEFTKSGWGFAFPRDSPLAIDMSTAILTLSENGELQRIHDKW 822 (953)
Q Consensus 756 ~~a~~~~~~~~~~~~~~~~-~l~~~~~~~~~~~~~~~~~k~spl~~~~n~~i~~l~e~G~~~~~~~~w 822 (953)
+|+.+...+++.-...+.. +-......-.++-..++++++.-=.+.+.+.+..++....-+.|.++|
T Consensus 183 vDaa~v~~~~~~~agl~~~~~~i~~e~~~~~~~n~l~~r~~~~~~~~~~~lv~~~~s~~v~~~i~~~~ 250 (258)
T TIGR00363 183 VDLAVINTTYAGQVGLNPQDDGVFVEDKDSPYVNIIVSREDNKDAENVKDFIQSYQSEEVYQAAQKHF 250 (258)
T ss_pred ccEEEEChHHHHHcCCCcCcCceeecCCCCCeeEEEEEcCCccCCHHHHHHHHHHcCHHHHHHHHHHc
Confidence 9999988877654322211 111111111122234556655335566666777777666555555554
No 260
>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=91.65 E-value=0.78 Score=44.19 Aligned_cols=98 Identities=15% Similarity=0.194 Sum_probs=65.3
Q ss_pred HHHHHHcCCcEEEEEEe--cCccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHH-HHhcCCceEEEEEcc
Q 002211 174 AEMVSYFGWGEVIAIFN--DDDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELV-KVRMMEARVIVVHGY 250 (953)
Q Consensus 174 ~~~l~~~~w~~vaii~~--d~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~-~i~~~~~~vii~~~~ 250 (953)
++++.+.|.+++++|.. ++.+.....+.|.+++++.|+........... ...+...... .+++..||+||+ .+
T Consensus 1 ~~~L~~~G~r~i~~i~~~~~~~~~~~r~~gf~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~l~~~~pdaii~-~~ 76 (160)
T PF13377_consen 1 VDYLIERGHRRIAFIGGPPNSSVSRERLEGFREALKEHGIEFEELIFFSDD---DSEDAREAQLLWLRRLRPDAIIC-SN 76 (160)
T ss_dssp HHHHHHTT-SSEEEEESSTTSHHHHHHHHHHHHHHHHTTSEEEGEEEEESS---SHHHHHHHHHHHHHTCSSSEEEE-SS
T ss_pred ChHHHHCCCCeEEEEecCCCChhHHHHHHHHHHHHHHCCCCCCeeEeecCC---cchhHHHHHHHHHhcCCCcEEEE-cC
Confidence 46788889999999993 34556667889999999999986544433333 1333332222 244347887666 67
Q ss_pred hhhHHHHHHHHHHcCCCCCceEEEE
Q 002211 251 SRTGLMVFDVAQRLGMMDSGYVWIA 275 (953)
Q Consensus 251 ~~~~~~~~~~a~~~g~~~~~~~wi~ 275 (953)
...+..+++.+.+.|+..++-+-|.
T Consensus 77 ~~~a~~~~~~l~~~g~~vP~di~vv 101 (160)
T PF13377_consen 77 DRLALGVLRALRELGIRVPQDISVV 101 (160)
T ss_dssp HHHHHHHHHHHHHTTSCTTTTSEEE
T ss_pred HHHHHHHHHHHHHcCCcccccccEE
Confidence 7788899999999998655433333
No 261
>PRK11233 nitrogen assimilation transcriptional regulator; Provisional
Probab=91.64 E-value=5 Score=43.57 Aligned_cols=84 Identities=17% Similarity=0.225 Sum_probs=51.8
Q ss_pred CcceEEEecCcccccccEEeeCCcceEEEeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEec
Q 002211 484 GRQLRIGVPNRVSYRDFVFKVNGTDIVHGYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGD 563 (953)
Q Consensus 484 g~~lri~v~~~~~~~p~~~~~~~~~~~~G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~ 563 (953)
.++|+||++. ... ...+..+++..+.++.+ .+++.+.. +...++...|.+|++|+++..
T Consensus 90 ~g~l~I~~~~--~~~-----------~~~~~~~~l~~~~~~~p-~i~l~~~~-------~~~~~~~~~l~~g~~Di~i~~ 148 (305)
T PRK11233 90 SGQVSIGLAP--GTA-----------ASSLTMPLLQAVRAEFP-GIVLYLHE-------NSGATLNEKLMNGQLDMAVIY 148 (305)
T ss_pred CceEEEEccc--chh-----------hHHHHHHHHHHHHHHCC-CcEEEEEE-------CCcHHHHHHHHCCCCCEEEEc
Confidence 3579998853 111 12344567888888763 24455543 446789999999999999852
Q ss_pred EEEecCccceeeccccceecceEEEEecc
Q 002211 564 IAIVTNRTKAVDFTQPYIESGLVVVAPVR 592 (953)
Q Consensus 564 ~~~t~~r~~~vdft~p~~~~~~~~~v~~~ 592 (953)
-. .....+ ...|+.+..++++++..
T Consensus 149 ~~---~~~~~~-~~~~l~~~~~~lv~~~~ 173 (305)
T PRK11233 149 EH---SPVAGL-SSQPLLKEDLFLVGTQD 173 (305)
T ss_pred CC---cCCCCc-EEEEEeeeeEEEEEcCc
Confidence 21 111222 24577778888777654
No 262
>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=91.60 E-value=13 Score=36.44 Aligned_cols=72 Identities=19% Similarity=0.267 Sum_probs=47.2
Q ss_pred EeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEecEEEecCccceeeccccceecceEEEEec
Q 002211 512 GYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGDIAIVTNRTKAVDFTQPYIESGLVVVAPV 591 (953)
Q Consensus 512 G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~~~~t~~r~~~vdft~p~~~~~~~~~v~~ 591 (953)
.+-.+++..+.+..+ .++++... ++..++++.+.+|++|+++.... ...+...+. ..|+....+++++++
T Consensus 13 ~~l~~~l~~~~~~~P-~v~i~i~~-------~~~~~~~~~l~~~~~Dl~i~~~~-~~~~~~~~~-~~~l~~~~~~~~~~~ 82 (201)
T cd08435 13 VLLPPAIARLLARHP-RLTVRVVE-------GTSDELLEGLRAGELDLAIGRLA-DDEQPPDLA-SEELADEPLVVVARP 82 (201)
T ss_pred HHHHHHHHHHHHHCC-CeEEEEEe-------CCHHHHHHHHHcCCccEEEEecC-cccCCCCcE-EEEcccCcEEEEEeC
Confidence 345677888888765 35555543 45788999999999999885321 111122333 457778888888876
Q ss_pred cc
Q 002211 592 RK 593 (953)
Q Consensus 592 ~~ 593 (953)
..
T Consensus 83 ~~ 84 (201)
T cd08435 83 GH 84 (201)
T ss_pred CC
Confidence 55
No 263
>cd08466 PBP2_LeuO The C-terminal substrate binding domain of LysR-type transcriptional regulator LeuO, an activator of leucine synthesis operon, contains the type 2 periplasmic binding fold. LeuO, a LysR-type transcriptional regulator, was originally identified as an activator of the leucine synthesis operon (leuABCD). Subsequently, LeuO was found to be not a specific regulator of the leu gene but a global regulator of unrelated various genes. LeuO activates bglGFB (utilization of beta-D-glucoside) and represses cadCBA (lysine decarboxylation) and dsrA (encoding a regulatory small RNA for translational control of rpoS and hns). LeuO also regulates the yjjQ-bglJ operon which coding for a LuxR-type transcription factor. In Salmonella enterica serovar Typhi, LeuO is a positive regulator of ompS1 (encoding an outer membrane), ompS2 (encoding a pathogenicity determinant), and assT, while LeuO represses the expression of OmpX and Tpx. Both osmS1 and osmS2 influence virulence in the mouse mo
Probab=91.55 E-value=6.9 Score=38.63 Aligned_cols=70 Identities=16% Similarity=0.208 Sum_probs=47.7
Q ss_pred EeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEecEEEecCccceeeccccceecceEEEEec
Q 002211 512 GYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGDIAIVTNRTKAVDFTQPYIESGLVVVAPV 591 (953)
Q Consensus 512 G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~~~~t~~r~~~vdft~p~~~~~~~~~v~~ 591 (953)
.+-.+++..+.++++ .++++... ++..++...|.+|++|+++... +.....+. +.++....++++++.
T Consensus 13 ~~l~~~l~~f~~~~P-~v~l~~~~-------~~~~~~~~~l~~g~~Dl~i~~~---~~~~~~~~-~~~l~~~~~~lv~~~ 80 (200)
T cd08466 13 LLLPRLLARLKQLAP-NISLRESP-------SSEEDLFEDLRLQEVDLVIDYV---PFRDPSFK-SELLFEDELVCVARK 80 (200)
T ss_pred HHHHHHHHHHHHHCC-CCEEEEec-------CchHhHHHHHHcCCccEEEecc---cCCCCCce-eeeecccceEEEEeC
Confidence 455677888888774 25566554 5678899999999999998621 11122232 457778888888876
Q ss_pred cc
Q 002211 592 RK 593 (953)
Q Consensus 592 ~~ 593 (953)
..
T Consensus 81 ~~ 82 (200)
T cd08466 81 DH 82 (200)
T ss_pred CC
Confidence 65
No 264
>cd08419 PBP2_CbbR_RubisCO_like The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO operon, which is involved in the carbon dioxide fixation, contains the type 2 periplasmic binding fold. CbbR, a LysR-type transcriptional regulator, is required to activate expression of RubisCO, one of two unique enzymes in the Calvin-Benson-Bassham (CBB) cycle pathway. All plants, cyanobacteria, and many autotrophic bacteria use the CBB cycle to fix carbon dioxide. Thus, this cycle plays an essential role in assimilating CO2 into organic carbon on earth. The key CBB cycle enzyme is ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO), which catalyzes the actual CO2 fixation reaction. The CO2 concentration affects the expression of RubisCO genes. It has also shown that NADPH enhances the DNA-binding ability of the CbbR. RubisCO is composed of eight large (CbbL) and eight small subunits (CbbS). The topology of this substrate-binding domain is most similar to t
Probab=91.50 E-value=12 Score=36.63 Aligned_cols=70 Identities=17% Similarity=0.222 Sum_probs=45.8
Q ss_pred EeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEecEEEecCccceeeccccceecceEEEEec
Q 002211 512 GYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGDIAIVTNRTKAVDFTQPYIESGLVVVAPV 591 (953)
Q Consensus 512 G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~~~~t~~r~~~vdft~p~~~~~~~~~v~~ 591 (953)
.+..+++..+.++.+- ++++... +....++..+.+|++|+++...... ...+ ...++....++++++.
T Consensus 12 ~~l~~~l~~~~~~~P~-i~l~i~~-------~~~~~~~~~l~~g~~Dl~i~~~~~~---~~~~-~~~~l~~~~~~~~~~~ 79 (197)
T cd08419 12 YFAPRLLGAFCRRHPG-VEVSLRV-------GNREQVLERLADNEDDLAIMGRPPE---DLDL-VAEPFLDNPLVVIAPP 79 (197)
T ss_pred hHhhHHHHHHHHHCCC-ceEEEEE-------CCHHHHHHHHhcCCccEEEecCCCC---CCCe-EEEEeccCCEEEEecC
Confidence 3566778888887632 4455553 4577899999999999998532211 1112 2456777788888775
Q ss_pred cc
Q 002211 592 RK 593 (953)
Q Consensus 592 ~~ 593 (953)
..
T Consensus 80 ~~ 81 (197)
T cd08419 80 DH 81 (197)
T ss_pred CC
Confidence 54
No 265
>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=91.16 E-value=2 Score=44.37 Aligned_cols=193 Identities=17% Similarity=0.079 Sum_probs=117.2
Q ss_pred EeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcC-ceeEEEecEEEecCc---cceee--ccccceecce
Q 002211 512 GYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTG-VFDAAVGDIAIVTNR---TKAVD--FTQPYIESGL 585 (953)
Q Consensus 512 G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g-~~Di~~~~~~~t~~r---~~~vd--ft~p~~~~~~ 585 (953)
+..-++.+.+.++.|+++++... .-.++...|..| ++|+.+.+-....++ ...++ -..|+..+.+
T Consensus 11 ~~~~~l~~~f~~~~g~~v~v~~~---------~s~~~~~~l~~g~~~Dv~~~~~~~~~~~l~~~g~~~~~~~~~~~~~~~ 81 (230)
T PF13531_consen 11 PALEELAEAFEKQPGIKVEVSFG---------GSGELVRRLQAGKKPDVFIPASSEWLERLAAAGLVDPGSPAPLARSPL 81 (230)
T ss_dssp HHHHHHHHHHHHHHCEEEEEEEE---------CHHHHHHHHHTT-S-SEEEESSHHHHHHHHHTTTCSGGGEEEEEEEEE
T ss_pred HHHHHHHHHHHhccCCeEEEEEC---------ChHHHHHHHhcCCCceEEEECCHHHHHHHHhcccccCCcccccccCce
Confidence 44567888888888877666654 357888888877 788877643211111 12333 6678889999
Q ss_pred EEEEecccCCcCcceeeccCchhHHHHHHHHHHHHHHHhhhhhcccCCCCCCCCcccchhhHHHHHHHhhccccCCcccc
Q 002211 586 VVVAPVRKLNSSAWAFLRPFTPLMWAVTGVFFLVVGTVVWILEHRLNDEFRGPPRKQIVTVLWFSFSTMFFAHRENTVST 665 (953)
Q Consensus 586 ~~~v~~~~~~~~~~~~l~PF~~~vW~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~s~ 665 (953)
++++++..+
T Consensus 82 vl~~~~~~~----------------------------------------------------------------------- 90 (230)
T PF13531_consen 82 VLAVPKGNP----------------------------------------------------------------------- 90 (230)
T ss_dssp EEEEETTST-----------------------------------------------------------------------
T ss_pred EEEeccCcc-----------------------------------------------------------------------
Confidence 999988772
Q ss_pred hhHHHHHHHHHHHHHhhhhcccceeeeeeeccccCCCCChHHhhhCCCeEEEEeC------chHHHHHHHhhC---C---
Q 002211 666 LGRVVLIIWLFVVLIITSSYTASLTSILTVQQLSSPIKGIDTLMTSNDRVGYQVG------SFAENYLIEELS---I--- 733 (953)
Q Consensus 666 ~~R~l~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~I~sl~dL~~~~~~ig~~~~------s~~~~~l~~~~~---~--- 733 (953)
..+.+++||.+.+.+|++.+. ......+.+ .+ .
T Consensus 91 ----------------------------------~~~~~~~dL~~~~~~i~~~dP~~s~~g~~~~~~l~~-~g~~~~~~~ 135 (230)
T PF13531_consen 91 ----------------------------------KGIRSWADLAQPGLRIAIPDPSTSPSGLAALQVLAA-AGGQELLDA 135 (230)
T ss_dssp ----------------------------------TSTTCHHHHCSTT--EEEE-TTTTHHHHHHHHHHHH-HTHCHHHHH
T ss_pred ----------------------------------cccCCHHHHhhccCEEEecCcccChhhHHHHHHHHH-cccHHHHHH
Confidence 467889999877778888762 122233322 11 0
Q ss_pred CccceE-eCCCHHHHHHHHHcCCcEEEEccchhHHHHHhcCcceE--EeCCccc--cCccEEEecCCCcchHHHHHHHHh
Q 002211 734 PKSRLV-ALGSPEEYAIALENRTVAAVVDERPYIDLFLSDHCQFS--VRGQEFT--KSGWGFAFPRDSPLAIDMSTAILT 808 (953)
Q Consensus 734 ~~~~~~-~~~~~~~~~~~l~~g~~~a~~~~~~~~~~~~~~~~~l~--~~~~~~~--~~~~~~~~~k~spl~~~~n~~i~~ 808 (953)
-..++. ..++..+....+.+|+.|+.+.......+. .+...+. .+.+... +..+.+++.++++-.+.-...+..
T Consensus 136 l~~~~~~~~~~~~~~~~~v~~g~~d~~~~~~s~~~~~-~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~a~~f~~~ 214 (230)
T PF13531_consen 136 LQKNIVQYVPSTSQVLSAVASGEADAGIVYESQAIFA-RQGDPLSYVYPPDGVNSPPIDYPIAILKNAPHPEAARAFIDF 214 (230)
T ss_dssp HHHTEEEEESSHHHHHHHHHTTSSSEEEEEHHHHHHC-TSHTTEEEEE-STTTSSSEEEEEEEEBTTCTTHHHHHHHHHH
T ss_pred HHHhCcccccchHHHHHHHHcCCCcceeeHHHHHHHh-hcCCCeEEEECCchhcCCCEEEEEEEecCCCCHHHHHHHHHH
Confidence 012343 466788999999999999999766555322 2222333 3444443 245778888888766666666666
Q ss_pred hhccccHHHHHHH
Q 002211 809 LSENGELQRIHDK 821 (953)
Q Consensus 809 l~e~G~~~~~~~~ 821 (953)
|.... -+++..+
T Consensus 215 L~s~~-~q~~l~~ 226 (230)
T PF13531_consen 215 LLSPE-GQQILAK 226 (230)
T ss_dssp HTSHH-HHHHHHH
T ss_pred HCCHH-HHHHHHH
Confidence 65533 4444443
No 266
>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=91.13 E-value=9.1 Score=37.67 Aligned_cols=70 Identities=17% Similarity=0.157 Sum_probs=46.1
Q ss_pred EeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEecEEEecCccceeeccccceecceEEEEec
Q 002211 512 GYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGDIAIVTNRTKAVDFTQPYIESGLVVVAPV 591 (953)
Q Consensus 512 G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~~~~t~~r~~~vdft~p~~~~~~~~~v~~ 591 (953)
.+-.+++..+.++.+ .++++... ++.+++...+.+|++|+++.... .....+. +.++....++++++.
T Consensus 13 ~~l~~~l~~f~~~~P-~v~i~i~~-------~~~~~~~~~l~~~~~Di~i~~~~---~~~~~~~-~~~l~~~~~~lv~~~ 80 (198)
T cd08461 13 AILPPLLAALRQEAP-GVRVAIRD-------LESDNLEAQLERGEVDLALTTPE---YAPDGLR-SRPLFEERYVCVTRR 80 (198)
T ss_pred HHhHHHHHHHHHHCC-CcEEEEee-------CCcccHHHHHhcCCCcEEEecCc---cCCccce-eeeeecCcEEEEEcC
Confidence 456778888888774 24455443 34567899999999999885321 1122232 567777888888876
Q ss_pred cc
Q 002211 592 RK 593 (953)
Q Consensus 592 ~~ 593 (953)
..
T Consensus 81 ~~ 82 (198)
T cd08461 81 GH 82 (198)
T ss_pred CC
Confidence 54
No 267
>TIGR00035 asp_race aspartate racemase.
Probab=90.77 E-value=2.4 Score=43.81 Aligned_cols=87 Identities=11% Similarity=0.087 Sum_probs=54.9
Q ss_pred ChHHHHHHHHH-HHhcCcEEEEccCChhhHHHHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHH
Q 002211 99 NGFLSIMGALQ-FMETDTLAIVGPQSAVMAHVLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMV 177 (953)
Q Consensus 99 ~~~~a~~~a~~-li~~~v~aiiGp~~S~~a~av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l 177 (953)
++...+..+.+ |.+.++.+|+=|..+.... +..+-+..++|+|+. .++.++.+
T Consensus 59 ~~~~~l~~~~~~L~~~g~d~iviaCNTah~~-~~~l~~~~~iPii~i-------------------------~~~~~~~~ 112 (229)
T TIGR00035 59 RPRPILIDIAVKLENAGADFIIMPCNTAHKF-AEDIQKAIGIPLISM-------------------------IEETAEAV 112 (229)
T ss_pred hHHHHHHHHHHHHHHcCCCEEEECCccHHHH-HHHHHHhCCCCEech-------------------------HHHHHHHH
Confidence 45554544444 4445898888777665443 456666778998862 23344455
Q ss_pred HHcCCcEEEEEEecCccccchHHHHHHHHHhcCcEEE
Q 002211 178 SYFGWGEVIAIFNDDDQGRNGVTALGDKLAEIRCKIS 214 (953)
Q Consensus 178 ~~~~w~~vaii~~d~~~g~~~~~~l~~~l~~~g~~v~ 214 (953)
+..|.++|+++.....- ....+++.+++.|+++.
T Consensus 113 ~~~~~~~VgvLaT~~T~---~s~~y~~~l~~~g~~v~ 146 (229)
T TIGR00035 113 KEDGVKKAGLLGTKGTM---KDGVYEREMKKHGIEIV 146 (229)
T ss_pred HHcCCCEEEEEecHHHH---HhHHHHHHHHHCCCEEE
Confidence 66688899999754332 22447777888887665
No 268
>PRK10837 putative DNA-binding transcriptional regulator; Provisional
Probab=90.76 E-value=15 Score=39.39 Aligned_cols=83 Identities=18% Similarity=0.203 Sum_probs=52.5
Q ss_pred cceEEEecCcccccccEEeeCCcceEEEeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEecE
Q 002211 485 RQLRIGVPNRVSYRDFVFKVNGTDIVHGYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGDI 564 (953)
Q Consensus 485 ~~lri~v~~~~~~~p~~~~~~~~~~~~G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~~ 564 (953)
+.++|++.. .. ...+..+++..+.++.+- +.+.... +...+++..+.+|++|+++...
T Consensus 89 g~l~i~~~~--~~------------~~~~~~~~l~~~~~~~P~-i~i~v~~-------~~~~~~~~~l~~g~~Di~i~~~ 146 (290)
T PRK10837 89 GALRIYASS--TI------------GNYILPAMIARYRRDYPQ-LPLELSV-------GNSQDVINAVLDFRVDIGLIEG 146 (290)
T ss_pred CeEEEEecc--hh------------HhhhhHHHHHHHHHHCCC-ceEEEEE-------CCHHHHHHHHHhCCceEEEecC
Confidence 578998874 11 124456778888887642 4455543 4577899999999999988532
Q ss_pred EEecCccceeeccccceecceEEEEeccc
Q 002211 565 AIVTNRTKAVDFTQPYIESGLVVVAPVRK 593 (953)
Q Consensus 565 ~~t~~r~~~vdft~p~~~~~~~~~v~~~~ 593 (953)
. .....+ ...|+....++++++...
T Consensus 147 ~---~~~~~~-~~~~l~~~~~~lv~~~~h 171 (290)
T PRK10837 147 P---CHSPEL-ISEPWLEDELVVFAAPDS 171 (290)
T ss_pred C---CCCCce-eEEEeecceEEEEEcCCC
Confidence 1 111122 235666777888877555
No 269
>PRK11063 metQ DL-methionine transporter substrate-binding subunit; Provisional
Probab=90.43 E-value=6.5 Score=41.71 Aligned_cols=120 Identities=12% Similarity=0.084 Sum_probs=64.8
Q ss_pred CCCCChHHhhhCCCeEEEEeCc-hHH---HHHHHhhCC--------------------CccceEeCCCHHHHHHHHHcCC
Q 002211 700 SPIKGIDTLMTSNDRVGYQVGS-FAE---NYLIEELSI--------------------PKSRLVALGSPEEYAIALENRT 755 (953)
Q Consensus 700 ~~I~sl~dL~~~~~~ig~~~~s-~~~---~~l~~~~~~--------------------~~~~~~~~~~~~~~~~~l~~g~ 755 (953)
..|++++||. .|.+|++.... ... .+| ++.+. ...+++.. ...+...++.+|+
T Consensus 119 ~~i~si~DL~-~Gk~IAip~d~~n~~r~L~lL-~~~Gli~l~~~~~~~~t~~di~~n~~~v~~v~~-~~~~~~~al~~g~ 195 (271)
T PRK11063 119 KKIKSLDELQ-DGSQVAVPNDPTNLGRSLLLL-QKVGLIKLKDGVGLLPTVLDIVENPKNLKIVEL-EAPQLPRSLDDAQ 195 (271)
T ss_pred cCCCCHHHhc-CCCEEEecCCCccHHHHHHHH-HHCCCEEecCCCCCCCCHHHHhcCCCCCEEEEC-cHHHHHHhccccc
Confidence 5799999995 58899998632 111 123 22111 12233443 6667888899999
Q ss_pred cEEEEccchhHHHHHhcC-cceEEeCCccccCccEEEecCCCcchHHHHHHHHhhhccccHHHHHHHh
Q 002211 756 VAAVVDERPYIDLFLSDH-CQFSVRGQEFTKSGWGFAFPRDSPLAIDMSTAILTLSENGELQRIHDKW 822 (953)
Q Consensus 756 ~~a~~~~~~~~~~~~~~~-~~l~~~~~~~~~~~~~~~~~k~spl~~~~n~~i~~l~e~G~~~~~~~~w 822 (953)
+|+.+...+++.....+. .+-......-.++-..++++++.-=.+.+.+.+.-++....-+.+.++|
T Consensus 196 vDaa~i~~~~a~~a~~~~~~~~l~~e~~~~~~~~~~~v~~~~~~~~~~~~l~~a~~s~~v~~~i~~~~ 263 (271)
T PRK11063 196 IALAVINTTYASQIGLTPAKDGIFVEDKDSPYVNLIVAREDNKDAENVKKFVQAYQSDEVYEAANKVF 263 (271)
T ss_pred ccEEEEChHHHHHcCCCCCCCeeEECCCCCCeEEEEEECCcccCCHHHHHHHHHHcCHHHHHHHHHHc
Confidence 999999888876532222 1211222111122234556655443445555555455444444555554
No 270
>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=90.29 E-value=3 Score=40.84 Aligned_cols=101 Identities=9% Similarity=-0.026 Sum_probs=69.7
Q ss_pred HHHHHHHHHHHHcCCcEEEEEEecCccccchHHHHHHHHHhc--CcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEE
Q 002211 168 YLMSAIAEMVSYFGWGEVIAIFNDDDQGRNGVTALGDKLAEI--RCKISYKSALPPDQSVTETDVRNELVKVRMMEARVI 245 (953)
Q Consensus 168 ~~~~ai~~~l~~~~w~~vaii~~d~~~g~~~~~~l~~~l~~~--g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vi 245 (953)
.....+.+.+...+ .++.++..+.+ ..+.+.+.+++. |+.|+....-+. +..+....++.|++++||+|
T Consensus 35 dl~~~l~~~~~~~~-~~ifllG~~~~----~~~~~~~~l~~~yP~l~ivg~~~g~f----~~~~~~~i~~~I~~~~pdiv 105 (172)
T PF03808_consen 35 DLFPDLLRRAEQRG-KRIFLLGGSEE----VLEKAAANLRRRYPGLRIVGYHHGYF----DEEEEEAIINRINASGPDIV 105 (172)
T ss_pred HHHHHHHHHHHHcC-CeEEEEeCCHH----HHHHHHHHHHHHCCCeEEEEecCCCC----ChhhHHHHHHHHHHcCCCEE
Confidence 34556666666665 48888886654 455556666665 677765432222 36788899999999999999
Q ss_pred EEEcchhhHHHHHHHHHHcCCCCCceEEEEeCccc
Q 002211 246 VVHGYSRTGLMVFDVAQRLGMMDSGYVWIATTWLS 280 (953)
Q Consensus 246 i~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~ 280 (953)
++.+..+.-..++.+.++.. ... +|+..++..
T Consensus 106 ~vglG~PkQE~~~~~~~~~l--~~~-v~i~vG~~~ 137 (172)
T PF03808_consen 106 FVGLGAPKQERWIARHRQRL--PAG-VIIGVGGAF 137 (172)
T ss_pred EEECCCCHHHHHHHHHHHHC--CCC-EEEEECchh
Confidence 99998888888888777743 223 777776544
No 271
>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=90.12 E-value=21 Score=35.30 Aligned_cols=72 Identities=15% Similarity=0.142 Sum_probs=48.0
Q ss_pred EEeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEecEEEecCccceeeccccceecceEEEEe
Q 002211 511 HGYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGDIAIVTNRTKAVDFTQPYIESGLVVVAP 590 (953)
Q Consensus 511 ~G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~~~~t~~r~~~vdft~p~~~~~~~~~v~ 590 (953)
..+-.+++..+.++.+ .++++... ++..++...+.+|++|+++..-. ......+. +.++....++++++
T Consensus 12 ~~~l~~~l~~f~~~~P-~~~i~i~~-------~~~~~~~~~l~~g~~Dl~i~~~~--~~~~~~~~-~~~l~~~~~~~v~~ 80 (198)
T cd08443 12 RYVLPPVIKGFIERYP-RVSLQMHQ-------GSPTQIAEMVSKGLVDFAIATEA--LHDYDDLI-TLPCYHWNRCVVVK 80 (198)
T ss_pred eeECcHHHHHHHHHCC-CeEEEEEe-------CCHHHHHHHHHCCCccEEEEecc--ccccCCce-EeeeeeceEEEEEc
Confidence 4567788889888764 24455543 55778999999999999985211 11112233 46677788888877
Q ss_pred ccc
Q 002211 591 VRK 593 (953)
Q Consensus 591 ~~~ 593 (953)
...
T Consensus 81 ~~h 83 (198)
T cd08443 81 RDH 83 (198)
T ss_pred CCC
Confidence 655
No 272
>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=90.04 E-value=14 Score=36.20 Aligned_cols=70 Identities=11% Similarity=0.129 Sum_probs=46.8
Q ss_pred EeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEecEEEecCccceeeccccceecceEEEEec
Q 002211 512 GYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGDIAIVTNRTKAVDFTQPYIESGLVVVAPV 591 (953)
Q Consensus 512 G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~~~~t~~r~~~vdft~p~~~~~~~~~v~~ 591 (953)
.+...++..+.++.+ .+.++... ....++.+.|.+|++|+++... +.....+. ..++.+..+++++++
T Consensus 14 ~~l~~~l~~~~~~~P-~v~i~i~~-------~~~~~~~~~l~~g~~Dl~i~~~---~~~~~~~~-~~~l~~~~~~~v~~~ 81 (197)
T cd08425 14 YLIGPLIDRFHARYP-GIALSLRE-------MPQERIEAALADDRLDLGIAFA---PVRSPDID-AQPLFDERLALVVGA 81 (197)
T ss_pred hhhHHHHHHHHHHCC-CcEEEEEE-------CcHHHHHHHHHcCCccEEEEec---CCCCCCcE-EEEeccccEEEEecC
Confidence 345678888888765 35566654 4467899999999999998532 22222232 456777788888776
Q ss_pred cc
Q 002211 592 RK 593 (953)
Q Consensus 592 ~~ 593 (953)
+.
T Consensus 82 ~~ 83 (197)
T cd08425 82 TH 83 (197)
T ss_pred CC
Confidence 55
No 273
>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=90.04 E-value=1.5 Score=46.25 Aligned_cols=86 Identities=14% Similarity=0.118 Sum_probs=69.2
Q ss_pred EEeEEEecCCCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEEccCChhhHHHH
Q 002211 51 NVGAIFSFGTVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIVGPQSAVMAHVL 130 (953)
Q Consensus 51 ~IG~l~~~~~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aiiGp~~S~~a~av 130 (953)
+||++.+...+.-.....|+...++..| |+.++...+..+..|+.++.+.+..|+++++.+|.+.. + ...+
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-D--SPGV 192 (258)
T ss_pred cEEEEcCcccHHHHHHHHHHHHHHHHHC------CCcEEEEEEecCCCCcHHHHHHHHHHHHCCCcEEEecC-C--ChHH
Confidence 7999988876655667789999998888 45677777777888999999999999999999888766 2 2456
Q ss_pred HHhhhhCCCcEEEee
Q 002211 131 SHLANELQVPLLSFT 145 (953)
Q Consensus 131 ~~v~~~~~vP~Is~~ 145 (953)
...+.+.++..|.+.
T Consensus 193 ~~aa~~~g~~~IG~d 207 (258)
T cd06353 193 IQAAEEKGVYAIGYV 207 (258)
T ss_pred HHHHHHhCCEEEeec
Confidence 677788899999864
No 274
>TIGR02424 TF_pcaQ pca operon transcription factor PcaQ. Members of this family are LysR-family transcription factors associated with operons for catabolism of protocatechuate. Members occur only in Proteobacteria.
Probab=89.71 E-value=12 Score=40.37 Aligned_cols=86 Identities=16% Similarity=0.275 Sum_probs=55.3
Q ss_pred CcceEEEecCcccccccEEeeCCcceEEEeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEec
Q 002211 484 GRQLRIGVPNRVSYRDFVFKVNGTDIVHGYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGD 563 (953)
Q Consensus 484 g~~lri~v~~~~~~~p~~~~~~~~~~~~G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~ 563 (953)
.++|+||++. .. ...+-.+++..+.++.+ .+.+.... .+..+++.++.+|++|++++.
T Consensus 92 ~~~l~I~~~~--~~------------~~~~~~~~l~~~~~~~P-~~~i~~~~-------~~~~~~~~~l~~g~~D~~i~~ 149 (300)
T TIGR02424 92 GPTVRIGALP--TV------------AARLMPEVVKRFLARAP-RLRVRIMT-------GPNAYLLDQLRVGALDLVVGR 149 (300)
T ss_pred CceEEEeccc--HH------------HHhhhHHHHHHHHHhCC-CcEEEEEe-------CchHHHHHHHHCCCCCEEEEe
Confidence 4679998874 11 12345567778887775 35566654 457889999999999999863
Q ss_pred EEEecCccceeeccccceecceEEEEeccc
Q 002211 564 IAIVTNRTKAVDFTQPYIESGLVVVAPVRK 593 (953)
Q Consensus 564 ~~~t~~r~~~vdft~p~~~~~~~~~v~~~~ 593 (953)
... ......+. ..|.....+++++++..
T Consensus 150 ~~~-~~~~~~~~-~~~l~~~~~~~~~~~~h 177 (300)
T TIGR02424 150 LGA-PETMQGLS-FEHLYNEPVVFVVRAGH 177 (300)
T ss_pred cCC-ccccccee-eeeecCCceEEEEcCCC
Confidence 321 11112232 44677778888887554
No 275
>cd08413 PBP2_CysB_like The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains type 2 periplasmic binding fold. CysB is a transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the regulation of transcription in response to sulfur source is attributed to two transcriptional regulators, CysB and Cbl. CysB, in association with Cbl, downregulates the expression of ssuEADCB operon which is required for the utilization of sulfur from aliphatic sulfonates, in the presence of cysteine. Also, Cbl and CysB together directly function as transcriptional activators of tauABCD genes, which are required for utilization of taurine as sulfur source for growth. Like many other members of the LTTR family, CysB is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-bi
Probab=89.70 E-value=14 Score=36.46 Aligned_cols=71 Identities=20% Similarity=0.165 Sum_probs=48.0
Q ss_pred EeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEecEEEecCccceeeccccceecceEEEEec
Q 002211 512 GYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGDIAIVTNRTKAVDFTQPYIESGLVVVAPV 591 (953)
Q Consensus 512 G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~~~~t~~r~~~vdft~p~~~~~~~~~v~~ 591 (953)
.+..+++..+.++.+- +++++.. +...++.+.+.+|++|+++..... .....+. +.+.....++++++.
T Consensus 13 ~~l~~~l~~~~~~~P~-i~v~~~~-------~~~~~~~~~l~~g~~D~~i~~~~~--~~~~~~~-~~~l~~~~~~~v~~~ 81 (198)
T cd08413 13 YVLPPVIAAFRKRYPK-VKLSLHQ-------GTPSQIAEMVLKGEADIAIATEAL--DDHPDLV-TLPCYRWNHCVIVPP 81 (198)
T ss_pred hhccHHHHHHHHhCCc-eEEEEEe-------CCHHHHHHHHHcCCCCEEEEccCC--CCCCCcE-EEEeeeeeEEEEecC
Confidence 4556788888888752 4555554 557889999999999998852211 1112233 467778888888876
Q ss_pred cc
Q 002211 592 RK 593 (953)
Q Consensus 592 ~~ 593 (953)
..
T Consensus 82 ~h 83 (198)
T cd08413 82 GH 83 (198)
T ss_pred CC
Confidence 55
No 276
>cd08467 PBP2_SyrM The C-terminal substrate binding of LysR-type symbiotic regulator SyrM, which activates expression of nodulation gene NodD3, contains the type 2 periplasmic binding fold. Rhizobium is a nitrogen fixing bacteria present in the roots of leguminous plants, which fixes atmospheric nitrogen to the soil. Most Rhizobium species possess multiple nodulation (nod) genes for the development of nodules. For example, Rhizobium meliloti possesses three copies of nodD genes. NodD1 and NodD2 activate nod operons when Rhizobium is exposed to inducers synthesized by the host plant, while NodD3 acts independent of plant inducers and requires the symbiotic regulator SyrM for nod gene expression. SyrM activates the expression of the regulatory nodulation gene nodD3. In turn, NodD3 activates expression of syrM. In addition, SyrM is involved in exopolysaccharide synthesis. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are
Probab=89.67 E-value=13 Score=36.88 Aligned_cols=70 Identities=11% Similarity=0.115 Sum_probs=47.1
Q ss_pred EeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEecEEEecCccceeeccccceecceEEEEec
Q 002211 512 GYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGDIAIVTNRTKAVDFTQPYIESGLVVVAPV 591 (953)
Q Consensus 512 G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~~~~t~~r~~~vdft~p~~~~~~~~~v~~ 591 (953)
.+-.+++..+.++.+- ++++... +...++++.|.+|++|+++... ......+. ..+.....+++++++
T Consensus 13 ~~l~~~l~~~~~~~P~-i~l~~~~-------~~~~~~~~~l~~g~~D~~i~~~---~~~~~~~~-~~~l~~~~~~~v~~~ 80 (200)
T cd08467 13 ALLPRLAPRLRERAPG-LDLRLCP-------IGDDLAERGLEQGTIDLAVGRF---AVPPDGLV-VRRLYDDGFACLVRH 80 (200)
T ss_pred HHHHHHHHHHHhhCCC-CEEEEec-------CCcccHHHHhhCCCcCEEEecC---CCCCccce-eEEeeeccEEEEEcC
Confidence 4556788888887752 5566554 4567899999999999988532 11122233 357778888888875
Q ss_pred cc
Q 002211 592 RK 593 (953)
Q Consensus 592 ~~ 593 (953)
..
T Consensus 81 ~h 82 (200)
T cd08467 81 GH 82 (200)
T ss_pred CC
Confidence 54
No 277
>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=89.63 E-value=20 Score=34.94 Aligned_cols=72 Identities=14% Similarity=0.084 Sum_probs=47.0
Q ss_pred EeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEecEEEecCccceeeccccceecceEEEEec
Q 002211 512 GYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGDIAIVTNRTKAVDFTQPYIESGLVVVAPV 591 (953)
Q Consensus 512 G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~~~~t~~r~~~vdft~p~~~~~~~~~v~~ 591 (953)
.+...++..+.++.+ .++++... +...++++.+.+|++|++++...... +...+. ..++....++++++.
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 456778888888874 24555554 45788999999999999986322110 112222 356777778887765
Q ss_pred cc
Q 002211 592 RK 593 (953)
Q Consensus 592 ~~ 593 (953)
..
T Consensus 83 ~~ 84 (197)
T cd08449 83 EH 84 (197)
T ss_pred CC
Confidence 54
No 278
>COG3473 Maleate cis-trans isomerase [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=89.55 E-value=11 Score=36.99 Aligned_cols=90 Identities=12% Similarity=0.001 Sum_probs=64.8
Q ss_pred HHHHHHHHHcCCcEEEEEEecCccccchHHHHHHHHHhcCcEEEEEEecCCCC-----CCChHHHHHHHHHHhcCCceEE
Q 002211 171 SAIAEMVSYFGWGEVIAIFNDDDQGRNGVTALGDKLAEIRCKISYKSALPPDQ-----SVTETDVRNELVKVRMMEARVI 245 (953)
Q Consensus 171 ~ai~~~l~~~~w~~vaii~~d~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~-----~~~~~d~~~~l~~i~~~~~~vi 245 (953)
.|.++-++.++.+++.++. +|-....+...+.++++|.+|+....+-... .......-...+++..-++|.|
T Consensus 107 ~Avv~aL~al~a~ri~vlT---PY~~evn~~e~ef~~~~Gfeiv~~~~Lgi~dn~eigr~~P~~~y~lAk~~~~~~~Dai 183 (238)
T COG3473 107 TAVVEALNALGAQRISVLT---PYIDEVNQREIEFLEANGFEIVDFKGLGITDNLEIGRQEPWAVYRLAKEVFTPDADAI 183 (238)
T ss_pred HHHHHHHHhhCcceEEEec---cchhhhhhHHHHHHHhCCeEEEEeeccCCcccchhcccChHHHHHHHHHhcCCCCCeE
Confidence 5677789999999999997 5667788888899999999998766543321 0122334455566677899999
Q ss_pred EEEcchhhHHHHHHHHHH
Q 002211 246 VVHGYSRTGLMVFDVAQR 263 (953)
Q Consensus 246 i~~~~~~~~~~~~~~a~~ 263 (953)
++.|..-....++....+
T Consensus 184 FiSCTnlRt~eii~~lE~ 201 (238)
T COG3473 184 FISCTNLRTFEIIEKLER 201 (238)
T ss_pred EEEeeccccHHHHHHHHH
Confidence 998877666666665544
No 279
>PRK12682 transcriptional regulator CysB-like protein; Reviewed
Probab=89.43 E-value=19 Score=39.03 Aligned_cols=84 Identities=15% Similarity=0.178 Sum_probs=54.7
Q ss_pred cceEEEecCcccccccEEeeCCcceEEEeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEecE
Q 002211 485 RQLRIGVPNRVSYRDFVFKVNGTDIVHGYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGDI 564 (953)
Q Consensus 485 ~~lri~v~~~~~~~p~~~~~~~~~~~~G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~~ 564 (953)
..|+||+.+ .+ ...+..+++..+.++.+ .+++.... ++.+++++.+.+|++|++++.-
T Consensus 93 g~l~Ig~~~--~~------------~~~~l~~~l~~~~~~~P-~i~i~i~~-------~~~~~~~~~l~~g~~D~~i~~~ 150 (309)
T PRK12682 93 GTLTIATTH--TQ------------ARYVLPRVVAAFRKRYP-KVNLSLHQ-------GSPDEIARMVISGEADIGIATE 150 (309)
T ss_pred CeEEEeeCc--hH------------HHHHHHHHHHHHHHhCC-CeEEEEec-------CCHHHHHHHHHcCCccEEEecC
Confidence 468998874 11 12455677888888764 24455543 4568899999999999998632
Q ss_pred EEecCccceeeccccceecceEEEEeccc
Q 002211 565 AIVTNRTKAVDFTQPYIESGLVVVAPVRK 593 (953)
Q Consensus 565 ~~t~~r~~~vdft~p~~~~~~~~~v~~~~ 593 (953)
.. .....++ +.|+.....+++++...
T Consensus 151 ~~--~~~~~l~-~~~l~~~~~~~~~~~~~ 176 (309)
T PRK12682 151 SL--ADDPDLA-TLPCYDWQHAVIVPPDH 176 (309)
T ss_pred cc--cCCCcce-EEEeeeeeEEEEecCCC
Confidence 11 1122333 45778888888887665
No 280
>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=89.32 E-value=14 Score=36.22 Aligned_cols=73 Identities=16% Similarity=0.153 Sum_probs=47.2
Q ss_pred EeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEecEEEe--cCccceeeccccceecceEEEE
Q 002211 512 GYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGDIAIV--TNRTKAVDFTQPYIESGLVVVA 589 (953)
Q Consensus 512 G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~~~~t--~~r~~~vdft~p~~~~~~~~~v 589 (953)
.+..+++..+.++.+ .+++.... ++..+++..+.+|++|+++...... ......+ ...+..+..+++++
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 345677888888874 34565554 4567899999999999988632110 1122223 35667778888888
Q ss_pred eccc
Q 002211 590 PVRK 593 (953)
Q Consensus 590 ~~~~ 593 (953)
+...
T Consensus 84 ~~~~ 87 (200)
T cd08423 84 PADH 87 (200)
T ss_pred cCCC
Confidence 7655
No 281
>PRK11482 putative DNA-binding transcriptional regulator; Provisional
Probab=89.32 E-value=13 Score=40.64 Aligned_cols=82 Identities=15% Similarity=0.132 Sum_probs=54.5
Q ss_pred CcceEEEecCcccccccEEeeCCcceEEEeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEec
Q 002211 484 GRQLRIGVPNRVSYRDFVFKVNGTDIVHGYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGD 563 (953)
Q Consensus 484 g~~lri~v~~~~~~~p~~~~~~~~~~~~G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~ 563 (953)
.++++||+.. .. ...+-..++..+.+..+ .++++.. .++++++.|.+|++|+++..
T Consensus 116 ~~~l~Ig~~~--~~------------~~~~l~~~l~~f~~~~P-~i~i~~~---------~~~~~~~~l~~g~~Dl~i~~ 171 (317)
T PRK11482 116 QRTITIATTP--SV------------GALVMPVIYQAIKTHYP-QLLLRNI---------PISDAENQLSQFQTDLIIDT 171 (317)
T ss_pred CceEEEEecH--HH------------HHHHHHHHHHHHHHHCC-CCEEEEe---------cchhHHHHHHCCCcCEEEec
Confidence 3579999874 11 12355677788888775 3444432 35689999999999999864
Q ss_pred EEEecCccceeeccccceecceEEEEeccc
Q 002211 564 IAIVTNRTKAVDFTQPYIESGLVVVAPVRK 593 (953)
Q Consensus 564 ~~~t~~r~~~vdft~p~~~~~~~~~v~~~~ 593 (953)
.. .....+. +.|+....++++++...
T Consensus 172 ~~---~~~~~~~-~~~l~~~~~~lv~~~~h 197 (317)
T PRK11482 172 HS---CSNRTIQ-HHVLFTDNVVLVCRQGH 197 (317)
T ss_pred cC---CCCCceE-EEEEecCcEEEEEeCCC
Confidence 32 2223344 35778888888887665
No 282
>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=89.31 E-value=18 Score=35.59 Aligned_cols=69 Identities=12% Similarity=0.159 Sum_probs=44.8
Q ss_pred eeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEecEEEecCccceeeccccceecceEEEEecc
Q 002211 513 YCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGDIAIVTNRTKAVDFTQPYIESGLVVVAPVR 592 (953)
Q Consensus 513 ~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~~~~t~~r~~~vdft~p~~~~~~~~~v~~~ 592 (953)
+-..++..+.++.+- ++++... ++..++.+.|.+|++|+++..-.. ....+. ..++....++++++..
T Consensus 14 ~~~~~l~~~~~~~P~-i~i~i~~-------~~~~~~~~~l~~g~~Dl~i~~~~~---~~~~~~-~~~l~~~~~~~~~~~~ 81 (198)
T cd08441 14 WLMPVLDQFRERWPD-VELDLSS-------GFHFDPLPALLRGELDLVITSDPL---PLPGIA-YEPLFDYEVVLVVAPD 81 (198)
T ss_pred hhHHHHHHHHHhCCC-eEEEEEe-------CCchhHHHHHHcCCceEEEecCCc---CCCCcE-EEEccCCcEEEEEcCC
Confidence 456788888888753 4455543 457789999999999999852211 112222 3466677777777655
Q ss_pred c
Q 002211 593 K 593 (953)
Q Consensus 593 ~ 593 (953)
.
T Consensus 82 ~ 82 (198)
T cd08441 82 H 82 (198)
T ss_pred C
Confidence 4
No 283
>cd08444 PBP2_Cbl The C-terminal substrate binding domain of LysR-type transcriptional regulator Cbl, which is required for expression of sulfate starvation-inducible (ssi) genes, contains the type 2 periplasmic binding fold. Cbl is a member of the LysR transcriptional regulators that comprise the largest family of prokaryotic transcription factor. Cbl shows high sequence similarity to CysB, the LysR-type transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the function of Cbl is required for expression of sulfate starvation-inducible (ssi) genes, coupled with the biosynthesis of cysteine from the organic sulfur sources (sulfonates). The ssi genes include the ssuEADCB and tauABCD operons encoding uptake systems for organosulfur compounds, aliphatic sulfonates, and taurine. The genes in these operons encode an ABC-type transport system required for uptake of aliphatic sulfonates and a desulfonati
Probab=88.97 E-value=22 Score=35.11 Aligned_cols=72 Identities=17% Similarity=0.188 Sum_probs=48.1
Q ss_pred EEeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEecEEEecCccceeeccccceecceEEEEe
Q 002211 511 HGYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGDIAIVTNRTKAVDFTQPYIESGLVVVAP 590 (953)
Q Consensus 511 ~G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~~~~t~~r~~~vdft~p~~~~~~~~~v~ 590 (953)
.++..+++..+.++.+ .++++... ++..++++.+.+|++|+++..-.. .....+ .+.++....++++++
T Consensus 12 ~~~l~~~l~~~~~~~P-~v~l~i~~-------~~~~~~~~~l~~g~~Dl~i~~~~~--~~~~~~-~~~~l~~~~~~~~~~ 80 (198)
T cd08444 12 RYALPWVVQAFKEQFP-NVHLVLHQ-------GSPEEIASMLANGQADIGIATEAL--ENHPEL-VSFPYYDWHHHIIVP 80 (198)
T ss_pred hhhhhHHHHHHHHHCC-CeEEEEEe-------CCHHHHHHHHHCCCccEEEecccc--CCCcCc-EEeeccccceeEEec
Confidence 3566788888988874 24555543 557789999999999998852111 111223 246777788888887
Q ss_pred ccc
Q 002211 591 VRK 593 (953)
Q Consensus 591 ~~~ 593 (953)
...
T Consensus 81 ~~h 83 (198)
T cd08444 81 VGH 83 (198)
T ss_pred CCC
Confidence 665
No 284
>COG1910 Periplasmic molybdate-binding protein/domain [Inorganic ion transport and metabolism]
Probab=88.83 E-value=6 Score=39.32 Aligned_cols=107 Identities=18% Similarity=0.190 Sum_probs=66.3
Q ss_pred CCCCChHHhhhCCCeE-EEEeCchHHHHHHHhh---CCCccceEeCC----CHHHHHHHHHcCCcEEEEccchhHHHHHh
Q 002211 700 SPIKGIDTLMTSNDRV-GYQVGSFAENYLIEEL---SIPKSRLVALG----SPEEYAIALENRTVAAVVDERPYIDLFLS 771 (953)
Q Consensus 700 ~~I~sl~dL~~~~~~i-g~~~~s~~~~~l~~~~---~~~~~~~~~~~----~~~~~~~~l~~g~~~a~~~~~~~~~~~~~ 771 (953)
..|++++||.+.+.++ --.+||-.+..|.+.+ +.....+.-|. +......++..|+.|+-+.-+..++-+
T Consensus 87 k~i~~~edl~~~d~~fVNR~rGSGTR~LlD~~L~~~~~~~~~I~GY~~e~~th~avA~aVa~G~AD~GvGlr~~A~~~-- 164 (223)
T COG1910 87 KNISSLEDLLRKDLRFVNRNRGSGTRILLDELLGELNILPDSIKGYSDEATTHDAVASAVASGRADAGVGLRHAAEKY-- 164 (223)
T ss_pred CccccHHHHhhcCcEEEecCCCccHHHHHHHHHHHcCcCchhcCCccccccccHHHHHHHHcCCCCccccHHHHHHHc--
Confidence 4599999999665442 2245777777665433 33334444343 555667788899999999865554332
Q ss_pred cCcceEEeCCccccCccEEEecCCCcchHHHHHHHHhhhccc
Q 002211 772 DHCQFSVRGQEFTKSGWGFAFPRDSPLAIDMSTAILTLSENG 813 (953)
Q Consensus 772 ~~~~l~~~~~~~~~~~~~~~~~k~spl~~~~n~~i~~l~e~G 813 (953)
.-+|.- +....|-|+++|+.--.+.+...+..|...+
T Consensus 165 -gL~Fip----l~~E~YD~virke~~~~~~vr~fi~~L~s~~ 201 (223)
T COG1910 165 -GLDFIP----LGDEEYDFVIRKERLDKPVVRAFIKALKSEG 201 (223)
T ss_pred -CCceEE----cccceEEEEEehhHccCHHHHHHHHHhcccc
Confidence 113333 3355788999998655556666666665533
No 285
>PRK09860 putative alcohol dehydrogenase; Provisional
Probab=88.69 E-value=2.1 Score=48.01 Aligned_cols=88 Identities=10% Similarity=0.094 Sum_probs=66.7
Q ss_pred HHHHHHHHHcCCcEEEEEEecCccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcc
Q 002211 171 SAIAEMVSYFGWGEVIAIFNDDDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGY 250 (953)
Q Consensus 171 ~ai~~~l~~~~w~~vaii~~d~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~ 250 (953)
..+.+.++.+|.+++.+++...-...+..+.+.+.|++.|+.+.....+.++ .+.+++...+..+++.++|+||-.+.
T Consensus 20 ~~l~~~~~~~g~~~~livt~~~~~~~g~~~~v~~~L~~~~i~~~~f~~v~~n--p~~~~v~~~~~~~~~~~~D~IiaiGG 97 (383)
T PRK09860 20 TDAMNMMADYGFTRTLIVTDNMLTKLGMAGDVQKALEERNIFSVIYDGTQPN--PTTENVAAGLKLLKENNCDSVISLGG 97 (383)
T ss_pred HHHHHHHHhcCCCEEEEEcCcchhhCccHHHHHHHHHHcCCeEEEeCCCCCC--cCHHHHHHHHHHHHHcCCCEEEEeCC
Confidence 4577788999999999988654444567889999999999886554455555 56788999999999999999997665
Q ss_pred h--hhHHHHHHH
Q 002211 251 S--RTGLMVFDV 260 (953)
Q Consensus 251 ~--~~~~~~~~~ 260 (953)
+ -|+.+.+..
T Consensus 98 GS~iD~AK~ia~ 109 (383)
T PRK09860 98 GSPHDCAKGIAL 109 (383)
T ss_pred chHHHHHHHHHH
Confidence 4 455555544
No 286
>cd08429 PBP2_NhaR The C-terminal substrate binding domain of LysR-type transcriptional activator of the nhaA gene, encoding Na+/H+ antiporter, contains the type 2 periplasmic binding fold. NhaR is a positive regulator of the LysR family and is known to be an activator of the nhaA gene encoding a Na(+)/H(+) antiporter. In Escherichia coli, NhaA is the vital antiporter that protects against high sodium stress, and it is essential for growth in high sodium levels, while NhaB becomes essential only if NhaA is not available. The nhaA gene of nhaAR operon is induced by monovalent cations. The nhaR of the operon activates nhaAR, as well as the osmC transcription which is induced at elevated osmolarity. OsmC is transcribed from the two overlapping promoters (osmCp1 and osmP2) and that NhaR is shown to activate only the expression of osmCp1. NhaR also activates the transcription of the pgaABCD operon which is required for production of the biofilm adhesion, poly-beta-1,6-N-acetyl-d-glucosamine
Probab=88.67 E-value=26 Score=34.96 Aligned_cols=71 Identities=11% Similarity=0.145 Sum_probs=45.1
Q ss_pred EeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEecEEEecCccceeeccccceecceEEEEec
Q 002211 512 GYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGDIAIVTNRTKAVDFTQPYIESGLVVVAPV 591 (953)
Q Consensus 512 G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~~~~t~~r~~~vdft~p~~~~~~~~~v~~ 591 (953)
.+..+++..+.++.+ .++++... ++.++++..|.+|++|+++.......+-...+ ...|+.+..++++++.
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 455678888888764 35566554 67899999999999999885322111100111 2347777777776654
No 287
>cd08464 PBP2_DntR_like_2 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold. This CD includes an uncharacterized LysR-type transcriptional regulator similar to DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytra
Probab=88.62 E-value=19 Score=35.33 Aligned_cols=70 Identities=13% Similarity=0.083 Sum_probs=45.1
Q ss_pred EeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEecEEEecCccceeeccccceecceEEEEec
Q 002211 512 GYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGDIAIVTNRTKAVDFTQPYIESGLVVVAPV 591 (953)
Q Consensus 512 G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~~~~t~~r~~~vdft~p~~~~~~~~~v~~ 591 (953)
++...++..+.++.+ .++++... ++..++++.+.+|++|+++.... .....+ -..+.....++++++.
T Consensus 13 ~~l~~~l~~~~~~~P-~v~l~i~~-------~~~~~~~~~l~~g~~D~~i~~~~---~~~~~~-~~~~l~~~~~~~v~~~ 80 (200)
T cd08464 13 WLAPPLLAALRAEAP-GVRLVFRQ-------VDPFNVGDMLDRGEIDLAIGVFG---ELPAWL-KREVLYTEGYACLFDP 80 (200)
T ss_pred HHHHHHHHHHHHHCC-CcEEEEec-------CCcccHHHHHhcCcccEEEecCC---CCcccc-eeeeecccceEEEEeC
Confidence 455677888888764 24555553 44678899999999999985221 111222 2456777777777765
Q ss_pred cc
Q 002211 592 RK 593 (953)
Q Consensus 592 ~~ 593 (953)
..
