Query 043276
Match_columns 829
No_of_seqs 479 out of 3247
Neff 9.1
Searched_HMMs 46136
Date Fri Mar 29 03:17:22 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/043276.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/043276hhsearch_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 2.1E-83 4.6E-88 669.6 43.1 670 8-711 138-846 (897)
2 KOG4440 NMDA selective glutama 100.0 9.2E-75 2E-79 607.3 31.2 644 1-712 149-859 (993)
3 KOG1053 Glutamate-gated NMDA-t 100.0 2E-71 4.4E-76 602.9 49.6 634 2-704 154-850 (1258)
4 KOG1052 Glutamate-gated kainat 100.0 4.9E-68 1.1E-72 628.6 57.7 599 69-710 4-624 (656)
5 cd06390 PBP1_iGluR_AMPA_GluR1 100.0 2E-35 4.3E-40 323.0 27.7 256 8-271 104-363 (364)
6 cd06387 PBP1_iGluR_AMPA_GluR3 100.0 8.1E-34 1.8E-38 309.4 27.6 257 8-271 111-371 (372)
7 cd06365 PBP1_Pheromone_recepto 100.0 1.2E-33 2.7E-38 320.8 27.3 272 1-290 152-469 (469)
8 cd06364 PBP1_CaSR Ligand-bindi 100.0 2.1E-32 4.6E-37 312.6 30.4 276 1-290 167-510 (510)
9 cd06391 PBP1_iGluR_delta_2 N-t 100.0 1E-31 2.2E-36 296.9 27.1 259 5-271 122-398 (400)
10 KOG1056 Glutamate-gated metabo 100.0 5.1E-32 1.1E-36 307.5 23.8 291 1-314 174-510 (878)
11 cd06392 PBP1_iGluR_delta_1 N-t 100.0 1.6E-31 3.5E-36 292.3 25.8 252 6-271 123-398 (400)
12 cd06376 PBP1_mGluR_groupIII Li 100.0 3E-31 6.4E-36 302.1 28.6 256 1-267 152-452 (463)
13 cd06375 PBP1_mGluR_groupII Lig 100.0 3.4E-31 7.4E-36 299.6 28.0 254 1-267 154-454 (458)
14 cd06374 PBP1_mGluR_groupI Liga 100.0 5.5E-31 1.2E-35 300.4 27.1 256 1-267 166-464 (472)
15 cd06379 PBP1_iGluR_NMDA_NR1 N- 100.0 1.1E-30 2.4E-35 290.1 27.2 237 1-292 134-377 (377)
16 cd06361 PBP1_GPC6A_like Ligand 100.0 6.2E-30 1.3E-34 284.5 27.4 234 1-270 152-396 (403)
17 cd06367 PBP1_iGluR_NMDA N-term 100.0 4.2E-30 9.1E-35 284.1 25.9 240 1-291 116-362 (362)
18 cd06362 PBP1_mGluR Ligand bind 100.0 8.2E-30 1.8E-34 290.2 27.6 259 1-270 152-449 (452)
19 cd06388 PBP1_iGluR_AMPA_GluR4 100.0 5.8E-29 1.3E-33 273.3 27.2 255 8-271 111-369 (371)
20 cd06389 PBP1_iGluR_AMPA_GluR2 100.0 1.5E-28 3.2E-33 270.7 27.4 257 8-271 105-368 (370)
21 cd06378 PBP1_iGluR_NMDA_NR2 N- 100.0 6.7E-29 1.4E-33 271.1 23.5 242 1-292 115-362 (362)
22 cd06393 PBP1_iGluR_Kainate_Glu 100.0 6.7E-28 1.5E-32 268.0 26.7 255 2-272 120-382 (384)
23 cd06380 PBP1_iGluR_AMPA N-term 100.0 6.1E-27 1.3E-31 260.8 27.9 259 9-271 114-381 (382)
24 cd06386 PBP1_NPR_C_like Ligand 100.0 1.2E-26 2.6E-31 258.0 26.5 243 1-268 117-379 (387)
25 cd06363 PBP1_Taste_receptor Li 99.9 3.8E-25 8.3E-30 248.2 27.0 248 1-291 156-410 (410)
26 PF01094 ANF_receptor: Recepto 99.9 3.7E-25 7.9E-30 243.3 25.3 244 1-256 101-348 (348)
27 cd06385 PBP1_NPR_A Ligand-bind 99.9 9.2E-25 2E-29 245.1 27.2 244 1-269 123-392 (405)
28 cd06370 PBP1_Speract_GC_like L 99.9 2.4E-24 5.3E-29 241.2 23.6 235 1-256 116-382 (404)
29 cd06372 PBP1_GC_G_like Ligand- 99.9 8.2E-24 1.8E-28 236.3 24.7 246 1-268 117-386 (391)
30 cd06371 PBP1_sensory_GC_DEF_li 99.9 2.2E-23 4.7E-28 231.3 25.9 232 9-265 120-369 (382)
31 cd06384 PBP1_NPR_B Ligand-bind 99.9 3.3E-23 7.1E-28 231.8 25.6 246 1-268 123-392 (399)
32 cd06373 PBP1_NPR_like Ligand b 99.9 2.3E-23 5E-28 233.1 24.2 247 1-268 122-389 (396)
33 cd06352 PBP1_NPR_GC_like Ligan 99.9 5.6E-23 1.2E-27 229.7 25.8 250 1-270 117-384 (389)
34 cd06394 PBP1_iGluR_Kainate_KA1 99.9 3.9E-24 8.4E-29 229.9 15.3 214 2-272 115-332 (333)
35 cd06366 PBP1_GABAb_receptor Li 99.9 2.9E-23 6.3E-28 228.5 22.6 226 1-272 115-347 (350)
36 cd06381 PBP1_iGluR_delta_like 99.9 1.1E-22 2.3E-27 222.7 23.4 222 6-271 123-362 (363)
37 PRK10797 glutamate and asparta 99.9 2.7E-21 5.9E-26 206.6 23.1 224 306-659 38-272 (302)
38 PRK09495 glnH glutamine ABC tr 99.9 2.8E-21 6.1E-26 201.6 22.5 220 307-659 24-244 (247)
39 cd06382 PBP1_iGluR_Kainate N-t 99.9 1.2E-21 2.5E-26 213.6 20.3 213 1-271 109-326 (327)
40 cd06383 PBP1_iGluR_AMPA_Like N 99.9 1.1E-21 2.4E-26 215.1 16.6 239 1-255 113-358 (368)
41 PRK11260 cystine transporter s 99.9 1.6E-20 3.5E-25 198.0 22.2 225 305-660 38-263 (266)
42 cd06377 PBP1_iGluR_NMDA_NR3 N- 99.9 5.9E-20 1.3E-24 197.7 25.2 233 2-291 132-382 (382)
43 cd06368 PBP1_iGluR_non_NMDA_li 99.9 1.4E-20 3.1E-25 204.9 19.8 214 2-271 108-323 (324)
44 PF00497 SBP_bac_3: Bacterial 99.9 7.5E-21 1.6E-25 195.0 16.5 223 310-659 1-225 (225)
45 PRK11917 bifunctional adhesin/ 99.8 1.2E-19 2.6E-24 190.0 22.5 219 305-657 35-258 (259)
46 PRK15007 putative ABC transpor 99.8 1.2E-19 2.5E-24 189.0 22.0 217 307-658 20-242 (243)
47 PRK15010 ABC transporter lysin 99.8 2.7E-19 5.8E-24 188.1 22.1 222 306-658 24-254 (260)
48 TIGR02995 ectoine_ehuB ectoine 99.8 1.8E-19 3.9E-24 190.9 20.4 226 304-657 29-260 (275)
49 TIGR01096 3A0103s03R lysine-ar 99.8 3.6E-19 7.8E-24 186.2 21.4 218 308-657 24-250 (250)
50 PRK15437 histidine ABC transpo 99.8 1.7E-18 3.7E-23 181.9 21.9 222 307-659 25-255 (259)
51 cd06342 PBP1_ABC_LIVBP_like Ty 99.8 2.9E-18 6.3E-23 187.5 21.1 217 1-255 114-334 (334)
52 PRK09959 hybrid sensory histid 99.8 9.9E-18 2.1E-22 213.8 25.9 217 307-658 301-520 (1197)
53 cd06350 PBP1_GPCR_family_C_lik 99.8 3.8E-18 8.2E-23 187.7 19.1 195 1-268 140-340 (348)
54 PRK10859 membrane-bound lytic 99.8 6.4E-18 1.4E-22 192.2 19.1 222 305-659 40-267 (482)
55 cd06351 PBP1_iGluR_N_LIVBP_lik 99.8 1.8E-17 3.8E-22 180.7 19.3 207 1-267 112-322 (328)
56 PF00060 Lig_chan: Ligand-gate 99.7 5.5E-19 1.2E-23 168.8 2.9 107 436-542 1-115 (148)
57 TIGR03870 ABC_MoxJ methanol ox 99.7 6.9E-17 1.5E-21 168.1 17.5 210 309-656 1-241 (246)
58 cd06338 PBP1_ABC_ligand_bindin 99.7 2.2E-16 4.7E-21 173.6 20.4 217 1-255 119-345 (345)
59 PRK15404 leucine ABC transport 99.7 3.1E-16 6.7E-21 173.2 20.9 220 1-258 140-363 (369)
60 COG0834 HisJ ABC-type amino ac 99.7 6.4E-16 1.4E-20 163.9 21.0 226 306-659 32-265 (275)
61 cd06346 PBP1_ABC_ligand_bindin 99.7 2.2E-16 4.8E-21 170.8 17.6 194 1-253 117-311 (312)
62 cd06345 PBP1_ABC_ligand_bindin 99.7 4.4E-16 9.5E-21 171.0 19.8 209 1-246 119-337 (344)
63 TIGR02285 conserved hypothetic 99.7 3.3E-16 7.2E-21 165.3 16.3 230 307-659 17-262 (268)
64 KOG1055 GABA-B ion channel rec 99.7 6.3E-17 1.4E-21 178.8 9.2 255 1-270 161-432 (865)
65 cd06348 PBP1_ABC_ligand_bindin 99.7 1.7E-15 3.6E-20 166.5 20.3 220 3-250 116-341 (344)
66 TIGR03871 ABC_peri_MoxJ_2 quin 99.7 1.6E-15 3.4E-20 156.7 18.8 212 309-657 1-228 (232)
67 PRK09959 hybrid sensory histid 99.7 8.4E-16 1.8E-20 196.2 19.1 222 306-659 54-278 (1197)
68 cd00134 PBPb Bacterial peripla 99.7 8E-15 1.7E-19 148.4 21.4 214 310-657 1-218 (218)
69 cd06347 PBP1_ABC_ligand_bindin 99.7 4.8E-15 1E-19 162.0 20.4 209 2-248 115-329 (334)
70 cd06360 PBP1_alkylbenzenes_lik 99.6 1.1E-14 2.4E-19 159.4 21.0 215 2-250 115-332 (336)
71 smart00062 PBPb Bacterial peri 99.6 1.1E-14 2.4E-19 147.2 19.4 216 309-657 1-219 (219)
72 cd06340 PBP1_ABC_ligand_bindin 99.6 9.3E-15 2E-19 160.6 19.0 211 1-247 118-341 (347)
73 cd06355 PBP1_FmdD_like Peripla 99.6 5E-14 1.1E-18 154.8 22.4 222 2-258 113-340 (348)
74 cd06344 PBP1_ABC_ligand_bindin 99.6 2.3E-14 4.9E-19 156.6 18.4 210 1-248 113-327 (332)
75 cd06330 PBP1_Arsenic_SBP_like 99.6 2.3E-14 4.9E-19 157.6 17.8 209 1-242 116-332 (346)
76 cd06329 PBP1_SBP_like_3 Peripl 99.6 5E-14 1.1E-18 154.5 20.1 207 1-245 122-335 (342)
77 cd06336 PBP1_ABC_ligand_bindin 99.6 3E-14 6.5E-19 156.6 18.3 214 1-250 118-344 (347)
78 cd06369 PBP1_GC_C_enterotoxin_ 99.6 1.1E-13 2.5E-18 145.3 21.3 226 2-270 128-367 (380)
79 cd06269 PBP1_glutamate_recepto 99.6 1.5E-14 3.3E-19 154.8 15.1 116 1-119 120-235 (298)
80 cd06331 PBP1_AmiC_like Type I 99.6 9E-14 2E-18 151.9 19.8 209 2-244 113-324 (333)
81 cd06327 PBP1_SBP_like_1 Peripl 99.6 9E-14 2E-18 152.0 19.6 211 1-248 115-330 (334)
82 PF13458 Peripla_BP_6: Peripla 99.6 2.7E-13 5.8E-18 148.8 23.1 221 2-258 115-342 (343)
83 cd06332 PBP1_aromatic_compound 99.6 1.9E-13 4.1E-18 149.4 20.1 210 2-248 115-327 (333)
84 cd06359 PBP1_Nba_like Type I p 99.6 2.2E-13 4.7E-18 148.9 20.5 214 2-253 115-331 (333)
85 TIGR03407 urea_ABC_UrtA urea A 99.5 7.6E-13 1.7E-17 146.0 24.3 211 1-245 113-328 (359)
86 TIGR03669 urea_ABC_arch urea A 99.5 6.1E-13 1.3E-17 146.9 23.1 229 1-266 113-349 (374)
87 cd06349 PBP1_ABC_ligand_bindin 99.5 4.3E-13 9.3E-18 147.0 21.1 217 1-256 114-336 (340)
88 cd06343 PBP1_ABC_ligand_bindin 99.5 6.2E-13 1.3E-17 147.2 22.3 221 2-256 124-358 (362)
89 cd06357 PBP1_AmiC Periplasmic 99.5 1.3E-12 2.8E-17 144.2 23.6 221 3-255 114-337 (360)
90 cd06358 PBP1_NHase Type I peri 99.5 4.9E-13 1.1E-17 146.1 19.9 209 2-245 112-325 (333)
91 COG0683 LivK ABC-type branched 99.5 6.4E-13 1.4E-17 146.6 20.5 221 1-256 127-353 (366)
92 cd06328 PBP1_SBP_like_2 Peripl 99.5 1.7E-12 3.6E-17 141.8 20.4 210 2-250 118-331 (333)
93 cd06335 PBP1_ABC_ligand_bindin 99.4 3.6E-12 7.8E-17 140.1 20.1 206 1-238 117-328 (347)
94 cd06356 PBP1_Amide_Urea_BP_lik 99.4 8.6E-12 1.9E-16 136.2 19.6 210 2-246 113-328 (334)
95 cd06339 PBP1_YraM_LppC_lipopro 99.4 5.7E-12 1.2E-16 137.7 15.7 201 2-246 105-330 (336)
96 cd06334 PBP1_ABC_ligand_bindin 99.4 2.4E-11 5.2E-16 133.4 18.7 222 1-241 115-343 (351)
97 cd06337 PBP1_ABC_ligand_bindin 99.3 1.8E-11 3.8E-16 135.1 17.0 203 3-241 126-340 (357)
98 smart00079 PBPe Eukaryotic hom 99.3 1.4E-11 3.1E-16 115.2 12.1 122 531-658 1-133 (134)
99 COG4623 Predicted soluble lyti 99.3 2.5E-11 5.4E-16 124.3 14.3 223 305-660 20-249 (473)
100 cd04509 PBP1_ABC_transporter_G 99.2 6.1E-11 1.3E-15 126.8 13.0 174 1-183 116-290 (299)
101 cd06326 PBP1_STKc_like Type I 99.2 3.8E-10 8.2E-15 123.5 19.1 207 2-244 117-328 (336)
102 PF13433 Peripla_BP_5: Peripla 99.2 1.8E-09 3.9E-14 114.4 19.4 201 7-241 119-322 (363)
103 TIGR03863 PQQ_ABC_bind ABC tra 99.1 1.7E-09 3.6E-14 117.9 15.5 194 1-248 108-309 (347)
104 cd06341 PBP1_ABC_ligand_bindin 99.1 4.4E-09 9.4E-14 115.4 18.7 203 2-238 113-320 (341)
105 cd06333 PBP1_ABC-type_HAAT_lik 99.1 2.9E-09 6.3E-14 115.2 16.0 170 2-185 114-293 (312)
106 cd06268 PBP1_ABC_transporter_L 99.0 8.3E-09 1.8E-13 110.2 15.8 169 2-185 115-287 (298)
107 TIGR01098 3A0109s03R phosphate 98.9 2.5E-08 5.4E-13 104.4 14.7 199 307-643 31-254 (254)
108 PF10613 Lig_chan-Glu_bd: Liga 98.8 7.1E-10 1.5E-14 86.7 0.8 61 322-383 1-65 (65)
109 PRK00489 hisG ATP phosphoribos 98.8 3.1E-08 6.7E-13 105.0 12.6 164 373-659 52-220 (287)
110 TIGR03431 PhnD phosphonate ABC 98.1 6.7E-05 1.4E-09 80.1 16.5 115 532-652 127-258 (288)
111 cd01391 Periplasmic_Binding_Pr 97.7 0.00028 6.1E-09 73.3 12.6 116 2-119 105-222 (269)
112 PRK11553 alkanesulfonate trans 97.5 0.0016 3.4E-08 70.5 13.7 69 532-606 121-194 (314)
113 PF12974 Phosphonate-bd: ABC t 97.3 0.003 6.5E-08 65.5 12.4 119 532-656 97-230 (243)
114 TIGR01729 taurine_ABC_bnd taur 96.3 0.026 5.7E-07 60.5 11.2 68 532-605 92-164 (300)
115 PF13379 NMT1_2: NMT1-like fam 96.3 0.016 3.5E-07 60.4 8.8 71 532-607 106-189 (252)
116 TIGR03427 ABC_peri_uca ABC tra 96.2 0.033 7E-07 60.2 11.0 67 532-605 98-170 (328)
117 PF03466 LysR_substrate: LysR 96.0 0.08 1.7E-06 52.5 12.3 180 340-644 20-205 (209)
118 PF04348 LppC: LppC putative l 95.9 0.083 1.8E-06 61.0 12.8 128 4-140 328-457 (536)
119 COG3221 PhnD ABC-type phosphat 95.8 0.2 4.4E-06 53.0 14.4 110 530-645 134-260 (299)
120 TIGR02122 TRAP_TAXI TRAP trans 95.7 0.057 1.2E-06 58.4 10.2 58 532-595 133-197 (320)
121 cd05466 PBP2_LTTR_substrate Th 95.6 0.62 1.3E-05 44.8 16.6 69 339-421 13-81 (197)
122 PF09084 NMT1: NMT1/THI5 like; 95.5 0.088 1.9E-06 53.3 10.4 56 532-593 85-145 (216)
123 cd08459 PBP2_DntR_NahR_LinR_li 95.4 0.54 1.2E-05 46.1 15.4 69 339-421 13-81 (201)
124 TIGR01728 SsuA_fam ABC transpo 95.3 0.25 5.4E-06 52.3 13.2 68 532-605 93-165 (288)
125 PF07885 Ion_trans_2: Ion chan 95.3 0.16 3.5E-06 42.2 9.2 56 469-524 21-78 (79)
126 cd08442 PBP2_YofA_SoxR_like Th 95.2 1.4 2.9E-05 42.7 17.6 70 338-421 12-81 (193)
127 cd08468 PBP2_Pa0477 The C-term 95.0 1.3 2.8E-05 43.6 16.9 72 339-421 13-84 (202)
128 cd08418 PBP2_TdcA The C-termin 94.9 1.5 3.2E-05 42.7 16.9 72 338-421 12-83 (201)
129 cd08463 PBP2_DntR_like_4 The C 94.9 1.7 3.6E-05 43.0 17.2 72 338-422 12-83 (203)
130 cd08438 PBP2_CidR The C-termin 94.7 2.2 4.8E-05 41.3 17.4 69 339-421 13-81 (197)
131 cd08421 PBP2_LTTR_like_1 The C 94.4 2.8 6.2E-05 40.6 17.5 69 339-421 13-81 (198)
132 cd08440 PBP2_LTTR_like_4 TThe 94.4 3.4 7.4E-05 39.8 18.0 70 338-421 12-81 (197)
133 PRK11480 tauA taurine transpor 94.2 0.29 6.3E-06 52.9 10.5 66 532-603 114-184 (320)
134 cd08433 PBP2_Nac The C-teminal 94.2 4 8.6E-05 39.6 18.1 69 339-421 13-81 (198)
135 cd08412 PBP2_PAO1_like The C-t 94.2 2.9 6.3E-05 40.5 17.0 70 338-421 12-81 (198)
136 cd08461 PBP2_DntR_like_3 The C 94.1 2.4 5.2E-05 41.2 16.2 69 339-421 13-81 (198)
137 PRK11151 DNA-binding transcrip 94.0 2.4 5.1E-05 45.4 17.1 69 339-421 104-172 (305)
138 cd08466 PBP2_LeuO The C-termin 94.0 1.9 4.1E-05 42.0 15.2 69 339-421 13-81 (200)
139 PRK12679 cbl transcriptional r 94.0 3.2 6.9E-05 44.7 18.0 209 307-658 92-306 (316)
140 cd08411 PBP2_OxyR The C-termin 93.9 2.8 6E-05 40.8 16.3 69 339-421 14-82 (200)
141 cd08415 PBP2_LysR_opines_like 93.8 3.7 7.9E-05 39.7 16.8 70 338-421 12-81 (196)
142 TIGR00363 lipoprotein, YaeC fa 93.8 2.2 4.7E-05 44.4 15.4 120 531-656 107-250 (258)
143 PRK12684 transcriptional regul 93.7 2.8 6.1E-05 45.1 17.0 207 307-657 92-304 (313)
144 PRK11233 nitrogen assimilation 93.6 2.9 6.2E-05 44.8 16.9 69 339-421 105-173 (305)
145 CHL00180 rbcR LysR transcripti 93.6 4 8.6E-05 43.7 18.0 87 307-422 94-180 (305)
146 cd08426 PBP2_LTTR_like_5 The C 93.6 4.7 0.0001 39.1 17.3 69 339-421 13-81 (199)
147 cd08434 PBP2_GltC_like The sub 93.4 4.4 9.6E-05 38.9 16.6 69 339-421 13-81 (195)
148 cd08417 PBP2_Nitroaromatics_li 93.4 3.6 7.7E-05 40.0 16.0 69 339-421 13-81 (200)
149 PRK11242 DNA-binding transcrip 93.3 3.5 7.5E-05 43.8 16.8 69 339-421 104-172 (296)
150 cd08441 PBP2_MetR The C-termin 93.0 5.6 0.00012 38.6 16.8 68 340-421 14-81 (198)
151 cd08435 PBP2_GbpR The C-termin 92.8 7.1 0.00015 37.7 17.1 71 339-421 13-83 (201)
152 PRK09791 putative DNA-binding 92.7 3.4 7.3E-05 44.1 15.7 85 307-421 94-178 (302)
153 cd08464 PBP2_DntR_like_2 The C 92.7 4.9 0.00011 39.0 15.8 69 339-421 13-81 (200)
154 cd08419 PBP2_CbbR_RubisCO_like 92.6 9.4 0.0002 36.7 17.8 69 339-421 12-80 (197)
155 cd08420 PBP2_CysL_like C-termi 92.6 8.2 0.00018 37.1 17.2 70 338-421 12-81 (201)
156 cd08460 PBP2_DntR_like_1 The C 92.5 4.4 9.4E-05 39.6 15.3 69 338-421 12-80 (200)
157 cd08462 PBP2_NodD The C-termin 92.3 6.1 0.00013 38.6 16.0 67 340-421 14-80 (200)
158 cd08465 PBP2_ToxR The C-termin 92.2 2.7 5.9E-05 41.2 13.3 69 339-421 13-81 (200)
159 TIGR02424 TF_pcaQ pca operon t 92.1 6 0.00013 42.1 16.7 85 307-421 92-176 (300)
160 PRK12682 transcriptional regul 92.0 6.9 0.00015 41.9 17.1 84 307-421 92-175 (309)
161 cd08425 PBP2_CynR The C-termin 92.0 6.7 0.00014 37.9 15.7 69 339-421 14-82 (197)
162 cd08457 PBP2_OccR The C-termin 91.9 12 0.00025 36.2 17.4 70 338-421 12-81 (196)
163 PRK10341 DNA-binding transcrip 91.9 6.1 0.00013 42.4 16.5 70 340-421 111-180 (312)
164 cd08413 PBP2_CysB_like The C-t 91.9 6.5 0.00014 38.3 15.6 71 338-421 12-82 (198)
165 cd08429 PBP2_NhaR The C-termin 91.8 12 0.00025 37.0 17.4 71 339-420 13-83 (204)
166 PRK12683 transcriptional regul 91.8 6.8 0.00015 42.0 16.6 197 307-646 92-294 (309)
167 PRK12680 transcriptional regul 91.8 6.5 0.00014 42.6 16.5 84 307-421 92-175 (327)
168 cd08430 PBP2_IlvY The C-termin 91.6 11 0.00025 36.2 17.0 71 338-421 12-82 (199)
169 cd08436 PBP2_LTTR_like_3 The C 91.6 12 0.00026 35.8 17.1 70 339-421 13-82 (194)
170 TIGR00787 dctP tripartite ATP- 91.6 0.39 8.5E-06 50.1 6.6 104 530-645 126-232 (257)
171 cd08458 PBP2_NocR The C-termin 91.5 9.9 0.00021 36.9 16.4 69 339-421 13-81 (196)
172 PRK11482 putative DNA-binding 91.5 7.3 0.00016 42.0 16.5 81 307-421 116-196 (317)
173 cd08456 PBP2_LysR The C-termin 91.5 7.5 0.00016 37.5 15.4 70 338-421 12-81 (196)
174 cd08444 PBP2_Cbl The C-termina 91.4 13 0.00029 36.1 17.2 71 338-421 12-82 (198)
175 cd08443 PBP2_CysB The C-termin 91.3 12 0.00026 36.5 16.7 71 338-421 12-82 (198)
176 PRK10837 putative DNA-binding 91.1 13 0.00028 39.2 17.9 83 307-421 88-170 (290)
177 cd01536 PBP1_ABC_sugar_binding 91.1 2.3 5.1E-05 43.9 12.0 100 3-104 101-206 (267)
178 PRK12681 cysB transcriptional 91.0 5.9 0.00013 42.9 15.2 84 307-421 92-175 (324)
179 cd01537 PBP1_Repressors_Sugar_ 90.7 1.8 3.9E-05 44.6 10.6 107 3-112 100-211 (264)
180 cd08427 PBP2_LTTR_like_2 The C 90.6 14 0.0003 35.4 16.4 71 339-421 13-83 (195)
181 cd08451 PBP2_BudR The C-termin 90.5 17 0.00037 35.0 18.5 69 340-421 15-83 (199)
182 cd08437 PBP2_MleR The substrat 90.5 12 0.00027 36.1 16.0 71 339-421 13-83 (198)
183 PRK11063 metQ DL-methionine tr 90.3 8.2 0.00018 40.5 14.9 118 531-655 120-262 (271)
184 cd08469 PBP2_PnbR The C-termin 90.2 13 0.00028 36.8 16.2 69 339-421 13-81 (221)
185 cd08467 PBP2_SyrM The C-termin 90.1 18 0.00039 35.1 16.9 69 339-421 13-81 (200)
186 cd08416 PBP2_MdcR The C-termin 90.1 15 0.00032 35.4 16.2 72 338-421 12-83 (199)
187 cd08449 PBP2_XapR The C-termin 89.9 16 0.00035 35.0 16.3 71 339-421 13-83 (197)
188 cd08446 PBP2_Chlorocatechol Th 89.8 16 0.00035 35.2 16.3 69 339-421 14-82 (198)
189 PRK11013 DNA-binding transcrip 89.8 11 0.00025 40.2 16.2 69 339-421 107-175 (309)
190 PRK09508 leuO leucine transcri 89.7 7.3 0.00016 41.8 14.6 69 339-421 125-193 (314)
191 cd06267 PBP1_LacI_sugar_bindin 89.2 3.1 6.8E-05 42.8 11.0 109 4-113 99-211 (264)
192 PRK15421 DNA-binding transcrip 89.1 16 0.00036 39.2 16.8 68 340-421 103-170 (317)
193 PF12727 PBP_like: PBP superfa 89.0 11 0.00023 37.4 13.9 101 531-642 82-191 (193)
194 cd08445 PBP2_BenM_CatM_CatR Th 88.7 21 0.00046 34.6 16.2 70 338-421 13-82 (203)
195 cd06282 PBP1_GntR_like_2 Ligan 88.6 3.4 7.4E-05 42.8 10.8 107 3-112 98-209 (266)
196 cd08486 PBP2_CbnR The C-termin 88.3 9.7 0.00021 37.1 13.4 69 339-421 14-82 (198)
197 cd06273 PBP1_GntR_like_1 This 88.2 4 8.7E-05 42.4 11.0 107 4-111 99-210 (268)
198 cd08414 PBP2_LTTR_aromatics_li 88.2 25 0.00054 33.6 17.2 69 339-421 13-81 (197)
199 PRK11062 nhaR transcriptional 87.9 23 0.0005 37.6 16.8 85 307-420 92-176 (296)
200 cd08450 PBP2_HcaR The C-termin 87.9 22 0.00047 34.1 15.5 69 339-421 13-81 (196)
201 COG1910 Periplasmic molybdate- 87.5 13 0.00028 36.8 12.7 104 532-647 89-201 (223)
202 cd08448 PBP2_LTTR_aromatics_li 87.1 29 0.00062 33.2 17.3 69 339-421 13-81 (197)
203 PF13531 SBP_bac_11: Bacterial 86.7 8.3 0.00018 39.2 12.0 193 338-654 10-225 (230)
204 cd08423 PBP2_LTTR_like_6 The C 86.0 33 0.00072 32.8 16.2 72 339-421 13-86 (200)
205 TIGR01256 modA molybdenum ABC 85.5 23 0.0005 35.5 14.4 70 569-644 134-204 (216)
206 TIGR02990 ectoine_eutA ectoine 85.4 7.9 0.00017 39.7 10.8 90 8-100 107-203 (239)
207 PF03480 SBP_bac_7: Bacterial 85.1 7.2 0.00016 41.3 11.0 102 530-643 126-230 (286)
208 PRK11074 putative DNA-binding 85.1 32 0.0007 36.5 16.1 85 307-421 91-175 (300)
209 PRK11716 DNA-binding transcrip 84.7 25 0.00054 36.4 14.8 70 339-421 80-149 (269)
210 cd08453 PBP2_IlvR The C-termin 84.2 41 0.00089 32.4 16.5 72 339-421 13-84 (200)
211 cd08485 PBP2_ClcR The C-termin 84.1 42 0.00092 32.4 16.3 69 339-421 14-82 (198)
212 PF13377 Peripla_BP_3: Peripla 83.6 5.6 0.00012 37.6 8.5 99 13-113 1-102 (160)
213 PRK09860 putative alcohol dehy 83.6 5.2 0.00011 44.4 9.3 79 10-88 20-98 (383)
214 TIGR03339 phn_lysR aminoethylp 83.2 61 0.0013 33.6 17.9 68 340-421 98-165 (279)
215 cd06298 PBP1_CcpA_like Ligand- 83.1 9.7 0.00021 39.4 10.8 110 4-114 99-213 (268)
216 PRK09906 DNA-binding transcrip 82.5 52 0.0011 34.7 16.4 69 339-421 103-171 (296)
217 cd06288 PBP1_sucrose_transcrip 82.4 8.9 0.00019 39.7 10.2 110 3-113 98-211 (269)
218 cd01545 PBP1_SalR Ligand-bindi 81.3 14 0.0003 38.2 11.3 103 6-109 103-209 (270)
219 COG0725 ModA ABC-type molybdat 80.9 44 0.00095 34.7 14.3 114 533-656 125-252 (258)
220 COG0715 TauA ABC-type nitrate/ 80.8 7.1 0.00015 42.3 9.1 71 531-607 127-203 (335)
221 COG1638 DctP TRAP-type C4-dica 80.6 24 0.00051 38.3 12.7 103 531-647 158-265 (332)
222 PRK15454 ethanol dehydrogenase 80.6 8.2 0.00018 43.0 9.5 79 10-88 38-116 (395)
223 PF14503 YhfZ_C: YhfZ C-termin 80.6 2.4 5.3E-05 42.7 4.7 105 541-657 113-224 (232)
224 TIGR01481 ccpA catabolite cont 80.0 17 0.00037 39.1 11.7 102 7-109 162-266 (329)
225 cd06271 PBP1_AglR_RafR_like Li 80.0 16 0.00034 37.8 11.1 108 4-112 103-214 (268)
226 cd08192 Fe-ADH7 Iron-containin 79.9 8.4 0.00018 42.6 9.3 87 10-96 13-101 (370)
227 cd08190 HOT Hydroxyacid-oxoaci 79.9 8.3 0.00018 43.3 9.3 79 10-88 12-90 (414)
228 PF00465 Fe-ADH: Iron-containi 79.9 5.9 0.00013 43.7 8.1 89 10-100 12-102 (366)
229 cd06284 PBP1_LacI_like_6 Ligan 78.8 16 0.00034 37.7 10.7 104 4-108 98-205 (267)
230 cd06310 PBP1_ABC_sugar_binding 78.5 33 0.00071 35.5 13.0 103 7-112 107-215 (273)
231 PRK10423 transcriptional repre 78.4 20 0.00043 38.5 11.6 105 9-113 162-269 (327)
232 PRK10624 L-1,2-propanediol oxi 78.3 10 0.00022 42.0 9.4 79 10-88 19-97 (382)
233 COG1454 EutG Alcohol dehydroge 78.2 11 0.00024 41.2 9.2 89 10-98 18-108 (377)
234 cd06325 PBP1_ABC_uncharacteriz 78.2 11 0.00023 39.4 9.2 93 5-103 113-208 (281)
235 PF00532 Peripla_BP_1: Peripla 77.9 46 0.001 35.0 13.9 111 8-118 105-220 (279)
236 cd06320 PBP1_allose_binding Pe 77.6 29 0.00064 36.0 12.4 98 4-103 103-206 (275)
237 cd08193 HVD 5-hydroxyvalerate 77.5 11 0.00024 41.7 9.3 87 10-96 15-103 (376)
238 PRK10727 DNA-binding transcrip 77.4 18 0.00038 39.3 10.9 108 5-112 160-270 (343)
239 cd06295 PBP1_CelR Ligand bindi 77.3 16 0.00036 37.9 10.3 109 4-113 108-220 (275)
240 cd08551 Fe-ADH iron-containing 77.1 12 0.00027 41.2 9.6 88 10-97 12-101 (370)
241 cd08447 PBP2_LTTR_aromatics_li 76.4 73 0.0016 30.4 16.1 69 338-420 12-80 (198)
242 cd06319 PBP1_ABC_sugar_binding 76.2 26 0.00057 36.3 11.5 101 9-112 107-216 (277)
243 cd06293 PBP1_LacI_like_11 Liga 76.2 29 0.00063 35.9 11.8 109 3-112 98-210 (269)
244 cd06272 PBP1_hexuronate_repres 75.3 19 0.00042 37.0 10.1 109 4-112 94-205 (261)
245 PRK10014 DNA-binding transcrip 75.3 29 0.00062 37.6 11.9 103 4-106 165-270 (342)
246 cd06297 PBP1_LacI_like_12 Liga 75.3 23 0.0005 36.8 10.7 109 4-113 97-214 (269)
247 PRK11041 DNA-binding transcrip 75.2 22 0.00049 37.7 10.8 108 5-113 136-247 (309)
248 cd06285 PBP1_LacI_like_7 Ligan 75.2 25 0.00054 36.3 10.9 105 5-109 98-205 (265)