T Consensus 81 ~~ 82 (200)
T cd08464 81 QQ 82 (200)
T ss_pred CC
Confidence 44
No 288
>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=88.47 E-value=8.4 Score=38.52 Aligned_cols=102 Identities=15% Similarity=0.113 Sum_probs=65.5
Q ss_pred CCCCChHHhhhCCCeE-EEEeCchHHHHHHHhh---CCCccceE----eCCCHHHHHHHHHcCCcEEEEccchhHHHHHh
Q 002211 700 SPIKGIDTLMTSNDRV-GYQVGSFAENYLIEEL---SIPKSRLV----ALGSPEEYAIALENRTVAAVVDERPYIDLFLS 771 (953)
Q Consensus 700 ~~I~sl~dL~~~~~~i-g~~~~s~~~~~l~~~~---~~~~~~~~----~~~~~~~~~~~l~~g~~~a~~~~~~~~~~~~~ 771 (953)
..|.+++||.+.+.++ .-+.||-.+.+|...+ ++....+. ...+..+...+|..|..|+-+.....+.-+
T Consensus 81 ~~i~~~~dL~~~~~r~vnR~~GSGtR~l~d~~l~~~gi~~~~i~gy~~~~~th~~vA~aVa~G~AD~G~g~~~~A~~~-- 158 (193)
T PF12727_consen 81 KGITSLEDLADPGLRFVNRQPGSGTRILFDQLLAEEGIDPEDIPGYAQEANTHLAVAAAVASGKADAGIGIRAAAEEF-- 158 (193)
T ss_pred ccCCCHHHhccCCcEEEECCCCCHHHHHHHHHHHHcCCChhhCCCccccccChHHHHHHHHcCCCCEEeehHHHHHhh--
Confidence 4799999998767664 3456887777775544 23333332 345778889999999999999866555321
Q ss_pred cCcceEEeCCccccCccEEEecCCCcchHHHHHHHH
Q 002211 772 DHCQFSVRGQEFTKSGWGFAFPRDSPLAIDMSTAIL 807 (953)
Q Consensus 772 ~~~~l~~~~~~~~~~~~~~~~~k~spl~~~~n~~i~ 807 (953)
..-++.-+ ....|-++++|..-..+.+.+.|.
T Consensus 159 ~gL~Fvpl----~~E~~dlv~~~~~~~~~~vq~ll~ 190 (193)
T PF12727_consen 159 YGLDFVPL----AEERYDLVIRREDLEDPAVQALLD 190 (193)
T ss_pred cCCCcEEc----cccceEEEEEhhHcCCHHHHHHHH
Confidence 01123322 235678888887765666555554
No 289
>PRK12683 transcriptional regulator CysB-like protein; Reviewed
Probab=88.46 E-value=24 Score=38.31 Aligned_cols=196 Identities=13% Similarity=0.085 Sum_probs=113.9
Q ss_pred cceEEEecCcccccccEEeeCCcceEEEeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEecE
Q 002211 485 RQLRIGVPNRVSYRDFVFKVNGTDIVHGYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGDI 564 (953)
Q Consensus 485 ~~lri~v~~~~~~~p~~~~~~~~~~~~G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~~ 564 (953)
++|+||+.. ... ..+-..+++.+.++.+ .+++.... +++++++..|.+|++|+++...
T Consensus 93 g~l~Ig~~~--~~~------------~~~l~~~i~~f~~~~P-~i~l~~~~-------~~~~~~~~~L~~~~~D~~i~~~ 150 (309)
T PRK12683 93 GHLTVATTH--TQA------------RYALPKVVRQFKEVFP-KVHLALRQ-------GSPQEIAEMLLNGEADIGIATE 150 (309)
T ss_pred ceEEEEecc--chH------------HHHHHHHHHHHHHHCC-CceEEEEe-------CCHHHHHHHHHcCCccEEEecC
Confidence 569998864 111 1344567788877764 24555554 5689999999999999987522
Q ss_pred EEecCccceeeccccceecceEEEEecccCCcCcceeeccCchhHHHHHHHHHHHHHHHhhhhhcccCCCCCCCCcccch
Q 002211 565 AIVTNRTKAVDFTQPYIESGLVVVAPVRKLNSSAWAFLRPFTPLMWAVTGVFFLVVGTVVWILEHRLNDEFRGPPRKQIV 644 (953)
Q Consensus 565 ~~t~~r~~~vdft~p~~~~~~~~~v~~~~~~~~~~~~l~PF~~~vW~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~ 644 (953)
.. .....+.+ .|+....++++++...+...
T Consensus 151 ~~--~~~~~l~~-~~l~~~~~~~v~~~~hpl~~----------------------------------------------- 180 (309)
T PRK12683 151 AL--DREPDLVS-FPYYSWHHVVVVPKGHPLTG----------------------------------------------- 180 (309)
T ss_pred CC--CCCCCceE-EEcccCeEEEEecCCCCccc-----------------------------------------------
Confidence 11 11222333 46777788888876552110
Q ss_pred hhHHHHHHHhhccccCCcccchhHHHHHHHHHHHHHhhhhcccceeeeeeeccccCCCCChHHhhhCCCe-EEEEeCchH
Q 002211 645 TVLWFSFSTMFFAHRENTVSTLGRVVLIIWLFVVLIITSSYTASLTSILTVQQLSSPIKGIDTLMTSNDR-VGYQVGSFA 723 (953)
Q Consensus 645 ~~~~~~~~~l~~~~~~~~~s~~~R~l~~~w~~~~lil~~~Yta~L~s~Lt~~~~~~~I~sl~dL~~~~~~-ig~~~~s~~ 723 (953)
..--+++||. +.+ |....++..
T Consensus 181 -------------------------------------------------------~~~~~~~~L~--~~~~i~~~~~~~~ 203 (309)
T PRK12683 181 -------------------------------------------------------RENLTLEAIA--EYPIITYDQGFTG 203 (309)
T ss_pred -------------------------------------------------------CCccCHHHHh--cCCeEeccCCCcH
Confidence 1235678886 333 444444433
Q ss_pred HHHHH---HhhCCCccceEeCCCHHHHHHHHHcCCcEEEEccchhHHHHHhcCcceEEeC--CccccCccEEEecCCCcc
Q 002211 724 ENYLI---EELSIPKSRLVALGSPEEYAIALENRTVAAVVDERPYIDLFLSDHCQFSVRG--QEFTKSGWGFAFPRDSPL 798 (953)
Q Consensus 724 ~~~l~---~~~~~~~~~~~~~~~~~~~~~~l~~g~~~a~~~~~~~~~~~~~~~~~l~~~~--~~~~~~~~~~~~~k~spl 798 (953)
...+. +..+.........++.+...+.+..|.--+++-.. ..... ...++..+. +......++++.+|+.++
T Consensus 204 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~Gi~~lp~~-~~~~~--~~~~l~~~~~~~~~~~~~~~l~~~~~~~~ 280 (309)
T PRK12683 204 RSRIDQAFAEAGLVPDIVLTALDADVIKTYVELGMGVGIVAAM-AYDPQ--RDTGLVALDTDHLFEANTTRVGLRRGAYL 280 (309)
T ss_pred HHHHHHHHHHCCCCceeEEEeccHHHHHHHHHhCCCeEEeehh-hcccc--CCCceEEEeCCCCcccceEEEEEECCCcC
Confidence 33222 23343333445677888888888887665666432 22221 123455443 222345688899999887
Q ss_pred hHHHHHHHHhhhcc
Q 002211 799 AIDMSTAILTLSEN 812 (953)
Q Consensus 799 ~~~~n~~i~~l~e~ 812 (953)
.......+..+.+.
T Consensus 281 ~~~~~~fi~~l~~~ 294 (309)
T PRK12683 281 RGYAYRFIELFAPH 294 (309)
T ss_pred CHHHHHHHHHHHhh
Confidence 77666666555543
No 290
>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=88.35 E-value=23 Score=34.42 Aligned_cols=72 Identities=22% Similarity=0.307 Sum_probs=46.9
Q ss_pred EeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEecEEEecCccceeeccccceecceEEEEec
Q 002211 512 GYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGDIAIVTNRTKAVDFTQPYIESGLVVVAPV 591 (953)
Q Consensus 512 G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~~~~t~~r~~~vdft~p~~~~~~~~~v~~ 591 (953)
.+-.+++..+.+..+ .++++... ++.+++++.+.+|++|+++..-.. ......+ .+.+.....+++++++
T Consensus 13 ~~l~~~l~~~~~~~P-~i~l~~~~-------~~~~~~~~~l~~g~~Dl~i~~~~~-~~~~~~~-~~~~l~~~~~~~v~~~ 82 (195)
T cd08427 13 GLLPRALARLRRRHP-DLEVHIVP-------GLSAELLARVDAGELDAAIVVEPP-FPLPKDL-VWTPLVREPLVLIAPA 82 (195)
T ss_pred HHhHHHHHHHHHHCC-CceEEEEe-------CCcHHHHHHHHCCCCCEEEEcCCC-CccccCc-eEEEcccCcEEEEECC
Confidence 455678888888774 24565554 557899999999999998863211 1101222 2456777788888776
Q ss_pred cc
Q 002211 592 RK 593 (953)
Q Consensus 592 ~~ 593 (953)
..
T Consensus 83 ~~ 84 (195)
T cd08427 83 EL 84 (195)
T ss_pred CC
Confidence 54
No 291
>cd08469 PBP2_PnbR The C-terminal substrate binding domain of LysR-type transcriptional regulator PnbR, which is involved in regulating the pnb genes encoding enzymes for 4-nitrobenzoate catabolism, contains the type 2 periplasmic binding fold. PnbR is the regulator of one or both of the two pnb genes that encoding enzymes for 4-nitrobenzoate catabolism. In Pseudomonas putida strain, pnbA encodes a 4-nitrobenzoate reductase, which is responsible for catalyzing the direct reduction of 4-nitrobenzoate to 4-hydroxylaminobenzoate, and pnbB encodes a 4-hydroxylaminobenzoate lyase, which catalyzes the conversion of 4-hydroxylaminobenzoate to 3, 4-dihydroxybenzoic acid and ammonium. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft bet
Probab=88.33 E-value=16 Score=36.90 Aligned_cols=70 Identities=14% Similarity=0.136 Sum_probs=47.3
Q ss_pred EeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEecEEEecCccceeeccccceecceEEEEec
Q 002211 512 GYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGDIAIVTNRTKAVDFTQPYIESGLVVVAPV 591 (953)
Q Consensus 512 G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~~~~t~~r~~~vdft~p~~~~~~~~~v~~ 591 (953)
.+..+++..+.++.+ .+++.... .+..++.+.+.+|++|++++.. ......+. ..|.....++++++.
T Consensus 13 ~~l~~~l~~f~~~~P-~v~l~i~~-------~~~~~~~~~l~~g~~Di~i~~~---~~~~~~l~-~~~l~~~~~~~v~~~ 80 (221)
T cd08469 13 VLLPALVRRLETEAP-GIDLRIRP-------VTRLDLAEQLDLGRIDLVIGIF---EQIPPRFR-RRTLFDEDEVWVMRK 80 (221)
T ss_pred HHHHHHHHHHHHHCC-CcEEEEee-------CChhhHHHHHHCCCccEEEecC---CCCCccce-eeeeeccceEEEEeC
Confidence 345677888888765 24555554 4577899999999999998632 22223343 457778888888876
Q ss_pred cc
Q 002211 592 RK 593 (953)
Q Consensus 592 ~~ 593 (953)
..
T Consensus 81 ~~ 82 (221)
T cd08469 81 DH 82 (221)
T ss_pred CC
Confidence 55
No 292
>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=88.27 E-value=19 Score=35.20 Aligned_cols=70 Identities=10% Similarity=0.107 Sum_probs=46.7
Q ss_pred EeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEecEEEecCccceeeccccceecceEEEEec
Q 002211 512 GYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGDIAIVTNRTKAVDFTQPYIESGLVVVAPV 591 (953)
Q Consensus 512 G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~~~~t~~r~~~vdft~p~~~~~~~~~v~~ 591 (953)
.+..+++..+.++.+ .++++... +....+++.+.+|++|+++.... .....+. +.+.....++++++.
T Consensus 13 ~~l~~~l~~~~~~~P-~i~~~i~~-------~~~~~~~~~l~~g~~Dl~i~~~~---~~~~~~~-~~~l~~~~~~~~~~~ 80 (196)
T cd08456 13 SFLPRAIKAFLQRHP-DVTISIHT-------RDSPTVEQWLSAQQCDLGLVSTL---HEPPGIE-RERLLRIDGVCVLPP 80 (196)
T ss_pred hhHHHHHHHHHHHCC-CcEEEEEe-------CCHHHHHHHHHcCCccEEEEecC---CCCCCee-EEEeeccCeEEEecC
Confidence 456788888888874 35566654 45778899999999999885221 1112222 456667778777765
Q ss_pred cc
Q 002211 592 RK 593 (953)
Q Consensus 592 ~~ 593 (953)
..
T Consensus 81 ~~ 82 (196)
T cd08456 81 GH 82 (196)
T ss_pred CC
Confidence 54
No 293
>PRK12680 transcriptional regulator CysB-like protein; Reviewed
Probab=88.08 E-value=24 Score=38.63 Aligned_cols=84 Identities=17% Similarity=0.094 Sum_probs=56.5
Q ss_pred cceEEEecCcccccccEEeeCCcceEEEeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEecE
Q 002211 485 RQLRIGVPNRVSYRDFVFKVNGTDIVHGYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGDI 564 (953)
Q Consensus 485 ~~lri~v~~~~~~~p~~~~~~~~~~~~G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~~ 564 (953)
++||||+... . ...+..++++.+.++.+ .+.+.... +..+++++.|.+|++|+++...
T Consensus 93 g~lrIg~~~~--~------------~~~~l~~~l~~f~~~~P-~v~i~l~~-------~~~~~~~~~l~~g~~Dl~i~~~ 150 (327)
T PRK12680 93 GQLTLTTTHT--Q------------ARFVLPPAVAQIKQAYP-QVSVHLQQ-------AAESAALDLLGQGDADIAIVST 150 (327)
T ss_pred eEEEEEecch--h------------HHHhhHHHHHHHHHHCC-CcEEEEEe-------CChHHHHHHHHCCCCcEEEEec
Confidence 5799998751 1 12456678888888886 24555554 5578999999999999988532
Q ss_pred EEecCccceeeccccceecceEEEEeccc
Q 002211 565 AIVTNRTKAVDFTQPYIESGLVVVAPVRK 593 (953)
Q Consensus 565 ~~t~~r~~~vdft~p~~~~~~~~~v~~~~ 593 (953)
.. ....... ..|+....++++++...
T Consensus 151 ~~--~~~~~~~-~~~l~~~~~~l~~~~~h 176 (327)
T PRK12680 151 AG--GEPSAGI-AVPLYRWRRLVVVPRGH 176 (327)
T ss_pred CC--CCCCcce-EEEeeccceEEEEeCCC
Confidence 11 1111222 46788888888887655
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=88.02 E-value=27 Score=33.95 Aligned_cols=70 Identities=17% Similarity=0.237 Sum_probs=46.3
Q ss_pred EeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEecEEEecCccceeeccccceecceEEEEec
Q 002211 512 GYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGDIAIVTNRTKAVDFTQPYIESGLVVVAPV 591 (953)
Q Consensus 512 G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~~~~t~~r~~~vdft~p~~~~~~~~~v~~ 591 (953)
.+..+++..+.++.+ .+++.... ++..++...+.+|++|+++..... ....+. ..++....++++++.
T Consensus 13 ~~l~~~l~~~~~~~p-~i~i~i~~-------~~~~~~~~~l~~~~~Dl~i~~~~~---~~~~~~-~~~l~~~~~~~v~~~ 80 (197)
T cd08414 13 GLLPRLLRRFRARYP-DVELELRE-------MTTAEQLEALRAGRLDVGFVRPPP---DPPGLA-SRPLLREPLVVALPA 80 (197)
T ss_pred HHHHHHHHHHHHHCC-CcEEEEec-------CChHHHHHHHHcCCccEEEEcCCC---CCCCee-EEEEeeccEEEEecC
Confidence 345677788887764 24555543 457889999999999998863221 122222 466777888888876
Q ss_pred cc
Q 002211 592 RK 593 (953)
Q Consensus 592 ~~ 593 (953)
..
T Consensus 81 ~~ 82 (197)
T cd08414 81 DH 82 (197)
T ss_pred CC
Confidence 54
No 295
>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=88.01 E-value=5.3 Score=39.07 Aligned_cols=99 Identities=13% Similarity=-0.017 Sum_probs=65.7
Q ss_pred HHHHHHHHHHHHcCCcEEEEEEecCccccchHHHHHHHHHhc--CcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEE
Q 002211 168 YLMSAIAEMVSYFGWGEVIAIFNDDDQGRNGVTALGDKLAEI--RCKISYKSALPPDQSVTETDVRNELVKVRMMEARVI 245 (953)
Q Consensus 168 ~~~~ai~~~l~~~~w~~vaii~~d~~~g~~~~~~l~~~l~~~--g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vi 245 (953)
.....+.+.....+ .+|.++....+ ..+.+.+.+++. |+.|+....-+.+ ..+-...+++|++++||+|
T Consensus 33 dl~~~ll~~~~~~~-~~v~llG~~~~----~~~~~~~~l~~~yp~l~i~g~~~g~~~----~~~~~~i~~~I~~~~pdiv 103 (171)
T cd06533 33 DLMPALLELAAQKG-LRVFLLGAKPE----VLEKAAERLRARYPGLKIVGYHHGYFG----PEEEEEIIERINASGADIL 103 (171)
T ss_pred HHHHHHHHHHHHcC-CeEEEECCCHH----HHHHHHHHHHHHCCCcEEEEecCCCCC----hhhHHHHHHHHHHcCCCEE
Confidence 34555666665554 78888876654 344444555554 7777764333333 4444558999999999999
Q ss_pred EEEcchhhHHHHHHHHHHcCCCCCceEEEEeCc
Q 002211 246 VVHGYSRTGLMVFDVAQRLGMMDSGYVWIATTW 278 (953)
Q Consensus 246 i~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~ 278 (953)
++.+..+.-..++...++.. +.-+++..++
T Consensus 104 ~vglG~PkQE~~~~~~~~~l---~~~v~~~vG~ 133 (171)
T cd06533 104 FVGLGAPKQELWIARHKDRL---PVPVAIGVGG 133 (171)
T ss_pred EEECCCCHHHHHHHHHHHHC---CCCEEEEece
Confidence 99999888888888877754 2335666554
No 296
>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=87.89 E-value=22 Score=35.10 Aligned_cols=70 Identities=10% Similarity=0.096 Sum_probs=47.4
Q ss_pred EeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEecEEEecCccceeeccccceecceEEEEec
Q 002211 512 GYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGDIAIVTNRTKAVDFTQPYIESGLVVVAPV 591 (953)
Q Consensus 512 G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~~~~t~~r~~~vdft~p~~~~~~~~~v~~ 591 (953)
.+-.+++..+.++++ .++++... ++.+++++.|.+|++|+++... ......++ +.++....++++++.
T Consensus 14 ~~l~~~l~~f~~~~P-~v~i~i~~-------~~~~~l~~~l~~g~~D~~~~~~---~~~~~~~~-~~~l~~~~~~lv~~~ 81 (198)
T cd08486 14 RSLPLLLRAFLTSTP-TATVSLTH-------MTKDEQVEGLLAGTIHVGFSRF---FPRHPGIE-IVNIAQEDLYLAVHR 81 (198)
T ss_pred HHHHHHHHHHHHhCC-CeEEEEEE-------CCHHHHHHHHHcCCceEEEecC---CCCCCceE-EEEEeeccEEEEecC
Confidence 455678888888874 25565554 5688999999999999988522 11122232 456667788888875
Q ss_pred cc
Q 002211 592 RK 593 (953)
Q Consensus 592 ~~ 593 (953)
..
T Consensus 82 ~h 83 (198)
T cd08486 82 SQ 83 (198)
T ss_pred CC
Confidence 54
No 297
>COG1454 EutG Alcohol dehydrogenase, class IV [Energy production and conversion]
Probab=87.75 E-value=5.2 Score=44.17 Aligned_cols=92 Identities=12% Similarity=0.072 Sum_probs=74.7
Q ss_pred HHHHHHHHHcCCcEEEEEEecCccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcc
Q 002211 171 SAIAEMVSYFGWGEVIAIFNDDDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGY 250 (953)
Q Consensus 171 ~ai~~~l~~~~w~~vaii~~d~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~ 250 (953)
+.+.+.++.+|++++-+|.+..-...+..+.+.+.|++.|+.+.....+.++ .+.+.....+..+++.++|.||-.+.
T Consensus 18 ~~l~~~~~~~g~~r~liVTd~~~~~~g~~~~v~~~L~~~~i~~~if~~v~p~--P~~~~v~~~~~~~~~~~~D~iIalGG 95 (377)
T COG1454 18 KELGEEVKRLGAKRALIVTDRGLAKLGLLDKVLDSLDAAGIEYEVFDEVEPE--PTIETVEAGAEVAREFGPDTIIALGG 95 (377)
T ss_pred HHHHHHHHhcCCCceEEEECCccccchhHHHHHHHHHhcCCeEEEecCCCCC--CCHHHHHHHHHHHHhcCCCEEEEeCC
Confidence 5577778889999999999777777788999999999999887766667666 67888899999999999999998765
Q ss_pred h--hhHHHHHHHHHHc
Q 002211 251 S--RTGLMVFDVAQRL 264 (953)
Q Consensus 251 ~--~~~~~~~~~a~~~ 264 (953)
+ -|+.+.+......
T Consensus 96 GS~~D~AK~i~~~~~~ 111 (377)
T COG1454 96 GSVIDAAKAIALLAEN 111 (377)
T ss_pred ccHHHHHHHHHHHhhC
Confidence 4 5666666665553
No 298
>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=87.68 E-value=29 Score=33.94 Aligned_cols=72 Identities=11% Similarity=0.093 Sum_probs=47.9
Q ss_pred EeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEecEEEecCccceeeccccceecceEEEEec
Q 002211 512 GYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGDIAIVTNRTKAVDFTQPYIESGLVVVAPV 591 (953)
Q Consensus 512 G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~~~~t~~r~~~vdft~p~~~~~~~~~v~~ 591 (953)
.+..+++..+.++.+ .++++... .+...+++.|.+|++|+++.... .......++ ..++.+..++++++.
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 345678888888875 35566654 45789999999999999885221 111222333 456777788888776
Q ss_pred cc
Q 002211 592 RK 593 (953)
Q Consensus 592 ~~ 593 (953)
..
T Consensus 83 ~h 84 (198)
T cd08437 83 DH 84 (198)
T ss_pred CC
Confidence 54
No 299
>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=87.67 E-value=29 Score=33.80 Aligned_cols=70 Identities=11% Similarity=0.086 Sum_probs=47.2
Q ss_pred EeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEecEEEecCccceeeccccceecceEEEEec
Q 002211 512 GYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGDIAIVTNRTKAVDFTQPYIESGLVVVAPV 591 (953)
Q Consensus 512 G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~~~~t~~r~~~vdft~p~~~~~~~~~v~~ 591 (953)
.+..+++..+.++.+ .++++... ++..++...+.+|++|+++... ......+. +.++....++++++.
T Consensus 13 ~~l~~~l~~~~~~~P-~i~i~i~~-------~~~~~~~~~l~~~~~Di~i~~~---~~~~~~~~-~~~l~~~~~~~~~~~ 80 (197)
T cd08448 13 RGLPRILRAFRAEYP-GIEVALHE-------MSSAEQIEALLRGELDLGFVHS---RRLPAGLS-ARLLHREPFVCCLPA 80 (197)
T ss_pred HHHHHHHHHHHHHCC-CCeEEEEe-------CCHHHHHHHHHcCCcceEEEeC---CCCCcCce-EEEEecCcEEEEeeC
Confidence 456788888888874 24565554 5688999999999999987522 22222232 456777788877765
Q ss_pred cc
Q 002211 592 RK 593 (953)
Q Consensus 592 ~~ 593 (953)
..
T Consensus 81 ~h 82 (197)
T cd08448 81 GH 82 (197)
T ss_pred CC
Confidence 54
No 300
>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=87.63 E-value=15 Score=36.32 Aligned_cols=70 Identities=13% Similarity=0.178 Sum_probs=46.8
Q ss_pred EeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEecEEEecCccceeeccccceecceEEEEec
Q 002211 512 GYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGDIAIVTNRTKAVDFTQPYIESGLVVVAPV 591 (953)
Q Consensus 512 G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~~~~t~~r~~~vdft~p~~~~~~~~~v~~ 591 (953)
++-.+++..+.++.+ .++++... ++..++++.|.+|++|+++...... ...++ +.+..+..++++++.
T Consensus 13 ~~l~~~l~~f~~~~P-~i~l~i~~-------~~~~~~~~~L~~g~~Dl~i~~~~~~---~~~~~-~~~l~~~~~~lv~~~ 80 (200)
T cd08465 13 LVLPALMRQLRAEAP-GIDLAVSQ-------ASREAMLAQVADGEIDLALGVFPEL---PEELH-AETLFEERFVCLADR 80 (200)
T ss_pred HhhhHHHHHHHHHCC-CcEEEEec-------CChHhHHHHHHCCCccEEEeccccC---CcCee-EEEeeeccEEEEEeC
Confidence 556678888877764 25555553 5688999999999999988632211 12233 246667788888876
Q ss_pred cc
Q 002211 592 RK 593 (953)
Q Consensus 592 ~~ 593 (953)
..
T Consensus 81 ~h 82 (200)
T cd08465 81 AT 82 (200)
T ss_pred CC
Confidence 54
No 301
>cd08445 PBP2_BenM_CatM_CatR The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in benzoate catabolism; contains the type 2 periplasmic binding fold. This CD includes the C-terminal of LysR-type transcription regulators, BenM, CatM, and CatR, which are involved in the benzoate catabolism. The BenM and CatM are paralogs with overlapping functions. BenM responds synergistically to two effectors, benzoate and cis,cis-muconate, to activate expression of the benABCDE operon which is involved in benzoate catabolism, while CatM responses only to muconate. BenM and CatM share high protein sequence identity and bind to the operator-promoter regions that have similar DNA sequences. In Pseudomonas species, phenolic compounds are converted by different enzymes to central intermediates, such as protocatechuate and catechols. Generally, unsubstituted compounds, such as benzoate, are metabolized by an ortho-cleavage pathway. The catBCA operon encodes three enzymes
Probab=87.34 E-value=27 Score=34.43 Aligned_cols=70 Identities=23% Similarity=0.299 Sum_probs=47.1
Q ss_pred EeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEecEEEecCccceeeccccceecceEEEEec
Q 002211 512 GYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGDIAIVTNRTKAVDFTQPYIESGLVVVAPV 591 (953)
Q Consensus 512 G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~~~~t~~r~~~vdft~p~~~~~~~~~v~~ 591 (953)
.+..+++..+.++.+ .++++... ++..+++..+.+|++|++++.... ....+. +.++....++++++.
T Consensus 14 ~~l~~~l~~~~~~~P-~i~l~i~~-------~~~~~~~~~l~~~~~Dl~i~~~~~---~~~~~~-~~~l~~~~~~~v~~~ 81 (203)
T cd08445 14 GLLPELIRRFRQAAP-DVEIELIE-------MTTVQQIEALKEGRIDVGFGRLRI---EDPAIR-RIVLREEPLVVALPA 81 (203)
T ss_pred hHHHHHHHHHHHHCC-CeEEEEEe-------CChHHHHHHHHcCCCcEEEecCCC---CCCCce-eEEEEeccEEEEeeC
Confidence 566778888888775 24555553 457899999999999998853211 112232 456777788888876
Q ss_pred cc
Q 002211 592 RK 593 (953)
Q Consensus 592 ~~ 593 (953)
..
T Consensus 82 ~h 83 (203)
T cd08445 82 GH 83 (203)
T ss_pred CC
Confidence 54
No 302
>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=87.33 E-value=1.1 Score=48.30 Aligned_cols=113 Identities=14% Similarity=0.167 Sum_probs=66.8
Q ss_pred cccceeeeeeeccccCCCCChHHhhhCCCeEEEEeCchHHHHHHHhhCCCccceEeCCCHHHHHHHHHcCCcEEEEccch
Q 002211 685 YTASLTSILTVQQLSSPIKGIDTLMTSNDRVGYQVGSFAENYLIEELSIPKSRLVALGSPEEYAIALENRTVAAVVDERP 764 (953)
Q Consensus 685 Yta~L~s~Lt~~~~~~~I~sl~dL~~~~~~ig~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~g~~~a~~~~~~ 764 (953)
|......+.+. ..+|++++||. |.++.+..+.....++ +.++. .-+.. ...|...+|++|.+|+......
T Consensus 114 ~~~g~~~~~~~---~~pi~s~~Dlk--G~kiR~~~~~~~~~~~-~~lGa---~pv~i-p~~evy~aLq~G~vDg~~~~~~ 183 (286)
T PF03480_consen 114 FPGGPRQFFST---KKPIRSPEDLK--GLKIRVPGSPVMSDFF-EALGA---SPVPI-PWSEVYQALQQGVVDGAENSAS 183 (286)
T ss_dssp EEEEEEEEEES---SS--SSGGGGT--TEEEEETSSHHHHHHH-HHCTS---EEEE--TGGGHHHHHHTTSSSEEEEEHH
T ss_pred ecCCceEEEec---ccCCccHhhHh--hCeEEecCCHHHHHHH-HHcCC---eeecC-cHHHHHHHHhcCCcCeEecCHH
Confidence 44444444442 26899999996 9999988666667777 45553 23333 5668999999999999998766
Q ss_pred hHHHH-HhcCcceEEeCCccccCccEEEecCCCc--chHHHHHHHHh
Q 002211 765 YIDLF-LSDHCQFSVRGQEFTKSGWGFAFPRDSP--LAIDMSTAILT 808 (953)
Q Consensus 765 ~~~~~-~~~~~~l~~~~~~~~~~~~~~~~~k~sp--l~~~~n~~i~~ 808 (953)
..... +.+.+++..... +...++.+++.++.- |-+....+|.+
T Consensus 184 ~~~~~~~~ev~~y~~~~~-~~~~~~~~~~n~~~w~~L~~e~q~~l~~ 229 (286)
T PF03480_consen 184 SIYSLGLYEVAKYFTDTN-HGWSPYAVIMNKDWWDSLPDEDQEALDD 229 (286)
T ss_dssp HHHHTTGGGTSSEEEEEE-EEEEEEEEEEEHHHHHHS-HHHHHHHHH
T ss_pred HHHhcChhhhCCeeEeec-ccCcceEEEEcHHHHhcCCHHHHHHHHH
Confidence 55222 122355444433 344566777766532 44444444433
No 303
>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=87.23 E-value=30 Score=33.55 Aligned_cols=71 Identities=15% Similarity=0.187 Sum_probs=46.5
Q ss_pred EeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEecEEEecCccceeeccccceecceEEEEec
Q 002211 512 GYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGDIAIVTNRTKAVDFTQPYIESGLVVVAPV 591 (953)
Q Consensus 512 G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~~~~t~~r~~~vdft~p~~~~~~~~~v~~ 591 (953)
.+..+++..+.++.+ .+.++... ++..++.+.+.+|++|+++..... .....+. ..+.....++++++.
T Consensus 13 ~~l~~~l~~~~~~~P-~v~i~i~~-------~~~~~~~~~l~~~~~Dl~i~~~~~--~~~~~~~-~~~l~~~~~~~~~~~ 81 (194)
T cd08436 13 VDLPELLARFHRRHP-GVDIRLRQ-------AGSDDLLAAVREGRLDLAFVGLPE--RRPPGLA-SRELAREPLVAVVAP 81 (194)
T ss_pred HHHHHHHHHHHHHCC-CcEEEEec-------CCHHHHHHHHHcCCccEEEEecCC--CCCCCcE-EEEeecceEEEEecC
Confidence 456778888888774 34555553 457789999999999999863222 1222232 356667777777765
Q ss_pred cc
Q 002211 592 RK 593 (953)
Q Consensus 592 ~~ 593 (953)
..
T Consensus 82 ~~ 83 (194)
T cd08436 82 DH 83 (194)
T ss_pred CC
Confidence 54
No 304
>PRK10341 DNA-binding transcriptional activator TdcA; Provisional
Probab=87.12 E-value=22 Score=38.68 Aligned_cols=85 Identities=19% Similarity=0.342 Sum_probs=55.5
Q ss_pred cceEEEecCcccccccEEeeCCcceEEEeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEecE
Q 002211 485 RQLRIGVPNRVSYRDFVFKVNGTDIVHGYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGDI 564 (953)
Q Consensus 485 ~~lri~v~~~~~~~p~~~~~~~~~~~~G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~~ 564 (953)
.+++||++. ... ..+-.+++..+.+..+ .+++.... ++..+++..|.+|++|+++...
T Consensus 97 ~~l~ig~~~--~~~------------~~~l~~~l~~~~~~~p-~v~i~~~~-------~~~~~~~~~l~~g~~Dl~i~~~ 154 (312)
T PRK10341 97 VDVSFGFPS--LIG------------FTFMSDMINKFKEVFP-KAQVSMYE-------AQLSSFLPAIRDGRLDFAIGTL 154 (312)
T ss_pred eEEEEEech--HHh------------HhhHHHHHHHHHHhCC-CCEEEEEe-------CCHHHHHHHHHcCCCcEEEecC
Confidence 468888864 111 1344578888888765 25566654 5578999999999999998532
Q ss_pred EEecCccceeeccccceecceEEEEeccc
Q 002211 565 AIVTNRTKAVDFTQPYIESGLVVVAPVRK 593 (953)
Q Consensus 565 ~~t~~r~~~vdft~p~~~~~~~~~v~~~~ 593 (953)
... .....+ ...|+.+..++++++...
T Consensus 155 ~~~-~~~~~l-~~~~l~~~~~~lv~~~~~ 181 (312)
T PRK10341 155 SNE-MKLQDL-HVEPLFESEFVLVASKSR 181 (312)
T ss_pred Ccc-cccCCe-eEEEEecccEEEEEcCCC
Confidence 111 111222 356778888888887654
No 305
>PRK15454 ethanol dehydrogenase EutG; Provisional
Probab=87.07 E-value=2.7 Score=47.34 Aligned_cols=88 Identities=11% Similarity=0.048 Sum_probs=65.4
Q ss_pred HHHHHHHHHcCCcEEEEEEecCccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcc
Q 002211 171 SAIAEMVSYFGWGEVIAIFNDDDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGY 250 (953)
Q Consensus 171 ~ai~~~l~~~~w~~vaii~~d~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~ 250 (953)
+.+.+.++.+|.+++.++....-...+..+.+.+.|++.|+.+.....+.++ .+.+++...++..++.++|+||-.+.
T Consensus 38 ~~l~~~~~~~g~~~~lvv~~~~~~~~g~~~~v~~~L~~~gi~~~~~~~v~~~--P~~~~v~~~~~~~r~~~~D~IiavGG 115 (395)
T PRK15454 38 SSCGQQAQTRGLKHLFVMADSFLHQAGMTAGLTRSLAVKGIAMTLWPCPVGE--PCITDVCAAVAQLRESGCDGVIAFGG 115 (395)
T ss_pred HHHHHHHHhcCCCEEEEEcCcchhhCccHHHHHHHHHHcCCeEEEECCCCCC--cCHHHHHHHHHHHHhcCcCEEEEeCC
Confidence 5577788889988888776544444567888999999999887654445544 55778889999999999999999876
Q ss_pred h--hhHHHHHHH
Q 002211 251 S--RTGLMVFDV 260 (953)
Q Consensus 251 ~--~~~~~~~~~ 260 (953)
+ -|+.+.+..
T Consensus 116 GS~iD~AKaia~ 127 (395)
T PRK15454 116 GSVLDAAKAVAL 127 (395)
T ss_pred hHHHHHHHHHHH
Confidence 5 345544443
No 306
>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=86.73 E-value=5.4 Score=44.68 Aligned_cols=91 Identities=14% Similarity=0.130 Sum_probs=67.4
Q ss_pred HHHHHHHHHcCCcEEEEEEecCccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcc
Q 002211 171 SAIAEMVSYFGWGEVIAIFNDDDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGY 250 (953)
Q Consensus 171 ~ai~~~l~~~~w~~vaii~~d~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~ 250 (953)
+.+.+.++.+|-+++.+++....+..+..+.+.+.|++.|+.+.....+.++ .+.+++...+..+++.++|+||-.+.
T Consensus 15 ~~l~~~l~~~g~~~~lvvt~~~~~~~g~~~~v~~~L~~~g~~~~~~~~v~~~--p~~~~v~~~~~~~~~~~~d~IIaiGG 92 (374)
T cd08189 15 AQLPAAISQLGVKKVLIVTDKGLVKLGLLDKVLEALEGAGIEYAVYDGVPPD--PTIENVEAGLALYRENGCDAILAVGG 92 (374)
T ss_pred HHHHHHHHhcCCCeEEEEeCcchhhcccHHHHHHHHHhcCCeEEEeCCCCCC--cCHHHHHHHHHHHHhcCCCEEEEeCC
Confidence 4577788889989999998655444456788999999999877654455554 56788899999999999999997655
Q ss_pred h--hhHHHHHHHHHH
Q 002211 251 S--RTGLMVFDVAQR 263 (953)
Q Consensus 251 ~--~~~~~~~~~a~~ 263 (953)
+ -|+.+++.....
T Consensus 93 GS~~D~aK~ia~~~~ 107 (374)
T cd08189 93 GSVIDCAKAIAARAA 107 (374)
T ss_pred ccHHHHHHHHHHHHh
Confidence 4 566666554433
No 307
>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=86.67 E-value=5.5 Score=44.58 Aligned_cols=90 Identities=12% Similarity=0.091 Sum_probs=67.0
Q ss_pred HHHHHHHHHcCCcEEEEEEecCccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcc
Q 002211 171 SAIAEMVSYFGWGEVIAIFNDDDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGY 250 (953)
Q Consensus 171 ~ai~~~l~~~~w~~vaii~~d~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~ 250 (953)
..+.++++.+|.+++.+++....+..+..+.+.+.|++.|+++.....+.++ .+.+++...+...++.++|+||-.+.
T Consensus 13 ~~l~~~l~~~g~~~~liv~~~~~~~~~~~~~v~~~L~~~g~~~~~~~~v~~~--p~~~~v~~~~~~~~~~~~d~IIaiGG 90 (370)
T cd08192 13 KELPAECAELGIKRPLIVTDPGLAALGLVARVLALLEDAGLAAALFDEVPPN--PTEAAVEAGLAAYRAGGCDGVIAFGG 90 (370)
T ss_pred HHHHHHHHHcCCCeEEEEcCcchhhCccHHHHHHHHHHcCCeEEEeCCCCCC--CCHHHHHHHHHHHHhcCCCEEEEeCC
Confidence 4577788889999999988655544456788999999999887544445544 56778889999999999999997655
Q ss_pred h--hhHHHHHHHHH
Q 002211 251 S--RTGLMVFDVAQ 262 (953)
Q Consensus 251 ~--~~~~~~~~~a~ 262 (953)
+ -|+.+++....
T Consensus 91 GSviD~aK~ia~~~ 104 (370)
T cd08192 91 GSALDLAKAVALMA 104 (370)
T ss_pred chHHHHHHHHHHHH
Confidence 4 56666655543
No 308
>cd08451 PBP2_BudR The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is responsible for activation of the expression of the butanediol operon genes; contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of BudR regulator, which is responsible for induction of the butanediol formation pathway under fermentative growth conditions. Three enzymes are involved in the production of 1 mol of 2,3 butanediol from the condensation of 2 mol of pyruvate with acetolactate and acetoin as intermediates: acetolactate synthetase, acetolactate decarboxylase, and acetoin reductase. In Klebsiella terrigena, BudR regulates the expression of the budABC operon genes, encoding these three enzymes of the butanediol pathway. In many bacterial species, the use of this pathway can prevent intracellular acidification by diverting metabolism from acid production to the formation of neutral compounds (acetoin and butanediol). This substra
Probab=86.51 E-value=34 Score=33.40 Aligned_cols=70 Identities=17% Similarity=0.264 Sum_probs=47.0
Q ss_pred eeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEecEEEecCccceeeccccceecceEEEEecc
Q 002211 513 YCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGDIAIVTNRTKAVDFTQPYIESGLVVVAPVR 592 (953)
Q Consensus 513 ~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~~~~t~~r~~~vdft~p~~~~~~~~~v~~~ 592 (953)
+..++++.+.++.+ .++++... ++.+++...+.+|++|+++...... ....+ .+.+.....++++++..
T Consensus 15 ~l~~~l~~~~~~~P-~i~l~i~~-------~~~~~~~~~l~~g~~Dl~i~~~~~~--~~~~~-~~~~l~~~~~~~v~~~~ 83 (199)
T cd08451 15 LVPGLIRRFREAYP-DVELTLEE-------ANTAELLEALREGRLDAAFVRPPVA--RSDGL-VLELLLEEPMLVALPAG 83 (199)
T ss_pred ccHHHHHHHHHHCC-CcEEEEec-------CChHHHHHHHHCCCccEEEEecCCC--CCCce-eEEEeecccEEEEecCC
Confidence 56778889988875 24555553 4578899999999999998532211 11222 34667778888887655
Q ss_pred c
Q 002211 593 K 593 (953)
Q Consensus 593 ~ 593 (953)
.
T Consensus 84 ~ 84 (199)
T cd08451 84 H 84 (199)
T ss_pred C
Confidence 4
No 309
>cd08457 PBP2_OccR The C-terminal substrate-domain of LysR-type transcriptional regulator, OccR, involved in the catabolism of octopine, contains the type 2 periplasmic binding fold. This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulator OccR, which is involved in the catabolism of octopine. Opines are low molecular weight compounds found in plant crown gall tumors produced by the parasitic bacterium Agrobacterium. There are at least 30 different opines identified so far. Opines are utilized by tumor-colonizing bacteria as a source of carbon, nitrogen, and energy. In Agrobacterium tumefaciens, OccR protein activates the occQ operon of the Ti plasmid in response to octopine. This operon encodes proteins required for the uptake and catabolism of octopine, an arginine derivative. The occ operon also encodes the TraR protein, which is a quorum-sensing transcriptional regulator of the Ti plasmid tra regulon. This substrate-binding domain shows significant h
Probab=85.93 E-value=36 Score=33.24 Aligned_cols=71 Identities=17% Similarity=0.218 Sum_probs=45.8
Q ss_pred EEeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEecEEEecCccceeeccccceecceEEEEe
Q 002211 511 HGYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGDIAIVTNRTKAVDFTQPYIESGLVVVAP 590 (953)
Q Consensus 511 ~G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~~~~t~~r~~~vdft~p~~~~~~~~~v~ 590 (953)
..+..+++..+.++.+ .+++.... +.-.++...+.+|++|+++.... .....+. ..++.+..++++++
T Consensus 12 ~~~l~~~l~~~~~~~P-~i~l~~~~-------~~~~~~~~~l~~~~~Dl~i~~~~---~~~~~~~-~~~l~~~~~~~~~~ 79 (196)
T cd08457 12 NGFLPRFLAAFLRLRP-NLHLSLMG-------LSSSQVLEAVASGRADLGIADGP---LEERQGF-LIETRSLPAVVAVP 79 (196)
T ss_pred ccccHHHHHHHHHHCC-CeEEEEEe-------cCcHHHHHHHHcCCccEEEeccC---CCCCCcE-EEEeccCCeEEEee
Confidence 3456788889988875 24555553 33568889999999999886322 1122222 34566777777776
Q ss_pred ccc
Q 002211 591 VRK 593 (953)
Q Consensus 591 ~~~ 593 (953)
...
T Consensus 80 ~~~ 82 (196)
T cd08457 80 MGH 82 (196)
T ss_pred CCC
Confidence 543
No 310
>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=85.84 E-value=3.6 Score=46.74 Aligned_cols=89 Identities=9% Similarity=0.056 Sum_probs=66.7
Q ss_pred HHHHHHHHHHcCCcEEEEEEecCccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEc
Q 002211 170 MSAIAEMVSYFGWGEVIAIFNDDDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHG 249 (953)
Q Consensus 170 ~~ai~~~l~~~~w~~vaii~~d~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~ 249 (953)
.+.+.++++.+|.+++.+++....+..+..+.+.+.|++.|+++.....+.++ .+.+.+...++.+++.++|+||-.+
T Consensus 11 ~~~l~~~l~~~g~~~vlivt~~~~~~~g~~~~v~~~L~~~gi~~~~f~~v~~~--p~~~~v~~~~~~~~~~~~D~IIaiG 88 (414)
T cd08190 11 TAEVGMDLKNLGARRVCLVTDPNLAQLPPVKVVLDSLEAAGINFEVYDDVRVE--PTDESFKDAIAFAKKGQFDAFVAVG 88 (414)
T ss_pred HHHHHHHHHHcCCCeEEEEECcchhhcchHHHHHHHHHHcCCcEEEeCCCCCC--cCHHHHHHHHHHHHhcCCCEEEEeC
Confidence 35567788899999999998766555556788999999999887654444444 5577888889999999999999876
Q ss_pred ch--hhHHHHHHH
Q 002211 250 YS--RTGLMVFDV 260 (953)
Q Consensus 250 ~~--~~~~~~~~~ 260 (953)
.+ -|+.+.+..
T Consensus 89 GGSviD~AKaia~ 101 (414)
T cd08190 89 GGSVIDTAKAANL 101 (414)
T ss_pred CccHHHHHHHHHH
Confidence 65 455555443
No 311
>PRK10624 L-1,2-propanediol oxidoreductase; Provisional
Probab=85.55 E-value=3.9 Score=45.97 Aligned_cols=88 Identities=13% Similarity=0.131 Sum_probs=65.1
Q ss_pred HHHHHHHHHHcCCcEEEEEEecCccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEc
Q 002211 170 MSAIAEMVSYFGWGEVIAIFNDDDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHG 249 (953)
Q Consensus 170 ~~ai~~~l~~~~w~~vaii~~d~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~ 249 (953)
...+.+.++.+|.+++.+++....+-.+..+.+.+.+++.|+++.....+.++ .+.+++...+..+++.++|+||-.+
T Consensus 18 l~~l~~~~~~~g~~~~lvvtd~~~~~~g~~~~v~~~L~~~g~~~~~~~~v~~~--p~~~~v~~~~~~~~~~~~D~IIaiG 95 (382)
T PRK10624 18 IGALTDEVKRRGFKKALIVTDKTLVKCGVVAKVTDVLDAAGLAYEIYDGVKPN--PTIEVVKEGVEVFKASGADYLIAIG 95 (382)
T ss_pred HHHHHHHHHhcCCCEEEEEeCcchhhCcchHHHHHHHHHCCCeEEEeCCCCCC--cCHHHHHHHHHHHHhcCCCEEEEeC
Confidence 35577888889999999988655544457888999999999876544444444 4577888888999999999999776
Q ss_pred ch--hhHHHHHH
Q 002211 250 YS--RTGLMVFD 259 (953)
Q Consensus 250 ~~--~~~~~~~~ 259 (953)
.+ -|+.+.+.
T Consensus 96 GGS~iD~aK~ia 107 (382)
T PRK10624 96 GGSPQDTCKAIG 107 (382)
T ss_pred ChHHHHHHHHHH
Confidence 54 45555444
No 312
>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=85.48 E-value=6.7 Score=44.00 Aligned_cols=89 Identities=13% Similarity=0.117 Sum_probs=66.4
Q ss_pred HHHHHHHHHcCCcEEEEEEecCccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcc
Q 002211 171 SAIAEMVSYFGWGEVIAIFNDDDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGY 250 (953)
Q Consensus 171 ~ai~~~l~~~~w~~vaii~~d~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~ 250 (953)
..+.++++.+|.+++.+++.......+..+.+.+.+++.|+++.....+.++ .+.+++...++.+++.++|+||-.+.
T Consensus 15 ~~l~~~l~~~~~~~~livt~~~~~~~~~~~~v~~~L~~~~~~~~~~~~v~~~--p~~~~v~~~~~~~~~~~~D~IIaiGG 92 (376)
T cd08193 15 ARLGELLAALGAKRVLVVTDPGILKAGLIDPLLASLEAAGIEVTVFDDVEAD--PPEAVVEAAVEAARAAGADGVIGFGG 92 (376)
T ss_pred HHHHHHHHHcCCCeEEEEcCcchhhCccHHHHHHHHHHcCCeEEEECCCCCC--cCHHHHHHHHHHHHhcCCCEEEEeCC
Confidence 4567778888999999888655444556788999999999877544444444 56788999999999999999998866
Q ss_pred h--hhHHHHHHHH
Q 002211 251 S--RTGLMVFDVA 261 (953)
Q Consensus 251 ~--~~~~~~~~~a 261 (953)
+ -|+.+++...
T Consensus 93 Gs~iD~aK~ia~~ 105 (376)
T cd08193 93 GSSMDVAKLVAVL 105 (376)
T ss_pred chHHHHHHHHHHH
Confidence 5 4555555443
No 313
>cd08551 Fe-ADH iron-containing alcohol dehydrogenases (Fe-ADH)-like. Large metal-containing alcohol dehydrogenases (ADH), known as iron-containing alcohol dehydrogenases. They contain a dehydroquinate synthase-like protein structural fold and mostly contain iron. They are distinct from other alcohol dehydrogenases which contains different protein domains. There are several distinct families of alcohol dehydrogenases: Zinc-containing long-chain alcohol dehydrogenases; insect-type, or short-chain alcohol dehydrogenases; iron-containing alcohol dehydrogenases, and others. The iron-containing family has a Rossmann fold-like topology that resembles the fold of the zinc-dependent alcohol dehydrogenases, but lacks sequence homology, and differs in strand arrangement. ADH catalyzes the reversible oxidation of alcohol to acetaldehyde with the simultaneous reduction of NAD(P)+ to NAD(P)H.
Probab=85.40 E-value=6.8 Score=43.88 Aligned_cols=90 Identities=11% Similarity=0.112 Sum_probs=67.0
Q ss_pred HHHHHHHHHcCCcEEEEEEecCccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcc
Q 002211 171 SAIAEMVSYFGWGEVIAIFNDDDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGY 250 (953)
Q Consensus 171 ~ai~~~l~~~~w~~vaii~~d~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~ 250 (953)
+.+.++++.++.+++.+++....+.....+.+.+.|++.|+++.....+... .+.+++...+..++..++|+||..+.
T Consensus 12 ~~l~~~l~~~~~~~~lvv~~~~~~~~~~~~~v~~~L~~~~~~~~~~~~~~~~--p~~~~v~~~~~~~~~~~~d~IiaiGG 89 (370)
T cd08551 12 EKLGEEIKNLGGRKALIVTDPGLVKTGVLDKVIDSLKEAGIEVVIFDGVEPN--PTLSNVDAAVAAYREEGCDGVIAVGG 89 (370)
T ss_pred HHHHHHHHHcCCCeEEEEeCcchhhCccHHHHHHHHHHcCCeEEEECCCCCC--CCHHHHHHHHHHHHhcCCCEEEEeCC
Confidence 5677778888999999998655444467788999999988876544445444 56788999999999999999998765
Q ss_pred h--hhHHHHHHHHH
Q 002211 251 S--RTGLMVFDVAQ 262 (953)
Q Consensus 251 ~--~~~~~~~~~a~ 262 (953)
+ -|+.+++....
T Consensus 90 Gs~~D~AK~va~~~ 103 (370)
T cd08551 90 GSVLDTAKAIALLA 103 (370)
T ss_pred chHHHHHHHHHHHH
Confidence 4 45666655443
No 314
>PRK11074 putative DNA-binding transcriptional regulator; Provisional
Probab=85.39 E-value=24 Score=38.08 Aligned_cols=85 Identities=14% Similarity=0.085 Sum_probs=53.7
Q ss_pred cceEEEecCcccccccEEeeCCcceEEEeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEecE
Q 002211 485 RQLRIGVPNRVSYRDFVFKVNGTDIVHGYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGDI 564 (953)
Q Consensus 485 ~~lri~v~~~~~~~p~~~~~~~~~~~~G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~~ 564 (953)
++++||+.. .+ ...+..+++..+.++.+- +++.... ++..++++.|.+|++|++++..
T Consensus 92 g~l~Ig~~~--~~------------~~~~l~~~l~~~~~~~p~-i~i~i~~-------~~~~~~~~~l~~g~~Dl~i~~~ 149 (300)
T PRK11074 92 GQLSIAVDN--IV------------RPDRTRQLIVDFYRHFDD-VELIIRQ-------EVFNGVWDALADGRVDIAIGAT 149 (300)
T ss_pred ceEEEEEcC--cc------------chhHHHHHHHHHHHhCCC-ceEEEEe-------hhhhHHHHHHHCCCCCEEEecC
Confidence 679999874 11 123456778888877762 4455543 4567899999999999998632
Q ss_pred EEecCccceeeccccceecceEEEEeccc
Q 002211 565 AIVTNRTKAVDFTQPYIESGLVVVAPVRK 593 (953)
Q Consensus 565 ~~t~~r~~~vdft~p~~~~~~~~~v~~~~ 593 (953)
.. ......+ -..++....+++++++..
T Consensus 150 ~~-~~~~~~l-~~~~l~~~~~~~v~~~~h 176 (300)
T PRK11074 150 RA-IPVGGRF-AFRDMGMLSWACVVSSDH 176 (300)
T ss_pred cc-CCccccc-ceeecccceEEEEEcCCC
Confidence 11 1111112 245567777888887655
No 315
>PRK15421 DNA-binding transcriptional regulator MetR; Provisional
Probab=84.76 E-value=33 Score=37.40 Aligned_cols=83 Identities=12% Similarity=0.113 Sum_probs=53.2
Q ss_pred cceEEEecCcccccccEEeeCCcceEEEeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEecE
Q 002211 485 RQLRIGVPNRVSYRDFVFKVNGTDIVHGYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGDI 564 (953)
Q Consensus 485 ~~lri~v~~~~~~~p~~~~~~~~~~~~G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~~ 564 (953)
++|+||+.. ... ..+-.+++..+.++.+ .+.++... ..-.++...|.+|++|+++..-
T Consensus 89 g~l~Ig~~~--~~~------------~~~l~~~l~~~~~~~P-~i~l~~~~-------~~~~~~~~~L~~g~~Dl~i~~~ 146 (317)
T PRK15421 89 TRLRIAIEC--HSC------------IQWLTPALENFHKNWP-QVEMDFKS-------GVTFDPQPALQQGELDLVMTSD 146 (317)
T ss_pred eeEEEEecc--cch------------HHHHHHHHHHHHHHCC-CceEEEEe-------CccHHHHHHHHCCCcCEEEecC
Confidence 468998863 111 1244667788877764 34555543 3456889999999999998632
Q ss_pred EEecCccceeeccccceecceEEEEeccc
Q 002211 565 AIVTNRTKAVDFTQPYIESGLVVVAPVRK 593 (953)
Q Consensus 565 ~~t~~r~~~vdft~p~~~~~~~~~v~~~~ 593 (953)
......+. ..++....++++++...
T Consensus 147 ---~~~~~~~~-~~~l~~~~~~lv~~~~h 171 (317)
T PRK15421 147 ---ILPRSGLH-YSPMFDYEVRLVLAPDH 171 (317)
T ss_pred ---cccCCCce-EEEeccceEEEEEcCCC
Confidence 22222343 36777788888887665
No 316
>PRK10200 putative racemase; Provisional
Probab=84.71 E-value=12 Score=38.61 Aligned_cols=88 Identities=11% Similarity=-0.004 Sum_probs=57.6
Q ss_pred CChHHHHHHHHHHHhc-CcEEEEccCChhhHHHHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHH
Q 002211 98 FNGFLSIMGALQFMET-DTLAIVGPQSAVMAHVLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEM 176 (953)
Q Consensus 98 ~~~~~a~~~a~~li~~-~v~aiiGp~~S~~a~av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~ 176 (953)
-+|........+.+.+ |+.+|+=|..+..+. .-.+-+..++|+|+- .++..+.
T Consensus 58 ~~~~~~l~~~~~~L~~~g~~~iviaCNTah~~-~~~l~~~~~iPii~i-------------------------i~~~~~~ 111 (230)
T PRK10200 58 DKTGDILAEAALGLQRAGAEGIVLCTNTMHKV-ADAIESRCSLPFLHI-------------------------ADATGRA 111 (230)
T ss_pred chHHHHHHHHHHHHHHcCCCEEEECCchHHHH-HHHHHHhCCCCEeeh-------------------------HHHHHHH
Confidence 3577666665555544 899998887776665 456777778998862 2344445
Q ss_pred HHHcCCcEEEEEEecCccccchHHHHHHHHHhc-CcEEE
Q 002211 177 VSYFGWGEVIAIFNDDDQGRNGVTALGDKLAEI-RCKIS 214 (953)
Q Consensus 177 l~~~~w~~vaii~~d~~~g~~~~~~l~~~l~~~-g~~v~ 214 (953)
++..+-++|+++..... -....+++.+++. |+++.