249 cd01575 PBP1_GntR Ligand-bindi 74.8 30 0.00064 35.6 11.4 108 4-112 99-210 (268)
250 cd08452 PBP2_AlsR The C-termin 74.7 82 0.0018 30.2 16.6 69 339-421 13-81 (197)
251 cd06286 PBP1_CcpB_like Ligand- 74.7 25 0.00054 36.2 10.7 108 4-112 97-208 (260)
252 cd08189 Fe-ADH5 Iron-containin 74.7 14 0.00031 40.8 9.2 87 10-96 15-103 (374)
253 PLN02245 ATP phosphoribosyl tr 74.6 18 0.00039 39.7 9.5 103 532-643 179-294 (403)
254 PRK10401 DNA-binding transcrip 74.6 30 0.00065 37.6 11.8 103 9-112 164-270 (346)
255 cd06300 PBP1_ABC_sugar_binding 74.4 19 0.00042 37.3 9.9 98 3-103 105-208 (272)
256 cd08194 Fe-ADH6 Iron-containin 74.3 15 0.00033 40.5 9.4 79 10-88 12-90 (375)
257 PLN03192 Voltage-dependent pot 74.2 8.8 0.00019 47.4 8.2 53 473-525 251-305 (823)
258 TIGR02638 lactal_redase lactal 74.2 15 0.00032 40.8 9.2 79 10-88 18-96 (379)
259 cd06317 PBP1_ABC_sugar_binding 74.2 43 0.00094 34.6 12.5 105 5-112 107-218 (275)
260 PRK09861 cytoplasmic membrane 74.0 91 0.002 32.7 14.5 120 531-656 121-264 (272)
261 cd06270 PBP1_GalS_like Ligand 74.0 36 0.00079 35.1 11.8 108 4-112 99-210 (268)
262 cd06275 PBP1_PurR Ligand-bindi 73.8 26 0.00056 36.2 10.6 108 6-113 102-212 (269)
263 PF13685 Fe-ADH_2: Iron-contai 73.7 26 0.00057 36.1 10.1 100 11-114 9-108 (250)
264 PRK10703 DNA-binding transcrip 73.5 24 0.00051 38.2 10.6 104 8-112 165-272 (341)
265 cd01544 PBP1_GalR Ligand-bindi 73.2 29 0.00063 36.0 10.9 108 4-113 95-213 (270)
266 cd08481 PBP2_GcdR_like The C-t 73.2 48 0.001 31.5 11.8 98 533-639 86-190 (194)
267 PRK03635 chromosome replicatio 73.1 98 0.0021 32.6 15.0 66 341-421 105-170 (294)
268 COG1609 PurR Transcriptional r 72.2 48 0.001 36.0 12.4 103 4-107 158-265 (333)
269 cd06294 PBP1_ycjW_transcriptio 71.3 31 0.00068 35.6 10.6 105 6-110 107-214 (270)
270 PRK09986 DNA-binding transcrip 71.2 1.4E+02 0.003 31.3 18.3 72 339-422 110-181 (294)
271 cd06296 PBP1_CatR_like Ligand- 70.9 27 0.00058 36.1 10.0 109 4-112 100-211 (270)
272 cd08188 Fe-ADH4 Iron-containin 70.9 21 0.00045 39.5 9.4 79 10-88 17-95 (377)
273 cd06290 PBP1_LacI_like_9 Ligan 70.7 37 0.00079 35.0 10.9 104 5-109 99-206 (265)
274 cd08185 Fe-ADH1 Iron-containin 70.5 20 0.00043 39.7 9.2 86 10-96 15-103 (380)
275 cd06292 PBP1_LacI_like_10 Liga 70.3 36 0.00078 35.2 10.8 109 4-113 105-215 (273)
276 cd06283 PBP1_RegR_EndR_KdgR_li 69.8 47 0.001 34.1 11.5 109 5-113 100-212 (267)
277 PRK13348 chromosome replicatio 69.1 1.5E+02 0.0034 31.0 16.2 64 343-421 107-170 (294)
278 cd06323 PBP1_ribose_binding Pe 68.7 43 0.00093 34.4 10.9 96 6-103 104-205 (268)
279 cd08181 PPD-like 1,3-propanedi 68.3 26 0.00056 38.5 9.3 78 10-88 15-93 (357)
280 cd08191 HHD 6-hydroxyhexanoate 68.1 26 0.00057 38.9 9.5 86 10-96 12-99 (386)
281 cd06289 PBP1_MalI_like Ligand- 67.5 41 0.0009 34.5 10.5 104 4-108 100-207 (268)
282 PRK11119 proX glycine betaine 67.3 37 0.00081 36.8 10.1 63 304-395 25-88 (331)
283 cd08431 PBP2_HupR The C-termin 67.0 1.2E+02 0.0026 28.9 14.3 71 338-421 12-82 (195)
284 cd06303 PBP1_LuxPQ_Quorum_Sens 66.8 79 0.0017 32.9 12.6 98 5-104 113-215 (280)
285 cd06291 PBP1_Qymf_like Ligand 65.3 69 0.0015 32.9 11.7 106 6-112 97-206 (265)
286 cd08170 GlyDH Glycerol dehydro 65.2 26 0.00056 38.4 8.6 76 10-88 12-87 (351)
287 cd01574 PBP1_LacI Ligand-bindi 65.2 82 0.0018 32.3 12.2 107 4-113 99-208 (264)
288 cd08176 LPO Lactadehyde:propan 65.1 28 0.0006 38.5 8.9 79 10-88 17-95 (377)
289 PRK09526 lacI lac repressor; R 65.0 78 0.0017 34.1 12.4 106 5-112 165-273 (342)
290 cd06305 PBP1_methylthioribose_ 64.8 65 0.0014 33.2 11.4 101 4-104 101-208 (273)
291 PRK10537 voltage-gated potassi 64.7 28 0.00061 38.6 8.7 56 468-523 164-221 (393)
292 PF03808 Glyco_tran_WecB: Glyc 64.7 1.2E+02 0.0025 29.4 12.1 100 8-117 36-137 (172)
293 cd08187 BDH Butanol dehydrogen 64.2 31 0.00068 38.2 9.1 78 10-88 18-96 (382)
294 PRK10094 DNA-binding transcrip 64.0 2E+02 0.0044 30.5 17.0 69 341-421 108-176 (308)
295 cd01542 PBP1_TreR_like Ligand- 63.9 56 0.0012 33.4 10.6 107 4-113 97-207 (259)
296 cd08428 PBP2_IciA_ArgP The C-t 63.7 1.4E+02 0.003 28.4 15.6 64 341-419 15-78 (195)
297 PRK10677 modA molybdate transp 63.0 1.1E+02 0.0024 31.7 12.5 70 342-422 42-117 (257)
298 PRK11303 DNA-binding transcrip 62.8 95 0.0021 33.2 12.5 106 4-112 162-271 (328)
299 cd06299 PBP1_LacI_like_13 Liga 62.2 60 0.0013 33.3 10.5 104 9-113 104-209 (265)
300 TIGR03298 argP transcriptional 61.9 2.1E+02 0.0045 30.0 16.6 63 343-420 107-169 (292)
301 cd06279 PBP1_LacI_like_3 Ligan 61.8 72 0.0016 33.3 11.1 106 4-109 99-225 (283)
302 PRK11139 DNA-binding transcrip 61.7 2E+02 0.0044 30.2 14.7 101 533-641 181-286 (297)
303 PRK14498 putative molybdopteri 61.7 57 0.0012 38.9 11.3 67 19-88 184-262 (633)
304 PF13407 Peripla_BP_4: Peripla 61.6 20 0.00044 36.8 6.7 78 24-103 1-81 (257)
305 cd06287 PBP1_LacI_like_8 Ligan 61.5 98 0.0021 32.1 11.9 107 6-113 103-212 (269)
306 TIGR02417 fruct_sucro_rep D-fr 61.3 77 0.0017 33.9 11.5 102 7-112 164-270 (327)
307 cd06313 PBP1_ABC_sugar_binding 61.1 1.2E+02 0.0025 31.5 12.5 99 3-103 103-207 (272)
308 PF01634 HisG: ATP phosphoribo 61.0 16 0.00034 35.0 5.1 100 532-643 58-159 (163)
309 KOG3857 Alcohol dehydrogenase, 60.9 38 0.00083 35.9 8.1 77 12-88 61-137 (465)
310 cd08186 Fe-ADH8 Iron-containin 60.8 38 0.00082 37.6 9.0 87 10-96 12-104 (383)
311 cd08182 HEPD Hydroxyethylphosp 60.7 42 0.00091 37.0 9.3 85 10-97 12-98 (367)
312 cd06307 PBP1_uncharacterized_s 60.5 1E+02 0.0022 31.9 11.9 96 7-104 108-210 (275)
313 PRK14987 gluconate operon tran 60.1 77 0.0017 34.0 11.2 108 5-113 164-273 (331)
314 cd06274 PBP1_FruR Ligand bindi 60.1 1.1E+02 0.0023 31.5 11.9 108 5-113 99-212 (264)
315 cd08470 PBP2_CrgA_like_1 The C 59.9 32 0.0007 33.0 7.5 69 568-643 123-193 (197)
316 PF08374 Protocadherin: Protoc 59.8 37 0.0008 33.5 7.3 36 674-709 31-66 (221)
317 cd06280 PBP1_LacI_like_4 Ligan 59.2 84 0.0018 32.3 10.9 104 5-112 99-205 (263)
318 cd06309 PBP1_YtfQ_like Peripla 58.8 1.1E+02 0.0025 31.4 12.0 108 4-114 105-220 (273)
319 KOG1419 Voltage-gated K+ chann 58.5 18 0.0004 40.6 5.6 85 438-522 235-321 (654)
320 cd07766 DHQ_Fe-ADH Dehydroquin 58.5 43 0.00093 36.3 8.8 100 11-115 13-114 (332)
321 cd08171 GlyDH-like2 Glycerol d 58.2 44 0.00096 36.4 8.8 77 10-88 12-88 (345)
322 cd01540 PBP1_arabinose_binding 58.2 1.1E+02 0.0025 31.8 11.9 100 15-114 121-229 (289)
323 PRK13583 hisG ATP phosphoribos 58.0 87 0.0019 31.8 10.0 91 532-631 111-212 (228)
324 cd08422 PBP2_CrgA_like The C-t 57.8 55 0.0012 31.1 8.8 65 338-419 13-77 (197)
325 PRK03601 transcriptional regul 57.7 21 0.00045 37.4 6.0 83 307-421 88-170 (275)
326 cd08478 PBP2_CrgA The C-termin 57.6 49 0.0011 31.8 8.4 65 339-420 16-80 (199)
327 cd08432 PBP2_GcdR_TrpI_HvrB_Am 57.0 1.6E+02 0.0035 27.7 12.1 64 340-420 14-77 (194)
328 cd06301 PBP1_rhizopine_binding 57.0 1.3E+02 0.0029 30.9 12.0 98 4-104 104-208 (272)
329 PRK09423 gldA glycerol dehydro 56.8 48 0.001 36.5 8.9 76 10-88 19-94 (366)
330 PF03401 TctC: Tripartite tric 56.5 1.1E+02 0.0023 32.2 11.1 123 528-655 86-241 (274)
331 cd06324 PBP1_ABC_sugar_binding 56.4 1.1E+02 0.0023 32.5 11.4 106 4-112 117-235 (305)
332 cd01324 cbb3_Oxidase_CcoQ Cyto 56.2 13 0.00028 27.5 2.8 28 438-465 12-39 (48)
333 PRK01686 hisG ATP phosphoribos 55.8 85 0.0018 31.6 9.5 92 541-643 114-207 (215)
334 PRK10339 DNA-binding transcrip 55.4 93 0.002 33.3 10.8 103 8-112 161-267 (327)
335 cd06312 PBP1_ABC_sugar_binding 55.4 1.1E+02 0.0023 31.6 11.0 105 3-112 106-214 (271)
336 cd06322 PBP1_ABC_sugar_binding 54.9 1.6E+02 0.0034 30.2 12.2 100 7-113 105-210 (267)
337 PF12273 RCR: Chitin synthesis 53.5 10 0.00023 34.8 2.5 10 809-818 97-106 (130)
338 cd06305 PBP1_methylthioribose_ 53.4 57 0.0012 33.6 8.6 77 24-103 2-81 (273)
339 COG2358 Imp TRAP-type uncharac 53.1 1E+02 0.0022 33.1 9.9 59 532-596 129-194 (321)
340 cd08479 PBP2_CrgA_like_9 The C 53.0 1.1E+02 0.0024 29.2 10.1 64 339-419 14-77 (198)
341 cd06321 PBP1_ABC_sugar_binding 53.0 1.7E+02 0.0036 30.1 12.0 108 4-115 102-215 (271)
342 TIGR00070 hisG ATP phosphoribo 52.7 67 0.0015 31.3 8.0 74 532-617 101-174 (182)
343 PRK07377 hypothetical protein; 52.4 27 0.00059 33.6 5.0 62 307-391 74-135 (184)
344 COG3107 LppC Putative lipoprot 52.3 1.7E+02 0.0037 33.3 11.7 48 6-53 368-415 (604)
345 cd06308 PBP1_sensor_kinase_lik 52.1 2.2E+02 0.0048 29.2 12.8 108 4-115 103-217 (270)
346 PRK09492 treR trehalose repres 51.8 1.5E+02 0.0033 31.4 11.7 95 5-103 159-256 (315)
347 TIGR03414 ABC_choline_bnd chol 51.7 2.8E+02 0.006 29.4 13.3 42 341-393 23-64 (290)
348 cd01541 PBP1_AraR Ligand-bindi 51.5 1.5E+02 0.0032 30.6 11.3 108 4-112 104-216 (273)
349 PF14981 FAM165: FAM165 family 51.3 24 0.00052 25.3 3.3 33 677-709 3-35 (51)
350 cd08483 PBP2_HvrB The C-termin 51.0 2.2E+02 0.0047 26.8 12.6 63 340-419 14-76 (190)
351 PF06305 DUF1049: Protein of u 50.7 47 0.001 26.3 5.7 27 683-709 24-50 (68)
352 cd08550 GlyDH-like Glycerol_de 50.5 68 0.0015 35.0 8.7 76 10-88 12-87 (349)
353 cd08183 Fe-ADH2 Iron-containin 50.5 74 0.0016 35.1 9.1 82 10-96 12-95 (374)
354 cd08471 PBP2_CrgA_like_2 The C 50.2 1E+02 0.0022 29.4 9.3 64 339-419 14-77 (201)
355 cd01543 PBP1_XylR Ligand-bindi 49.9 1.3E+02 0.0029 30.8 10.7 110 4-114 92-207 (265)
356 cd08472 PBP2_CrgA_like_3 The C 49.7 1.8E+02 0.004 27.6 11.2 64 339-419 14-77 (202)
357 cd06311 PBP1_ABC_sugar_binding 49.7 2.4E+02 0.0051 29.0 12.6 95 6-103 110-209 (274)
358 cd08474 PBP2_CrgA_like_5 The C 49.3 1.3E+02 0.0028 28.8 9.9 64 568-638 132-197 (202)
359 cd08178 AAD_C C-terminal alcoh 48.7 67 0.0014 35.8 8.5 80 17-96 17-98 (398)
360 cd06353 PBP1_BmpA_Med_like Per 48.5 1.2E+02 0.0026 31.5 9.8 85 23-115 1-89 (258)
361 cd06533 Glyco_transf_WecG_TagA 48.5 1.7E+02 0.0037 28.2 10.2 96 10-115 36-133 (171)
362 cd06301 PBP1_rhizopine_binding 47.8 73 0.0016 32.9 8.3 78 23-103 1-82 (272)
363 cd06277 PBP1_LacI_like_1 Ligan 47.7 1.5E+02 0.0033 30.3 10.7 100 8-109 105-207 (268)
364 PF04273 DUF442: Putative phos 47.6 1.7E+02 0.0038 25.9 9.2 81 16-96 23-104 (110)
365 cd03770 SR_TndX_transposase Se 47.4 1.8E+02 0.0038 26.9 9.8 20 6-25 21-40 (140)
366 PRK10653 D-ribose transporter 47.0 2.7E+02 0.0058 29.2 12.6 98 4-103 128-231 (295)
367 TIGR02667 moaB_proteo molybden 46.8 1.2E+02 0.0027 29.0 8.8 67 20-88 3-73 (163)
368 cd06306 PBP1_TorT-like TorT-li 46.5 1.9E+02 0.0041 29.8 11.2 102 5-112 104-214 (268)
369 cd06267 PBP1_LacI_sugar_bindin 46.4 76 0.0016 32.2 8.1 76 24-103 2-79 (264)
370 cd06281 PBP1_LacI_like_5 Ligan 46.1 1.4E+02 0.0031 30.6 10.2 106 5-112 99-209 (269)
371 cd06303 PBP1_LuxPQ_Quorum_Sens 46.0 67 0.0014 33.5 7.7 80 23-102 1-84 (280)
372 cd00338 Ser_Recombinase Serine 45.7 2.1E+02 0.0046 25.8 10.2 27 4-31 15-41 (137)
373 cd00886 MogA_MoaB MogA_MoaB fa 45.7 1.1E+02 0.0023 28.9 8.2 64 23-88 2-71 (152)
374 PRK09801 transcriptional activ 44.4 1.2E+02 0.0027 32.2 9.5 70 568-644 223-293 (310)
375 TIGR00249 sixA phosphohistidin 44.2 1.2E+02 0.0025 28.6 8.2 93 6-99 28-120 (152)
376 TIGR02405 trehalos_R_Ecol treh 43.7 2.6E+02 0.0057 29.5 12.0 95 5-103 156-253 (311)
377 PRK10632 transcriptional regul 43.6 2.5E+02 0.0055 29.7 11.8 78 307-419 91-168 (309)
378 cd06278 PBP1_LacI_like_2 Ligan 43.4 2.1E+02 0.0046 29.1 11.0 96 4-102 98-197 (266)
379 PF15179 Myc_target_1: Myc tar 42.5 35 0.00076 32.6 4.1 38 672-709 13-51 (197)
380 cd01537 PBP1_Repressors_Sugar_ 42.2 74 0.0016 32.3 7.2 76 24-102 2-79 (264)
381 cd06304 PBP1_BmpA_like Peripla 41.8 1.5E+02 0.0032 30.5 9.4 89 13-102 111-202 (260)
382 cd08487 PBP2_BlaA The C-termin 41.8 3E+02 0.0065 25.8 12.9 99 534-640 85-186 (189)
383 COG2984 ABC-type uncharacteriz 41.3 2.3E+02 0.0049 30.3 10.2 94 4-102 140-239 (322)
384 cd08473 PBP2_CrgA_like_4 The C 41.0 2E+02 0.0044 27.2 9.9 66 340-420 17-82 (202)
385 cd03522 MoeA_like MoeA_like. T 40.6 2.7E+02 0.0058 29.9 11.0 68 19-88 157-229 (312)
386 cd00758 MoCF_BD MoCF_BD: molyb 40.4 1.2E+02 0.0027 27.7 7.6 62 24-88 2-68 (133)
387 PRK10086 DNA-binding transcrip 40.4 4E+02 0.0086 28.2 12.7 79 307-420 101-179 (311)
388 KOG0498 K+-channel ERG and rel 40.3 41 0.00088 40.1 5.2 69 473-541 295-370 (727)
389 cd06354 PBP1_BmpA_PnrA_like Pe 40.3 1.7E+02 0.0037 30.2 9.6 89 13-102 112-206 (265)
390 PF05545 FixQ: Cbb3-type cytoc 40.2 30 0.00065 25.6 2.7 26 438-463 11-36 (49)
391 PF01102 Glycophorin_A: Glycop 39.1 46 0.00099 30.1 4.1 27 683-709 67-93 (122)
392 cd08197 DOIS 2-deoxy-scyllo-in 38.9 3.1E+02 0.0067 30.0 11.5 99 11-114 13-119 (355)
393 cd06312 PBP1_ABC_sugar_binding 38.9 1.1E+02 0.0023 31.6 7.9 79 23-103 1-83 (271)
394 PF03180 Lipoprotein_9: NLPA l 38.9 1.3E+02 0.0027 30.9 7.9 101 544-650 2-123 (237)
395 cd08175 G1PDH Glycerol-1-phosp 38.5 1.3E+02 0.0027 32.9 8.5 84 10-95 12-99 (348)
396 cd08177 MAR Maleylacetate redu 38.4 96 0.0021 33.7 7.5 98 10-115 12-111 (337)
397 cd06289 PBP1_MalI_like Ligand- 38.3 1.2E+02 0.0025 31.1 8.0 77 24-103 2-80 (268)
398 cd01538 PBP1_ABC_xylose_bindin 38.1 1.6E+02 0.0034 30.8 9.0 77 24-103 2-81 (288)
399 cd06299 PBP1_LacI_like_13 Liga 37.9 1.9E+02 0.0041 29.5 9.6 76 24-103 2-79 (265)
400 cd06306 PBP1_TorT-like TorT-li 37.7 1.2E+02 0.0026 31.3 8.0 79 24-103 2-82 (268)
401 cd08180 PDD 1,3-propanediol de 37.5 80 0.0017 34.2 6.7 72 16-88 17-88 (332)
402 PRK10936 TMAO reductase system 37.0 3.2E+02 0.007 29.5 11.5 103 5-113 151-262 (343)
403 cd08549 G1PDH_related Glycerol 37.0 1.3E+02 0.0028 32.6 8.3 98 10-114 12-113 (332)
404 PF13380 CoA_binding_2: CoA bi 36.9 49 0.0011 29.6 4.1 87 22-115 1-89 (116)
405 cd00885 cinA Competence-damage 36.9 1.4E+02 0.0031 28.7 7.6 47 37-86 20-66 (170)
406 PRK00002 aroB 3-dehydroquinate 36.8 3.1E+02 0.0066 30.1 11.2 101 10-114 20-127 (358)
407 cd08480 PBP2_CrgA_like_10 The 36.7 2.9E+02 0.0062 26.3 10.2 64 340-420 15-78 (198)
408 cd06277 PBP1_LacI_like_1 Ligan 36.4 1.5E+02 0.0032 30.5 8.4 75 24-103 2-81 (268)
409 PF10777 YlaC: Inner membrane 36.1 90 0.0019 29.0 5.5 23 437-459 36-58 (155)
410 TIGR00854 pts-sorbose PTS syst 36.1 2.4E+02 0.0052 26.6 8.8 81 8-96 13-93 (151)
411 TIGR00177 molyb_syn molybdenum 35.8 1.7E+02 0.0037 27.3 7.8 50 36-88 27-76 (144)
412 TIGR02955 TMAO_TorT TMAO reduc 35.8 3.5E+02 0.0076 28.3 11.3 99 9-113 108-215 (295)
413 cd00001 PTS_IIB_man PTS_IIB, P 35.6 2.4E+02 0.0053 26.6 8.7 81 8-96 12-92 (151)
414 cd06318 PBP1_ABC_sugar_binding 35.5 5.1E+02 0.011 26.6 12.6 107 4-112 103-221 (282)
415 KOG0025 Zn2+-binding dehydroge 35.4 2.2E+02 0.0048 29.9 8.8 85 5-102 170-257 (354)
416 PF07302 AroM: AroM protein; 35.2 3.4E+02 0.0074 27.4 10.0 74 22-99 126-201 (221)
417 cd08477 PBP2_CrgA_like_8 The C 35.0 2.5E+02 0.0054 26.5 9.4 64 339-419 14-77 (197)
418 KOG3713 Voltage-gated K+ chann 35.0 45 0.00098 37.2 4.1 60 450-513 359-420 (477)
419 COG0521 MoaB Molybdopterin bio 34.9 1.9E+02 0.004 27.9 7.7 63 23-87 9-76 (169)
420 cd06302 PBP1_LsrB_Quorum_Sensi 34.7 4.9E+02 0.011 27.2 12.3 101 4-104 104-210 (298)
421 PF01007 IRK: Inward rectifier 34.6 2.2E+02 0.0047 30.9 9.3 59 471-529 83-145 (336)
422 cd06282 PBP1_GntR_like_2 Ligan 34.5 1.4E+02 0.0031 30.4 7.9 77 24-103 2-80 (266)
423 cd06300 PBP1_ABC_sugar_binding 34.3 1.6E+02 0.0035 30.3 8.3 80 23-103 1-86 (272)
424 PRK09756 PTS system N-acetylga 33.9 3E+02 0.0065 26.2 9.1 80 8-96 17-97 (158)
425 cd06322 PBP1_ABC_sugar_binding 33.9 1.7E+02 0.0037 29.9 8.4 77 24-103 2-81 (267)
426 cd08179 NADPH_BDH NADPH-depend 33.6 95 0.0021 34.3 6.6 72 17-88 19-91 (375)
427 cd06316 PBP1_ABC_sugar_binding 33.2 4.8E+02 0.01 27.1 11.9 106 5-114 107-219 (294)
428 KOG1420 Ca2+-activated K+ chan 33.2 26 0.00057 39.3 2.0 60 465-524 281-342 (1103)
429 cd08184 Fe-ADH3 Iron-containin 33.0 2E+02 0.0044 31.3 8.9 75 10-88 12-91 (347)
430 cd01536 PBP1_ABC_sugar_binding 32.9 1.7E+02 0.0037 29.7 8.2 77 23-102 1-80 (267)
431 smart00857 Resolvase Resolvase 32.8 3.4E+02 0.0074 24.9 9.5 37 66-102 53-95 (148)
432 PRK09701 D-allose transporter 32.8 6E+02 0.013 26.8 12.6 97 4-103 136-240 (311)
433 PRK15408 autoinducer 2-binding 32.3 2.3E+02 0.005 30.7 9.3 82 20-103 22-106 (336)
434 cd06310 PBP1_ABC_sugar_binding 32.2 1.6E+02 0.0036 30.2 8.0 79 23-102 1-82 (273)
435 cd00757 ThiF_MoeB_HesA_family 32.0 4.8E+02 0.01 26.4 11.0 88 9-102 33-136 (228)
436 cd01391 Periplasmic_Binding_Pr 32.0 1.7E+02 0.0037 29.2 8.0 77 24-103 2-83 (269)
437 cd08173 Gro1PDH Sn-glycerol-1- 31.7 1.8E+02 0.004 31.5 8.4 95 12-115 15-112 (339)
438 PF10566 Glyco_hydro_97: Glyco 31.6 3.9E+02 0.0083 28.0 10.1 99 4-105 29-153 (273)
439 PRK00072 hemC porphobilinogen 31.5 6.5E+02 0.014 26.7 13.2 60 533-600 113-174 (295)
440 cd08484 PBP2_LTTR_beta_lactama 31.5 4.4E+02 0.0095 24.6 12.5 99 534-640 85-186 (189)
441 PRK11425 PTS system N-acetylga 31.4 3.2E+02 0.007 25.9 8.9 80 8-96 15-94 (157)
442 TIGR00696 wecB_tagA_cpsF bacte 31.2 5E+02 0.011 25.2 10.8 80 11-98 39-120 (177)
443 cd01545 PBP1_SalR Ligand-bindi 30.6 1.8E+02 0.0039 29.7 8.0 77 24-102 2-80 (270)
444 cd06318 PBP1_ABC_sugar_binding 30.6 1.7E+02 0.0037 30.2 7.8 77 24-103 2-81 (282)
445 PRK01215 competence damage-ind 30.4 2.4E+02 0.0052 29.4 8.5 62 23-87 5-71 (264)
446 cd08475 PBP2_CrgA_like_6 The C 30.0 4.7E+02 0.01 24.5 12.1 67 567-640 128-196 (199)
447 PRK03692 putative UDP-N-acetyl 29.9 5.3E+02 0.012 26.5 10.8 82 12-100 97-179 (243)
448 PF03830 PTSIIB_sorb: PTS syst 29.6 1.7E+02 0.0036 27.7 6.6 83 9-99 14-96 (151)
449 PF13314 DUF4083: Domain of un 29.1 2.7E+02 0.0058 21.4 6.4 15 716-730 43-57 (58)
450 COG3473 Maleate cis-trans isom 28.9 6E+02 0.013 25.4 10.1 76 10-88 107-189 (238)
451 PF00218 IGPS: Indole-3-glycer 28.9 3.7E+02 0.008 27.9 9.4 89 7-103 68-159 (254)
452 cd08439 PBP2_LrhA_like The C-t 28.4 1.7E+02 0.0037 27.6 6.8 66 340-421 14-79 (185)
453 COG1058 CinA Predicted nucleot 28.2 1.4E+02 0.0031 30.8 6.2 62 23-87 3-69 (255)
454 PF02310 B12-binding: B12 bind 28.0 2.6E+02 0.0056 24.7 7.5 70 9-86 17-87 (121)
455 PF02608 Bmp: Basic membrane p 28.0 1.9E+02 0.0042 30.8 7.7 88 23-117 3-95 (306)
456 PF00731 AIRC: AIR carboxylase 27.9 3.8E+02 0.0083 25.3 8.4 65 23-89 2-66 (150)
457 PF09651 Cas_APE2256: CRISPR-a 27.6 2.1E+02 0.0046 26.4 6.8 50 6-55 4-56 (136)
458 PRK09061 D-glutamate deacylase 27.6 4.2E+02 0.009 30.7 10.7 97 6-103 165-276 (509)
459 cd06281 PBP1_LacI_like_5 Ligan 27.5 2.3E+02 0.005 29.0 8.1 76 24-102 2-79 (269)
460 cd01540 PBP1_arabinose_binding 27.5 2E+02 0.0044 29.8 7.8 76 24-103 2-80 (289)
461 cd03364 TOPRIM_DnaG_primases T 27.5 1.1E+02 0.0024 25.0 4.4 41 12-53 35-75 (79)
462 PLN02428 lipoic acid synthase 27.4 5.3E+02 0.011 28.1 10.7 75 5-82 131-209 (349)
463 PRK13957 indole-3-glycerol-pho 27.3 4.8E+02 0.01 26.9 9.8 87 9-103 63-152 (247)
464 PF02602 HEM4: Uroporphyrinoge 27.3 62 0.0013 32.7 3.6 90 4-100 99-189 (231)
465 cd03767 SR_Res_par Serine reco 27.2 5.1E+02 0.011 24.0 10.0 28 6-34 15-42 (146)
466 COG0134 TrpC Indole-3-glycerol 27.2 1.6E+02 0.0036 30.3 6.4 88 8-103 67-157 (254)
467 TIGR02976 phageshock_pspB phag 27.2 2.6E+02 0.0057 22.9 6.3 17 718-734 55-71 (75)
468 PRK00843 egsA NAD(P)-dependent 27.1 2.6E+02 0.0057 30.5 8.6 97 10-115 22-121 (350)
469 PRK03670 competence damage-ind 26.7 3.1E+02 0.0068 28.3 8.5 61 24-86 3-68 (252)
470 cd01538 PBP1_ABC_xylose_bindin 26.5 7.2E+02 0.016 25.7 11.8 96 9-105 107-216 (288)
471 cd06273 PBP1_GntR_like_1 This 26.4 2.6E+02 0.0055 28.6 8.2 75 24-102 2-78 (268)
472 PRK10936 TMAO reductase system 26.3 2.8E+02 0.006 30.1 8.7 80 22-103 47-129 (343)
473 cd06324 PBP1_ABC_sugar_binding 25.9 2.3E+02 0.005 29.9 7.8 77 24-103 2-83 (305)
474 cd06323 PBP1_ribose_binding Pe 25.7 2.7E+02 0.0059 28.3 8.2 76 24-102 2-80 (268)
475 PF06679 DUF1180: Protein of u 25.7 79 0.0017 30.2 3.6 30 679-708 93-122 (163)
476 COG3181 Uncharacterized protei 25.6 7E+02 0.015 26.8 11.0 124 527-655 129-284 (319)
477 PF13407 Peripla_BP_4: Peripla 25.6 5.5E+02 0.012 25.9 10.4 107 3-112 102-213 (257)
478 cd01539 PBP1_GGBP Periplasmic 25.6 3E+02 0.0066 29.0 8.7 78 23-103 1-83 (303)
479 cd06320 PBP1_allose_binding Pe 25.4 2.8E+02 0.0061 28.4 8.3 79 24-103 2-83 (275)
480 COG0807 RibA GTP cyclohydrolas 24.6 2.6E+02 0.0057 27.5 7.0 54 3-64 123-176 (193)
481 PRK10014 DNA-binding transcrip 24.4 2.6E+02 0.0057 29.9 8.1 78 22-102 65-144 (342)
482 cd00494 HMBS Hydroxymethylbila 24.3 8.7E+02 0.019 25.7 12.7 60 533-600 109-170 (292)
483 COG0040 HisG ATP phosphoribosy 24.2 3.8E+02 0.0082 28.3 8.5 102 532-645 107-211 (290)
484 cd06317 PBP1_ABC_sugar_binding 24.1 2.9E+02 0.0063 28.2 8.1 77 24-103 2-82 (275)
485 KOG3603 Predicted phospholipas 24.1 1.9E+02 0.0041 32.0 6.4 91 26-118 303-402 (456)
486 PRK10653 D-ribose transporter 23.9 3.4E+02 0.0073 28.4 8.6 80 21-103 26-108 (295)
487 cd06321 PBP1_ABC_sugar_binding 23.9 3.4E+02 0.0073 27.8 8.6 76 24-102 2-82 (271)
488 cd06296 PBP1_CatR_like Ligand- 23.9 4E+02 0.0087 27.1 9.1 75 24-102 2-78 (270)
489 cd06270 PBP1_GalS_like Ligand 23.8 4.3E+02 0.0092 26.9 9.3 75 24-102 2-78 (268)
490 cd02071 MM_CoA_mut_B12_BD meth 23.6 5.1E+02 0.011 23.1 8.5 68 30-103 8-79 (122)
491 smart00852 MoCF_biosynth Proba 23.6 3.2E+02 0.007 24.9 7.3 50 35-87 17-66 (135)
492 cd01542 PBP1_TreR_like Ligand- 23.5 2.7E+02 0.0059 28.2 7.7 75 24-102 2-78 (259)
493 TIGR02136 ptsS_2 phosphate bin 23.3 94 0.002 32.8 4.1 72 340-421 49-126 (287)
494 cd06274 PBP1_FruR Ligand bindi 23.1 3E+02 0.0065 28.0 7.9 75 24-102 2-78 (264)
495 cd06285 PBP1_LacI_like_7 Ligan 23.0 3.1E+02 0.0068 27.9 8.0 75 24-102 2-78 (265)
496 PF01936 NYN: NYN domain; Int 23.0 4.4E+02 0.0094 24.0 8.3 100 8-113 21-126 (146)
497 cd06314 PBP1_tmGBP Periplasmic 22.9 8.1E+02 0.018 24.9 12.6 96 7-104 104-204 (271)
498 PRK10355 xylF D-xylose transpo 22.9 3.8E+02 0.0082 28.8 8.9 78 22-102 26-106 (330)
499 PF03908 Sec20: Sec20; InterP 22.9 89 0.0019 26.6 3.1 23 438-460 69-91 (92)
500 PRK13209 L-xylulose 5-phosphat 22.8 6.3E+02 0.014 26.2 10.4 94 10-103 24-152 (283)
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=2.1e-83 Score=669.63 Aligned_cols=670 Identities=20% Similarity=0.315 Sum_probs=548.2
Q ss_pred HHHHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcC
Q 043276 8 QVGAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHML 87 (829)
Q Consensus 8 q~~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~ 87 (829)
...|+++++.||+|.+++.+| |.+-|...++++.+.+.+++..|.....-.. .+..+++.++..|...+.+-+++.|.