T Consensus 112 ~~~~~~~~VglLaT~~T---i~s~~Y~~~l~~~~g~~~~ 147 (230)
T PRK10200 112 ITGAGMTRVALLGTRYT---MEQDFYRGRLTEQFSINCL 147 (230)
T ss_pred HHHcCCCeEEEeccHHH---HHHhHHHHHHHHhcCCeEe
Confidence 55567889999986543 2344566666655 87764
No 317
>PRK09861 cytoplasmic membrane lipoprotein-28; Provisional
Probab=84.40 E-value=24 Score=37.40 Aligned_cols=120 Identities=9% Similarity=0.072 Sum_probs=65.0
Q ss_pred CCCCChHHhhhCCCeEEEEe--CchHHHHH-HHhh---------CC-----------CccceEeCCCHHHHHHHHHcCCc
Q 002211 700 SPIKGIDTLMTSNDRVGYQV--GSFAENYL-IEEL---------SI-----------PKSRLVALGSPEEYAIALENRTV 756 (953)
Q Consensus 700 ~~I~sl~dL~~~~~~ig~~~--~s~~~~~l-~~~~---------~~-----------~~~~~~~~~~~~~~~~~l~~g~~ 756 (953)
..|++++||. .|.+|++.+ +...+.++ .+.. +. ...+++.. ...+...++.+|++
T Consensus 120 ~~iksl~DL~-~Ga~IAipnd~~n~~ral~lL~~agli~l~~~~g~~~t~~di~~np~~l~~ve~-~~~q~~~al~dg~v 197 (272)
T PRK09861 120 KKIKTVAQIK-EGATVAIPNDPTNLGRALLLLQKEKLITLKEGKGLLPTALDITDNPRHLQIMEL-EGAQLPRVLDDPKV 197 (272)
T ss_pred cCCCCHHHcC-CCCEEEEeCCCccHHHHHHHHHHCCCEEEcCCCCCCCCHhHHhcCCCCCEEEEc-CHHHhHhhccCccc
Confidence 6799999995 688999986 33233222 1221 11 11223332 66678888888999
Q ss_pred EEEEccchhHHHHHhcCc--ceEEeCCccccCccEEEecCCCcchHHHHHHHHhhhccccHHHHHHHh
Q 002211 757 AAVVDERPYIDLFLSDHC--QFSVRGQEFTKSGWGFAFPRDSPLAIDMSTAILTLSENGELQRIHDKW 822 (953)
Q Consensus 757 ~a~~~~~~~~~~~~~~~~--~l~~~~~~~~~~~~~~~~~k~spl~~~~n~~i~~l~e~G~~~~~~~~w 822 (953)
|+++...+++.-- .-.+ +-......-.++--.++++.+..=.+.+.+.+..++....-+.|.++|
T Consensus 198 D~a~i~~~~~~~a-g~~~~~~~l~~e~~~~~~~n~~~~r~~~~~~~~~~~lv~~~~s~~v~~~i~~~~ 264 (272)
T PRK09861 198 DVAIISTTYIQQT-GLSPVHDSVFIEDKNSPYVNILVAREDNKNAENVKEFLQSYQSPEVAKAAETIF 264 (272)
T ss_pred CEEEEchhHHHHc-CCCcccceeEEcCCCCCeEEEEEEcCCccCCHHHHHHHHHHcCHHHHHHHHHHc
Confidence 9999887776431 1111 111111111112223455554334566666666666555555555554
No 318
>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=83.90 E-value=5.2 Score=44.82 Aligned_cols=87 Identities=11% Similarity=0.058 Sum_probs=65.6
Q ss_pred HHHHHHHHHcCCcEEEEEEecCccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcc
Q 002211 171 SAIAEMVSYFGWGEVIAIFNDDDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGY 250 (953)
Q Consensus 171 ~ai~~~l~~~~w~~vaii~~d~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~ 250 (953)
..+.++++.++.+++.+|+....+..+..+.+.+.|++.|+++.....+.++ .+.+++...+..++..++|+||-.+.
T Consensus 12 ~~l~~~~~~~~~~r~livt~~~~~~~g~~~~v~~~L~~~gi~~~~~~~v~~~--p~~~~v~~~~~~~~~~~~D~IIaiGG 89 (375)
T cd08194 12 DETGAVLADLGGKRPLIVTDKVMVKLGLVDKLTDSLKKEGIESAIFDDVVSE--PTDESVEEGVKLAKEGGCDVIIALGG 89 (375)
T ss_pred HHHHHHHHHcCCCeEEEEcCcchhhcchHHHHHHHHHHCCCeEEEECCCCCC--cCHHHHHHHHHHHHhcCCCEEEEeCC
Confidence 4566777878889999998655554457788999999999887655455555 56788899999999999999998765
Q ss_pred h--hhHHHHHH
Q 002211 251 S--RTGLMVFD 259 (953)
Q Consensus 251 ~--~~~~~~~~ 259 (953)
+ -|+.+.+.
T Consensus 90 GS~~D~AKaia 100 (375)
T cd08194 90 GSPIDTAKAIA 100 (375)
T ss_pred chHHHHHHHHH
Confidence 5 45555544
No 319
>COG0715 TauA ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]
Probab=83.84 E-value=7.1 Score=42.96 Aligned_cols=73 Identities=21% Similarity=0.204 Sum_probs=50.7
Q ss_pred CCCCChHHhhhCCCeEEEEeCch-HHHHHH---HhhCCCccceE-eCCCHHHHHHHHHcCCcEEEEccchhHHHHHhcCc
Q 002211 700 SPIKGIDTLMTSNDRVGYQVGSF-AENYLI---EELSIPKSRLV-ALGSPEEYAIALENRTVAAVVDERPYIDLFLSDHC 774 (953)
Q Consensus 700 ~~I~sl~dL~~~~~~ig~~~~s~-~~~~l~---~~~~~~~~~~~-~~~~~~~~~~~l~~g~~~a~~~~~~~~~~~~~~~~ 774 (953)
.+|++++||. |++||+..++. ....+. ...+...+++. ..-.+.+...++..|++||++...++......+..
T Consensus 126 ~~i~~~adlk--Gk~vg~~~~~~~~~~~l~~~L~~~Gl~~~dv~~v~~~~~~~~~al~~g~vda~~~~ep~~~~~~~~~~ 203 (335)
T COG0715 126 SGIKSVADLK--GKKVGVPFGGSTSDFLLRYALAKAGLDPDDVELVNLPPADAVAALAAGQVDAFVVWEPWNAAAEGEGG 203 (335)
T ss_pred CCcccccCCC--CceEEEeCCCchHHHHHHHHHHHcCCCcccceEEeeCcHHHHHHHhcCCcceEEecCCchhhhhccCC
Confidence 6888999996 99999998774 333222 33444444332 23355588999999999999988888777665543
No 320
>cd08458 PBP2_NocR The C-terminal substrate-domain of LysR-type transcriptional regulator, NocR, involved in the catabolism of nopaline, contains the type 2 periplasmic binding fold. This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulator NocR, which is involved in the catabolism of nopaline. Opines are low molecular weight compounds found in plant crown gall tumors produced by the parasitic bacterium Agrobacterium. There are at least 30 different opines identified so far. Opines are utilized by tumor-colonizing bacteria as a source of carbon, nitrogen, and energy. In Agrobacterium tumefaciens, NocR regulates expression of the divergently transcribed nocB and nocR genes of the nopaline catabolism (noc) region. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, an
Probab=83.82 E-value=45 Score=32.60 Aligned_cols=70 Identities=13% Similarity=0.141 Sum_probs=46.1
Q ss_pred EeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEecEEEecCccceeeccccceecceEEEEec
Q 002211 512 GYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGDIAIVTNRTKAVDFTQPYIESGLVVVAPV 591 (953)
Q Consensus 512 G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~~~~t~~r~~~vdft~p~~~~~~~~~v~~ 591 (953)
.+-.+++..+.++.+ .++++... ++..++.+.+.+|++|+++..... . ...+ -+.++.+..++++++.
T Consensus 13 ~~l~~~l~~f~~~~P-~v~i~~~~-------~~~~~~~~~l~~g~~Dl~i~~~~~--~-~~~~-~~~~l~~~~~~~v~~~ 80 (196)
T cd08458 13 SFMSGVIQTFIADRP-DVSVYLDT-------VPSQTVLELVSLQHYDLGISILAG--D-YPGL-TTEPVPSFRAVCLLPP 80 (196)
T ss_pred hhhHHHHHHHHHHCC-CcEEEEec-------cChHHHHHHHHcCCCCEEEEeccC--C-CCCc-eEEEeccCceEEEecC
Confidence 455678888888875 25565553 456789999999999998863221 1 1222 2356677777877765
Q ss_pred cc
Q 002211 592 RK 593 (953)
Q Consensus 592 ~~ 593 (953)
..
T Consensus 81 ~h 82 (196)
T cd08458 81 GH 82 (196)
T ss_pred CC
Confidence 44
No 321
>COG0725 ModA ABC-type molybdate transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=83.76 E-value=23 Score=37.22 Aligned_cols=116 Identities=18% Similarity=0.156 Sum_probs=68.3
Q ss_pred CCCChHHhhhC-CCeEEEEe------CchHHHHHHHhhCCC---ccceEeCCCHHHHHHHHHcCCcEEEEccchhHHHHH
Q 002211 701 PIKGIDTLMTS-NDRVGYQV------GSFAENYLIEELSIP---KSRLVALGSPEEYAIALENRTVAAVVDERPYIDLFL 770 (953)
Q Consensus 701 ~I~sl~dL~~~-~~~ig~~~------~s~~~~~l~~~~~~~---~~~~~~~~~~~~~~~~l~~g~~~a~~~~~~~~~~~~ 770 (953)
.+..+++|.+. +.++++.+ |.+..+.|+ ..+.. ..+++.-.+..+.+..+..|+.|+.+.-...+....
T Consensus 123 ~~~~~~~l~~~~~~~lai~~p~~~P~G~ya~~~l~-~~g~~~~~~~k~v~~~~v~~~l~~V~~G~ad~g~vy~sd~~~~~ 201 (258)
T COG0725 123 KIESLEDLLERPDVRLAIGDPKTVPAGKYAKEALE-LLGLWYTLKDKLVLATNVRQALAYVETGEADAGFVYVSDALLSK 201 (258)
T ss_pred CcccHHHHhcCcCcEEEecCCCCCCchHHHHHHHH-HhchhhhccccEEecCcHHHHHHHHHcCCCCeEEEEEEhhhccC
Confidence 34447777763 55677653 667777774 33332 246777888899999999999998776544332221
Q ss_pred hcCcceEEeCCcc-ccCccEEEecCCCcc---hHHHHHHHHhhhccccHHHHHHHh
Q 002211 771 SDHCQFSVRGQEF-TKSGWGFAFPRDSPL---AIDMSTAILTLSENGELQRIHDKW 822 (953)
Q Consensus 771 ~~~~~l~~~~~~~-~~~~~~~~~~k~spl---~~~~n~~i~~l~e~G~~~~~~~~w 822 (953)
+...+..++... .+..|.+++.+++.- ...|-..+.. ..-+++.++|
T Consensus 202 -~~~~~~~~~~~~~~Pi~y~iav~~~~~~~~~A~~f~~fl~s----~~a~~il~~~ 252 (258)
T COG0725 202 -KVKIVGVFPEDLHSPIVYPIAVLKNAKNPELAKEFVDFLLS----PEAQEILEKY 252 (258)
T ss_pred -CceEEEEcccccCCCeEEEEEEEcCCCCHHHHHHHHHHHhC----HHHHHHHHHc
Confidence 112233444332 245678888888664 5555555543 3334444444
No 322
>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=83.55 E-value=5.1 Score=44.98 Aligned_cols=88 Identities=15% Similarity=0.140 Sum_probs=64.6
Q ss_pred HHHHHHHHHcCCcEEEEEEecCccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcc
Q 002211 171 SAIAEMVSYFGWGEVIAIFNDDDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGY 250 (953)
Q Consensus 171 ~ai~~~l~~~~w~~vaii~~d~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~ 250 (953)
..+.+.++.+|.+++.+++.....-.+..+.+.+.|++.|+++.....+.++ .+.+++......+++.++|+||..+.
T Consensus 18 ~~l~~~l~~~g~~r~lvvt~~~~~~~g~~~~v~~~L~~~~i~~~~~~~v~~~--p~~~~v~~~~~~~~~~~~D~IiaiGG 95 (379)
T TIGR02638 18 EDIVDEVKRRGFKKALVVTDKDLIKFGVADKVTDLLDEAGIAYELFDEVKPN--PTITVVKAGVAAFKASGADYLIAIGG 95 (379)
T ss_pred HHHHHHHHhcCCCEEEEEcCcchhhccchHHHHHHHHHCCCeEEEECCCCCC--cCHHHHHHHHHHHHhcCCCEEEEeCC
Confidence 4567778889999999988655444457888999999999876554444444 55778888899999999999998765
Q ss_pred h--hhHHHHHHH
Q 002211 251 S--RTGLMVFDV 260 (953)
Q Consensus 251 ~--~~~~~~~~~ 260 (953)
+ -|+.+.+..
T Consensus 96 GSviD~aKaia~ 107 (379)
T TIGR02638 96 GSPIDTAKAIGI 107 (379)
T ss_pred hHHHHHHHHHHH
Confidence 4 455554443
No 323
>cd08430 PBP2_IlvY The C-terminal substrate binding of LysR-type transcriptional regulator IlvY, which activates the expression of ilvC gene that encoding acetohydroxy acid isomeroreductase for the biosynthesis of branched amino acids; contains the type 2 periplasmic binding fold. In Escherichia coli, IlvY is required for the regulation of ilvC gene expression that encodes acetohydroxy acid isomeroreductase (AHIR), a key enzyme in the biosynthesis of branched-chain amino acids (isoleucine, valine, and leucine). The ilvGMEDA operon genes encode remaining enzyme activities required for the biosynthesis of these amino acids. Activation of ilvC transcription by IlvY requires the additional binding of a co-inducer molecule (either alpha-acetolactate or alpha-acetohydoxybutyrate, the substrates for AHIR) to a preformed complex of IlvY protein-DNA. Like many other LysR-family members, IlvY negatively auto-regulates the transcription of its own divergently transcribed ilvY gene in an inducer-i
Probab=83.29 E-value=47 Score=32.34 Aligned_cols=72 Identities=18% Similarity=0.172 Sum_probs=47.2
Q ss_pred EEeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEecEEEecCccceeeccccceecceEEEEe
Q 002211 511 HGYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGDIAIVTNRTKAVDFTQPYIESGLVVVAP 590 (953)
Q Consensus 511 ~G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~~~~t~~r~~~vdft~p~~~~~~~~~v~ 590 (953)
..+-.+++..+.++.+ .++++... ++..++++.+.+|++|+++..... .....+. ..++.+..++++++
T Consensus 12 ~~~l~~~l~~~~~~~P-~v~l~~~~-------~~~~~~~~~l~~g~~Dl~i~~~~~--~~~~~l~-~~~l~~~~~~~~~~ 80 (199)
T cd08430 12 YSFLPPILERFRAQHP-QVEIKLHT-------GDPADAIDKVLNGEADIAIAARPD--KLPARLA-FLPLATSPLVFIAP 80 (199)
T ss_pred eeeccHHHHHHHHHCC-CceEEEEe-------CCHHHHHHHHHCCCCCEEEEecCC--CCCcccE-EEeeccceEEEEEe
Confidence 3566778899999884 24565554 557889999999999998853211 1112232 35566777777776
Q ss_pred ccc
Q 002211 591 VRK 593 (953)
Q Consensus 591 ~~~ 593 (953)
...
T Consensus 81 ~~~ 83 (199)
T cd08430 81 NIA 83 (199)
T ss_pred CCc
Confidence 554
No 324
>PRK11062 nhaR transcriptional activator NhaR; Provisional
Probab=83.16 E-value=27 Score=37.63 Aligned_cols=86 Identities=16% Similarity=0.253 Sum_probs=52.1
Q ss_pred cceEEEecCcccccccEEeeCCcceEEEeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEecE
Q 002211 485 RQLRIGVPNRVSYRDFVFKVNGTDIVHGYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGDI 564 (953)
Q Consensus 485 ~~lri~v~~~~~~~p~~~~~~~~~~~~G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~~ 564 (953)
+.|||++.. .+ ..++-.+++..+.++.+ .+++.... ++.+++...|.+|++|+++...
T Consensus 93 g~l~i~~~~--~~------------~~~~l~~~l~~f~~~~P-~i~l~~~~-------~~~~~~~~~l~~g~~D~~i~~~ 150 (296)
T PRK11062 93 LLFDVGVAD--AL------------SKRLVSRVLLTAVPEDE-SIHLRCFE-------STHEMLLEQLSQHKLDMILSDC 150 (296)
T ss_pred eEEEEEecc--hh------------hHhhHHHHHHHHHhcCC-ceEEEEEe-------CCHHHHHHHHHcCCCCEEEecC
Confidence 469998874 11 13566777888877654 34555443 4578999999999999987532
Q ss_pred EEecCccceeeccccceecceEEEEeccc
Q 002211 565 AIVTNRTKAVDFTQPYIESGLVVVAPVRK 593 (953)
Q Consensus 565 ~~t~~r~~~vdft~p~~~~~~~~~v~~~~ 593 (953)
.........+ ...|+....++++++.+.
T Consensus 151 ~~~~~~~~~l-~~~~l~~~~~~~~~~~~~ 178 (296)
T PRK11062 151 PVDSTQQEGL-FSKKLGECGVSFFCTNPL 178 (296)
T ss_pred CCccccccch-hhhhhhccCcceEecCCC
Confidence 1111111222 235666666766665443
No 325
>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=83.07 E-value=5.6 Score=44.44 Aligned_cols=89 Identities=17% Similarity=0.183 Sum_probs=69.0
Q ss_pred HHHHHHHHHcCCcEEEEEEecCccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcc
Q 002211 171 SAIAEMVSYFGWGEVIAIFNDDDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGY 250 (953)
Q Consensus 171 ~ai~~~l~~~~w~~vaii~~d~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~ 250 (953)
..+.+.++.+| ++.+|+...-...+..+.+.+.|++.|+++.....+... .+.+++...+..+++.++|+||..+.
T Consensus 12 ~~l~~~l~~~g--r~lvVt~~~~~~~~~~~~v~~~L~~~~i~~~~~~~~~~~--p~~~~v~~~~~~~~~~~~D~IIaiGG 87 (366)
T PF00465_consen 12 EELGEELKRLG--RVLVVTDPSLSKSGLVDRVLDALEEAGIEVQVFDGVGPN--PTLEDVDEAAEQARKFGADCIIAIGG 87 (366)
T ss_dssp GGHHHHHHCTT--EEEEEEEHHHHHHTHHHHHHHHHHHTTCEEEEEEEESSS---BHHHHHHHHHHHHHTTSSEEEEEES
T ss_pred HHHHHHHHhcC--CEEEEECchHHhCccHHHHHHHHhhCceEEEEEecCCCC--CcHHHHHHHHHHHHhcCCCEEEEcCC
Confidence 44667788887 999998764344447899999999999998776666666 66889999999999999999999876
Q ss_pred h--hhHHHHHHHHHH
Q 002211 251 S--RTGLMVFDVAQR 263 (953)
Q Consensus 251 ~--~~~~~~~~~a~~ 263 (953)
+ -++.+.+.....
T Consensus 88 GS~~D~aK~va~~~~ 102 (366)
T PF00465_consen 88 GSVMDAAKAVALLLA 102 (366)
T ss_dssp HHHHHHHHHHHHHHT
T ss_pred CCcCcHHHHHHhhcc
Confidence 5 456666666555
No 326
>PRK11013 DNA-binding transcriptional regulator LysR; Provisional
Probab=82.95 E-value=50 Score=35.70 Aligned_cols=83 Identities=13% Similarity=0.127 Sum_probs=50.7
Q ss_pred cceEEEecCcccccccEEeeCCcceEEEeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEecE
Q 002211 485 RQLRIGVPNRVSYRDFVFKVNGTDIVHGYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGDI 564 (953)
Q Consensus 485 ~~lri~v~~~~~~~p~~~~~~~~~~~~G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~~ 564 (953)
+.++||++.. . ...+..+++..+.+..+ .+++.... .+-.++...+.+|++|+++...
T Consensus 94 g~l~I~~~~~---~-----------~~~~l~~~l~~~~~~~P-~v~i~i~~-------~~~~~~~~~l~~~~~Dl~i~~~ 151 (309)
T PRK11013 94 GQLSIACLPV---F-----------SQSLLPGLCQPFLARYP-DVSLNIVP-------QESPLLEEWLSAQRHDLGLTET 151 (309)
T ss_pred CcEEEEEcHH---H-----------HHhhHHHHHHHHHHHCC-CCeEEEEe-------CCHHHHHHHHHcCCCCEEEEcC
Confidence 4688887631 1 12456778888888774 24555554 3456788999999999988632
Q ss_pred EEecCccceeeccccceecceEEEEeccc
Q 002211 565 AIVTNRTKAVDFTQPYIESGLVVVAPVRK 593 (953)
Q Consensus 565 ~~t~~r~~~vdft~p~~~~~~~~~v~~~~ 593 (953)
.. ....+. ..+......+++++...
T Consensus 152 ~~---~~~~~~-~~~l~~~~~~~~~~~~~ 176 (309)
T PRK11013 152 LH---TPAGTE-RTELLTLDEVCVLPAGH 176 (309)
T ss_pred CC---CCCCce-eeeecceeEEEEEcCCC
Confidence 21 111222 33555566667766554
No 327
>PRK10094 DNA-binding transcriptional activator AllS; Provisional
Probab=82.63 E-value=54 Score=35.51 Aligned_cols=87 Identities=14% Similarity=0.183 Sum_probs=54.2
Q ss_pred CcceEEEecCcccccccEEeeCCcceEEEeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEec
Q 002211 484 GRQLRIGVPNRVSYRDFVFKVNGTDIVHGYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGD 563 (953)
Q Consensus 484 g~~lri~v~~~~~~~p~~~~~~~~~~~~G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~ 563 (953)
.++|+||+... .+. ..+-.+++..+.++++- +++.... ++..++.+.|.+|++|++++
T Consensus 91 ~g~l~Ig~~~~-~~~------------~~~l~~~l~~~~~~~P~-i~l~l~~-------~~~~~~~~~l~~g~~D~~i~- 148 (308)
T PRK10094 91 ERQVNIVINNL-LYN------------PQAVAQLLAWLNERYPF-TQFHISR-------QIYMGVWDSLLYEGFSLAIG- 148 (308)
T ss_pred CccEEEEeccc-ccC------------HHHHHHHHHHHHHhCCC-cEEEEEe-------ehhhhHHHHHhCCCccEEEe-
Confidence 35799988631 011 12345788888888764 4566554 45678899999999999886
Q ss_pred EEEecCccceeeccccceecceEEEEeccc
Q 002211 564 IAIVTNRTKAVDFTQPYIESGLVVVAPVRK 593 (953)
Q Consensus 564 ~~~t~~r~~~vdft~p~~~~~~~~~v~~~~ 593 (953)
+.........+. ..+.....++++++...
T Consensus 149 ~~~~~~~~~~l~-~~~l~~~~~~~v~~~~h 177 (308)
T PRK10094 149 VTGTEALANTFS-LDPLGSVQWRFVMAADH 177 (308)
T ss_pred cccCccccCCee-EEEecceeEEEEECCCC
Confidence 211111122232 34777778888876554
No 328
>PLN02245 ATP phosphoribosyl transferase
Probab=82.48 E-value=13 Score=40.99 Aligned_cols=105 Identities=10% Similarity=-0.009 Sum_probs=63.4
Q ss_pred CCCCChHHhhh-------CCCeEEEEeCchHHHHHHHhhCCCccceEeCCCHHHHHHHHHcCCcEEEEccchhHHHHHhc
Q 002211 700 SPIKGIDTLMT-------SNDRVGYQVGSFAENYLIEELSIPKSRLVALGSPEEYAIALENRTVAAVVDERPYIDLFLSD 772 (953)
Q Consensus 700 ~~I~sl~dL~~-------~~~~ig~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~g~~~a~~~~~~~~~~~~~~ 772 (953)
..+++++||.. ..++|+...-...++||. +.++...+++.....-|. +..-|-.|++++-......+.+
T Consensus 177 ~~~~s~~dL~g~~~~~~~~~~RIATkYp~ltr~ff~-~~Gv~~v~Iv~l~GAvE~--AP~lGlADaIvDIVsTGtTLra- 252 (403)
T PLN02245 177 ENINSLKELAQMPQWTEERPLRVVTGFTYLGPKFMK-DNGFKHVTFSTADGALEA--APAMGIADAILDLVSSGTTLRE- 252 (403)
T ss_pred cccCCHHHhcccccccccCceEEEeCCHHHHHHHHH-HcCCCeEEEEECcCceec--ccccCchhhhcchhccHHHHHH-
Confidence 35788889873 116888888888899995 456644566665554444 3444777788776555554433
Q ss_pred CcceEEeC-CccccCccEEEecCCCc-----chHHHHHHHHhh
Q 002211 773 HCQFSVRG-QEFTKSGWGFAFPRDSP-----LAIDMSTAILTL 809 (953)
Q Consensus 773 ~~~l~~~~-~~~~~~~~~~~~~k~sp-----l~~~~n~~i~~l 809 (953)
.+|++++ +.+....-.++..|++. -++.++..+.+|
T Consensus 253 -NgLk~i~~~~Il~S~A~LIan~~sl~~~~~~~~~i~~ll~rl 294 (403)
T PLN02245 253 -NNLKEIEGGVVLESQAVLVASRRALLERKGALEVVHEILERL 294 (403)
T ss_pred -CCCEEccCceEEEEEEEEEEecchhhcchhHHHHHHHHHHHH
Confidence 4677775 44444455566677654 223444444444
No 329
>PRK09508 leuO leucine transcriptional activator; Reviewed
Probab=82.32 E-value=22 Score=38.70 Aligned_cols=84 Identities=11% Similarity=0.153 Sum_probs=55.8
Q ss_pred CcceEEEecCcccccccEEeeCCcceEEEeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEec
Q 002211 484 GRQLRIGVPNRVSYRDFVFKVNGTDIVHGYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGD 563 (953)
Q Consensus 484 g~~lri~v~~~~~~~p~~~~~~~~~~~~G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~ 563 (953)
++.++|++.. + . ..++-.+++..+.++.+- +.+.+.. ++...++..|.+|++|+++..
T Consensus 111 ~~~i~i~~~~--~---~---------~~~~l~~~l~~f~~~~P~-i~l~i~~-------~~~~~~~~~l~~g~~Di~i~~ 168 (314)
T PRK09508 111 ERVFNLCICS--P---L---------DIRLTSQIYNRIEQIAPN-IHVVFKS-------SLNQNIEHQLRYQETEFVISY 168 (314)
T ss_pred ccEEEEEech--h---H---------HHHHHHHHHHHHHHhCCC-cEEEEEe-------CcchhHHHHHhcCCccEEEec
Confidence 4678888753 1 0 124667888999888752 4565554 456789999999999999864
Q ss_pred EEEecCccceeeccccceecceEEEEeccc
Q 002211 564 IAIVTNRTKAVDFTQPYIESGLVVVAPVRK 593 (953)
Q Consensus 564 ~~~t~~r~~~vdft~p~~~~~~~~~v~~~~ 593 (953)
... ....+. ..++....++++++...
T Consensus 169 ~~~---~~~~l~-~~~l~~~~~~lv~~~~h 194 (314)
T PRK09508 169 EEF---DRPEFT-SVPLFKDELVLVASKNH 194 (314)
T ss_pred CCC---Cccccc-eeeeecCceEEEEcCCC
Confidence 321 122233 34667788888887655
No 330
>COG1744 Med Uncharacterized ABC-type transport system, periplasmic component/surface lipoprotein [General function prediction only]
Probab=81.84 E-value=29 Score=38.20 Aligned_cols=92 Identities=13% Similarity=0.030 Sum_probs=69.1
Q ss_pred eEEEeEEEecCCCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEEccCChhhHH
Q 002211 49 VLNVGAIFSFGTVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIVGPQSAVMAH 128 (953)
Q Consensus 49 ~i~IG~l~~~~~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aiiGp~~S~~a~ 128 (953)
.-+||.+..+..+.-.....|+++.++..|.+ .++...+..+=.||..+.+++..|+++||++|.....+....
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 56788888888777778889999999999954 678888888888999999999999999999999766655444
Q ss_pred HHHHhhhhCCCcEEEeecC
Q 002211 129 VLSHLANELQVPLLSFTAL 147 (953)
Q Consensus 129 av~~v~~~~~vP~Is~~at 147 (953)
.+- .+.+.+.=-|.+.+.
T Consensus 235 v~~-~A~~~~~~~iGvdsD 252 (345)
T COG1744 235 VFQ-AAKELGAYAIGVDSD 252 (345)
T ss_pred HHH-HHHHhCCCeEEEecc
Confidence 321 233333333765433
No 331
>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=81.26 E-value=7.6 Score=43.58 Aligned_cols=88 Identities=13% Similarity=0.044 Sum_probs=64.1
Q ss_pred HHHHHHHHHcCCcEEEEEEecCccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcc
Q 002211 171 SAIAEMVSYFGWGEVIAIFNDDDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGY 250 (953)
Q Consensus 171 ~ai~~~l~~~~w~~vaii~~d~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~ 250 (953)
..+.++++.+|.+++.+++.......+..+.+.+.+++.|+.+.....+.++ .+..++...+..+++.++|+||-.+.
T Consensus 17 ~~l~~~l~~~g~~~~livt~~~~~~~~~~~~v~~~L~~~~~~~~~~~~v~~~--p~~~~v~~~~~~~~~~~~d~IIaiGG 94 (377)
T cd08188 17 KLAGRYARRLGAKKVLLVSDPGVIKAGWVDRVIESLEEAGLEYVVFSDVSPN--PRDEEVMAGAELYLENGCDVIIAVGG 94 (377)
T ss_pred HHHHHHHHHcCCCeEEEEeCcchhhCccHHHHHHHHHHcCCeEEEeCCCCCC--CCHHHHHHHHHHHHhcCCCEEEEeCC
Confidence 5577778888999999998654444456788999999888876544444444 45777888899999999999998765
Q ss_pred h--hhHHHHHHH
Q 002211 251 S--RTGLMVFDV 260 (953)
Q Consensus 251 ~--~~~~~~~~~ 260 (953)
+ -|+.+.+..
T Consensus 95 GsviD~AK~ia~ 106 (377)
T cd08188 95 GSPIDCAKGIGI 106 (377)
T ss_pred chHHHHHHHHHH
Confidence 4 455544443
No 332
>COG1638 DctP TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]
Probab=81.01 E-value=6.1 Score=43.18 Aligned_cols=103 Identities=13% Similarity=0.100 Sum_probs=65.6
Q ss_pred CCCCChHHhhhCCCeEEEEeCchHHHHHHHhhCCCccceEeCCCHHHHHHHHHcCCcEEEEccchhHH----HHHhcCcc
Q 002211 700 SPIKGIDTLMTSNDRVGYQVGSFAENYLIEELSIPKSRLVALGSPEEYAIALENRTVAAVVDERPYID----LFLSDHCQ 775 (953)
Q Consensus 700 ~~I~sl~dL~~~~~~ig~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~g~~~a~~~~~~~~~----~~~~~~~~ 775 (953)
.+|.+.+||. |.++.+.........+ +.++.....+ ...|...+|+.|-+|+.-.....+. |-.++++
T Consensus 157 ~PI~~peDlk--GlkiRv~~s~~~~~~~-~a~GA~P~pm----~f~Evy~aLqtGvVDGqEnp~~~i~~~k~~EVqky~- 228 (332)
T COG1638 157 RPIKTPEDLK--GLKIRVPQSPLLLAMF-KALGANPTPM----PFAEVYTALQTGVVDGQENPLSNIYSAKLYEVQKYL- 228 (332)
T ss_pred CCCCChHHhC--CCeeecCCCHHHHHHH-HHcCCCCCCC----CHHHHHHHHHcCCcccccCCHHHHhhccHHHHhHHh-
Confidence 4999999996 9999999988888888 4565443332 6789999999999998766544321 1111111
Q ss_pred eEEeCCccccCccEEEecCCC--cchHHHHHHHHhhhccc
Q 002211 776 FSVRGQEFTKSGWGFAFPRDS--PLAIDMSTAILTLSENG 813 (953)
Q Consensus 776 l~~~~~~~~~~~~~~~~~k~s--pl~~~~n~~i~~l~e~G 813 (953)
...+- ...++.+.+.+.. -|-+...++|++..+..
T Consensus 229 -t~tnH--~~~~~~~~~s~~~w~~L~~e~q~il~~aa~e~ 265 (332)
T COG1638 229 -TLTNH--IYLPLAVLVSKAFWDSLPEEDQTILLEAAKEA 265 (332)
T ss_pred -hhccc--cccceeeEEcHHHHhcCCHHHHHHHHHHHHHH
Confidence 11111 1234556666652 36777777776665544
No 333
>PRK13583 hisG ATP phosphoribosyltransferase catalytic subunit; Provisional
Probab=80.93 E-value=24 Score=36.03 Aligned_cols=93 Identities=13% Similarity=0.115 Sum_probs=55.3
Q ss_pred CCCCChHHhhh--------CC--CeEEEEeCchHHHHHHHhhCCCccceEeCCCHHHHHHHHHcCCcEEEEccchhHHHH
Q 002211 700 SPIKGIDTLMT--------SN--DRVGYQVGSFAENYLIEELSIPKSRLVALGSPEEYAIALENRTVAAVVDERPYIDLF 769 (953)
Q Consensus 700 ~~I~sl~dL~~--------~~--~~ig~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~g~~~a~~~~~~~~~~~ 769 (953)
..+++++||.+ .+ .+|+...-...+.||. +.+....+++.....-|. +-.-|-.|++++-......+
T Consensus 109 ~~~~~~~dl~~~~~~~~~~~g~~~RIATkYp~it~~yf~-~~Gv~~~~Iv~l~GsvEl--aP~~GlAD~IvDivsTG~TL 185 (228)
T PRK13583 109 IDVDTMADLDDVAADFRARHGRRLRIATKYWRLTQQFLS-QKGVQDYRIVESLGATEG--APANGSAEIIVDITSTGETL 185 (228)
T ss_pred cccCCHHHhhhhhhhhhhccCCceEEEeCCHHHHHHHHH-HcCCceeEEEECCCceec--ccccCcchhhhhhhchhHHH
Confidence 35677777751 12 5788888888899995 445543356665444443 23336777777765555544
Q ss_pred HhcCcceEEeC-CccccCccEEEecCCCc
Q 002211 770 LSDHCQFSVRG-QEFTKSGWGFAFPRDSP 797 (953)
Q Consensus 770 ~~~~~~l~~~~-~~~~~~~~~~~~~k~sp 797 (953)
.+ .+|.+++ +.+....-.++..+.|.
T Consensus 186 r~--NgL~~i~~~~Il~SsA~LI~n~~s~ 212 (228)
T PRK13583 186 RA--NHLKILSDGVILRSQACLVRARKAD 212 (228)
T ss_pred HH--CCCEEecCceEEEEEEEEEEecccc
Confidence 32 4677776 34444455566677764
No 334
>PRK10677 modA molybdate transporter periplasmic protein; Provisional
Probab=80.93 E-value=17 Score=38.34 Aligned_cols=71 Identities=27% Similarity=0.223 Sum_probs=42.4
Q ss_pred eHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCc-eeEEEecEEEecCcc---ceee-cc-ccceecceEE
Q 002211 514 CIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGV-FDAAVGDIAIVTNRT---KAVD-FT-QPYIESGLVV 587 (953)
Q Consensus 514 ~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~-~Di~~~~~~~t~~r~---~~vd-ft-~p~~~~~~~~ 587 (953)
.-++.+.+.++.|.++++.+- .-..+..++.+|. +|+.+.+-.-..++. ..+. .+ .+|....+++
T Consensus 41 ~~~l~~~Fe~~~g~~v~~~~~---------~Sg~l~~qi~~g~~~Dv~~~a~~~~~~~l~~~gl~~~~~~~~~a~n~lvl 111 (257)
T PRK10677 41 LQDIAAQYKKEKGVDVVSSFA---------SSSTLARQIEQGAPADLFISADQKWMDYAVDKKAIDTATRYTLLGNSLVV 111 (257)
T ss_pred HHHHHHHHHhhhCCeEEEEec---------ccHHHHHHHHcCCCCCEEEECCHHHHHHHHHCCCCCCcchheeecCEEEE
Confidence 445666777777866665543 2346777888877 998877432212121 1221 11 3577788888
Q ss_pred EEeccc
Q 002211 588 VAPVRK 593 (953)
Q Consensus 588 ~v~~~~ 593 (953)
++++..
T Consensus 112 ~~~~~~ 117 (257)
T PRK10677 112 VAPKAS 117 (257)
T ss_pred EEECCC
Confidence 888765
No 335
>KOG3857 consensus Alcohol dehydrogenase, class IV [Energy production and conversion]
Probab=80.83 E-value=11 Score=40.04 Aligned_cols=97 Identities=12% Similarity=0.088 Sum_probs=75.8
Q ss_pred CCCCcEEEccCChHHHHHH----HHHHHHHcCCcEEEEEEecCccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHH
Q 002211 154 LQYPFFVQTAPNDLYLMSA----IAEMVSYFGWGEVIAIFNDDDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETD 229 (953)
Q Consensus 154 ~~~p~~fr~~p~d~~~~~a----i~~~l~~~~w~~vaii~~d~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d 229 (953)
...+|-|-+.|+....++. +++.++.+|.|++.++.+.+---....+..++.|++.|+++.......+. .+...
T Consensus 38 k~~~~af~m~~s~~rfG~gv~~Evg~dikn~gaKk~llvTDkni~~~~~~~~a~~~L~~~~I~~~vyD~v~~e--Ptv~s 115 (465)
T KOG3857|consen 38 KMMSVAFFMIPSTSRFGKGVLAEVGDDIKNLGAKKTLLVTDKNIAKLGLVKVAQDSLEENGINVEVYDKVQPE--PTVGS 115 (465)
T ss_pred ccceeeEEeccchhhhcchhHHHHHHHHHhcCccceEEeeCCChhhcccHHHHHHHHHHcCCceEEecCccCC--Cchhh
Confidence 3356777777777766654 34457889999999999777777778889999999999998766655555 56788
Q ss_pred HHHHHHHHhcCCceEEEEEcchh
Q 002211 230 VRNELVKVRMMEARVIVVHGYSR 252 (953)
Q Consensus 230 ~~~~l~~i~~~~~~vii~~~~~~ 252 (953)
+...+.-+|..+.|.+|..+.+.
T Consensus 116 ~~~alefak~~~fDs~vaiGGGS 138 (465)
T KOG3857|consen 116 VTAALEFAKKKNFDSFVAIGGGS 138 (465)
T ss_pred HHHHHHHHHhcccceEEEEcCcc
Confidence 99999999999999999876653
No 336
>COG1794 RacX Aspartate racemase [Cell envelope biogenesis, outer membrane]
Probab=80.75 E-value=29 Score=34.95 Aligned_cols=86 Identities=17% Similarity=0.164 Sum_probs=59.2
Q ss_pred ChHHHHHHHHHHHhc-CcEEEEccCChhhHHHHHH-hhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHH
Q 002211 99 NGFLSIMGALQFMET-DTLAIVGPQSAVMAHVLSH-LANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEM 176 (953)
Q Consensus 99 ~~~~a~~~a~~li~~-~v~aiiGp~~S~~a~av~~-v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~ 176 (953)
++...+..+.+-+++ |+..|+=|.. +++.+++ +-+..+||+|+ ..++.++-
T Consensus 59 ~~~~~L~~~a~~Le~~GAd~i~l~~N--T~H~~~d~iq~~~~iPllh-------------------------IidaTa~~ 111 (230)
T COG1794 59 EAGEILIDAAKKLERAGADFIVLPTN--TMHKVADDIQKAVGIPLLH-------------------------IIDATAKA 111 (230)
T ss_pred cHHHHHHHHHHHHHhcCCCEEEEeCC--cHHHHHHHHHHhcCCCeeh-------------------------HHHHHHHH
Confidence 455555544444444 8888887654 4556565 44577999996 24667777
Q ss_pred HHHcCCcEEEEEEecCccccchHHHHHHHHHhcCcEEE
Q 002211 177 VSYFGWGEVIAIFNDDDQGRNGVTALGDKLAEIRCKIS 214 (953)
Q Consensus 177 l~~~~w~~vaii~~d~~~g~~~~~~l~~~l~~~g~~v~ 214 (953)
+++.|.++|+++..... -...-.++.|+++|++++
T Consensus 112 ik~~g~kkvgLLgT~~T---m~~~fY~~~l~~~gievv 146 (230)
T COG1794 112 IKAAGAKKVGLLGTRFT---MEQGFYRKRLEEKGIEVV 146 (230)
T ss_pred HHhcCCceeEEeeccch---HHhHHHHHHHHHCCceEe
Confidence 88899999999986543 223456788999998876
No 337
>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=80.49 E-value=8.2 Score=43.38 Aligned_cols=88 Identities=11% Similarity=0.078 Sum_probs=64.6
Q ss_pred HHHHHHHHHcCCcEEEEEEecCcc-ccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEc
Q 002211 171 SAIAEMVSYFGWGEVIAIFNDDDQ-GRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHG 249 (953)
Q Consensus 171 ~ai~~~l~~~~w~~vaii~~d~~~-g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~ 249 (953)
..+.++++.+| +++.+|+..... ..+..+.+.+.|++.|+++.....+.++ .+.+++...+..+++.++|+||-.+
T Consensus 15 ~~l~~~~~~~g-~r~livt~~~~~~~~g~~~~v~~~L~~~~~~~~~~~~v~~~--p~~~~v~~~~~~~~~~~~D~IiavG 91 (380)
T cd08185 15 NELGEEALKPG-KKALIVTGNGSSKKTGYLDRVIELLKQAGVEVVVFDKVEPN--PTTTTVMEGAALAREEGCDFVVGLG 91 (380)
T ss_pred HHHHHHHHhcC-CeEEEEeCCCchhhccHHHHHHHHHHHcCCeEEEeCCccCC--CCHHHHHHHHHHHHHcCCCEEEEeC
Confidence 44667777788 899988865542 4567888999999999887644445555 5678888888999999999999765
Q ss_pred ch--hhHHHHHHHH
Q 002211 250 YS--RTGLMVFDVA 261 (953)
Q Consensus 250 ~~--~~~~~~~~~a 261 (953)
.+ -|+.+.+...
T Consensus 92 GGS~iD~aK~ia~~ 105 (380)
T cd08185 92 GGSSMDTAKAIAFM 105 (380)
T ss_pred CccHHHHHHHHHHH
Confidence 54 4555555443
No 338
>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=80.46 E-value=60 Score=31.70 Aligned_cols=73 Identities=15% Similarity=0.134 Sum_probs=46.6
Q ss_pred EeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEecEEEecCccceeeccccceecceEEEEec
Q 002211 512 GYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGDIAIVTNRTKAVDFTQPYIESGLVVVAPV 591 (953)
Q Consensus 512 G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~~~~t~~r~~~vdft~p~~~~~~~~~v~~ 591 (953)
.+-.+++..+.++.+- ++++... +...++...+.+|++|+++............+ -+.+.....++++++.
T Consensus 13 ~~l~~~l~~~~~~~P~-i~l~i~~-------~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~~~-~~~~l~~~~~~~v~~~ 83 (200)
T cd08453 13 SVLPELVRRFREAYPD-VELQLRE-------ATSDVQLEALLAGEIDAGIVIPPPGASAPPAL-AYRPLLSEPLVLAVPA 83 (200)
T ss_pred HHHHHHHHHHHHhCCC-ceEEEEe-------CCHHHHHHHHHcCCCCEEEEecCcccCCCcce-eEEEeeeCceEEEEEC
Confidence 4556788888887642 4555554 45778999999999999885221111011222 2566777888888876
Q ss_pred cc
Q 002211 592 RK 593 (953)
Q Consensus 592 ~~ 593 (953)
..
T Consensus 84 ~h 85 (200)
T cd08453 84 AW 85 (200)
T ss_pred CC
Confidence 54
No 339
>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=79.65 E-value=7.7 Score=43.50 Aligned_cols=87 Identities=15% Similarity=0.181 Sum_probs=63.6
Q ss_pred HHHHHHHHHcCCcEEEEEEecCccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcc
Q 002211 171 SAIAEMVSYFGWGEVIAIFNDDDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGY 250 (953)
Q Consensus 171 ~ai~~~l~~~~w~~vaii~~d~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~ 250 (953)
..+.+.++.+|-+++.+++....+-....+.+.+.|++.|+++.....+.++ .+.+.+...+..+++.++|+||-.+.
T Consensus 17 ~~l~~~l~~~g~~~~lvv~~~~~~~~~~~~~v~~~L~~~~~~~~~f~~v~~~--p~~~~v~~~~~~~~~~~~D~IIavGG 94 (377)
T cd08176 17 KEIGDELKNLGFKKALIVTDKGLVKIGVVEKVTDVLDEAGIDYVIYDGVKPN--PTITNVKDGLAVFKKEGCDFIISIGG 94 (377)
T ss_pred HHHHHHHHHhCCCeEEEECCchHhhcCcHHHHHHHHHHcCCeEEEeCCCCCC--CCHHHHHHHHHHHHhcCCCEEEEeCC
Confidence 4567778888888988887544433367888999999989876544444444 55778888999999999999998766
Q ss_pred h--hhHHHHHH
Q 002211 251 S--RTGLMVFD 259 (953)
Q Consensus 251 ~--~~~~~~~~ 259 (953)
+ -|+.+.+.
T Consensus 95 GS~iD~aK~ia 105 (377)
T cd08176 95 GSPHDCAKAIG 105 (377)
T ss_pred cHHHHHHHHHH
Confidence 5 34555544
No 340
>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=79.43 E-value=9.3 Score=41.46 Aligned_cols=89 Identities=12% Similarity=0.026 Sum_probs=65.6
Q ss_pred EEeEEE---ecCCCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEEccCChhhH
Q 002211 51 NVGAIF---SFGTVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIVGPQSAVMA 127 (953)
Q Consensus 51 ~IG~l~---~~~~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aiiGp~~S~~a 127 (953)
++|.+. ....+.-.....|+...++.+| |+.++...+..+-.||..+.+.+..|+++|+.+|.+ ......
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------PDIKVNVSYTGSFNDPAKAKEAAEALIDQGADVIFP-VAGGSG 200 (306)
T ss_dssp EEEEEEEEES--SCTTHHHHHHHHHHHHHTT------TT-EEEEEE-SSSS-HHHHHHHHHHHHHTT-SEEEE-E-CCCH
T ss_pred cccccccccCCCcHhHHHHHHHHHHHHHHhC------cCceEEEEEcCCcCchHHHHHHHHHHhhcCCeEEEE-CCCCCc
Confidence 566666 6666555678899999999999 567888888888889999999999999999998887 344556
Q ss_pred HHHHHhhhhCCCc--EEEeec
Q 002211 128 HVLSHLANELQVP--LLSFTA 146 (953)
Q Consensus 128 ~av~~v~~~~~vP--~Is~~a 146 (953)
..+.+.+.+.+.. .|....
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 6777888888888 777543
No 341
>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=79.41 E-value=17 Score=40.90 Aligned_cols=89 Identities=11% Similarity=0.157 Sum_probs=62.1
Q ss_pred HHHHHHHHHcCCcEEEEEEecCccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcc
Q 002211 171 SAIAEMVSYFGWGEVIAIFNDDDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGY 250 (953)
Q Consensus 171 ~ai~~~l~~~~w~~vaii~~d~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~ 250 (953)
..+.++++.+| +++.+|+....+.....+.+.+.+++.|+++.....+.+. .+..+....+...++.++|+||-.+.
T Consensus 12 ~~l~~~~~~~g-~~~livt~~~~~~~~~~~~v~~~L~~~~~~~~~f~~v~~~--~~~~~v~~~~~~~~~~~~D~IIaiGG 88 (386)
T cd08191 12 RQLPRLAARLG-SRALIVTDERMAGTPVFAELVQALAAAGVEVEVFDGVLPD--LPRSELCDAASAAARAGPDVIIGLGG 88 (386)
T ss_pred HHHHHHHHHcC-CeEEEEECcchhhcchHHHHHHHHHHcCCeEEEECCCCCC--cCHHHHHHHHHHHHhcCCCEEEEeCC
Confidence 44677788888 8998888544444467888999999999876543333322 34566777788888899999998766
Q ss_pred h--hhHHHHHHHHH
Q 002211 251 S--RTGLMVFDVAQ 262 (953)
Q Consensus 251 ~--~~~~~~~~~a~ 262 (953)
+ -|+.+++....
T Consensus 89 GS~iD~aK~ia~~~ 102 (386)
T cd08191 89 GSCIDLAKIAGLLL 102 (386)
T ss_pred chHHHHHHHHHHHH
Confidence 5 45665655443
No 342
>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=79.17 E-value=89 Score=32.91 Aligned_cols=69 Identities=16% Similarity=0.174 Sum_probs=45.5
Q ss_pred eeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEecEEEecCccceeeccccceecceEEEEecc
Q 002211 513 YCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGDIAIVTNRTKAVDFTQPYIESGLVVVAPVR 592 (953)
Q Consensus 513 ~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~~~~t~~r~~~vdft~p~~~~~~~~~v~~~ 592 (953)
+-.+++..+.++.+ .+++.... ++..+++..+.+|++|+++..-... ...+. ..|+....++++++..
T Consensus 98 ~~~~~l~~~~~~~p-~v~l~i~~-------~~~~~~~~~l~~g~~Dl~i~~~~~~---~~~~~-~~~l~~~~~~lv~s~~ 165 (279)
T TIGR03339 98 YVLDLVARFRQRYP-GIEVSVRI-------GNSQEVLQALQSYRVDVAVSSEVVD---DPRLD-RVVLGNDPLVAVVHRQ 165 (279)
T ss_pred HHHHHHHHHHHHCC-CcEEEEEE-------CCHHHHHHHHHcCCCcEEEEecccC---CCceE-EEEcCCceEEEEECCC
Confidence 45677888887765 24455543 4577899999999999998532221 12222 3566777888888765
Q ss_pred c
Q 002211 593 K 593 (953)
Q Consensus 593 ~ 593 (953)
.
T Consensus 166 ~ 166 (279)
T TIGR03339 166 H 166 (279)
T ss_pred C
Confidence 5
No 343
>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=79.08 E-value=10 Score=42.25 Aligned_cols=86 Identities=7% Similarity=0.107 Sum_probs=62.6
Q ss_pred HHHHHHHHHcCCcEEEEEEecCccc-cchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEc
Q 002211 171 SAIAEMVSYFGWGEVIAIFNDDDQG-RNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHG 249 (953)
Q Consensus 171 ~ai~~~l~~~~w~~vaii~~d~~~g-~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~ 249 (953)
..+.++++.+| +++.+++....+- .+..+.+.+.|++.|+++.....+.++ .+.+++...++.+++.++|+||-.+
T Consensus 15 ~~l~~~~~~~g-~r~lvVt~~~~~~~~g~~~~v~~~L~~~g~~~~~~~~v~~~--p~~~~v~~~~~~~~~~~~D~IIavG 91 (357)
T cd08181 15 EKHGEELAALG-KRALIVTGKSSAKKNGSLDDVTKALEELGIEYEIFDEVEEN--PSLETIMEAVEIAKKFNADFVIGIG 91 (357)
T ss_pred HHHHHHHHHcC-CEEEEEeCCchHhhcCcHHHHHHHHHHcCCeEEEeCCCCCC--cCHHHHHHHHHHHHhcCCCEEEEeC
Confidence 34567788888 8988887655433 345688999999999887654445544 5678889999999999999999987
Q ss_pred ch--hhHHHHHH
Q 002211 250 YS--RTGLMVFD 259 (953)
Q Consensus 250 ~~--~~~~~~~~ 259 (953)
.+ -|+.+.+.
T Consensus 92 GGSviD~aK~ia 103 (357)
T cd08181 92 GGSPLDAAKAIA 103 (357)
T ss_pred CchHHHHHHHHH
Confidence 65 34555443
No 344
>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=78.77 E-value=7.8 Score=43.03 Aligned_cols=84 Identities=12% Similarity=0.107 Sum_probs=61.9
Q ss_pred HHHHHHHHHcCCcEEEEEEecCccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcc
Q 002211 171 SAIAEMVSYFGWGEVIAIFNDDDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGY 250 (953)
Q Consensus 171 ~ai~~~l~~~~w~~vaii~~d~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~ 250 (953)
..+.+.++.++ +++.+|+....+. ...+.+.+.+++.|+.+.+. .+... .+.+++...++.+++.++|+||-.+.
T Consensus 12 ~~l~~~~~~~~-~r~livt~~~~~~-~~~~~v~~~L~~~~i~~~~~-~~~~~--p~~~~v~~~~~~~~~~~~D~IIavGG 86 (351)
T cd08170 12 DELGEYLARLG-KRALIIADEFVLD-LVGAKIEESLAAAGIDARFE-VFGGE--CTRAEIERLAEIARDNGADVVIGIGG 86 (351)
T ss_pred HHHHHHHHHhC-CeEEEEECHHHHH-HHHHHHHHHHHhCCCeEEEE-EeCCc--CCHHHHHHHHHHHhhcCCCEEEEecC
Confidence 44667777776 8998888544444 77888999999999887643 35554 55788888899999999999998876
Q ss_pred h--hhHHHHHH
Q 002211 251 S--RTGLMVFD 259 (953)
Q Consensus 251 ~--~~~~~~~~ 259 (953)
+ -|+.+.+.
T Consensus 87 GS~iD~aK~ia 97 (351)
T cd08170 87 GKTLDTAKAVA 97 (351)
T ss_pred chhhHHHHHHH
Confidence 5 34444444
No 345
>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=78.73 E-value=37 Score=33.31 Aligned_cols=128 Identities=16% Similarity=0.241 Sum_probs=75.0
Q ss_pred CChHHHHHHHHHH-HhcCcEEEEccCChhhHHHHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHH
Q 002211 98 FNGFLSIMGALQF-METDTLAIVGPQSAVMAHVLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEM 176 (953)
Q Consensus 98 ~~~~~a~~~a~~l-i~~~v~aiiGp~~S~~a~av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~ 176 (953)
++-..++..+.++ ..+++.+||.-.. ++ ..+-+..++|+|... ++.....+++.+.
T Consensus 17 ~~~e~~v~~a~~~~~~~g~dViIsRG~--ta---~~lr~~~~iPVV~I~------------------~s~~Dil~al~~a 73 (176)
T PF06506_consen 17 ASLEEAVEEARQLLESEGADVIISRGG--TA---ELLRKHVSIPVVEIP------------------ISGFDILRALAKA 73 (176)
T ss_dssp --HHHHHHHHHHHHTTTT-SEEEEEHH--HH---HHHHCC-SS-EEEE---------------------HHHHHHHHHHC
T ss_pred ecHHHHHHHHHHhhHhcCCeEEEECCH--HH---HHHHHhCCCCEEEEC------------------CCHhHHHHHHHHH
Confidence 3557889999999 7789999997322 22 234445589999741 1222233444332
Q ss_pred HHHcCCcEEEEEEecCccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHH
Q 002211 177 VSYFGWGEVIAIFNDDDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLM 256 (953)
Q Consensus 177 l~~~~w~~vaii~~d~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~ 256 (953)
- .++ ++++++...+.. .....+.+.+ |..+.... +. +.+|+...+.+++..+.|+||-.+.
T Consensus 74 ~-~~~-~~Iavv~~~~~~--~~~~~~~~ll---~~~i~~~~-~~-----~~~e~~~~i~~~~~~G~~viVGg~~------ 134 (176)
T PF06506_consen 74 K-KYG-PKIAVVGYPNII--PGLESIEELL---GVDIKIYP-YD-----SEEEIEAAIKQAKAEGVDVIVGGGV------ 134 (176)
T ss_dssp C-CCT-SEEEEEEESS-S--CCHHHHHHHH---T-EEEEEE-ES-----SHHHHHHHHHHHHHTT--EEEESHH------
T ss_pred H-hcC-CcEEEEeccccc--HHHHHHHHHh---CCceEEEE-EC-----CHHHHHHHHHHHHHcCCcEEECCHH------
Confidence 2 334 899999865543 2255555555 56655432 21 2789999999999999999887653
Q ss_pred HHHHHHHcCCC
Q 002211 257 VFDVAQRLGMM 267 (953)
Q Consensus 257 ~~~~a~~~g~~ 267 (953)
..+.|++.|+.
T Consensus 135 ~~~~A~~~gl~ 145 (176)
T PF06506_consen 135 VCRLARKLGLP 145 (176)
T ss_dssp HHHHHHHTTSE
T ss_pred HHHHHHHcCCc
Confidence 35667888874
No 346
>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=78.61 E-value=68 Score=31.20 Aligned_cols=72 Identities=11% Similarity=0.211 Sum_probs=46.4
Q ss_pred EeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEecEEEecCccceeeccccceecceEEEEec
Q 002211 512 GYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGDIAIVTNRTKAVDFTQPYIESGLVVVAPV 591 (953)
Q Consensus 512 G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~~~~t~~r~~~vdft~p~~~~~~~~~v~~ 591 (953)
++..+++..+.++.+ .+++.... +...++...+.+|++|+++..... ......+. +.++....+++++++
T Consensus 13 ~~l~~~l~~~~~~~P-~i~l~i~~-------~~~~~~~~~l~~~~~Dl~i~~~~~-~~~~~~l~-~~~l~~~~~~~v~~~ 82 (199)
T cd08416 13 NTVPRIIMGLKLRRP-ELDIELTL-------GSNKDLLKKLKDGELDAILVATPE-GLNDPDFE-VVPLFEDDIFLAVPA 82 (199)
T ss_pred hhhHHHHHHHHHhCC-CeEEEEEE-------cCcHHHHHHHhCCCCCEEEEecCC-cCCCCCeE-EEEeecceEEEEECC
Confidence 556778888888874 24455543 446788999999999998863211 00112222 456677778888876
Q ss_pred cc
Q 002211 592 RK 593 (953)
Q Consensus 592 ~~ 593 (953)
..
T Consensus 83 ~h 84 (199)
T cd08416 83 TS 84 (199)
T ss_pred CC
Confidence 54
No 347
>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=78.50 E-value=17 Score=40.52 Aligned_cols=86 Identities=10% Similarity=0.133 Sum_probs=62.4
Q ss_pred HHHHHHHHHcCCcEEEEEEecCccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcc
Q 002211 171 SAIAEMVSYFGWGEVIAIFNDDDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGY 250 (953)
Q Consensus 171 ~ai~~~l~~~~w~~vaii~~d~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~ 250 (953)
..+.+.++.+|.+++.+|+....+ ..+.+.+.+++.|+.+.....+.++ .+.+.....+..+++.++|+||-.+.
T Consensus 12 ~~l~~~~~~~g~~~~livtd~~~~---~~~~~~~~l~~~~~~~~~~~~~~~~--p~~~~v~~~~~~~~~~~~D~IIavGG 86 (367)
T cd08182 12 AKLPSLLKGLGGKRVLLVTGPRSA---IASGLTDILKPLGTLVVVFDDVQPN--PDLEDLAAGIRLLREFGPDAVLAVGG 86 (367)
T ss_pred HHHHHHHHhcCCCeEEEEeCchHH---HHHHHHHHHHHcCCeEEEEcCcCCC--cCHHHHHHHHHHHHhcCcCEEEEeCC
Confidence 456677888898999999865544 4566788888888776544445444 55778888888899999999998765
Q ss_pred h--hhHHHHHHHH
Q 002211 251 S--RTGLMVFDVA 261 (953)
Q Consensus 251 ~--~~~~~~~~~a 261 (953)
+ -|+.+++...
T Consensus 87 Gs~~D~aK~ia~~ 99 (367)
T cd08182 87 GSVLDTAKALAAL 99 (367)
T ss_pred cHHHHHHHHHHHH
Confidence 4 5666665554
No 348
>PRK09906 DNA-binding transcriptional regulator HcaR; Provisional
Probab=78.38 E-value=75 Score=34.01 Aligned_cols=70 Identities=16% Similarity=0.194 Sum_probs=49.1
Q ss_pred EeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEecEEEecCccceeeccccceecceEEEEec
Q 002211 512 GYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGDIAIVTNRTKAVDFTQPYIESGLVVVAPV 591 (953)
Q Consensus 512 G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~~~~t~~r~~~vdft~p~~~~~~~~~v~~ 591 (953)
.+..+++..+.++.+ .+.+.... .+.++++..+.+|++|+++..... ....++ +.|+....+++++++
T Consensus 103 ~~l~~~~~~~~~~~p-~v~i~~~~-------~~~~~~~~~l~~~~~D~~i~~~~~---~~~~l~-~~~l~~~~~~~v~~~ 170 (296)
T PRK09906 103 NLLPKVLPMFRLRHP-DTLIELVS-------LITTQQEEKLRRGELDVGFMRHPV---YSDEID-YLELLDEPLVVVLPV 170 (296)
T ss_pred hHHHHHHHHHHHHCC-CeEEEEEe-------CCcHHHHHHHHcCCeeEEEecCCC---CCCCce-EEEEecccEEEEecC
Confidence 345677788888764 35566554 456889999999999999863322 233344 368888899999886
Q ss_pred cc
Q 002211 592 RK 593 (953)
Q Consensus 592 ~~ 593 (953)
..
T Consensus 171 ~~ 172 (296)
T PRK09906 171 DH 172 (296)
T ss_pred CC
Confidence 65
No 349
>PRK03692 putative UDP-N-acetyl-D-mannosaminuronic acid transferase; Provisional
Probab=78.07 E-value=26 Score=36.40 Aligned_cols=88 Identities=13% Similarity=0.040 Sum_probs=58.6
Q ss_pred HHHHHHHHHHHHcCCcEEEEEEecCccccchHHHHHHHHHh-cCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEE
Q 002211 168 YLMSAIAEMVSYFGWGEVIAIFNDDDQGRNGVTALGDKLAE-IRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIV 246 (953)
Q Consensus 168 ~~~~ai~~~l~~~~w~~vaii~~d~~~g~~~~~~l~~~l~~-~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii 246 (953)
.....+.+.....| .+|.++..+.+ ..+.+.+.+++ .|+.|+....=. .+.++....+++|.+++||+++
T Consensus 92 dl~~~ll~~~~~~~-~~v~llG~~~~----v~~~a~~~l~~~y~l~i~g~~~Gy----f~~~e~~~i~~~I~~s~~dil~ 162 (243)
T PRK03692 92 DLWEALMARAGKEG-TPVFLVGGKPE----VLAQTEAKLRTQWNVNIVGSQDGY----FTPEQRQALFERIHASGAKIVT 162 (243)
T ss_pred HHHHHHHHHHHhcC-CeEEEECCCHH----HHHHHHHHHHHHhCCEEEEEeCCC----CCHHHHHHHHHHHHhcCCCEEE
Confidence 34555666666666 78888876554 44455555543 377776543211 1245567789999999999999
Q ss_pred EEcchhhHHHHHHHHHHc
Q 002211 247 VHGYSRTGLMVFDVAQRL 264 (953)
Q Consensus 247 ~~~~~~~~~~~~~~a~~~ 264 (953)
+.+..+.-..++...++.
T Consensus 163 VglG~PkQE~~~~~~~~~ 180 (243)
T PRK03692 163 VAMGSPKQEIFMRDCRLV 180 (243)
T ss_pred EECCCcHHHHHHHHHHHh
Confidence 998887777777766553
No 350
>PF14503 YhfZ_C: YhfZ C-terminal domain; PDB: 2OZZ_B.
Probab=77.46 E-value=7.8 Score=39.47 Aligned_cols=103 Identities=15% Similarity=0.120 Sum_probs=49.6
Q ss_pred CCCeEEEEeCchHHHHHHHhhCCCccc--eEeCCCHHHHHHHHHcCCcEEEEccchhHHHHHhcCcceEEeC--C--c-c
Q 002211 711 SNDRVGYQVGSFAENYLIEELSIPKSR--LVALGSPEEYAIALENRTVAAVVDERPYIDLFLSDHCQFSVRG--Q--E-F 783 (953)
Q Consensus 711 ~~~~ig~~~~s~~~~~l~~~~~~~~~~--~~~~~~~~~~~~~l~~g~~~a~~~~~~~~~~~~~~~~~l~~~~--~--~-~ 783 (953)
.|.+||+-..|.-+..+.+..- ...+ ++.. +..+.++.+.+|.+||.+-+..... .+..++.... . . .
T Consensus 113 dGmRVGiD~~S~Dq~~LT~~~~-~gk~Ve~Vei-~Y~q~~~~l~~g~IDA~IWN~d~i~---~~~~~l~~~~l~~~~~~~ 187 (232)
T PF14503_consen 113 DGMRVGIDPSSIDQKILTEAEF-EGKNVEFVEI-PYNQLLELLRSGEIDAAIWNYDEIE---DKNFGLKYVPLKDDPMSK 187 (232)
T ss_dssp ---EEEE-TT-HHHHHHHHHHH-TTS--EEEE---HHHHHHHHHHTS--EEEEE--HHC---CHHCTEEEEE--SSCHHH
T ss_pred eeeEeecCCCCccHHHHHHHHh-CCCceEEEEe-cHHHHHHHHHCCCccEEEECCcccc---cccCCeeEEeCCchHHHH
Confidence 3789999999988888765432 2223 3333 7889999999999999997654111 1112333322 1 1 1
Q ss_pred ccCccEEEecCCCc-chHHHHHHHHhhhccccHHHHHHHh
Q 002211 784 TKSGWGFAFPRDSP-LAIDMSTAILTLSENGELQRIHDKW 822 (953)
Q Consensus 784 ~~~~~~~~~~k~sp-l~~~~n~~i~~l~e~G~~~~~~~~w 822 (953)
....-.++++|+.+ +...+++.| ....+-++.++=
T Consensus 188 ~~seAVivi~~~~~~i~~ll~~~i----d~~~vl~iQ~~V 223 (232)
T PF14503_consen 188 DASEAVIVIRKDNEPIKALLRKLI----DVEKVLEIQKKV 223 (232)
T ss_dssp HTT-EEEEEETT-HHHHHHHHHH------HHHHHHHHHHH
T ss_pred hcCeeEEEEeCCCHHHHHHHHHhc----CHHHHHHHHHHH
Confidence 12345677888886 444444333 334444444443
No 351
>PRK10537 voltage-gated potassium channel; Provisional
Probab=77.37 E-value=4.9 Score=45.02 Aligned_cols=54 Identities=20% Similarity=0.293 Sum_probs=42.0
Q ss_pred CCcccchhhHHHHHHHhhccccC--CcccchhHHHHHHHHHHHHHhhhhcccceee
Q 002211 638 PPRKQIVTVLWFSFSTMFFAHRE--NTVSTLGRVVLIIWLFVVLIITSSYTASLTS 691 (953)
Q Consensus 638 ~~~~~~~~~~~~~~~~l~~~~~~--~~~s~~~R~l~~~w~~~~lil~~~Yta~L~s 691 (953)
+...++.+++||++.++...|.. .|.+..+|++.+++.++++.+.....+.++.
T Consensus 164 ~~~~s~~dA~y~svvt~tTvGyGdi~p~t~~grl~~i~~ii~Gi~vf~~~is~i~~ 219 (393)
T PRK10537 164 PPIESLSTAFYFSIVTMSTVGYGDIVPVSESARLFTISVIILGITVFATSISAIFG 219 (393)
T ss_pred cCCCCHHHHHHhhheeeecccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44567999999999998877644 6889999999999999988776555454444
No 352
>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=77.20 E-value=28 Score=34.21 Aligned_cols=98 Identities=15% Similarity=0.035 Sum_probs=63.9
Q ss_pred HHHHHHHHHHHHcCCcEEEEEEecCccccchHHHHHHHHHhc--CcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEE
Q 002211 168 YLMSAIAEMVSYFGWGEVIAIFNDDDQGRNGVTALGDKLAEI--RCKISYKSALPPDQSVTETDVRNELVKVRMMEARVI 245 (953)
Q Consensus 168 ~~~~ai~~~l~~~~w~~vaii~~d~~~g~~~~~~l~~~l~~~--g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vi 245 (953)
..+..+.+.....+ .+|.++....+ ..+.+.+.+++. |++|+.. ... .+.++-...+++|.+++||++
T Consensus 35 dl~~~l~~~~~~~~-~~vfllG~~~~----v~~~~~~~l~~~yP~l~i~g~---~g~--f~~~~~~~i~~~I~~s~~dil 104 (177)
T TIGR00696 35 DLMEELCQRAGKEK-LPIFLYGGKPD----VLQQLKVKLIKEYPKLKIVGA---FGP--LEPEERKAALAKIARSGAGIV 104 (177)
T ss_pred HHHHHHHHHHHHcC-CeEEEECCCHH----HHHHHHHHHHHHCCCCEEEEE---CCC--CChHHHHHHHHHHHHcCCCEE
Confidence 44566666666566 68888875543 455666666655 7777764 211 224555678999999999999
Q ss_pred EEEcchhhHHHHHHHHHHcCCCCCceEEEEeCc
Q 002211 246 VVHGYSRTGLMVFDVAQRLGMMDSGYVWIATTW 278 (953)
Q Consensus 246 i~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~ 278 (953)
++.+..+.-..++.+.++.- +.-++++.++
T Consensus 105 ~VglG~PkQE~~~~~~~~~~---~~~v~~gvGg 134 (177)
T TIGR00696 105 FVGLGCPKQEIWMRNHRHLK---PDAVMIGVGG 134 (177)
T ss_pred EEEcCCcHhHHHHHHhHHhC---CCcEEEEece
Confidence 99988877777776664432 2235555443
No 353
>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=77.06 E-value=7.6 Score=40.70 Aligned_cols=78 Identities=9% Similarity=0.066 Sum_probs=59.8
Q ss_pred EEEEEe--cCccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEc-chhhHHHHHHHH
Q 002211 185 VIAIFN--DDDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHG-YSRTGLMVFDVA 261 (953)
Q Consensus 185 vaii~~--d~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~-~~~~~~~~~~~a 261 (953)
|++|.. ++.|.......+++++++.|..+... .+.. .+.......++++.+.++|.||+.. .+.....+++++
T Consensus 1 I~vi~~~~~~~~~~~~~~g~~~~a~~~g~~~~~~--~~~~--~d~~~q~~~i~~~i~~~~d~Iiv~~~~~~~~~~~l~~~ 76 (257)
T PF13407_consen 1 IGVIVPSMDNPFWQQVIKGAKAAAKELGYEVEIV--FDAQ--NDPEEQIEQIEQAISQGVDGIIVSPVDPDSLAPFLEKA 76 (257)
T ss_dssp EEEEESSSSSHHHHHHHHHHHHHHHHHTCEEEEE--EEST--TTHHHHHHHHHHHHHTTESEEEEESSSTTTTHHHHHHH
T ss_pred cEEEeCCCCCHHHHHHHHHHHHHHHHcCCEEEEe--CCCC--CCHHHHHHHHHHHHHhcCCEEEecCCCHHHHHHHHHHH
Confidence 456653 56688889999999999999988765 2222 3356677788888889999999874 456678899999
Q ss_pred HHcCC
Q 002211 262 QRLGM 266 (953)
Q Consensus 262 ~~~g~ 266 (953)
.+.|+
T Consensus 77 ~~~gI 81 (257)
T PF13407_consen 77 KAAGI 81 (257)
T ss_dssp HHTTS
T ss_pred hhcCc
Confidence 99886
No 354
>cd08428 PBP2_IciA_ArgP The C-terminal substrate binding domain of LysR-type transcriptional regulator, ArgP (IciA), for arginine exporter (ArgO); contains the type 2 periplasmic binding fold. The inhibitor of chromosomal replication (iciA) protein encoded by Mycobacterium tuberculosis, which is implicated in chromosome replication initiation in vitro, has been identified as arginine permease (ArgP), a LysR-type transcriptional regulator for arginine outward transport, based on the same amino sequence and similar DNA binding targets. Arp has been shown to regulate various targets including DnaA (replication), ArgO (arginine export), dapB (lysine biosynthesis), and gdhA (glutamate biosynthesis). With abundant nutrition, ArgP activates the DnaA gene (to increase replication) and the ArgO (to export redundant molecules). However, when nutrition supply is limited, it is suggested that ArgP might function as an inhibitor of chromosome replication in order to slow replication. This substrate-
Probab=76.41 E-value=78 Score=30.76 Aligned_cols=100 Identities=11% Similarity=0.020 Sum_probs=52.8
Q ss_pred CCChHHhhhCCCe-EEEEeCchHH-HHHHHhhCCCc--cceEeCCCHHHHHHHHHcCCcEEEEccchhHHHHHhcCcceE
Q 002211 702 IKGIDTLMTSNDR-VGYQVGSFAE-NYLIEELSIPK--SRLVALGSPEEYAIALENRTVAAVVDERPYIDLFLSDHCQFS 777 (953)
Q Consensus 702 I~sl~dL~~~~~~-ig~~~~s~~~-~~l~~~~~~~~--~~~~~~~~~~~~~~~l~~g~~~a~~~~~~~~~~~~~~~~~l~ 777 (953)
.-+++||. +.+ |....++... .++.+..+... .....+++.+.....+.+|.--+++.+.. +.....+ ..+.
T Consensus 89 ~i~~~~L~--~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~G~Gi~~lp~~~-~~~~~~~-~~l~ 164 (195)
T cd08428 89 GLTREALL--KAPAVAFNRKDDLHQSFLQQHFGLPPGSYPCHYVPSSEAFVDLAAQGLAYGMIPELQ-IEPELAS-GELI 164 (195)
T ss_pred CCCHHHHh--cCcEEEEcCCCchhHHHHHHHhccCCCCceEEEECCHHHHHHHHHhCCeeEeccHHH-HHHHhcC-CCEE
Confidence 34678887 444 4444443332 34333222221 12345778888888888877666665533 3322222 2344
Q ss_pred EeCCccccCccEEEecCCCcchHHHHHHH
Q 002211 778 VRGQEFTKSGWGFAFPRDSPLAIDMSTAI 806 (953)
Q Consensus 778 ~~~~~~~~~~~~~~~~k~spl~~~~n~~i 806 (953)
.+.+. ....++++.+++.+....+...+
T Consensus 165 ~l~~~-~~~~~~l~~~~~~~~s~~~~~~~ 192 (195)
T cd08428 165 DLAPG-HLLRVTLYWHRWNLESGLMKRLS 192 (195)
T ss_pred EccCc-ccccceEEEecccccCHHHHHhh
Confidence 44332 24567788888866555544443
No 355
>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=76.27 E-value=21 Score=40.10 Aligned_cols=89 Identities=13% Similarity=0.137 Sum_probs=63.4
Q ss_pred HHHHHHHHHc---CCcEEEEEEecCccc-cchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEE
Q 002211 171 SAIAEMVSYF---GWGEVIAIFNDDDQG-RNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIV 246 (953)
Q Consensus 171 ~ai~~~l~~~---~w~~vaii~~d~~~g-~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii 246 (953)
+.+.++++.+ |.+++.+|+....+. .+..+.+.+.+++.|+++.....+.++ .+.+++...+..+++.++|+||
T Consensus 12 ~~l~~~l~~~~~~g~kr~livtd~~~~~~~g~~~~v~~~L~~~gi~~~~f~~v~~~--p~~~~v~~~~~~~~~~~~D~II 89 (383)
T cd08186 12 EKIGEILKDLKSKGISKVLLVTGKSAYKKSGAWDKVEPALDEHGIEYVLYNKVTPN--PTVDQVDEAAKLGREFGAQAVI 89 (383)
T ss_pred HHHHHHHHHhcccCCCEEEEEcCccHHhhcChHHHHHHHHHHcCCeEEEeCCCCCC--CCHHHHHHHHHHHHHcCCCEEE
Confidence 4466667776 789999888544433 345688999999999876544444444 5678888999999999999999
Q ss_pred EEcch--hhHHHHHHHH
Q 002211 247 VHGYS--RTGLMVFDVA 261 (953)
Q Consensus 247 ~~~~~--~~~~~~~~~a 261 (953)
..+.+ -|..+++...
T Consensus 90 aiGGGS~iD~aK~ia~~ 106 (383)
T cd08186 90 AIGGGSPIDSAKSAAIL 106 (383)
T ss_pred EeCCccHHHHHHHHHHH
Confidence 77554 4566555543
No 356
>PRK07475 hypothetical protein; Provisional
Probab=76.17 E-value=17 Score=37.94 Aligned_cols=84 Identities=14% Similarity=0.072 Sum_probs=51.4
Q ss_pred CCChHHHHHHH-HHHHhcCcEEEEccCChhhHHHHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHH
Q 002211 97 KFNGFLSIMGA-LQFMETDTLAIVGPQSAVMAHVLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAE 175 (953)
Q Consensus 97 ~~~~~~a~~~a-~~li~~~v~aiiGp~~S~~a~av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~ 175 (953)
..++......+ ++|...++.+|+.|. .........+.+..+||+++. +.+..+
T Consensus 60 ~~~~~~~l~~aa~~L~~~G~d~I~~~C-gt~~~~~~~l~~~~~VPv~~s-------------------------s~~~v~ 113 (245)
T PRK07475 60 DPSLLDAFVAAARELEAEGVRAITTSC-GFLALFQRELAAALGVPVATS-------------------------SLLQVP 113 (245)
T ss_pred CccHHHHHHHHHHHHHHcCCCEEEech-HHHHHHHHHHHHHcCCCEecc-------------------------HHHHHH
Confidence 34555555444 445555999999976 333444556777789999851 122233
Q ss_pred HHHHc--CCcEEEEEEecCccccchHHHHHHHHHhcCcE
Q 002211 176 MVSYF--GWGEVIAIFNDDDQGRNGVTALGDKLAEIRCK 212 (953)
Q Consensus 176 ~l~~~--~w~~vaii~~d~~~g~~~~~~l~~~l~~~g~~ 212 (953)
.++.. +-++|+++..+.. .. ..+.+++.|++
T Consensus 114 ~l~~~~~~~~kIGILtt~~t---~l---~~~~l~~~Gi~ 146 (245)
T PRK07475 114 LIQALLPAGQKVGILTADAS---SL---TPAHLLAVGVP 146 (245)
T ss_pred HHHHhccCCCeEEEEeCCch---hh---hHHHHHhCCCC
Confidence 34443 3689999986654 22 35668888875
No 357
>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=76.10 E-value=65 Score=32.60 Aligned_cols=125 Identities=10% Similarity=0.073 Sum_probs=75.3
Q ss_pred HHHHhcCcEEEEccCChhhHHHHHHhh-hhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCCcEEE
Q 002211 108 LQFMETDTLAIVGPQSAVMAHVLSHLA-NELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVI 186 (953)
Q Consensus 108 ~~li~~~v~aiiGp~~S~~a~av~~v~-~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~va 186 (953)
.+|...++.+|+=+.+|. ...+..+- ...++|+++. .++..+-+.. +-++++
T Consensus 59 ~~l~~~g~d~i~i~C~s~-~~~~~~~~~~~~~iPv~~~-------------------------~~a~~~~~~~-~~~ri~ 111 (216)
T PF01177_consen 59 EKLEKAGVDAIVIACNSA-HPFVDELRKERVGIPVVGI-------------------------VEAALEAAKA-GGKRIG 111 (216)
T ss_dssp HHHHHTTESEEEESSHHH-HHHHHHHHHHHHSSEEEES-------------------------HHHHHHHHHH-TSSEEE
T ss_pred HHHHhCCCCEEEEcCCch-hhhHHHHhhhcCceEEEec-------------------------cHHHHHHHHh-cCCEEE
Confidence 333444899988765544 23344444 6679998863 1223444555 889999
Q ss_pred EEEecCccccchHHHHHHHHHhc-Cc--EEEEEE--ecC----CCCCCChH---HHHHHHHHH-hcCCceEEEEEcchhh
Q 002211 187 AIFNDDDQGRNGVTALGDKLAEI-RC--KISYKS--ALP----PDQSVTET---DVRNELVKV-RMMEARVIVVHGYSRT 253 (953)
Q Consensus 187 ii~~d~~~g~~~~~~l~~~l~~~-g~--~v~~~~--~~~----~~~~~~~~---d~~~~l~~i-~~~~~~vii~~~~~~~ 253 (953)
++.. ++......+.+.+++. |+ +++... .+. .+. .+.. .+...+.++ +..++|+|++.|..-.
T Consensus 112 vl~t---~~~~~~~~~~~~~~~~~gi~~~~~~~i~~~~~~~~e~~~-~~~~~~~~~~~~~~~l~~~~~~d~iiLgCt~l~ 187 (216)
T PF01177_consen 112 VLTT---YTTEKSPLYEEFIEEAAGIDDEVVAGIHNAIYDVIELGD-IPPEQIEILAEAARELIKEDGADAIILGCTHLP 187 (216)
T ss_dssp EEES---HHHHHHTHHHHHHHHCTTEECEEEEEEEEEHTHHHHTTC-TTHHHHHHHHHHHHHHHHCTTSSEEEEESTTGG
T ss_pred EEec---CcccchHHHHHHHHHhcCCcHHHHHHHHhhcHHHHhhhc-CCHHHHHHHHHHHHHHhccCCCCEEEECCCchH
Confidence 9985 4556677788888887 87 555421 111 220 1222 345555555 3789999999887644
Q ss_pred HH-HHHHHHHH
Q 002211 254 GL-MVFDVAQR 263 (953)
Q Consensus 254 ~~-~~~~~a~~ 263 (953)
.. ...+.+.+
T Consensus 188 ~~~~~~~~l~~ 198 (216)
T PF01177_consen 188 LLLGAIEALEE 198 (216)
T ss_dssp GGHHHHHHHHH
T ss_pred HHHHHHHhhcc
Confidence 33 55655554
No 358
>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=75.65 E-value=22 Score=39.14 Aligned_cols=100 Identities=14% Similarity=0.190 Sum_probs=66.9
Q ss_pred HHHHHHHHHcCCcEEEEEEecCccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcc
Q 002211 171 SAIAEMVSYFGWGEVIAIFNDDDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGY 250 (953)
Q Consensus 171 ~ai~~~l~~~~w~~vaii~~d~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~ 250 (953)
..+.+.++.+|.+++.+|+....+- ...+.+.+.+++. +++.......++ .+.++....+..+++.++|+||..+.
T Consensus 12 ~~l~~~~~~~g~~~~liv~~~~~~~-~~~~~v~~~l~~~-~~~~~~~~~~~~--p~~~~v~~~~~~~~~~~~d~IIaiGG 87 (332)
T cd07766 12 EKIGEEIKRGGFDRALVVSDEGVVK-GVGEKVADSLKKL-IAVHIFDGVGPN--PTFEEVKEAVERARAAEVDAVIAVGG 87 (332)
T ss_pred HHHHHHHHhcCCCeEEEEeCCchhh-hHHHHHHHHHHhc-CcEEEeCCcCCC--cCHHHHHHHHHHHHhcCcCEEEEeCC
Confidence 3466778888989999998544433 6778888888876 655433333333 45778888999999999999998765
Q ss_pred h--hhHHHHHHHHHHcCCCCCceEEEEeC
Q 002211 251 S--RTGLMVFDVAQRLGMMDSGYVWIATT 277 (953)
Q Consensus 251 ~--~~~~~~~~~a~~~g~~~~~~~wi~~~ 277 (953)
+ -|..+++......| ..++-|.|.
T Consensus 88 Gs~~D~aK~ia~~~~~~---~p~i~iPTt 113 (332)
T cd07766 88 GSTLDTAKAVAALLNRG---LPIIIVPTT 113 (332)
T ss_pred chHHHHHHHHHHHhcCC---CCEEEEeCC
Confidence 4 45555555444323 344555554
No 359
>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=75.37 E-value=13 Score=41.79 Aligned_cols=87 Identities=11% Similarity=0.152 Sum_probs=61.9
Q ss_pred HHHHHHHHHcCCcEEEEEEecCcc-ccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEc
Q 002211 171 SAIAEMVSYFGWGEVIAIFNDDDQ-GRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHG 249 (953)
Q Consensus 171 ~ai~~~l~~~~w~~vaii~~d~~~-g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~ 249 (953)
+.+.+.++.++ +++.+|.....+ ..+..+.+.+.|++.|+++.....+.++ .+.++....+..+++.++|+||-.+
T Consensus 18 ~~l~~~~~~~~-~r~livt~~~~~~~~~~~~~v~~~L~~~g~~~~~~~~v~~~--p~~~~v~~~~~~~~~~~~D~IIaiG 94 (382)
T cd08187 18 SELGKELKKYG-KKVLLVYGGGSIKKNGLYDRVIASLKEAGIEVVELGGVEPN--PRLETVREGIELCKEEKVDFILAVG 94 (382)
T ss_pred HHHHHHHHHhC-CEEEEEeCCcHHHhcCcHHHHHHHHHHcCCeEEEECCccCC--CCHHHHHHHHHHHHHcCCCEEEEeC
Confidence 45667777775 898888754333 2356788999999999887654445544 5577888889999999999999876
Q ss_pred ch--hhHHHHHHH
Q 002211 250 YS--RTGLMVFDV 260 (953)
Q Consensus 250 ~~--~~~~~~~~~ 260 (953)
.+ -|+.+.+..
T Consensus 95 GGS~iD~aK~ia~ 107 (382)
T cd08187 95 GGSVIDSAKAIAA 107 (382)
T ss_pred ChHHHHHHHHHHh
Confidence 54 455555433
No 360
>cd08446 PBP2_Chlorocatechol The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the chlorocatechol catabolism, contains the type 2 periplasmic binding fold. This CD includes the substrate binding domain of LysR-type regulators CbnR, ClcR and TfdR, which are involved in the regulation of chlorocatechol breakdown. The chlorocatechol-degradative pathway is often found in bacteria that can use chlorinated aromatic compounds as carbon and energy sources. CbnR is found in the 3-chlorobenzoate degradative bacterium Ralstonia eutropha NH9 and forms a tetramer. CbnR activates the expression of the cbnABCD genes, which are responsible for the degradation of chlorocatechol converted from 3-chlorobenzoate and are transcribed divergently from cbnR. In soil bacterium Pseudomonas putida, the 3-chlorocatechol-degradative pathway is encoded by clcABD operon, which requires the divergently transcribed clcR for activation. TfdR is involved in the activation of tf
Probab=75.27 E-value=83 Score=30.54 Aligned_cols=70 Identities=14% Similarity=0.150 Sum_probs=47.2
Q ss_pred EeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEecEEEecCccceeeccccceecceEEEEec
Q 002211 512 GYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGDIAIVTNRTKAVDFTQPYIESGLVVVAPV 591 (953)
Q Consensus 512 G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~~~~t~~r~~~vdft~p~~~~~~~~~v~~ 591 (953)
++..+++..+.++.+ .++++... +.+.++.+.+.+|++|+++.... .....+ -+.++....++++++.
T Consensus 14 ~~l~~~i~~~~~~~P-~v~l~i~~-------~~~~~~~~~l~~~~~Dl~i~~~~---~~~~~~-~~~~l~~~~~~~v~~~ 81 (198)
T cd08446 14 DTVPRLLRAFLTARP-DVTVSLHN-------MTKDEQIEALRAGRIHIGFGRFY---PVEPDI-AVENVAQERLYLAVPK 81 (198)
T ss_pred HHHHHHHHHHHHHCC-CeEEEEee-------CCHHHHHHHHHCCCccEEEEecC---CCCCCc-eeEEeeeccEEEEEeC
Confidence 355778888888875 35565554 56888999999999999985321 111222 2456677788888776
Q ss_pred cc
Q 002211 592 RK 593 (953)
Q Consensus 592 ~~ 593 (953)
..
T Consensus 82 ~~ 83 (198)
T cd08446 82 SH 83 (198)
T ss_pred CC
Confidence 55
No 361
>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=74.74 E-value=14 Score=40.90 Aligned_cols=87 Identities=16% Similarity=0.106 Sum_probs=61.7
Q ss_pred HHHHHHHHHcCCcEEEEEEecCccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcc
Q 002211 171 SAIAEMVSYFGWGEVIAIFNDDDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGY 250 (953)
Q Consensus 171 ~ai~~~l~~~~w~~vaii~~d~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~ 250 (953)
..+.++++.+| +++.+|+....+ ....+.+.+.+++.|+.+.....+..+ .+.+++....+..++.++|+||-.+.
T Consensus 12 ~~l~~~~~~~~-~r~liv~d~~~~-~~~~~~v~~~l~~~~~~~~~~~~~~~~--p~~~~v~~~~~~~~~~~~d~iiavGG 87 (345)
T cd08171 12 KKIPEVCEKYG-KKVVVIGGKTAL-AAAKDKIKAALEQSGIEITDFIWYGGE--STYENVERLKKNPAVQEADMIFAVGG 87 (345)
T ss_pred HHHHHHHHhcC-CEEEEEeCHHHH-HHHHHHHHHHHHHCCCeEEEEEecCCC--CCHHHHHHHHHHHhhcCCCEEEEeCC
Confidence 44667777777 898888765444 345778888898889877644455554 55777888888888899999998766
Q ss_pred h--hhHHHHHHHH
Q 002211 251 S--RTGLMVFDVA 261 (953)
Q Consensus 251 ~--~~~~~~~~~a 261 (953)
+ -|+.+++...
T Consensus 88 Gs~~D~aK~ia~~ 100 (345)
T cd08171 88 GKAIDTVKVLADK 100 (345)
T ss_pred cHHHHHHHHHHHH
Confidence 5 4555555443
No 362
>PF03401 TctC: Tripartite tricarboxylate transporter family receptor; InterPro: IPR005064 Bordetella pertussis, the causative agent of human whooping cough (pertussis), is an obligate human pathogen with diverse high-affinity transport systems for the assimilation of iron, a biometal that is essential for growth []. Periplasmic binding proteins of a new family, particularly well represented in this organism (and more generally in beta-proteobacteria), have been called Bug receptors []. They adopt a characteristic Venus flytrap fold with two globular domains bisected by a ligand-binding cleft. The family is specific for carboxylated solutes, with a characteristic mode of binding involving two highly conserved beta strand-beta turn-alpha helix motifs originating from each domain. These two motifs form hydrogen bonds with a carboxylate group of the ligand, both directly and via conserved water molecules, and have thus been termed the carboxylate pincers. Domain 1 recognises the ligand and the carboxylate group serves as an initial anchoring point. Domain 2 discriminates between productively and non-productively bound ligands as proper interactions with this domain is needed for the of the closed conformation []. BugE has a glutamate bound ligand. No charged residues are involved in glutamate binding by BugE, unlike what has been described for all glutamate receptors reported so far. The Bug architecture is highly conserved despite limited sequence identity [].; GO: 0030288 outer membrane-bounded periplasmic space; PDB: 2QPQ_C 2DVZ_A 2F5X_A.
Probab=74.32 E-value=76 Score=33.72 Aligned_cols=122 Identities=22% Similarity=0.231 Sum_probs=74.2
Q ss_pred CCCCChHHhhh----CC--CeEEEE-eCch---HHHHHHHhhCCCccceEeCCCHHHHHHHHHcCCcEEEEccchhHHHH
Q 002211 700 SPIKGIDTLMT----SN--DRVGYQ-VGSF---AENYLIEELSIPKSRLVALGSPEEYAIALENRTVAAVVDERPYIDLF 769 (953)
Q Consensus 700 ~~I~sl~dL~~----~~--~~ig~~-~~s~---~~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~g~~~a~~~~~~~~~~~ 769 (953)
.+++|++||++ +. .++|.. .|+. ....|.+..+.. .+.++|++..+.+.+|..|.+|+.+.......-+
T Consensus 88 sp~~t~~eli~~ak~~p~~~~~g~~g~g~~~hl~~~~l~~~~G~~-~~~Vpy~G~~~~~~allgG~vd~~~~~~~~~~~~ 166 (274)
T PF03401_consen 88 SPYKTLEELIEYAKANPGKLTFGSSGPGSSDHLAAALLAKAAGIK-FTHVPYDGGAEALTALLGGHVDAAFGSPGEALPY 166 (274)
T ss_dssp SS-SSHHHHHHHHHCSCCC-EEEESSTTSHHHHHHHHHHHHHT----EEEE-SSHHHHHHHHHTTSSSEEEEEHHHHHHH
T ss_pred CccccHHHHHHHHHhCCCCeEEEecCCCchHHHHHHHHHHHhCCc-eEEEEeCCccHHHHHHhCCeeeEEeecHHHHHHH
Confidence 57889999864 22 356654 2332 234455566654 5678999999999999999999998875544333
Q ss_pred Hhc-Ccc-eEE--------------eCC----cc-ccCccEEEecCCCc--chHHHHHHHHhhhccccHHHHHHHh
Q 002211 770 LSD-HCQ-FSV--------------RGQ----EF-TKSGWGFAFPRDSP--LAIDMSTAILTLSENGELQRIHDKW 822 (953)
Q Consensus 770 ~~~-~~~-l~~--------------~~~----~~-~~~~~~~~~~k~sp--l~~~~n~~i~~l~e~G~~~~~~~~w 822 (953)
+.. .-+ +-+ ..+ .+ .....++.+|||-| .++.+..++.+..++-.+++..++.
T Consensus 167 ~~~G~~k~Lav~~~~r~~~~pdvPT~~E~G~~d~~~~~~~g~~~p~gtp~~~~~~l~~a~~~~~~~pe~~~~~~~~ 242 (274)
T PF03401_consen 167 VEAGDLKPLAVFSDERSPALPDVPTFKEQGYPDIVFGSWRGLFAPKGTPDEIVDKLADAIKKALEDPEFQEFLEKM 242 (274)
T ss_dssp HHTTSEEEEEECSSS-BTTCTTS-BTTTTT-TTG--EEEEEEEEETTS-HHHHHHHHHHHHHHHT-HHHHHHHHHH
T ss_pred HhCCCceEEEEecCccccccCCCCCHHHhCccceeeeeeeeeecCCCCCHHHHHHHHHHHHHHhCCHHHHHHHHHC
Confidence 332 111 111 111 11 11235888999988 9999999999999988776665543
No 363
>PF13685 Fe-ADH_2: Iron-containing alcohol dehydrogenase; PDB: 3CE9_C.
Probab=73.10 E-value=21 Score=37.18 Aligned_cols=100 Identities=16% Similarity=0.229 Sum_probs=58.2
Q ss_pred HHHHHHHHcCCcEEEEEEecCccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcch
Q 002211 172 AIAEMVSYFGWGEVIAIFNDDDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYS 251 (953)
Q Consensus 172 ai~~~l~~~~w~~vaii~~d~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~ 251 (953)
.+.+++++++.+++.+|...+.| ....+.+.+.+++.|+++......... .+..+......+++..++|+||-.+.+
T Consensus 9 ~l~~~l~~~~~~~~lvv~d~~t~-~~~g~~v~~~l~~~g~~v~~~~~~~~~--~~~~~~~~~~~~~~~~~~d~ii~vGgG 85 (250)
T PF13685_consen 9 KLPEILSELGLKKVLVVTDENTY-KAAGEKVEESLKSAGIEVAVIEEFVGD--ADEDEVEKLVEALRPKDADLIIGVGGG 85 (250)
T ss_dssp GHHHHHGGGT-SEEEEEEETTHH-HHHHHHHHHHHHTTT-EEEEEE-EE-----BHHHHHHHHTTS--TT--EEEEEESH
T ss_pred HHHHHHHhcCCCcEEEEEcCCHH-HHHHHHHHHHHHHcCCeEEEEecCCCC--CCHHHHHHHHHHhcccCCCEEEEeCCc
Confidence 35677888888999999876654 345577888899999988743322222 335666677777777889999988887
Q ss_pred hhHHHHHHHHHHcCCCCCceEEEEeC
Q 002211 252 RTGLMVFDVAQRLGMMDSGYVWIATT 277 (953)
Q Consensus 252 ~~~~~~~~~a~~~g~~~~~~~wi~~~ 277 (953)
.-.-.-=-.|.+.| ..|+-+.|.
T Consensus 86 ~i~D~~K~~A~~~~---~p~isVPTa 108 (250)
T PF13685_consen 86 TIIDIAKYAAFELG---IPFISVPTA 108 (250)
T ss_dssp HHHHHHHHHHHHHT-----EEEEES-
T ss_pred HHHHHHHHHHHhcC---CCEEEeccc
Confidence 53322222344545 355656554
No 364
>KOG1419 consensus Voltage-gated K+ channel KCNQ [Inorganic ion transport and metabolism]
Probab=72.60 E-value=7.1 Score=43.99 Aligned_cols=89 Identities=13% Similarity=0.184 Sum_probs=69.4
Q ss_pred hhHHHHHHHHHHHHHHHhhhhhcccCCCCCCCCcccchhhHHHHHHHhhccccC--CcccchhHHHHHHHHHHHHHhhhh
Q 002211 607 PLMWAVTGVFFLVVGTVVWILEHRLNDEFRGPPRKQIVTVLWFSFSTMFFAHRE--NTVSTLGRVVLIIWLFVVLIITSS 684 (953)
Q Consensus 607 ~~vW~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~--~~~s~~~R~l~~~w~~~~lil~~~ 684 (953)
...|..-++.+++.++++|+.|.....+-......+.-.++|+...++...|.. .|..+.+|++..+.-++++=+-+.
T Consensus 234 iTt~YIGFL~LIfsSflVYLaEKd~~~e~~n~~F~TyADALWWG~ITltTIGYGDk~P~TWlGr~laa~fsligiSFFAL 313 (654)
T KOG1419|consen 234 ITTWYIGFLVLIFSSFLVYLAEKDAQGEGTNDEFPTYADALWWGVITLTTIGYGDKTPQTWLGRLLAACFSLIGISFFAL 313 (654)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhcccccccccccchhHHHHHHhhheeEEeeccCCcCcccchhHHHHHHHHHHHHHHHhc
Confidence 357888899999999999999988544333334446788999999999988754 899999999999888888766666
Q ss_pred cccceeeeeee
Q 002211 685 YTASLTSILTV 695 (953)
Q Consensus 685 Yta~L~s~Lt~ 695 (953)
=.+.|-|=++.
T Consensus 314 PAGILGSGfAL 324 (654)
T KOG1419|consen 314 PAGILGSGFAL 324 (654)
T ss_pred ccccccchhhh
Confidence 66666665554
No 365
>cd08485 PBP2_ClcR The C-terminal substrate binding domain of LysR-type transcriptional regulator ClcR involved in the chlorocatechol catabolism, contains type 2 periplasmic binding fold. In soil bacterium Pseudomonas putida, the ortho-pathways of catechol and 3-chlorocatechol are central catabolic pathways that convert aromatic and chloroaromaric compounds to tricarboxylic acid (TCA) cycle intermediates. The 3-chlorocatechol-degradative pathway is encoded by clcABD operon, which requires the divergently transcribed clcR and an intermediate of the pathway, 2-chloromuconate, as an inducer for activation. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding th
Probab=72.43 E-value=1e+02 Score=30.20 Aligned_cols=70 Identities=11% Similarity=0.122 Sum_probs=44.2
Q ss_pred EeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEecEEEecCccceeeccccceecceEEEEec
Q 002211 512 GYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGDIAIVTNRTKAVDFTQPYIESGLVVVAPV 591 (953)
Q Consensus 512 G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~~~~t~~r~~~vdft~p~~~~~~~~~v~~ 591 (953)
.+-.+++..+.++.+ .++++... ++-++++++|.+|++|+++...... ...+. +.++.+..++++++.
T Consensus 14 ~~l~~~l~~~~~~~P-~i~l~~~~-------~~~~~~~~~l~~~~~D~~i~~~~~~---~~~l~-~~~l~~~~~~~~~~~ 81 (198)
T cd08485 14 HTLPLLLRQLLSVAP-SATVSLTQ-------MSKNRQIEALDAGTIDIGFGRFYPY---QEGVV-VRNVTNERLFLGAQK 81 (198)
T ss_pred HHHHHHHHHHHHhCC-CcEEEEEE-------CCHHHHHHHHHcCCccEEEecCCCC---CCCeE-EEEeeccceEEEeCC
Confidence 455677888877764 35555553 4567899999999999988632111 12232 346666677766654
Q ss_pred cc
Q 002211 592 RK 593 (953)
Q Consensus 592 ~~ 593 (953)
..
T Consensus 82 ~~ 83 (198)
T cd08485 82 SR 83 (198)
T ss_pred CC
Confidence 43
No 366
>PRK11716 DNA-binding transcriptional regulator IlvY; Provisional
Probab=71.93 E-value=1.2e+02 Score=31.53 Aligned_cols=83 Identities=17% Similarity=0.140 Sum_probs=52.3
Q ss_pred cceEEEecCcccccccEEeeCCcceEEEeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEecE
Q 002211 485 RQLRIGVPNRVSYRDFVFKVNGTDIVHGYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGDI 564 (953)
Q Consensus 485 ~~lri~v~~~~~~~p~~~~~~~~~~~~G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~~ 564 (953)
+.++||++.. . ...+..+++..+.++.+- +++.... ++..+++..+.+|++|+++...
T Consensus 67 ~~l~I~~~~~--~------------~~~~~~~~l~~~~~~~p~-i~l~i~~-------~~~~~~~~~l~~~~~D~~i~~~ 124 (269)
T PRK11716 67 GELSLFCSVT--A------------AYSHLPPILDRFRAEHPL-VEIKLTT-------GDAADAVEKVQSGEADLAIAAK 124 (269)
T ss_pred ceEEEEecch--H------------HHHHHHHHHHHHHHHCCC-eEEEEEE-------CCHHHHHHHHHCCCccEEEEec
Confidence 5688887641 1 123556788888888752 4555554 4577999999999999998532
Q ss_pred EEecCccceeeccccceecceEEEEecc
Q 002211 565 AIVTNRTKAVDFTQPYIESGLVVVAPVR 592 (953)
Q Consensus 565 ~~t~~r~~~vdft~p~~~~~~~~~v~~~ 592 (953)
.. .....+. ..+.....++++++..
T Consensus 125 ~~--~~~~~~~-~~~l~~~~~~~v~~~~ 149 (269)
T PRK11716 125 PE--TLPASVA-FSPIDEIPLVLIAPAL 149 (269)
T ss_pred CC--CCCcceE-EEEcccceEEEEEcCC
Confidence 11 1111222 3556677777777654
No 367
>PRK09423 gldA glycerol dehydrogenase; Provisional
Probab=70.67 E-value=18 Score=40.43 Aligned_cols=84 Identities=8% Similarity=0.095 Sum_probs=60.7
Q ss_pred HHHHHHHHHcCCcEEEEEEecCccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcc
Q 002211 171 SAIAEMVSYFGWGEVIAIFNDDDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGY 250 (953)
Q Consensus 171 ~ai~~~l~~~~w~~vaii~~d~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~ 250 (953)
..+.+.++.+| +++.+|+....+ ....+.+.+.+++.|+++.+. .++.. .+.+++...++.+++.++|+||..+.
T Consensus 19 ~~l~~~l~~~g-~~~livtd~~~~-~~~~~~v~~~l~~~~~~~~~~-~~~~e--p~~~~v~~~~~~~~~~~~d~IIavGG 93 (366)
T PRK09423 19 ARLGEYLKPLG-KRALVIADEFVL-GIVGDRVEASLKEAGLTVVFE-VFNGE--CSDNEIDRLVAIAEENGCDVVIGIGG 93 (366)
T ss_pred HHHHHHHHHcC-CEEEEEEChhHH-HHHHHHHHHHHHhCCCeEEEE-EeCCC--CCHHHHHHHHHHHHhcCCCEEEEecC
Confidence 44667788888 999888854444 346788888898888887543 34544 45678888888888899999998766
Q ss_pred h--hhHHHHHH
Q 002211 251 S--RTGLMVFD 259 (953)
Q Consensus 251 ~--~~~~~~~~ 259 (953)
+ -|+.+++.
T Consensus 94 Gsv~D~aK~iA 104 (366)
T PRK09423 94 GKTLDTAKAVA 104 (366)
T ss_pred hHHHHHHHHHH
Confidence 5 45555554
No 368
>PRK13348 chromosome replication initiation inhibitor protein; Provisional
Probab=70.32 E-value=1.5e+02 Score=31.49 Aligned_cols=103 Identities=9% Similarity=0.014 Sum_probs=54.4
Q ss_pred CChHHhhhCCCe-EEEEeCch-HHHHHHHhhCCC--ccceEeCCCHHHHHHHHHcCCcEEEEccchhHHHHHhcCcceEE
Q 002211 703 KGIDTLMTSNDR-VGYQVGSF-AENYLIEELSIP--KSRLVALGSPEEYAIALENRTVAAVVDERPYIDLFLSDHCQFSV 778 (953)
Q Consensus 703 ~sl~dL~~~~~~-ig~~~~s~-~~~~l~~~~~~~--~~~~~~~~~~~~~~~~l~~g~~~a~~~~~~~~~~~~~~~~~l~~ 778 (953)
-+++||. +.+ |.+..+.. ...++....+.. .......++.....+.+..|.-.+++-+... ..... ...+..
T Consensus 180 v~~~~l~--~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~lp~~~~-~~~~~-~~~l~~ 255 (294)
T PRK13348 180 LTRHSAL--KAPAVAFNRKDTLQDSFLEQLFGLPVGAYPRHYVPSTHAHLAAIRHGLGYGMVPELLI-GPLLA-AGRLVD 255 (294)
T ss_pred CCHHHHc--CCCEEEecCCchHHHHHHHHHHhccccccceEEeCcHHHHHHHHHcCCeeEeCCHHHH-HHHHh-cCeeee
Confidence 4678886 444 44444432 334553322211 1223356788888888888776565554433 32222 234444
Q ss_pred eCCccccCccEEEecCCCcchHHHHHHHHhhh
Q 002211 779 RGQEFTKSGWGFAFPRDSPLAIDMSTAILTLS 810 (953)
Q Consensus 779 ~~~~~~~~~~~~~~~k~spl~~~~n~~i~~l~ 810 (953)
+.... ...++++.+|+.+....+...+..+.
T Consensus 256 l~~~~-~~~~~l~~~~~~~~~~~~~~~~~~i~ 286 (294)
T PRK13348 256 LAPGH-PVDVALYWHHWEVESPTMEALSQRVV 286 (294)
T ss_pred cCCCC-CCCceeEEeeccccChHHHHHHHHHH
Confidence 44332 45677888888765555544444443
No 369
>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=70.24 E-value=1.1e+02 Score=29.62 Aligned_cols=70 Identities=19% Similarity=0.236 Sum_probs=46.7
Q ss_pred EeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEecEEEecCccceeeccccceecceEEEEec
Q 002211 512 GYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGDIAIVTNRTKAVDFTQPYIESGLVVVAPV 591 (953)
Q Consensus 512 G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~~~~t~~r~~~vdft~p~~~~~~~~~v~~ 591 (953)
.+-.++++.+.++.+- ++++... ++..++++.+.+|++|+++..... . ...+. ..+.....++++++.
T Consensus 13 ~~l~~~l~~~~~~~P~-i~l~i~~-------~~~~~~~~~l~~~~~Dl~i~~~~~--~-~~~~~-~~~l~~~~~~~~~~~ 80 (196)
T cd08450 13 QWLPEVLPILREEHPD-LDVELSS-------LFSPQLAEALMRGKLDVAFMRPEI--Q-SDGID-YQLLLKEPLIVVLPA 80 (196)
T ss_pred hhHHHHHHHHHhhCCC-cEEEEEe-------cChHHHHHHHhcCCccEEEEeCCC--C-CCCcE-EEEEEccceEEEecC
Confidence 4557788888888752 4555554 457789999999999998852211 1 12232 456777788888776
Q ss_pred cc
Q 002211 592 RK 593 (953)
Q Consensus 592 ~~ 593 (953)
..
T Consensus 81 ~~ 82 (196)
T cd08450 81 DH 82 (196)
T ss_pred CC
Confidence 54
No 370
>PRK09986 DNA-binding transcriptional activator XapR; Provisional
Probab=70.12 E-value=1.6e+02 Score=31.42 Aligned_cols=85 Identities=15% Similarity=0.181 Sum_probs=53.9
Q ss_pred cceEEEecCcccccccEEeeCCcceEEEeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEecE
Q 002211 485 RQLRIGVPNRVSYRDFVFKVNGTDIVHGYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGDI 564 (953)
Q Consensus 485 ~~lri~v~~~~~~~p~~~~~~~~~~~~G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~~ 564 (953)
++++||+... + ...+..+++..+.++.+ .+.+.... .+-++++..+.+|++|+++...
T Consensus 97 ~~l~I~~~~~--~------------~~~~l~~~l~~f~~~~p-~i~l~i~~-------~~~~~~~~~l~~g~~D~~i~~~ 154 (294)
T PRK09986 97 GRIEIGIVGT--A------------LWGRLRPAMRHFLKENP-NVEWLLRE-------LSPSMQMAALERRELDAGIWRM 154 (294)
T ss_pred ceEEEEEehH--H------------hHHHHHHHHHHHHHhCC-CeEEEEEe-------CCHHHHHHHHHcCCCCEEEecC
Confidence 5699988641 1 12344667788887775 24455543 3457899999999999987521
Q ss_pred EEecCccceeeccccceecceEEEEeccc
Q 002211 565 AIVTNRTKAVDFTQPYIESGLVVVAPVRK 593 (953)
Q Consensus 565 ~~t~~r~~~vdft~p~~~~~~~~~v~~~~ 593 (953)
. .......+. +.|+....+++++++..
T Consensus 155 ~-~~~~~~~l~-~~~l~~~~~~~v~~~~~ 181 (294)
T PRK09986 155 A-DLEPNPGFT-SRRLHESAFAVAVPEEH 181 (294)
T ss_pred C-ccCCCCCeE-EEEeecccEEEEEcCCC
Confidence 1 011223344 36777788888887665
No 371
>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=69.86 E-value=32 Score=33.92 Aligned_cols=130 Identities=15% Similarity=0.150 Sum_probs=67.7
Q ss_pred CcEEEEccCChhhHHHHHHhhhhCC--CcE-EEeecCCCCCCC-CCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEE
Q 002211 114 DTLAIVGPQSAVMAHVLSHLANELQ--VPL-LSFTALDPTLSP-LQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIF 189 (953)
Q Consensus 114 ~v~aiiGp~~S~~a~av~~v~~~~~--vP~-Is~~at~~~ls~-~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~ 189 (953)
++++++||.+|+-...+..+.+... +.. ++++.-.|...+ ..-.|.|-. .. .+-+.++.-..=...- |
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----KE---EFERMIKAGEFIEYGE-Y 74 (183)
T ss_dssp SEEEEESSTTSSHHHHHHHHHHHSTTTEEEEEEEESS-GGTTS-TTTSEEE------HH---HHHHHHHTTHEEEEEE-E
T ss_pred CEEEEECCCCCCHHHHHHHHHHhcccccccceeecccCCcccccCCcceEEEe----ec---hhhhhhccccEEEEee-e
Confidence 6789999999998877777877653 433 444333344333 344566642 11 1222222211111121 4
Q ss_pred ecCccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHHHcC
Q 002211 190 NDDDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQRLG 265 (953)
Q Consensus 190 ~d~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~~~g 265 (953)
.++-||.. .+.+.+.+++...+|... .+ .-+.+++....+.++++..++....+-+.+++.|
T Consensus 75 ~g~~YGt~-~~~i~~~~~~gk~~il~~---~~----------~g~~~L~~~~~~~~~IfI~~~s~~~l~~~l~~r~ 136 (183)
T PF00625_consen 75 DGNYYGTS-KSAIDKVLEEGKHCILDV---DP----------EGVKQLKKAGFNPIVIFIKPPSPEVLKRRLRRRG 136 (183)
T ss_dssp TTEEEEEE-HHHHHHHHHTTTEEEEEE---TH----------HHHHHHHHCTTTEEEEEEEESSHHHHHHHHHTTT
T ss_pred cchhhhhc-cchhhHhhhcCCcEEEEc---cH----------HHHHHHHhcccCceEEEEEccchHHHHHHHhccc
Confidence 46677855 577777777777766542 11 2245555555555555554444444444444433
No 372
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=69.77 E-value=1.6e+02 Score=34.20 Aligned_cols=141 Identities=11% Similarity=0.178 Sum_probs=75.6
Q ss_pred EEccCChhhHHHHHHhhh-hCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEec-Cccc
Q 002211 118 IVGPQSAVMAHVLSHLAN-ELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFND-DDQG 195 (953)
Q Consensus 118 iiGp~~S~~a~av~~v~~-~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d-~~~g 195 (953)
|+||.+...-.++..+.+ ...+=+|.++- .-++|- +.....+.-.++.....-+++.|+|.. +...
T Consensus 198 i~~p~~~~v~~~l~~~~~l~l~~~~i~p~H----------G~i~r~--~~~~~l~~Y~~~~~~~~~~kv~IvY~S~~GnT 265 (479)
T PRK05452 198 ILTPFSRLVTPKITEILGFNLPVDMIATSH----------GVVWRD--NPTQIVELYLKWAADYQEDRITIFYDTMSNNT 265 (479)
T ss_pred hhhhhHHHHHHHHHHHhhcCCCCCEEECCC----------CceEeC--CHHHHHHHHHHHhhccCcCcEEEEEECCccHH
Confidence 789988876666666664 23444454321 124553 111122222233333345789999843 2333
Q ss_pred cchHHHHHHHHHhc--CcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcch------hhHHHHHHHHHHcCCC
Q 002211 196 RNGVTALGDKLAEI--RCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYS------RTGLMVFDVAQRLGMM 267 (953)
Q Consensus 196 ~~~~~~l~~~l~~~--g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~------~~~~~~~~~a~~~g~~ 267 (953)
+.+++.+.+.+++. |+++.... +. +.+....+..+ .++|.|++.++. +....++.......+.
T Consensus 266 e~mA~~ia~gl~~~g~gv~v~~~~-v~------~~~~~~i~~~~--~~ad~vilGspT~~~~~~p~~~~fl~~l~~~~l~ 336 (479)
T PRK05452 266 RMMADAIAQGIAEVDPRVAVKIFN-VA------RSDKNEILTNV--FRSKGVLVGSSTMNNVMMPKIAGLLEEITGLRFR 336 (479)
T ss_pred HHHHHHHHHHHHhhCCCceEEEEE-CC------CCCHHHHHhHH--hhCCEEEEECCccCCcchHHHHHHHHHhhccCcC
Confidence 56788899999877 44544322 22 22334444444 357788887543 3456666666666555
Q ss_pred CCceEEEEeCcc
Q 002211 268 DSGYVWIATTWL 279 (953)
Q Consensus 268 ~~~~~wi~~~~~ 279 (953)
++....+++.+|
T Consensus 337 gK~~~vFGSygw 348 (479)
T PRK05452 337 NKRASAFGSHGW 348 (479)
T ss_pred CCEEEEEECCCc
Confidence 444444555444
No 373
>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=69.76 E-value=36 Score=38.09 Aligned_cols=84 Identities=10% Similarity=0.097 Sum_probs=60.3
Q ss_pred HHHHHHHHHcCCcEEEEEEecCccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcc
Q 002211 171 SAIAEMVSYFGWGEVIAIFNDDDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGY 250 (953)
Q Consensus 171 ~ai~~~l~~~~w~~vaii~~d~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~ 250 (953)
..+.++++.++ +++.+|+..... ..+.+.+.|++.|+.+.... +..+ .+.+++...+..+++.++|+||-.+.