T Consensus 138 l~~al~s~i~hy~W~~fv~ly-D~~rg~s~Lqai~~~a~~~nw~VtA~~v~~~-~d~~~yr~~f~~l~~r~e~rv~iDce 215 (897)
T KOG1054|consen 138 LKGALLSLIDHYKWEKFVYLY-DTDRGLSILQAIMEAAAQNNWQVTAINVGNI-NDVKEYRMLFEMLDRRQENRVLIDCE 215 (897)
T ss_pred HHHHHHHHHHhcccceEEEEE-cccchHHHHHHHHHHHHhcCceEEEEEcCCc-ccHHHHHHHHHHHhccccceEEEEcc
Confidence 346899999999999999999 8888999999999999999999987654322 23456888888888889999999999
Q ss_pred hhHHHHHHHHHHHcCccccCeEEEEcCccccccccCCccccccccceEEEEeccCCChhHHHHHHHHHHhhcccCCCCCc
Q 043276 88 PSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLEPSVTDSMQGVIGVRPYVPKTKALENFRVRWKRKFLQENPSLFD 167 (829)
Q Consensus 88 ~~~~~~i~~~a~~~gm~~~~~vwI~t~~~~~~~~~~~~~~~~~~~g~l~~~~~~~~~~~~~~F~~~w~~~~~~~~~~~~~ 167 (829)
.+....++.++.+.|-...+|++|+.+---. +...........++.||++...+.|-.+.|.++|++.-..++++...
T Consensus 216 ~~~~~~il~q~i~~~k~~~~YHYvlaNl~f~--d~dl~~f~~g~aNitgFqivn~~~~~~~k~~~~~~~l~~~~~~g~~~ 293 (897)
T KOG1054|consen 216 SERRNRILLQVIELGKHVKGYHYVLANLGFT--DIDLERFQHGGANITGFQIVNKNNPMVKKFIQRWKELDEREYPGASN 293 (897)
T ss_pred cHHHHHHHHHHHHHhhhccceEEEEeeCCCc--hhhHHHHhcCCcceeEEEEecCCChHHHHHHHHHhhhcccccCCCCC
Confidence 9999999999999887778999999763211 11111233445667899999999999999999999988887887776
Q ss_pred cccchhHHHHHHHHHHHHHHHHHhcccCccccCCCCCCCCCCCc--cccCCCChHHHHHHHhccceecccccEEEe-cCc
Q 043276 168 AELNIFGLLAYDATSALAVAVEKAGITGFGFDKTNVSSNATDLE--AFGISQNGPKLLQALSSIRFRGLTGDYIFV-DGQ 244 (829)
Q Consensus 168 ~~~~~~~~~~YDAV~~~A~Al~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~g~~l~~~L~~~~f~G~tG~~~F~-~G~ 244 (829)
..+..-++..|||+..+|+|++.+..+..+..+. +...||. ....|..|..+.++|+++.++|+||+++|| .|.
T Consensus 294 ~~~k~tsAlthDailV~~eaf~~~~~q~~~~~rR---G~~GD~~an~~~p~~qG~~I~ralk~v~~eGLTGniqFd~~G~ 370 (897)
T KOG1054|consen 294 DPIKYTSALTHDAILVMAEAFRSLRRQRIDISRR---GNAGDCLANPAVPWEQGIDIERALKQVQVEGLTGNIQFDKYGR 370 (897)
T ss_pred CCcchhhhhhhhHHHHHHHHHHHHHHhhhchhcc---CCCccccCCCCCchhcchhHHHHHHheeecccccceeecccCc
Confidence 6677778999999999999999987665433222 1224443 245678899999999999999999999998 999
Q ss_pred cccceEEEEEcc-CCcEEEEEecCCCCcccccCCCccccCCccceecCCCCCCCCCCc-ccCCCCceEEEecccccCccc
Q 043276 245 LQSSAFEIINVN-NGARGVGFWSPEKGLTQKLSSNSTTKSKLRPIIWPGDSTSDPKGW-EIPTNEKKLRVGVPVKKGFSD 322 (829)
Q Consensus 245 ~~~~~y~I~n~~-~g~~~VG~w~~~~g~~~~l~~~~~~~~~~~~i~Wpg~~~~~P~~~-~~p~~~~~lrv~v~~~~~~~p 322 (829)
+.+-..+|+.+. ++.+++|+|....++....+ ..+.+. ......++..|......|
T Consensus 371 R~Nyt~~i~elk~~~~rk~~~W~e~~~fv~~~t-------------------~a~~~~d~~~~~n~tvvvttiL~sp--- 428 (897)
T KOG1054|consen 371 RTNYTIDIVELKSNGSRKVGYWNEGEGFVPGST-------------------VAQSRNDQASKENRTVVVTTILESP--- 428 (897)
T ss_pred cccceEEEEEeccCCcceeeeecccCceeeccc-------------------cccccccccccccceEEEEEecCCc---
Confidence 988788899999 89999999998888664321 001111 111223444444444444
Q ss_pred eEEEeec--CCCCCceEEEeeHHHHHHHHHHCCCcccEEEEecCCCCCC--CCCC-hhHHHHhHhcCcccEEEecccccc
Q 043276 323 FVKVTID--PKTQETSVVGYSIDVFKAVIEELPYAVAYDFVPYAQPDGT--SSGS-YNDLIYQVFLGEFDAVVGDTTIVF 397 (829)
Q Consensus 323 ~~~~~~~--~~~~~~~~~G~~idll~~ia~~l~f~~~~~~~~~~~~~g~--~ng~-~~~li~~l~~g~~Di~~~~~~it~ 397 (829)
|++..++ ...++.++.|||+||+.+||++.++++++.++..+ .+|. +.++ |+||+++|..|++|++++++|||.
T Consensus 429 yvm~kkn~~~~egn~ryEGyCvdLa~~iAkhi~~~Y~l~iv~dg-kyGardaD~k~WnGMvGeLv~grAdiavApLTIt~ 507 (897)
T KOG1054|consen 429 YVMLKKNHEQLEGNERYEGYCVDLAAEIAKHIGIKYKLFIVGDG-KYGARDADTKIWNGMVGELVYGRADIAVAPLTITL 507 (897)
T ss_pred hhHHHhhHHHhcCCcccceeHHHHHHHHHHhcCceEEEEEecCC-cccccCCCcccccchhHHHhcCccceEEeeeeeeh
Confidence 4554443 23678899999999999999999986665555432 3332 4555 999999999999999999999999
Q ss_pred ccceeccccccccccceEEEEEccCCCCCCceeeeccCCHhHHHHHHHHHHHHHHHHHhhhcccCCCCCC------Cc--
Q 043276 398 NRSNYVDFTLPYTESGVSMIVPIKDSKKRNAWVFLQPLTWDLWVTSGCFFIFIGFVVWVLEHRVNEDFRG------PA-- 469 (829)
Q Consensus 398 ~R~~~vdft~p~~~~~~~~vv~~~~~~~~~~~~fl~PF~~~vW~~i~~~~~~~~~v~~~~~~~~~~~~~~------~~-- 469 (829)
+|++.+|||.||+..|+++|.++|+...+..+.||.|+..++|++++..++.+++++++..|+++.+|+- +.
T Consensus 508 ~REeviDFSKPfMslGISIMIKKPqKsk~gVFSFldPLa~eIWm~ivfaYiGVSvvlFLVSrFSPYEwh~Ee~~rg~~t~ 587 (897)
T KOG1054|consen 508 VREEVIDFSKPFMSLGISIMIKKPQKSKPGVFSFLDPLAYEIWMCIVFAYIGVSVVLFLVSRFSPYEWHTEEFERGRFTP 587 (897)
T ss_pred hhhhhhccccchhhcCeEEEEeCcccCCCCeeeecchhHHHHHHHHHHHHhcceEEEEEEeccCchheeccccccCCCCC
Confidence 9999999999999999999999999999999999999999999999999999999999999999877642 11
Q ss_pred -----cCccchhHHHHHHHhhhcCc-cccccchhHHHHHHHHHHHHHHHHHhHHHHHHHhhcccCCCCCCCHHHHHhCCC
Q 043276 470 -----RHQVGTSFWFSFSTMVFSQR-ERVISNLARFVVIVWCFVVLILIQSYTASLTSLLTVDQLQPTITDVNLLIKRGD 543 (829)
Q Consensus 470 -----~~~~~~~~~~~~~~l~~~~~-~~~~s~~~R~v~~~w~~~~lil~~~YtA~L~s~Lt~~~~~~~I~s~~dL~~~~~ 543 (829)
..++.|++||+++++++||- ..|+|.++|++..+||||+|||.++|||||++|||++++.+||++.+||.++.+
T Consensus 588 ~~~~NeFgifNsLWFsLgAFMQQG~DI~PRslSGRIvggvWWFFTlIIiSSYTANLAAFLTvErMvsPIESaEDLAkQte 667 (897)
T KOG1054|consen 588 SDPPNEFGIFNSLWFSLGAFMQQGCDISPRSLSGRIVGGVWWFFTLIIISSYTANLAAFLTVERMVSPIESAEDLAKQTE 667 (897)
T ss_pred CCCCccchhhHHHHHHHHHHHhcCCCCCccccccceeccchhhhhhhhhhhhhhHHHHHHhHHhhcCcchhHHHHhhcce
Confidence 23577999999999999995 578999999999999999999999999999999999999999999999999887
Q ss_pred -cEEEEeCchHHHHHHhcCCC----------ccc-eeecCChHHHHHHHhcCCcCCceeEEEcchhHHHHHHhc-CCCce
Q 043276 544 -NVGYQKGSFVLGILKQLGFD----------ERK-LVVYNSHEECDELFQKGSANGGIAAAFDEIPYAKLLIGQ-HCSKY 610 (829)
Q Consensus 544 -~vg~~~~s~~~~~l~~~~~~----------~~~-~~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~-~c~~l 610 (829)
.+|+..+....+++++...+ ... -+.+.+..|.++++++.+ |-+|++.|...-+|...+ .|+ -
T Consensus 668 IaYGt~~~GSTkeFFr~Skiavy~kMW~yM~SaepsVFv~t~aeGv~rVRksK---GkyAfLLEsTmNey~eqRkPCD-T 743 (897)
T KOG1054|consen 668 IAYGTLDSGSTKEFFRRSKIAVYEKMWTYMKSAEPSVFVRTTAEGVARVRKSK---GKYAFLLESTMNEYIEQRKPCD-T 743 (897)
T ss_pred eeeeecCCCchHHHHhhhhHHHHHHHHHHHhcCCcceeeehhhhHHHHHHhcC---CceEeehHhhhhhhhhccCCcc-c
Confidence 68888888778887642211 011 134456677888887655 689999999888887654 597 5
Q ss_pred EEeCcccccCCceeeecCCCCchhhHHHHHHhhhccChhHHHHHHHccCCCCCCCCC--CccccccccccchhHHHHHHH
Q 043276 611 TMVEPTFKTAGFGFAFPLHSPLVHDVSKAILNVTEGDKMKEIEDAWFKKHSSCPDAG--TVVSARSLGLNSFWGLFLIAG 688 (829)
Q Consensus 611 ~~v~~~~~~~~~~~~~~k~spl~~~in~~il~l~e~G~~~~~~~~w~~~~~~c~~~~--~~~~~~~L~l~~~~g~f~il~ 688 (829)
+.||..+.+.+||+|.||||.|+..+|.|++.|.|.|+++++++|||.+++.|.... ..++...|+|.+++|+||||.
T Consensus 744 MKVGgNLds~GYGiATp~Gsslr~~vNLAvLkL~E~G~LdKLkNKWWYDkGeC~sg~~ds~~ktsaLsLSnVAGvFYIL~ 823 (897)
T KOG1054|consen 744 MKVGGNLDSKGYGIATPKGSSLRNAVNLAVLKLNEQGLLDKLKNKWWYDKGECGSGGGDSKDKTSALSLSNVAGVFYILV 823 (897)
T ss_pred eecccccCCcceeecCCCCcccccchhhhhhhhcccchHHHhhhhhcccccccCCCCCCCCcchhhcchhhccceeeeeh
Confidence 678999999999999999999999999999999999999999999999999999876 344557999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHhhcccc
Q 043276 689 IAAILALIIFLAVFVHEHWNVLK 711 (829)
Q Consensus 689 vg~~lallvf~~E~~~~~~~~~~ 711 (829)
.|++||.++.++|++|+.|...+
T Consensus 824 gGl~laMlvALiEF~yksr~Eak 846 (897)
T KOG1054|consen 824 GGLGLAMLVALIEFCYKSRAEAK 846 (897)
T ss_pred hhHHHHHHHHHHHHHHHhhHHHH
Confidence 99999999999999999887644
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=9.2e-75 Score=607.35 Aligned_cols=644 Identities=22% Similarity=0.361 Sum_probs=529.5
Q ss_pred CCCChHHHHHHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCe
Q 043276 1 GALNDSSQVGAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTR 80 (829)
Q Consensus 1 t~psD~~q~~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~ar 80 (829)
|+|+-++|+.+..++|.+|.|++|.++.+||.-|+.....++..+++...++.....+.++ .+.++..|-.+|+.++|
T Consensus 149 tvpPyshqa~VwleMl~~~~y~~vi~l~s~d~~gra~~~r~qt~~e~~~~~~e~v~~f~p~--~~~~t~~l~~~k~~~~r 226 (993)
T KOG4440|consen 149 TVPPYSHQASVWLEMLRVYSYNHVILLVSDDHEGRAAQKRLQTLLEERESKAEKVLQFDPG--TKNVTALLMEAKELEAR 226 (993)
T ss_pred cCCCccchhHHHHHHHHHhhcceEEEEEcccccchhHHhHHHHHHHHHhhhhhhheecCcc--cchHHHHHhhhhhhhhe
Confidence 6899999999999999999999999999999999888888888888776666555556555 34788899999999999
Q ss_pred EEEEEcChhHHHHHHHHHHHcCccccCeEEEEcCccccccccCCccccccccceEEEEeccCCChhHHHHHHHHHHhhcc
Q 043276 81 VFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLEPSVTDSMQGVIGVRPYVPKTKALENFRVRWKRKFLQ 160 (829)
Q Consensus 81 ViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t~~~~~~~~~~~~~~~~~~~g~l~~~~~~~~~~~~~~F~~~w~~~~~~ 160 (829)
|+++..+.++|..+++.|-+++|++.|||||.++.-... ....+|++|.+.....+
T Consensus 227 v~~~~as~dDA~~ifr~Ag~lnmTG~G~VWiV~E~a~~~--------nn~PdG~LGlqL~~~~~---------------- 282 (993)
T KOG4440|consen 227 VIILSASEDDAATIFRAAGMLNMTGSGYVWIVGERAISG--------NNLPDGILGLQLINGKN---------------- 282 (993)
T ss_pred eEEeecccchHHHHHHhhhhhcccCceEEEEEecccccc--------CCCCCceeeeEeecCcc----------------
Confidence 999999999999999999999999999999999764422 13368999998754321
Q ss_pred cCCCCCccccchhHHHHHHHHHHHHHHHHHhcccCccccCCCCCCCCCCCccccCCCChHHHHHHHhccc-eecccccEE
Q 043276 161 ENPSLFDAELNIFGLLAYDATSALAVAVEKAGITGFGFDKTNVSSNATDLEAFGISQNGPKLLQALSSIR-FRGLTGDYI 239 (829)
Q Consensus 161 ~~~~~~~~~~~~~~~~~YDAV~~~A~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~L~~~~-f~G~tG~~~ 239 (829)
-.+..-|+|+++|.|+|.+.....-...+ ++| |++..+|..|+.|.+.+...+ -.|.||.+.
T Consensus 283 ------------~~~hirDsv~vlasAv~e~~~~e~I~~~P---~~c--~d~~~~w~~g~~l~~~l~s~~~~~g~TgrV~ 345 (993)
T KOG4440|consen 283 ------------ESAHIRDSVGVLASAVHELLEKENITDPP---RGC--VDNTNIWKTGPLLKRVLMSSKYADGVTGRVE 345 (993)
T ss_pred ------------ccceehhhHHHHHHHHHHHHhhccCCCCC---Ccc--cCccchhcccHHHHHHHhhhcccCCcceeEE
Confidence 12345699999999999987543221222 122 345557888999999887654 579999999
Q ss_pred Ee-cCccccceEEEEEcc-C-CcEEEEEecCCCCcccccCCCccccCCccceecCCCCCCCCCCcccCCCCceEEEeccc
Q 043276 240 FV-DGQLQSSAFEIINVN-N-GARGVGFWSPEKGLTQKLSSNSTTKSKLRPIIWPGDSTSDPKGWEIPTNEKKLRVGVPV 316 (829)
Q Consensus 240 F~-~G~~~~~~y~I~n~~-~-g~~~VG~w~~~~g~~~~l~~~~~~~~~~~~i~Wpg~~~~~P~~~~~p~~~~~lrv~v~~ 316 (829)
|+ +||++...|+|+|+. + ..+.+|.|+.. .+. .|.+.|+|||+.+..|++...| +.||+.+..
T Consensus 346 Fnd~gdRi~a~YdiiN~hq~rk~Vg~~~yd~~-----r~~------~nd~~IiWpGg~~~KP~gi~~p---thLrivTi~ 411 (993)
T KOG4440|consen 346 FNDDGDRIFANYDIINLHQNRKLVGVGIYDGT-----RVI------PNDRKIIWPGGETEKPRGIQMP---THLRIVTIH 411 (993)
T ss_pred EcCCCceeeccceeEehhhhhhhhhhccccce-----eec------cCCceeecCCCCcCCCcccccc---ceeEEEEec
Confidence 95 999999999999996 3 35556666532 111 3668999999999999999987 567877776
Q ss_pred ccCccceEEEee---------------c--------------CCC----CCceEEEeeHHHHHHHHHHCCCcccEEEEec
Q 043276 317 KKGFSDFVKVTI---------------D--------------PKT----QETSVVGYSIDVFKAVIEELPYAVAYDFVPY 363 (829)
Q Consensus 317 ~~~~~p~~~~~~---------------~--------------~~~----~~~~~~G~~idll~~ia~~l~f~~~~~~~~~ 363 (829)
.+| |+++.. | |.+ ..-++.||||||+-.+++.+||+++..+++.
T Consensus 412 ~~P---FVYv~p~~sd~~c~eef~~~~d~~~k~~c~gpn~s~p~s~~~t~~fCC~G~cIDLLi~Ls~~~Nftyd~~l~~d 488 (993)
T KOG4440|consen 412 QEP---FVYVKPTLSDGTCKEEFTVNGDPVKKVICTGPNDSSPGSPRHTVPFCCYGFCIDLLIKLSRTMNFTYDVHLVAD 488 (993)
T ss_pred cCC---eEEEecCCCCcchhhhccccCCcccceeecCCCCCCCCCcccCcchhhhHHHHHHHHHHHHhhcceEEEEEeec
Confidence 666 454331 1 111 1235689999999999999999888877764
Q ss_pred CCCC---C-----CCC-CChhHHHHhHhcCcccEEEeccccccccceeccccccccccceEEEEEccCCCCCCceeeecc
Q 043276 364 AQPD---G-----TSS-GSYNDLIYQVFLGEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMIVPIKDSKKRNAWVFLQP 434 (829)
Q Consensus 364 ~~~~---g-----~~n-g~~~~li~~l~~g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv~~~~~~~~~~~~fl~P 434 (829)
+.-+ + ..+ ..|+|++++|..|++||+++++||++||.++++||.||...|+.++.+++... .....||+|
T Consensus 489 g~fg~~~~vnnsseT~~kew~G~iGEL~~~~ADMivaplTINpERa~yieFskPfkYqGitILeKk~~r~-Stl~SFlQP 567 (993)
T KOG4440|consen 489 GKFGTQERVNNSSETNKKEWNGMIGELLSGQADMIVAPLTINPERAQYIEFSKPFKYQGITILEKKEIRR-STLDSFLQP 567 (993)
T ss_pred ccccceeeeecccccccceehhhhhhhhCCccceEeeceeeChhhhhheeccCcccccceEEEeeCCCCC-chHHHHHhH
Confidence 4211 1 122 37999999999999999999999999999999999999999999999988654 588999999
Q ss_pred CCHhHHHHHHHHHHHHHHHHHhhhcccCCC-CCC-------CccCccchhHHHHHHHhhhcC-cc-ccccchhHHHHHHH
Q 043276 435 LTWDLWVTSGCFFIFIGFVVWVLEHRVNED-FRG-------PARHQVGTSFWFSFSTMVFSQ-RE-RVISNLARFVVIVW 504 (829)
Q Consensus 435 F~~~vW~~i~~~~~~~~~v~~~~~~~~~~~-~~~-------~~~~~~~~~~~~~~~~l~~~~-~~-~~~s~~~R~v~~~w 504 (829)
|+..+|+++++++.+++++++++.|+++-+ |.. .....++.++||+|+.|+-+| ++ .|+|+++|++.++|
T Consensus 568 fqstLW~lv~~SVhvVal~lYlLDrfSPFgRFk~~ds~~~ee~alnlssAmWF~WGVLLNSGigEgtPRSfSARvLGmVW 647 (993)
T KOG4440|consen 568 FQSTLWLLVGLSVHVVALMLYLLDRFSPFGRFKVNDSEEEEEDALNLSSAMWFSWGVLLNSGIGEGTPRSFSARVLGMVW 647 (993)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhcCcccceeeccCccchhhhcchhhhHHHHhHhhhccccCCCCCcchhHHHHHHHH
Confidence 999999999999999999999999988743 221 123478999999999999888 55 78999999999999
Q ss_pred HHHHHHHHHHhHHHHHHHhhcccCCCCCCCHHHHHhCC----CcEEEEeCchHHHHHHhc-----CCCccceeecCChHH
Q 043276 505 CFVVLILIQSYTASLTSLLTVDQLQPTITDVNLLIKRG----DNVGYQKGSFVLGILKQL-----GFDERKLVVYNSHEE 575 (829)
Q Consensus 505 ~~~~lil~~~YtA~L~s~Lt~~~~~~~I~s~~dL~~~~----~~vg~~~~s~~~~~l~~~-----~~~~~~~~~~~~~~~ 575 (829)
+-|+|||.++|||||++||...+.+..++.+.|-.-.+ ..++.+.+|.+..|+++. -+..-.-..|.+.+|
T Consensus 648 aGFaMIiVASYTANLAAFLVLdrPe~~ltGinDpRLRNps~nf~~aTVk~SsVd~YFrRqVELS~MyR~ME~hNy~~A~e 727 (993)
T KOG4440|consen 648 AGFAMIIVASYTANLAAFLVLDRPEERLTGINDPRLRNPSDNFIYATVKQSSVDIYFRRQVELSTMYRHMEKHNYESAAE 727 (993)
T ss_pred hhhheeeehhhhhhhhhheeecCccccccCCCCccccCcccceeEEEecCccHHHHHHHHhHHHHHHHhhhhcchhhHHH
Confidence 99999999999999999999999999999998865443 257889999999999752 122223346778889
Q ss_pred HHHHHhcCCcCCceeEEEcchhHHHHHHhcCCCceEEeCcccccCCceeeecCCCCchhhHHHHHHhhhccChhHHHHHH
Q 043276 576 CDELFQKGSANGGIAAAFDEIPYAKLLIGQHCSKYTMVEPTFKTAGFGFAFPLHSPLVHDVSKAILNVTEGDKMKEIEDA 655 (829)
Q Consensus 576 ~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~~c~~l~~v~~~~~~~~~~~~~~k~spl~~~in~~il~l~e~G~~~~~~~~ 655 (829)
+++++++|+ .+||+.|+..++|-.++.|. +...|+.|...+||++++||||+.+.+..+|+++.|+|+|+++.++
T Consensus 728 Aiq~v~~gk----L~AFIWDS~rLEfEAs~~Ce-LvT~GeLFgRSgyGIGlqK~SPWt~~vtlaIL~~hEsGfMEkLDk~ 802 (993)
T KOG4440|consen 728 AIQAVRDGK----LHAFIWDSARLEFEASQKCE-LVTTGELFGRSGYGIGLQKDSPWTQNVTLAILKSHESGFMEKLDKT 802 (993)
T ss_pred HHHHHHcCc----eeEEEeecceeeehhhcccc-eEeccccccccccccccccCCCCcchhhHHHHHhhhcchHHHHHHH
Confidence 999999999 99999999999999999996 8889999999999999999999999999999999999999999999
Q ss_pred HccCCC--CCCCCCCccccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhccccc
Q 043276 656 WFKKHS--SCPDAGTVVSARSLGLNSFWGLFLIAGIAAILALIIFLAVFVHEHWNVLKN 712 (829)
Q Consensus 656 w~~~~~--~c~~~~~~~~~~~L~l~~~~g~f~il~vg~~lallvf~~E~~~~~~~~~~~ 712 (829)
|....+ .|.. ....+..|++.++.|+|++.+.|+.+++++.++|..|+|++..++
T Consensus 803 Wi~~Ggpq~c~~--~~k~PatLgl~NMagvFiLV~~Gia~GifLifiEv~Ykrh~~~k~ 859 (993)
T KOG4440|consen 803 WIRYGGPQECDS--RSKAPATLGLENMAGVFILVAGGIAAGIFLIFIEVAYKRHKDAKR 859 (993)
T ss_pred HHhcCCcchhhh--hccCcccccccccccEEEEEecchhheeeEEEEeehhhhhhhhhh
Confidence 996533 3333 233678899999999999999999999999999999998877543
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=2e-71 Score=602.88 Aligned_cols=634 Identities=21% Similarity=0.371 Sum_probs=498.2
Q ss_pred CCChHHHHHHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHh--CCceeeeEEecCCCCChhHHHHHHHHhhcCCC
Q 043276 2 ALNDSSQVGAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQA--IDTRVPYRSVISPLATDDQIEKELYKLFTMQT 79 (829)
Q Consensus 2 ~psD~~q~~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~--~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~a 79 (829)
.||-++|+++|.+||+.|+|..+++|.+.-+..+.....++....+ .|..+.-...+..+.+ +........||+-++
T Consensus 154 g~Sieqqa~Vml~iL~~ydW~~Fs~vtt~~pg~~~f~~~ir~~~d~s~vgwe~i~v~~l~~s~~-d~~a~~q~qLkki~a 232 (1258)
T KOG1053|consen 154 GPSIEQQAQVMLKILEEYDWYNFSLVTTQFPGNRTFVSLIRQTNDNSHVGWEMINVLTLDPSTD-DLLAKLQAQLKKIQA 232 (1258)
T ss_pred CCcHHHHHHHHHHHHHHcCcceeEEEEeecCchHHHHHHHHHhhhhccccceeeeeeecCCCCC-chHHHHHHHHHhcCC
Confidence 4678899999999999999999999999888777777777766655 3544433333333322 223334445666779
Q ss_pred eEEEEEcChhHHHHHHHHHHHcCccccCeEEEEcCccccccccCCccccccccceEEEEeccCCChhHHHHHHHHHHhhc
Q 043276 80 RVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLEPSVTDSMQGVIGVRPYVPKTKALENFRVRWKRKFL 159 (829)
Q Consensus 80 rViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t~~~~~~~~~~~~~~~~~~~g~l~~~~~~~~~~~~~~F~~~w~~~~~ 159 (829)
.||+++|+.++|..||++|.++||++++|+||++....+.. . .-.+..-|.+.+.. +.|+.