T Consensus 12 ~~l~~~l~~~~-~r~livtd~~~~---~~~~v~~~L~~~g~~~~~~~-~~~~--p~~~~v~~~~~~~~~~~~D~IIaiGG 84 (374)
T cd08183 12 KELPALAAELG-RRVLLVTGASSL---RAAWLIEALRAAGIEVTHVV-VAGE--PSVELVDAAVAEARNAGCDVVIAIGG 84 (374)
T ss_pred HHHHHHHHHcC-CcEEEEECCchH---HHHHHHHHHHHcCCeEEEec-CCCC--cCHHHHHHHHHHHHhcCCCEEEEecC
Confidence 44667777775 899888854443 67788888999998765433 3334 55778888899999999999998766
Q ss_pred h--hhHHHHHHHH
Q 002211 251 S--RTGLMVFDVA 261 (953)
Q Consensus 251 ~--~~~~~~~~~a 261 (953)
+ -|+.+++...
T Consensus 85 GS~~D~aK~ia~~ 97 (374)
T cd08183 85 GSVIDAGKAIAAL 97 (374)
T ss_pred chHHHHHHHHHHH
Confidence 5 4555555443
No 374
>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=69.57 E-value=45 Score=32.30 Aligned_cols=65 Identities=11% Similarity=0.081 Sum_probs=39.0
Q ss_pred eeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEecEEEecCccceeeccccceecceEEEEecc
Q 002211 513 YCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGDIAIVTNRTKAVDFTQPYIESGLVVVAPVR 592 (953)
Q Consensus 513 ~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~~~~t~~r~~~vdft~p~~~~~~~~~v~~~ 592 (953)
+...++..+.++.+ .++++... + + .+..+.+|++|+++... +.....+ .+.+.....++++++..
T Consensus 14 ~l~~~l~~~~~~~P-~v~i~~~~-------~--~-~~~~l~~g~~D~~i~~~---~~~~~~~-~~~~l~~~~~~~v~~~~ 78 (194)
T cd08432 14 WLIPRLARFQARHP-DIDLRLST-------S--D-RLVDFAREGIDLAIRYG---DGDWPGL-EAERLMDEELVPVCSPA 78 (194)
T ss_pred HHHHHhHHHHHHCC-CeEEEEEe-------c--C-CccccccccccEEEEec---CCCCCCc-ceEEccCCcEEEecCHH
Confidence 34566777777765 35565553 1 1 45678899999988521 1111222 25567777777777643
No 375
>PRK14498 putative molybdopterin biosynthesis protein MoeA/LysR substrate binding-domain-containing protein; Provisional
Probab=68.02 E-value=40 Score=40.86 Aligned_cols=67 Identities=19% Similarity=0.242 Sum_probs=48.3
Q ss_pred cCCcEEEEEEecCcc---------cc---chHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEE
Q 002211 180 FGWGEVIAIFNDDDQ---------GR---NGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVV 247 (953)
Q Consensus 180 ~~w~~vaii~~d~~~---------g~---~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~ 247 (953)
|..-+|++|...|+- |+ .....+...+++.|.++.....++.+ .+.+...+.++.+ ++|+||.
T Consensus 184 ~~~prv~vi~tG~El~~~~~~~~~g~i~dsn~~~l~~~l~~~g~~~~~~~~v~Dd----~~~i~~~l~~~~~-~~D~iIt 258 (633)
T PRK14498 184 YKKPRVGIISTGDELVEPGEPLKPGKIYDVNSYTLAAAVEEAGGEPVRYGIVPDD----EEELEAALRKALK-ECDLVLL 258 (633)
T ss_pred ecCcEEEEEecCccccCCCCCCCCCEEEEChHHHHHHHHHHCCCEEEEEEEeCCC----HHHHHHHHHHHHh-cCCEEEE
Confidence 345588888765441 22 34567888899999998887777655 7778888888764 7999999
Q ss_pred Ecch
Q 002211 248 HGYS 251 (953)
Q Consensus 248 ~~~~ 251 (953)
.+..
T Consensus 259 tGG~ 262 (633)
T PRK14498 259 SGGT 262 (633)
T ss_pred CCCC
Confidence 7553
No 376
>PRK03635 chromosome replication initiation inhibitor protein; Validated
Probab=67.64 E-value=1.3e+02 Score=32.11 Aligned_cols=82 Identities=12% Similarity=0.072 Sum_probs=52.4
Q ss_pred cceEEEecCcccccccEEeeCCcceEEEeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEecE
Q 002211 485 RQLRIGVPNRVSYRDFVFKVNGTDIVHGYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGDI 564 (953)
Q Consensus 485 ~~lri~v~~~~~~~p~~~~~~~~~~~~G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~~ 564 (953)
++|+||+.. ... ..+...++..+.++. .++++... +.-.+.+..+.+|++|+++..-
T Consensus 90 g~l~I~~~~--~~~------------~~~l~~~l~~f~~~~--~i~i~l~~-------~~~~~~~~~l~~~~~d~~i~~~ 146 (294)
T PRK03635 90 LTLSIAVNA--DSL------------ATWFLPALAPVLARS--GVLLDLVV-------EDQDHTAELLRRGEVVGAVTTE 146 (294)
T ss_pred eEEEEeecc--hhH------------HHHHHHHHHHHHhCC--CcEEEEEe-------cCcHHHHHHHhCCCceEEEecc
Confidence 569999863 111 123345677777764 45566654 4456889999999999987532
Q ss_pred EEecCccceeeccccceecceEEEEeccc
Q 002211 565 AIVTNRTKAVDFTQPYIESGLVVVAPVRK 593 (953)
Q Consensus 565 ~~t~~r~~~vdft~p~~~~~~~~~v~~~~ 593 (953)
......+ .+.|+.+..++++++...
T Consensus 147 ---~~~~~~l-~~~~l~~~~~~lv~~~~~ 171 (294)
T PRK03635 147 ---PQPVQGC-RVDPLGAMRYLAVASPAF 171 (294)
T ss_pred ---CCCCCCc-eeeecccceEEEEEcchH
Confidence 2222223 467788888888887553
No 377
>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=67.26 E-value=24 Score=37.14 Aligned_cols=77 Identities=5% Similarity=0.026 Sum_probs=55.0
Q ss_pred EEEEEe--cCccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcc-hhhHHHHHHHH
Q 002211 185 VIAIFN--DDDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGY-SRTGLMVFDVA 261 (953)
Q Consensus 185 vaii~~--d~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~-~~~~~~~~~~a 261 (953)
++++.. ++.|.......+.+++++.|.++.... .. .+.......+..+...++|.||+... .......++++
T Consensus 2 Ig~i~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~---~~--~~~~~~~~~l~~~~~~~vdgii~~~~~~~~~~~~i~~~ 76 (273)
T cd06305 2 IAVVRYGGSGDFDQAYLAGTKAEAEALGGDLRVYD---AG--GDDAKQADQIDQAIAQKVDAIIIQHGRAEVLKPWVKRA 76 (273)
T ss_pred eEEEeecCCCcHHHHHHHHHHHHHHHcCCEEEEEC---CC--CCHHHHHHHHHHHHHcCCCEEEEecCChhhhHHHHHHH
Confidence 566665 577888889999999999999877632 11 22445566777777789999999753 33345667888
Q ss_pred HHcCC
Q 002211 262 QRLGM 266 (953)
Q Consensus 262 ~~~g~ 266 (953)
.+.|+
T Consensus 77 ~~~~i 81 (273)
T cd06305 77 LDAGI 81 (273)
T ss_pred HHcCC
Confidence 88775
No 378
>cd08431 PBP2_HupR The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which regulates expression of the heme uptake receptor HupA; contains the type 2 periplasmic binding fold. HupR, a member of the LysR family, activates hupA transcription under low-iron conditions in the presence of hemin. The expression of many iron-uptake genes, such as hupA, is regulated at the transcriptional level by iron and an iron-binding repressor protein called Fur (ferric uptake regulation). Under iron-abundant conditions with heme, the active Fur repressor protein represses transcription of the iron-uptake gene hupA, and prevents transcriptional activation via HupR. Under low-iron conditions with heme, the Fur repressor is inactive and transcription of the hupA is allowed. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, p
Probab=66.34 E-value=1.3e+02 Score=29.08 Aligned_cols=71 Identities=13% Similarity=0.081 Sum_probs=46.0
Q ss_pred EeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEecEEEecCccceeeccccceecceEEEEec
Q 002211 512 GYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGDIAIVTNRTKAVDFTQPYIESGLVVVAPV 591 (953)
Q Consensus 512 G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~~~~t~~r~~~vdft~p~~~~~~~~~v~~ 591 (953)
.+-.+++..+.++.+- ++++... ++.++++.++.+|++|+++..... .....+ .+.++....++++++.
T Consensus 13 ~~l~~~l~~~~~~~P~-v~i~i~~-------~~~~~~~~~l~~g~~D~~i~~~~~--~~~~~~-~~~~l~~~~~~~v~~~ 81 (195)
T cd08431 13 QPLYPLIAEFYQLNKA-TRIRLSE-------EVLGGTWDALASGRADLVIGATGE--LPPGGV-KTRPLGEVEFVFAVAP 81 (195)
T ss_pred HHHHHHHHHHHHHCCC-CceEEEE-------eccchHHHHHhCCCCCEEEEecCC--CCCCce-EEEecccceEEEEEcC
Confidence 5567888899888752 4555554 446788999999999998852111 111122 2456666777777765
Q ss_pred cc
Q 002211 592 RK 593 (953)
Q Consensus 592 ~~ 593 (953)
..
T Consensus 82 ~h 83 (195)
T cd08431 82 NH 83 (195)
T ss_pred CC
Confidence 54
No 379
>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=66.32 E-value=41 Score=38.04 Aligned_cols=79 Identities=15% Similarity=0.070 Sum_probs=57.7
Q ss_pred cCCcEEEEEEecCccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcch--hhHHHH
Q 002211 180 FGWGEVIAIFNDDDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYS--RTGLMV 257 (953)
Q Consensus 180 ~~w~~vaii~~d~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~--~~~~~~ 257 (953)
.+.+++.+|+.......+..+.+.+.|++.|+++.....+.++ .+.+.+...+..+++.++|+||-.+.+ -|+.++
T Consensus 19 ~~~~k~liVtd~~~~~~g~~~~v~~~L~~~gi~~~~f~~v~~~--p~~~~v~~~~~~~~~~~~D~IIaiGGGS~iD~AK~ 96 (398)
T cd08178 19 KGKKRAFIVTDRFMVKLGYVDKVIDVLKRRGVETEVFSDVEPD--PSLETVRKGLELMNSFKPDTIIALGGGSPMDAAKI 96 (398)
T ss_pred cCCCeEEEEcChhHHhCccHHHHHHHHHHCCCeEEEecCCCCC--cCHHHHHHHHHHHHhcCCCEEEEeCCccHHHHHHH
Confidence 4668988888544444457888999999999887654445555 557788888999999999999976554 566666
Q ss_pred HHH
Q 002211 258 FDV 260 (953)
Q Consensus 258 ~~~ 260 (953)
+..
T Consensus 97 iA~ 99 (398)
T cd08178 97 MWL 99 (398)
T ss_pred HHH
Confidence 554
No 380
>COG2358 Imp TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]
Probab=65.83 E-value=31 Score=37.09 Aligned_cols=79 Identities=28% Similarity=0.161 Sum_probs=47.1
Q ss_pred CCCCChHHhhhCCCeEEEEe-Cch----HHHHHHHhhCCCccceEe--CCCHHHHHHHHHcCCcEEEEccch---hHHHH
Q 002211 700 SPIKGIDTLMTSNDRVGYQV-GSF----AENYLIEELSIPKSRLVA--LGSPEEYAIALENRTVAAVVDERP---YIDLF 769 (953)
Q Consensus 700 ~~I~sl~dL~~~~~~ig~~~-~s~----~~~~l~~~~~~~~~~~~~--~~~~~~~~~~l~~g~~~a~~~~~~---~~~~~ 769 (953)
..|+++.||. |++|.+.. ||- .+..| +.+++....+.. .-...|..+++++|.+||.+.-.. -.-..
T Consensus 127 ~~Ikti~DL~--GKrV~iG~~gSgt~~~a~~il-~a~Gi~~~~~~~~~~~~~a~~~~~l~~g~iDA~~~~~G~p~~ai~e 203 (321)
T COG2358 127 AGIKTIADLK--GKRVAIGPPGSGTEATARQIL-EALGITYDDYELDLGLGDAESADALKNGTIDAAFYVAGVPNPAISE 203 (321)
T ss_pred CCcceehhcC--CCEEeecCCCCccHHHHHHHH-HHcCCCCcchhhhhhcCchhhHHHhhCCcccEEEEecCCCCccHHH
Confidence 4799999997 99988753 332 33333 445554433322 123445578899999999876422 12233
Q ss_pred HhcCcceEEeCC
Q 002211 770 LSDHCQFSVRGQ 781 (953)
Q Consensus 770 ~~~~~~l~~~~~ 781 (953)
+...|++.+++-
T Consensus 204 l~~~~~i~lv~i 215 (321)
T COG2358 204 LATTCDIVLVPI 215 (321)
T ss_pred HHhhCCeEEEeC
Confidence 445677766653
No 381
>PLN03192 Voltage-dependent potassium channel; Provisional
Probab=65.82 E-value=6.6 Score=49.19 Aligned_cols=53 Identities=17% Similarity=0.367 Sum_probs=46.5
Q ss_pred chhhHHHHHHHhhccccC--CcccchhHHHHHHHHHHHHHhhhhcccceeeeeee
Q 002211 643 IVTVLWFSFSTMFFAHRE--NTVSTLGRVVLIIWLFVVLIITSSYTASLTSILTV 695 (953)
Q Consensus 643 ~~~~~~~~~~~l~~~~~~--~~~s~~~R~l~~~w~~~~lil~~~Yta~L~s~Lt~ 695 (953)
...++|+++.++...|.. .|.+...|++.++|.++++++.++..+++++++..
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 455899999999988744 78999999999999999999999999999987754
No 382
>cd08550 GlyDH-like Glycerol_dehydrogenase-like. Families of proteins related to glycerol dehydrogenases. Glycerol dehydrogenases (GlyDH) is a key enzyme in the glycerol dissimilation pathway. In anaerobic conditions, many microorganisms utilize glycerol as a source of carbon through coupled oxidative and reductive pathways. One of the pathways involves the oxidation of glycerol to dihydroxyacetone with the reduction of NAD+ to NADH catalyzed by glycerol dehydrogenases. Dihydroxyacetone is then phosphorylated by dihydroxyacetone kinase and enters the glycolytic pathway for further degradation. The activity of GlyDH is zinc-dependent. The zinc ion plays a role in stabilizing an alkoxide intermediate at the active site. Some subfamilies have not been characterized till now.
Probab=64.78 E-value=28 Score=38.57 Aligned_cols=84 Identities=18% Similarity=0.150 Sum_probs=57.4
Q ss_pred HHHHHHHHHcCCcEEEEEEecCccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcc
Q 002211 171 SAIAEMVSYFGWGEVIAIFNDDDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGY 250 (953)
Q Consensus 171 ~ai~~~l~~~~w~~vaii~~d~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~ 250 (953)
..+.++++.+| +++.+|+....+- ...+.+.+.+++.|+.+.... +... .+.+.+...+..+++.++|+||-.+.
T Consensus 12 ~~l~~~~~~~g-~~~liv~~~~~~~-~~~~~v~~~l~~~~i~~~~~~-~~~~--p~~~~v~~~~~~~~~~~~d~IIavGG 86 (349)
T cd08550 12 KEIAAILSTFG-SKVAVVGGKTVLK-KSRPRFEAALAKSIIVVDVIV-FGGE--CSTEEVVKALCGAEEQEADVIIGVGG 86 (349)
T ss_pred HHHHHHHHHcC-CeEEEEEChHHHH-HHHHHHHHHHHhcCCeeEEEE-cCCC--CCHHHHHHHHHHHHhcCCCEEEEecC
Confidence 44667788888 8888877444332 556788888988887653332 4433 34677888888888899999998765
Q ss_pred h--hhHHHHHH
Q 002211 251 S--RTGLMVFD 259 (953)
Q Consensus 251 ~--~~~~~~~~ 259 (953)
+ -|..+++.
T Consensus 87 Gs~~D~aK~ia 97 (349)
T cd08550 87 GKTLDTAKAVA 97 (349)
T ss_pred cHHHHHHHHHH
Confidence 5 44555543
No 383
>cd08452 PBP2_AlsR The C-terminal substrate binding domain of LysR-type trnascriptional regulator AlsR, which regulates acetoin formation under stationary phase growth conditions; contains the type 2 periplasmic binding fold. AlsR is responsible for activating the expression of the acetoin operon (alsSD) in response to inducing signals such as glucose and acetate. Like many other LysR family proteins, AlsR is transcribed divergently from the alsSD operon. The alsS gene encodes acetolactate synthase, an enzyme involved in the production of acetoin in cells of stationary-phase. AlsS catalyzes the conversion of two pyruvate molecules to acetolactate and carbon dioxide. Acetolactate is then converted to acetoin at low pH by acetolactate decarboxylase which encoded by the alsD gene. Acetoin is an important physiological metabolite excreted by many microorganisms grown on glucose or other fermentable carbon sources. This substrate-binding domain shows significant homology to the type 2 perip
Probab=64.20 E-value=1.5e+02 Score=28.90 Aligned_cols=70 Identities=11% Similarity=0.158 Sum_probs=46.3
Q ss_pred EeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEecEEEecCccceeeccccceecceEEEEec
Q 002211 512 GYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGDIAIVTNRTKAVDFTQPYIESGLVVVAPV 591 (953)
Q Consensus 512 G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~~~~t~~r~~~vdft~p~~~~~~~~~v~~ 591 (953)
.+-.+++..+.++.+ .++++... ++..++...|.+|++|+++.. .......+. +.++....++++++.
T Consensus 13 ~~l~~~l~~~~~~~P-~v~i~i~~-------~~~~~~~~~l~~~~~Dl~i~~---~~~~~~~~~-~~~l~~~~~~lv~~~ 80 (197)
T cd08452 13 EFLPPIVREYRKKFP-SVKVELRE-------LSSPDQVEELLKGRIDIGFLH---PPIQHTALH-IETVQSSPCVLALPK 80 (197)
T ss_pred hHHHHHHHHHHHHCC-CcEEEEEe-------cChHHHHHHHHCCCccEEEee---CCCCCCCee-EEEeeeccEEEEEeC
Confidence 345678888888775 24565554 557889999999999998852 122222333 356667777777765
Q ss_pred cc
Q 002211 592 RK 593 (953)
Q Consensus 592 ~~ 593 (953)
..
T Consensus 81 ~h 82 (197)
T cd08452 81 QH 82 (197)
T ss_pred CC
Confidence 44
No 384
>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=64.15 E-value=25 Score=36.97 Aligned_cols=78 Identities=9% Similarity=0.054 Sum_probs=56.3
Q ss_pred EEEEEEec--CccccchHHHHHHHHHh-cCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchh-hHHHHHH
Q 002211 184 EVIAIFND--DDQGRNGVTALGDKLAE-IRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSR-TGLMVFD 259 (953)
Q Consensus 184 ~vaii~~d--~~~g~~~~~~l~~~l~~-~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~-~~~~~~~ 259 (953)
+|++|..+ ++|.....+.+.+++++ .|..+..... . .+.......++++.+.++|.+|+..... ....++.
T Consensus 1 ~igvi~~~~~~~~~~~~~~gi~~~~~~~~~~~~~~~~~---~--~~~~~~~~~i~~l~~~~vdgiii~~~~~~~~~~~~~ 75 (272)
T cd06301 1 KIGVSMANFDDNFLTLLRNAMKEHAKVLGGVELQFEDA---K--NDVATQLSQVENFIAQGVDAIIVVPVDTAATAPIVK 75 (272)
T ss_pred CeeEeecccCCHHHHHHHHHHHHHHHHcCCcEEEEeCC---C--CCHHHHHHHHHHHHHcCCCEEEEecCchhhhHHHHH
Confidence 46777754 77888889999999999 8988876432 1 2245666778888888999999876443 3456777
Q ss_pred HHHHcCC
Q 002211 260 VAQRLGM 266 (953)
Q Consensus 260 ~a~~~g~ 266 (953)
++.+.|.
T Consensus 76 ~l~~~~i 82 (272)
T cd06301 76 AANAAGI 82 (272)
T ss_pred HHHHCCC
Confidence 7777664
No 385
>PRK11139 DNA-binding transcriptional activator GcvA; Provisional
Probab=64.08 E-value=1e+02 Score=32.93 Aligned_cols=102 Identities=5% Similarity=-0.079 Sum_probs=51.9
Q ss_pred CCChHHhhhCCCe-EEEEeCchHHHHHHHhhCCC---ccceEeCCCHHHHHHHHHcCCcEEEEccchhHHHHHhcCcceE
Q 002211 702 IKGIDTLMTSNDR-VGYQVGSFAENYLIEELSIP---KSRLVALGSPEEYAIALENRTVAAVVDERPYIDLFLSDHCQFS 777 (953)
Q Consensus 702 I~sl~dL~~~~~~-ig~~~~s~~~~~l~~~~~~~---~~~~~~~~~~~~~~~~l~~g~~~a~~~~~~~~~~~~~~~~~l~ 777 (953)
.-+++||. +.+ |....+.....++.. .+.. ......+++.+...+.+..|..-+++.+.. .........-..
T Consensus 180 ~i~~~dL~--~~p~i~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~lp~~~-~~~~~~~~~l~~ 255 (297)
T PRK11139 180 LKTPEDLA--RHTLLHDDSREDWRAWFRA-AGLDDLNVQQGPIFSHSSMALQAAIHGQGVALGNRVL-AQPEIEAGRLVC 255 (297)
T ss_pred CCCHHHhh--cCceEeecCcccHHHHHHH-hCCCCcCcccceeeCCHHHHHHHHHhCCCeEecchhh-hHHHHHCCceec
Confidence 34788887 444 333333344556643 3331 112245678887888888777666655433 332222221111
Q ss_pred EeCCcc-ccCccEEEecCCCcchHHHHHHHH
Q 002211 778 VRGQEF-TKSGWGFAFPRDSPLAIDMSTAIL 807 (953)
Q Consensus 778 ~~~~~~-~~~~~~~~~~k~spl~~~~n~~i~ 807 (953)
.+.+.. ....+.++.+|+.+....+...+.
T Consensus 256 ~~~~~~~~~~~~~l~~~~~~~~~~~~~~f~~ 286 (297)
T PRK11139 256 PFDTVLPSPNAFYLVCPDSQAELPKVAAFRQ 286 (297)
T ss_pred ccccCcCCCccEEEEeccccccChhHHHHHH
Confidence 222221 234678888887665555544443
No 386
>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=63.78 E-value=27 Score=36.79 Aligned_cols=79 Identities=11% Similarity=0.039 Sum_probs=55.2
Q ss_pred EEEEEEe---cCccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchh-hHHHHHH
Q 002211 184 EVIAIFN---DDDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSR-TGLMVFD 259 (953)
Q Consensus 184 ~vaii~~---d~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~-~~~~~~~ 259 (953)
+|++|.. ++.|.....+.+.+++++.|..+.....-. .+.......++++...++|.+|+..... .....++
T Consensus 1 ~i~~i~~~~~~~~~~~~~~~g~~~~~~~~g~~v~~~~~~~----~~~~~~~~~i~~l~~~~vdgiii~~~~~~~~~~~l~ 76 (271)
T cd06312 1 KIAFVTHGPAGDPFWTVVKNGAEDAAKDLGVDVEYRGPET----FDVADMARLIEAAIAAKPDGIVVTIPDPDALDPAIK 76 (271)
T ss_pred CEEEecCCCCCCcHHHHHHHHHHHHHHHhCCEEEEECCCC----CCHHHHHHHHHHHHHhCCCEEEEeCCChHHhHHHHH
Confidence 4667764 357888899999999999999876542211 1245566778888888999999876433 2345677
Q ss_pred HHHHcCC
Q 002211 260 VAQRLGM 266 (953)
Q Consensus 260 ~a~~~g~ 266 (953)
.+.+.|.
T Consensus 77 ~~~~~~i 83 (271)
T cd06312 77 RAVAAGI 83 (271)
T ss_pred HHHHCCC
Confidence 7777664
No 387
>TIGR03298 argP transcriptional regulator, ArgP family. ArgP used to be known as IciA. ArgP is a positive regulator of argK. It is a negative autoregulator in presence of arginine. It competes with DnaA for oriC iteron (13-mer) binding. It activates dnaA and nrd transcription. It has been demonstrated to be part of the pho regulon (PubMed:10589831). ArgP mutants convey canavanine (an L-arginine structural homolog) sensitivity (PubMed: 15150242).
Probab=63.45 E-value=2.1e+02 Score=30.45 Aligned_cols=64 Identities=13% Similarity=0.074 Sum_probs=40.9
Q ss_pred HHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEecEEEecCccceeeccccceecceEEEEecc
Q 002211 516 DVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGDIAIVTNRTKAVDFTQPYIESGLVVVAPVR 592 (953)
Q Consensus 516 dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~~~~t~~r~~~vdft~p~~~~~~~~~v~~~ 592 (953)
.++..+.++.+ +++.... ++-..+++.|.+|++|+++.... .....+. +.++.+..++++++++
T Consensus 107 ~~l~~~~~~~~--i~i~l~~-------~~~~~~~~~l~~g~~d~~i~~~~---~~~~~l~-~~~l~~~~~~~v~~~~ 170 (292)
T TIGR03298 107 PALAPVLAQEG--VLLDLVV-------EDQDHTAELLRSGEVLGAVTTQA---KPVQGCR-VVPLGAMRYLAVASPA 170 (292)
T ss_pred HHHHHHHhCCC--ceEEEEe-------CcchhHHHHHhCCCceEEEecCC---CCCCCce-EEecCCceEEEEECch
Confidence 45666666643 5555543 44567899999999999886322 1122333 4677788888887654
No 388
>PRK00865 glutamate racemase; Provisional
Probab=63.20 E-value=82 Score=33.20 Aligned_cols=37 Identities=16% Similarity=0.217 Sum_probs=28.2
Q ss_pred HHHHHhcCcEEEEccCChhhHHHHHHhhhhCCCcEEE
Q 002211 107 ALQFMETDTLAIVGPQSAVMAHVLSHLANELQVPLLS 143 (953)
Q Consensus 107 a~~li~~~v~aiiGp~~S~~a~av~~v~~~~~vP~Is 143 (953)
+..|.+.++.+|+=+..+..+.++..+-+..++|+|+
T Consensus 60 ~~~L~~~g~d~iVIaCNTa~~~~l~~lr~~~~iPvig 96 (261)
T PRK00865 60 VEFLLEYGVKMLVIACNTASAVALPDLRERYDIPVVG 96 (261)
T ss_pred HHHHHhCCCCEEEEeCchHHHHHHHHHHHhCCCCEEe
Confidence 3444455899998888887777777777888999996
No 389
>PF07287 DUF1446: Protein of unknown function (DUF1446); InterPro: IPR010839 This family consists of several bacterial and plant proteins of around 400 residues in length. The function of this family is unknown.
Probab=63.03 E-value=2.3e+02 Score=31.43 Aligned_cols=173 Identities=13% Similarity=0.106 Sum_probs=87.3
Q ss_pred CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEEccCChhhHHHHHHhhhhCCC
Q 002211 60 TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIVGPQSAVMAHVLSHLANELQV 139 (953)
Q Consensus 60 ~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aiiGp~~S~~a~av~~v~~~~~v 139 (953)
...|.....+.+++ +. -.+.+++.|.-.....+..+..++-+.. .. --|.--..-..+.+.+.+.+|
T Consensus 6 Gf~gD~~~a~~~l~-----~~------g~~d~l~~d~LaE~tma~~~~~~~~~p~-~g-Y~~~~~~~L~~~L~~~~~~gI 72 (362)
T PF07287_consen 6 GFWGDRPDAAVRLA-----RG------GDVDYLVGDYLAERTMAILARAKRKDPT-KG-YAPDFVRDLRPLLPAAAEKGI 72 (362)
T ss_pred ccccCcHHHHHHHH-----hc------CCCCEEEEecHHHHHHHHHHHHHhhCCC-CC-chHHHHHHHHHHHHHHHhCCC
Confidence 34455566666665 12 2467778887766555555433332211 10 001111233456677788899
Q ss_pred cEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCC-cEEEEEEecCccccchHHHHHHHHHhcCcEEEEEEe
Q 002211 140 PLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGW-GEVIAIFNDDDQGRNGVTALGDKLAEIRCKISYKSA 218 (953)
Q Consensus 140 P~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w-~~vaii~~d~~~g~~~~~~l~~~l~~~g~~v~~~~~ 218 (953)
|+|+-++.. +....++.+.+++++.|. -||++|+.|+. .+.+.+.++ .|..+..-..
T Consensus 73 kvI~NaGg~----------------np~~~a~~v~eia~e~Gl~lkvA~V~gDd~-----~~~v~~~~~-~g~~~~~l~~ 130 (362)
T PF07287_consen 73 KVITNAGGL----------------NPAGCADIVREIARELGLSLKVAVVYGDDL-----KDEVKELLA-EGETIRPLDT 130 (362)
T ss_pred CEEEeCCCC----------------CHHHHHHHHHHHHHhcCCCeeEEEEECccc-----hHhHHHHHh-CCCCCccCCC
Confidence 999743221 123367888888888876 58899987765 344444443 2211111000
Q ss_pred cCCCCC-------CC-hHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHHHcCCCC
Q 002211 219 LPPDQS-------VT-ETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQRLGMMD 268 (953)
Q Consensus 219 ~~~~~~-------~~-~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~~~g~~~ 268 (953)
-++-.. .+ .--..++++.|+ .++||||..=..+.+.-+--.+.+.|...
T Consensus 131 ~~~l~~~~~~~~~a~aylGa~pI~~AL~-~GADIVI~GR~~D~Al~~a~~~~~~GW~~ 187 (362)
T PF07287_consen 131 GPPLSEWDDRIVSANAYLGAEPIVEALE-AGADIVITGRVADPALFAAPAIHEFGWSE 187 (362)
T ss_pred CCCcchhccccceEEEecChHHHHHHHH-cCCCEEEeCcccchHHHHhHHHHHcCCCc
Confidence 000000 00 000233444444 67998887544444444445555667543
No 390
>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=62.80 E-value=25 Score=36.54 Aligned_cols=78 Identities=8% Similarity=0.080 Sum_probs=54.9
Q ss_pred EEEEEEec--CccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHH
Q 002211 184 EVIAIFND--DDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVA 261 (953)
Q Consensus 184 ~vaii~~d--~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a 261 (953)
+++++.+. ..+.......+++++++.|+++.... .. .+.+.....++++.+.++|.||+..........+..+
T Consensus 1 ~ig~v~~~~~~~~~~~~~~g~~~~~~~~g~~l~~~~---~~--~~~~~~~~~~~~~~~~~~d~ii~~~~~~~~~~~~~~l 75 (264)
T cd01537 1 TIGVLVPDLDNPFFAQVLKGIEEAAKAAGYQVLLAN---SQ--NDAEKQLSALENLIARGVDGIIIAPSDLTAPTIVKLA 75 (264)
T ss_pred CeEEEEcCCCChHHHHHHHHHHHHHHHcCCeEEEEe---CC--CCHHHHHHHHHHHHHcCCCEEEEecCCCcchhHHHHh
Confidence 36777754 67888889999999999998876542 22 2245567778888888999999876554443356666
Q ss_pred HHcCC
Q 002211 262 QRLGM 266 (953)
Q Consensus 262 ~~~g~ 266 (953)
.+.|.
T Consensus 76 ~~~~i 80 (264)
T cd01537 76 RKAGI 80 (264)
T ss_pred hhcCC
Confidence 66554
No 391
>PRK15408 autoinducer 2-binding protein lsrB; Provisional
Probab=62.75 E-value=36 Score=37.42 Aligned_cols=82 Identities=11% Similarity=0.060 Sum_probs=59.3
Q ss_pred CCcEEEEEEe--cCccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcc-hhhHHHH
Q 002211 181 GWGEVIAIFN--DDDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGY-SRTGLMV 257 (953)
Q Consensus 181 ~w~~vaii~~--d~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~-~~~~~~~ 257 (953)
.-++++++.. +++|.....+.+.++.++.|.++.... +.. .+...-...++.+.+.++|.|++... +......
T Consensus 22 ~~~~i~~v~k~~~~pf~~~~~~Gi~~aa~~~G~~v~~~~--~~~--~d~~~q~~~i~~li~~~vdgIiv~~~d~~al~~~ 97 (336)
T PRK15408 22 AAERIAFIPKLVGVGFFTSGGNGAKEAGKELGVDVTYDG--PTE--PSVSGQVQLINNFVNQGYNAIIVSAVSPDGLCPA 97 (336)
T ss_pred CCcEEEEEECCCCCHHHHHHHHHHHHHHHHhCCEEEEEC--CCC--CCHHHHHHHHHHHHHcCCCEEEEecCCHHHHHHH
Confidence 4468888874 578888889999999999999887532 222 22333346778888899999999754 3444678
Q ss_pred HHHHHHcCC
Q 002211 258 FDVAQRLGM 266 (953)
Q Consensus 258 ~~~a~~~g~ 266 (953)
++++.+.|.
T Consensus 98 l~~a~~~gI 106 (336)
T PRK15408 98 LKRAMQRGV 106 (336)
T ss_pred HHHHHHCCC
Confidence 889998875
No 392
>cd06267 PBP1_LacI_sugar_binding_like Ligand binding domain of the LacI tanscriptional regulator family belonging to the type I periplasmic-binding fold protein superfamily. Ligand binding domain of the LacI tanscriptional regulator family belonging to the type I periplasmic-binding fold protein superfamily. In most cases, ligands are monosaccharide including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the domain sugar binding changes the DNA binding activity of the repressor domain.
Probab=62.71 E-value=29 Score=36.06 Aligned_cols=76 Identities=12% Similarity=0.080 Sum_probs=55.7
Q ss_pred EEEEEec--CccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHH
Q 002211 185 VIAIFND--DDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQ 262 (953)
Q Consensus 185 vaii~~d--~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~ 262 (953)
++++..+ ++|.....+.+++++++.|+.+.... .+ .+.......++++.+.++|+|++......... ++.+.
T Consensus 2 i~~v~~~~~~~~~~~~~~g~~~~~~~~g~~~~~~~---~~--~~~~~~~~~~~~~~~~~~d~iii~~~~~~~~~-~~~~~ 75 (264)
T cd06267 2 IGVIVPDISNPFFAELLRGIEEAAREAGYSVLLCN---SD--EDPEKEREALELLLSRRVDGIILAPSRLDDEL-LEELA 75 (264)
T ss_pred EEEEECCCCCHHHHHHHHHHHHHHHHcCCEEEEEc---CC--CCHHHHHHHHHHHHHcCcCEEEEecCCcchHH-HHHHH
Confidence 5666644 78888899999999999998876532 22 22445667788888889999999777655555 77777
Q ss_pred HcCC
Q 002211 263 RLGM 266 (953)
Q Consensus 263 ~~g~ 266 (953)
+.|.
T Consensus 76 ~~~i 79 (264)
T cd06267 76 ALGI 79 (264)
T ss_pred HcCC
Confidence 7775
No 393
>TIGR03414 ABC_choline_bnd choline ABC transporter, periplasmic binding protein. Partial phylogenetic profiling (PubMed:16930487) vs. the genome property of glycine betaine biosynthesis from choline consistently reveals a member of this ABC transporter periplasmic binding protein as the best match, save for the betaine biosynthesis enzymes themselves. Genomes often carry several paralogs, one encoded together with the permease and ATP-binding components and another encoded next to a choline-sulfatase gene, suggesting that different members of this protein family interact with shared components and give some flexibility in substrate. Of two members from Sinorhizobium meliloti 1021, one designated ChoX has been shown experimentally to bind choline (though not various related compounds such as betaine) and to be required for about 60 % of choline uptake. Members of this protein have an invariant Cys residue near the N-terminus and likely are lipoproteins.
Probab=61.88 E-value=2.1e+02 Score=30.73 Aligned_cols=41 Identities=12% Similarity=0.100 Sum_probs=30.3
Q ss_pred eHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEec
Q 002211 514 CIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGD 563 (953)
Q Consensus 514 ~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~ 563 (953)
.-.|+..+.+.+||++++. . .+-.-+...|.+|++|+.+..
T Consensus 23 ~~~i~~~iLE~~Gy~Ve~~--~-------~~~~~~~~al~~GdiD~~~e~ 63 (290)
T TIGR03414 23 TTALASVLLEGLGYQPKVT--L-------LSVPVTYAGLKDGDLDVFLGN 63 (290)
T ss_pred HHHHHHHHHHHcCCcceeE--E-------ccHHHHHHHHHcCCceEeccc
Confidence 3466777777889887764 2 335677888999999998764
No 394
>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=61.79 E-value=96 Score=34.38 Aligned_cols=102 Identities=15% Similarity=0.109 Sum_probs=66.3
Q ss_pred HHHHHHHHHcCCcEEEEEEecCccccchHHHHHHHHHhcCcEEEEEEecCCC-CCCChHHHHHHHHHHhcCCce---EEE
Q 002211 171 SAIAEMVSYFGWGEVIAIFNDDDQGRNGVTALGDKLAEIRCKISYKSALPPD-QSVTETDVRNELVKVRMMEAR---VIV 246 (953)
Q Consensus 171 ~ai~~~l~~~~w~~vaii~~d~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~-~~~~~~d~~~~l~~i~~~~~~---vii 246 (953)
..+.++++.++.+++.+++....+ ....+.+.+.+++.|+.+... .++.. ...+.+.+...+..+++.++| +||
T Consensus 12 ~~l~~~l~~~g~~rvlvVtd~~v~-~~~~~~l~~~L~~~g~~~~~~-~~~~~e~~k~~~~v~~~~~~~~~~~~dr~~~II 89 (355)
T cd08197 12 DSVLGYLPELNADKYLLVTDSNVE-DLYGHRLLEYLREAGAPVELL-SVPSGEEHKTLSTLSDLVERALALGATRRSVIV 89 (355)
T ss_pred HHHHHHHHhcCCCeEEEEECccHH-HHHHHHHHHHHHhcCCceEEE-EeCCCCCCCCHHHHHHHHHHHHHcCCCCCcEEE
Confidence 335667777888999988865544 336678889999888765322 23322 113467788888899888888 888
Q ss_pred EEcch--hhHHHHHHHHHHcCCCCCceEEEEeC
Q 002211 247 VHGYS--RTGLMVFDVAQRLGMMDSGYVWIATT 277 (953)
Q Consensus 247 ~~~~~--~~~~~~~~~a~~~g~~~~~~~wi~~~ 277 (953)
..+.+ -|+..++......| ..++.|.|.
T Consensus 90 AvGGGsv~D~ak~~A~~~~rg---ip~I~IPTT 119 (355)
T cd08197 90 ALGGGVVGNIAGLLAALLFRG---IRLVHIPTT 119 (355)
T ss_pred EECCcHHHHHHHHHHHHhccC---CCEEEecCc
Confidence 76654 56666655443334 356666664
No 395
>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=61.36 E-value=31 Score=36.31 Aligned_cols=80 Identities=10% Similarity=0.015 Sum_probs=54.4
Q ss_pred EEEEEEec--CccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHH
Q 002211 184 EVIAIFND--DDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVA 261 (953)
Q Consensus 184 ~vaii~~d--~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a 261 (953)
++++|..+ +.|.......+.+++++.|..+.....-. . .+..+-...++.+...++|.||+.....+....++++
T Consensus 1 ~Igvi~~~~~~~f~~~~~~gi~~~a~~~g~~~~~~~~~~-~--~~~~~~~~~i~~~~~~~vdgiI~~~~~~~~~~~~~~~ 77 (268)
T cd06306 1 KLCVLYPHLKDAYWLSVNYGMVEEAKRLGVSLKLLEAGG-Y--PNLAKQIAQLEDCAAWGADAILLGAVSPDGLNEILQQ 77 (268)
T ss_pred CeEEEcCCCCCHHHHHHHHHHHHHHHHcCCEEEEecCCC-C--CCHHHHHHHHHHHHHcCCCEEEEcCCChhhHHHHHHH
Confidence 36777754 67888888999999999999877642211 1 1134455678888888999999876544332256777
Q ss_pred HHcCC
Q 002211 262 QRLGM 266 (953)
Q Consensus 262 ~~~g~ 266 (953)
.+.|+
T Consensus 78 ~~~gi 82 (268)
T cd06306 78 VAASI 82 (268)
T ss_pred HHCCC
Confidence 77665
No 396
>cd08422 PBP2_CrgA_like The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain. This CD includes the substrate binding domain of LysR-type transcriptional regulator (LTTR) CrgA and its related homologs. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis further showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own
Probab=61.27 E-value=42 Score=32.52 Aligned_cols=66 Identities=9% Similarity=-0.049 Sum_probs=37.1
Q ss_pred eEeCCCHHHHHHHHHcCCcEEEEccchhHHHHHhcCcceEEeCC--ccccCccEEEecCCCcchHHHHHH
Q 002211 738 LVALGSPEEYAIALENRTVAAVVDERPYIDLFLSDHCQFSVRGQ--EFTKSGWGFAFPRDSPLAIDMSTA 805 (953)
Q Consensus 738 ~~~~~~~~~~~~~l~~g~~~a~~~~~~~~~~~~~~~~~l~~~~~--~~~~~~~~~~~~k~spl~~~~n~~ 805 (953)
....++.+...+.+..|..-+++.+...... .. ...+..+.. ......++++.+|+......+...
T Consensus 126 ~~~~~~~~~~~~~v~~g~gi~~~p~~~~~~~-~~-~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~ 193 (197)
T cd08422 126 RLVVNDGEALRAAALAGLGIALLPDFLVAED-LA-SGRLVRVLPDWRPPPLPIYAVYPSRRHLPAKVRAF 193 (197)
T ss_pred cEEEccHHHHHHHHHcCCcEEEecHHHHhhh-cc-CCeEEEecCcccCCCceEEEEEcccccCCHHHHHH
Confidence 4557888888999998776666655432222 12 222333321 223456778888776554444433
No 397
>PRK01686 hisG ATP phosphoribosyltransferase catalytic subunit; Reviewed
Probab=60.92 E-value=1.7e+02 Score=29.64 Aligned_cols=93 Identities=16% Similarity=0.072 Sum_probs=58.0
Q ss_pred CCCeEEEEeCchHHHHHHHhhCCCccceEeCCCHHHHHHHHHcCCcEEEEccchhHHHHHhcCcceEEeCCccccCccEE
Q 002211 711 SNDRVGYQVGSFAENYLIEELSIPKSRLVALGSPEEYAIALENRTVAAVVDERPYIDLFLSDHCQFSVRGQEFTKSGWGF 790 (953)
Q Consensus 711 ~~~~ig~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~g~~~a~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~ 790 (953)
.+.+|+...-...+.||.+ .+.. .+++.....-|. +-..|-.|++++-......+.++ +|.++...+. ..-.+
T Consensus 114 ~~~rIATkYp~it~~yf~~-~gv~-~~iv~l~GsvE~--aP~~GlAD~IvDivsTG~TLr~N--gL~~ie~Il~-s~A~L 186 (215)
T PRK01686 114 PRLRVATKYPNIARRYFAE-KGEQ-VEIIKLYGSVEL--APLVGLADAIVDIVETGNTLRAN--GLVEVEEIMD-ISARL 186 (215)
T ss_pred CCCEEEeCCHHHHHHHHHH-cCCe-EEEEECcCceee--ccccCCccEEEEeecChHHHHHC--cCEEeeEEEe-eEEEE
Confidence 4678998888888999954 4554 566665544444 23347889999877776665443 4566654443 44456
Q ss_pred EecCCCc--chHHHHHHHHhhh
Q 002211 791 AFPRDSP--LAIDMSTAILTLS 810 (953)
Q Consensus 791 ~~~k~sp--l~~~~n~~i~~l~ 810 (953)
+.++.|. -.+.++..+.++.
T Consensus 187 I~n~~s~~~k~~~i~~l~~~l~ 208 (215)
T PRK01686 187 IVNRASLKLKREEIRPLIEKLR 208 (215)
T ss_pred EEecccchhhHHHHHHHHHHHH
Confidence 6677765 2345666655553
No 398
>PRK00945 acetyl-CoA decarbonylase/synthase complex subunit epsilon; Provisional
Probab=60.67 E-value=71 Score=31.04 Aligned_cols=120 Identities=14% Similarity=0.130 Sum_probs=68.2
Q ss_pred HHHHhc--CcEEEEccCChh---hHHHHHHhhhhCCCcEEEeecCCCCCCCCC-CCcEEEccCChHHHHHHHHHHHHHcC
Q 002211 108 LQFMET--DTLAIVGPQSAV---MAHVLSHLANELQVPLLSFTALDPTLSPLQ-YPFFVQTAPNDLYLMSAIAEMVSYFG 181 (953)
Q Consensus 108 ~~li~~--~v~aiiGp~~S~---~a~av~~v~~~~~vP~Is~~at~~~ls~~~-~p~~fr~~p~d~~~~~ai~~~l~~~~ 181 (953)
.+++.+ +.+.++|..... ....+.+++++.++|+++...+...|.+.. .|. ....-.+..++..-+
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 344444 899999987644 677789999999999997555444454422 121 222234555554433
Q ss_pred C---------cEEEEEEecCccccchHHHHHHHHHhcCcE-EEEEEecCCCC-----CCChHHHHHHHHHHh
Q 002211 182 W---------GEVIAIFNDDDQGRNGVTALGDKLAEIRCK-ISYKSALPPDQ-----SVTETDVRNELVKVR 238 (953)
Q Consensus 182 w---------~~vaii~~d~~~g~~~~~~l~~~l~~~g~~-v~~~~~~~~~~-----~~~~~d~~~~l~~i~ 238 (953)
| .-|.++..+..|.......++.... ++ |.....|.++. ..+.+++...|+++.
T Consensus 100 ~e~~~g~~~~DlvlfvG~~~~~~~~~l~~lk~f~~---~~~~~~~~~y~~~a~~s~~~~~~~~~~~~l~~li 168 (171)
T PRK00945 100 WKGLDGNGNYDLVIFIGVTYYYASQGLSALKHFSP---LKTITIDRYYHPNADMSFPNLSKEEYLEYLDELI 168 (171)
T ss_pred hhhhcCCCCcCEEEEecCCchhHHHHHHHHhhcCC---ceEEEecCCcCCCCceecCCCCHHHHHHHHHHHH
Confidence 3 3445566677766666665554332 32 22233333321 134667777777764
No 399
>PRK11119 proX glycine betaine transporter periplasmic subunit; Provisional
Probab=60.44 E-value=42 Score=36.73 Aligned_cols=62 Identities=16% Similarity=0.193 Sum_probs=42.8
Q ss_pred cCCCcceEEEecCcccccccEEeeCCcceEEEeeHHHHHHHHHhCCCcc-cEEEeeCCCCCCCCChHHHHHHHHcCceeE
Q 002211 481 PNNGRQLRIGVPNRVSYRDFVFKVNGTDIVHGYCIDVFLAAVRLLPYAV-PYKFIPYGDGHKNPTYSELINQITTGVFDA 559 (953)
Q Consensus 481 ~~~g~~lri~v~~~~~~~p~~~~~~~~~~~~G~~~dll~~la~~l~~~~-~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di 559 (953)
|.+|+++++++. +|.. .-+.-.+++.+.+.+||++ ++... +-.-+...|.+|++|+
T Consensus 25 ~~~~~~V~~~~~---~W~~-----------~~~~t~v~~~iLe~~GY~V~e~~~~---------~~~~~~~ala~GdiDv 81 (331)
T PRK11119 25 PGKGITVQPAQS---TIAE-----------ETFQTLLVSRALEKLGYDVNKPKEV---------DYNVFYTSIANGDATF 81 (331)
T ss_pred CCCCeEEEEeec---CccH-----------HHHHHHHHHHHHHHcCCceeeeccc---------CcHHHHHHHHcCCCeE
Confidence 457889999887 3431 1234567778888899876 55433 2467788999999999
Q ss_pred EEecEE
Q 002211 560 AVGDIA 565 (953)
Q Consensus 560 ~~~~~~ 565 (953)
......
T Consensus 82 ~~~~W~ 87 (331)
T PRK11119 82 TAVNWF 87 (331)
T ss_pred ehhhcc
Confidence 876444
No 400
>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=60.15 E-value=41 Score=37.23 Aligned_cols=87 Identities=11% Similarity=0.157 Sum_probs=57.4
Q ss_pred HHHHHHHHHcCCcEEEEEEecCccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcc
Q 002211 171 SAIAEMVSYFGWGEVIAIFNDDDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGY 250 (953)
Q Consensus 171 ~ai~~~l~~~~w~~vaii~~d~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~ 250 (953)
..+.++++.++.+++.+|+....+.. ..+.+.+.+++.|+.+............+.+.+...+..+++ ++|+||..+.
T Consensus 12 ~~l~~~~~~~~~~~~livtd~~~~~~-~~~~v~~~l~~~~i~~~~~~~~~~~~~pt~~~v~~~~~~~~~-~~d~IIaIGG 89 (348)
T cd08175 12 ERLPEILKEFGYKKALIVADENTYAA-AGKKVEALLKRAGVVVLLIVLPAGDLIADEKAVGRVLKELER-DTDLIIAVGS 89 (348)
T ss_pred HHHHHHHHhcCCCcEEEEECCcHHHH-HHHHHHHHHHHCCCeeEEeecCCCcccCCHHHHHHHHHHhhc-cCCEEEEECC
Confidence 44677788888899988884433322 257888889988986643332222112446777777788777 9999998765
Q ss_pred h--hhHHHHHH
Q 002211 251 S--RTGLMVFD 259 (953)
Q Consensus 251 ~--~~~~~~~~ 259 (953)
+ -|+.+++.
T Consensus 90 Gs~~D~aK~vA 100 (348)
T cd08175 90 GTINDITKYVS 100 (348)
T ss_pred cHHHHHHHHHH
Confidence 4 45555554
No 401
>TIGR00070 hisG ATP phosphoribosyltransferase. Members of this family from B. subtilis, Aquifex aeolicus, and Synechocystis PCC6803 (and related taxa) lack the C-terminal third of the sequence. The sole homolog from Archaeoglobus fulgidus lacks the N-terminal 50 residues (as reported) and is otherwise atypical of the rest of the family. This model excludes the C-terminal extension.
Probab=59.62 E-value=57 Score=32.09 Aligned_cols=74 Identities=16% Similarity=0.179 Sum_probs=48.5
Q ss_pred CCCChHHhhhCCCeEEEEeCchHHHHHHHhhCCCccceEeCCCHHHHHHHHHcCCcEEEEccchhHHHHHhcCcceEEeC
Q 002211 701 PIKGIDTLMTSNDRVGYQVGSFAENYLIEELSIPKSRLVALGSPEEYAIALENRTVAAVVDERPYIDLFLSDHCQFSVRG 780 (953)
Q Consensus 701 ~I~sl~dL~~~~~~ig~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~g~~~a~~~~~~~~~~~~~~~~~l~~~~ 780 (953)
++++.+||. +++|+...-...+.||. +.+. ...++.....-|. +-..|-.|++++-......+.++ +|.++.
T Consensus 100 ~~~~~~~l~--~~rIATkyp~i~~~~f~-~~Gi-~v~ii~l~GsvE~--aP~~GlaD~IvDiv~TG~TL~~N--gL~~ie 171 (182)
T TIGR00070 100 DISSVEDLK--GKRIATKYPNLARRYFE-KKGI-DVEIIKLNGSVEL--APLLGLADAIVDIVSTGTTLREN--GLRIIE 171 (182)
T ss_pred CCCChHHhC--CCEEEECCHHHHHHHHH-HcCC-eEEEEECcceeec--ccCCCceeEEEEEeCCHHHHHHC--CCEEee
Confidence 467889985 88999988888899994 4555 3455555444443 22358889998877666665443 344444
Q ss_pred Cc
Q 002211 781 QE 782 (953)
Q Consensus 781 ~~ 782 (953)
+.
T Consensus 172 ~i 173 (182)
T TIGR00070 172 VI 173 (182)
T ss_pred EE
Confidence 33
No 402
>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=59.20 E-value=40 Score=35.16 Aligned_cols=77 Identities=5% Similarity=0.015 Sum_probs=53.5
Q ss_pred EEEEEe--cCccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHH
Q 002211 185 VIAIFN--DDDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQ 262 (953)
Q Consensus 185 vaii~~--d~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~ 262 (953)
|+++.. +++|.......+.+++++.|..+..... . .+.......++++.+.++|.||+..........++.+.
T Consensus 2 igvv~~~~~~~~~~~~~~~i~~~~~~~g~~~~~~~~---~--~~~~~~~~~~~~l~~~~vdgiii~~~~~~~~~~~~~~~ 76 (266)
T cd06282 2 VGVVLPSLANPVFAECVQGIQEEARAAGYSLLLATT---D--YDAEREADAVETLLRQRVDGLILTVADAATSPALDLLD 76 (266)
T ss_pred eEEEeCCCCcchHHHHHHHHHHHHHHCCCEEEEeeC---C--CCHHHHHHHHHHHHhcCCCEEEEecCCCCchHHHHHHh
Confidence 456664 4667788889999999999998876432 1 12445567778888889999998643333334677887
Q ss_pred HcCC
Q 002211 263 RLGM 266 (953)
Q Consensus 263 ~~g~ 266 (953)
+.|.
T Consensus 77 ~~~i 80 (266)
T cd06282 77 AERV 80 (266)
T ss_pred hCCC
Confidence 7775
No 403
>COG2247 LytB Putative cell wall-binding domain [Cell envelope biogenesis, outer membrane]
Probab=58.58 E-value=1.2e+02 Score=32.40 Aligned_cols=50 Identities=16% Similarity=0.147 Sum_probs=29.3
Q ss_pred EEccCChHH-HHHHHHHHHH-----HcCCcEEEEEEecCccccchHHHHHHHHHhcCcEEEE
Q 002211 160 VQTAPNDLY-LMSAIAEMVS-----YFGWGEVIAIFNDDDQGRNGVTALGDKLAEIRCKISY 215 (953)
Q Consensus 160 fr~~p~d~~-~~~ai~~~l~-----~~~w~~vaii~~d~~~g~~~~~~l~~~l~~~g~~v~~ 215 (953)
-|..-++.+ -+..++.+++ .|+-.+++++|.-| ..+.+.+.+++ |++.++
T Consensus 104 ~RigG~nR~ETa~~v~~~~~~~yp~af~n~kvvvv~GwD-----y~~~~~e~~k~-~~~p~~ 159 (337)
T COG2247 104 KRIGGANRYETAEKVAKFFREDYPNAFKNVKVVVVYGWD-----YADALMELMKE-GIVPVI 159 (337)
T ss_pred EEecCcchHHHHHHHHHHHHhhchhhhcCeEEEEEeccc-----cHHHHHHHHhc-CcceeE
Confidence 344433433 3556666775 24444788887433 33378888888 887665
No 404
>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=58.55 E-value=76 Score=28.90 Aligned_cols=62 Identities=15% Similarity=0.168 Sum_probs=41.7
Q ss_pred chHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcch----hhHHHHHHHHHHcCC
Q 002211 197 NGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYS----RTGLMVFDVAQRLGM 266 (953)
Q Consensus 197 ~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~----~~~~~~~~~a~~~g~ 266 (953)
-+...+...++..|.+|.+-.... .....+..+.+.+||+|.+++.. ..+..+++++++.|.