T Consensus 233 ~VillyC~~eea~~IF~~A~q~Gl~g~~y~Wi~pqlv~g~~-~---~pa~~P~GLisv~~------------~~w~~--- 293 (1258)
T KOG1053|consen 233 PVILLYCSREEAERIFEEAEQAGLTGPGYVWIVPQLVEGLE-P---RPAEFPLGLISVSY------------DTWRY--- 293 (1258)
T ss_pred cEEEEEecHHHHHHHHHHHHhcCCcCCceEEEeehhccCCC-C---CCccCccceeeeec------------cchhh---
Confidence 99999999999999999999999999999999976554421 1 11234556666543 12332
Q ss_pred ccCCCCCccccchhHHHHHHHHHHHHHHHHHhcccCccccCCCCCCCCCCCcc--ccCCCChHHHHHHHhccceeccccc
Q 043276 160 QENPSLFDAELNIFGLLAYDATSALAVAVEKAGITGFGFDKTNVSSNATDLEA--FGISQNGPKLLQALSSIRFRGLTGD 237 (829)
Q Consensus 160 ~~~~~~~~~~~~~~~~~~YDAV~~~A~Al~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~g~~l~~~L~~~~f~G~tG~ 237 (829)
.+..++-|+|-++|.|.+.+....... + ... .+|-. ......+..|..+|.|++|+| ++
T Consensus 294 ------------~l~~rVrdgvaiva~aa~s~~~~~~~l-p-~~~---~~C~~~~~~~~~~~~~l~r~l~NvT~~g--~~ 354 (1258)
T KOG1053|consen 294 ------------SLEARVRDGVAIVARAASSMLRIHGFL-P-EPK---MDCREQEETRLTSGETLHRFLANVTWDG--RD 354 (1258)
T ss_pred ------------hHHHHHhhhHHHHHHHHHHHHhhcccC-C-Ccc---cccccccCccccchhhhhhhhheeeecc--cc
Confidence 255678899999999999987554321 1 111 22322 123345788999999999999 78
Q ss_pred EEEe-cCccccceEEEEEcc--CCcEEEEEecCCCCcccccCCCccccCCccceecCCCCCCCCCCcccCCCCceEEEec
Q 043276 238 YIFV-DGQLQSSAFEIINVN--NGARGVGFWSPEKGLTQKLSSNSTTKSKLRPIIWPGDSTSDPKGWEIPTNEKKLRVGV 314 (829)
Q Consensus 238 ~~F~-~G~~~~~~y~I~n~~--~g~~~VG~w~~~~g~~~~l~~~~~~~~~~~~i~Wpg~~~~~P~~~~~p~~~~~lrv~v 314 (829)
+.|+ +|-..+++.-|+... .-|.+||.|.... +..+..+||.... ..++.| ...+|+|.+
T Consensus 355 lsf~~~g~~v~p~lvvI~l~~~r~We~VG~We~~~-------------L~M~y~vWPr~~~---~~q~~~-d~~HL~VvT 417 (1258)
T KOG1053|consen 355 LSFNEDGYLVHPNLVVIDLNRDRTWERVGSWENGT-------------LVMKYPVWPRYHK---FLQPVP-DKLHLTVVT 417 (1258)
T ss_pred eeecCCceeeccceEEEecCCCcchheeceecCCe-------------EEEeccccccccC---ccCCCC-CcceeEEEE
Confidence 9996 887777777666665 3499999998532 2457789994332 122222 234788888
Q ss_pred ccccCccceEEEe-ecCCC---------------------------CCceEEEeeHHHHHHHHHHCCCcccEEEEecCCC
Q 043276 315 PVKKGFSDFVKVT-IDPKT---------------------------QETSVVGYSIDVFKAVIEELPYAVAYDFVPYAQP 366 (829)
Q Consensus 315 ~~~~~~~p~~~~~-~~~~~---------------------------~~~~~~G~~idll~~ia~~l~f~~~~~~~~~~~~ 366 (829)
.+++|| +.+. -||.+ -+.+++||||||+++||+.+||++++..+..+ +
T Consensus 418 LeE~PF---Vive~vDP~t~~C~~ntvpc~s~~~~t~ss~~~~~~tvKkCCkGfCIDiLkKlA~~v~FtYDLYlVtnG-K 493 (1258)
T KOG1053|consen 418 LEERPF---VIVEDVDPLTQTCVRNTVPCRSQLNSTFSSGDEANRTVKKCCKGFCIDILKKLARDVKFTYDLYLVTNG-K 493 (1258)
T ss_pred eccCCe---EEEecCCCCcCcCCCCCCcchhhhhhccCCCccCCchHHhhhhhhhHHHHHHHHhhcCcceEEEEecCC-c
Confidence 877765 4331 13221 14578999999999999999997776555443 4
Q ss_pred CC-CCCCChhHHHHhHhcCcccEEEeccccccccceeccccccccccceEEEEEccCCCCCCceeeeccCCHhHHHHHHH
Q 043276 367 DG-TSSGSYNDLIYQVFLGEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMIVPIKDSKKRNAWVFLQPLTWDLWVTSGC 445 (829)
Q Consensus 367 ~g-~~ng~~~~li~~l~~g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv~~~~~~~~~~~~fl~PF~~~vW~~i~~ 445 (829)
.| +.||.|+|||++|..+++||++++++|+++|.+.||||.||.++|+++||...+.. .+..+||.||++.+|+++++
T Consensus 494 hGkk~ng~WnGmIGev~~~rA~MAVgSltINeeRSevVDFSvPFveTgIsVmV~rsngt-vspsAFLePfs~svWVmmFV 572 (1258)
T KOG1053|consen 494 HGKKINGVWNGMIGEVVYQRADMAVGSLTINEERSEVVDFSVPFVETGISVMVARSNGT-VSPSAFLEPFSPSVWVMMFV 572 (1258)
T ss_pred ccceecCcchhhHHHHHhhhhheeeeeeEechhhhccccccccccccceEEEEEecCCc-cCchhhcCCcchHHHHHHHH
Confidence 45 48999999999999999999999999999999999999999999999999977654 68999999999999999999
Q ss_pred HHHHH-HHHHHhhhcccCCCCC---------CCccCccchhHHHHHHHhhhcC--ccccccchhHHHHHHHHHHHHHHHH
Q 043276 446 FFIFI-GFVVWVLEHRVNEDFR---------GPARHQVGTSFWFSFSTMVFSQ--RERVISNLARFVVIVWCFVVLILIQ 513 (829)
Q Consensus 446 ~~~~~-~~v~~~~~~~~~~~~~---------~~~~~~~~~~~~~~~~~l~~~~--~~~~~s~~~R~v~~~w~~~~lil~~ 513 (829)
+++++ ++.++++|+.++-.+. +.+.++++.++|..|+.++... .+.|++..+|+++.+|.||++|..+
T Consensus 573 m~livaai~vFlFEy~SPvgyn~~l~~gkkpggp~FtigkaiwllwaLvFnnsVpv~nPKgtTskiMv~VWAfFavifLA 652 (1258)
T KOG1053|consen 573 MCLIVAAITVFLFEYFSPVGYNRNLANGKKPGGPSFTIGKAIWLLWALVFNNSVPVENPKGTTSKIMVLVWAFFAVIFLA 652 (1258)
T ss_pred HHHHHHHHHHHHHhhcCcccccccccCCCCCCCcceehhhHHHHHHHHHhCCCcCCCCCCchHHHHHHHHHHHHHHHHHH
Confidence 98855 6667899998764432 2346789999999997777554 4688999999999999999999999
Q ss_pred HhHHHHHHHhhcccCCCCCCCHHHHHhC-------CCcEEEEeCchHHHHHHhcCCCcc--ceeec--CChHHHHHHHhc
Q 043276 514 SYTASLTSLLTVDQLQPTITDVNLLIKR-------GDNVGYQKGSFVLGILKQLGFDER--KLVVY--NSHEECDELFQK 582 (829)
Q Consensus 514 ~YtA~L~s~Lt~~~~~~~I~s~~dL~~~-------~~~vg~~~~s~~~~~l~~~~~~~~--~~~~~--~~~~~~~~~l~~ 582 (829)
+|||||++||..+.+..++..+.|-.-+ +.+.|.+.++..++++++ ++++- -++.| ...+++++.|++
T Consensus 653 sYTANLAAfMIqE~~~d~vSGlsD~KfqrP~dq~PpFRFGTVpngSTE~niR~-Nyp~MHeYM~kyNq~~v~dal~sLK~ 731 (1258)
T KOG1053|consen 653 SYTANLAAFMIQEEYYDTVSGLSDPKFQRPHDQYPPFRFGTVPNGSTERNIRS-NYPEMHEYMVKYNQPGVEDALESLKN 731 (1258)
T ss_pred HHHHHHHHHHhhhhhhhhccccCcccccCccccCCCcccccCCCCchhhhHHh-ccHHHHHHHHHhccCchHHHHHHHhc
Confidence 9999999999999999999999886533 347899988888888875 24321 22333 367899999999
Q ss_pred CCcCCceeEEEcchhHHHHHHhcC--CCceEEeC--cccccCCceeeecCCCCchhhHHHHHHhhhccChhHHHHHHHcc
Q 043276 583 GSANGGIAAAFDEIPYAKLLIGQH--CSKYTMVE--PTFKTAGFGFAFPLHSPLVHDVSKAILNVTEGDKMKEIEDAWFK 658 (829)
Q Consensus 583 g~~~~g~~a~~~~~~~~~~~~~~~--c~~l~~v~--~~~~~~~~~~~~~k~spl~~~in~~il~l~e~G~~~~~~~~w~~ 658 (829)
|+ .|||+.|...++|...++ |+ +..+| ..|.+.+||+++|||||++..||.+|+++...|+|+.+++.|+
T Consensus 732 gK----LDAFIyDaAVLnY~agkDegCK-LvTIGsgKvFAttGYGIal~k~Spwkr~IdlallQy~gdGeme~Le~~Wl- 805 (1258)
T KOG1053|consen 732 GK----LDAFIYDAAVLNYMAGKDEGCK-LVTIGSGKVFATTGYGIALPKNSPWKRQIDLALLQYLGDGEMEMLETLWL- 805 (1258)
T ss_pred cc----chhHHHHHHHHHHhhccCCCce-EEEecCCceeeecceeeecCCCCcchhhHHHHHHHHhccchHHHHHHHHh-
Confidence 99 999999999999999876 96 66676 8999999999999999999999999999999999999999999
Q ss_pred CCCCCCCCCCccccccccccchhHHHHHHHHHHHHHHHHHHHHHHH
Q 043276 659 KHSSCPDAGTVVSARSLGLNSFWGLFLIAGIAAILALIIFLAVFVH 704 (829)
Q Consensus 659 ~~~~c~~~~~~~~~~~L~l~~~~g~f~il~vg~~lallvf~~E~~~ 704 (829)
.+.|.+....+.+.+|++++|.|+||+|++|++||+++|++|-++
T Consensus 806 -tgic~n~k~evmSsqLdIdnmaGvFymL~~amgLSllvfi~EHlv 850 (1258)
T KOG1053|consen 806 -TGICHNSKNEVMSSQLDIDNMAGVFYMLAVAMGLSLLVFIWEHLV 850 (1258)
T ss_pred -hcccccchhhhhhcccChhhhhhHHHHHHHHHHHHHHHHHHHHHH
Confidence 688888778889999999999999999999999999999999554
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=4.9e-68 Score=628.63 Aligned_cols=599 Identities=35% Similarity=0.601 Sum_probs=504.9
Q ss_pred HHHHHhhcCCCeEEEEEcChhHHHHHHHHHHHcCccccCeEEEEcCccccccccCC-ccccccccceEEEEeccCCChhH
Q 043276 69 KELYKLFTMQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLE-PSVTDSMQGVIGVRPYVPKTKAL 147 (829)
Q Consensus 69 ~~l~~lk~~~arViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t~~~~~~~~~~~-~~~~~~~~g~l~~~~~~~~~~~~ 147 (829)
.++.+++....+++++++.+..+..++.+|.++||+..+|+|+.++......+... ....+.++|.++.+.+.+.+...
T Consensus 4 ~~~~~~~~~~~~~~v~~~~~~~~~~~~~~a~~~~~~~~~~~~i~t~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~s~~~ 83 (656)
T KOG1052|consen 4 KLLLKLKAMRTRVFVLHMFPILALAIFSQAEELGMMQFGYVWILTNLLTDALDLDELYSLIDVMNGVLGLRGHIPRSELL 83 (656)
T ss_pred hHHHHhhccCceEEEEeCCHHHHHHHHHHHHHhCccccCeEEEEEecchhhhcccccccchhheeeEEeeccCCCccHHH
Confidence 34556667899999999999999999999999999999999999998776655544 34567789999999999999999
Q ss_pred HHHHHHHHHhhcccCCCCCccccchhHHHHHHHHHHHHHHHHHhcccCccccCCCCCCCCCCCccccCCCChHHHHHHHh
Q 043276 148 ENFRVRWKRKFLQENPSLFDAELNIFGLLAYDATSALAVAVEKAGITGFGFDKTNVSSNATDLEAFGISQNGPKLLQALS 227 (829)
Q Consensus 148 ~~F~~~w~~~~~~~~~~~~~~~~~~~~~~~YDAV~~~A~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~L~ 227 (829)
++|..+|+.. .. .++.++.++||+++++|.|++.+..... . ...|...+.+..+..+.+.++
T Consensus 84 ~~~~~~~~~~-~~--------~~~~~~~~~~D~~~~~a~~~~~~~~~~~----~-----~~~~~~~~~~~~~~~~~~~~~ 145 (656)
T KOG1052|consen 84 QNFVTRWQTS-NV--------ELLVYALWAYDAIQALARAVESLLNIGN----L-----SLSCGRNNSWLDALGVFNFGK 145 (656)
T ss_pred HHHHHHHhhc-cc--------cccchhhHHHHHHHHHHHHHHHhhcCCC----C-----ceecCCCCcccchhHHHHHHH
Confidence 9999999876 22 3567899999999999999999864110 0 122333334566777888877
Q ss_pred ccceec---ccccEEEe-cCccccceEEEEEcc-CCcEEEEEecCCCCcccccCCCccccCCccceecCCCCCCCCCCcc
Q 043276 228 SIRFRG---LTGDYIFV-DGQLQSSAFEIINVN-NGARGVGFWSPEKGLTQKLSSNSTTKSKLRPIIWPGDSTSDPKGWE 302 (829)
Q Consensus 228 ~~~f~G---~tG~~~F~-~G~~~~~~y~I~n~~-~g~~~VG~w~~~~g~~~~l~~~~~~~~~~~~i~Wpg~~~~~P~~~~ 302 (829)
.....+ .+|.+.+. +|.+....|+|+|.. .+.+.||.|++..+ ..|.||+.....|+++.
T Consensus 146 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~n~~~~~~~~ig~W~~~~~---------------~~i~~~~~~~~~~~~~~ 210 (656)
T KOG1052|consen 146 KLLVVNLSGVTGQFQFFRGGLLEYFKYEILNLNGSGERRIGYWYPRGG---------------ENISWPGKDYFVPKGWF 210 (656)
T ss_pred hhhhhccccceeEEEecCCCccccceEEEEEecCcCceeEEEecCCCC---------------ceeeccCCcccCcCCcc
Confidence 765544 45666665 778888899999999 88888999998654 36899999999999999
Q ss_pred cCCCCceEEEecccccCccceEEEeecCCCCCceEEEeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHh
Q 043276 303 IPTNEKKLRVGVPVKKGFSDFVKVTIDPKTQETSVVGYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVF 382 (829)
Q Consensus 303 ~p~~~~~lrv~v~~~~~~~p~~~~~~~~~~~~~~~~G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~ 382 (829)
.|.+++++||+++..+||..++... ....++.++.|||+||+++++++|||+++++.++.+.....++|+|+|++++|.
T Consensus 211 ~~~~~~~l~v~~~~~~P~~~~~~~~-~~~~~~~~~~G~~idll~~l~~~l~f~~~~~~~~~~~g~~~~~g~~~g~v~~l~ 289 (656)
T KOG1052|consen 211 FPTNGKPLRVGVVTEPPFVDLVEDL-AILNGNDRIEGFEIDLLQALAKRLNFSYEIIFVPDGSGSRDPNGNWDGLVGQLV 289 (656)
T ss_pred ccCCCceEEEEEeccCCceeeeecc-cccCCCCccceEEehHHHHHHHhCCCceEEEEcCCCCCCCCCCCChhHHHHHHh
Confidence 8888999999999888765444322 133456799999999999999999999888888877633345689999999999
Q ss_pred cCcccEEEeccccccccceeccccccccccceEEEEEccCCCCCCceeeeccCCHhHHHHHHHHHHHHHHHHHhhhcccC
Q 043276 383 LGEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMIVPIKDSKKRNAWVFLQPLTWDLWVTSGCFFIFIGFVVWVLEHRVN 462 (829)
Q Consensus 383 ~g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv~~~~~~~~~~~~fl~PF~~~vW~~i~~~~~~~~~v~~~~~~~~~ 462 (829)
+|++|++ ++++++++|+.+||||.||++.++++++++++.... .|.|+.||++++|++++++++++++++|+++|+.+
T Consensus 290 ~~~advg-~~~tit~~R~~~vdfT~p~~~~~~~i~~~~~~~~~~-~~~fl~Pf~~~vW~~i~~~~l~~~~~~~~~~~~~~ 367 (656)
T KOG1052|consen 290 DGEADVG-ADITITPERSKYVDFTIPYLQFGIVIIVRKPDSRSK-LWNFLAPFSPEVWLLILASLLLVGLLLWILERLSP 367 (656)
T ss_pred cCccccc-cceEEeecccccEEeccceEeccEEEEEEecCCccc-ceEEecCCcHHHHHHHHHHHHHHHHHHHHHhcccc
Confidence 9999999 899999999999999999999999999999987765 99999999999999999999999999999999999
Q ss_pred CCCCCCc-----cCccchhHHHHHHHhhhcC-ccccccchhHHHHHHHHHHHHHHHHHhHHHHHHHhhcccCCCCCCCHH
Q 043276 463 EDFRGPA-----RHQVGTSFWFSFSTMVFSQ-RERVISNLARFVVIVWCFVVLILIQSYTASLTSLLTVDQLQPTITDVN 536 (829)
Q Consensus 463 ~~~~~~~-----~~~~~~~~~~~~~~l~~~~-~~~~~s~~~R~v~~~w~~~~lil~~~YtA~L~s~Lt~~~~~~~I~s~~ 536 (829)
.++ .++ .....+++|+++++++.++ .+.|++.++|+++++|||+++||+++|||+|+|+||++++.++|++++
T Consensus 368 ~~~-~~~~~~~~~~~~~~~~~~~~~~~~~q~~~~~p~~~~~Rll~~~w~~~~lil~ssYTa~L~a~Lt~~~~~~~i~~~~ 446 (656)
T KOG1052|consen 368 YEL-PPRQIVTSLFSLLNCLWLTVGSLLQQGSDEIPRSLSTRLLLGAWWLFVLILISSYTANLTAFLTVPRLRSPIDSLD 446 (656)
T ss_pred ccC-CccccceeEeecccchhhhhHHHhccCCCccccchhhhHHHHHHHHHHHHHHHHHHHHHHHHhcccccCCcccCHH
Confidence 988 222 1124457899999999887 468999999999999999999999999999999999999999999999
Q ss_pred HHHh-CCCcEEEEeCchHHHHHHhc----CCCcc-ceeecCChHHHHHHHhcCCcCCceeEEEcchhHHHHHHhcC-CCc
Q 043276 537 LLIK-RGDNVGYQKGSFVLGILKQL----GFDER-KLVVYNSHEECDELFQKGSANGGIAAAFDEIPYAKLLIGQH-CSK 609 (829)
Q Consensus 537 dL~~-~~~~vg~~~~s~~~~~l~~~----~~~~~-~~~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~~-c~~ 609 (829)
||.+ ++..+|+..+++...++++. .+... ..+.+.+.+++.+++.+|.. +|+.++.++.++.+...+++ | .
T Consensus 447 dL~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~v~~~~~-~~~~~~~~~~~~~~~~~~~~~c-~ 524 (656)
T KOG1052|consen 447 DLADQSNIPYGTQRGSFTRIYLEESEDMWAFKVSQRSVPLASPEEGVERVRKGPS-GGYAFASDELYLAYLFLRDEIC-D 524 (656)
T ss_pred HHHHhcCCeEEEEecchHHHHHHHHHHHHhhhccCCCccCCCHHHHHHHHHcCCC-CceEEEeccHHHHHHHhhcCCC-c
Confidence 9995 77799999999999999764 23333 66788999999999999976 54666666666555555554 7 5
Q ss_pred eEEeCcccccCCceeeecCCCCchhhHHHHHHhhhccChhHHHHHHHccCC---CCCCCCCCccccccccccchhHHHHH
Q 043276 610 YTMVEPTFKTAGFGFAFPLHSPLVHDVSKAILNVTEGDKMKEIEDAWFKKH---SSCPDAGTVVSARSLGLNSFWGLFLI 686 (829)
Q Consensus 610 l~~v~~~~~~~~~~~~~~k~spl~~~in~~il~l~e~G~~~~~~~~w~~~~---~~c~~~~~~~~~~~L~l~~~~g~f~i 686 (829)
++++++.+...+++ ++||||||++.++++|+++.|.|++++++++|+.+. ..|.... +...|++++++|+|++
T Consensus 525 ~~~v~~~~~~~~~~-~~~~~Spl~~~is~~Il~l~e~g~l~~~~~kw~~~~~~~~~~~~~~---~~~~l~~~~~~g~F~i 600 (656)
T KOG1052|consen 525 LTEVGEPFLYKGYG-AFPKGSPLRSLISRAILKLQETGILQKLKRKWFSKKPCLPKCSQTE---KTKALDLESFWGLFLI 600 (656)
T ss_pred eEEeCCcccCCCcc-eecCCCccHHHHHHHHHhhccccHHHHHHHHhccCCCCCCCCCCcc---cccccchhhHHHHHHH
Confidence 99999999999999 999999999999999999999999999999999864 4455443 5778999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHhhccc
Q 043276 687 AGIAAILALIIFLAVFVHEHWNVL 710 (829)
Q Consensus 687 l~vg~~lallvf~~E~~~~~~~~~ 710 (829)
+++|+++|+++|++|++|++++..
T Consensus 601 ~~~g~~lal~vfi~E~~~~~~~~~ 624 (656)
T KOG1052|consen 601 LLVGYLLALLVFILELLYSRRRTL 624 (656)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhh
Confidence 999999999999999999988875
No 5
>cd06390 PBP1_iGluR_AMPA_GluR1 N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the GluR1 subunit of the AMPA receptor. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the GluR1 subunit of the AMPA (alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid) receptor. The AMPA receptor is a member of the glutamate-receptor ion channels (iGluRs) which are the major mediators of excitatory synaptic transmission in the central nervous system. AMPA receptors are composed of four types of subunits (GluR1, GluR2, GluR3, and GluR4) which combine to form a tetramer and play an important role in mediating the rapid excitatory synaptic current. Furthermore, this N-terminal domain of the iGluRs has homology with LIVBP, a bacterial periplasmic binding protein, as well as with the structurally related glutamate-binding domain of the G-protein-coupled metabotropic receptors (mGluRs).
Probab=100.00 E-value=2e-35 Score=322.99 Aligned_cols=256 Identities=18% Similarity=0.285 Sum_probs=215.2
Q ss_pred HHHHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcC
Q 043276 8 QVGAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHML 87 (829)
Q Consensus 8 q~~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~ 87 (829)
+++||++|+++|||++|++||+ ++||...++.|.+++++.|+||.+...++.. +++++.+|++|+++++|+||++|+
T Consensus 104 ~~~Ai~diI~~~~W~~v~iIYd-~d~g~~~lq~l~~~~~~~~~~I~~~~~~~~~--~~d~~~~L~~ik~~~~rvIVl~~~ 180 (364)
T cd06390 104 LQDALISVIEHYKWQKFVYIYD-ADRGLSVLQKVLDTAAEKNWQVTAVNILTTT--EEGYRKLFQDLDKKKERLIVVDCE 180 (364)
T ss_pred HHHHHHHHHHHcCCcEEEEEEe-CCccHHHHHHHHHhhhccCceeeEEEeecCC--hHHHHHHHHhccccCCeEEEEECC
Confidence 8999999999999999999995 5599999999999999999999988776533 568999999999999999999999
Q ss_pred hhHHHHHHHHHHHcCccccCeEEEEcCccccccccCCccccccccceEEEEeccCCChhHHHHHHHHHHhhcccCCCCCc
Q 043276 88 PSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLEPSVTDSMQGVIGVRPYVPKTKALENFRVRWKRKFLQENPSLFD 167 (829)
Q Consensus 88 ~~~~~~i~~~a~~~gm~~~~~vwI~t~~~~~~~~~~~~~~~~~~~g~l~~~~~~~~~~~~~~F~~~w~~~~~~~~~~~~~ 167 (829)
++.+..++.++.+.+|+..+|+||+|+.-....+ .......+.|++|++++.++++.+++|..+|++.+...+|....
T Consensus 181 ~~~~~~~L~~a~~~~~~~~gy~wI~t~l~~~~~~--~~~~~~~~~nitg~r~~~~~~~~~~~~~~~w~~~~~~~~~~~~~ 258 (364)
T cd06390 181 SERLNAILNQIIKLEKNGIGYHYILANLGFMDID--LTKFRESGANVTGFQLVNYTDTTVSRIMQQWKNFDARDLPRVDW 258 (364)
T ss_pred HHHHHHHHHHHHHhhccCCceEEEecCCCccccc--HHHHhcCCcCceEEEEecCCCHHHHHHHHHHHhhccccCCCCCc
Confidence 9999999999999999999999999982211111 22355678999999999999999999999999887766665555
Q ss_pred cccchhHHHHHHHHHHHHHHHHHhcccCccccCCCCCCCCCCCcc--ccCCCChHHHHHHHhccceecccccEEEe-cCc
Q 043276 168 AELNIFGLLAYDATSALAVAVEKAGITGFGFDKTNVSSNATDLEA--FGISQNGPKLLQALSSIRFRGLTGDYIFV-DGQ 244 (829)
Q Consensus 168 ~~~~~~~~~~YDAV~~~A~Al~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~g~~l~~~L~~~~f~G~tG~~~F~-~G~ 244 (829)
.+++.+++++|||||++|+|++++......... ..+..+|.. ...|..|..|+++|++++|+|+||++.|+ +|+
T Consensus 259 ~~~~~~~~l~yDaV~~~A~A~~~l~~~~~~~~~---~~~~~~C~~~~~~~w~~G~~l~~~i~~~~f~GlTG~i~F~~~G~ 335 (364)
T cd06390 259 KRPKYTSALTYDGVRVMAEAFQNLRKQRIDISR---RGNAGDCLANPAVPWGQGIDIQRALQQVRFEGLTGNVQFNEKGR 335 (364)
T ss_pred CCcchHHHHHHHHHHHHHHHHHHHHHcCCCccc---CCCCCCCCCCCCCCCccHHHHHHHHHhhcccccccceeeCCCCC
Confidence 567889999999999999999998543321111 111124533 23588999999999999999999999996 899
Q ss_pred cccceEEEEEcc-CCcEEEEEecCCCCc
Q 043276 245 LQSSAFEIINVN-NGARGVGFWSPEKGL 271 (829)
Q Consensus 245 ~~~~~y~I~n~~-~g~~~VG~w~~~~g~ 271 (829)
+.+..|+|+|+. +|+++||+|++..|+
T Consensus 336 r~~~~~~I~~~~~~g~~~vG~W~~~~g~ 363 (364)
T cd06390 336 RTNYTLHVIEMKHDGIRKIGYWNEDEKL 363 (364)
T ss_pred cccceEEEEEecCCcceEEEEECCCCCc
Confidence 999999999999 999999999998775
No 6
>cd06387 PBP1_iGluR_AMPA_GluR3 N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the GluR3 subunit of the AMPA receptor. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the GluR3 subunit of the AMPA (alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid) receptor. The AMPA receptor is a member of the glutamate-receptor ion channels (iGluRs) which are the major mediators of excitatory synaptic transmission in the central nervous system. AMPA receptors are composed of four types of subunits (GluR1, GluR2, GluR3, and GluR4) which combine to form a tetramer and play an important role in mediating the rapid excitatory synaptic current. Furthermore, this N-terminal domain of the iGluRs has homology with LIVBP, a bacterial periplasmic binding protein, as well as with the structurally related glutamate-binding domain of the G-protein-coupled metabotropic receptors (mGluRs).
Probab=100.00 E-value=8.1e-34 Score=309.43 Aligned_cols=257 Identities=18% Similarity=0.271 Sum_probs=213.0
Q ss_pred HHHHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcC
Q 043276 8 QVGAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHML 87 (829)
Q Consensus 8 q~~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~ 87 (829)
...|+++|+++|||++|++|| |++||...++.|.+.++..+..|.++...+.. ..++++..++.|++++.|+|||+|+
T Consensus 111 l~~Ai~diI~~~~Wr~~~~iY-d~d~gl~~Lq~L~~~~~~~~~~V~~~~v~~~~-~~~~~~~~l~el~~~~~r~iIld~s 188 (372)
T cd06387 111 LKGAILSLLAHYKWEKFVYLY-DTERGFSILQAIMEAAVQNNWQVTARSVGNIK-DVQEFRRIIEEMDRRQEKRYLIDCE 188 (372)
T ss_pred HHHHHHHHHHhcCCCEEEEEe-cCchhHHHHHHHHHhhccCCceEEEEEeccCC-chHHHHHHHHHhccccceEEEEECC
Confidence 689999999999999999999 88999999999999999999999888655533 3457888999999999999999999
Q ss_pred hhHHHHHHHHHHHcCccccCeEEEEcCccccccccCCccccccccceEEEEeccCCChhHHHHHHHHHHhhcccCCCCCc
Q 043276 88 PSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLEPSVTDSMQGVIGVRPYVPKTKALENFRVRWKRKFLQENPSLFD 167 (829)
Q Consensus 88 ~~~~~~i~~~a~~~gm~~~~~vwI~t~~~~~~~~~~~~~~~~~~~g~l~~~~~~~~~~~~~~F~~~w~~~~~~~~~~~~~ 167 (829)
++.+..++++|.++||+..+|+||+|+-.....+.. +......+++|++++.++.+.+++|..+|++.+...+++...
T Consensus 189 ~~~~~~il~~a~e~gM~~~~y~~ilt~ld~~~~dl~--~~~~g~~NItg~rl~~~~~~~~~~f~~~w~~~~~~~~~~~~~ 266 (372)
T cd06387 189 VERINTILEQVVILGKHSRGYHYMLANLGFTDISLE--RVMHGGANITGFQIVNNENPMVQQFLQRWVRLDEREFPEAKN 266 (372)
T ss_pred HHHHHHHHHHHHHcCccccceEEEEecCCcccccHH--HhccCCcceeEEEEecCCCchHHHHHHHHHhCCcccCCCCCC
Confidence 999999999999999999999999998333222221 122223339999999999999999999999887777665554
Q ss_pred cccchhHHHHHHHHHHHHHHHHHhcccCccccCCCCCCCCCCCcc--ccCCCChHHHHHHHhccceecccccEEEe-cCc
Q 043276 168 AELNIFGLLAYDATSALAVAVEKAGITGFGFDKTNVSSNATDLEA--FGISQNGPKLLQALSSIRFRGLTGDYIFV-DGQ 244 (829)
Q Consensus 168 ~~~~~~~~~~YDAV~~~A~Al~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~g~~l~~~L~~~~f~G~tG~~~F~-~G~ 244 (829)
.++..+++++|||||++|+|++++..........+ ...+|.. ...|..|..|+++|++++|+|+||++.|+ +|+
T Consensus 267 ~~l~~~~al~yDaV~~~A~A~~~l~~~~~~~~~~~---~~~~C~~~~~~~W~~G~~l~~~ik~v~~~GLTG~i~F~~~G~ 343 (372)
T cd06387 267 SPLKYTSALTHDAILVIAEAFRYLRRQRVDVSRRG---SAGDCLANPAVPWSQGIDIERALKMVQVQGMTGNIQFDTYGR 343 (372)
T ss_pred CCcchHHHHHHHHHHHHHHHHHHHHhcCCCcccCC---CCCCcCCCCCCCccchHHHHHHHHhcccCCCccceeeCCCCC
Confidence 55778999999999999999999854332211111 1224532 34688999999999999999999999996 899
Q ss_pred cccceEEEEEcc-CCcEEEEEecCCCCc
Q 043276 245 LQSSAFEIINVN-NGARGVGFWSPEKGL 271 (829)
Q Consensus 245 ~~~~~y~I~n~~-~g~~~VG~w~~~~g~ 271 (829)
+.+..|+|+|+. +|+++||+|++..|+
T Consensus 344 R~~~~ldIinl~~~g~~kIG~W~~~~g~ 371 (372)
T cd06387 344 RTNYTIDVYEMKPSGSRKAGYWNEYERF 371 (372)
T ss_pred cccceEEEEEecCCCceeEEEECCCCCc
Confidence 999999999999 999999999998875
No 7
>cd06365 PBP1_Pheromone_receptor Ligand-binding domain of the V2R phermone receptor, a member of the family C receptors within the G-protein coupled receptor superfamily. Ligand-binding domain of the V2R phermone receptor, a member of the family C receptors within the G-protein coupled receptor superfamily, which also includes the metabotropic glutamate receptor, the GABAb receptor, the calcium-sensing receptor (CaSR), the T1R taste receptor, and a small group of uncharacterized orphan receptors.
Probab=100.00 E-value=1.2e-33 Score=320.75 Aligned_cols=272 Identities=18% Similarity=0.188 Sum_probs=216.2
Q ss_pred CCCChHHHHHHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCCh--hHHHHHHHHhhcCC
Q 043276 1 GALNDSSQVGAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATD--DQIEKELYKLFTMQ 78 (829)
Q Consensus 1 t~psD~~q~~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~--~~~~~~l~~lk~~~ 78 (829)
|+|+|..|+.||++++++|||+||++|++|++||+.+++.|.+++++.|+||++.+.++....+ .++...+.+|++++
T Consensus 152 t~psd~~q~~ai~~li~~f~W~~Vaiv~~d~~yg~~~~~~~~~~~~~~gi~I~~~~~i~~~~~~~~~~~~~~l~~i~~~~ 231 (469)
T cd06365 152 MAPKDTSLPLGMVSLMLHFSWTWVGLVISDDDRGEQFLSDLREEMQRNGICLAFVEKIPVNMQLYLTRAEKYYNQIMTSS 231 (469)
T ss_pred ecCCchhHHHHHHHHHHhcCCeEEEEEEecChhHHHHHHHHHHHHHHCCeEEEEEEEecCCchhhHHHHHHHHHHhhcCC
Confidence 6899999999999999999999999999999999999999999999999999999999876543 37888999999999
Q ss_pred CeEEEEEcChhHHHHHHHHHHHcCccccCeEEEEcCccccccccCCccccccccceEEEEeccCCChhHHHHHH------
Q 043276 79 TRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLEPSVTDSMQGVIGVRPYVPKTKALENFRV------ 152 (829)
Q Consensus 79 arViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t~~~~~~~~~~~~~~~~~~~g~l~~~~~~~~~~~~~~F~~------ 152 (829)
+||||++++.+.+..++.++.+.+ +.+++||++++|....... ....+.++|++++.++.++.+++++|+.
T Consensus 232 arvIvl~~~~~~~~~l~~~~~~~~--~~~~~wi~s~~w~~~~~~~-~~~~~~~~G~lg~~~~~~~~~~f~~fl~~l~~~~ 308 (469)
T cd06365 232 AKVIIIYGDTDSLLEVSFRLWQYL--LIGKVWITTSQWDVTTSPK-DFTLNSFHGTLIFSHHHSEIPGFKDFLQTVNPSK 308 (469)
T ss_pred CeEEEEEcCcHHHHHHHHHHHHhc--cCceEEEeecccccccccc-ccccceeeEEEEEEeccCcCcchHHHhhccCccc
Confidence 999999999988877766666554 3679999999997544222 2356789999999999999999999864
Q ss_pred ---------HHHHhhcccCCCCC-----------cc--------c--cchhHHHHHHHHHHHHHHHHHhcccCccccCCC
Q 043276 153 ---------RWKRKFLQENPSLF-----------DA--------E--LNIFGLLAYDATSALAVAVEKAGITGFGFDKTN 202 (829)
Q Consensus 153 ---------~w~~~~~~~~~~~~-----------~~--------~--~~~~~~~~YDAV~~~A~Al~~~~~~~~~~~~~~ 202 (829)
.|+..|+|..+... .. + ...++.++||||||+|||||+++.|.+...+.
T Consensus 309 ~~~npw~~efwe~~f~c~~~~~~~~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~v~dAVya~AhALh~~l~c~~~~~~~- 387 (469)
T cd06365 309 YPEDIFLEKLWWIYFNCSLSKSSCKTLKNCLSNASLEWLPLHYFDMAMSEESYNVYNAVYAVAHALHEMLLQQVETQSE- 387 (469)
T ss_pred CCCccHHHhhHhHhcCcccCcCCccccCCCCCCccccccccccccchhhhhHHHHHHHHHHHHHHHHHHHHhhccCCCc-
Confidence 58999988742110 10 0 23467889999999999999999876532111
Q ss_pred CCCCCCCCccccCCCChHHHHHHHhccceeccccc-EEEe-cCccccceEEEEEcc-C--C---cEEEEEecCCCCcccc
Q 043276 203 VSSNATDLEAFGISQNGPKLLQALSSIRFRGLTGD-YIFV-DGQLQSSAFEIINVN-N--G---ARGVGFWSPEKGLTQK 274 (829)
Q Consensus 203 ~~~~~~~~~~~~~~~~g~~l~~~L~~~~f~G~tG~-~~F~-~G~~~~~~y~I~n~~-~--g---~~~VG~w~~~~g~~~~ 274 (829)
.+|.. ....+++|+++|++++|+|.+|. +.|+ |||+ .+.|+|+||+ . + +++||+|++..+....
T Consensus 388 -----~~~~~--~~~~~~~l~~~l~~v~F~~~~g~~v~Fd~nGd~-~~~YdI~n~q~~~~~~~~~~~VG~~~~~~~~~~~ 459 (469)
T cd06365 388 -----NNGKR--LIFLPWQLHSFLKNIQFKNPAGDEVNLNQKRKL-DTEYDILNYWNFPQGLGLKVKVGEFSPQAPSGQQ 459 (469)
T ss_pred -----CCCCC--CCccHHHHHHHHHhccccCCCCCEEEecCCCCc-CceeeEEEEEECCCCCEEEEEEEEEeCCCCCCcE
Confidence 11211 23458899999999999999995 7897 9998 4899999998 2 2 7999999865443333
Q ss_pred cCCCccccCCccceec
Q 043276 275 LSSNSTTKSKLRPIIW 290 (829)
Q Consensus 275 l~~~~~~~~~~~~i~W 290 (829)
|. ++.+.|.|
T Consensus 460 l~------i~~~~i~W 469 (469)
T cd06365 460 LS------ISEEMIEW 469 (469)
T ss_pred EE------EehhhccC
Confidence 43 56677877
No 8
>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=2.1e-32 Score=312.62 Aligned_cols=276 Identities=18% Similarity=0.267 Sum_probs=222.6
Q ss_pred CCCChHHHHHHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCe
Q 043276 1 GALNDSSQVGAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTR 80 (829)
Q Consensus 1 t~psD~~q~~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~ar 80 (829)
|+|+|..|++|+++++++|||+||++|+.|++||+.+++.|.+++++.|+||++.+.++...+..++.+.+.+|+++++|
T Consensus 167 t~psd~~q~~Ai~~l~~~f~wk~VaiI~~dd~yG~~~~~~~~~~~~~~Gi~I~~~~~i~~~~~~~d~~~~l~klk~~~a~ 246 (510)
T cd06364 167 TIPNDEHQATAMADIIEYFRWNWVGTIAADDDYGRPGIEKFREEAEERDICIDFSELISQYSDEEEIQRVVEVIQNSTAK 246 (510)
T ss_pred cCCChHHHHHHHHHHHHHcCCeEEEEEEecCcchHHHHHHHHHHHHHCCcEEEEEEEeCCCCCHHHHHHHHHHHHhcCCe
Confidence 68999999999999999999999999999999999999999999999999999998887655567899999999999999
Q ss_pred EEEEEcChhHHHHHHHHHHHcCccccCeEEEEcCccccccccCCccccccccceEEEEeccCCChhHHHHHH--------
Q 043276 81 VFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLEPSVTDSMQGVIGVRPYVPKTKALENFRV-------- 152 (829)
Q Consensus 81 ViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t~~~~~~~~~~~~~~~~~~~g~l~~~~~~~~~~~~~~F~~-------- 152 (829)
|||+++..+.+..++++|+++|+ .+++||++++|............+.++|++|+.++....++|++|+.
T Consensus 247 vVvl~~~~~~~~~ll~qa~~~g~--~~~iwI~s~~w~~~~~~~~~~~~~~~gg~lg~~~~~~~i~~f~~~l~~l~p~~~~ 324 (510)
T cd06364 247 VIVVFSSGPDLEPLIKEIVRRNI--TGKIWLASEAWASSSLIAMPEYFDVMGGTIGFALKAGQIPGFREFLQKVHPKKSS 324 (510)
T ss_pred EEEEEeCcHHHHHHHHHHHHhCC--CCcEEEEEchhhcccccccCCccceeeEEEEEEECCCcCccHHHHHHhCCcccCC
Confidence 99999999999999999999997 46899999999865444444566789999999999988998888764
Q ss_pred -------HHHHhhcccCCC--C-------------------------C-c------c--------c--cchhHHHHHHHH
Q 043276 153 -------RWKRKFLQENPS--L-------------------------F-D------A--------E--LNIFGLLAYDAT 181 (829)
Q Consensus 153 -------~w~~~~~~~~~~--~-------------------------~-~------~--------~--~~~~~~~~YDAV 181 (829)
.|+..|+|..+. . . . . + ...+++++||||
T Consensus 325 ~~~~~~~~we~~f~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~~~~~~~~~~~~~~~~~~~~~~~v~~AV 404 (510)
T cd06364 325 HNGFAKEFWEETFNCYLEDSPKNALPVDTFLGHEESGDDSENGSTAFRPLCTGDENIASVETPYLDYTHLRISYNVYLAV 404 (510)
T ss_pred CChHHHHHHHHhcCCCCCCCcccccccccccccccccccccccccccCCCCCChhhhcccCCccccccchhhHHHHHHHH
Confidence 588999987432 0 0 0 0 0 123578899999
Q ss_pred HHHHHHHHHhcccCccccCCCCCCCCCCCccccCCCChHHHHHHHhccceeccccc-EEEe-cCccccceEEEEEcc--C
Q 043276 182 SALAVAVEKAGITGFGFDKTNVSSNATDLEAFGISQNGPKLLQALSSIRFRGLTGD-YIFV-DGQLQSSAFEIINVN--N 257 (829)
Q Consensus 182 ~~~A~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~L~~~~f~G~tG~-~~F~-~G~~~~~~y~I~n~~--~ 257 (829)
||+|||||++..|..... ..+ ...|.... ...+++|+++|++++|+|.+|. +.|+ +||.. +.|+|+||+ .
T Consensus 405 yAvAhaLh~~~~c~~~~~--~~~--~~~c~~~~-~~~~~~l~~~L~~v~F~~~~g~~v~Fd~~Gd~~-~~YdI~n~q~~~ 478 (510)
T cd06364 405 YSIAHALQDIYTCTPGKG--LFT--NGSCADIK-KVEAWQVLKHLRHLNFTDNMGEQVRFDEGGDLV-GNYSIINWHLSP 478 (510)
T ss_pred HHHHHHHHHHhcCCCCCC--Ccc--CCCCCCCC-CCCHHHHHHHHHhcEEecCCCCEEEEecCCCCc-cceeEEEeeecC
Confidence 999999999987653211 000 02343321 2358999999999999999985 6797 99984 899999999 2
Q ss_pred --C---cEEEEEecCCCCcccccCCCccccCCccceec
Q 043276 258 --G---ARGVGFWSPEKGLTQKLSSNSTTKSKLRPIIW 290 (829)
Q Consensus 258 --g---~~~VG~w~~~~g~~~~l~~~~~~~~~~~~i~W 290 (829)
| +++||.|++..+....|. ++.+.|.|
T Consensus 479 ~~~~~~~v~VG~~~~~~~~~~~l~------i~~~~i~W 510 (510)
T cd06364 479 EDGSVVFKEVGYYNVYAKKGERLF------INESKILW 510 (510)
T ss_pred CCCcEEEEEEEEEcCCCCCCceEE------eccccccC
Confidence 2 689999987654444454 56677888
No 9
>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=1e-31 Score=296.86 Aligned_cols=259 Identities=20% Similarity=0.273 Sum_probs=204.1
Q ss_pred hHHHHHHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCCh---hHHHH-HHHHhhc--CC
Q 043276 5 DSSQVGAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATD---DQIEK-ELYKLFT--MQ 78 (829)
Q Consensus 5 D~~q~~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~---~~~~~-~l~~lk~--~~ 78 (829)
+..|.+|+++|+++|||++|+++ .|++||...++.|.+++++.|+||+.... .....+ ..+.. .+.+|++ .+
T Consensus 122 ~~~~~~ai~~li~~f~W~~v~i~-~d~~~~~~~l~~l~~~~~~~~i~I~~~~~-~~~~~~~~~~~~~~~~~~~l~~~~~~ 199 (400)
T cd06391 122 PVYLNDVILRVVTEYAWQKFIIF-YDTDYDIRGIQEFLDKVSQQGMDVALQKV-ENNINKMITGLFRTMRIEELNRYRDT 199 (400)
T ss_pred hHHHHHHHHHHHHHcCCcEEEEE-EeCCccHHHHHHHHHHHHHcCCeEEEEec-CcchhhhhHHHHHHHHHHHHHhhccc
Confidence 35689999999999999999975 57889999999999999999999997543 222111 12222 4455655 67
Q ss_pred CeEEEEEcChhHHHHHHHHHHHcCccccCeEEEEcCccccccccCCccccccccceEEEEeccCCChhHHHHHHHHHHhh
Q 043276 79 TRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLEPSVTDSMQGVIGVRPYVPKTKALENFRVRWKRKF 158 (829)
Q Consensus 79 arViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t~~~~~~~~~~~~~~~~~~~g~l~~~~~~~~~~~~~~F~~~w~~~~ 158 (829)
.|+||++|+++.+..+|++|.++||++.+|+||++++.....+... ...+.++|+.+++++.+.+..+.+|..+|...+
T Consensus 200 ~rviVl~~~~~~~~~ll~~a~~~gm~~~~y~wi~t~~~~~~~dl~~-~~~~~~~~v~~~r~~~~~~~~~~~~~~r~~~~~ 278 (400)
T cd06391 200 LRRAILVMNPATAKSFITEVVETNLVAFDCHWIIINEEISDMDVQE-LVRRSIGRLTIIRQTFPLPQNISQRCFRGNHRI 278 (400)
T ss_pred ccEEEEECCcHHHHHHHHHHHHcCCCCCCeEEEEeCccccccccch-HHhcccceEEEeccCCchHHHHHHHHHHHhhhc
Confidence 7999999999999999999999999999999999999887777533 334567888999999998889999999998876
Q ss_pred cccC--CCCC-ccccchhHHHHHHHHHHHHHHHHHhcccCccccCCCCCCCCCCCc--cccCCCChHHHHHHHhccceec
Q 043276 159 LQEN--PSLF-DAELNIFGLLAYDATSALAVAVEKAGITGFGFDKTNVSSNATDLE--AFGISQNGPKLLQALSSIRFRG 233 (829)
Q Consensus 159 ~~~~--~~~~-~~~~~~~~~~~YDAV~~~A~Al~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~g~~l~~~L~~~~f~G 233 (829)
.... +..+ ...++.+++++|||||++|+|++++........ .. ..+|. ...+|..|..|+++|++++|+|
T Consensus 279 ~~~~~~~~~~~~~~~~~~~alayDaV~~~A~A~~~l~~~~~~~~---~~--~~~c~~~~~~~w~~G~~ll~~i~~~~f~G 353 (400)
T cd06391 279 SSSLCDPKDPFAQMMEISNLYIYDTVLLLANAFHKKLEDRKWHS---MA--SLSCIRKNSKPWQGGRSMLETIKKGGVSG 353 (400)
T ss_pred cccccCccccccccccchhhHHHHHHHHHHHHHHHHHhhccccC---CC--CcccccCCCCCCCChHHHHHHHHhcCccc
Confidence 4322 2211 123568999999999999999998752221111 11 12333 3457889999999999999999
Q ss_pred ccccEEEe-cCccccceEEEEEc-----c-CCcEEEEEecCCCCc
Q 043276 234 LTGDYIFV-DGQLQSSAFEIINV-----N-NGARGVGFWSPEKGL 271 (829)
Q Consensus 234 ~tG~~~F~-~G~~~~~~y~I~n~-----~-~g~~~VG~w~~~~g~ 271 (829)
+||++.|+ +|++.+..|+|+|+ . +|+++||+|++..|+
T Consensus 354 lTG~i~f~~~g~r~~~~~dIin~~~~~~~~~g~rkiG~Ws~~~gl 398 (400)
T cd06391 354 LTGELEFNENGGNPNVHFEILGTNYGEDLGRGVRKLGCWNPITGL 398 (400)
T ss_pred ceeceEECCCCCccCCceEEEEeeccccCCCcceEEEEEcCCcCC
Confidence 99999996 79999999999999 3 679999999998875
No 10
>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=5.1e-32 Score=307.46 Aligned_cols=291 Identities=22% Similarity=0.352 Sum_probs=242.2
Q ss_pred CCCChHHHHHHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhc-CCC
Q 043276 1 GALNDSSQVGAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFT-MQT 79 (829)
Q Consensus 1 t~psD~~q~~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~-~~a 79 (829)
|+|+|.+|++||++|+++|||+||+.++++++||+.++++|.++.++.|+||++.+.++..+.+..+...++++.+ .++
T Consensus 174 tVP~D~~Qa~Am~~il~~f~W~yVstv~s~~dYGE~Gieaf~~~a~~~~iCIa~s~ki~~~~~~~~~~~~l~kl~~~~~a 253 (878)
T KOG1056|consen 174 TVPSDVFQAQAMVDILKKFNWNYVSTVASEGDYGESGIEAFKEEAAERGICIAFSEKIYQLSIEQEFDCVLRKLLETPNA 253 (878)
T ss_pred ecCChHHHHHHHHHHHHHhCeeEeeehhcCccchhhhHHHHHHhHHhcCceEEehhhcccccchhHHHHHHHHHhhcCCC
Confidence 6899999999999999999999999999999999999999999999999999999888877677789999999886 899
Q ss_pred eEEEEEcChhHHHHHHHHHHHcCccccCeEEEEcCccccccccCCccccccccceEEEEeccCCChhHHHHHH-------
Q 043276 80 RVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLEPSVTDSMQGVIGVRPYVPKTKALENFRV------- 152 (829)
Q Consensus 80 rViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t~~~~~~~~~~~~~~~~~~~g~l~~~~~~~~~~~~~~F~~------- 152 (829)
||+|+++..+.+.+++++|.++++.+ .++||++|+|....+... ...+..+|++++.+..+..+.|++|.+
T Consensus 254 ~vvV~F~~~~~~r~~~~aa~~~n~~g-~~~wiaSd~W~~~~~~~~-~~e~~a~g~i~i~l~~~~v~~F~~y~~s~~p~nn 331 (878)
T KOG1056|consen 254 RVVVVFCRGEDARRLLKAARRANLTG-EFLWIASDGWASQNSPTE-APEREAEGAITIKLASPQVPGFDRYFQSLHPENN 331 (878)
T ss_pred eEEEEecCcchHHHHHHHHHHhCCCc-ceEEEecchhhccCChhh-hhhhhhceeEEEEecCCcchhHHHHHHhcCcccc
Confidence 99999999999999999999999743 599999999997544433 233478999999999999999998864
Q ss_pred --------HHHHhhcccCCCCC----c-------c---------ccchhHHHHHHHHHHHHHHHHHhcccCccccCCCCC
Q 043276 153 --------RWKRKFLQENPSLF----D-------A---------ELNIFGLLAYDATSALAVAVEKAGITGFGFDKTNVS 204 (829)
Q Consensus 153 --------~w~~~~~~~~~~~~----~-------~---------~~~~~~~~~YDAV~~~A~Al~~~~~~~~~~~~~~~~ 204 (829)
+|+..|+|.++... + . +-..-...++||||++|||||++..+.+...
T Consensus 332 ~~n~w~~e~w~~~f~C~l~~~~~~~~~~~~~Ct~~e~~~~~~~~~q~~k~~~Vi~aVya~A~aLh~m~~~lc~~~----- 406 (878)
T KOG1056|consen 332 RRNPWFAEFWEDKFNCSLPNSAFKNENLIRLCTAVERITLDSAYEQDSKVQFVIDAVYAMAHALHNMHQDLCPGT----- 406 (878)
T ss_pred ccCcccchhhhhcccCCCCcccccchhhhhhcccchhhccccchhhhcccccHHHHHHHHHHHHHHHHHhhcCCc-----
Confidence 69999999886321 0 0 0112357899999999999999987765321
Q ss_pred CCCCCCccccCCCChHHHHHHHhccceecccccEEEe-cCccccceEEEEEcc--C---CcEEEEEecCCCCcccccCCC
Q 043276 205 SNATDLEAFGISQNGPKLLQALSSIRFRGLTGDYIFV-DGQLQSSAFEIINVN--N---GARGVGFWSPEKGLTQKLSSN 278 (829)
Q Consensus 205 ~~~~~~~~~~~~~~g~~l~~~L~~~~f~G~tG~~~F~-~G~~~~~~y~I~n~~--~---g~~~VG~w~~~~g~~~~l~~~ 278 (829)
...|..... .+|++|++++++++|.|..|.+.|+ +||.. +.|+|++++ + .+..||+|+....
T Consensus 407 --~~~C~~m~~-~dg~~L~~~l~~vnF~~~~~~v~Fd~~gD~~-~~y~I~~~~~~~~~~~y~~vg~w~~~~~-------- 474 (878)
T KOG1056|consen 407 --SGLCSAMKA-IDGSLLLKYLLNVNFTGPAGSVRFDENGDGP-GRYDILNYQLTNGSYTYKEVGYWSEGLS-------- 474 (878)
T ss_pred --cccCcCccc-cCHHHHHhhhheeEEecCCCceeecCCCCCc-cceeEEEeeccCCCccceeeeeeccccc--------
Confidence 134554433 5799999999999999999999997 99984 899999999 4 2899999997543
Q ss_pred ccccCCccceecCCCCCCCCCCcc----cCCCCceEEEec
Q 043276 279 STTKSKLRPIIWPGDSTSDPKGWE----IPTNEKKLRVGV 314 (829)
Q Consensus 279 ~~~~~~~~~i~Wpg~~~~~P~~~~----~p~~~~~lrv~v 314 (829)
++...+.|.++...+|++.| .|++.|+++-++
T Consensus 475 ----l~i~~~~w~~~~~~v~~S~CS~pC~~g~~k~~~~~~ 510 (878)
T KOG1056|consen 475 ----LNIEDLDWTTKPSGVPKSVCSEPCLPGQRKKVTKGV 510 (878)
T ss_pred ----ccceeeeeccCCCCCccccccCcCCcchhcccccCc
Confidence 35678999999999999997 567777665443
No 11
>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=1.6e-31 Score=292.27 Aligned_cols=252 Identities=20% Similarity=0.301 Sum_probs=194.8
Q ss_pred HHHHHHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEe-------cCCCCChhHHHHHHHHhhcCC
Q 043276 6 SSQVGAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSV-------ISPLATDDQIEKELYKLFTMQ 78 (829)
Q Consensus 6 ~~q~~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~-------i~~~~~~~~~~~~l~~lk~~~ 78 (829)
..+..||++|+.+|||++|++|| |++||...++.|.+++.+.+..|.++.. +++.. .+...++|.+++.+.
T Consensus 123 ~~~~~Ai~dlV~~~~W~~v~~iY-D~d~gl~~lq~L~~~~~~~~~~I~~~~v~~~~~~~~~~~l-~~~~~~~L~~~~~~~ 200 (400)
T cd06392 123 VRLNDVMLKLVTELRWQKFIVFY-DSEYDIRGLQSFLDQASRLGLDVSLQKVDRNISRVFTNLF-TTMKTEELNRYRDTL 200 (400)
T ss_pred hHHHHHHHHHHHhCCCcEEEEEE-ECcccHHHHHHHHHHHhhcCceEEEEEcccCcchhhhhHH-HHHHHhhhhhccccc
Confidence 34788999999999999999999 8999999999999999999999997762 22111 223445666676666
Q ss_pred CeEEEEEcChhHHHHHHHHHHHcCccccCeEEEEcCccccccccCCccccccccceEE----EEeccCCChhHHHHH---
Q 043276 79 TRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLEPSVTDSMQGVIG----VRPYVPKTKALENFR--- 151 (829)
Q Consensus 79 arViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t~~~~~~~~~~~~~~~~~~~g~l~----~~~~~~~~~~~~~F~--- 151 (829)
|+|||+|+++.+..+|++|.++|||..+|+||+|+......+ ..+.++|.++ ++.+.+.+....+|.
T Consensus 201 -r~iVv~~s~~~~~~il~qA~~lgM~~~~y~wI~t~~~~~~~d-----l~~~~~g~~~niT~~r~~~~~~~~~~~~~~~~ 274 (400)
T cd06392 201 -RRAILLLSPRGAQTFINEAVETNLASKDSHWVFVNEEISDTE-----ILELVHSALGRMTVIRQIFPLSKDNNQRCIRN 274 (400)
T ss_pred -eEEEEEcCcHHHHHHHHHHHHhCcccCCeEEEEecCCccccc-----HHHHhcccccceeeEEEecCCcHHHHHHHHHH
Confidence 999999999999999999999999999999999998665433 3334555554 999888777565554
Q ss_pred -HHHHHhhcccCCCCCccccchhHHHHHHHHHHHHHHHHHhcccCccccCCCCCCCCCCC--ccccCCCChHHHHHHHhc
Q 043276 152 -VRWKRKFLQENPSLFDAELNIFGLLAYDATSALAVAVEKAGITGFGFDKTNVSSNATDL--EAFGISQNGPKLLQALSS 228 (829)
Q Consensus 152 -~~w~~~~~~~~~~~~~~~~~~~~~~~YDAV~~~A~Al~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~g~~l~~~L~~ 228 (829)
.+|++........ ....++.+++++|||||++|+|++++....... .....+| ....+|..|..|+++|++
T Consensus 275 ~~r~~~~~~~~~~~-~~~~l~~~aalayDaV~~~A~Al~~ll~~~~~~-----~~~~l~C~~~~~~~w~~G~~ll~~ik~ 348 (400)
T cd06392 275 NHRISSLLCDPQEG-YLQMLQVSNLYLYDSVLMLANAFHRKLEDRKWH-----SMASLNCIRKSTKPWNGGRSMLETIKK 348 (400)
T ss_pred HHHHHhhhcccccc-cccccchhHHHHHHHHHHHHHHHHHHhhccccC-----CCCCCccCCCCCCCCCChHHHHHHHHh
Confidence 5675443321111 111467899999999999999999864221111 1111345 446789999999999999
Q ss_pred cceecccccEEEe-cCccccceEEEEEcc------CCcEEEEEecCCCCc
Q 043276 229 IRFRGLTGDYIFV-DGQLQSSAFEIINVN------NGARGVGFWSPEKGL 271 (829)
Q Consensus 229 ~~f~G~tG~~~F~-~G~~~~~~y~I~n~~------~g~~~VG~w~~~~g~ 271 (829)
++|+|+||++.|+ +|++.+..|+|+|+. .|.++||+|++..|+
T Consensus 349 v~f~GLTG~I~F~~~G~r~~~~ldIi~l~~~~~~g~g~~~iG~W~~~~gl 398 (400)
T cd06392 349 GHITGLTGVMEFKEDGANPHVQFEILGTSYSETFGKDVRRLATWDSEKGL 398 (400)
T ss_pred CCCccCccceeECCCCCCcCCceEEEeccccccCCCCceEeEEecCCCCC
Confidence 9999999999996 999999999999965 349999999998875
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=3e-31 Score=302.05 Aligned_cols=256 Identities=19% Similarity=0.282 Sum_probs=208.8
Q ss_pred CCCChHHHHHHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhC-CceeeeEEecCCCCChhHHHHHHHHhhc-CC
Q 043276 1 GALNDSSQVGAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAI-DTRVPYRSVISPLATDDQIEKELYKLFT-MQ 78 (829)
Q Consensus 1 t~psD~~q~~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~-gi~I~~~~~i~~~~~~~~~~~~l~~lk~-~~ 78 (829)
|+|+|..|+.|+++++++|||++|++||++++||...++.|.+++++. ++||+....++....+.++..++.+||+ ++
T Consensus 152 ~~p~d~~~~~ai~~~i~~~~w~~Vaii~~~~~yg~~~~~~~~~~~~~~g~~~v~~~~~i~~~~~~~d~~~~l~~ik~~~~ 231 (463)
T cd06376 152 VVPPDSFQAQAMVDIVKALGWNYVSTLASEGNYGESGVEAFTQISREAGGVCIAQSIKIPREPRPGEFDKIIKRLLETPN 231 (463)
T ss_pred ccCCHHHHHHHHHHHHHHcCCeEEEEEEeCChHHHHHHHHHHHHHHHcCCceEEEEEecCCCCCHHHHHHHHHHHhccCC
Confidence 579999999999999999999999999999999999999999999987 5899877777666666789999999986 79
Q ss_pred CeEEEEEcChhHHHHHHHHHHHcCccccCeEEEEcCccccccccCCccccccccceEEEEeccCCChhHHHHHH------
Q 043276 79 TRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLEPSVTDSMQGVIGVRPYVPKTKALENFRV------ 152 (829)
Q Consensus 79 arViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t~~~~~~~~~~~~~~~~~~~g~l~~~~~~~~~~~~~~F~~------ 152 (829)
+||||++++.+.+..++++|+++||++ .|+||++++|........ ...+.+.|++++.++....++|++|+.