T Consensus 14 lG~~~~~~~l~~~G~~vi~lG~~v--------p~e~~~~~a~~~~~d~V~iS~~~~~~~~~~~~~~~~L~~~~~ 79 (122)
T cd02071 14 RGAKVIARALRDAGFEVIYTGLRQ--------TPEEIVEAAIQEDVDVIGLSSLSGGHMTLFPEVIELLRELGA 79 (122)
T ss_pred HHHHHHHHHHHHCCCEEEECCCCC--------CHHHHHHHHHHcCCCEEEEcccchhhHHHHHHHHHHHHhcCC
Confidence 345666777888999988643222 22345667777899999998754 455666777777665
No 405
>PRK00002 aroB 3-dehydroquinate synthase; Reviewed
Probab=57.51 E-value=96 Score=34.45 Aligned_cols=102 Identities=12% Similarity=0.072 Sum_probs=64.9
Q ss_pred HHHHHHHHHcCCcEEEEEEecCccccchHHHHHHHHHhcCcEEEEEEecCCC-CCCChHHHHHHHHHHhcCCc---eEEE
Q 002211 171 SAIAEMVSYFGWGEVIAIFNDDDQGRNGVTALGDKLAEIRCKISYKSALPPD-QSVTETDVRNELVKVRMMEA---RVIV 246 (953)
Q Consensus 171 ~ai~~~l~~~~w~~vaii~~d~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~-~~~~~~d~~~~l~~i~~~~~---~vii 246 (953)
..+.+.++.++.+++.+++.... .....+.+.+.+++.|+.+... .++.. ...+.+.+...++.+++.++ |+||
T Consensus 20 ~~l~~~l~~~~~~~~livtd~~~-~~~~~~~v~~~L~~~gi~~~~~-~~~~~e~~~~~~~v~~~~~~~~~~~~~r~d~II 97 (358)
T PRK00002 20 SELGELLAPLKGKKVAIVTDETV-APLYLEKLRASLEAAGFEVDVV-VLPDGEQYKSLETLEKIYDALLEAGLDRSDTLI 97 (358)
T ss_pred HHHHHHHHhcCCCeEEEEECCch-HHHHHHHHHHHHHhcCCceEEE-EeCCCCCCCCHHHHHHHHHHHHHcCCCCCCEEE
Confidence 44666777778899999985544 3457788888898888866421 12221 11346778888888887655 9998
Q ss_pred EEcch--hhHHHHHHHHHHcCCCCCceEEEEeC
Q 002211 247 VHGYS--RTGLMVFDVAQRLGMMDSGYVWIATT 277 (953)
Q Consensus 247 ~~~~~--~~~~~~~~~a~~~g~~~~~~~wi~~~ 277 (953)
..+.+ -|+..++......| ..++-|.|.
T Consensus 98 avGGGsv~D~aK~iA~~~~~g---ip~i~IPTT 127 (358)
T PRK00002 98 ALGGGVIGDLAGFAAATYMRG---IRFIQVPTT 127 (358)
T ss_pred EEcCcHHHHHHHHHHHHhcCC---CCEEEcCch
Confidence 87665 45665655444444 244445554
No 406
>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=57.14 E-value=40 Score=35.68 Aligned_cols=78 Identities=8% Similarity=-0.026 Sum_probs=54.0
Q ss_pred EEEEEEe--cCccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhh-HHHHHHH
Q 002211 184 EVIAIFN--DDDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRT-GLMVFDV 260 (953)
Q Consensus 184 ~vaii~~--d~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~-~~~~~~~ 260 (953)
+|+++.. .+.|.......+.+++++.|..+..... . .+...-...+..+...++|.||+.....+ ....++.
T Consensus 1 ~igv~~~~~~~~~~~~~~~~i~~~~~~~g~~v~~~~~---~--~~~~~~~~~i~~~~~~~~Dgiii~~~~~~~~~~~i~~ 75 (282)
T cd06318 1 KIGFSQYTLNSPFFAALTEAAKAHAKALGYELISTDA---Q--GDLTKQIADVEDLLTRGVNVLIINPVDPEGLVPAVAA 75 (282)
T ss_pred CeeEEeccccCHHHHHHHHHHHHHHHHcCCEEEEEcC---C--CCHHHHHHHHHHHHHcCCCEEEEecCCccchHHHHHH
Confidence 3566664 3677788899999999999998765321 1 12444556788888899999998754332 2456777
Q ss_pred HHHcCC
Q 002211 261 AQRLGM 266 (953)
Q Consensus 261 a~~~g~ 266 (953)
+.+.|.
T Consensus 76 ~~~~~i 81 (282)
T cd06318 76 AKAAGV 81 (282)
T ss_pred HHHCCC
Confidence 777664
No 407
>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=56.68 E-value=1.3e+02 Score=28.98 Aligned_cols=120 Identities=13% Similarity=0.174 Sum_probs=64.6
Q ss_pred HHHhc--CcEEEEccCCh--hhHHHHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCCcE
Q 002211 109 QFMET--DTLAIVGPQSA--VMAHVLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGWGE 184 (953)
Q Consensus 109 ~li~~--~v~aiiGp~~S--~~a~av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~ 184 (953)
+++.+ +.+.++|+... .....+..+++..++|+++.......+.+.. +. ..| ...-.+..++.+-+|+-
T Consensus 22 ~lLk~AKRPvIivG~ga~~~~a~e~l~~laEklgiPVvtT~~~~~~~~~kg---v~-~~~---~~lg~~g~~~~~p~~e~ 94 (162)
T TIGR00315 22 MMIKRAKRPLLIVGPENLEDEEKELIVKFIEKFDLPVVATADTYRALIEAG---IE-SEE---MNLHEITQFLADPSWEG 94 (162)
T ss_pred HHHHcCCCcEEEECCCcCcccHHHHHHHHHHHHCCCEEEcCccccccccCC---ee-cCC---CCHHHHHHhccCchhhh
Confidence 34444 89999998764 7788889999999999997433323333321 11 111 11234555555534433
Q ss_pred ---------EEEEEecCccccchHHHHHHHHHhcCcE-EEEEEecCCCC-----CCChHHHHHHHHHHh
Q 002211 185 ---------VIAIFNDDDQGRNGVTALGDKLAEIRCK-ISYKSALPPDQ-----SVTETDVRNELVKVR 238 (953)
Q Consensus 185 ---------vaii~~d~~~g~~~~~~l~~~l~~~g~~-v~~~~~~~~~~-----~~~~~d~~~~l~~i~ 238 (953)
|.++..+..++..+...++... .++ |.....|.++. ....+++...|+++.
T Consensus 95 ~~g~g~~DlvlfvG~~~y~~~~~ls~lk~f~---~~~~i~l~~~y~pnA~~Sf~n~~~~~~~~~l~~~~ 160 (162)
T TIGR00315 95 FDGEGNYDLVLFLGIIYYYLSQMLSSLKHFS---HIVTIAIDKYYQPNADYSFPNLSKDEYLDYLRKLL 160 (162)
T ss_pred ccCCCCcCEEEEeCCcchHHHHHHHHHHhhc---CcEEEEecCCCCCCCceeccccCHHHHHHHHHHHh
Confidence 4455555555555555555333 232 33333333331 123566777777654
No 408
>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=56.29 E-value=30 Score=38.06 Aligned_cols=98 Identities=13% Similarity=0.078 Sum_probs=64.1
Q ss_pred HHHHHHHHHcCCcEEEEEEecCccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcc
Q 002211 171 SAIAEMVSYFGWGEVIAIFNDDDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGY 250 (953)
Q Consensus 171 ~ai~~~l~~~~w~~vaii~~d~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~ 250 (953)
+.+.+.++.+|.+++.+++....+-. ..+.+.+.+++.+..+ + ..+.+. .+.+.+...+..+++.++|.||..+.
T Consensus 12 ~~l~~~l~~~g~~~~livt~~~~~~~-~~~~v~~~l~~~~~~~-~-~~~~~~--p~~~~v~~~~~~~~~~~~d~IIaiGG 86 (337)
T cd08177 12 AALAAELERLGASRALVLTTPSLATK-LAERVASALGDRVAGT-F-DGAVMH--TPVEVTEAAVAAAREAGADGIVAIGG 86 (337)
T ss_pred HHHHHHHHHcCCCeEEEEcChHHHHH-HHHHHHHHhccCCcEE-e-CCCCCC--CCHHHHHHHHHHHHhcCCCEEEEeCC
Confidence 55777889999999998885544443 6667788887765432 2 223333 44677888888888899999998766
Q ss_pred h--hhHHHHHHHHHHcCCCCCceEEEEeCc
Q 002211 251 S--RTGLMVFDVAQRLGMMDSGYVWIATTW 278 (953)
Q Consensus 251 ~--~~~~~~~~~a~~~g~~~~~~~wi~~~~ 278 (953)
+ -|..+++.... + ..++-|.|..
T Consensus 87 Gs~iD~aK~ia~~~--~---~p~i~IPTta 111 (337)
T cd08177 87 GSTIDLAKAIALRT--G---LPIIAIPTTL 111 (337)
T ss_pred cHHHHHHHHHHHHh--c---CCEEEEcCCc
Confidence 5 45555554332 2 3455555543
No 409
>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=56.13 E-value=46 Score=34.64 Aligned_cols=78 Identities=6% Similarity=-0.013 Sum_probs=53.7
Q ss_pred EEEEEEec--CccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchh-hHHHHHHH
Q 002211 184 EVIAIFND--DDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSR-TGLMVFDV 260 (953)
Q Consensus 184 ~vaii~~d--~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~-~~~~~~~~ 260 (953)
+|++|..+ +.|.....+.+.+++++.|+.+.....- .+.......++++...+.|.||+..... .....++.
T Consensus 1 ~ig~i~p~~~~~~~~~~~~~~~~~a~~~g~~~~~~~~~-----~~~~~~~~~~~~l~~~~vdgvi~~~~~~~~~~~~~~~ 75 (267)
T cd01536 1 KIGLVVPSLNNPFWQAMNKGAEAAAKELGVELIVLDAQ-----NDVSKQIQQIEDLIAQGVDGIIISPVDSAALTPALKK 75 (267)
T ss_pred CEEEEeccccCHHHHHHHHHHHHHHHhcCceEEEECCC-----CCHHHHHHHHHHHHHcCCCEEEEeCCCchhHHHHHHH
Confidence 46777754 6788889999999999999887653221 1244556778888888999998875443 33346667
Q ss_pred HHHcCC
Q 002211 261 AQRLGM 266 (953)
Q Consensus 261 a~~~g~ 266 (953)
+.+.+.
T Consensus 76 l~~~~i 81 (267)
T cd01536 76 ANAAGI 81 (267)
T ss_pred HHHCCC
Confidence 766553
No 410
>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=55.98 E-value=1.7e+02 Score=27.44 Aligned_cols=95 Identities=11% Similarity=0.020 Sum_probs=56.9
Q ss_pred HHHHHHHHHcCCcEEEEEEecCccccchHHHHHHHHHhcCcEEEEEEecC--CCCCCChHHH-HHHHHHHhcCCceEEEE
Q 002211 171 SAIAEMVSYFGWGEVIAIFNDDDQGRNGVTALGDKLAEIRCKISYKSALP--PDQSVTETDV-RNELVKVRMMEARVIVV 247 (953)
Q Consensus 171 ~ai~~~l~~~~w~~vaii~~d~~~g~~~~~~l~~~l~~~g~~v~~~~~~~--~~~~~~~~d~-~~~l~~i~~~~~~vii~ 247 (953)
..+.+.+...+-....-+|.+.... .....+.+++++.|.++....... ......+..+ ...+..+...+.|.|++
T Consensus 27 ~~l~~~~~~~~~~~~~r~y~~~~~~-~~~~~~~~~L~~~g~~~~~~~~~~~~~~~~~~D~~l~~d~~~~~~~~~~d~ivL 105 (149)
T cd06167 27 RKLLEFLRDGGEIVLARAYGNWTSP-ERQRGFLDALRRLGFEPIQKPLRTRGSGKKGVDVALAIDALELAYKRRIDTIVL 105 (149)
T ss_pred HHHHHHHHhCCeEEEEEEEEecCCc-hhHHHHHHHHHHCCcEEEEEcceecCCcccCccHHHHHHHHHHhhhcCCCEEEE
Confidence 3344444443323333444333211 456889999999999987654321 1100112222 33344444457899999
Q ss_pred EcchhhHHHHHHHHHHcCC
Q 002211 248 HGYSRTGLMVFDVAQRLGM 266 (953)
Q Consensus 248 ~~~~~~~~~~~~~a~~~g~ 266 (953)
.+...+...+++.+++.|.
T Consensus 106 vSgD~Df~~~i~~lr~~G~ 124 (149)
T cd06167 106 VSGDSDFVPLVERLRELGK 124 (149)
T ss_pred EECCccHHHHHHHHHHcCC
Confidence 9999999999999999874
No 411
>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=55.97 E-value=50 Score=36.97 Aligned_cols=80 Identities=11% Similarity=0.051 Sum_probs=56.2
Q ss_pred HcCCcEEEEEEecCccc-cchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcch--hhHH
Q 002211 179 YFGWGEVIAIFNDDDQG-RNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYS--RTGL 255 (953)
Q Consensus 179 ~~~w~~vaii~~d~~~g-~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~--~~~~ 255 (953)
.++.+++.+|+....+- .+..+.+.+.|++.|+++.....+.++ .+.+.+...+..+++.++|+||-.+.+ -|+.
T Consensus 20 ~~~~~r~livt~~~~~~~~g~~~~v~~~L~~~g~~~~~~~~v~~~--p~~~~v~~~~~~~~~~~~D~IIavGGGSviD~A 97 (375)
T cd08179 20 TLKGKKAFIVTGGGSMKKFGFLDKVEAYLKEAGIEVEVFEGVEPD--PSVETVLKGAEAMREFEPDWIIALGGGSPIDAA 97 (375)
T ss_pred HhcCCeEEEEeCchHHHhCChHHHHHHHHHHcCCeEEEeCCCCCC--cCHHHHHHHHHHHHhcCCCEEEEeCCccHHHHH
Confidence 34458888887544332 356678899999889887644444444 557788899999999999999987665 4555
Q ss_pred HHHHH
Q 002211 256 MVFDV 260 (953)
Q Consensus 256 ~~~~~ 260 (953)
+.+..
T Consensus 98 K~ia~ 102 (375)
T cd08179 98 KAMWI 102 (375)
T ss_pred HHHHH
Confidence 55543
No 412
>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=55.24 E-value=51 Score=34.53 Aligned_cols=78 Identities=4% Similarity=-0.007 Sum_probs=51.7
Q ss_pred EEEEEe--cCccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHH
Q 002211 185 VIAIFN--DDDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQ 262 (953)
Q Consensus 185 vaii~~--d~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~ 262 (953)
|+++.. ++.|.....+.+.+++++.|..+.....- .+ ........++.+...+.|.||+..........++.+.
T Consensus 2 I~vi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~~-~~---~~~~~~~~~~~l~~~~vdgiii~~~~~~~~~~~~~~~ 77 (270)
T cd01545 2 IGLLYDNPSPGYVSEIQLGALDACRDTGYQLVIEPCD-SG---SPDLAERVRALLQRSRVDGVILTPPLSDNPELLDLLD 77 (270)
T ss_pred EEEEEcCCCcccHHHHHHHHHHHHHhCCCeEEEEeCC-CC---chHHHHHHHHHHHHCCCCEEEEeCCCCCccHHHHHHH
Confidence 466664 46788889999999999999887654322 11 1224555666677788999988644322345667776
Q ss_pred HcCC
Q 002211 263 RLGM 266 (953)
Q Consensus 263 ~~g~ 266 (953)
+.|.
T Consensus 78 ~~~i 81 (270)
T cd01545 78 EAGV 81 (270)
T ss_pred hcCC
Confidence 6664
No 413
>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=55.23 E-value=46 Score=34.99 Aligned_cols=80 Identities=10% Similarity=0.068 Sum_probs=53.9
Q ss_pred EEEEEEec--CccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhh-HHHHHHH
Q 002211 184 EVIAIFND--DDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRT-GLMVFDV 260 (953)
Q Consensus 184 ~vaii~~d--~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~-~~~~~~~ 260 (953)
||++|..+ ++|.......+.+++++.|..+.....-.. .+.......+.++...+.|.+|+...... ....++.
T Consensus 1 ~Igvi~~~~~~~~~~~~~~g~~~~~~~~g~~~~~~~~~~~---~~~~~~~~~i~~l~~~~vdgvii~~~~~~~~~~~l~~ 77 (273)
T cd06310 1 KIALVPKGTTSDFWQAVKAGAEAAAKELGVKVTFQGPASE---TDVAGQVNLLENAIARGPDAILLAPTDAKALVPPLKE 77 (273)
T ss_pred CeEEEecCCCcHHHHHHHHHHHHHHHHcCCEEEEecCccC---CCHHHHHHHHHHHHHhCCCEEEEcCCChhhhHHHHHH
Confidence 46777754 667788889999999999998775432111 12445566777777789999998654433 2456677
Q ss_pred HHHcCC
Q 002211 261 AQRLGM 266 (953)
Q Consensus 261 a~~~g~ 266 (953)
+.+.|+
T Consensus 78 ~~~~~i 83 (273)
T cd06310 78 AKDAGI 83 (273)
T ss_pred HHHCCC
Confidence 766554
No 414
>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=55.11 E-value=43 Score=35.83 Aligned_cols=79 Identities=8% Similarity=0.154 Sum_probs=52.7
Q ss_pred EEEEEEec--CccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchh-hHHHHHHH
Q 002211 184 EVIAIFND--DDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSR-TGLMVFDV 260 (953)
Q Consensus 184 ~vaii~~d--~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~-~~~~~~~~ 260 (953)
||++|..+ +.|.......+.+++++.|..+.... ... .+.......+..+...++|.||+..... .....+++
T Consensus 1 ~i~~i~~~~~~~~~~~~~~gi~~~a~~~g~~~~~~~--~~~--~~~~~~~~~l~~~~~~~~dgiii~~~~~~~~~~~i~~ 76 (294)
T cd06316 1 KAAIVMHTSGSDWSNAQVRGAKDEFAKLGIEVVATT--DAQ--FDPAKQVADIETTISQKPDIIISIPVDPVSTAAAYKK 76 (294)
T ss_pred CeEEEecCCCChHHHHHHHHHHHHHHHcCCEEEEec--CCC--CCHHHHHHHHHHHHHhCCCEEEEcCCCchhhhHHHHH
Confidence 46666643 55666788889999999998876321 221 2244455677777778999998865432 23567788
Q ss_pred HHHcCC
Q 002211 261 AQRLGM 266 (953)
Q Consensus 261 a~~~g~ 266 (953)
+.+.|.
T Consensus 77 ~~~~~i 82 (294)
T cd06316 77 VAEAGI 82 (294)
T ss_pred HHHcCC
Confidence 888775
No 415
>cd01540 PBP1_arabinose_binding Periplasmic L-arabinose-binding protein (ABP), a member of a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily. Periplasmic L-arabinose-binding protein (ABP), a member of a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily. ABP is only involved in transport contrary to other related sugar-binding proteins such as the glucose/galactose-binding protein (GGBP) and the ribose-binding protein (RBP), both of which are involved in chemotaxis as well as transport. The periplasmic ABP consists of two alpha/beta globular domains connected by a three-stranded hinge, a Venus flytrap-like domain, which undergoes a transition from an open to a closed conformational state upon ligand binding. Moreover, ABP is homologous to the ligand-binding domain of eukaryotic receptors such as metabotropic glutamate receptor (mGluR) and DNA-binding transcriptional repressors such a
Probab=54.83 E-value=40 Score=35.86 Aligned_cols=77 Identities=12% Similarity=0.036 Sum_probs=54.2
Q ss_pred EEEEEEec--CccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcch-hhHHHHHHH
Q 002211 184 EVIAIFND--DDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYS-RTGLMVFDV 260 (953)
Q Consensus 184 ~vaii~~d--~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~-~~~~~~~~~ 260 (953)
+|++|..+ +.|.....+.+.+++++.|..+...... + .......++++...++|.||+.... ......+++
T Consensus 1 ~Ig~v~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~~--~----~~~~~~~i~~~~~~~~dgiii~~~~~~~~~~~~~~ 74 (289)
T cd01540 1 KIGFIVKQPEEPWFQTEWKFAKKAAKEKGFTVVKIDVP--D----GEKVLSAIDNLGAQGAKGFVICVPDVKLGPAIVAK 74 (289)
T ss_pred CeeeecCCCCCcHHHHHHHHHHHHHHHcCCEEEEccCC--C----HHHHHHHHHHHHHcCCCEEEEccCchhhhHHHHHH
Confidence 35666643 5678888899999999999887643211 2 3444567778888899999987543 334567888
Q ss_pred HHHcCC
Q 002211 261 AQRLGM 266 (953)
Q Consensus 261 a~~~g~ 266 (953)
+.+.|.
T Consensus 75 ~~~~~i 80 (289)
T cd01540 75 AKAYNM 80 (289)
T ss_pred HHhCCC
Confidence 888764
No 416
>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=54.80 E-value=51 Score=35.44 Aligned_cols=78 Identities=10% Similarity=0.019 Sum_probs=54.0
Q ss_pred EEEEEe--cCccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcch-hhHHHHHHHH
Q 002211 185 VIAIFN--DDDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYS-RTGLMVFDVA 261 (953)
Q Consensus 185 vaii~~--d~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~-~~~~~~~~~a 261 (953)
|++|.. ++.|.......+.+++++.|..+.... +.. .+.......++.+...++|.||+.... ......++++
T Consensus 2 I~vi~~~~~~~f~~~i~~gi~~~a~~~g~~v~~~~--~~~--~d~~~~~~~i~~~~~~~~DgiIi~~~~~~~~~~~~~~~ 77 (298)
T cd06302 2 IAFVPKVTGIPYFNRMEEGAKEAAKELGVDAIYVG--PTT--ADAAGQVQIIEDLIAQGVDAIAVVPNDPDALEPVLKKA 77 (298)
T ss_pred EEEEEcCCCChHHHHHHHHHHHHHHHhCCeEEEEC--CCC--CCHHHHHHHHHHHHhcCCCEEEEecCCHHHHHHHHHHH
Confidence 555653 467788889999999999998876421 111 124556677888878899999997543 3345677788
Q ss_pred HHcCC
Q 002211 262 QRLGM 266 (953)
Q Consensus 262 ~~~g~ 266 (953)
.+.|+
T Consensus 78 ~~~~i 82 (298)
T cd06302 78 REAGI 82 (298)
T ss_pred HHCCC
Confidence 77664
No 417
>smart00072 GuKc Guanylate kinase homologues. Active enzymes catalyze ATP-dependent phosphorylation of GMP to GDP. Structure resembles that of adenylate kinase. So-called membrane-associated guanylate kinase homologues (MAGUKs) do not possess guanylate kinase activities; instead at least some possess protein-binding functions.
Probab=54.65 E-value=2e+02 Score=28.23 Aligned_cols=130 Identities=10% Similarity=0.076 Sum_probs=67.1
Q ss_pred CcEEEEccCChhhHHHHHHhhhhC--CCcEEEeecCCCCCCC--CCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEE
Q 002211 114 DTLAIVGPQSAVMAHVLSHLANEL--QVPLLSFTALDPTLSP--LQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIF 189 (953)
Q Consensus 114 ~v~aiiGp~~S~~a~av~~v~~~~--~vP~Is~~at~~~ls~--~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~ 189 (953)
.+++++||.+|+=...+..+.+.. ++..+-...|-+.-.. .+-.|.|-+. +.+-+.++.-.+-.... +
T Consensus 3 r~ivl~Gpsg~GK~tl~~~L~~~~~~~~~~~~~~TtR~~r~~e~~g~dy~fvs~-------~ef~~~i~~g~fve~~~-~ 74 (184)
T smart00072 3 RPIVLSGPSGVGKGTLLAELIQEIPDAFERVVSHTTRPPRPGEVNGVDYHFVSR-------EEFEDDIKSGLFLEWGE-Y 74 (184)
T ss_pred cEEEEECCCCCCHHHHHHHHHhcCCcceEeeeeecCCCCCCCCcCCceEEECCH-------HHHHHHHHcCCeEEEEE-E
Confidence 468899999998887777777775 3433332333333222 2335666431 22333333322222222 2
Q ss_pred ecCccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHHHcC
Q 002211 190 NDDDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQRLG 265 (953)
Q Consensus 190 ~d~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~~~g 265 (953)
.++-||.. .+.+.+.+++...+|... . + ..+.++++..++.++++..+++...+.+...+.|
T Consensus 75 ~g~~YGt~-~~~i~~~~~~~~~~ild~-~-~-----------~~~~~l~~~~~~~~vIfi~~~s~~~l~~rl~~R~ 136 (184)
T smart00072 75 SGNYYGTS-KETIRQVAEQGKHCLLDI-D-P-----------QGVKQLRKAQLYPIVIFIAPPSSEELERRLRGRG 136 (184)
T ss_pred cCcCcccC-HHHHHHHHHcCCeEEEEE-C-H-----------HHHHHHHHhCCCcEEEEEeCcCHHHHHHHHHhcC
Confidence 24556654 455666666555555432 1 1 1244555555666666666555555555555433
No 418
>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=54.35 E-value=54 Score=34.29 Aligned_cols=77 Identities=8% Similarity=0.009 Sum_probs=53.6
Q ss_pred EEEEEec--CccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchh-hHHHHHHHH
Q 002211 185 VIAIFND--DDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSR-TGLMVFDVA 261 (953)
Q Consensus 185 vaii~~d--~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~-~~~~~~~~a 261 (953)
|+++..+ +.|.....+.+.+++++.|..+.... .. .+.......+.++.+.++|.+|+..... .....++++
T Consensus 2 i~~~~~~~~~~~~~~~~~~i~~~~~~~g~~~~i~~---~~--~~~~~~~~~~~~~~~~~vdgiii~~~~~~~~~~~~~~~ 76 (267)
T cd06322 2 IGASLLTQQHPFYIELANAMKEEAKKQKVNLIVSI---AN--QDLNKQLSDVEDFITKKVDAIVLSPVDSKGIRAAIAKA 76 (267)
T ss_pred eeEeecCcccHHHHHHHHHHHHHHHhcCCEEEEec---CC--CCHHHHHHHHHHHHHcCCCEEEEcCCChhhhHHHHHHH
Confidence 4566654 67888889999999999998876532 11 1244556778888888999999965433 235567777
Q ss_pred HHcCC
Q 002211 262 QRLGM 266 (953)
Q Consensus 262 ~~~g~ 266 (953)
.+.|+
T Consensus 77 ~~~~i 81 (267)
T cd06322 77 KKAGI 81 (267)
T ss_pred HHCCC
Confidence 77664
No 419
>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=54.25 E-value=55 Score=34.16 Aligned_cols=77 Identities=10% Similarity=0.012 Sum_probs=53.4
Q ss_pred EEEEEe--cCccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHH
Q 002211 185 VIAIFN--DDDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQ 262 (953)
Q Consensus 185 vaii~~--d~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~ 262 (953)
+++|.. .+.|.......+.+++++.|.++... ... .+...-...++++.+.++|.|++..........++++.
T Consensus 2 I~vi~~~~~~~~~~~~~~g~~~~a~~~g~~~~~~---~~~--~~~~~~~~~i~~~~~~~vdgiii~~~~~~~~~~~~~~~ 76 (268)
T cd06289 2 IGLVINDLTNPFFAELAAGLEEVLEEAGYTVFLA---NSG--EDVERQEQLLSTMLEHGVAGIILCPAAGTSPDLLKRLA 76 (268)
T ss_pred EEEEecCCCcchHHHHHHHHHHHHHHcCCeEEEe---cCC--CChHHHHHHHHHHHHcCCCEEEEeCCCCccHHHHHHHH
Confidence 566664 46677788899999999999887542 211 12444566788888889999998765444444677787
Q ss_pred HcCC
Q 002211 263 RLGM 266 (953)
Q Consensus 263 ~~g~ 266 (953)
+.|.
T Consensus 77 ~~~i 80 (268)
T cd06289 77 ESGI 80 (268)
T ss_pred hcCC
Confidence 7665
No 420
>cd06277 PBP1_LacI_like_1 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=54.22 E-value=69 Score=33.55 Aligned_cols=75 Identities=11% Similarity=0.034 Sum_probs=50.8
Q ss_pred EEEEEec-----CccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHH
Q 002211 185 VIAIFND-----DDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFD 259 (953)
Q Consensus 185 vaii~~d-----~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~ 259 (953)
|+++.++ +.|.....+.+.+++++.|..+.... .... .......+..+.+.++|.||+.....+. .++
T Consensus 2 vgv~~~~~~~~~~~~~~~~~~~i~~~~~~~g~~~~~~~-~~~~----~~~~~~~~~~l~~~~vdgiii~~~~~~~--~~~ 74 (268)
T cd06277 2 IGLIASKRILNSPAFYSEIYRAIEEEAKKYGYNLILKF-VSDE----DEEEFELPSFLEDGKVDGIILLGGISTE--YIK 74 (268)
T ss_pred eEEEEeccccccCCcHHHHHHHHHHHHHHcCCEEEEEe-CCCC----hHHHHHHHHHHHHCCCCEEEEeCCCChH--HHH
Confidence 5666655 77888889999999999998876543 2222 3334455666777889999987654332 366
Q ss_pred HHHHcCC
Q 002211 260 VAQRLGM 266 (953)
Q Consensus 260 ~a~~~g~ 266 (953)
.+.+.|.
T Consensus 75 ~l~~~~i 81 (268)
T cd06277 75 EIKELGI 81 (268)
T ss_pred HHhhcCC
Confidence 7777664
No 421
>TIGR00067 glut_race glutamate racemase. The most closely related proteins differing in function are aspartate racemases.
Probab=53.32 E-value=1.7e+02 Score=30.56 Aligned_cols=40 Identities=13% Similarity=0.114 Sum_probs=31.2
Q ss_pred HHHHHHH-hcCcEEEEccCChhhHHHHHHhhhhCCCcEEEe
Q 002211 105 MGALQFM-ETDTLAIVGPQSAVMAHVLSHLANELQVPLLSF 144 (953)
Q Consensus 105 ~~a~~li-~~~v~aiiGp~~S~~a~av~~v~~~~~vP~Is~ 144 (953)
+.+..|. +.++.+|+=|..+..+.+...+-+..++|+|+.
T Consensus 51 ~~~~~L~~~~g~d~ivIaCNTA~a~~~~~l~~~~~iPii~i 91 (251)
T TIGR00067 51 ELLTFLKERHNIKLLVVACNTASALALEDLQRNFDFPVVGV 91 (251)
T ss_pred HHHHHHHHhCCCCEEEEeCchHHHHHHHHHHHHCCCCEEee
Confidence 3344555 558999999888888788888888889999973
No 422
>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=53.29 E-value=1.4e+02 Score=26.70 Aligned_cols=84 Identities=14% Similarity=0.163 Sum_probs=46.0
Q ss_pred HHHcCCcEEEEEEecCc-cccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHH
Q 002211 177 VSYFGWGEVIAIFNDDD-QGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGL 255 (953)
Q Consensus 177 l~~~~w~~vaii~~d~~-~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~ 255 (953)
++..|.+.|.-+-.|.+ -++...+.+.+..++.|+..++. .+..+ ..+.+++....+.+......|.+.|.++..+.
T Consensus 23 la~~GfktVInlRpd~E~~~qp~~~~~~~~a~~~Gl~y~~i-Pv~~~-~~~~~~v~~f~~~l~~~~~Pvl~hC~sG~Ra~ 100 (110)
T PF04273_consen 23 LAAQGFKTVINLRPDGEEPGQPSSAEEAAAAEALGLQYVHI-PVDGG-AITEEDVEAFADALESLPKPVLAHCRSGTRAS 100 (110)
T ss_dssp HHHCT--EEEE-S-TTSTTT-T-HHCHHHHHHHCT-EEEE-----TT-T--HHHHHHHHHHHHTTTTSEEEE-SCSHHHH
T ss_pred HHHCCCcEEEECCCCCCCCCCCCHHHHHHHHHHcCCeEEEe-ecCCC-CCCHHHHHHHHHHHHhCCCCEEEECCCChhHH
Confidence 55689999998887754 35566777889999999986642 23222 14566776666666655445666666666665
Q ss_pred HHHHHHH
Q 002211 256 MVFDVAQ 262 (953)
Q Consensus 256 ~~~~~a~ 262 (953)
.+...++
T Consensus 101 ~l~~l~~ 107 (110)
T PF04273_consen 101 ALWALAQ 107 (110)
T ss_dssp HHHHHHH
T ss_pred HHHHHHh
Confidence 5554443
No 423
>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=53.12 E-value=1.8e+02 Score=30.30 Aligned_cols=126 Identities=11% Similarity=0.012 Sum_probs=72.3
Q ss_pred EEEeEEEecCCCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEEccCChhhHHH
Q 002211 50 LNVGAIFSFGTVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIVGPQSAVMAHV 129 (953)
Q Consensus 50 i~IG~l~~~~~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aiiGp~~S~~a~a 129 (953)
-+||.+.+........-..|+.-|+++.+. ..+...+...+..+...+...+.++++.+..+|+... ...+..
T Consensus 121 ~~I~~i~~~~~~~~~~R~~Gf~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~ai~~~~-d~~A~g 193 (260)
T cd06304 121 GKVGFVGGMPIPEVNRFINGFAAGAKSVNP------DITVLVIYTGSFFDPAKGKEAALALIDQGADVIFAAA-GGTGPG 193 (260)
T ss_pred CceEEEeccccHHHHHHHHHHHHHHHHhCC------CcEEEEEEecCccCcHHHHHHHHHHHhCCCCEEEEcC-CCCchH
Confidence 457776542222233445677777766431 2333333333434456677778888877678888744 445656
Q ss_pred HHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcCCcE
Q 002211 130 LSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFGWGE 184 (953)
Q Consensus 130 v~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~ 184 (953)
+...+.+.++-++++..+. ......|-+-....+....+..+++.+..-.|+.
T Consensus 194 v~~al~~~gv~vigfD~~~--~~~~~~p~lttv~~~~~~~~~~~~~~~~~~~~~~ 246 (260)
T cd06304 194 VIQAAKEAGVYAIGVDSDQ--SALAPDAVLTSAVKNVDVAVYDAIKAVLDGTWKG 246 (260)
T ss_pred HHHHHHHcCCEEEeecCch--hhhcCccEEEEEEeccHHHHHHHHHHHHcCCCCC
Confidence 6667777777777665432 2222235555555566666777777666655544
No 424
>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=52.67 E-value=1.4e+02 Score=26.70 Aligned_cols=64 Identities=9% Similarity=0.062 Sum_probs=34.1
Q ss_pred CccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEc-ch---hhHHHHHHHHHH
Q 002211 192 DDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHG-YS---RTGLMVFDVAQR 263 (953)
Q Consensus 192 ~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~-~~---~~~~~~~~~a~~ 263 (953)
.++-.-+...+...+++.|.+|..... . .+.....+.+++.+||+|.+.+ .. .....+.+.+++
T Consensus 10 ~~~~~lGl~~la~~l~~~G~~v~~~d~---~-----~~~~~l~~~~~~~~pd~V~iS~~~~~~~~~~~~l~~~~k~ 77 (121)
T PF02310_consen 10 GEVHPLGLLYLAAYLRKAGHEVDILDA---N-----VPPEELVEALRAERPDVVGISVSMTPNLPEAKRLARAIKE 77 (121)
T ss_dssp TSSTSHHHHHHHHHHHHTTBEEEEEES---S-----B-HHHHHHHHHHTTCSEEEEEESSSTHHHHHHHHHHHHHT
T ss_pred CcchhHHHHHHHHHHHHCCCeEEEECC---C-----CCHHHHHHHHhcCCCcEEEEEccCcCcHHHHHHHHHHHHh
Confidence 333334566667777777777664321 1 1114445566667778777766 33 334444444443
No 425
>COG3340 PepE Peptidase E [Amino acid transport and metabolism]
Probab=52.66 E-value=1.4e+02 Score=29.98 Aligned_cols=85 Identities=19% Similarity=0.177 Sum_probs=53.5
Q ss_pred HHHHHHHHHcCCcEEEEEEecCccc--cchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEE
Q 002211 171 SAIAEMVSYFGWGEVIAIFNDDDQG--RNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVH 248 (953)
Q Consensus 171 ~ai~~~l~~~~w~~vaii~~d~~~g--~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~ 248 (953)
.-|.+.++.. -++|+.|=.-..-. ....+.++++|++.|..|..-....+. ..++...| .++|+|++.
T Consensus 22 ~~i~n~l~g~-~~~i~FIPtAs~~~~~~~Yv~k~~~~l~~lg~~v~~L~l~~~~----~~~Ie~~l-----~~~d~IyVg 91 (224)
T COG3340 22 PFIANFLQGK-RKTIAFIPTASVDSEDDFYVEKVRNALAKLGLEVSELHLSKPP----LAAIENKL-----MKADIIYVG 91 (224)
T ss_pred HHHHHHhcCC-CceEEEEecCccccchHHHHHHHHHHHHHcCCeeeeeeccCCC----HHHHHHhh-----hhccEEEEC
Confidence 4455555554 46888885322111 236789999999999998865444433 44444443 357888876
Q ss_pred cchhhHHHHHHHHHHcCCC
Q 002211 249 GYSRTGLMVFDVAQRLGMM 267 (953)
Q Consensus 249 ~~~~~~~~~~~~a~~~g~~ 267 (953)
+. ....+++++++.|+.
T Consensus 92 GG--NTF~LL~~lke~gld 108 (224)
T COG3340 92 GG--NTFNLLQELKETGLD 108 (224)
T ss_pred Cc--hHHHHHHHHHHhCcH
Confidence 54 456677777777753
No 426
>cd08481 PBP2_GcdR_like The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, contains the type 2 periplasmic binding fold. GcdR is involved in the glutaconate/glutarate-specific activation of the Pg promoter driving expression of a glutaryl-CoA dehydrogenase-encoding gene (gcdH). The GcdH protein is essential for the anaerobic catabolism of many aromatic compounds and some alicyclic and dicarboxylic acids. The structural topology of this substrate-binding domain is most similar to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplas
Probab=51.94 E-value=1.6e+02 Score=28.29 Aligned_cols=97 Identities=9% Similarity=0.005 Sum_probs=49.4
Q ss_pred CChHHhhhCCCeEEE-EeC-chHHHHHHHhhCCCc---cceEeCCCHHHHHHHHHcCCcEEEEccchhHHHHHhcCcceE
Q 002211 703 KGIDTLMTSNDRVGY-QVG-SFAENYLIEELSIPK---SRLVALGSPEEYAIALENRTVAAVVDERPYIDLFLSDHCQFS 777 (953)
Q Consensus 703 ~sl~dL~~~~~~ig~-~~~-s~~~~~l~~~~~~~~---~~~~~~~~~~~~~~~l~~g~~~a~~~~~~~~~~~~~~~~~l~ 777 (953)
-+++||. +.++-. ... .....++.+ .+... .....+++.+...+.+..|.--+++.+.....+. . ...+.
T Consensus 86 ~~~~dl~--~~~~i~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~v~~g~Gi~~~p~~~~~~~~-~-~~~l~ 160 (194)
T cd08481 86 AAPADLA--HLPLLQQTTRPEAWRDWFEE-VGLEVPTAYRGMRFEQFSMLAQAAVAGLGVALLPRFLIEEEL-A-RGRLV 160 (194)
T ss_pred CcHHHHh--hCceEecCCCCcCHHHHHHH-cCCCCCCccCceEeccHHHHHHHHHhCCCeEEecHHHHHHHH-H-CCCEE
Confidence 3678886 333322 211 223455532 33221 1224457888888888887776776654433332 2 22333
Q ss_pred EeC--CccccCccEEEecCCCcchHHHHH
Q 002211 778 VRG--QEFTKSGWGFAFPRDSPLAIDMST 804 (953)
Q Consensus 778 ~~~--~~~~~~~~~~~~~k~spl~~~~n~ 804 (953)
... +......++++.+|+.+....+..
T Consensus 161 ~~~~~~~~~~~~~~l~~~~~~~~~~~~~~ 189 (194)
T cd08481 161 VPFNLPLTSDKAYYLVYPEDKAESPPVQA 189 (194)
T ss_pred eecCccccCCCeEEEEeCcccccCHHHHH
Confidence 222 222234678888887665444443
No 427
>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=51.64 E-value=83 Score=34.52 Aligned_cols=98 Identities=9% Similarity=0.144 Sum_probs=62.0
Q ss_pred HHHHHHHHHcCC-cEEEEEEecCccccchHHHHHHHHHhcCcEEEEEE-ecCCCCCCChHHHHHHHHHHhcCCceEEEEE
Q 002211 171 SAIAEMVSYFGW-GEVIAIFNDDDQGRNGVTALGDKLAEIRCKISYKS-ALPPDQSVTETDVRNELVKVRMMEARVIVVH 248 (953)
Q Consensus 171 ~ai~~~l~~~~w-~~vaii~~d~~~g~~~~~~l~~~l~~~g~~v~~~~-~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~ 248 (953)
..+.++++.++. +++.+|+....+... .+.+.+.|++.|+++.... ...++ .+.+.+...+..+++ ++|+||..
T Consensus 12 ~~l~~~~~~~~~~~kvlivtd~~~~~~~-~~~i~~~L~~~~~~~~i~~~~~~~~--p~~~~v~~~~~~~~~-~~d~IIai 87 (332)
T cd08549 12 NDIGPIINKIGVNSKIMIVCGNNTYKVA-GKEIIERLESNNFTKEVLERDSLLI--PDEYELGEVLIKLDK-DTEFLLGI 87 (332)
T ss_pred HHHHHHHHHcCCCCcEEEEECCcHHHHH-HHHHHHHHHHcCCeEEEEecCCCCC--CCHHHHHHHHHHhhc-CCCEEEEE
Confidence 446667777776 788888865544332 4778888988887654211 12222 346778888888887 99999987
Q ss_pred cch--hhHHHHHHHHHHcCCCCCceEEEEeC
Q 002211 249 GYS--RTGLMVFDVAQRLGMMDSGYVWIATT 277 (953)
Q Consensus 249 ~~~--~~~~~~~~~a~~~g~~~~~~~wi~~~ 277 (953)
+.+ -|+..++. ...| ..++-|.|.
T Consensus 88 GGGsv~D~aK~iA--~~~g---ip~I~VPTT 113 (332)
T cd08549 88 GSGTIIDLVKFVS--FKVG---KPFISVPTA 113 (332)
T ss_pred CCcHHHHHHHHHH--HHcC---CCEEEeCCC
Confidence 665 56666654 2233 345555554
No 428
>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=51.60 E-value=71 Score=34.03 Aligned_cols=77 Identities=9% Similarity=0.098 Sum_probs=55.5
Q ss_pred EEEEEec--CccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcc-hhhHHHHHHHH
Q 002211 185 VIAIFND--DDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGY-SRTGLMVFDVA 261 (953)
Q Consensus 185 vaii~~d--~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~-~~~~~~~~~~a 261 (953)
|++|..+ +.|.....+.+.+++++.|..+..... . .+.......++++.+.++|.||+... .......++++
T Consensus 2 I~vi~~~~~~~~~~~~~~gi~~~a~~~g~~~~~~~~---~--~~~~~~~~~i~~~~~~~vdgiii~~~~~~~~~~~l~~l 76 (288)
T cd01538 2 IGLSLPTKTEERWIRDRPNFEAALKELGAEVIVQNA---N--GDPAKQISQIENMIAKGVDVLVIAPVDGEALASAVEKA 76 (288)
T ss_pred eEEEEeCCCcHHHHHHHHHHHHHHHHcCCEEEEECC---C--CCHHHHHHHHHHHHHcCCCEEEEecCChhhHHHHHHHH
Confidence 5677753 677788889999999999998776432 1 12445567788888889999998754 33346678888
Q ss_pred HHcCC
Q 002211 262 QRLGM 266 (953)
Q Consensus 262 ~~~g~ 266 (953)
.+.|.
T Consensus 77 ~~~~i 81 (288)
T cd01538 77 ADAGI 81 (288)
T ss_pred HHCCC
Confidence 87664
No 429
>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=51.58 E-value=77 Score=30.19 Aligned_cols=63 Identities=19% Similarity=0.257 Sum_probs=44.3
Q ss_pred EEEEEEecCc--ccc---chHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhc-CCceEEEEEcc
Q 002211 184 EVIAIFNDDD--QGR---NGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRM-MEARVIVVHGY 250 (953)
Q Consensus 184 ~vaii~~d~~--~g~---~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~-~~~~vii~~~~ 250 (953)
++++|...++ .|+ .....+.+.+++.|.++.....++.+ .+++...+++..+ +++|+||..+.
T Consensus 2 ~~~ii~~~~e~~~g~i~d~n~~~l~~~l~~~G~~v~~~~~v~Dd----~~~i~~~l~~~~~~~~~DlVittGG 70 (152)
T cd00886 2 RAAVLTVSDTRSAGEAEDRSGPALVELLEEAGHEVVAYEIVPDD----KDEIREALIEWADEDGVDLILTTGG 70 (152)
T ss_pred EEEEEEEcCcccCCCCccchHHHHHHHHHHcCCeeeeEEEcCCC----HHHHHHHHHHHHhcCCCCEEEECCC
Confidence 5677765542 222 23457888899999998887777766 7778888877654 37899998654
No 430
>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=51.18 E-value=39 Score=37.08 Aligned_cols=79 Identities=11% Similarity=0.054 Sum_probs=53.1
Q ss_pred HHcCCcEEEEEEecCccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcch--hhHH
Q 002211 178 SYFGWGEVIAIFNDDDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYS--RTGL 255 (953)
Q Consensus 178 ~~~~w~~vaii~~d~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~--~~~~ 255 (953)
..++.+++.+|+....+..+..+.+.+.+++. +.+.....+.++ .+.+.+...+..+++.++|+||-.+.+ -|+.
T Consensus 18 ~~~~~~~~lvv~~~~~~~~g~~~~v~~~l~~~-~~~~~~~~v~~~--p~~~~v~~~~~~~~~~~~d~IiaiGGGs~~D~a 94 (332)
T cd08180 18 KELKNKRVLIVTDPFMVKSGMLDKVTDHLDSS-IEVEIFSDVVPD--PPIEVVAKGIKKFLDFKPDIVIALGGGSAIDAA 94 (332)
T ss_pred HHhCCCeEEEEeCchhhhCccHHHHHHHHHhc-CcEEEeCCCCCC--cCHHHHHHHHHHHHhcCCCEEEEECCchHHHHH
Confidence 44556899988854444444677888888876 554433334444 457778888899999999999977654 4555
Q ss_pred HHHH
Q 002211 256 MVFD 259 (953)
Q Consensus 256 ~~~~ 259 (953)
+.+.
T Consensus 95 Ka~a 98 (332)
T cd08180 95 KAII 98 (332)
T ss_pred HHHH
Confidence 5443
No 431
>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=51.13 E-value=90 Score=30.18 Aligned_cols=65 Identities=14% Similarity=0.167 Sum_probs=46.4
Q ss_pred CcEEEEEEecCcccc---chHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhc-CCceEEEEEcc
Q 002211 182 WGEVIAIFNDDDQGR---NGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRM-MEARVIVVHGY 250 (953)
Q Consensus 182 w~~vaii~~d~~~g~---~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~-~~~~vii~~~~ 250 (953)
..++++|...|.-+. .....+...+++.|.++.....++.+ .+.+...+++..+ .+.|+|+..+.
T Consensus 4 ~~rv~vit~~d~~~~~~d~n~~~l~~~L~~~G~~v~~~~iv~Dd----~~~i~~~l~~~~~~~~~DlVIttGG 72 (163)
T TIGR02667 4 PLRIAILTVSDTRTEEDDTSGQYLVERLTEAGHRLADRAIVKDD----IYQIRAQVSAWIADPDVQVILITGG 72 (163)
T ss_pred ccEEEEEEEeCcCCccCCCcHHHHHHHHHHCCCeEEEEEEcCCC----HHHHHHHHHHHHhcCCCCEEEECCC
Confidence 357788765443222 23457788899999998887777766 7788888888753 57999998654
No 432
>COG1922 WecG Teichoic acid biosynthesis proteins [Cell envelope biogenesis, outer membrane]
Probab=51.13 E-value=1.1e+02 Score=31.79 Aligned_cols=102 Identities=11% Similarity=-0.066 Sum_probs=62.7
Q ss_pred HHHHHHHHHHHHcCCcEEEEEEecCccccchHHHHHHHHHhc--CcEEEEEE-ecCCCCCCChHHHHHHHHHHhcCCceE
Q 002211 168 YLMSAIAEMVSYFGWGEVIAIFNDDDQGRNGVTALGDKLAEI--RCKISYKS-ALPPDQSVTETDVRNELVKVRMMEARV 244 (953)
Q Consensus 168 ~~~~ai~~~l~~~~w~~vaii~~d~~~g~~~~~~l~~~l~~~--g~~v~~~~-~~~~~~~~~~~d~~~~l~~i~~~~~~v 244 (953)
....++.+.+..- -++|.++....+ ..+.....+++. |..|+... .|-.. .++ ...+++|++++||+
T Consensus 95 Dl~~~Ll~~a~~~-~~~vfllGgkp~----V~~~a~~~l~~~~p~l~ivg~h~GYf~~----~e~-~~i~~~I~~s~pdi 164 (253)
T COG1922 95 DLVEALLKRAAEE-GKRVFLLGGKPG----VAEQAAAKLRAKYPGLKIVGSHDGYFDP----EEE-EAIVERIAASGPDI 164 (253)
T ss_pred HHHHHHHHHhCcc-CceEEEecCCHH----HHHHHHHHHHHHCCCceEEEecCCCCCh----hhH-HHHHHHHHhcCCCE
Confidence 3455566555444 367777765443 344444444443 34665543 23222 333 68999999999999
Q ss_pred EEEEcchhhHHHHHHHHHHcCCCCCceEEEEeCccccc
Q 002211 245 IVVHGYSRTGLMVFDVAQRLGMMDSGYVWIATTWLSTF 282 (953)
Q Consensus 245 ii~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~~~~~~ 282 (953)
+++.+..+.-..++.+-++.= +.-++++.++.-+.
T Consensus 165 l~VgmG~P~QE~wi~~~~~~~---~~~v~igVGg~fDv 199 (253)
T COG1922 165 LLVGMGVPRQEIWIARNRQQL---PVAVAIGVGGSFDV 199 (253)
T ss_pred EEEeCCCchhHHHHHHhHHhc---CCceEEeccceEEE
Confidence 999988887777777766632 24467777654433
No 433
>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=51.04 E-value=74 Score=33.16 Aligned_cols=76 Identities=12% Similarity=0.033 Sum_probs=54.1
Q ss_pred EEEEEe--cCccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHH
Q 002211 185 VIAIFN--DDDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQ 262 (953)
Q Consensus 185 vaii~~--d~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~ 262 (953)
|+++.. +++|-....+.+.+++++.|..+..... . .+.+.....+..+.+.+.|.||+....... ..++++.
T Consensus 2 igvv~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~---~--~~~~~~~~~~~~l~~~~vdgiIi~~~~~~~-~~~~~l~ 75 (265)
T cd06299 2 IGVIVPDIRNPYFASLATAIQDAASAAGYSTIIGNS---D--ENPETENRYLDNLLSQRVDGIIVVPHEQSA-EQLEDLL 75 (265)
T ss_pred EEEEecCCCCccHHHHHHHHHHHHHHcCCEEEEEeC---C--CCHHHHHHHHHHHHhcCCCEEEEcCCCCCh-HHHHHHH
Confidence 566665 4678788889999999999998775432 1 124455677888888999999987654333 3478888
Q ss_pred HcCC
Q 002211 263 RLGM 266 (953)
Q Consensus 263 ~~g~ 266 (953)
+.|.
T Consensus 76 ~~~i 79 (265)
T cd06299 76 KRGI 79 (265)
T ss_pred hCCC
Confidence 7664
No 434
>PF01634 HisG: ATP phosphoribosyltransferase; InterPro: IPR013820 ATP phosphoribosyltransferase (2.4.2.17 from EC) is the enzyme that catalyzes the first step in the biosynthesis of histidine in bacteria, fungi and plants as shown below. It is a member of the larger phosphoribosyltransferase superfamily of enzymes which catalyse the condensation of 5-phospho-alpha-D-ribose 1-diphosphate with nitrogenous bases in the presence of divalent metal ions []. ATP + 5-phospho-alpha-D-ribose 1-diphosphate = 1-(5-phospho-D-ribosyl)-ATP + diphosphate Histidine biosynthesis is an energetically expensive process and ATP phosphoribosyltransferase activity is subject to control at several levels. Transcriptional regulation is based primarily on nutrient conditions and determines the amount of enzyme present in the cell, while feedback inihibition rapidly modulates activity in response to cellular conditions. The enzyme has been shown to be inhibited by 1-(5-phospho-D-ribosyl)-ATP, histidine, ppGpp (a signal associated with adverse environmental conditions) and ADP and AMP (which reflect the overall energy status of the cell). As this pathway of histidine biosynthesis is present only in prokayrotes, plants and fungi, this enzyme is a promising target for the development of novel antimicrobial compounds and herbicides. ATP phosphoribosyltransferase is found in two distinct forms: a long form containing two catalytic domains and a C-terminal regulatory domain, and a short form in which the regulatory domain is missing. The long form is catalytically competent, but in organisms with the short form, a histidyl-tRNA synthetase paralogue, HisZ, is required for enzyme activity []. This entry represents the catalytic region of this enzyme. The structures of the long form enzymes from Escherichia coli (P60757 from SWISSPROT) and Mycobacterium tuberculosis (P60759 from SWISSPROT) have been determined [, ]. The enzyme itself exists in equilibrium between an active dimeric form, an inactive hexameric form and higher aggregates. Interconversion between the various forms is largely reversible and is influenced by the binding of the natural substrates and inhibitors of the enzyme. The two catalytic domains are linked by a two-stranded beta-sheet and togther form a "periplasmic binding protein fold". A crevice between these domains contains the active site. The C-terminal domain is not directly involved in catalysis but appears to be involved the formation of hexamers, induced by the binding of inhibitors such as histidine to the enzyme, thus regulating activity.; GO: 0003879 ATP phosphoribosyltransferase activity, 0000105 histidine biosynthetic process, 0005737 cytoplasm; PDB: 1VE4_A 2VD3_B 1NH7_A 1NH8_A 1Z7N_G 1Z7M_E 1O64_A 1O63_A 1USY_F 1Q1K_A ....
Probab=50.91 E-value=22 Score=34.27 Aligned_cols=102 Identities=16% Similarity=0.156 Sum_probs=60.2
Q ss_pred CCCChHHhhhCCCeEEEEeCchHHHHHHHhhCCCccceEeCCCHHHHHHHHHcCCcEEEEccchhHHHHHhcCcceEEeC
Q 002211 701 PIKGIDTLMTSNDRVGYQVGSFAENYLIEELSIPKSRLVALGSPEEYAIALENRTVAAVVDERPYIDLFLSDHCQFSVRG 780 (953)
Q Consensus 701 ~I~sl~dL~~~~~~ig~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~g~~~a~~~~~~~~~~~~~~~~~l~~~~ 780 (953)
.+.+++||.+ +.+|+...-...+.||.+ .+. ..+++.....-|.. ...|-.|++++-......+.++ +|.+++
T Consensus 57 ~~~~~~~l~~-~~rIATkyp~l~~~yf~~-~g~-~~~ii~l~GsvE~a--p~~glAD~IvDiv~TG~TLr~N--gL~~i~ 129 (163)
T PF01634_consen 57 PYKSVEDLKA-GLRIATKYPNLTRRYFAE-KGI-NVEIIKLSGSVELA--PPLGLADAIVDIVETGTTLRAN--GLKEIE 129 (163)
T ss_dssp CGCCGGGGSS-TEEEEES-HHHHHHHHHH-CT--EEEEEE-SS-TTHH--HHTTSSSEEEEEESSSHHHHHT--TEEEEE
T ss_pred CCCCHHHhcc-CCEEEECCHHHHHHHHHH-cCC-cEEEEEccCCcccc--CCCCCCCEEEEeccCcHHHHHC--CCEEeE
Confidence 3678888853 778998888888999954 443 34555554444433 3347899999877776665443 566665
Q ss_pred CccccCccEEEecCCCc--chHHHHHHHHhhh
Q 002211 781 QEFTKSGWGFAFPRDSP--LAIDMSTAILTLS 810 (953)
Q Consensus 781 ~~~~~~~~~~~~~k~sp--l~~~~n~~i~~l~ 810 (953)
..+. ..-.+...+.+- -.+.++..+.+|.
T Consensus 130 ~i~~-s~a~LI~n~~~~~~k~~~i~~l~~~l~ 160 (163)
T PF01634_consen 130 TILE-SSARLIANKASLKEKEEKIDELVTRLR 160 (163)
T ss_dssp EEEE-EEEEEEEEHHHHHHCHHHHHHHHHHHH
T ss_pred EEEE-EEEEEEEcCccchhhHHHHHHHHHHHH
Confidence 4443 344555555543 3334555555543
No 435
>PRK09701 D-allose transporter subunit; Provisional
Probab=50.58 E-value=74 Score=34.43 Aligned_cols=84 Identities=11% Similarity=0.079 Sum_probs=57.8
Q ss_pred cCCcEEEEEEe--cCccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchh-hHHH
Q 002211 180 FGWGEVIAIFN--DDDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSR-TGLM 256 (953)
Q Consensus 180 ~~w~~vaii~~--d~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~-~~~~ 256 (953)
+.-.+++++.. ++.|.....+.+.+++++.|..+..... +.. .+...-...++.+...++|.||+..... ....