T Consensus 232 ~~vIvl~~~~~~~~~ll~~a~~~~~~g-~~~wig~d~~~~~~~~~~-~~~~~~~G~~~~~~~~~~~~~F~~~~~~l~~~~ 309 (463)
T cd06376 232 ARAVIIFANEDDIRRVLEAAKRANQVG-HFLWVGSDSWGAKISPIL-QQEDVAEGAITILPKRASIEGFDAYFTSRTLEN 309 (463)
T ss_pred CeEEEEecChHHHHHHHHHHHhcCCcC-ceEEEEeccccccccccc-cCcceeeeEEEEEeccccchhHHHHHHhCCccc
Confidence 999999999999999999999999853 599999999975433322 134568999999999999999998765
Q ss_pred ---------HHHHhhcccCCC--CC---------c---------cccchhHHHHHHHHHHHHHHHHHhcccCccccCCCC
Q 043276 153 ---------RWKRKFLQENPS--LF---------D---------AELNIFGLLAYDATSALAVAVEKAGITGFGFDKTNV 203 (829)
Q Consensus 153 ---------~w~~~~~~~~~~--~~---------~---------~~~~~~~~~~YDAV~~~A~Al~~~~~~~~~~~~~~~ 203 (829)
.|+..|+|..+. .. . ......++++|||||++|||||++..+.+...
T Consensus 310 ~~~~~~~~~~w~~~f~c~~~~~~~~~~~~~~~C~~~~~~~~~~~~~~~~~~~~v~dAVyaiA~ALh~l~~~~c~~~---- 385 (463)
T cd06376 310 NRRNVWFAEFWEENFNCKLTISGSKKEDTDRKCTGQERIGRDSTYEQEGKVQFVIDAVYAMAHALHSMHKDLCPGY---- 385 (463)
T ss_pred CCCCcHHHHHHHHhCCCcccCCCCccccccCcCcchhhccccCcccccchhHHHHHHHHHHHHHHHHHHHhhCCCC----
Confidence 699999987531 10 0 00123688999999999999999976554211
Q ss_pred CCCCCCCccccCCCChHHHHHHHhccceecccc-cEEEe-cCccccceEEEEEcc-C-----CcEEEEEecC
Q 043276 204 SSNATDLEAFGISQNGPKLLQALSSIRFRGLTG-DYIFV-DGQLQSSAFEIINVN-N-----GARGVGFWSP 267 (829)
Q Consensus 204 ~~~~~~~~~~~~~~~g~~l~~~L~~~~f~G~tG-~~~F~-~G~~~~~~y~I~n~~-~-----g~~~VG~w~~ 267 (829)
. ..|... .+..|++|+++|++++|+|.+| .+.|+ +|++. +.|+|+|++ . ++++||.|++
T Consensus 386 ~---~~C~~~-~~~~~~~l~~~L~~v~F~g~tg~~v~Fd~~G~~~-~~Ydi~n~q~~~~~~~~~~~VG~w~~ 452 (463)
T cd06376 386 T---GVCPEM-EPADGKKLLKYIRAVNFNGSAGTPVMFNENGDAP-GRYDIFQYQITNTSSPGYRLIGQWTD 452 (463)
T ss_pred C---CCCccC-CCCCHHHHHHHHHhCCccCCCCCeEEeCCCCCCC-CceEEEEEEecCCCceeEEEEEEECC
Confidence 1 124332 2456899999999999999999 68997 99985 689999999 2 2899999974
No 13
>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=3.4e-31 Score=299.59 Aligned_cols=254 Identities=19% Similarity=0.261 Sum_probs=209.2
Q ss_pred CCCChHHHHHHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhc-CCC
Q 043276 1 GALNDSSQVGAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFT-MQT 79 (829)
Q Consensus 1 t~psD~~q~~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~-~~a 79 (829)
|+|+|..|+.||++++++|||+||++||+|++||+.+++.|.+++++.|+||++.+.++......++.+++++|++ .++
T Consensus 154 t~psd~~qa~ai~~ll~~~~W~~Vaii~~~~~yG~~~~~~~~~~~~~~gi~i~~~~~i~~~~~~~d~~~~l~~l~~~~~a 233 (458)
T cd06375 154 TVPPDFYQAKAMAEILRFFNWTYVSTVASEGDYGETGIEAFEQEARLRNICIATSEKVGRSADRKSYDSVIRKLLQKPNA 233 (458)
T ss_pred ecCCcHHHHHHHHHHHHHCCCeEEEEEEeCchHHHHHHHHHHHHHHHCCeeEEEEEEecCCCCHHHHHHHHHHHhccCCC
Confidence 6899999999999999999999999999999999999999999999999999999988876566789999999875 799
Q ss_pred eEEEEEcChhHHHHHHHHHHHcCccccCeEEEEcCccccccccCCccccccccceEEEEeccCCChhHHHHHH-------
Q 043276 80 RVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLEPSVTDSMQGVIGVRPYVPKTKALENFRV------- 152 (829)
Q Consensus 80 rViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t~~~~~~~~~~~~~~~~~~~g~l~~~~~~~~~~~~~~F~~------- 152 (829)
||||++++.+.+..++++|.++|+. ++||++++|........ .....++|++++.++....++|++|+.
T Consensus 234 ~vVvl~~~~~~~~~ll~~a~~~g~~---~~wigs~~~~~~~~~~~-~~~~~~~G~i~~~~~~~~i~~f~~yl~~l~p~~~ 309 (458)
T cd06375 234 RVVVLFTRSEDARELLAAAKRLNAS---FTWVASDGWGAQESIVK-GSEDVAEGAITIELASHPIPDFDRYFQSLTPETN 309 (458)
T ss_pred EEEEEecChHHHHHHHHHHHHcCCc---EEEEEeccccccchhhh-ccchhhceEEEEEeccccchhHHHHHHhCCcCcC
Confidence 9999999999999999999999973 89999999974322222 234678999999999999999999874
Q ss_pred --------HHHHhhcccCCCCCc----------------cccchhHHHHHHHHHHHHHHHHHhcccCccccCCCCCCCCC
Q 043276 153 --------RWKRKFLQENPSLFD----------------AELNIFGLLAYDATSALAVAVEKAGITGFGFDKTNVSSNAT 208 (829)
Q Consensus 153 --------~w~~~~~~~~~~~~~----------------~~~~~~~~~~YDAV~~~A~Al~~~~~~~~~~~~~~~~~~~~ 208 (829)
.|+..|+|..+.... .....++.++||||||+|||||++..+.|.... .
T Consensus 310 ~~n~w~~e~w~~~f~c~~~~~~~~~~~C~~~~~~~~~~~~~~~~~~~~v~~AVyA~AhaLh~~l~~~c~~~~-------~ 382 (458)
T cd06375 310 TRNPWFKDFWEQKFQCSLQNRDCANTTTNDKERLLDKVNYEQESKIMFVVNAVYAMAHALHNMQRDLCPNTT-------K 382 (458)
T ss_pred CCCcHHHHHHHHHcCCCCCCCCccCCCCCchhcccccCcccccchHHHHHHHHHHHHHHHHHHHHhcCCCCC-------C
Confidence 599999998642210 012347889999999999999999876653211 2
Q ss_pred CCccccCCCChHHHH-HHHhcccee-----ccccc-EEEe-cCccccceEEEEEcc---CC----cEEEEEecC
Q 043276 209 DLEAFGISQNGPKLL-QALSSIRFR-----GLTGD-YIFV-DGQLQSSAFEIINVN---NG----ARGVGFWSP 267 (829)
Q Consensus 209 ~~~~~~~~~~g~~l~-~~L~~~~f~-----G~tG~-~~F~-~G~~~~~~y~I~n~~---~g----~~~VG~w~~ 267 (829)
.|.... ...+++|+ ++|++++|+ |.+|. +.|+ |||. .+.|+|+||+ ++ +++||.|+.
T Consensus 383 ~c~~~~-~~~~~~l~~~~L~~v~F~~~~~~~~~g~~v~Fd~nGd~-~~~YdI~n~q~~~~~~~~~~~~VG~w~~ 454 (458)
T cd06375 383 LCDAMK-PLDGKKLYKEYLLNVSFTAPFRPDLADSEVKFDSQGDG-LGRYNIFNYQRTGNSYGYRYVGVGAWAN 454 (458)
T ss_pred CCCCCC-CCCHHHHHHHHHHhccccccccCCCCCCeeEECCCCCC-CcceEEEEEEEcCCCCcEEEEEEEEEec
Confidence 243321 23589999 599999999 99884 6797 9997 4899999999 33 689999963
No 14
>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=99.98 E-value=5.5e-31 Score=300.39 Aligned_cols=256 Identities=18% Similarity=0.253 Sum_probs=207.9
Q ss_pred CCCChHHHHHHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhc--CC
Q 043276 1 GALNDSSQVGAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFT--MQ 78 (829)
Q Consensus 1 t~psD~~q~~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~--~~ 78 (829)
|+|+|..|+.|+++++++|||+||++||++++||+..++.|.+.+++.|+||++.+.++......++..++.+||+ .+
T Consensus 166 t~p~d~~~~~al~~l~~~~~W~~Vaii~~~~~yg~~~~~~~~~~~~~~gi~i~~~~~i~~~~~~~d~~~~l~~lk~~~~d 245 (472)
T cd06374 166 VVPSDTLQARAMLDIVKRYNWTYVSAVHTEGNYGESGMEAFKELAAHEGLCIAHSDKIYSNAGEQSFDRLLRKLRSRLPK 245 (472)
T ss_pred cCCChHHHHHHHHHHHHHCCCcEEEEEEecchHHHHHHHHHHHHHHHCCeeEEEEEEecCCCchHHHHHHHHHHHhcCCC
Confidence 6799999999999999999999999999999999999999999999999999998888665556789999999996 46
Q ss_pred CeEEEEEcChhHHHHHHHHHHHcCccccCeEEEEcCccccccccCCccccccccceEEEEeccCCChhHHHHH-------
Q 043276 79 TRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLEPSVTDSMQGVIGVRPYVPKTKALENFR------- 151 (829)
Q Consensus 79 arViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t~~~~~~~~~~~~~~~~~~~g~l~~~~~~~~~~~~~~F~------- 151 (829)
+|||++++....+..++++|+++||. .+++||.+++|........ ...+.++|++++.++.++.++|++|+
T Consensus 246 a~vvv~~~~~~~~~~~l~~a~~~g~~-~~~~wi~s~~~~~~~~~~~-~~~~~~~G~l~~~~~~~~~~~F~~~l~~l~~~~ 323 (472)
T cd06374 246 ARVVVCFCEGMTVRGLLMAMRRLGVG-GEFQLIGSDGWADRDDVVE-GYEEEAEGGITIKLQSPEVPSFDDYYLKLRPET 323 (472)
T ss_pred cEEEEEEechHHHHHHHHHHHHhcCC-CceEEEEecccccchHhhh-cchhhhheeEEEEecCCCCccHHHHHHhCCccc
Confidence 88888888888899999999999984 5589999999986433332 34567899999999999999999864
Q ss_pred --------HHHHHhhcccCCCCCc--------------c----ccchhHHHHHHHHHHHHHHHHHhcccCccccCCCCCC
Q 043276 152 --------VRWKRKFLQENPSLFD--------------A----ELNIFGLLAYDATSALAVAVEKAGITGFGFDKTNVSS 205 (829)
Q Consensus 152 --------~~w~~~~~~~~~~~~~--------------~----~~~~~~~~~YDAV~~~A~Al~~~~~~~~~~~~~~~~~ 205 (829)
+.|+..|+|..+.... . ....++.++|||||++|+|||++..+.+... .
T Consensus 324 ~~~~~~~~~~w~~~f~c~~~~~~~~~~~~~~~c~~~~~~~~~~~~~~~~~~vyDAVyaiA~ALh~~~~~~~~~~----~- 398 (472)
T cd06374 324 NTRNPWFREFWQHRFQCRLPGHPQENPNYIKICTGNESLDEQYVQDSKMGFVINAIYAMAHGLHNMHQDLCPGH----V- 398 (472)
T ss_pred CCCChHHHHHHHHhcCCCcCCccCcCCccCCCCCCcccccccccccceeHHHHHHHHHHHHHHHHHHHhhCCCC----C-
Confidence 4799999997521100 0 0124566999999999999999976553211 1
Q ss_pred CCCCCccccCCCChHHHHHHHhccceecccc-cEEEe-cCccccceEEEEEcc-C--C---cEEEEEecC
Q 043276 206 NATDLEAFGISQNGPKLLQALSSIRFRGLTG-DYIFV-DGQLQSSAFEIINVN-N--G---ARGVGFWSP 267 (829)
Q Consensus 206 ~~~~~~~~~~~~~g~~l~~~L~~~~f~G~tG-~~~F~-~G~~~~~~y~I~n~~-~--g---~~~VG~w~~ 267 (829)
..|.... ...|++|+++|++++|+|++| .+.|+ +|++. +.|+|+|++ . | +++||.|++
T Consensus 399 --~~c~~~~-~~~~~~l~~~l~~v~F~g~tG~~v~Fd~~G~~~-~~ydI~n~~~~~~~~~~~~~VG~w~~ 464 (472)
T cd06374 399 --GLCDAMK-PIDGRKLLEYLLKTSFSGVSGEEVYFDENGDSP-GRYDIMNLQYTEDLRFDYINVGSWHE 464 (472)
T ss_pred --CCCcCCC-CCCHHHHHHHHHhCcccCCCCCeEEEcCCCCCC-CceEEEEEEECCCCCEEEEEEEEEeC
Confidence 1233221 346899999999999999999 68997 99985 699999999 2 2 899999974
No 15
>cd06379 PBP1_iGluR_NMDA_NR1 N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the NR1, an essential channel-forming subunit of the NMDA receptor. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the NR1, an essential channel-forming subunit of the NMDA receptor. The ionotropic N-methyl-d-asparate (NMDA) subtype of glutamate receptor serves critical functions in neuronal development, functioning, and degeneration in the mammalian central nervous system. The functional NMDA receptor is a heterotetramer ccomposed of two NR1 and two NR2 (A, B, C, and D) or of NR3 (A and B) subunits. The receptor controls a cation channel that is highly permeable to monovalent ions and calcium and exhibits voltage-dependent inhibition by magnesium. Dual agonists, glutamate and glycine, are required for efficient activation of the NMDA receptor. When co-expressed with NR1, the NR3 subunits form receptors that are activated by glycine alone and therefore
Probab=99.97 E-value=1.1e-30 Score=290.06 Aligned_cols=237 Identities=22% Similarity=0.344 Sum_probs=198.4
Q ss_pred CCCChHHHHHHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCc----eeeeEEecCCCCChhHHHHHHHHhhc
Q 043276 1 GALNDSSQVGAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDT----RVPYRSVISPLATDDQIEKELYKLFT 76 (829)
Q Consensus 1 t~psD~~q~~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi----~I~~~~~i~~~~~~~~~~~~l~~lk~ 76 (829)
++|+|..|+.|+++++++|||++|++||++++||.+.++.|++++++.|+ ||+..+.++.+ +.++..++.+||+
T Consensus 134 ~~psd~~~~~a~~~~l~~~~w~~vaii~~~~~~g~~~~~~~~~~~~~~g~~~~~~v~~~~~~~~~--~~d~~~~l~~ik~ 211 (377)
T cd06379 134 TVPPYSHQADVWLEMLRSFKWNKVILLVSDDHEGRAAQKRFETLLEEREIEFKIKVEKVVEFEPG--EKNVTSLLQEAKE 211 (377)
T ss_pred ecCCHHHHHHHHHHHHHHcCCeEEEEEEEcCcchhHHHHHHHHHHHhcCCccceeeeEEEecCCc--hhhHHHHHHHHhh
Confidence 47999999999999999999999999999999999999999999999999 88887777654 4689999999999
Q ss_pred CCCeEEEEEcChhHHHHHHHHHHHcCccccCeEEEEcCccccccccCCccccccccceEEEEeccCCChhHHHHHHHHHH
Q 043276 77 MQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLEPSVTDSMQGVIGVRPYVPKTKALENFRVRWKR 156 (829)
Q Consensus 77 ~~arViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t~~~~~~~~~~~~~~~~~~~g~l~~~~~~~~~~~~~~F~~~w~~ 156 (829)
.++|+||++++.+.+..++++|+++||++.+|+||.++.|... .+...|++|+++..+.
T Consensus 212 ~~~~vIvl~~~~~~~~~l~~qa~~~g~~~~~~~wi~t~~~~~~--------~~~~~g~~g~~~~~~~------------- 270 (377)
T cd06379 212 LTSRVILLSASEDDAAVIYRNAGMLNMTGEGYVWIVSEQAGAA--------RNAPDGVLGLQLINGK------------- 270 (377)
T ss_pred cCCeEEEEEcCHHHHHHHHHHHHHcCCCCCCEEEEEecccccc--------ccCCCceEEEEECCCC-------------
Confidence 9999999999999999999999999999889999999998432 2346899999875421
Q ss_pred hhcccCCCCCccccchhHHHHHHHHHHHHHHHHHhcccCccccCCCCCCCCCCCcccc-CCCChHHHHHHHhccceeccc
Q 043276 157 KFLQENPSLFDAELNIFGLLAYDATSALAVAVEKAGITGFGFDKTNVSSNATDLEAFG-ISQNGPKLLQALSSIRFRGLT 235 (829)
Q Consensus 157 ~~~~~~~~~~~~~~~~~~~~~YDAV~~~A~Al~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~g~~l~~~L~~~~f~G~t 235 (829)
.+++++|||||++|+|+|++..+... .. ....|.... .|..|+.|+++|++++|+|+|
T Consensus 271 ---------------~~~~~~yDAV~~~A~Al~~~~~~~~~---~~---~~~~c~~~~~~~~~g~~l~~~l~~v~f~G~t 329 (377)
T cd06379 271 ---------------NESSHIRDAVAVLASAIQELFEKENI---TE---PPRECVGNTVIWETGPLFKRALMSSKYPGET 329 (377)
T ss_pred ---------------CHHHHHHHHHHHHHHHHHHHHcCCCC---CC---CCccccCCCCCCcchHHHHHHHHhCCcCCcc
Confidence 24678999999999999998653211 00 012343322 467899999999999999999
Q ss_pred ccEEEe-cCccccceEEEEEcc-CCcEEEEEecCCCCcccccCCCccccCCccceecCC
Q 043276 236 GDYIFV-DGQLQSSAFEIINVN-NGARGVGFWSPEKGLTQKLSSNSTTKSKLRPIIWPG 292 (829)
Q Consensus 236 G~~~F~-~G~~~~~~y~I~n~~-~g~~~VG~w~~~~g~~~~l~~~~~~~~~~~~i~Wpg 292 (829)
|++.|+ +|++....|+|+|++ .++++||+|++. .+. .+.+.|.||+
T Consensus 330 g~i~Fd~~Gd~~~~~~~I~~~~~~~~~~VG~w~~~-----~l~------~~~~~i~W~~ 377 (377)
T cd06379 330 GRVEFNDDGDRKFANYDIMNIQNRKLVQVGLYNGD-----ILR------LNDRSIIWPG 377 (377)
T ss_pred CceEECCCCCccCccEEEEEecCCCceEeeEEcCc-----EEE------ecCceeeCCC
Confidence 999996 999976899999999 889999999863 222 3557899985
No 16
>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=99.97 E-value=6.2e-30 Score=284.49 Aligned_cols=234 Identities=18% Similarity=0.223 Sum_probs=193.6
Q ss_pred CCCChHHHHHHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCCh-----hHHHHHHHHhh
Q 043276 1 GALNDSSQVGAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATD-----DQIEKELYKLF 75 (829)
Q Consensus 1 t~psD~~q~~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~-----~~~~~~l~~lk 75 (829)
|+|+|..|++||++++++|||+||++|++|++||+++++.|.+++++.|+||+..+.++...++ .++...+++++
T Consensus 152 t~p~D~~qa~ai~~li~~~~w~~Vaii~~~d~yG~~~~~~f~~~~~~~GicIa~~e~~~~~~~~~~~~~~~~~~~~~~ik 231 (403)
T cd06361 152 TVPSDFYQTKAMAHLIKKSGWNWVGIIITDDDYGRSALETFIIQAEANGVCIAFKEILPASLSDNTKLNRIIRTTEKIIE 231 (403)
T ss_pred CCCchHhHHHHHHHHHHHcCCcEEEEEEecCchHHHHHHHHHHHHHHCCeEEEEEEEecCccCcchhHHHHHHHHHHHHh
Confidence 6899999999999999999999999999999999999999999999999999999998875422 23445555678
Q ss_pred cCCCeEEEEEcChhHHHHHHHHHHHcCccccCeEEEEcCccccccccCCccccccccceEEEEeccCCChhHHHHHHHHH
Q 043276 76 TMQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLEPSVTDSMQGVIGVRPYVPKTKALENFRVRWK 155 (829)
Q Consensus 76 ~~~arViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t~~~~~~~~~~~~~~~~~~~g~l~~~~~~~~~~~~~~F~~~w~ 155 (829)
++++||||++++.+++..++++|+++|| +++||++++|..............++|++++.++.++.++|.+|+.
T Consensus 232 ~~~a~vVvv~~~~~~~~~l~~~a~~~g~---~~~wigs~~w~~~~~~~~~~~~~~~~g~ig~~~~~~~~~~F~~~~~--- 305 (403)
T cd06361 232 ENKVNVIVVFARQFHVFLLFNKAIERNI---NKVWIASDNWSTAKKILTDPNVKKIGKVVGFTFKSGNISSFHQFLK--- 305 (403)
T ss_pred cCCCeEEEEEeChHHHHHHHHHHHHhCC---CeEEEEECcccCccccccCCcccccceEEEEEecCCccchHHHHHH---
Confidence 8999999999999999999999999997 7999999999865444443344678899999998877777666554
Q ss_pred HhhcccCCCCCccccchhHHHHHHHHHHHHHHHHHhcccCccccCCCCCCCCCCCccccCCCChHHHHHHHhccceeccc
Q 043276 156 RKFLQENPSLFDAELNIFGLLAYDATSALAVAVEKAGITGFGFDKTNVSSNATDLEAFGISQNGPKLLQALSSIRFRGLT 235 (829)
Q Consensus 156 ~~~~~~~~~~~~~~~~~~~~~~YDAV~~~A~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~L~~~~f~G~t 235 (829)
+. +..++|||||++|+|||++..+. .|... ...++++|+++|++++|+|.+
T Consensus 306 ~~---------------~~~~v~~AVyaiA~Al~~~~~~~-------------~c~~~-~~~~~~~l~~~L~~~~f~g~~ 356 (403)
T cd06361 306 NL---------------LIHSIQLAVFALAHAIRDLCQER-------------QCQNP-NAFQPWELLGQLKNVTFEDGG 356 (403)
T ss_pred Hh---------------hHHHHHHHHHHHHHHHHHhccCC-------------CCCCC-CCcCHHHHHHHHheeEEecCC
Confidence 32 24468999999999999975432 12221 123589999999999999998
Q ss_pred ccEEEe-cCccccceEEEEEcc--CC---cEEEEEecCCCC
Q 043276 236 GDYIFV-DGQLQSSAFEIINVN--NG---ARGVGFWSPEKG 270 (829)
Q Consensus 236 G~~~F~-~G~~~~~~y~I~n~~--~g---~~~VG~w~~~~g 270 (829)
|.+.|+ +||. ...|+|+||+ +| +++||.|++.+.
T Consensus 357 ~~v~Fd~~gd~-~~~y~I~~~~~~~~~~~~~~vg~~~~~~~ 396 (403)
T cd06361 357 NMYHFDANGDL-NLGYDVVLWKEDNGHMTVTIMAEYDPQND 396 (403)
T ss_pred ceEEECCCCCC-CcceEEEEeEecCCcEEEEEEEEEeCCCC
Confidence 899997 9997 5799999999 44 799999998654
No 17
>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=99.97 E-value=4.2e-30 Score=284.05 Aligned_cols=240 Identities=22% Similarity=0.272 Sum_probs=197.8
Q ss_pred CCCChHHHHHHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCce--eeeEEecCCCCChhHHHHHHHHhhcCC
Q 043276 1 GALNDSSQVGAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTR--VPYRSVISPLATDDQIEKELYKLFTMQ 78 (829)
Q Consensus 1 t~psD~~q~~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~--I~~~~~i~~~~~~~~~~~~l~~lk~~~ 78 (829)
|.|+|..|++|+++++++|||++|++||++++||++.++.|++.+++.|+| |.....++.... +++...+.++++.+
T Consensus 116 ~~p~~~~~~~ai~~ll~~~~w~~vaii~~~~~~g~~~~~~l~~~l~~~g~~~~i~~~~~~~~~~~-~~~~~~l~~l~~~~ 194 (362)
T cd06367 116 TGPSLEQQADVMLEILEEYDWHQFSVVTSRDPGYRDFLDRVETTLEESFVGWEFQLVLTLDLSDD-DGDARLLRQLKKLE 194 (362)
T ss_pred ecCcHHHHHHHHHHHHHHcCCeEEEEEEEcCcccHHHHHHHHHHHHhcccceeeeeeEEeccCCC-cchHHHHHHHHhcC
Confidence 579999999999999999999999999999999999999999999999999 776666655432 26788899999999
Q ss_pred CeEEEEEcChhHHHHHHHHHHHcCccccCeEEEEcCccccccccCCccccccccceEEEEeccCCChhHHHHHHHHHHhh
Q 043276 79 TRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLEPSVTDSMQGVIGVRPYVPKTKALENFRVRWKRKF 158 (829)
Q Consensus 79 arViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t~~~~~~~~~~~~~~~~~~~g~l~~~~~~~~~~~~~~F~~~w~~~~ 158 (829)
+|+||++|+.+++..++++|.++||+.++|+||+++.|..... ...+...|++++++...
T Consensus 195 ~~vivl~~~~~~~~~il~~a~~~g~~~~~~~wI~~~~~~~~~~----~~~~~~~G~~g~~~~~~---------------- 254 (362)
T cd06367 195 SRVILLYCSKEEAERIFEAAASLGLTGPGYVWIVGELALGSGL----APEGLPVGLLGVGLDTW---------------- 254 (362)
T ss_pred CcEEEEeCCHHHHHHHHHHHHHcCCCCCCcEEEECcccccccC----CccCCCCeeEEEEeccc----------------
Confidence 9999999999999999999999999988999999999975211 23456789999987542
Q ss_pred cccCCCCCccccchhHHHHHHHHHHHHHHHHHhcccCccccCCCCCCCCCCCcccc--CCCChHHHHHHHhccceecccc
Q 043276 159 LQENPSLFDAELNIFGLLAYDATSALAVAVEKAGITGFGFDKTNVSSNATDLEAFG--ISQNGPKLLQALSSIRFRGLTG 236 (829)
Q Consensus 159 ~~~~~~~~~~~~~~~~~~~YDAV~~~A~Al~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~g~~l~~~L~~~~f~G~tG 236 (829)
..+.+++||||+++|+|++++..+...... ...+|.... .+..|..|+++|++++|.|+||
T Consensus 255 ------------~~~~~~~~Dav~~~a~Al~~~~~~~~~~~~-----~~~~C~~~~~~~~~~g~~l~~~l~~~~f~G~tg 317 (362)
T cd06367 255 ------------YSLEARVRDAVAIVARAAESLLRDKGALPE-----PPVNCYDTANKRESSGQYLARFLMNVTFDGETG 317 (362)
T ss_pred ------------ccHHHHHHHHHHHHHHHHHHHHHhcCCCCC-----CCCCcCCCCCCCCCchHHHHHHHhcccccCCCC
Confidence 136788999999999999998755321111 112354432 2678999999999999999999
Q ss_pred cEEEe-cCccccceEEEEEcc--CCcEEEEEecCCCCcccccCCCccccCCccceecC
Q 043276 237 DYIFV-DGQLQSSAFEIINVN--NGARGVGFWSPEKGLTQKLSSNSTTKSKLRPIIWP 291 (829)
Q Consensus 237 ~~~F~-~G~~~~~~y~I~n~~--~g~~~VG~w~~~~g~~~~l~~~~~~~~~~~~i~Wp 291 (829)
++.|+ +|++..+.|+|+|++ .+|++||.|++ . . ++.+.|.||
T Consensus 318 ~v~F~~~G~~~~~~~~I~~l~~~~~~~~VG~W~~---~--~--------~~~~~i~w~ 362 (362)
T cd06367 318 DVSFNEDGYLSNPKLVIINLRRNRKWERVGSWEN---G--K--------LVMRYIVWP 362 (362)
T ss_pred ceeECCCcccccceEEEEEecCCCcceEEEEEcC---C--c--------eecCcCCCC
Confidence 99996 999877899999998 57999999974 1 1 355789997
No 18
>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=99.97 E-value=8.2e-30 Score=290.18 Aligned_cols=259 Identities=22% Similarity=0.276 Sum_probs=211.1
Q ss_pred CCCChHHHHHHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhc-CCC
Q 043276 1 GALNDSSQVGAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFT-MQT 79 (829)
Q Consensus 1 t~psD~~q~~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~-~~a 79 (829)
|+|+|..|+.|+++++++|||++|++||+|++||....+.|.+++++.|+||+..+.++......++...+.+|++ .++
T Consensus 152 ~~p~d~~~~~a~~~~l~~~~w~~vaii~~~~~~G~~~~~~~~~~~~~~gi~i~~~~~~~~~~~~~d~~~~l~~l~~~~~a 231 (452)
T cd06362 152 TVPPDSFQAQAMVDIVKAFNWTYVSTVASEGNYGEKGIEAFEKLAAERGICIAGSEKIPSSATEEEFDNIIRKLLSKPNA 231 (452)
T ss_pred ecCChHHHHHHHHHHHHHCCCcEEEEEEeCCHHHHHHHHHHHHHHHHCCeeEEEEEEcCCCCCHHHHHHHHHHHhhcCCC
Confidence 5799999999999999999999999999999999999999999999999999998888765556789999999987 579
Q ss_pred eEEEEEcChhHHHHHHHHHHHcCccccCeEEEEcCccccccccCCccccccccceEEEEeccCCChhHHHHH--------
Q 043276 80 RVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLEPSVTDSMQGVIGVRPYVPKTKALENFR-------- 151 (829)
Q Consensus 80 rViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t~~~~~~~~~~~~~~~~~~~g~l~~~~~~~~~~~~~~F~-------- 151 (829)
||||+++..+.+..++++|+++||+ .+++||.+++|....... ......++|++++.++....++|++|+
T Consensus 232 ~viil~~~~~~~~~~~~~a~~~g~~-~~~~~i~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~i~~f~~~l~~l~~~~~ 309 (452)
T cd06362 232 RVVVLFCREDDIRGLLAAAKRLNAE-GHFQWIASDGWGARNSVV-EGLEDVAEGAITIELQSAEVPGFDEYFLSLTPENN 309 (452)
T ss_pred eEEEEEcChHHHHHHHHHHHHcCCc-CceEEEEeccccccchhh-cccccccceEEEEEecccccccHHHHhhhCCcCcC
Confidence 9999999999999999999999986 568999999997643222 234567899999999888888877754
Q ss_pred -------HHHHHhhcccCCCCCc----------------cccchhHHHHHHHHHHHHHHHHHhcccCccccCCCCCCCCC
Q 043276 152 -------VRWKRKFLQENPSLFD----------------AELNIFGLLAYDATSALAVAVEKAGITGFGFDKTNVSSNAT 208 (829)
Q Consensus 152 -------~~w~~~~~~~~~~~~~----------------~~~~~~~~~~YDAV~~~A~Al~~~~~~~~~~~~~~~~~~~~ 208 (829)
+.|+..|+|..+.... .....+++++|||||++|+|||++..+.+.... .