T Consensus 22 ~~~~~Igvi~~~~~~~f~~~~~~gi~~~a~~~g~~v~~~~~-~~~--~~~~~~~~~i~~l~~~~vDgiIi~~~~~~~~~~ 98 (311)
T PRK09701 22 FAAAEYAVVLKTLSNPFWVDMKKGIEDEAKTLGVSVDIFAS-PSE--GDFQSQLQLFEDLSNKNYKGIAFAPLSSVNLVM 98 (311)
T ss_pred ccCCeEEEEeCCCCCHHHHHHHHHHHHHHHHcCCeEEEecC-CCC--CCHHHHHHHHHHHHHcCCCEEEEeCCChHHHHH
Confidence 44578999985 4778888899999999999988765321 111 1234456677788888999999876543 2334
Q ss_pred HHHHHHHcCC
Q 002211 257 VFDVAQRLGM 266 (953)
Q Consensus 257 ~~~~a~~~g~ 266 (953)
.+.++.+.|+
T Consensus 99 ~l~~~~~~gi 108 (311)
T PRK09701 99 PVARAWKKGI 108 (311)
T ss_pred HHHHHHHCCC
Confidence 4666777664
No 436
>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=50.49 E-value=53 Score=33.75 Aligned_cols=78 Identities=12% Similarity=0.075 Sum_probs=55.2
Q ss_pred EEEEEEec---CccccchHHHHHHHHHh--cCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHH
Q 002211 184 EVIAIFND---DDQGRNGVTALGDKLAE--IRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVF 258 (953)
Q Consensus 184 ~vaii~~d---~~~g~~~~~~l~~~l~~--~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~ 258 (953)
+|++|..+ +.|+....+.+.+++++ .++++.... .. .+..+....+.++...++|+|++.........+.
T Consensus 1 ~Ig~i~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~---~~--~~~~~~~~~~~~~~~~~~d~ii~~~~~~~~~~~~ 75 (269)
T cd01391 1 KIGVLLPLSGSAPFGAQLLAGIELAAEEIGRGLEVILAD---SQ--SDPERALEALRDLIQQGVDGIIGPPSSSSALAVV 75 (269)
T ss_pred CceEEeecCCCcHHHHHHHHHHHHHHHHhCCceEEEEec---CC--CCHHHHHHHHHHHHHcCCCEEEecCCCHHHHHHH
Confidence 36777753 57788888999999999 777765432 22 2245677778888888999999987766555577
Q ss_pred HHHHHcCC
Q 002211 259 DVAQRLGM 266 (953)
Q Consensus 259 ~~a~~~g~ 266 (953)
..+.+.|.
T Consensus 76 ~~~~~~~i 83 (269)
T cd01391 76 ELAAAAGI 83 (269)
T ss_pred HHHHHcCC
Confidence 77777664
No 437
>cd06300 PBP1_ABC_sugar_binding_like_1 Periplasmic sugar-binding component of uncharacterized ABC-type transport systems that are members of the pentose/hexose sugar-binding protein family of the type I periplasmic binding protein superfamily. Periplasmic sugar-binding component of uncharacterized ABC-type transport systems that are members of the pentose/hexose sugar-binding protein family of the type I periplasmic binding protein superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding. Members of this group are predicted to be involved in the transport of sugar-containing molecules across cellular and organellar membranes; however their substrate specificity is not known in detail.
Probab=50.49 E-value=70 Score=33.57 Aligned_cols=80 Identities=9% Similarity=0.022 Sum_probs=52.9
Q ss_pred EEEEEEe--cCccccchHHHHHHHHHhc---CcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchh-hHHHH
Q 002211 184 EVIAIFN--DDDQGRNGVTALGDKLAEI---RCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSR-TGLMV 257 (953)
Q Consensus 184 ~vaii~~--d~~~g~~~~~~l~~~l~~~---g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~-~~~~~ 257 (953)
||+++.. ++.|-....+.+.+++++. |.++.... +... .+.+.....++++...++|.||+..... .....
T Consensus 1 ~Ig~i~~~~~~~~~~~~~~~i~~~~~~~~~~g~~~~l~i-~~~~--~~~~~~~~~~~~~~~~~vdgiIi~~~~~~~~~~~ 77 (272)
T cd06300 1 KIGLSNSYAGNTWRAQMLDEFKAQAKELKKAGLISEFIV-TSAD--GDVAQQIADIRNLIAQGVDAIIINPASPTALNPV 77 (272)
T ss_pred CeEEeccccCChHHHHHHHHHHHHHHhhhccCCeeEEEE-ecCC--CCHHHHHHHHHHHHHcCCCEEEEeCCChhhhHHH
Confidence 4666663 4567778888999999988 87432221 1222 2345567888888888999999976543 33446
Q ss_pred HHHHHHcCC
Q 002211 258 FDVAQRLGM 266 (953)
Q Consensus 258 ~~~a~~~g~ 266 (953)
+..+.+.|.
T Consensus 78 l~~~~~~~i 86 (272)
T cd06300 78 IEEACEAGI 86 (272)
T ss_pred HHHHHHCCC
Confidence 777777664
No 438
>PRK15424 propionate catabolism operon regulatory protein PrpR; Provisional
Probab=50.46 E-value=2.7e+02 Score=32.87 Aligned_cols=129 Identities=19% Similarity=0.235 Sum_probs=78.0
Q ss_pred CChHHHHHHHHH-HHhcCcEEEEccCChhhHHHHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHH
Q 002211 98 FNGFLSIMGALQ-FMETDTLAIVGPQSAVMAHVLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEM 176 (953)
Q Consensus 98 ~~~~~a~~~a~~-li~~~v~aiiGp~~S~~a~av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~ 176 (953)
..-..++..+.+ +..+++++||.-.+++ .-+-+...||+|....+ .-| ..+++. .
T Consensus 47 ~~~~~~v~~~~~~~~~~~~dviIsrG~ta-----~~i~~~~~iPVv~i~~s----------------~~D--il~al~-~ 102 (538)
T PRK15424 47 LGFEKAVTYIRKRLATERCDAIIAAGSNG-----AYLKSRLSVPVILIKPS----------------GFD--VMQALA-R 102 (538)
T ss_pred hhHHHHHHHHHHHHhhCCCcEEEECchHH-----HHHHhhCCCCEEEecCC----------------HhH--HHHHHH-H
Confidence 344677777855 5566899999754332 22334568999964221 112 233332 2
Q ss_pred HHHcCCcEEEEEEecCccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHH
Q 002211 177 VSYFGWGEVIAIFNDDDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLM 256 (953)
Q Consensus 177 l~~~~w~~vaii~~d~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~ 256 (953)
.+.++ .++++|.-.+.. ...+.+.+.+ |..+.... +. +.+|....+.++++.+.++||-.+.
T Consensus 103 a~~~~-~~iavv~~~~~~--~~~~~~~~~l---~~~i~~~~-~~-----~~~e~~~~v~~lk~~G~~~vvG~~~------ 164 (538)
T PRK15424 103 ARKLT-SSIGVVTYQETI--PALVAFQKTF---NLRIEQRS-YV-----TEEDARGQINELKANGIEAVVGAGL------ 164 (538)
T ss_pred HHhcC-CcEEEEecCccc--HHHHHHHHHh---CCceEEEE-ec-----CHHHHHHHHHHHHHCCCCEEEcCch------
Confidence 34555 578887644331 2345555554 55554332 21 3679999999999999999985543
Q ss_pred HHHHHHHcCCCC
Q 002211 257 VFDVAQRLGMMD 268 (953)
Q Consensus 257 ~~~~a~~~g~~~ 268 (953)
....|.++|+.+
T Consensus 165 ~~~~A~~~g~~g 176 (538)
T PRK15424 165 ITDLAEEAGMTG 176 (538)
T ss_pred HHHHHHHhCCce
Confidence 356778888764
No 439
>COG1464 NlpA ABC-type metal ion transport system, periplasmic component/surface antigen [Inorganic ion transport and metabolism]
Probab=50.32 E-value=69 Score=33.33 Aligned_cols=47 Identities=17% Similarity=0.205 Sum_probs=33.1
Q ss_pred ceEEEeEEEecCCCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHH
Q 002211 48 EVLNVGAIFSFGTVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIM 105 (953)
Q Consensus 48 ~~i~IG~l~~~~~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~ 105 (953)
.+|+||+.- .+.+...+..++-+.++ .|.+|+++.+.+...|..|+.
T Consensus 29 ~~I~vg~~~---~p~a~ile~~~k~~~~k--------~Gi~l~i~~FtDY~~PN~AL~ 75 (268)
T COG1464 29 KTIKVGATP---GPHAEILEVVVKPALKK--------KGLDLKIVEFTDYVQPNEALA 75 (268)
T ss_pred CcEEEeecC---CchHHHHHHHHHHHHHh--------cCceEEEEEecCCcchhHHHh
Confidence 589999852 22333344466666655 378999999999998888875
No 440
>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=50.08 E-value=53 Score=34.84 Aligned_cols=81 Identities=9% Similarity=0.083 Sum_probs=52.2
Q ss_pred EEEEEEec---CccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHH
Q 002211 184 EVIAIFND---DDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDV 260 (953)
Q Consensus 184 ~vaii~~d---~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~ 260 (953)
++++|..+ ++|.....+.+.+++++.|..+......+.. ..+...-...++++.+.++|.||+..........++.
T Consensus 1 ~Igvi~~~~~~~~~~~~~~~~i~~~~~~~g~~~~~~~~~~~~-~~~~~~~~~~i~~l~~~~vDgiIv~~~~~~~~~~~~~ 79 (280)
T cd06303 1 KIAVIYPGQQISDYWVRNIASFTARLEELNIPYELTQFSSRP-GIDHRLQSQQLNEALQSKPDYLIFTLDSLRHRKLIER 79 (280)
T ss_pred CeeEEecCccHHHHHHHHHHHHHHHHHHcCCcEEEEEeccCc-ccCHHHHHHHHHHHHHcCCCEEEEcCCchhhHHHHHH
Confidence 36777764 4677788889999999999876653211111 0113444566778888999999987543333455666
Q ss_pred HHHcC
Q 002211 261 AQRLG 265 (953)
Q Consensus 261 a~~~g 265 (953)
+.+.+
T Consensus 80 l~~~~ 84 (280)
T cd06303 80 VLASG 84 (280)
T ss_pred HHhCC
Confidence 66655
No 441
>PF00218 IGPS: Indole-3-glycerol phosphate synthase; InterPro: IPR013798 Indole-3-glycerol phosphate synthase (4.1.1.48 from EC) (IGPS) catalyses the fourth step in the biosynthesis of tryptophan, the ring closure of 1-(2-carboxy-phenylamino)-1-deoxyribulose into indol-3-glycerol-phosphate. In some bacteria, IGPS is a single chain enzyme. In others, such as Escherichia coli, it is the N-terminal domain of a bifunctional enzyme that also catalyses N-(5'-phosphoribosyl)anthranilate isomerase (5.3.1.24 from EC) (PRAI) activity (see IPR001240 from INTERPRO), the third step of tryptophan biosynthesis. In fungi, IGPS is the central domain of a trifunctional enzyme that contains a PRAI C-terminal domain and a glutamine amidotransferase (2.4.2 from EC) (GATase) N-terminal domain (see IPR000991 from INTERPRO). A structure of the IGPS domain of the bifunctional enzyme from the mesophilic bacterium E. coli (eIGPS) has been compared with the monomeric indole-3-glycerol phosphate synthase from the hyperthermophilic archaeon Sulfolobus solfataricus (sIGPS). Both are single-domain (beta/alpha)8 barrel proteins, with one (eIGPS) or two (sIGPS) additional helices inserted before the first beta strand []. ; GO: 0004425 indole-3-glycerol-phosphate synthase activity; PDB: 1VC4_A 1PII_A 1JCM_P 1I4N_B 1J5T_A 3TSM_B 4FB7_A 3QJA_A 1JUL_A 2C3Z_A ....
Probab=49.47 E-value=1e+02 Score=32.19 Aligned_cols=88 Identities=11% Similarity=0.094 Sum_probs=60.1
Q ss_pred HHHHHHHHHHcCCcEEEEEEecCccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEc
Q 002211 170 MSAIAEMVSYFGWGEVIAIFNDDDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHG 249 (953)
Q Consensus 170 ~~ai~~~l~~~~w~~vaii~~d~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~ 249 (953)
...++......|..-+.+++ |..|..+..+.+...-+..++.+..+..+-. .-++.+.+..++|+|++..
T Consensus 70 ~~~~a~~y~~~GA~aiSVlT-e~~~F~Gs~~dL~~v~~~~~~PvL~KDFIid---------~~QI~eA~~~GADaVLLI~ 139 (254)
T PF00218_consen 70 PAEIAKAYEEAGAAAISVLT-EPKFFGGSLEDLRAVRKAVDLPVLRKDFIID---------PYQIYEARAAGADAVLLIA 139 (254)
T ss_dssp HHHHHHHHHHTT-SEEEEE---SCCCHHHHHHHHHHHHHSSS-EEEES---S---------HHHHHHHHHTT-SEEEEEG
T ss_pred HHHHHHHHHhcCCCEEEEEC-CCCCCCCCHHHHHHHHHHhCCCcccccCCCC---------HHHHHHHHHcCCCEeehhH
Confidence 45677777888999999887 5556778888888877777887776543321 2367778889999999975
Q ss_pred c---hhhHHHHHHHHHHcCCC
Q 002211 250 Y---SRTGLMVFDVAQRLGMM 267 (953)
Q Consensus 250 ~---~~~~~~~~~~a~~~g~~ 267 (953)
. ......++..|.++||.
T Consensus 140 ~~L~~~~l~~l~~~a~~lGle 160 (254)
T PF00218_consen 140 AILSDDQLEELLELAHSLGLE 160 (254)
T ss_dssp GGSGHHHHHHHHHHHHHTT-E
T ss_pred HhCCHHHHHHHHHHHHHcCCC
Confidence 5 34557999999999985
No 442
>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=49.39 E-value=23 Score=32.00 Aligned_cols=86 Identities=15% Similarity=0.067 Sum_probs=46.8
Q ss_pred cEEEEEEecCccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHh--cCCceEEEEEcchhhHHHHHHH
Q 002211 183 GEVIAIFNDDDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVR--MMEARVIVVHGYSRTGLMVFDV 260 (953)
Q Consensus 183 ~~vaii~~d~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~--~~~~~vii~~~~~~~~~~~~~~ 260 (953)
|++|+|...+.-+.- ...+.+.+.+.|.+|... .+. ...-+=......+. -..+|+++++..+.....++++
T Consensus 1 ksiAVvGaS~~~~~~-g~~v~~~l~~~G~~v~~V---np~--~~~i~G~~~y~sl~e~p~~iDlavv~~~~~~~~~~v~~ 74 (116)
T PF13380_consen 1 KSIAVVGASDNPGKF-GYRVLRNLKAAGYEVYPV---NPK--GGEILGIKCYPSLAEIPEPIDLAVVCVPPDKVPEIVDE 74 (116)
T ss_dssp -EEEEET--SSTTSH-HHHHHHHHHHTT-EEEEE---STT--CSEETTEE-BSSGGGCSST-SEEEE-S-HHHHHHHHHH
T ss_pred CEEEEEcccCCCCCh-HHHHHHHHHhCCCEEEEE---CCC--ceEECcEEeeccccCCCCCCCEEEEEcCHHHHHHHHHH
Confidence 578888754433332 333444555577666532 222 10100011223333 3689999999999999999999
Q ss_pred HHHcCCCCCceEEEEeC
Q 002211 261 AQRLGMMDSGYVWIATT 277 (953)
Q Consensus 261 a~~~g~~~~~~~wi~~~ 277 (953)
+.++| .+.+|+.++
T Consensus 75 ~~~~g---~~~v~~~~g 88 (116)
T PF13380_consen 75 AAALG---VKAVWLQPG 88 (116)
T ss_dssp HHHHT----SEEEE-TT
T ss_pred HHHcC---CCEEEEEcc
Confidence 99988 467899887
No 443
>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=49.37 E-value=48 Score=33.03 Aligned_cols=70 Identities=19% Similarity=0.201 Sum_probs=51.8
Q ss_pred HHHHhcCCCCCCCcEEEEEEe-cCCCChHHHHHHHHHHHhc----CcEEEEccCChhhHHHHHHhhhhCCCcEEEe
Q 002211 74 QDDINSDPRVLGGRKLSITMH-DAKFNGFLSIMGALQFMET----DTLAIVGPQSAVMAHVLSHLANELQVPLLSF 144 (953)
Q Consensus 74 ve~iN~~g~il~g~~l~l~~~-D~~~~~~~a~~~a~~li~~----~v~aiiGp~~S~~a~av~~v~~~~~vP~Is~ 144 (953)
.+.+|+.+.++||--+....+ |.+.||......+..+.+. ++.+|+|+...+...+. .++...++|++-.
T Consensus 5 ~~~~~~~~~~~~~~~i~~~~~~~~~~~p~~l~~v~~~l~~~~~~~~~d~Vv~~ea~Gi~la~-~lA~~Lg~p~v~v 79 (191)
T TIGR01744 5 KQKIKEEGVVLPGGILKVDSFLNHQIDPKLMQEVGEEFARRFADDGITKIVTIEASGIAPAI-MTGLKLGVPVVFA 79 (191)
T ss_pred HHHHhcCCEEcCCCEEEEehhhccccCHHHHHHHHHHHHHHhccCCCCEEEEEccccHHHHH-HHHHHHCCCEEEE
Confidence 578999999999877777544 6666887666656555543 78999998887765543 4677789998864
No 444
>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=49.36 E-value=83 Score=34.75 Aligned_cols=85 Identities=9% Similarity=-0.017 Sum_probs=55.3
Q ss_pred HHHHHHHHHcCC--cEEEEEEecCccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcC---CceEE
Q 002211 171 SAIAEMVSYFGW--GEVIAIFNDDDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMM---EARVI 245 (953)
Q Consensus 171 ~ai~~~l~~~~w--~~vaii~~d~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~---~~~vi 245 (953)
..+.++++.+|. +++.+++ |...-. ..+.+.|++.|+.+.....+.++ .+.+++....+..++. ++|+|
T Consensus 12 ~~l~~~~~~~g~~~~~~lvvt-d~~~~~---~~v~~~L~~~g~~~~~f~~v~~n--Pt~~~v~~~~~~~~~~~~~~~D~I 85 (347)
T cd08184 12 DQLNDLLAPKRKNKDPAVFFV-DDVFQG---KDLISRLPVESEDMIIWVDATEE--PKTDQIDALTAQVKSFDGKLPCAI 85 (347)
T ss_pred HHHHHHHHHcCCCCCeEEEEE-Ccchhh---hHHHHHHHhcCCcEEEEcCCCCC--cCHHHHHHHHHHHHhhCCCCCCEE
Confidence 456677777763 5566666 322211 56777888888875544445555 5677788888888877 89999
Q ss_pred EEEcch--hhHHHHHHHH
Q 002211 246 VVHGYS--RTGLMVFDVA 261 (953)
Q Consensus 246 i~~~~~--~~~~~~~~~a 261 (953)
|-.+.+ -|+.+.+...
T Consensus 86 IaiGGGS~iD~AKaia~~ 103 (347)
T cd08184 86 VGIGGGSTLDVAKAVSNM 103 (347)
T ss_pred EEeCCcHHHHHHHHHHHH
Confidence 987654 4555554443
No 445
>TIGR00249 sixA phosphohistidine phosphatase SixA.
Probab=49.25 E-value=95 Score=29.56 Aligned_cols=98 Identities=10% Similarity=-0.070 Sum_probs=60.8
Q ss_pred cCChHHHHHHHHHHHHHcCCcEEEEEEecCccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCc
Q 002211 163 APNDLYLMSAIAEMVSYFGWGEVIAIFNDDDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEA 242 (953)
Q Consensus 163 ~p~d~~~~~ai~~~l~~~~w~~vaii~~d~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~ 242 (953)
++.-..|++.+++.++..+..--.++.+...-.+..++.+.+.+.. ...+.....+.++ .+..++...+.++...+.
T Consensus 24 t~~G~~qa~~~~~~l~~~~~~~d~i~sSp~~Ra~qTa~~l~~~~~~-~~~~~~~~~l~p~--~~~~~~~~~l~~~~~~~~ 100 (152)
T TIGR00249 24 TTNGCDESRLVAQWLKGQGVEIERILVSPFVRAEQTAEIVGDCLNL-PSSAEVLEGLTPC--GDIGLVSDYLEALTNEGV 100 (152)
T ss_pred CHHHHHHHHHHHHHHHhCCCCCCEEEECCcHHHHHHHHHHHHHcCC-CcceEEccCcCCC--CCHHHHHHHHHHHHhcCC
Confidence 4445678899999998866544445555554444555555444421 1233333334333 345667777777765556
Q ss_pred eEEEEEcchhhHHHHHHHHHH
Q 002211 243 RVIVVHGYSRTGLMVFDVAQR 263 (953)
Q Consensus 243 ~vii~~~~~~~~~~~~~~a~~ 263 (953)
+.++++++.+....++.++-.
T Consensus 101 ~~vliVgH~P~i~~l~~~l~~ 121 (152)
T TIGR00249 101 ASVLLVSHLPLVGYLVAELCP 121 (152)
T ss_pred CEEEEEeCCCCHHHHHHHHhC
Confidence 788888998888888888753
No 446
>COG0563 Adk Adenylate kinase and related kinases [Nucleotide transport and metabolism]
Probab=48.42 E-value=46 Score=32.73 Aligned_cols=28 Identities=32% Similarity=0.536 Sum_probs=26.0
Q ss_pred EEEEccCChhhHHHHHHhhhhCCCcEEE
Q 002211 116 LAIVGPQSAVMAHVLSHLANELQVPLLS 143 (953)
Q Consensus 116 ~aiiGp~~S~~a~av~~v~~~~~vP~Is 143 (953)
+.|+||..|+=+.-+..+++.+++|+|+
T Consensus 3 iiilG~pGaGK~T~A~~La~~~~i~hls 30 (178)
T COG0563 3 ILILGPPGAGKSTLAKKLAKKLGLPHLD 30 (178)
T ss_pred EEEECCCCCCHHHHHHHHHHHhCCcEEc
Confidence 6799999999999999999999999997
No 447
>PRK09189 uroporphyrinogen-III synthase; Validated
Probab=47.84 E-value=1.8e+02 Score=30.13 Aligned_cols=87 Identities=10% Similarity=-0.003 Sum_probs=53.1
Q ss_pred HHHHHHHHHHHc--CCcEEEEEEecCccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEE
Q 002211 169 LMSAIAEMVSYF--GWGEVIAIFNDDDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIV 246 (953)
Q Consensus 169 ~~~ai~~~l~~~--~w~~vaii~~d~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii 246 (953)
.++.+++++... .-++|.++. |....+.+.+.|++.|..|.....|... ....+-......+++.+.|+|+
T Consensus 103 ~~e~L~~~~~~~~~~~~~vL~~r-----g~~~r~~l~~~L~~~G~~v~~~~vY~~~--~~~~~~~~~~~~l~~~~~d~i~ 175 (240)
T PRK09189 103 DGVRLAETVAAALAPTARLLYLA-----GRPRAPVFEDRLAAAGIPFRVAECYDML--PVMYSPATLSAILGGAPFDAVL 175 (240)
T ss_pred CHHHHHHHHHHhcCCCCcEEEec-----cCcccchhHHHHHhCCCeeEEEEEEEee--cCCCChHHHHHHHhcCCCCEEE
Confidence 467777776542 446666665 3334578889999999887665555322 1111222344555666788777
Q ss_pred EEcchhhHHHHHHHHHH
Q 002211 247 VHGYSRTGLMVFDVAQR 263 (953)
Q Consensus 247 ~~~~~~~~~~~~~~a~~ 263 (953)
+.. +..+..|++....
T Consensus 176 f~S-~~~~~~f~~~~~~ 191 (240)
T PRK09189 176 LYS-RVAARRFFALMRL 191 (240)
T ss_pred EeC-HHHHHHHHHHHhh
Confidence 665 4567777777654
No 448
>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=47.15 E-value=87 Score=28.99 Aligned_cols=48 Identities=23% Similarity=0.472 Sum_probs=36.7
Q ss_pred hHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcc
Q 002211 198 GVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGY 250 (953)
Q Consensus 198 ~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~ 250 (953)
....+.+.+++.|.++.+....+.+ .+.+...+.+..+. +|+||..+.
T Consensus 20 n~~~l~~~l~~~G~~v~~~~~v~Dd----~~~i~~~i~~~~~~-~DlvittGG 67 (133)
T cd00758 20 NGPALEALLEDLGCEVIYAGVVPDD----ADSIRAALIEASRE-ADLVLTTGG 67 (133)
T ss_pred hHHHHHHHHHHCCCEEEEeeecCCC----HHHHHHHHHHHHhc-CCEEEECCC
Confidence 4567888889999998876666655 77788888887654 899998744
No 449
>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=47.05 E-value=1.5e+02 Score=32.61 Aligned_cols=101 Identities=12% Similarity=0.023 Sum_probs=61.9
Q ss_pred HHHHHHHHHcCCcEEEEEEecCccccchHHHHHHHHHh-cCcEEEEEEecCCCCCCChHHHHHHHHHHhcCC---ceEEE
Q 002211 171 SAIAEMVSYFGWGEVIAIFNDDDQGRNGVTALGDKLAE-IRCKISYKSALPPDQSVTETDVRNELVKVRMME---ARVIV 246 (953)
Q Consensus 171 ~ai~~~l~~~~w~~vaii~~d~~~g~~~~~~l~~~l~~-~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~---~~vii 246 (953)
..+.++++.++-+++.++.+...+. ...+.+.+.+++ .++.+......... .+.+.+...+..+++.+ .|+||
T Consensus 12 ~~l~~~~~~~~~~k~livtd~~v~~-~~~~~v~~~L~~~~~~~~~~~~~~e~~--k~~~~v~~~~~~~~~~~~~r~d~II 88 (344)
T cd08169 12 ESVESYTTRDLFDQYFFISDSGVAD-LIAHYIAEYLSKILPVHILVIEGGEEY--KTFETVTRILERAIALGANRRTAIV 88 (344)
T ss_pred HHHHHHHHhcCCCeEEEEECccHHH-HHHHHHHHHHHhhcCceEEEeCCCCCC--CCHHHHHHHHHHHHHcCCCCCcEEE
Confidence 3455677777888988887544433 566778888876 56654322222222 34667777777777544 89999
Q ss_pred EEcch--hhHHHHHHHHHHcCCCCCceEEEEeC
Q 002211 247 VHGYS--RTGLMVFDVAQRLGMMDSGYVWIATT 277 (953)
Q Consensus 247 ~~~~~--~~~~~~~~~a~~~g~~~~~~~wi~~~ 277 (953)
..+.+ -|...++......| ..++-|.|.
T Consensus 89 aiGGGsv~D~ak~vA~~~~rg---ip~i~VPTT 118 (344)
T cd08169 89 AVGGGATGDVAGFVASTLFRG---IAFIRVPTT 118 (344)
T ss_pred EECCcHHHHHHHHHHHHhccC---CcEEEecCC
Confidence 87654 55666665544434 345555554
No 450
>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=46.86 E-value=96 Score=32.41 Aligned_cols=76 Identities=4% Similarity=-0.058 Sum_probs=52.2
Q ss_pred EEEEEe--cCccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHH
Q 002211 185 VIAIFN--DDDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQ 262 (953)
Q Consensus 185 vaii~~--d~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~ 262 (953)
+++|.. +++|.......+.+++++.|..+..... . . +.+.-...++.+.+.++|.||+....... ..++++.
T Consensus 2 igvi~p~~~~~~~~~~~~g~~~~a~~~g~~~~~~~~-~-~---~~~~~~~~i~~~~~~~vdgii~~~~~~~~-~~~~~~~ 75 (268)
T cd06270 2 IGLVVSDLDGPFFGPLLSGVESVARKAGKHLIITAG-H-H---SAEKEREAIEFLLERRCDALILHSKALSD-DELIELA 75 (268)
T ss_pred EEEEEccccCcchHHHHHHHHHHHHHCCCEEEEEeC-C-C---chHHHHHHHHHHHHcCCCEEEEecCCCCH-HHHHHHh
Confidence 455553 4778888899999999999998775332 1 1 23445577888888899999997653222 2377777
Q ss_pred HcCC
Q 002211 263 RLGM 266 (953)
Q Consensus 263 ~~g~ 266 (953)
+.|.
T Consensus 76 ~~~i 79 (268)
T cd06270 76 AQVP 79 (268)
T ss_pred hCCC
Confidence 7664
No 451
>TIGR02329 propionate_PrpR propionate catabolism operon regulatory protein PrpR. At least five distinct pathways exists for the catabolism of propionate by way of propionyl-CoA. Members of this family represent the transcriptional regulatory protein PrpR, whose gene is found in most cases divergently transcribed from an operon for the methylcitric acid cycle of propionate catabolism. 2-methylcitric acid, a catabolite by this pathway, is a coactivator of PrpR.
Probab=46.60 E-value=3.4e+02 Score=31.96 Aligned_cols=129 Identities=17% Similarity=0.207 Sum_probs=78.3
Q ss_pred CChHHHHHHHHH-HHhcCcEEEEccCChhhHHHHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHH
Q 002211 98 FNGFLSIMGALQ-FMETDTLAIVGPQSAVMAHVLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEM 176 (953)
Q Consensus 98 ~~~~~a~~~a~~-li~~~v~aiiGp~~S~~a~av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~ 176 (953)
++-..++..+.+ +..+++++||.-..+ +.. +-+...+|+|...-+. -| ..+++ ..
T Consensus 37 ~~~~~~~~~a~~~~~~~~~dviIsrG~t--a~~---i~~~~~iPVv~i~~s~----------------~D--il~al-~~ 92 (526)
T TIGR02329 37 LGFEDAVREIRQRLGAERCDVVVAGGSN--GAY---LKSRLSLPVIVIKPTG----------------FD--VMQAL-AR 92 (526)
T ss_pred ccHHHHHHHHHHHHHhCCCcEEEECchH--HHH---HHHhCCCCEEEecCCh----------------hh--HHHHH-HH
Confidence 455778888855 556699999974432 222 3345579998642211 12 23333 23
Q ss_pred HHHcCCcEEEEEEecCccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHH
Q 002211 177 VSYFGWGEVIAIFNDDDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLM 256 (953)
Q Consensus 177 l~~~~w~~vaii~~d~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~ 256 (953)
.+.++ .++++|.-.+. ......+.+.+ ++.+.... +. +.+|....+.++++.+.++||-.+.
T Consensus 93 a~~~~-~~ia~vg~~~~--~~~~~~~~~ll---~~~i~~~~-~~-----~~~e~~~~~~~l~~~G~~~viG~~~------ 154 (526)
T TIGR02329 93 ARRIA-SSIGVVTHQDT--PPALRRFQAAF---NLDIVQRS-YV-----TEEDARSCVNDLRARGIGAVVGAGL------ 154 (526)
T ss_pred HHhcC-CcEEEEecCcc--cHHHHHHHHHh---CCceEEEE-ec-----CHHHHHHHHHHHHHCCCCEEECChH------
Confidence 35555 57888764433 13345555554 45544322 21 3679999999999999999985442
Q ss_pred HHHHHHHcCCCC
Q 002211 257 VFDVAQRLGMMD 268 (953)
Q Consensus 257 ~~~~a~~~g~~~ 268 (953)
....|++.||.+
T Consensus 155 ~~~~A~~~gl~~ 166 (526)
T TIGR02329 155 ITDLAEQAGLHG 166 (526)
T ss_pred HHHHHHHcCCce
Confidence 356788999854
No 452
>COG1880 CdhB CO dehydrogenase/acetyl-CoA synthase epsilon subunit [Energy production and conversion]
Probab=46.57 E-value=2.6e+02 Score=26.49 Aligned_cols=124 Identities=13% Similarity=0.133 Sum_probs=78.3
Q ss_pred HHHHHHhc--CcEEEEccCCh--hhHHHHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcC
Q 002211 106 GALQFMET--DTLAIVGPQSA--VMAHVLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFG 181 (953)
Q Consensus 106 ~a~~li~~--~v~aiiGp~~S--~~a~av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~ 181 (953)
.+..++.+ +...|+||..- ..-.-+..+.++.++|.+..+++...+.+.. .-+......++..+++.-.
T Consensus 27 v~ammIkkAkrPLlivGp~~~dee~~E~~vKi~ekfnipivaTa~~~~~~~~~~-------i~~~~~~lh~it~~l~Dp~ 99 (170)
T COG1880 27 VVAMMIKKAKRPLLIVGPLALDEELLELAVKIIEKFNIPIVATASSMGNLIGRG-------IGSEYINLHAITQYLTDPN 99 (170)
T ss_pred HHHHHHHhcCCceEEecccccCHHHHHHHHHHHHhcCCceEecchhhcchhhcc-------cccchhHHHHHHHHhcCCC
Confidence 34455655 89999999875 4555678899999999997666665555533 1244555677888888744
Q ss_pred C---------cEEEEEEecCccccchHHHHHHHHHhcCcEEEEEEecCCCC-----CCChHHHHHHHHHHh
Q 002211 182 W---------GEVIAIFNDDDQGRNGVTALGDKLAEIRCKISYKSALPPDQ-----SVTETDVRNELVKVR 238 (953)
Q Consensus 182 w---------~~vaii~~d~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~-----~~~~~d~~~~l~~i~ 238 (953)
| .-|.++..-..|.......++... .=.+|+....|.++. +...+++-..|+++-
T Consensus 100 w~G~dg~g~yDlviflG~~~yy~sq~Ls~lKhFs--~i~tiaId~~Y~pnAd~SFpNl~kde~~~~L~ell 168 (170)
T COG1880 100 WPGFDGNGNYDLVIFLGSIYYYLSQVLSGLKHFS--NIKTIAIDRYYQPNADYSFPNLSKDEYLAYLDELL 168 (170)
T ss_pred CCCcCCCCCcceEEEEeccHHHHHHHHHHhhhhh--cceEEEeccccCcCccccCCCcCHHHHHHHHHHHh
Confidence 4 456777766767766666665543 112344444444431 134566777777664
No 453
>COG0134 TrpC Indole-3-glycerol phosphate synthase [Amino acid transport and metabolism]
Probab=46.56 E-value=48 Score=34.37 Aligned_cols=86 Identities=16% Similarity=0.097 Sum_probs=67.1
Q ss_pred HHHHHHHHcCCcEEEEEEecCccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcc-
Q 002211 172 AIAEMVSYFGWGEVIAIFNDDDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGY- 250 (953)
Q Consensus 172 ai~~~l~~~~w~~vaii~~d~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~- 250 (953)
.+++..+++|..-+.+++ |..|.++..+.++..-+...+.|.-+..+.. .-++...+..++|+|.+...
T Consensus 70 ~ia~~Ye~~GAa~iSVLT-d~~~F~Gs~e~L~~v~~~v~~PvL~KDFiiD---------~yQI~~Ar~~GADavLLI~~~ 139 (254)
T COG0134 70 EIAKAYEEGGAAAISVLT-DPKYFQGSFEDLRAVRAAVDLPVLRKDFIID---------PYQIYEARAAGADAVLLIVAA 139 (254)
T ss_pred HHHHHHHHhCCeEEEEec-CccccCCCHHHHHHHHHhcCCCeeeccCCCC---------HHHHHHHHHcCcccHHHHHHh
Confidence 377778889999999887 6678889999998887777887765554432 24677778899999988543
Q ss_pred --hhhHHHHHHHHHHcCCC
Q 002211 251 --SRTGLMVFDVAQRLGMM 267 (953)
Q Consensus 251 --~~~~~~~~~~a~~~g~~ 267 (953)
......+...|.++||.
T Consensus 140 L~~~~l~el~~~A~~LGm~ 158 (254)
T COG0134 140 LDDEQLEELVDRAHELGME 158 (254)
T ss_pred cCHHHHHHHHHHHHHcCCe
Confidence 45689999999999995
No 454
>PHA03239 envelope glycoprotein M; Provisional
Probab=46.20 E-value=44 Score=37.31 Aligned_cols=28 Identities=11% Similarity=-0.028 Sum_probs=16.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q 002211 848 LFLICGIACFLALLAYFCLMLRQFKKYS 875 (953)
Q Consensus 848 ~f~il~~g~~lallvf~~e~~~~~~~~~ 875 (953)
+=..+++..+++++..++++++.+.-++
T Consensus 334 v~~~Laviail~l~~~ivRlvRa~~yHr 361 (429)
T PHA03239 334 AAGILAAFAVISIALAILRATRAYKFHK 361 (429)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3345666666677777777776544443
No 455
>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=46.10 E-value=78 Score=33.98 Aligned_cols=77 Identities=10% Similarity=0.095 Sum_probs=50.5
Q ss_pred EEEEe--cCccccchHHHHHHHHHhcCc-EEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcch-hhHHHHHHHH
Q 002211 186 IAIFN--DDDQGRNGVTALGDKLAEIRC-KISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYS-RTGLMVFDVA 261 (953)
Q Consensus 186 aii~~--d~~~g~~~~~~l~~~l~~~g~-~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~-~~~~~~~~~a 261 (953)
++|.. ++.|.....+.+.+++++.|. .+.... +.. .+.......++.+.+.++|.||+.... ......++++
T Consensus 2 gvi~~~~~~~f~~~~~~gi~~~a~~~g~~~~i~~~--~~~--~d~~~q~~~i~~l~~~~vdgiIi~~~~~~~~~~~l~~~ 77 (302)
T TIGR02637 2 GLVVKSLGNPFFEAANKGAEEAAKELGSVYIIYTG--PTG--TTAEGQIEVVNSLIAQKVDAIAISANDPDALVPALKKA 77 (302)
T ss_pred EEEeccCCCHHHHHHHHHHHHHHHHhCCeeEEEEC--CCC--CCHHHHHHHHHHHHHcCCCEEEEeCCChHHHHHHHHHH
Confidence 44443 366777888899999999994 443321 111 124445567888888899999987543 3345667888
Q ss_pred HHcCC
Q 002211 262 QRLGM 266 (953)
Q Consensus 262 ~~~g~ 266 (953)
++.|.
T Consensus 78 ~~~gi 82 (302)
T TIGR02637 78 MKRGI 82 (302)
T ss_pred HHCCC
Confidence 88774
No 456
>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=45.73 E-value=96 Score=32.47 Aligned_cols=77 Identities=8% Similarity=0.001 Sum_probs=53.2
Q ss_pred EEEEEe--cCccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHH
Q 002211 185 VIAIFN--DDDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQ 262 (953)
Q Consensus 185 vaii~~--d~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~ 262 (953)
|+++.. ++.|-..+.+.+.+++++.|..+..... . .+.+.-...++.+.+.+.|.||+.....+...++++++
T Consensus 2 Igvv~~~~~~~~~~~~~~~i~~~a~~~g~~~~~~~~---~--~~~~~~~~~i~~l~~~~vdgii~~~~~~~~~~~~~~~~ 76 (269)
T cd06281 2 IGCLVSDITNPLLAQLFSGAEDRLRAAGYSLLIANS---L--NDPERELEILRSFEQRRMDGIIIAPGDERDPELVDALA 76 (269)
T ss_pred EEEEecCCccccHHHHHHHHHHHHHHcCCEEEEEeC---C--CChHHHHHHHHHHHHcCCCEEEEecCCCCcHHHHHHHH
Confidence 566664 4677788889999999999998765432 1 12444566778888889999998754333445667777
Q ss_pred HcCC
Q 002211 263 RLGM 266 (953)
Q Consensus 263 ~~g~ 266 (953)
+.|.
T Consensus 77 ~~~i 80 (269)
T cd06281 77 SLDL 80 (269)
T ss_pred hCCC
Confidence 7553
No 457
>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=45.55 E-value=1.1e+02 Score=32.42 Aligned_cols=79 Identities=14% Similarity=0.142 Sum_probs=54.9
Q ss_pred cEEEEEEec--CccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhh-HHHHHH
Q 002211 183 GEVIAIFND--DDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRT-GLMVFD 259 (953)
Q Consensus 183 ~~vaii~~d--~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~-~~~~~~ 259 (953)
|+|+++..+ +.|.......+.+++++.|..+..... . .+.+.-...+..+...++|.||+.....+ ....++
T Consensus 1 ~~ig~i~~~~~~~~~~~~~~gi~~~a~~~gy~~~~~~~---~--~~~~~~~~~i~~l~~~~vdgiil~~~~~~~~~~~~~ 75 (280)
T cd06315 1 KNIIFVASDLKNGGILGVGEGVREAAKAIGWNLRILDG---R--GSEAGQAAALNQAIALKPDGIVLGGVDAAELQAELE 75 (280)
T ss_pred CeEEEEecccCCcHHHHHHHHHHHHHHHcCcEEEEECC---C--CCHHHHHHHHHHHHHcCCCEEEEcCCCHHHHHHHHH
Confidence 467888754 667778889999999999988765321 1 12455567888888899999999754322 234556
Q ss_pred HHHHcCC
Q 002211 260 VAQRLGM 266 (953)
Q Consensus 260 ~a~~~g~ 266 (953)
.+.+.|.
T Consensus 76 ~~~~~~i 82 (280)
T cd06315 76 LAQKAGI 82 (280)
T ss_pred HHHHCCC
Confidence 6666554
No 458
>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=45.50 E-value=63 Score=34.43 Aligned_cols=73 Identities=5% Similarity=-0.030 Sum_probs=53.1
Q ss_pred cEEEEEEec--CccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHH
Q 002211 183 GEVIAIFND--DDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDV 260 (953)
Q Consensus 183 ~~vaii~~d--~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~ 260 (953)
+.+++|.++ ++|....+..+.+++++.|..+.....-. +.+-...++.+.+.+.|.+|+.+...+-..+...
T Consensus 2 ~~IGvivp~~~npff~~ii~gIe~~a~~~Gy~l~l~~t~~------~~~~e~~i~~l~~~~vDGiI~~s~~~~~~~l~~~ 75 (279)
T PF00532_consen 2 KTIGVIVPDISNPFFAEIIRGIEQEAREHGYQLLLCNTGD------DEEKEEYIELLLQRRVDGIILASSENDDEELRRL 75 (279)
T ss_dssp CEEEEEESSSTSHHHHHHHHHHHHHHHHTTCEEEEEEETT------THHHHHHHHHHHHTTSSEEEEESSSCTCHHHHHH
T ss_pred CEEEEEECCCCCcHHHHHHHHHHHHHHHcCCEEEEecCCC------chHHHHHHHHHHhcCCCEEEEecccCChHHHHHH
Confidence 467888865 77888999999999999999876543222 2233388899999999999999776653334333
Q ss_pred H
Q 002211 261 A 261 (953)
Q Consensus 261 a 261 (953)
.
T Consensus 76 ~ 76 (279)
T PF00532_consen 76 I 76 (279)
T ss_dssp H
T ss_pred H
Confidence 3
No 459
>PRK10936 TMAO reductase system periplasmic protein TorT; Provisional
Probab=45.42 E-value=93 Score=34.26 Aligned_cols=80 Identities=10% Similarity=0.025 Sum_probs=54.8
Q ss_pred cEEEEEEec--CccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhH-HHHHH
Q 002211 183 GEVIAIFND--DDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTG-LMVFD 259 (953)
Q Consensus 183 ~~vaii~~d--~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~-~~~~~ 259 (953)
+.|+++..+ +.|.....+.+.+++++.|..+.....-.. .+.+.....++.+.+.++|.||+.....+. ...+
T Consensus 47 ~~Igvv~p~~~~~f~~~~~~gi~~aa~~~G~~l~i~~~~~~---~~~~~q~~~i~~l~~~~vdgIIl~~~~~~~~~~~l- 122 (343)
T PRK10936 47 WKLCALYPHLKDSYWLSVNYGMVEEAKRLGVDLKVLEAGGY---YNLAKQQQQLEQCVAWGADAILLGAVTPDGLNPDL- 122 (343)
T ss_pred eEEEEEecCCCchHHHHHHHHHHHHHHHhCCEEEEEcCCCC---CCHHHHHHHHHHHHHhCCCEEEEeCCChHHhHHHH-
Confidence 688888854 667777888999999999988776432211 113444567788888899999987644333 3445
Q ss_pred HHHHcCC
Q 002211 260 VAQRLGM 266 (953)
Q Consensus 260 ~a~~~g~ 266 (953)
++.+.|.
T Consensus 123 ~~~~~gi 129 (343)
T PRK10936 123 ELQAANI 129 (343)
T ss_pred HHHHCCC
Confidence 6777664
No 460
>PRK15116 sulfur acceptor protein CsdL; Provisional
Probab=45.40 E-value=3.3e+02 Score=28.82 Aligned_cols=79 Identities=11% Similarity=0.130 Sum_probs=48.1
Q ss_pred CchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEEccCCh-hhHHHHHHhhhhCCC
Q 002211 61 VNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIVGPQSA-VMAHVLSHLANELQV 139 (953)
Q Consensus 61 ~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aiiGp~~S-~~a~av~~v~~~~~v 139 (953)
..|+.-..++.-.+.+|| |..+++.+ +..-++. ...+++..+.+.||-...+ ..-.++...+.+.++
T Consensus 80 ~vG~~Kve~~~~rl~~IN------P~~~V~~i--~~~i~~e----~~~~ll~~~~D~VIdaiD~~~~k~~L~~~c~~~~i 147 (268)
T PRK15116 80 NVGLAKAEVMAERIRQIN------PECRVTVV--DDFITPD----NVAEYMSAGFSYVIDAIDSVRPKAALIAYCRRNKI 147 (268)
T ss_pred hcChHHHHHHHHHHHhHC------CCcEEEEE--ecccChh----hHHHHhcCCCCEEEEcCCCHHHHHHHHHHHHHcCC
Confidence 345444456666666776 44555543 4333322 2345555567778876666 455568889999999
Q ss_pred cEEEeecCCCCC
Q 002211 140 PLLSFTALDPTL 151 (953)
Q Consensus 140 P~Is~~at~~~l 151 (953)
|+|+.+.....+
T Consensus 148 p~I~~gGag~k~ 159 (268)
T PRK15116 148 PLVTTGGAGGQI 159 (268)
T ss_pred CEEEECCcccCC
Confidence 999876554333
No 461
>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=45.34 E-value=1e+02 Score=29.03 Aligned_cols=48 Identities=27% Similarity=0.300 Sum_probs=37.6
Q ss_pred hHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcc
Q 002211 198 GVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGY 250 (953)
Q Consensus 198 ~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~ 250 (953)
....+.+.+++.|.++......+.+ .+++...+.++.+ ++|+||..+.
T Consensus 28 n~~~l~~~l~~~G~~v~~~~~v~Dd----~~~i~~~l~~~~~-~~DliIttGG 75 (144)
T TIGR00177 28 NGPLLAALLEEAGFNVSRLGIVPDD----PEEIREILRKAVD-EADVVLTTGG 75 (144)
T ss_pred cHHHHHHHHHHCCCeEEEEeecCCC----HHHHHHHHHHHHh-CCCEEEECCC
Confidence 3567888899999998887777765 7778888887754 7999999754
No 462
>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=45.30 E-value=1.5e+02 Score=29.62 Aligned_cols=87 Identities=13% Similarity=0.069 Sum_probs=54.2
Q ss_pred cEEEEEEecCccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcc----hhhHHHHH
Q 002211 183 GEVIAIFNDDDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGY----SRTGLMVF 258 (953)
Q Consensus 183 ~~vaii~~d~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~----~~~~~~~~ 258 (953)
.+|.+....++.=.-+..-+...++..|.+|.+-- . +......++.+++.+||+|-+.+. ......++
T Consensus 85 ~~vv~~t~~gd~H~lG~~~v~~~l~~~G~~vi~LG---~-----~vp~e~~v~~~~~~~pd~v~lS~~~~~~~~~~~~~i 156 (197)
T TIGR02370 85 GKVVCGVAEGDVHDIGKNIVVTMLRANGFDVIDLG---R-----DVPIDTVVEKVKKEKPLMLTGSALMTTTMYGQKDIN 156 (197)
T ss_pred CeEEEEeCCCchhHHHHHHHHHHHHhCCcEEEECC---C-----CCCHHHHHHHHHHcCCCEEEEccccccCHHHHHHHH
Confidence 35555554444444456667777888898887531 1 122345566677788999888654 35677788
Q ss_pred HHHHHcCCCCCceEEEEeC
Q 002211 259 DVAQRLGMMDSGYVWIATT 277 (953)
Q Consensus 259 ~~a~~~g~~~~~~~wi~~~ 277 (953)
+++++.|....-.+|+++.
T Consensus 157 ~~l~~~~~~~~v~i~vGG~ 175 (197)
T TIGR02370 157 DKLKEEGYRDSVKFMVGGA 175 (197)
T ss_pred HHHHHcCCCCCCEEEEECh
Confidence 8888887654334555554
No 463
>cd01324 cbb3_Oxidase_CcoQ Cytochrome cbb oxidase CcoQ. Cytochrome cbb3 oxidase, the terminal oxidase in the respiratory chains of proteobacteria, is a multi-chain transmembrane protein located in the cell membrane. Like other cytochrome oxidases, it catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. Found exclusively in proteobacteria, cbb3 is believed to be a modern enzyme that has evolved independently to perform a specialized function in microaerobic energy metabolism. The cbb3 operon contains four genes (ccoNOQP or fixNOQP), with ccoN coding for subunit I. Instead of a CuA-containing subunit II analogous to other cytochrome oxidases, cbb3 utilizes subunits ccoO and ccoP, which contain one and two hemes, respectively, to transfer electrons to the binuclear center. ccoQ, the fourth subunit, is a single transmembrane helix protein. It has been shown to protect the core complex from proteolytic degradation by serine proteases. See cd00919, cd01322
Probab=44.75 E-value=23 Score=26.24 Aligned_cols=27 Identities=19% Similarity=0.463 Sum_probs=21.9
Q ss_pred hHHHHHHHHHHHHHHHhhhhhcccCCC
Q 002211 608 LMWAVTGVFFLVVGTVVWILEHRLNDE 634 (953)
Q Consensus 608 ~vW~~i~~~~~~~~~~~~~l~~~~~~~ 634 (953)
++|.++..+.+++++++|.+..+..+.
T Consensus 12 ~~~~l~~~~~~Figiv~wa~~p~~k~~ 38 (48)
T cd01324 12 DSWGLLYLALFFLGVVVWAFRPGRKKA 38 (48)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCCcchh
Confidence 678888999999999999997655443
No 464
>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=44.69 E-value=99 Score=32.04 Aligned_cols=75 Identities=11% Similarity=0.009 Sum_probs=51.2
Q ss_pred EEEEEec--CccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHH
Q 002211 185 VIAIFND--DDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQ 262 (953)
Q Consensus 185 vaii~~d--~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~ 262 (953)
|+++..+ +.|.....+.+.+++++.|.++..... . .+.+.....++++...++|.+|+...... ..++..+.
T Consensus 2 igvv~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~---~--~~~~~~~~~i~~l~~~~~dgii~~~~~~~-~~~~~~~~ 75 (259)
T cd01542 2 IGVIVPRLDSFSTSRTVKGILAALYENGYQMLLMNT---N--FSIEKEIEALELLARQKVDGIILLATTIT-DEHREAIK 75 (259)
T ss_pred eEEEecCCccchHHHHHHHHHHHHHHCCCEEEEEeC---C--CCHHHHHHHHHHHHhcCCCEEEEeCCCCC-HHHHHHHh
Confidence 5566643 566678889999999999998865321 1 12445567788888889999999765432 34556666
Q ss_pred HcC
Q 002211 263 RLG 265 (953)
Q Consensus 263 ~~g 265 (953)
+.|
T Consensus 76 ~~~ 78 (259)
T cd01542 76 KLN 78 (259)
T ss_pred cCC
Confidence 655
No 465
>PRK03601 transcriptional regulator HdfR; Provisional
Probab=44.36 E-value=4e+02 Score=27.99 Aligned_cols=84 Identities=12% Similarity=0.027 Sum_probs=56.3
Q ss_pred CcceEEEecCcccccccEEeeCCcceEEEeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEec
Q 002211 484 GRQLRIGVPNRVSYRDFVFKVNGTDIVHGYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVGD 563 (953)
Q Consensus 484 g~~lri~v~~~~~~~p~~~~~~~~~~~~G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~~ 563 (953)
+++++||+.. . ....+..+++..+.++.+- +++.... +...++++.|.+|++|+++..
T Consensus 88 ~~~l~Ig~~~--~------------~~~~~l~~~l~~f~~~~P~-v~v~~~~-------~~~~~~~~~l~~g~~Dl~i~~ 145 (275)
T PRK03601 88 HNELSIGASA--S------------LWECMLTPWLGRLYQNQEA-LQFEARI-------AQRQSLVKQLHERQLDLLITT 145 (275)
T ss_pred CceEEEeccH--H------------HHHHHHHHHHHHHHHhCCC-cEEEEEE-------CChHHHHHHHHcCCCCEEEEc
Confidence 3568998874 1 1135566778888777642 4555554 557899999999999999864
Q ss_pred EEEecCccceeeccccceecceEEEEeccc
Q 002211 564 IAIVTNRTKAVDFTQPYIESGLVVVAPVRK 593 (953)
Q Consensus 564 ~~~t~~r~~~vdft~p~~~~~~~~~v~~~~ 593 (953)
.... . ..+ ...|+....++++++...
T Consensus 146 ~~~~--~-~~l-~~~~l~~~~~~~v~~~~~ 171 (275)
T PRK03601 146 EAPK--M-DEF-SSQLLGHFTLALYTSAPS 171 (275)
T ss_pred CCCc--c-CCc-cEEEecceeEEEEecCch
Confidence 3222 1 223 355788888888887654
No 466
>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=44.29 E-value=1e+02 Score=33.96 Aligned_cols=95 Identities=15% Similarity=0.145 Sum_probs=61.5
Q ss_pred HHHHHHHH-cCCcEEEEEEecCccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcc
Q 002211 172 AIAEMVSY-FGWGEVIAIFNDDDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGY 250 (953)
Q Consensus 172 ai~~~l~~-~~w~~vaii~~d~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~ 250 (953)
.+.++++. .+.+++.+|+....+ ....+.+.+.+++.| .+... +.+. .+.+.+...+..+++.++|+||..+.
T Consensus 14 ~l~~~l~~~~~~~~~liv~d~~~~-~~~~~~v~~~l~~~~-~~~~~--~~~~--~~~~~v~~~~~~~~~~~~d~iIaiGG 87 (339)
T cd08173 14 KIPNVLRDLLLGGRVLVVTGPTTK-SIAGKKVEALLEDEG-EVDVV--IVED--ATYEEVEKVESSARDIGADFVIGVGG 87 (339)
T ss_pred HHHHHHHHhCCCCeEEEEECCchH-HHHHHHHHHHHHhcC-CeEEE--EeCC--CCHHHHHHHHHHhhhcCCCEEEEeCC
Confidence 35566663 567899888854433 356778888888887 44322 2233 45788888889999889999998765
Q ss_pred h--hhHHHHHHHHHHcCCCCCceEEEEeC
Q 002211 251 S--RTGLMVFDVAQRLGMMDSGYVWIATT 277 (953)
Q Consensus 251 ~--~~~~~~~~~a~~~g~~~~~~~wi~~~ 277 (953)
+ -|+.+++.. ..| ..++-|.|.
T Consensus 88 Gs~~D~aK~~a~--~~~---~p~i~iPTT 111 (339)
T cd08173 88 GRVIDVAKVAAY--KLG---IPFISVPTA 111 (339)
T ss_pred chHHHHHHHHHH--hcC---CCEEEecCc
Confidence 4 455555542 223 344555544
No 467
>COG0078 ArgF Ornithine carbamoyltransferase [Amino acid transport and metabolism]
Probab=44.28 E-value=4.3e+02 Score=28.28 Aligned_cols=163 Identities=17% Similarity=0.210 Sum_probs=99.4
Q ss_pred eEEEeEEEecCCCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEEccCChhhHH
Q 002211 49 VLNVGAIFSFGTVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIVGPQSAVMAH 128 (953)
Q Consensus 49 ~i~IG~l~~~~~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aiiGp~~S~~a~ 128 (953)
.=.|+.+|.-++. ..+.+++.|+-+. +|..+-+--.|.+-...+.+...-+.+++=+++|.-=..+. .
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 4568999988764 5688899999886 34555555556554444555556666777555555322222 2
Q ss_pred HHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHH---HHcC---CcEEEEEEecCccccchHHHH
Q 002211 129 VLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMV---SYFG---WGEVIAIFNDDDQGRNGVTAL 202 (953)
Q Consensus 129 av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l---~~~~---w~~vaii~~d~~~g~~~~~~l 202 (953)
.+-.+++...||+|. .|++...| -+++++++ +++| -.+++.+.+. .+....+
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 567899999999995 35554334 25566663 5555 3566665532 6788888
Q ss_pred HHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHH-hcCCceEEEEE
Q 002211 203 GDKLAEIRCKISYKSALPPDQSVTETDVRNELVKV-RMMEARVIVVH 248 (953)
Q Consensus 203 ~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i-~~~~~~vii~~ 248 (953)
.......|..+.... |.+... ..++-...+++ +++++.+.+..
T Consensus 170 ~~~~a~~G~dv~ia~--Pk~~~p-~~~~~~~a~~~a~~~g~~i~~t~ 213 (310)
T COG0078 170 LLAAAKLGMDVRIAT--PKGYEP-DPEVVEKAKENAKESGGKITLTE 213 (310)
T ss_pred HHHHHHhCCeEEEEC--CCcCCc-CHHHHHHHHHHHHhcCCeEEEec
Confidence 888888998876533 322112 34454444443 44455554443
No 468
>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=44.12 E-value=90 Score=32.77 Aligned_cols=80 Identities=6% Similarity=0.037 Sum_probs=52.5
Q ss_pred EEEEEEe--cCccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcch-hhHHHHHHH
Q 002211 184 EVIAIFN--DDDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYS-RTGLMVFDV 260 (953)
Q Consensus 184 ~vaii~~--d~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~-~~~~~~~~~ 260 (953)
++++|.. ++.|.....+.+.+++++.|..+.....-... +...-...+.++...++|.||+.... ......++.