T Consensus 310 ~~~~~~~~~w~~~~~c~~~~~~~~~~~~~c~~~~~~~~~~~~~~~~~~vyDAV~a~A~AL~~~l~~~~~~~~-------~ 382 (452)
T cd06362 310 SRNPWFREFWEQKFNCKLTGNGSTKDNTCCTERILLLSNYEQESKVQFVIDAVYAMAHALHNMHRDLCPGTT-------G 382 (452)
T ss_pred CCChHHHHHHHHhcCCCcCCCCccccCCCCccccccccccccccchhHHHHHHHHHHHHHHHHHHhhCCCCC-------C
Confidence 3577788886422110 112457899999999999999999765432111 1
Q ss_pred CCccccCCCChHHHHHHHhccceecccc-cEEEe-cCccccceEEEEEcc-C----CcEEEEEecCCCC
Q 043276 209 DLEAFGISQNGPKLLQALSSIRFRGLTG-DYIFV-DGQLQSSAFEIINVN-N----GARGVGFWSPEKG 270 (829)
Q Consensus 209 ~~~~~~~~~~g~~l~~~L~~~~f~G~tG-~~~F~-~G~~~~~~y~I~n~~-~----g~~~VG~w~~~~g 270 (829)
.|... .+.+|++|+++|++++|+|++| .+.|+ +|++. +.|+|+|++ + ++++||+|++..+
T Consensus 383 ~c~~~-~~~~~~~l~~~l~~v~f~g~tg~~v~Fd~~G~~~-~~y~I~~~~~~~~~~~~~~VG~w~~~~~ 449 (452)
T cd06362 383 LCDAM-KPIDGRKLLFYLRNVSFSGLAGGPVRFDANGDGP-GRYDIFNYQRTNGKYDYVKVGSWKGELS 449 (452)
T ss_pred CCcCc-cCCCHHHHHHHHHhCCcCCCCCceEEECCCCCCC-CceEEEEEEEcCCceEEEEEEEEecccc
Confidence 24322 2456999999999999999998 78997 99985 799999998 2 2899999987655
No 19
>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=99.97 E-value=5.8e-29 Score=273.32 Aligned_cols=255 Identities=20% Similarity=0.285 Sum_probs=202.2
Q ss_pred HHHHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcC
Q 043276 8 QVGAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHML 87 (829)
Q Consensus 8 q~~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~ 87 (829)
+..|+++++++|||++|++|| |+++|.+.++.|.+++++.|+.|+.....+.. +.+++.+|++|++++.++||+.|+
T Consensus 111 ~~~a~~~~i~~~~wk~vaiiY-d~~~~~~~lq~l~~~~~~~g~~v~~~~~~~~~--~~d~~~~L~~ik~~~~~~iil~~~ 187 (371)
T cd06388 111 LRGALLSLLDHYEWNRFVFLY-DTDRGYSILQAIMEKAGQNGWQVSAICVENFN--DASYRRLLEDLDRRQEKKFVIDCE 187 (371)
T ss_pred hhhHHHHHHHhcCceEEEEEe-cCCccHHHHHHHHHhhHhcCCeeeeEEeccCC--cHHHHHHHHHhcccccEEEEEECC
Confidence 457888899999999999999 55556677999999999999999876554333 458999999999999999999999
Q ss_pred hhHHHHHHHHHHHcCccccCeEEEEcCccccccccCCccccccccceEEEEeccCCChhHHHHHHHHHHhhcccCCCCCc
Q 043276 88 PSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLEPSVTDSMQGVIGVRPYVPKTKALENFRVRWKRKFLQENPSLFD 167 (829)
Q Consensus 88 ~~~~~~i~~~a~~~gm~~~~~vwI~t~~~~~~~~~~~~~~~~~~~g~l~~~~~~~~~~~~~~F~~~w~~~~~~~~~~~~~ 167 (829)
++.+..+++||+++||+.++|+||+++.-....+. .+....-.++.|+++..+..+.+++|..+|++.+...+++...
T Consensus 188 ~~~~~~il~qa~~~gm~~~~y~~il~~~~~~~~~l--~~~~~g~~nitg~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~ 265 (371)
T cd06388 188 IERLQNILEQIVSVGKHVKGYHYIIANLGFKDISL--ERFMHGGANVTGFQLVDFNTPMVTKLMQRWKKLDQREYPGSES 265 (371)
T ss_pred HHHHHHHHHHHHhcCccccceEEEEccCccccccH--HHHhccCCceEEEEeecCCChhHHHHHHHHHhcCccccCCCCC
Confidence 99999999999999999999999998742111111 0111222337889988888899999999999887766543221
Q ss_pred cccchhHHHHHHHHHHHHHHHHHhcccCccccCCCCCCCCCCCc--cccCCCChHHHHHHHhccceecccccEEEe-cCc
Q 043276 168 AELNIFGLLAYDATSALAVAVEKAGITGFGFDKTNVSSNATDLE--AFGISQNGPKLLQALSSIRFRGLTGDYIFV-DGQ 244 (829)
Q Consensus 168 ~~~~~~~~~~YDAV~~~A~Al~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~g~~l~~~L~~~~f~G~tG~~~F~-~G~ 244 (829)
.+..+++++||||+++|.|++++......... .+.+.+|. ...+|..|..|.++|++++|+|+||++.|+ +|+
T Consensus 266 -~~~~~aAl~YDaV~l~a~A~~~l~~~~~~~~~---~~~~~~C~~~~~~~w~~G~~i~~~lk~~~~~GlTG~i~Fd~~G~ 341 (371)
T cd06388 266 -PPKYTSALTYDGVLVMAEAFRNLRRQKIDISR---RGNAGDCLANPAAPWGQGIDMERTLKQVRIQGLTGNIQFDHYGR 341 (371)
T ss_pred -CccchHHHHHHHHHHHHHHHHHHHhcCCCccc---CCCCCCcCCCCCCCCcccHHHHHHHHhcCcCCCccceeECCCCC
Confidence 46778999999999999999997432211000 01112453 345788999999999999999999999996 999
Q ss_pred cccceEEEEEcc-CCcEEEEEecCCCCc
Q 043276 245 LQSSAFEIINVN-NGARGVGFWSPEKGL 271 (829)
Q Consensus 245 ~~~~~y~I~n~~-~g~~~VG~w~~~~g~ 271 (829)
+....++|+++. +|+++||+|++..|+
T Consensus 342 r~~~~l~Ii~l~~~g~~kvG~W~~~~g~ 369 (371)
T cd06388 342 RVNYTMDVFELKSNGPRKIGYWNDMDKL 369 (371)
T ss_pred cccceEEEEEccCCCceEEEEEcCCCCc
Confidence 987799999999 999999999998875
No 20
>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=99.97 E-value=1.5e-28 Score=270.74 Aligned_cols=257 Identities=21% Similarity=0.294 Sum_probs=203.8
Q ss_pred HHHHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEe--cCCCCChhHHHHHHHHhhcCCCeEEEEE
Q 043276 8 QVGAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSV--ISPLATDDQIEKELYKLFTMQTRVFILH 85 (829)
Q Consensus 8 q~~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~--i~~~~~~~~~~~~l~~lk~~~arViIv~ 85 (829)
...|+++++++|||++|++||+ ++||...++.|.+.+++.|+.|..... +.......+++.+|++||++++++||+.
T Consensus 105 ~~~ai~d~i~~~~wk~vailYd-sd~gl~~lq~l~~~~~~~g~~V~~~~~~~i~~~~~~~d~~~~L~~ik~~~~~~Iil~ 183 (370)
T cd06389 105 LKGALLSLIEYYQWDKFAYLYD-SDRGLSTLQAVLDSAAEKKWQVTAINVGNINNDRKDEAYRSLFQDLENKKERRVILD 183 (370)
T ss_pred hhhHHHHHHHhcCCcEEEEEec-CchHHHHHHHHHHhhccCCceEEEEEeecCCCccchHHHHHHHHHhccccceEEEEE
Confidence 5789999999999999999996 679999999999999999988765432 2222234589999999999999999999
Q ss_pred cChhHHHHHHHHHHHcCccccCeEEEEcCc-cccccccCCccccccccceEEEEeccCCChhHHHHHHHHHHhhcccCCC
Q 043276 86 MLPSLGSRIFEKANEIGLMNKGCVWIMTDG-MTNLLRTLEPSVTDSMQGVIGVRPYVPKTKALENFRVRWKRKFLQENPS 164 (829)
Q Consensus 86 ~~~~~~~~i~~~a~~~gm~~~~~vwI~t~~-~~~~~~~~~~~~~~~~~g~l~~~~~~~~~~~~~~F~~~w~~~~~~~~~~ 164 (829)
|+++.+..++++|.++||+..+|+||+++. +.. .+... ....-.++.|++...+..+..++|.++|++.....+++
T Consensus 184 ~~~~~~~~il~qa~~~gm~~~~y~~il~~~~~~~-~~l~~--~~~~~~nitg~~~~~~~~~~v~~f~~~~~~~~~~~~~~ 260 (370)
T cd06389 184 CERDKVNDIVDQVITIGKHVKGYHYIIANLGFTD-GDLSK--IQFGGANVSGFQIVDYDDPLVSKFIQRWSTLEEKEYPG 260 (370)
T ss_pred CCHHHHHHHHHHHHHhCccccceEEEEccCCccc-cchhh--hccCCcceEEEEEecCCCchHHHHHHHHHhcCccccCC
Confidence 999999999999999999999999999874 332 22111 11123357888888888899999999999755444443
Q ss_pred CCccccchhHHHHHHHHHHHHHHHHHhcccCccccCCCCCCCCCCCcc--ccCCCChHHHHHHHhccceecccccEEEe-
Q 043276 165 LFDAELNIFGLLAYDATSALAVAVEKAGITGFGFDKTNVSSNATDLEA--FGISQNGPKLLQALSSIRFRGLTGDYIFV- 241 (829)
Q Consensus 165 ~~~~~~~~~~~~~YDAV~~~A~Al~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~g~~l~~~L~~~~f~G~tG~~~F~- 241 (829)
.....++.+++++||||+++|.|++++.......... .+..+|.. ..+|..|..|.++|++++|+|+||++.|+
T Consensus 261 ~~~~~~~~~aAl~yDAV~v~a~A~~~l~~~~~~~~~~---~~~~~C~~~~~~~w~~G~~i~~~l~~~~~~GlTG~i~Fd~ 337 (370)
T cd06389 261 AHTKTIKYTSALTYDAVQVMTEAFRNLRKQRIEISRR---GNAGDCLANPAVPWGQGVEIERALKQVQVEGLTGNIKFDQ 337 (370)
T ss_pred CCCcCcchHHHHHHHHHHHHHHHHHHHHHcCCCcccC---CCCCCcCCCCCCCCCCcHHHHHHHHhcccCccccceEeCC
Confidence 3333577899999999999999999985433221111 11124432 44688999999999999999999999996
Q ss_pred cCccccceEEEEEcc-CCcEEEEEecCCCCc
Q 043276 242 DGQLQSSAFEIINVN-NGARGVGFWSPEKGL 271 (829)
Q Consensus 242 ~G~~~~~~y~I~n~~-~g~~~VG~w~~~~g~ 271 (829)
+|++....++|++++ +|+++||+|++..|+
T Consensus 338 ~G~r~~~~~~ii~l~~~g~~kvG~W~~~~~~ 368 (370)
T cd06389 338 NGKRINYTINVMELKSNGPRKIGYWSEVDKM 368 (370)
T ss_pred CCccccceEEEEEecCCcceEEEEEcCCCCc
Confidence 999987799999999 999999999998775
No 21
>cd06378 PBP1_iGluR_NMDA_NR2 N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the NR2 subunit of NMDA receptor family. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the NR2 subunit of NMDA receptor family. The ionotropic N-methyl-d-asparate (NMDA) subtype of glutamate receptor serves critical functions in neuronal development, functioning, and degeneration in the mammalian central nervous system. The functional NMDA receptor is a heterotetramer composed of two NR1 and two NR2 (A, B, C, and D) or of NR3 (A and B) subunits. The receptor controls a cation channel that is highly permeable to monovalent ions and calcium and exhibits voltage-dependent inhibition by magnesium. Dual agonists, glutamate and glycine, are required for efficient activation of the NMDA receptor. Among NMDA receptor subtypes, the NR2B subunit containing receptors appear particularly important for pain perception; thus NR2B-selective antagonists may be useful in
Probab=99.96 E-value=6.7e-29 Score=271.12 Aligned_cols=242 Identities=17% Similarity=0.224 Sum_probs=189.4
Q ss_pred CCCChHHHHHHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCCh-hHHHHHHHHhhcCCC
Q 043276 1 GALNDSSQVGAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATD-DQIEKELYKLFTMQT 79 (829)
Q Consensus 1 t~psD~~q~~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~-~~~~~~l~~lk~~~a 79 (829)
|+|+|.+|+.||++|+++|||++|++||++++.+..+.+.+++.+++.++|+.....++...++ ..+...+.++|++++
T Consensus 115 ~~Psd~~q~~Ai~~Ii~~f~W~~v~iV~~~~~g~~~~~~~l~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~l~~lk~~~a 194 (362)
T cd06378 115 FGPSIEQQAAVMLKIMEEYDWHAFSVVTSRFPGYDDFVSAVRTTVDNSFVGWELQSVLTLDMSDDDGDARTQRQLKKLES 194 (362)
T ss_pred eCCCHHHHHHHHHHHHHHCCCeEEEEEEEcCCCHHHHHHHHHHHHhhcccceeEEEEEeeccCCCcchHHHHHHHHhcCC
Confidence 5899999999999999999999999999999888888888888888778887766555544322 247788899999999
Q ss_pred eEEEEEcChhHHHHHHHHHHHcCccccCeEEEEcCccccccccCCccccccccceEEEEeccCCChhHHHHHHHHHHhhc
Q 043276 80 RVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLEPSVTDSMQGVIGVRPYVPKTKALENFRVRWKRKFL 159 (829)
Q Consensus 80 rViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t~~~~~~~~~~~~~~~~~~~g~l~~~~~~~~~~~~~~F~~~w~~~~~ 159 (829)
||||++|+.+.+..+|++|.++||++.+|+||++++.....+.. ..+...|+++++. ++|+.
T Consensus 195 rViVl~~s~~~a~~if~~A~~~gm~g~~yvWI~t~~~~~~~~~~---~~~~~~G~i~v~~------------~~w~~--- 256 (362)
T cd06378 195 QVILLYCSKEEAEYIFRAARSAGLTGPGYVWIVPSLVLGNTDLG---PSEFPVGLISVSY------------DGWRY--- 256 (362)
T ss_pred CEEEEECCHHHHHHHHHHHHHcCCcCCCeEEEecccccCCCccc---cccCCcceEeecc------------ccccc---
Confidence 99999999999999999999999999999999999876553211 1234577887663 23421
Q ss_pred ccCCCCCccccchhHHHHHHHHHHHHHHHHHhcccCccccCCCCCCCCCCCcc-cc-CCCChHHHHHHHhccceeccccc
Q 043276 160 QENPSLFDAELNIFGLLAYDATSALAVAVEKAGITGFGFDKTNVSSNATDLEA-FG-ISQNGPKLLQALSSIRFRGLTGD 237 (829)
Q Consensus 160 ~~~~~~~~~~~~~~~~~~YDAV~~~A~Al~~~~~~~~~~~~~~~~~~~~~~~~-~~-~~~~g~~l~~~L~~~~f~G~tG~ 237 (829)
.+.+.+||||+++|+|++.+....... .....+|.. .. .|..|..|+++|++++|+|+ +
T Consensus 257 ------------~~~a~~~DaV~vva~Al~~l~~~~~~~-----~~~~~~C~~~~~~~~~~G~~l~~~l~~v~~~G~--~ 317 (362)
T cd06378 257 ------------SLRARVRDGVAIIATGASAMLRQHGFI-----PEAKGSCYGQAEKRDLPPNTLHRYMMNVTWEGR--D 317 (362)
T ss_pred ------------cHHHHHHHHHHHHHHHHHHHHhccCCC-----CCCCCCcCCCCCCCCCchHHHHHHhhcceECCC--c
Confidence 135578999999999999885322111 111234533 22 37789999999999999997 9
Q ss_pred EEEe-cCccccceEEEEEcc-C-CcEEEEEecCCCCcccccCCCccccCCccceecCC
Q 043276 238 YIFV-DGQLQSSAFEIINVN-N-GARGVGFWSPEKGLTQKLSSNSTTKSKLRPIIWPG 292 (829)
Q Consensus 238 ~~F~-~G~~~~~~y~I~n~~-~-g~~~VG~w~~~~g~~~~l~~~~~~~~~~~~i~Wpg 292 (829)
+.|+ +|++.++.|+|+|+. + ||++||+|+.. ++ .++.+.|||
T Consensus 318 i~F~~~G~r~~~~ldIinl~~~~g~~kVG~W~~~-~L------------~~~~~~wp~ 362 (362)
T cd06378 318 LSFTEDGYLVNPKLVVISLNKERVWEEVGKWENG-SL------------RLKYPVWPR 362 (362)
T ss_pred eeECCCCeEccceEEEEEecCCCCceEEEEEcCC-eE------------EEecCCCCC
Confidence 9996 999999999999999 4 89999999942 32 347889996
No 22
>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=99.96 E-value=6.7e-28 Score=268.04 Aligned_cols=255 Identities=20% Similarity=0.291 Sum_probs=203.4
Q ss_pred CCChHHHHHHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeE
Q 043276 2 ALNDSSQVGAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRV 81 (829)
Q Consensus 2 ~psD~~q~~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arV 81 (829)
.|++..+..++++++++|||++|++||+++ +|...++.|.+++++.|+||... .++.+ +.+++.+|++||+.+.++
T Consensus 120 ~~~~~~~~~a~~~~~~~~~wk~vaily~~~-~g~~~l~~~~~~~~~~g~~v~~~-~~~~~--~~d~~~~L~~ik~~~~~~ 195 (384)
T cd06393 120 YPDYASLSHAILDLVQYLKWRSATVVYDDS-TGLIRLQELIMAPSRYNIRLKIR-QLPTD--SDDARPLLKEMKRGREFR 195 (384)
T ss_pred ccCHHHHHHHHHHHHHHcCCcEEEEEEeCc-hhHHHHHHHHHhhhccCceEEEE-ECCCC--chHHHHHHHHHhhcCceE
Confidence 477778999999999999999999999665 47666778888899999999864 45544 568999999999999999
Q ss_pred EEEEcChhHHHHHHHHHHHcCccccCeEEEEcCccccccccCCccccccccceEEEEeccCCChhHHHHHHHHHHh-hcc
Q 043276 82 FILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLEPSVTDSMQGVIGVRPYVPKTKALENFRVRWKRK-FLQ 160 (829)
Q Consensus 82 iIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t~~~~~~~~~~~~~~~~~~~g~l~~~~~~~~~~~~~~F~~~w~~~-~~~ 160 (829)
||++++.+.+..++++|+++||+.++|+|++++.-....+. .........+++++...+..+.+++|.++|+++ ++.
T Consensus 196 iil~~~~~~~~~il~qa~~~gm~~~~~~~~~~~~~~~~~~~--~~~~~~~~~it~~~~~~~~~~~~~~f~~~~~~~~~~~ 273 (384)
T cd06393 196 IIFDCSHQMAAQILKQAMAMGMMTEYYHFIFTTLDLYALDL--EPYRYSGVNLTGFRILNVDNPHVSSIVEKWSMERLQA 273 (384)
T ss_pred EEEECCHHHHHHHHHHHHHhccccCceEEEEccCccccccc--hhhhcCcceEEEEEecCCCcHHHHHHHHHHHhhhhcc
Confidence 99999999999999999999999999999988754332221 111111222578888888899999999999854 443
Q ss_pred cCCCCCc----cccchhHHHHHHHHHHHHHHHHHhcccCccccCCCCCCCCCCCccccCCCChHHHHHHHhccceecccc
Q 043276 161 ENPSLFD----AELNIFGLLAYDATSALAVAVEKAGITGFGFDKTNVSSNATDLEAFGISQNGPKLLQALSSIRFRGLTG 236 (829)
Q Consensus 161 ~~~~~~~----~~~~~~~~~~YDAV~~~A~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~L~~~~f~G~tG 236 (829)
. |..+. ..+..+++++|||||++|.|++++..... ...+|+...+|..|..|+++|++++|+|+||
T Consensus 274 ~-p~~~~~~~~~~~~~~aal~yDav~~~a~A~~~~~~~~~---------~~~~c~~~~~w~~G~~i~~~l~~~~~~GltG 343 (384)
T cd06393 274 A-PKPETGLLDGVMMTDAALLYDAVHMVSVCYQRAPQMTV---------NSLQCHRHKAWRFGGRFMNFIKEAQWEGLTG 343 (384)
T ss_pred c-cccccccccccccchhHHhhhhHHHHHHHHhhhhhcCC---------CCCCCCCCCCCcccHHHHHHHhheeeccccc
Confidence 2 21111 12356899999999999999997643210 1135666678999999999999999999999
Q ss_pred cEEEe--cCccccceEEEEEcc-CCcEEEEEecCCCCcc
Q 043276 237 DYIFV--DGQLQSSAFEIINVN-NGARGVGFWSPEKGLT 272 (829)
Q Consensus 237 ~~~F~--~G~~~~~~y~I~n~~-~g~~~VG~w~~~~g~~ 272 (829)
++.|+ +|.|.+..|+|+|+. +|+++||+|++..|+.
T Consensus 344 ~i~Fd~~~g~r~~~~~~i~~~~~~g~~~vg~W~~~~g~~ 382 (384)
T cd06393 344 RIVFNKTSGLRTDFDLDIISLKEDGLEKVGVWNPNTGLN 382 (384)
T ss_pred ceEecCCCCeeeeeEEEEEEecCCcceeeEEEcCCCCcC
Confidence 99995 578888999999999 9999999999988864
No 23
>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=99.95 E-value=6.1e-27 Score=260.77 Aligned_cols=259 Identities=22% Similarity=0.314 Sum_probs=197.9
Q ss_pred HHHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCC--ceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEc
Q 043276 9 VGAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAID--TRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHM 86 (829)
Q Consensus 9 ~~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~g--i~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~ 86 (829)
..++++++++|||++|++||++++ |...++.|.+.+++.| +.|... .+.....+++++.+|.+||++++|+||+++
T Consensus 114 ~~a~~~~~~~~~wk~vaii~~~~~-~~~~~~~~~~~~~~~g~~i~v~~~-~~~~~~~~~d~~~~L~~ik~~~~~~iil~~ 191 (382)
T cd06380 114 IQALVDLIEHYGWRKVVYLYDSDR-GLLRLQQLLDYLREKDNKWQVTAR-RVDNVTDEEEFLRLLEDLDRRKEKRIVLDC 191 (382)
T ss_pred hHHHHHHHHhcCCeEEEEEECCCc-chHHHHHHHHHHhccCCceEEEEE-EecCCCcHHHHHHHHHHhhcccceEEEEEC
Confidence 458899999999999999996665 6677888889999988 555543 233222346899999999999999999999
Q ss_pred ChhHHHHHHHHHHHcCccccCeEEEEcCccccccccCCccccccccceEEEEeccCCChhHHHHHHHHHHhhcccCCCCC
Q 043276 87 LPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLEPSVTDSMQGVIGVRPYVPKTKALENFRVRWKRKFLQENPSLF 166 (829)
Q Consensus 87 ~~~~~~~i~~~a~~~gm~~~~~vwI~t~~~~~~~~~~~~~~~~~~~g~l~~~~~~~~~~~~~~F~~~w~~~~~~~~~~~~ 166 (829)
+.+.+..++++|+++||+..+|+||+++.-....+.. .......++.++++..+..+..++|.++|++.+++.++...
T Consensus 192 ~~~~~~~i~~qa~~~gm~~~~y~~i~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~ 269 (382)
T cd06380 192 ESERLNKILEQIVDVGKNRKGYHYILANLGFDDIDLS--KFLFGGVNITGFQLVDNTNPTVQKFLQRWKKLDPREWPGAG 269 (382)
T ss_pred CHHHHHHHHHHHHHhhhcccceEEEEccCCcccccHH--HhccCceeeEEEeccCCCCHHHHHHHHHHHhcCccccCcCC
Confidence 9999999999999999999999999986533322221 11222345677877777788999999999998876554332
Q ss_pred ccccchhHHHHHHHHHHHHHHHHHhcccCccc---cCCCCCCCCCCCc--cccCCCChHHHHHHHhccceecccccEEEe
Q 043276 167 DAELNIFGLLAYDATSALAVAVEKAGITGFGF---DKTNVSSNATDLE--AFGISQNGPKLLQALSSIRFRGLTGDYIFV 241 (829)
Q Consensus 167 ~~~~~~~~~~~YDAV~~~A~Al~~~~~~~~~~---~~~~~~~~~~~~~--~~~~~~~g~~l~~~L~~~~f~G~tG~~~F~ 241 (829)
...++.+++++|||||++|.|+++++...... ........+..|. ....|..|..|.++|++++|+|+||.+.|+
T Consensus 270 ~~~~~~~aa~aYDav~~~a~Al~~~~~~~~~~~~~~~~~~~~~~~~C~~~~~~~~~~g~~i~~~l~~~~~~G~tG~i~Fd 349 (382)
T cd06380 270 TSPIKYTAALAHDAVLVMAEAFRSLRRQRGSGRHRIDISRRGNGGDCLANPAVPWEHGIDIERALKKVQFEGLTGNVQFD 349 (382)
T ss_pred cCCcchHHHHHHHHHHHHHHHHHHHHHhccccccccccccCCCCCcCCCCCCCCccchHHHHHHHHhcccCCcccceEEC
Confidence 23466789999999999999999986432100 0000001112333 345677899999999999999999999996
Q ss_pred -cCccccceEEEEEcc-CCcEEEEEecCCCCc
Q 043276 242 -DGQLQSSAFEIINVN-NGARGVGFWSPEKGL 271 (829)
Q Consensus 242 -~G~~~~~~y~I~n~~-~g~~~VG~w~~~~g~ 271 (829)
+|++....++|++++ ++.++||+|++..|+
T Consensus 350 ~~G~~~~~~~~i~~~~~~~~~~vg~w~~~~g~ 381 (382)
T cd06380 350 EFGQRTNYTLDVVELKTRGLRKVGYWNEDDGL 381 (382)
T ss_pred CCCCcccccEEEEEecCCCceEEEEECCCcCc
Confidence 999987789999999 889999999998775
No 24
>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=99.95 E-value=1.2e-26 Score=258.03 Aligned_cols=243 Identities=17% Similarity=0.206 Sum_probs=192.6
Q ss_pred CCCChHHHHHHHHHHHHHcCCcEEEEEEEeCccccch---HHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcC
Q 043276 1 GALNDSSQVGAITAIIKAFGWREAVPIYVDNQYGEEL---IPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTM 77 (829)
Q Consensus 1 t~psD~~q~~ai~~ll~~fgW~~V~iI~~dd~yG~~~---~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~ 77 (829)
|+|+|..|+.++++++++|||++|++||++++||++. ++.|.+++++.|+||...+..+.. +.++...|.++++.
T Consensus 117 ~~p~~~~~~~a~~~ll~~~~W~~vaiiy~~~~~~~~~~~~~~~l~~~~~~~gi~v~~~~~~~~~--~~d~~~~l~~ik~~ 194 (387)
T cd06386 117 VAPSYVKMGETFSALFERFHWRSALLVYEDDKQERNCYFTLEGVHHVFQEEGYHMSIYPFDETK--DLDLDEIIRAIQAS 194 (387)
T ss_pred ecCchHHHHHHHHHHHHhCCCeEEEEEEEcCCCCccceehHHHHHHHHHhcCceEEEEecCCCC--cccHHHHHHHHHhc
Confidence 5799999999999999999999999999999999886 999999999999999876554333 45789999999987
Q ss_pred CCeEEEEEcChhHHHHHHHHHHHcCccccCeEEEEcCccccc-c--------ccCC---ccccccccceEEEEeccCCCh
Q 043276 78 QTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNL-L--------RTLE---PSVTDSMQGVIGVRPYVPKTK 145 (829)
Q Consensus 78 ~arViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t~~~~~~-~--------~~~~---~~~~~~~~g~l~~~~~~~~~~ 145 (829)
+ ||||+|++.+.+..++++|+++||+..+|+||..|...+. . +..+ ....+.++|+.++++. .+
T Consensus 195 ~-rvii~~~~~~~~~~ll~~A~~~gm~~~~yv~i~~d~~~~~~~~~~~w~~~~~~~~~~~~a~~~~~~v~~~~~~---~~ 270 (387)
T cd06386 195 E-RVVIMCAGADTIRSIMLAAHRRGLTSGDYIFFNIELFNSSSYGDGSWKRGDKHDFEAKQAYSSLNTVTLLRTV---KP 270 (387)
T ss_pred C-cEEEEecCHHHHHHHHHHHHHcCCCCCCEEEEEEecccccccCCCCCccCCCcCHHHHHHHHhheEEeccCCC---Ch
Confidence 7 9999999999999999999999999999999999865311 0 0011 1123445565555544 57
Q ss_pred hHHHHHHHHHHhhcccCCCCCccccchhHHHHHHHHHHHHHHHHHhcccCccccCCCCCCCCCCCccccCCCChHHHHHH
Q 043276 146 ALENFRVRWKRKFLQENPSLFDAELNIFGLLAYDATSALAVAVEKAGITGFGFDKTNVSSNATDLEAFGISQNGPKLLQA 225 (829)
Q Consensus 146 ~~~~F~~~w~~~~~~~~~~~~~~~~~~~~~~~YDAV~~~A~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~ 225 (829)
++++|.+++++.+.......+...++.+++++|||||++|+||+++..... .+.+|..|.++
T Consensus 271 ~~~~f~~~~~~~~~~~~~~~~~~~~~~~aa~~yDav~l~A~Al~~~~~~g~------------------~~~~g~~l~~~ 332 (387)
T cd06386 271 EFEKFSMEVKSSVEKAGDLNDCDYVNMFVEGFHDAILLYALALHEVLKNGY------------------SKKDGTKITQR 332 (387)
T ss_pred HHHHHHHHHHHHHHhCCCCcccccchHHHHHHHHHHHHHHHHHHHHhhCCC------------------CCCCHHHHHHH
Confidence 788999988865543211111124568999999999999999999853321 12358999999
Q ss_pred HhccceecccccEEEe-cCccccceEEEEEcc---C-CcEEEEEecCC
Q 043276 226 LSSIRFRGLTGDYIFV-DGQLQSSAFEIINVN---N-GARGVGFWSPE 268 (829)
Q Consensus 226 L~~~~f~G~tG~~~F~-~G~~~~~~y~I~n~~---~-g~~~VG~w~~~ 268 (829)
|++++|+|+||.+.|+ +|++. ..|.|+.++ + +++.||+|...