T Consensus 1 ~igvi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~~~~~---~~~~~~~~i~~l~~~~vdgiIi~~~~~~~~~~~~~~ 77 (275)
T cd06320 1 KYGVVLKTLSNEFWRSLKEGYENEAKKLGVSVDIQAAPSEG---DQQGQLSIAENMINKGYKGLLFSPISDVNLVPAVER 77 (275)
T ss_pred CeeEEEecCCCHHHHHHHHHHHHHHHHhCCeEEEEccCCCC---CHHHHHHHHHHHHHhCCCEEEECCCChHHhHHHHHH
Confidence 3566664 46677788899999999999887653221111 23344567777888899998876543 323455677
Q ss_pred HHHcCC
Q 002211 261 AQRLGM 266 (953)
Q Consensus 261 a~~~g~ 266 (953)
+.+.|.
T Consensus 78 ~~~~~i 83 (275)
T cd06320 78 AKKKGI 83 (275)
T ss_pred HHHCCC
Confidence 777664
No 469
>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=43.88 E-value=98 Score=32.50 Aligned_cols=77 Identities=12% Similarity=-0.009 Sum_probs=49.7
Q ss_pred CcEEEEEEe---------cCccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchh
Q 002211 182 WGEVIAIFN---------DDDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSR 252 (953)
Q Consensus 182 w~~vaii~~---------d~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~ 252 (953)
.+.|++|.+ ++.|.....+.+.+.+++.|+.+.... .+ . . +.....+.+.+.++|.||+.....
T Consensus 3 s~~i~vi~p~~~~~~~~~~~~~~~~~~~gi~~~~~~~g~~~~v~~---~~--~-~-~~~~~~~~l~~~~~dgiii~~~~~ 75 (275)
T cd06295 3 TDTIALVVPEPHERDQSFSDPFFLSLLGGIADALAERGYDLLLSF---VS--S-P-DRDWLARYLASGRADGVILIGQHD 75 (275)
T ss_pred ceEEEEEecCccccccccCCchHHHHHHHHHHHHHHcCCEEEEEe---CC--c-h-hHHHHHHHHHhCCCCEEEEeCCCC
Confidence 467888885 344666778889999999998876532 12 1 1 233444556667899998865432
Q ss_pred hHHHHHHHHHHcCC
Q 002211 253 TGLMVFDVAQRLGM 266 (953)
Q Consensus 253 ~~~~~~~~a~~~g~ 266 (953)
. ...++++.+.|.
T Consensus 76 ~-~~~~~~~~~~~i 88 (275)
T cd06295 76 Q-DPLPERLAETGL 88 (275)
T ss_pred C-hHHHHHHHhCCC
Confidence 2 244677777665
No 470
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=43.82 E-value=1.2e+02 Score=33.00 Aligned_cols=80 Identities=8% Similarity=-0.002 Sum_probs=53.0
Q ss_pred CcEEEEEEe--cCccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHH
Q 002211 182 WGEVIAIFN--DDDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFD 259 (953)
Q Consensus 182 w~~vaii~~--d~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~ 259 (953)
-+.|+++.. ++.|.......+.+++++.|..+..... .. +.+.-...+..+...+.|.||+..........++
T Consensus 61 ~~~Igvv~~~~~~~~~~~l~~gi~~~~~~~g~~~~~~~~--~~---~~~~~~~~~~~l~~~~vdgiIi~~~~~~~~~~~~ 135 (328)
T PRK11303 61 TRSIGLIIPDLENTSYARIAKYLERQARQRGYQLLIACS--DD---QPDNEMRCAEHLLQRQVDALIVSTSLPPEHPFYQ 135 (328)
T ss_pred CceEEEEeCCCCCchHHHHHHHHHHHHHHcCCEEEEEeC--CC---CHHHHHHHHHHHHHcCCCEEEEcCCCCCChHHHH
Confidence 356888875 3567777888999999999998765422 11 1333445677777789999998754322234566
Q ss_pred HHHHcCC
Q 002211 260 VAQRLGM 266 (953)
Q Consensus 260 ~a~~~g~ 266 (953)
++.+.|.
T Consensus 136 ~l~~~~i 142 (328)
T PRK11303 136 RLQNDGL 142 (328)
T ss_pred HHHhcCC
Confidence 6666664
No 471
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=43.76 E-value=1.3e+02 Score=32.91 Aligned_cols=79 Identities=11% Similarity=0.072 Sum_probs=55.2
Q ss_pred cEEEEEEec--CccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHH
Q 002211 183 GEVIAIFND--DDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDV 260 (953)
Q Consensus 183 ~~vaii~~d--~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~ 260 (953)
+.++++..+ ++|.......+.+++++.|..+.... .. .+.......++.+.+.++|.||+..........++.
T Consensus 65 ~~Igvv~~~~~~~~~~~i~~gi~~~a~~~g~~~~~~~---~~--~~~~~~~~~~~~l~~~~vdgiIi~~~~~~~~~~~~~ 139 (342)
T PRK10014 65 GVIGLIVRDLSAPFYAELTAGLTEALEAQGRMVFLLQ---GG--KDGEQLAQRFSTLLNQGVDGVVIAGAAGSSDDLREM 139 (342)
T ss_pred CEEEEEeCCCccchHHHHHHHHHHHHHHcCCEEEEEe---CC--CCHHHHHHHHHHHHhCCCCEEEEeCCCCCcHHHHHH
Confidence 468888854 67888888999999999998765431 11 124455677888888899999997544333456677
Q ss_pred HHHcCC
Q 002211 261 AQRLGM 266 (953)
Q Consensus 261 a~~~g~ 266 (953)
+.+.|.
T Consensus 140 l~~~~i 145 (342)
T PRK10014 140 AEEKGI 145 (342)
T ss_pred HhhcCC
Confidence 777664
No 472
>PRK13010 purU formyltetrahydrofolate deformylase; Reviewed
Probab=43.73 E-value=4.4e+02 Score=28.23 Aligned_cols=89 Identities=12% Similarity=0.132 Sum_probs=56.0
Q ss_pred cEEEEccCChhhHHHHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEcc-----CC---hHHHHHHHHHHHHHcC-----
Q 002211 115 TLAIVGPQSAVMAHVLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTA-----PN---DLYLMSAIAEMVSYFG----- 181 (953)
Q Consensus 115 v~aiiGp~~S~~a~av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~-----p~---d~~~~~ai~~~l~~~~----- 181 (953)
++-++||-..+....++.++.+.++=++..+.... ...-.||.|+. |. ....-.++.++.+.+|
T Consensus 11 iitv~G~Dr~GIVA~Vs~~Lae~g~NI~disq~~d---~~~~~ffm~i~~~~~~~~~~~~~~l~~~l~~l~~~l~l~~~i 87 (289)
T PRK13010 11 VLTLACPSAPGIVAAVSGFLAEKGCYIVELTQFDD---DESGRFFMRVSFHAQSAEAASVDTFRQEFQPVAEKFDMQWAI 87 (289)
T ss_pred EEEEECCCCCCcHHHHHHHHHHCCCCEEecccccc---cccCcEEEEEEEEcCCCCCCCHHHHHHHHHHHHHHhCCeEEE
Confidence 78899999999999999999999888876544321 12224666622 22 2334455666655543
Q ss_pred -----CcEEEEEEecCccccchHHHHHHHHHhc
Q 002211 182 -----WGEVIAIFNDDDQGRNGVTALGDKLAEI 209 (953)
Q Consensus 182 -----w~~vaii~~d~~~g~~~~~~l~~~l~~~ 209 (953)
.++++++.+.. |. ..+++.++.++.
T Consensus 88 ~~~~~~~kiavl~Sg~--g~-nl~al~~~~~~~ 117 (289)
T PRK13010 88 HPDGQRPKVVIMVSKF--DH-CLNDLLYRWRMG 117 (289)
T ss_pred ecCCCCeEEEEEEeCC--Cc-cHHHHHHHHHCC
Confidence 56888888655 22 244555555443
No 473
>PRK10355 xylF D-xylose transporter subunit XylF; Provisional
Probab=43.67 E-value=1.1e+02 Score=33.36 Aligned_cols=80 Identities=13% Similarity=0.087 Sum_probs=58.1
Q ss_pred CcEEEEEEe--cCccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhh-HHHHH
Q 002211 182 WGEVIAIFN--DDDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRT-GLMVF 258 (953)
Q Consensus 182 w~~vaii~~--d~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~-~~~~~ 258 (953)
-.+|+++.. +++|.....+.+.+++++.|..+.... .. .+.......++.+.+.++|.||+...... ....+
T Consensus 25 ~~~Ig~i~~~~~~~f~~~~~~gi~~~a~~~g~~l~i~~---~~--~~~~~~~~~i~~l~~~~vDGiIi~~~~~~~~~~~l 99 (330)
T PRK10355 25 EVKIGMAIDDLRLERWQKDRDIFVKKAESLGAKVFVQS---AN--GNEETQMSQIENMINRGVDVLVIIPYNGQVLSNVI 99 (330)
T ss_pred CceEEEEecCCCchHHHHHHHHHHHHHHHcCCEEEEEC---CC--CCHHHHHHHHHHHHHcCCCEEEEeCCChhhHHHHH
Confidence 367887774 578899999999999999999877542 11 22455667888888899999999765332 34566
Q ss_pred HHHHHcCC
Q 002211 259 DVAQRLGM 266 (953)
Q Consensus 259 ~~a~~~g~ 266 (953)
+.+.+.|.
T Consensus 100 ~~~~~~~i 107 (330)
T PRK10355 100 KEAKQEGI 107 (330)
T ss_pred HHHHHCCC
Confidence 77777663
No 474
>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=43.65 E-value=1.6e+02 Score=25.61 Aligned_cols=58 Identities=10% Similarity=0.148 Sum_probs=40.5
Q ss_pred chHHHHHHHHHhcCc-EEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEc--chhhHHHHHHHHHHcC
Q 002211 197 NGVTALGDKLAEIRC-KISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHG--YSRTGLMVFDVAQRLG 265 (953)
Q Consensus 197 ~~~~~l~~~l~~~g~-~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~--~~~~~~~~~~~a~~~g 265 (953)
...+.+.+.++..|. .+.. ..+....+..++...+|++++.. ...++..++++.++.+
T Consensus 9 ~~~~~l~~~l~~~~~~~v~~-----------~~~~~~~~~~~~~~~~d~iiid~~~~~~~~~~~~~~i~~~~ 69 (112)
T PF00072_consen 9 EIRELLEKLLERAGYEEVTT-----------ASSGEEALELLKKHPPDLIIIDLELPDGDGLELLEQIRQIN 69 (112)
T ss_dssp HHHHHHHHHHHHTTEEEEEE-----------ESSHHHHHHHHHHSTESEEEEESSSSSSBHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHhCCCCEEEE-----------ECCHHHHHHHhcccCceEEEEEeeecccccccccccccccc
Confidence 456677777887787 4432 12344566777777899999874 4467888888888877
No 475
>PRK07377 hypothetical protein; Provisional
Probab=43.63 E-value=50 Score=32.03 Aligned_cols=61 Identities=18% Similarity=0.193 Sum_probs=44.3
Q ss_pred cceEEEecCcccccccEEeeCCcceEEEeeHHHHHHHHHhCCCcccEEEeeCCCCCCCCChHHHHHHHHcCceeEEEe
Q 002211 485 RQLRIGVPNRVSYRDFVFKVNGTDIVHGYCIDVFLAAVRLLPYAVPYKFIPYGDGHKNPTYSELINQITTGVFDAAVG 562 (953)
Q Consensus 485 ~~lri~v~~~~~~~p~~~~~~~~~~~~G~~~dll~~la~~l~~~~~~~~~~~~~~~~n~~~~~~i~~l~~g~~Di~~~ 562 (953)
.++|+|+-.. . ++ .+...+-.++.++.+.++++.+ .+++++ .+-+.+.+.+.+|++|++.+
T Consensus 75 ~~~Rlgv~~~-----~---~~-~~~~~~~l~~~l~~~~~~y~~r--lElv~y------~~~~~l~~aL~~~eVh~~c~ 135 (184)
T PRK07377 75 LVMRLGVLEI-----E---TE-TSSVFDQLIDQLRTILDKYHLR--LELVVY------PDLQALEQALRDKEVHAICL 135 (184)
T ss_pred cEEEEEEEec-----c---cc-ccccHHHHHHHHHHHHHHhCce--eeEEec------CCHHHHHHHHhcCCccEEec
Confidence 5689998652 0 11 2234455778889999999955 566665 45889999999999998876
No 476
>PRK00843 egsA NAD(P)-dependent glycerol-1-phosphate dehydrogenase; Reviewed
Probab=43.55 E-value=1.3e+02 Score=33.20 Aligned_cols=97 Identities=13% Similarity=0.164 Sum_probs=63.1
Q ss_pred HHHHHHHHHcCC-cEEEEEEecCccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEc
Q 002211 171 SAIAEMVSYFGW-GEVIAIFNDDDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHG 249 (953)
Q Consensus 171 ~ai~~~l~~~~w-~~vaii~~d~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~ 249 (953)
..+.++++.++. +++.+|.....+.. ..+.+.+.+++.| .+... +.+. .+.+.+...+.++++.++|+||..+
T Consensus 22 ~~l~~~l~~~~~~~~~livtd~~~~~~-~~~~l~~~l~~~~-~~~~~--~~~~--~t~~~v~~~~~~~~~~~~d~IIaiG 95 (350)
T PRK00843 22 DDIGDVCSDLKLTGRALIVTGPTTKKI-AGDRVEENLEDAG-DVEVV--IVDE--ATMEEVEKVEEKAKDVNAGFLIGVG 95 (350)
T ss_pred HHHHHHHHHhCCCCeEEEEECCcHHHH-HHHHHHHHHHhcC-CeeEE--eCCC--CCHHHHHHHHHHhhccCCCEEEEeC
Confidence 446677777775 78888886555433 4567888888777 44322 3333 4577888889999988999999876
Q ss_pred ch--hhHHHHHHHHHHcCCCCCceEEEEeCc
Q 002211 250 YS--RTGLMVFDVAQRLGMMDSGYVWIATTW 278 (953)
Q Consensus 250 ~~--~~~~~~~~~a~~~g~~~~~~~wi~~~~ 278 (953)
.+ -|...++. ...| ..++-|.|..
T Consensus 96 GGsv~D~ak~vA--~~rg---ip~I~IPTT~ 121 (350)
T PRK00843 96 GGKVIDVAKLAA--YRLG---IPFISVPTAA 121 (350)
T ss_pred CchHHHHHHHHH--HhcC---CCEEEeCCCc
Confidence 64 45555554 2233 3455555543
No 477
>KOG0025 consensus Zn2+-binding dehydrogenase (nuclear receptor binding factor-1) [Transcription; Energy production and conversion]
Probab=43.34 E-value=1.1e+02 Score=32.28 Aligned_cols=97 Identities=11% Similarity=0.103 Sum_probs=69.9
Q ss_pred CcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEecCccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHH
Q 002211 157 PFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFNDDDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVK 236 (953)
Q Consensus 157 p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~d~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~ 236 (953)
.++.+-..+ +.-++++.++.+.+|.+.+.+|-+.+ ..+.+++.|+..|.+.+..+.--.+ .++.. .+
T Consensus 162 D~vIQNgan-S~VG~~ViQlaka~GiktinvVRdR~-----~ieel~~~Lk~lGA~~ViTeeel~~-----~~~~k--~~ 228 (354)
T KOG0025|consen 162 DSVIQNGAN-SGVGQAVIQLAKALGIKTINVVRDRP-----NIEELKKQLKSLGATEVITEEELRD-----RKMKK--FK 228 (354)
T ss_pred CeeeecCcc-cHHHHHHHHHHHHhCcceEEEeecCc-----cHHHHHHHHHHcCCceEecHHHhcc-----hhhhh--hh
Confidence 467766554 45689999999999999999998554 4789999999999887765422211 12211 12
Q ss_pred HhcCCceEEEEEcchhhHHHHHHHHHHcCC
Q 002211 237 VRMMEARVIVVHGYSRTGLMVFDVAQRLGM 266 (953)
Q Consensus 237 i~~~~~~vii~~~~~~~~~~~~~~a~~~g~ 266 (953)
....+++.-+-|..+..+..+.+.+.+-|.
T Consensus 229 ~~~~~prLalNcVGGksa~~iar~L~~Ggt 258 (354)
T KOG0025|consen 229 GDNPRPRLALNCVGGKSATEIARYLERGGT 258 (354)
T ss_pred ccCCCceEEEeccCchhHHHHHHHHhcCce
Confidence 234678888888889999999998877553
No 478
>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=43.16 E-value=98 Score=32.41 Aligned_cols=77 Identities=9% Similarity=-0.015 Sum_probs=53.0
Q ss_pred EEEEEe---cCccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchh-hHHHHHHH
Q 002211 185 VIAIFN---DDDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSR-TGLMVFDV 260 (953)
Q Consensus 185 vaii~~---d~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~-~~~~~~~~ 260 (953)
|++|.. +++|.....+.+.+++++.|..+..... . .+.+.-...++.+...++|.||+..... .....+++
T Consensus 2 i~vi~p~~~~~~~~~~~~~g~~~~~~~~g~~~~~~~~---~--~~~~~~~~~~~~l~~~~vdgiii~~~~~~~~~~~l~~ 76 (275)
T cd06317 2 IGYTQNNVGSHSYQTTYNKAFQAAAEEDGVEVIVLDA---N--GDVARQAAQVEDLIAQKVDGIILWPTDGQAYIPGLRK 76 (275)
T ss_pred eEEEecccCCCHHHHHHHHHHHHHHHhcCCEEEEEcC---C--cCHHHHHHHHHHHHHcCCCEEEEecCCccccHHHHHH
Confidence 456663 4678888899999999999988765421 1 1244455667777778999998876433 23456677
Q ss_pred HHHcCC
Q 002211 261 AQRLGM 266 (953)
Q Consensus 261 a~~~g~ 266 (953)
+.+.|.
T Consensus 77 ~~~~~i 82 (275)
T cd06317 77 AKQAGI 82 (275)
T ss_pred HHHCCC
Confidence 777664
No 479
>cd08475 PBP2_CrgA_like_6 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 6. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene a
Probab=43.10 E-value=2.1e+02 Score=27.48 Aligned_cols=67 Identities=13% Similarity=0.002 Sum_probs=38.6
Q ss_pred eEeCCCHHHHHHHHHcCCcEEEEccchhHHHHHhcCcceEEeCC--ccccCccEEEecCCCcchHHHHHHH
Q 002211 738 LVALGSPEEYAIALENRTVAAVVDERPYIDLFLSDHCQFSVRGQ--EFTKSGWGFAFPRDSPLAIDMSTAI 806 (953)
Q Consensus 738 ~~~~~~~~~~~~~l~~g~~~a~~~~~~~~~~~~~~~~~l~~~~~--~~~~~~~~~~~~k~spl~~~~n~~i 806 (953)
....++.+..++.+..|.--+++.+. .++.... ...+..+.. ......+.++.+|+......+...+
T Consensus 128 ~~~~~~~~~~~~~v~~g~gi~~~p~~-~~~~~~~-~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 196 (199)
T cd08475 128 RLQFDDGEAIADAALAGLGIAQLPTW-LVADHLQ-RGELVEVLPELAPEGLPIHAVWPRTRHLPPKVRAAV 196 (199)
T ss_pred cEEECCHHHHHHHHHhCCCEEeeeHH-HHHhHhh-cCcEEEecCCCcCCCccEEEEeCCcccCCHHHHHHH
Confidence 45578888899999987766665543 3333222 223333321 2234567788888766555544443
No 480
>PRK10653 D-ribose transporter subunit RbsB; Provisional
Probab=42.81 E-value=1.1e+02 Score=32.67 Aligned_cols=80 Identities=1% Similarity=0.007 Sum_probs=55.4
Q ss_pred CcEEEEEEe--cCccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhh-HHHHH
Q 002211 182 WGEVIAIFN--DDDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRT-GLMVF 258 (953)
Q Consensus 182 w~~vaii~~--d~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~-~~~~~ 258 (953)
-+.++++.. ++.|.......+.+++++.|..+..... . .+.......++++...++|++++.....+ ....+
T Consensus 26 ~~~I~vi~~~~~~~f~~~~~~~i~~~~~~~G~~~~~~~~---~--~d~~~~~~~~~~l~~~~~dgiii~~~~~~~~~~~l 100 (295)
T PRK10653 26 KDTIALVVSTLNNPFFVSLKDGAQKEADKLGYNLVVLDS---Q--NNPAKELANVQDLTVRGTKILLINPTDSDAVGNAV 100 (295)
T ss_pred CCeEEEEecCCCChHHHHHHHHHHHHHHHcCCeEEEecC---C--CCHHHHHHHHHHHHHcCCCEEEEcCCChHHHHHHH
Confidence 467888875 4667888899999999999998765321 1 12444566777887788998887654333 23566
Q ss_pred HHHHHcCC
Q 002211 259 DVAQRLGM 266 (953)
Q Consensus 259 ~~a~~~g~ 266 (953)
+.+.+.|.
T Consensus 101 ~~~~~~~i 108 (295)
T PRK10653 101 KMANQANI 108 (295)
T ss_pred HHHHHCCC
Confidence 77777664
No 481
>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=42.62 E-value=1.3e+02 Score=32.56 Aligned_cols=67 Identities=19% Similarity=0.254 Sum_probs=49.9
Q ss_pred cCCcEEEEEEecCcc--cc---chHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcc
Q 002211 180 FGWGEVIAIFNDDDQ--GR---NGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGY 250 (953)
Q Consensus 180 ~~w~~vaii~~d~~~--g~---~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~ 250 (953)
|.-.+|++|...++- |+ .....+.+.+++.|.++......+.+ .+.+...+.++.+.++|+||..+.
T Consensus 157 ~r~~rv~II~TG~Ev~~G~i~D~~~~~l~~~L~~~G~~v~~~~iv~Dd----~~~I~~ai~~~~~~g~DlIItTGG 228 (312)
T cd03522 157 FRPLRVGLIVTGSEVYGGRIEDKFGPVLRARLAALGVELVEQVIVPHD----EAAIAAAIAEALEAGAELLILTGG 228 (312)
T ss_pred cCCCEEEEEEcCCcCCCCcEEEhHHHHHHHHHHHCCCEEEEEEEcCCC----HHHHHHHHHHHhcCCCCEEEEeCC
Confidence 345678888765432 22 23567888899999999887777766 788888888887667999998754
No 482
>PF14981 FAM165: FAM165 family
Probab=42.36 E-value=62 Score=23.25 Aligned_cols=33 Identities=18% Similarity=0.232 Sum_probs=26.8
Q ss_pred cccchHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 002211 842 IQSFRGLFLICGIACFLALLAYFCLMLRQFKKY 874 (953)
Q Consensus 842 l~~~~g~f~il~~g~~lallvf~~e~~~~~~~~ 874 (953)
++++-.++||++.-.++.++.|..--+|++++.
T Consensus 3 L~~vPlLlYILaaKtlilClaFAgvK~yQ~krl 35 (51)
T PF14981_consen 3 LDNVPLLLYILAAKTLILCLAFAGVKMYQRKRL 35 (51)
T ss_pred hhhchHHHHHHHHHHHHHHHHHhhHHHHHHHHH
Confidence 567778899999988888888888888876554
No 483
>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=42.24 E-value=91 Score=32.47 Aligned_cols=77 Identities=6% Similarity=0.032 Sum_probs=52.9
Q ss_pred EEEEEe--cCccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhh-HHHHHHHH
Q 002211 185 VIAIFN--DDDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRT-GLMVFDVA 261 (953)
Q Consensus 185 vaii~~--d~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~-~~~~~~~a 261 (953)
+++|.. ++.|.......+.+++++.|..+... ... .+..+....+.++...++|.||+...... ....++++
T Consensus 2 I~vv~~~~~~~~~~~~~~~i~~~~~~~g~~v~~~---~~~--~~~~~~~~~~~~~~~~~~dgii~~~~~~~~~~~~l~~l 76 (268)
T cd06323 2 IGLSVSTLNNPFFVTLKDGAQKEAKELGYELTVL---DAQ--NDAAKQLNDIEDLITRGVDAIIINPTDSDAVVPAVKAA 76 (268)
T ss_pred eeEecccccCHHHHHHHHHHHHHHHHcCceEEec---CCC--CCHHHHHHHHHHHHHcCCCEEEEcCCChHHHHHHHHHH
Confidence 455553 47788888999999999999887642 222 23455667888888889999888643322 24567777
Q ss_pred HHcCC
Q 002211 262 QRLGM 266 (953)
Q Consensus 262 ~~~g~ 266 (953)
.+.|.
T Consensus 77 ~~~~i 81 (268)
T cd06323 77 NEAGI 81 (268)
T ss_pred HHCCC
Confidence 77554
No 484
>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=42.13 E-value=2.3e+02 Score=28.36 Aligned_cols=65 Identities=15% Similarity=0.074 Sum_probs=42.6
Q ss_pred CcEEEEEEecCccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcch
Q 002211 182 WGEVIAIFNDDDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYS 251 (953)
Q Consensus 182 w~~vaii~~d~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~ 251 (953)
-++|++|..| .|-.+..+.++...+..|+.+.... ...+ ........+++.+..+.|+|++...+
T Consensus 29 ~~~v~lis~D-~~R~ga~eQL~~~a~~l~vp~~~~~-~~~~---~~~~~~~~l~~~~~~~~D~vlIDT~G 93 (196)
T PF00448_consen 29 GKKVALISAD-TYRIGAVEQLKTYAEILGVPFYVAR-TESD---PAEIAREALEKFRKKGYDLVLIDTAG 93 (196)
T ss_dssp T--EEEEEES-TSSTHHHHHHHHHHHHHTEEEEESS-TTSC---HHHHHHHHHHHHHHTTSSEEEEEE-S
T ss_pred cccceeecCC-CCCccHHHHHHHHHHHhccccchhh-cchh---hHHHHHHHHHHHhhcCCCEEEEecCC
Confidence 5789999864 4667888999999988898765321 1111 12334566777877889999998764
No 485
>cd01574 PBP1_LacI Ligand-binding domain of DNA transcription repressor LacI specific for lactose, a member of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressor LacI specific for lactose, a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of LacI is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA b
Probab=41.79 E-value=1.3e+02 Score=31.25 Aligned_cols=77 Identities=8% Similarity=0.042 Sum_probs=49.7
Q ss_pred EEEEEe--cCccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHH
Q 002211 185 VIAIFN--DDDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQ 262 (953)
Q Consensus 185 vaii~~--d~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~ 262 (953)
|++|.+ ++.|.......+.+++++.|..+..... .. .+...-...++.+.+.++|.+++........ .+.++.
T Consensus 2 i~vi~~~~~~~~~~~~~~gi~~~~~~~~~~~~~~~~--~~--~~~~~~~~~~~~l~~~~vdgiii~~~~~~~~-~~~~~~ 76 (264)
T cd01574 2 IGVVTTDLALHGPSSTLAAIESAAREAGYAVTLSML--AE--ADEEALRAAVRRLLAQRVDGVIVNAPLDDAD-AALAAA 76 (264)
T ss_pred EEEEeCCCCcccHHHHHHHHHHHHHHCCCeEEEEeC--CC--CchHHHHHHHHHHHhcCCCEEEEeCCCCChH-HHHHHH
Confidence 556664 4567778899999999999988765421 11 1134556678888888899999876543333 234445
Q ss_pred HcCC
Q 002211 263 RLGM 266 (953)
Q Consensus 263 ~~g~ 266 (953)
+.|.
T Consensus 77 ~~~i 80 (264)
T cd01574 77 PADV 80 (264)
T ss_pred hcCC
Confidence 5553
No 486
>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=41.21 E-value=1.2e+02 Score=31.48 Aligned_cols=76 Identities=14% Similarity=0.115 Sum_probs=51.9
Q ss_pred EEEEEe--cCccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHH
Q 002211 185 VIAIFN--DDDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQ 262 (953)
Q Consensus 185 vaii~~--d~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~ 262 (953)
|+++.. ++.|.......+.+++++.|..+... ... .+.......++++.+.+.|.+++...... ...++.+.
T Consensus 2 i~vv~p~~~~~~~~~~~~~i~~~~~~~g~~~~~~---~~~--~~~~~~~~~~~~l~~~~vdgiii~~~~~~-~~~~~~l~ 75 (268)
T cd06273 2 IGAIVPTLDNAIFARVIQAFQETLAAHGYTLLVA---SSG--YDLDREYAQARKLLERGVDGLALIGLDHS-PALLDLLA 75 (268)
T ss_pred eEEEeCCCCCchHHHHHHHHHHHHHHCCCEEEEe---cCC--CCHHHHHHHHHHHHhcCCCEEEEeCCCCC-HHHHHHHH
Confidence 566765 46777888899999999999887753 222 22445567788888888999888654322 34456666
Q ss_pred HcCC
Q 002211 263 RLGM 266 (953)
Q Consensus 263 ~~g~ 266 (953)
+.|.
T Consensus 76 ~~~i 79 (268)
T cd06273 76 RRGV 79 (268)
T ss_pred hCCC
Confidence 6653
No 487
>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=40.93 E-value=35 Score=31.77 Aligned_cols=57 Identities=19% Similarity=0.289 Sum_probs=40.2
Q ss_pred HHHHHHHhc--CcEEEEccCCh--hhHHHHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEc
Q 002211 105 MGALQFMET--DTLAIVGPQSA--VMAHVLSHLANELQVPLLSFTALDPTLSPLQYPFFVQT 162 (953)
Q Consensus 105 ~~a~~li~~--~v~aiiGp~~S--~~a~av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~ 162 (953)
+++.+++.+ +.+.++|.... .....+..++++.++|++..... ...-+...|+++-.
T Consensus 2 ~~~~~~L~~A~rP~il~G~g~~~~~a~~~l~~lae~~~~Pv~~t~~~-kg~i~~~hp~~~G~ 62 (137)
T PF00205_consen 2 DEAADLLSSAKRPVILAGRGARRSGAAEELRELAEKLGIPVATTPMG-KGVIPEDHPLFLGY 62 (137)
T ss_dssp HHHHHHHHH-SSEEEEE-HHHHHTTCHHHHHHHHHHHTSEEEEEGGG-TTSSTTTSTTEEEE
T ss_pred HHHHHHHHhCCCEEEEEcCCcChhhHHHHHHHHHHHHCCCEEecCcc-ccccCCCCchhccc
Confidence 445566655 89999998766 88899999999999999875433 33333445777653
No 488
>COG4521 TauA ABC-type taurine transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=40.78 E-value=2e+02 Score=29.34 Aligned_cols=106 Identities=16% Similarity=0.129 Sum_probs=63.0
Q ss_pred CCCCChHHhhhCCCeEEEEeCchHHH-HHH--HhhCCCccceEeCC-CHHHHHHHHHcCCcEEEEccchhHHHHHhcCc-
Q 002211 700 SPIKGIDTLMTSNDRVGYQVGSFAEN-YLI--EELSIPKSRLVALG-SPEEYAIALENRTVAAVVDERPYIDLFLSDHC- 774 (953)
Q Consensus 700 ~~I~sl~dL~~~~~~ig~~~~s~~~~-~l~--~~~~~~~~~~~~~~-~~~~~~~~l~~g~~~a~~~~~~~~~~~~~~~~- 774 (953)
..|...+||+ |++|++.--|.... +|. ++.+++..++..++ .+.+...+-++|.+|+.....|.+.-+.....
T Consensus 120 sgI~kpeDL~--GK~iavPFvSTtHysLLaaLkhw~idp~~V~IlNl~Pp~IaAAwqRGDIDgAyVW~PAl~el~ksGkV 197 (334)
T COG4521 120 SGIEKPEDLI--GKRIAVPFVSTTHYSLLAALKHWGIDPGQVEILNLQPPAIAAAWQRGDIDGAYVWAPALSELKKSGKV 197 (334)
T ss_pred CCcCChHHhc--cCeeccceeehhHHHHHHHHHHcCCCccceeEeccCCHHHHHHHHcCCCCceeeccHhHHHHhhcCcE
Confidence 5899999998 99999875544332 221 23455544443332 66778888899999988887777665543321
Q ss_pred --ceEEeCCccccCccEEEecCCC----c-chHHHHHHHH
Q 002211 775 --QFSVRGQEFTKSGWGFAFPRDS----P-LAIDMSTAIL 807 (953)
Q Consensus 775 --~l~~~~~~~~~~~~~~~~~k~s----p-l~~~~n~~i~ 807 (953)
+-..++..-.+..-+++++|+. | ....|-+..+
T Consensus 198 ltDs~qvgqwgaPTfdvwVvrkdfAekhPe~v~aFakv~~ 237 (334)
T COG4521 198 LTDSEQVGQWGAPTFDVWVVRKDFAEKHPEVVAAFAKVAL 237 (334)
T ss_pred eccHHHhhccCCCceeeEEeehHhhHhChHHHHHHHHHHH
Confidence 1122333333344567777774 4 4455544443
No 489
>cd06319 PBP1_ABC_sugar_binding_like_10 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=40.77 E-value=1.1e+02 Score=32.15 Aligned_cols=77 Identities=6% Similarity=-0.013 Sum_probs=51.8
Q ss_pred EEEEEe--cCccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhh-HHHHHHHH
Q 002211 185 VIAIFN--DDDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRT-GLMVFDVA 261 (953)
Q Consensus 185 vaii~~--d~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~-~~~~~~~a 261 (953)
+++|.. ++.|.......+.+.+++.|.++... ... .+...-...++++.+.++|.||+.....+ ....++.+
T Consensus 2 i~vi~~~~~~~~~~~~~~~i~~~~~~~g~~~~~~---~~~--~~~~~~~~~i~~~~~~~~dgiii~~~~~~~~~~~l~~~ 76 (277)
T cd06319 2 IAYIVSDLRIPFWQIMGRGVKSKAKALGYDAVEL---SAE--NSAKKELENLRTAIDKGVSGIIISPTNSSAAVTLLKLA 76 (277)
T ss_pred eEEEeCCCCchHHHHHHHHHHHHHHhcCCeEEEe---cCC--CCHHHHHHHHHHHHhcCCCEEEEcCCchhhhHHHHHHH
Confidence 566664 46788888899999999999887643 211 12344456777777789999988654332 34566777
Q ss_pred HHcCC
Q 002211 262 QRLGM 266 (953)
Q Consensus 262 ~~~g~ 266 (953)
.+.|.
T Consensus 77 ~~~~i 81 (277)
T cd06319 77 AQAKI 81 (277)
T ss_pred HHCCC
Confidence 77664
No 490
>TIGR01276 thiB thiamine ABC transporter, periplasmic binding protein. This model finds the thiamine (and thiamine pyrophosphate) ABC transporter periplasmic binding protein ThiB in proteobacteria. Completed genomes having this protein (E. coli, Vibrio cholera, Haemophilus influenzae) also have the permease ThiP, described by TIGRFAMs equivalog model TIGR01253.
Probab=40.68 E-value=4.9e+02 Score=27.92 Aligned_cols=83 Identities=7% Similarity=-0.205 Sum_probs=43.4
Q ss_pred eCCCHHHHHHHHHcCCcEEEEccchhHHH--HHhcCcce--EEeCCccccCccEEEecCCCcchHHHHHHHHhhhccccH
Q 002211 740 ALGSPEEYAIALENRTVAAVVDERPYIDL--FLSDHCQF--SVRGQEFTKSGWGFAFPRDSPLAIDMSTAILTLSENGEL 815 (953)
Q Consensus 740 ~~~~~~~~~~~l~~g~~~a~~~~~~~~~~--~~~~~~~l--~~~~~~~~~~~~~~~~~k~spl~~~~n~~i~~l~e~G~~ 815 (953)
...+..+....+.+|++++.+.......+ .......+ ...++-......+++++|++|-.+.-.+.|..+......
T Consensus 175 ~~~~~~~~~~~~~~Ge~~i~i~~~~~~~~~~~~~~~~~~~~~~~~eG~~~~~~~~ai~k~a~n~e~A~~Fidflls~e~Q 254 (309)
T TIGR01276 175 VTKGWSEAYGLFLKGESDLVLSYTTSPAYHILEEKKDNYAAANFSEGHYLQVEVAARTAASKQPELAQKFLQFLVSPAFQ 254 (309)
T ss_pred eCCChHHHHHHHHcCCcCEEEecCCcHHHHhhcccCcccceEecCCCCEeEEEEEEEeCCCCCHHHHHHHHHHHcCHHHH
Confidence 34455667788899999887754322111 11111122 222222222345788899998666555666555544323
Q ss_pred HHHHHHh
Q 002211 816 QRIHDKW 822 (953)
Q Consensus 816 ~~~~~~w 822 (953)
..+..++
T Consensus 255 ~~~~~~~ 261 (309)
T TIGR01276 255 NAIPTGN 261 (309)
T ss_pred HHHHhhC
Confidence 2344443
No 491
>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=40.67 E-value=1.2e+02 Score=32.68 Aligned_cols=78 Identities=9% Similarity=0.072 Sum_probs=53.0
Q ss_pred EEEEEEec--CccccchHHHHHHHHHh--cCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcc-hhhHHHHH
Q 002211 184 EVIAIFND--DDQGRNGVTALGDKLAE--IRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGY-SRTGLMVF 258 (953)
Q Consensus 184 ~vaii~~d--~~~g~~~~~~l~~~l~~--~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~-~~~~~~~~ 258 (953)
+|++|..+ +.|.......+.+++++ .|..+.... .. .+...-...++++...++|.||+... +......+
T Consensus 1 ~Igviv~~~~~~~~~~~~~gi~~~a~~~~~g~~~~~~~---~~--~~~~~q~~~i~~l~~~~vdgiii~~~~~~~~~~~~ 75 (303)
T cd01539 1 KIGVFLYKFDDTFISLVRKNLEDIQKENGGKVEFTFYD---AK--NNQSTQNEQIDTALAKGVDLLAVNLVDPTAAQTVI 75 (303)
T ss_pred CeEEEeeCCCChHHHHHHHHHHHHHHhhCCCeeEEEec---CC--CCHHHHHHHHHHHHHcCCCEEEEecCchhhHHHHH
Confidence 46666653 56777788899999998 777765432 22 22444556788888899999888643 33345677
Q ss_pred HHHHHcCC
Q 002211 259 DVAQRLGM 266 (953)
Q Consensus 259 ~~a~~~g~ 266 (953)
+++.+.|+
T Consensus 76 ~~~~~~gi 83 (303)
T cd01539 76 NKAKQKNI 83 (303)
T ss_pred HHHHHCCC
Confidence 88877775
No 492
>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=40.51 E-value=1.2e+02 Score=31.66 Aligned_cols=76 Identities=9% Similarity=0.107 Sum_probs=51.4
Q ss_pred EEEEEe--cCccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcchhhHHHHHHHHH
Q 002211 185 VIAIFN--DDDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYSRTGLMVFDVAQ 262 (953)
Q Consensus 185 vaii~~--d~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~~~~~~~~~~a~ 262 (953)
+++|.. ++.|.....+.+.+++++.|..+..... . .+..+....++++...++|.||+...... ...++.+.
T Consensus 2 Ig~i~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~---~--~~~~~~~~~~~~l~~~~vdgiii~~~~~~-~~~~~~~~ 75 (268)
T cd01575 2 VAVLVPSLSNSVFADVLQGISDVLEAAGYQLLLGNT---G--YSPEREEELLRTLLSRRPAGLILTGLEHT-ERTRQLLR 75 (268)
T ss_pred EEEEeCCCcchhHHHHHHHHHHHHHHcCCEEEEecC---C--CCchhHHHHHHHHHHcCCCEEEEeCCCCC-HHHHHHHH
Confidence 466664 3567777888999999999988765321 1 12445667788888889999998764432 34555666
Q ss_pred HcCC
Q 002211 263 RLGM 266 (953)
Q Consensus 263 ~~g~ 266 (953)
+.|.
T Consensus 76 ~~~i 79 (268)
T cd01575 76 AAGI 79 (268)
T ss_pred hcCC
Confidence 6554
No 493
>PRK14174 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=39.93 E-value=5e+02 Score=27.85 Aligned_cols=175 Identities=13% Similarity=0.057 Sum_probs=92.6
Q ss_pred EEeEEEecCCCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhc-CcEEEEc--cC--Chh
Q 002211 51 NVGAIFSFGTVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMET-DTLAIVG--PQ--SAV 125 (953)
Q Consensus 51 ~IG~l~~~~~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~-~v~aiiG--p~--~S~ 125 (953)
+++++.--+......+.+.-.-+.+++ |.+.+++-.+...+..+-.....+|=++ .|.+|+= |. .-.
T Consensus 33 ~Laii~vg~d~as~~Yv~~k~k~~~~~--------Gi~~~~~~l~~~~~~~el~~~I~~lN~D~~V~GIlvq~Plp~~id 104 (295)
T PRK14174 33 GLTVIIVGEDPASQVYVRNKAKSCKEI--------GMNSTVIELPADTTEEHLLKKIEDLNNDPDVHGILVQQPLPKQID 104 (295)
T ss_pred eEEEEEeCCChHHHHHHHHHHHHHHHc--------CCEEEEEECCCCCCHHHHHHHHHHHhCCCCCCEEEEeCCCCCCCC
Confidence 455554433333344455555555554 5677777777666666555555555444 6777662 32 222
Q ss_pred hHHHHHHhhhhCCCcEEEeecCCCCCCCCCCCcEEEccCChHHHHHHHHHHHHHcC----CcEEEEEEecCccccchHHH
Q 002211 126 MAHVLSHLANELQVPLLSFTALDPTLSPLQYPFFVQTAPNDLYLMSAIAEMVSYFG----WGEVIAIFNDDDQGRNGVTA 201 (953)
Q Consensus 126 ~a~av~~v~~~~~vP~Is~~at~~~ls~~~~p~~fr~~p~d~~~~~ai~~~l~~~~----w~~vaii~~d~~~g~~~~~~ 201 (953)
.-.....+.-+..|=-+++......+.....+.| .| --+.++.+++++|+ -++|++|.-..--|+-....
T Consensus 105 ~~~i~~~I~p~KDVDGl~~~n~g~l~~~~~~~~~---~P---cTp~ail~ll~~y~i~l~Gk~vvViGrS~iVG~Pla~l 178 (295)
T PRK14174 105 EFAVTLAIDPAKDVDGFHPENLGRLVMGHLDKCF---VS---CTPYGILELLGRYNIETKGKHCVVVGRSNIVGKPMANL 178 (295)
T ss_pred HHHHHhcCCccccccccChhhHHHHhcCCCCCCc---CC---CCHHHHHHHHHHhCCCCCCCEEEEECCCCcchHHHHHH
Confidence 2222222333333333322111111111000211 12 13468899999886 58999999888889888888
Q ss_pred HHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcch
Q 002211 202 LGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGYS 251 (953)
Q Consensus 202 l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~~ 251 (953)
|.+.++..|.+|..... . +.++...+ .++|++|.....
T Consensus 179 L~~~~~~~~atVt~~hs---~----t~~l~~~~-----~~ADIvI~Avg~ 216 (295)
T PRK14174 179 MLQKLKESNCTVTICHS---A----TKDIPSYT-----RQADILIAAIGK 216 (295)
T ss_pred HHhccccCCCEEEEEeC---C----chhHHHHH-----HhCCEEEEecCc
Confidence 77666666776654321 1 23332222 468999987743
No 494
>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=39.80 E-value=2.7e+02 Score=28.73 Aligned_cols=77 Identities=13% Similarity=0.134 Sum_probs=48.1
Q ss_pred CCchhHHHHHHHHHHHHHhcCCCCCCCcEEEEEEecCCCChHHHHHHHHHHHhcCcEEEEccCChh-hHHHHHHhhhhCC
Q 002211 60 TVNGQVSRIAMKAAQDDINSDPRVLGGRKLSITMHDAKFNGFLSIMGALQFMETDTLAIVGPQSAV-MAHVLSHLANELQ 138 (953)
Q Consensus 60 ~~~g~~~~~a~~lAve~iN~~g~il~g~~l~l~~~D~~~~~~~a~~~a~~li~~~v~aiiGp~~S~-~a~av~~v~~~~~ 138 (953)
...|+.-..++.-.+.++| |..+++. .+..-++. ...+++..+...||....+. .-..+...+.+.+
T Consensus 60 ~diG~~Kae~~~~~l~~in------P~~~V~~--~~~~i~~~----~~~~l~~~~~D~VvdaiD~~~~k~~L~~~c~~~~ 127 (231)
T cd00755 60 STVGKPKVEVMAERIRDIN------PECEVDA--VEEFLTPD----NSEDLLGGDPDFVVDAIDSIRAKVALIAYCRKRK 127 (231)
T ss_pred hhCCCcHHHHHHHHHHHHC------CCcEEEE--eeeecCHh----HHHHHhcCCCCEEEEcCCCHHHHHHHHHHHHHhC
Confidence 4456655666677777877 4445554 33333332 34456655677777765544 4455778899999
Q ss_pred CcEEEeecCC
Q 002211 139 VPLLSFTALD 148 (953)
Q Consensus 139 vP~Is~~at~ 148 (953)
+|+|+.....
T Consensus 128 ip~I~s~g~g 137 (231)
T cd00755 128 IPVISSMGAG 137 (231)
T ss_pred CCEEEEeCCc
Confidence 9999865544
No 495
>PRK02261 methylaspartate mutase subunit S; Provisional
Probab=39.78 E-value=3e+02 Score=25.65 Aligned_cols=86 Identities=14% Similarity=0.058 Sum_probs=52.4
Q ss_pred cEEEEEEecCccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEcc----hhhHHHHH
Q 002211 183 GEVIAIFNDDDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHGY----SRTGLMVF 258 (953)
Q Consensus 183 ~~vaii~~d~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~~----~~~~~~~~ 258 (953)
.+|.+.....+.=.-+...+...++..|.+|.+--. . ......+..+.+.+||+|.+.+. ...+..++
T Consensus 4 ~~vl~~~~~gD~H~lG~~iv~~~lr~~G~eVi~LG~---~-----vp~e~i~~~a~~~~~d~V~lS~~~~~~~~~~~~~~ 75 (137)
T PRK02261 4 KTVVLGVIGADCHAVGNKILDRALTEAGFEVINLGV---M-----TSQEEFIDAAIETDADAILVSSLYGHGEIDCRGLR 75 (137)
T ss_pred CEEEEEeCCCChhHHHHHHHHHHHHHCCCEEEECCC---C-----CCHHHHHHHHHHcCCCEEEEcCccccCHHHHHHHH
Confidence 344444433333334456777788899999886321 1 12234566677789999998753 35677888
Q ss_pred HHHHHcCCCCCceEEEEeC
Q 002211 259 DVAQRLGMMDSGYVWIATT 277 (953)
Q Consensus 259 ~~a~~~g~~~~~~~wi~~~ 277 (953)
+++++.|... -.+|+++.
T Consensus 76 ~~L~~~~~~~-~~i~vGG~ 93 (137)
T PRK02261 76 EKCIEAGLGD-ILLYVGGN 93 (137)
T ss_pred HHHHhcCCCC-CeEEEECC
Confidence 8888877642 23444443
No 496
>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=39.56 E-value=1.2e+02 Score=27.17 Aligned_cols=73 Identities=15% Similarity=0.109 Sum_probs=48.0
Q ss_pred HHHHHHHHHHHcCCcEEEEEEecCccccchHHHHHHHHHhcCcEEEEEEe-cCCCCCCChHHHHHHHHHHhcCCceEEEE
Q 002211 169 LMSAIAEMVSYFGWGEVIAIFNDDDQGRNGVTALGDKLAEIRCKISYKSA-LPPDQSVTETDVRNELVKVRMMEARVIVV 247 (953)
Q Consensus 169 ~~~ai~~~l~~~~w~~vaii~~d~~~g~~~~~~l~~~l~~~g~~v~~~~~-~~~~~~~~~~d~~~~l~~i~~~~~~vii~ 247 (953)
-...++.++++.|| +|.++-.+. ..+.+.+.+.+.+..++.-.. +... .......++.+|+..|++.++
T Consensus 16 Gl~~la~~l~~~G~-~v~~~d~~~-----~~~~l~~~~~~~~pd~V~iS~~~~~~----~~~~~~l~~~~k~~~p~~~iv 85 (121)
T PF02310_consen 16 GLLYLAAYLRKAGH-EVDILDANV-----PPEELVEALRAERPDVVGISVSMTPN----LPEAKRLARAIKERNPNIPIV 85 (121)
T ss_dssp HHHHHHHHHHHTTB-EEEEEESSB------HHHHHHHHHHTTCSEEEEEESSSTH----HHHHHHHHHHHHTTCTTSEEE
T ss_pred HHHHHHHHHHHCCC-eEEEECCCC-----CHHHHHHHHhcCCCcEEEEEccCcCc----HHHHHHHHHHHHhcCCCCEEE
Confidence 34667888899898 555553222 127777778777777666544 4433 667788888888888886666
Q ss_pred Ecch
Q 002211 248 HGYS 251 (953)
Q Consensus 248 ~~~~ 251 (953)
.+.+
T Consensus 86 ~GG~ 89 (121)
T PF02310_consen 86 VGGP 89 (121)
T ss_dssp EEES
T ss_pred EECC
Confidence 5543
No 497
>cd00885 cinA Competence-damaged protein. CinA is the first gene in the competence- inducible (cin) operon and is thought to be specifically required at some stage in the process of transformation. This domain is closely related to a domain, found in a variety of proteins involved in biosynthesis of molybdopterin cofactor, where the domain is presumed to bind molybdopterin.
Probab=39.42 E-value=1.2e+02 Score=29.49 Aligned_cols=46 Identities=20% Similarity=0.335 Sum_probs=31.3
Q ss_pred HHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEEEEc
Q 002211 199 VTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARVIVVHG 249 (953)
Q Consensus 199 ~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii~~~ 249 (953)
...+.+.+.+.|+++.....++.+ ...+...+.++.+ .+|+||..+
T Consensus 21 ~~~l~~~L~~~G~~v~~~~~v~Dd----~~~I~~~l~~~~~-~~dlVIttG 66 (170)
T cd00885 21 AAFLAKELAELGIEVYRVTVVGDD----EDRIAEALRRASE-RADLVITTG 66 (170)
T ss_pred HHHHHHHHHHCCCEEEEEEEeCCC----HHHHHHHHHHHHh-CCCEEEECC
Confidence 457777788888888776666655 6667777766653 467766654
No 498
>KOG3713 consensus Voltage-gated K+ channel KCNB/KCNC [Inorganic ion transport and metabolism]
Probab=39.33 E-value=41 Score=37.90 Aligned_cols=59 Identities=20% Similarity=0.344 Sum_probs=45.5
Q ss_pred HHHhhhhhcccCCCCCCCCcccchhhHHHHHHHhhccccC--CcccchhHHHHHHHHHHHHHhhh
Q 002211 621 GTVVWILEHRLNDEFRGPPRKQIVTVLWFSFSTMFFAHRE--NTVSTLGRVVLIIWLFVVLIITS 683 (953)
Q Consensus 621 ~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~--~~~s~~~R~l~~~w~~~~lil~~ 683 (953)
+.+++++|+-.+. ++..++-.++|++..+|..-|.. .|+...+|++...-.++++++.+
T Consensus 360 StlvY~~Ek~~~~----~~FtSIPa~~WWaiVTMTTVGYGDm~P~T~~Gklvas~cil~GVLvlA 420 (477)
T KOG3713|consen 360 STLVYFAEKDEPD----TKFTSIPAGFWWAVVTMTTVGYGDMVPVTVLGKLVASLCILCGVLVLA 420 (477)
T ss_pred HHHHHHhhhcCCC----CCCccccchhheeeEEEeeecccCccccccchHHHHHHHHHHhHHHhh
Confidence 4456777765433 23556888999999999988755 89999999999999998887754
No 499
>PRK14737 gmk guanylate kinase; Provisional
Probab=39.23 E-value=3.9e+02 Score=26.37 Aligned_cols=130 Identities=12% Similarity=0.028 Sum_probs=66.4
Q ss_pred CcEEEEccCChhhHHHHHHhhhhC-CCcE-EEeecCCCCCCC-CCCCcEEEccCChHHHHHHHHHHHHHcCCcEEEEEEe
Q 002211 114 DTLAIVGPQSAVMAHVLSHLANEL-QVPL-LSFTALDPTLSP-LQYPFFVQTAPNDLYLMSAIAEMVSYFGWGEVIAIFN 190 (953)
Q Consensus 114 ~v~aiiGp~~S~~a~av~~v~~~~-~vP~-Is~~at~~~ls~-~~~p~~fr~~p~d~~~~~ai~~~l~~~~w~~vaii~~ 190 (953)
.+++|+||.+|+=...+..+.+.. ++.. ++++...|.-.+ .+-.|+|-+. .+. ...++.-..=..+- |.
T Consensus 5 ~~ivl~GpsG~GK~tl~~~l~~~~~~~~~~v~~TTR~~r~gE~~G~dY~fvs~----~~F---~~~i~~~~f~e~~~-~~ 76 (186)
T PRK14737 5 KLFIISSVAGGGKSTIIQALLEEHPDFLFSISCTTRAPRPGDEEGKTYFFLTI----EEF---KKGIADGEFLEWAE-VH 76 (186)
T ss_pred eEEEEECCCCCCHHHHHHHHHhcCCccccccCccCCCCCCCCCCCceeEeCCH----HHH---HHHHHcCCeEEEEE-EC
Confidence 578899999999888888887765 2211 233333333333 3456777632 222 22222212111111 33
Q ss_pred cCccccchHHHHHHHHHhcCcEEEEEEecCCCCCCChHHHHHHHHHHhcCCceE-EEEEcchhhHHHHHHHHHHcC
Q 002211 191 DDDQGRNGVTALGDKLAEIRCKISYKSALPPDQSVTETDVRNELVKVRMMEARV-IVVHGYSRTGLMVFDVAQRLG 265 (953)
Q Consensus 191 d~~~g~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~v-ii~~~~~~~~~~~~~~a~~~g 265 (953)
++-||... +.+.+.+++..++|... . . .-+..++...++. ++++..++....+.+.+.+.|
T Consensus 77 g~~YGt~~-~~i~~~~~~g~~~i~d~---~------~----~g~~~l~~~~~~~~~~Ifi~pps~e~l~~RL~~R~ 138 (186)
T PRK14737 77 DNYYGTPK-AFIEDAFKEGRSAIMDI---D------V----QGAKIIKEKFPERIVTIFIEPPSEEEWEERLIHRG 138 (186)
T ss_pred CeeecCcH-HHHHHHHHcCCeEEEEc---C------H----HHHHHHHHhCCCCeEEEEEECCCHHHHHHHHHhcC
Confidence 56677544 55667776666665532 1 1 1234455444543 455555544555555555554
No 500
>PRK11070 ssDNA exonuclease RecJ; Provisional
Probab=39.06 E-value=2.1e+02 Score=34.06 Aligned_cols=101 Identities=14% Similarity=0.085 Sum_probs=0.0
Q ss_pred HHHHHHHHHH--cCCcEEEEEEecCccccchHHHHHHHHHhcCc-EEEEEEecCCCCCCChHHHHHHHHHHhcCCceEEE
Q 002211 170 MSAIAEMVSY--FGWGEVIAIFNDDDQGRNGVTALGDKLAEIRC-KISYKSALPPDQSVTETDVRNELVKVRMMEARVIV 246 (953)
Q Consensus 170 ~~ai~~~l~~--~~w~~vaii~~d~~~g~~~~~~l~~~l~~~g~-~v~~~~~~~~~~~~~~~d~~~~l~~i~~~~~~vii 246 (953)
+...++.+.+ ..-++|.|...-|.-|.....-+.+.|++.|. .+.+...-... ..-.--...+.++.+.+++.||
T Consensus 55 m~~a~~ri~~ai~~~e~I~I~gDyD~DGitstail~~~L~~~g~~~~~~~IP~R~~--eGYGl~~~~i~~~~~~~~~LiI 132 (575)
T PRK11070 55 IEKAVELLYNALREGTRIIVVGDFDADGATSTALSVLALRSLGCSNVDYLVPNRFE--DGYGLSPEVVDQAHARGAQLIV 132 (575)
T ss_pred HHHHHHHHHHHHHCCCEEEEEEecCccHHHHHHHHHHHHHHcCCCceEEEeCCCCc--CCCCCCHHHHHHHHhcCCCEEE
Q ss_pred EEcchhhHHHHHHHHHHcCCCCCceEEEEeC
Q 002211 247 VHGYSRTGLMVFDVAQRLGMMDSGYVWIATT 277 (953)
Q Consensus 247 ~~~~~~~~~~~~~~a~~~g~~~~~~~wi~~~ 277 (953)
.+..+.....-++.|++.|+. .|.+|
T Consensus 133 tvD~Gi~~~e~i~~a~~~gid-----vIVtD 158 (575)
T PRK11070 133 TVDNGISSHAGVAHAHALGIP-----VLVTD 158 (575)
T ss_pred EEcCCcCCHHHHHHHHHCCCC-----EEEEC
Done!