T Consensus 333 l~~~~f~G~tG~v~~d~~g~r~-~~~~v~~~~~~~~~~~~~~~~~~~~ 379 (387)
T cd06386 333 MWNRTFEGIAGQVSIDANGDRY-GDFSVIAMTDVEAGTYEVVGNYFGK 379 (387)
T ss_pred HhCCceeeccccEEECCCCCcc-ccEEEEEccCCCCccEEEEeEEccc
Confidence 9999999999999996 99996 699999997 3 39999999753
No 25
>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=99.94 E-value=3.8e-25 Score=248.18 Aligned_cols=248 Identities=18% Similarity=0.272 Sum_probs=199.5
Q ss_pred CCCChHHHHHHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCC-ChhHHHHHHHHhhcCCC
Q 043276 1 GALNDSSQVGAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLA-TDDQIEKELYKLFTMQT 79 (829)
Q Consensus 1 t~psD~~q~~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~-~~~~~~~~l~~lk~~~a 79 (829)
+.|+|..|+.++++++++|+|++|++|+++++||.+..+.|.+.+++.|+||+..+.++... .+.++..++.+|+++++
T Consensus 156 ~~~~~~~~~~al~~~l~~~~~k~vaii~~~~~~g~~~~~~~~~~l~~~gi~i~~~~~~~~~~~~~~d~~~~l~~i~~~~~ 235 (410)
T cd06363 156 TVPSDKDQIEAMVQLLQEFGWNWVAFLGSDDEYGRDGLQLFSELIANTGICIAYQGLIPLDTDPETDYQQILKQINQTKV 235 (410)
T ss_pred ecCCcHHHHHHHHHHHHHCCCcEEEEEEeCChhHHHHHHHHHHHHHHCCeEEEEEEEecCCCchHHHHHHHHHHHhcCCC
Confidence 46899999999999999999999999999999999999999999999999999988887532 35689999999999999
Q ss_pred eEEEEEcChhHHHHHHHHHHHcCccccCeEEEEcCccccccccCCccccccccceEEEEeccCCChhHHHHHHHHHHhhc
Q 043276 80 RVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLEPSVTDSMQGVIGVRPYVPKTKALENFRVRWKRKFL 159 (829)
Q Consensus 80 rViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t~~~~~~~~~~~~~~~~~~~g~l~~~~~~~~~~~~~~F~~~w~~~~~ 159 (829)
++||+++..+.+..++++|+++|| .+.+||.+++|...............++++++..+.+..+++++|.+.
T Consensus 236 dvIil~~~~~~~~~il~qa~~~g~--~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~------ 307 (410)
T cd06363 236 NVIVVFASRQPAEAFFNSVIQQNL--TGKVWIASEAWSLNDELPSLPGIRNIGTVLGVAQQTVTIPGFSDFIYS------ 307 (410)
T ss_pred eEEEEEcChHHHHHHHHHHHhcCC--CCCEEEEeCcccccccccCCccceeeccEEEEEeCCCCCccHHHHHHH------
Confidence 999999999999999999999997 356999999886432222222234566788888777778888887765
Q ss_pred ccCCCCCccccchhHHHHHHHHHHHHHHHHHhcccCccccCCCCCCCCCCCccccCCCChHHHHHHHhccceecccccEE
Q 043276 160 QENPSLFDAELNIFGLLAYDATSALAVAVEKAGITGFGFDKTNVSSNATDLEAFGISQNGPKLLQALSSIRFRGLTGDYI 239 (829)
Q Consensus 160 ~~~~~~~~~~~~~~~~~~YDAV~~~A~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~L~~~~f~G~tG~~~ 239 (829)
+++.+|||||++|+|++++..+.. ..|.. .....++.|.++|++++|.|++|++.
T Consensus 308 -------------~~~~~YDaV~~~a~Al~~a~~~~~-----------~~~~~-~~~~~~~~l~~~L~~~~~~g~~g~i~ 362 (410)
T cd06363 308 -------------FAFSVYAAVYAVAHALHNVLQCGS-----------GGCPK-RVPVYPWQLLEELKKVNFTLLGQTVR 362 (410)
T ss_pred -------------HHHHHHHHHHHHHHHHHHHhCCCC-----------CCCCC-CCCCCHHHHHHHHhccEEecCCcEEE
Confidence 456799999999999999865431 11211 01235788999999999999999999
Q ss_pred Ee-cCccccceEEEEEcc-C----CcEEEEEecCCCCcccccCCCccccCCccceecC
Q 043276 240 FV-DGQLQSSAFEIINVN-N----GARGVGFWSPEKGLTQKLSSNSTTKSKLRPIIWP 291 (829)
Q Consensus 240 F~-~G~~~~~~y~I~n~~-~----g~~~VG~w~~~~g~~~~l~~~~~~~~~~~~i~Wp 291 (829)
|+ +|++. ..|+|++++ + ++++||+|.+.+ ..|. ++.+.|.|+
T Consensus 363 fd~~G~~~-~~~~i~~~~~~~~~~~~~~vG~~~~~~---~~l~------~~~~~i~w~ 410 (410)
T cd06363 363 FDENGDPN-FGYDIVVWWWDNSSGTFEEVGSYSFYP---IRLT------INRSKIQWH 410 (410)
T ss_pred eCCCCCCc-cceEEEEEEEcCCceeEEEEEEEECCC---CEEE------EehHhcccC
Confidence 97 89974 689999997 3 389999998742 2232 355778896
No 26
>PF01094 ANF_receptor: Receptor family ligand binding region The Prosite family is a sub-family of the Pfam family; InterPro: IPR001828 This describes a ligand binding domain and includes extracellular ligand binding domains of a wide range of receptors, as well as the bacterial amino acid binding proteins of known structure [].; PDB: 3SAJ_D 3Q41_B 3QEM_C 3QEK_A 3QEL_C 3MQ4_A 3QLV_G 3OM1_A 3QLU_A 3OM0_A ....
Probab=99.94 E-value=3.7e-25 Score=243.35 Aligned_cols=244 Identities=31% Similarity=0.477 Sum_probs=195.0
Q ss_pred CCCChHHHHHHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHh-CCceeee-EEecCCCCChhHHHHHHHHhhcCC
Q 043276 1 GALNDSSQVGAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQA-IDTRVPY-RSVISPLATDDQIEKELYKLFTMQ 78 (829)
Q Consensus 1 t~psD~~q~~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~-~gi~I~~-~~~i~~~~~~~~~~~~l~~lk~~~ 78 (829)
++|++..+++|+++++++|+|++|++||+++++|....+.|.+.+++ .+.|+.. ........+..++...+.+ ++.+
T Consensus 101 ~~p~~~~~~~a~~~~l~~~~w~~v~vv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~-~~~~ 179 (348)
T PF01094_consen 101 TVPSDSSQARALVDLLKHFGWTRVSVVYSDDDYGNSLADSFQDLLRERGGICVAFISVVISSDSDAEELLKKLKE-IKSG 179 (348)
T ss_dssp SSB-HHHHHHHHHHHHHHTTSSEEEEEEESSHHHHHHHHHHHHHHHHHTTCEEEEEEEEETTTSHHHHHHHHHHH-HTTT
T ss_pred ccccHHHHHHHHHHhhhcCCCceeeeeccccccccccchhhhhhhcccccceecccccccccccchhhhhhhhhh-cccc
Confidence 57999999999999999999999999999999999999999999999 5677776 3333332223345455555 4599
Q ss_pred CeEEEEEcChhHHHHHHHHHHHcCccccCeEEEEcCccccccccCCccccccccceEEEEeccCCChhHHHHHHHHHHhh
Q 043276 79 TRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLEPSVTDSMQGVIGVRPYVPKTKALENFRVRWKRKF 158 (829)
Q Consensus 79 arViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t~~~~~~~~~~~~~~~~~~~g~l~~~~~~~~~~~~~~F~~~w~~~~ 158 (829)
+||||++++...+..++++|.++||...+|+||.++.+..............+.|+++++++.+..+.+++|...|+...
T Consensus 180 ~rvvil~~~~~~~~~~l~~a~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~ 259 (348)
T PF01094_consen 180 ARVVILCSSPEDARQFLEAAYELGMTSGDYVWILTDLDNSSFWQNNEDFREAFQGVLGFTPPPPSSPEFEDFMKKWKESN 259 (348)
T ss_dssp TSEEEEESBHHHHHHHHHHHHHTTTSSTTSEEEEETTTTTTHTSTHCHHHCCHTTEEEEEESTTTSHHHHHHHHHHHTTT
T ss_pred ceeeeeecccccccccccchhhhhccccceeEEeecccccccccccccccccccceeeeeeecccccchhhhhcccChhh
Confidence 99999999999999999999999999999999999998765322233466788999999999999999999999999764
Q ss_pred cccCCCCCccccchhHHHHHHHHHHHHHHHHHhcccCccccCCCCCCCCCCCccccCCCChHHHHHHHhccceecccccE
Q 043276 159 LQENPSLFDAELNIFGLLAYDATSALAVAVEKAGITGFGFDKTNVSSNATDLEAFGISQNGPKLLQALSSIRFRGLTGDY 238 (829)
Q Consensus 159 ~~~~~~~~~~~~~~~~~~~YDAV~~~A~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~L~~~~f~G~tG~~ 238 (829)
...........+..+++++||||+++|+|++++....+.... ....+..|..|.++|++++|+|++|++
T Consensus 260 ~~~~~~~~~~~~~~~~~~~yDAv~~~a~al~~~~~~~~~~~~-----------~~~~~~~g~~l~~~l~~~~f~G~tG~v 328 (348)
T PF01094_consen 260 NQSSTSGSDQEPSPYAAYAYDAVYLLAHALNRALQDGGPVTN-----------GRNPWQNGSQLLKYLRNVSFEGLTGRV 328 (348)
T ss_dssp HTTTTTTTTSSGCHHHHHHHHHHHHHHHHHHHHHHHHSTTTS-----------SSGTSTTHHHHHHHHHTEEEEETTEEE
T ss_pred ccCcccccccccceeeeeehhhhHHHHHHHHHHHHhccCCCC-----------CccccccHHHHHHHHhheeeeCCCCCE
Confidence 321111122356789999999999999999999765432110 013567799999999999999999999
Q ss_pred EEe--cCccccceEEEEEcc
Q 043276 239 IFV--DGQLQSSAFEIINVN 256 (829)
Q Consensus 239 ~F~--~G~~~~~~y~I~n~~ 256 (829)
.|+ +|++....|+|+|++
T Consensus 329 ~f~~~~G~~~~~~~~i~~~~ 348 (348)
T PF01094_consen 329 SFDSNDGDRTNYDYDILNMQ 348 (348)
T ss_dssp EEETTTSBEESEEEEEEEE-
T ss_pred EEeCCCCCcCCCEEEEEECC
Confidence 994 789988999999985
No 27
>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=99.94 E-value=9.2e-25 Score=245.06 Aligned_cols=244 Identities=18% Similarity=0.185 Sum_probs=191.2
Q ss_pred CCCChHHHHHHHHHHHHHcCCcEEEE-EEEeCcc-ccc---hHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhh
Q 043276 1 GALNDSSQVGAITAIIKAFGWREAVP-IYVDNQY-GEE---LIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLF 75 (829)
Q Consensus 1 t~psD~~q~~ai~~ll~~fgW~~V~i-I~~dd~y-G~~---~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk 75 (829)
|+|+|..|+.++++++++|||++|++ +|.++++ |+. .++.|.+.+++.|+||+..+..+.+ ..++...|++++
T Consensus 123 ~~p~~~~~~~a~~~~~~~~~w~~va~ii~~~~~~~~~~~~~~~~~l~~~~~~~gi~v~~~~~~~~~--~~d~~~~l~~ik 200 (405)
T cd06385 123 TGPTHKKLGEFVLHIHQHFGWRSHAMLIYSDNKVDDRPCYFAMEGLYMELKKNNITVVDLVFEEDD--LINYTTLLQDIK 200 (405)
T ss_pred ecCchHHHHHHHHHHHHhCCCeEEEEEEEecCcccccchHHHHHHHHHHHHhCCeEEEEeeccCCc--hhhHHHHHHHHh
Confidence 57999999999999999999999985 5554433 333 4688999999999999987643222 558999999998
Q ss_pred cCCCeEEEEEcChhHHHHHHHHHHHcCccccCeEEEEcCcccccccc------------CCccccccccceEEEEeccCC
Q 043276 76 TMQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRT------------LEPSVTDSMQGVIGVRPYVPK 143 (829)
Q Consensus 76 ~~~arViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t~~~~~~~~~------------~~~~~~~~~~g~l~~~~~~~~ 143 (829)
+. +||||++++.+.+..++++|.++||+.++|+||+++.+...... .+.....++++++.+....+.
T Consensus 201 ~~-~~iii~~~~~~~~~~i~~~a~~~g~~~~~y~~i~~~~~~~~~~~~~~~~~w~~~~~~~~~~~~a~~~v~~~~~~~~~ 279 (405)
T cd06385 201 QK-GRVIYVCCSPDIFRRLMLQFWREGLPSEDYVFFYIDLFGASLQGPDPKRPWYRGDADDAAAREAFQSVKILTYKEPQ 279 (405)
T ss_pred hc-ceEEEEeCCHHHHHHHHHHHHHcCCCCCcEEEEEeecchhhccCCCCCCCCCCCCcccHHHHHhhheeEEEeCCCCC
Confidence 65 49999999999999999999999999999999999776432221 011234567888888777777
Q ss_pred ChhHHHHHHHHHHh----hcccCCCCCccccchhHHHHHHHHHHHHHHHHHhcccCccccCCCCCCCCCCCccccCCCCh
Q 043276 144 TKALENFRVRWKRK----FLQENPSLFDAELNIFGLLAYDATSALAVAVEKAGITGFGFDKTNVSSNATDLEAFGISQNG 219 (829)
Q Consensus 144 ~~~~~~F~~~w~~~----~~~~~~~~~~~~~~~~~~~~YDAV~~~A~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g 219 (829)
++.+++|.++|+++ |++.. +...++.+++++|||||++|.||+++..... .+.+|
T Consensus 280 ~~~~~~f~~~~~~~~~~~~~~~~---~~~~~~~~aa~~YDav~l~a~Al~~~~~~~~------------------~~~~g 338 (405)
T cd06385 280 NPEYKEFLSDLKTDAKEMFNFTV---EDSLMNIIAGGFYDGVMLYAHALNETMAKGG------------------TRPPG 338 (405)
T ss_pred ChhHHHHHHHHHHHhhccCCCcc---chhhHHHHHHHHHHHHHHHHHHHHHHHhcCC------------------CCCCH
Confidence 78899999999986 43321 1112568999999999999999999743221 11248
Q ss_pred HHHHHHHhccceecccccEEEe-cCccccceEEEEEcc---C-CcEEEEEecCCC
Q 043276 220 PKLLQALSSIRFRGLTGDYIFV-DGQLQSSAFEIINVN---N-GARGVGFWSPEK 269 (829)
Q Consensus 220 ~~l~~~L~~~~f~G~tG~~~F~-~G~~~~~~y~I~n~~---~-g~~~VG~w~~~~ 269 (829)
..|.++|++++|.|++|.+.|+ +|++. +.|.|+.++ + .++.||+|+..+
T Consensus 339 ~~i~~~l~~~~f~G~tG~v~fd~~G~r~-~~~~~~~~~~~~~g~~~~v~~~~~~~ 392 (405)
T cd06385 339 TAITQRMWNRTFYGVTGFVKIDDNGDRE-TDFALWDMTDTESGDFQVVSVYNGTQ 392 (405)
T ss_pred HHHHHHhhCceEeeceeEEEEcCCCCEe-ceeEEEEccCCCCCcEEEEEEEcccC
Confidence 8999999999999999999996 99995 789998774 3 399999998643
No 28
>cd06370 PBP1_Speract_GC_like Ligand-binding domain of membrane bound guanylyl cyclases. Ligand-binding domain of membrane bound guanylyl cyclases (GCs), which are known to be activated by sperm-activating peptides (SAPs), such as speract or resact. These ligand peptides are released by a range of invertebrates to stimulate the metabolism and motility of spermatozoa and are also potent chemoattractants. These GCs contain a single transmembrane segment, an extracellular ligand binding domain, and intracellular protein kinase-like and cyclase catalytic domains. GCs of insect and nematodes, which exhibit high sequence similarity to the speract receptor are also included in this model.
Probab=99.93 E-value=2.4e-24 Score=241.20 Aligned_cols=235 Identities=15% Similarity=0.240 Sum_probs=186.5
Q ss_pred CCCChHHHHHHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCC-----ChhHHHHHHHHhh
Q 043276 1 GALNDSSQVGAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLA-----TDDQIEKELYKLF 75 (829)
Q Consensus 1 t~psD~~q~~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~-----~~~~~~~~l~~lk 75 (829)
++|+|..|+.++++++++|||++|++||.+++||++..+.|.+.+++.|+||+..+.++... ...++...|.+++
T Consensus 116 ~~~~~~~~~~a~~~~~~~~~w~~vaii~~~~~~g~~~~~~~~~~~~~~g~~iv~~~~~~~~~~~~~~~~~~~~~~l~~~~ 195 (404)
T cd06370 116 TVPPSIQVVKSVIALLKHFNWNKFSVVYENDSKYSSVFETLKEEAELRNITISHVEYYADFYPPDPIMDNPFEDIIQRTK 195 (404)
T ss_pred cCCCHHHHHHHHHHHHHHCCCcEEEEEEecCcccHHHHHHHHHHHHHcCCEEEEEEEECCCCCchhhhHHHHHHHHHhcc
Confidence 57899999999999999999999999999999999999999999999999999998887652 1357888888877
Q ss_pred cCCCeEEEEEcChhHHHHHHHHHHHcCcc-ccCeEEEEcCcc-------cc----------c-cccCCccccccccceEE
Q 043276 76 TMQTRVFILHMLPSLGSRIFEKANEIGLM-NKGCVWIMTDGM-------TN----------L-LRTLEPSVTDSMQGVIG 136 (829)
Q Consensus 76 ~~~arViIv~~~~~~~~~i~~~a~~~gm~-~~~~vwI~t~~~-------~~----------~-~~~~~~~~~~~~~g~l~ 136 (829)
. .++++|+++..+.+..++++|+++||+ ..+|+||.++.. .. . .........++++|+++
T Consensus 196 ~-~~~~~v~~~~~~~~~~~l~qa~~~g~~~~~~y~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~ 274 (404)
T cd06370 196 E-TTRIYVFIGEANELRQFLMSMLDEGLLESGDYMVLGVDIEYYDRDSQDYYSLHRGFQSREYNRSDDEKALEAMKSVLI 274 (404)
T ss_pred C-CCEEEEEEcCHHHHHHHHHHHHHcCCCCCCcEEEEEEchhhccccchhhhhhhhhhccccccccccHHHHHHhHheEE
Confidence 5 479999999888999999999999998 578999997631 10 0 00011123456889888
Q ss_pred EEeccCCChhHHHHHHHHHHhhcccC-CC-----CCccccchhHHHHHHHHHHHHHHHHHhcccCccccCCCCCCCCCCC
Q 043276 137 VRPYVPKTKALENFRVRWKRKFLQEN-PS-----LFDAELNIFGLLAYDATSALAVAVEKAGITGFGFDKTNVSSNATDL 210 (829)
Q Consensus 137 ~~~~~~~~~~~~~F~~~w~~~~~~~~-~~-----~~~~~~~~~~~~~YDAV~~~A~Al~~~~~~~~~~~~~~~~~~~~~~ 210 (829)
+.+..+ .+..++|.++|++.+.... +. .....++.+++++|||||++|+||+++..+...
T Consensus 275 ~~~~~~-~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~aa~~yDAv~~~a~Al~~~~~~~~~------------- 340 (404)
T cd06370 275 IVPTPV-SPDYDSFSIFVRKYNLEPPFNGDLGESELVLEIDIEAAYLYDAVMLYAKALDETLLEGGD------------- 340 (404)
T ss_pred EecCCC-CchHHHHHHHHHHhccCCCCcccccccccccccceeeehhHHHHHHHHHHHHHHHHhcCC-------------
Confidence 876555 7778999999998764421 10 011246678999999999999999998543210
Q ss_pred ccccCCCChHHHHHHHhccceecccc-cEEEe-cCccccceEEEEEcc
Q 043276 211 EAFGISQNGPKLLQALSSIRFRGLTG-DYIFV-DGQLQSSAFEIINVN 256 (829)
Q Consensus 211 ~~~~~~~~g~~l~~~L~~~~f~G~tG-~~~F~-~G~~~~~~y~I~n~~ 256 (829)
..+|.+|.++|++++|+|+|| .+.|+ +|++. ..|.|++++
T Consensus 341 -----~~~g~~i~~~l~~~~f~GvtG~~v~fd~~G~~~-~~y~v~~~~ 382 (404)
T cd06370 341 -----IYNGTAIVSHILNRTYRSITGFDMYIDENGDAE-GNYSVLALQ 382 (404)
T ss_pred -----CCCHHHHHHHHhCcccccccCceEEEcCCCCcc-cceEEEEec
Confidence 124789999999999999999 89997 99984 899999998
No 29
>cd06372 PBP1_GC_G_like Ligand-binding domain of membrane guanylyl cyclase G. This group includes the ligand-binding domain of membrane guanylyl cyclase G (GC-G) which is a sperm surface receptor and might function, similar to its sea urchin counterpart, in the early signaling event that regulates the Ca2+ influx/efflux and subsequent motility response in sperm. GC-G appears to be a pseudogene in human. Furthermore, in contrast to the other orphan receptor GCs, GC-G has a broad tissue distribution in rat, including lung, intestine, kidney, and skeletal muscle.
Probab=99.92 E-value=8.2e-24 Score=236.34 Aligned_cols=246 Identities=17% Similarity=0.226 Sum_probs=181.3
Q ss_pred CCCChHHHHHHHHHHHHHcCCcEEEEEEEeC---ccc--cchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhh
Q 043276 1 GALNDSSQVGAITAIIKAFGWREAVPIYVDN---QYG--EELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLF 75 (829)
Q Consensus 1 t~psD~~q~~ai~~ll~~fgW~~V~iI~~dd---~yG--~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk 75 (829)
|.|++..|+.++++++++|||++|++||+++ .|| ....+.+.+.++ .+++|...+.++.+ +.++...+.+.+
T Consensus 117 ~~p~~~~~~~a~~~l~~~~~w~~vaii~~~~~~~~~~~~~~~~~~~~~~~~-~~~~i~~~~~~~~~--~~d~~~~~l~~~ 193 (391)
T cd06372 117 LVPPKQKIGEVLQKSLQHFGWKHIGLFGGSSRDSSWDEVDELWKAVENQLK-FHFNITATVRYSSS--NPDLLQEKLRYI 193 (391)
T ss_pred ecCchhhHHHHHHHHHHHCCCeEEEEEEeccccchhhhHHHHHHHHHHHHh-hCEEEEEEEecCCC--ChHHHHHHHHhh
Confidence 4689999999999999999999999998543 333 223445555554 67899888777654 346666665666
Q ss_pred cCCCeEEEEEcChhHHHHHHHHHHHcCccccCeEEEEc-----Ccccccccc-CCccccccccceEEEEeccCC-ChhHH
Q 043276 76 TMQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMT-----DGMTNLLRT-LEPSVTDSMQGVIGVRPYVPK-TKALE 148 (829)
Q Consensus 76 ~~~arViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t-----~~~~~~~~~-~~~~~~~~~~g~l~~~~~~~~-~~~~~ 148 (829)
++++||||++++.+.+..++++|+++||+..+|+||.+ +.|...... ......+.++|++++.+..+. .+...
T Consensus 194 ~~~~~vii~~~~~~~~~~i~~~a~~~g~~~~~y~~i~~~~~~~~~w~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~ 273 (391)
T cd06372 194 SSVARVIILICSSEDAKAILQAAEKLGLMKGKFVFFLLQQFEDNFWKEVLTDDQVQHLPKVYESVFLIAPSSYGGYSGGY 273 (391)
T ss_pred hccceEEEEEcChHHHHHHHHHHHHcCCCCCCEEEEEehhhcCccccccCCCcchHHHHHHHhhEEEEecCCCCCCcchh
Confidence 78999999999999999999999999998878999995 334322111 111133467888888776532 35567
Q ss_pred HHHHHHHHhhccc-CCC--CCccccchhHHHHHHHHHHHHHHHHHhcccCccccCCCCCCCCCCCccccCCCChHHHHHH
Q 043276 149 NFRVRWKRKFLQE-NPS--LFDAELNIFGLLAYDATSALAVAVEKAGITGFGFDKTNVSSNATDLEAFGISQNGPKLLQA 225 (829)
Q Consensus 149 ~F~~~w~~~~~~~-~~~--~~~~~~~~~~~~~YDAV~~~A~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~ 225 (829)
+|.++|++++... +.. ......+.|++++|||||++|+||+++..+.. .+.+|..|.++
T Consensus 274 ~f~~~~~~~~~~~p~~~~~~~~~~~~~~a~~~yDav~~~A~Al~~~~~~g~------------------~~~~g~~l~~~ 335 (391)
T cd06372 274 EFRKQVYQKLKRPPFQSSLSSEEQVSPYSAYLHDAVLLYALAVKEMLKAGK------------------DFRNGRQLVST 335 (391)
T ss_pred HHHHHHHHHHhcCCccccccccccchHHHHHHHHHHHHHHHHHHHHHhcCC------------------CCCCHHHHHHH
Confidence 7888887776421 100 01113467899999999999999999864321 12358899999
Q ss_pred Hh---ccceecccccEEEe-cCccccceEEEEEcc-CC----cEEEEEecCC
Q 043276 226 LS---SIRFRGLTGDYIFV-DGQLQSSAFEIINVN-NG----ARGVGFWSPE 268 (829)
Q Consensus 226 L~---~~~f~G~tG~~~F~-~G~~~~~~y~I~n~~-~g----~~~VG~w~~~ 268 (829)
|+ +++|.|+||.+.|+ +|++. +.|.|++++ .+ ++.||+|+..
T Consensus 336 l~~~~~~~f~G~tG~v~fd~~G~r~-~~y~i~~~~~~~~~~~~~~vg~~~~~ 386 (391)
T cd06372 336 LRGANQVELQGITGLVLLDEQGKRQ-MDYSVYALQKSGNSSLFLPFLHYDSH 386 (391)
T ss_pred HhhccCceEeccceeEEECCCCCcc-eeEEEEeccccCCccceeeEEEecch
Confidence 99 68999999999996 99995 899999998 22 7899999864
No 30
>cd06371 PBP1_sensory_GC_DEF_like Ligand-binding domain of membrane guanylyl cyclases (GC-D, GC-E, and GC-F) that are specifically expressed in sensory tissues. This group includes the ligand-binding domain of membrane guanylyl cyclases (GC-D, GC-E, and GC-F) that are specifically expressed in sensory tissues. They share a similar topology with an N-terminal extracellular ligand-binding domain, a single transmembrane domain, and a C-terminal cytosolic region that contains kinase-like and catalytic domains. GC-D is specifically expressed in a subpopulation of olfactory sensory neurons. GC-E and GC-F are colocalized within the same photoreceptor cells of the retina and have important roles in phototransduction. Unlike the other family members, GC-E and GC-F have no known extracellular ligands. Instead, they are activated under low calcium conditions by guanylyl cyclase activating proteins called GCAPs. GC-D expressing neurons have been implicated in pheromone detection and GC-D is phyloge
Probab=99.92 E-value=2.2e-23 Score=231.27 Aligned_cols=232 Identities=20% Similarity=0.255 Sum_probs=178.7
Q ss_pred HHHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCC-CeEEEEEcC
Q 043276 9 VGAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQ-TRVFILHML 87 (829)
Q Consensus 9 ~~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~-arViIv~~~ 87 (829)
..++++++++|+|++|++||++++||.+..+.|.+.+++.|+||+....++.+ +.+++.+|++||+++ +||||+|++
T Consensus 120 ~~~~~~~~~~~~w~~vaii~~~~~~~~~~~~~l~~~l~~~gi~v~~~~~~~~~--~~d~~~~L~~lk~~~~~~viv~~~~ 197 (382)
T cd06371 120 SRVLFTVLRYFRWAHVAIVSSPQDIWVETAQKLASALRAHGLPVGLVTSMGPD--EKGAREALKKVRSADRVRVVIMCMH 197 (382)
T ss_pred HHHHHHHHHHCCCeEEEEEEecccchHHHHHHHHHHHHHCCCcEEEEEEecCC--HHHHHHHHHHHhcCCCcEEEEEEee
Confidence 46788999999999999999999999999999999999999999988887654 568999999999987 699999987
Q ss_pred h-----hHHHHHHHHHHHcCccccCeEEEEcCcccccccc-----C----CccccccccceEEEEeccCCChhHHHHHHH
Q 043276 88 P-----SLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRT-----L----EPSVTDSMQGVIGVRPYVPKTKALENFRVR 153 (829)
Q Consensus 88 ~-----~~~~~i~~~a~~~gm~~~~~vwI~t~~~~~~~~~-----~----~~~~~~~~~g~l~~~~~~~~~~~~~~F~~~ 153 (829)
. ..+..++++|+++||+..+|+||.+++.....+. . +....+++++++++.+..+..+..+.|.+.
T Consensus 198 ~~~~~~~~~~~i~~qa~~~Gm~~~~y~~i~~d~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~f~~~ 277 (382)
T cd06371 198 SVLIGGEEQRLLLETALEMGMTDGRYVFIPYDTLLYSLPYRNVSYPALRNNSKLRRAYDAVLTITMDSGEQSFYEAFRAA 277 (382)
T ss_pred ccccCcHHHHHHHHHHHHcCCcCCcEEEEEeccccccCCCCCccccCCCCCHHHHHHhHhhEEEEecCCCCcHHHHHHHH
Confidence 6 6778999999999999899999999864311110 0 112235688888887765444444445444
Q ss_pred HHHhhcccCCC-CCccccchhHHHHHHHHHHHHHHHHHhcccCccccCCCCCCCCCCCccccCCCChHHHHHHHhcccee
Q 043276 154 WKRKFLQENPS-LFDAELNIFGLLAYDATSALAVAVEKAGITGFGFDKTNVSSNATDLEAFGISQNGPKLLQALSSIRFR 232 (829)
Q Consensus 154 w~~~~~~~~~~-~~~~~~~~~~~~~YDAV~~~A~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~L~~~~f~ 232 (829)
|+.. ..+. .+....+.|++++|||+|++|+|+++++.... ..+|.++.++|++++|+
T Consensus 278 ~~~~---~~~~~~~~~~~~~~~~~~YDav~~~a~Al~~a~~~g~-------------------~~d~~~l~~~l~~~~f~ 335 (382)
T cd06371 278 QERG---EIPSDLEPEQVSPLFGTIYNSIYLLAHAVENARAAGG-------------------GVSGANLAQHTRNLEFQ 335 (382)
T ss_pred HhcC---CCCCCCCccccchhHHHHHHHHHHHHHHHHHHHHhCC-------------------CccHHHHHHHHhCcccc
Confidence 3211 1111 01113456777899999999999999864321 02378999999999999
Q ss_pred cccccEEEe-cCccccceEEEEEcc-CCcEEEEEe
Q 043276 233 GLTGDYIFV-DGQLQSSAFEIINVN-NGARGVGFW 265 (829)
Q Consensus 233 G~tG~~~F~-~G~~~~~~y~I~n~~-~g~~~VG~w 265 (829)
|++|.+.|+ +|++ .+.|.|+++. +|++-+-.+
T Consensus 336 GvtG~v~fd~~g~~-~~~~~v~~~~~~~~~~~~~~ 369 (382)
T cd06371 336 GFNQRLRTDSGGGG-QAPYVVLDTDGKGDQLYPTY 369 (382)
T ss_pred ccceEEEecCCCCc-ccceEEEecCCCCCeeeeeE
Confidence 999999997 9998 4899999999 887766554
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=99.91 E-value=3.3e-23 Score=231.79 Aligned_cols=246 Identities=15% Similarity=0.171 Sum_probs=189.2
Q ss_pred CCCChHHHHHHHHHHHHHcCCc-EEEEEEEeCcccc----chHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhh
Q 043276 1 GALNDSSQVGAITAIIKAFGWR-EAVPIYVDNQYGE----ELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLF 75 (829)
Q Consensus 1 t~psD~~q~~ai~~ll~~fgW~-~V~iI~~dd~yG~----~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk 75 (829)
|+|+|..|+.++..++++|+|+ ++++||.++.++. ...+.+.+.+++.|++|+.......+ +.++..+|.++|
T Consensus 123 ~~p~~~~~~~~~~~i~~~~~w~~~vaiiy~~~~~~~~~~~~~~~~~~~~~~~~gi~v~~~~~~~~~--~~d~~~~l~~ik 200 (399)
T cd06384 123 TGPSTTKLGEFVNHLHEHFNWTSRAALLYLDLKTDDRPHYFISEGVFLALQEENANVSAHPYHIEK--NSDIIEIIQFIK 200 (399)
T ss_pred ecCcHHHHHHHHHHHHHhCCCcEEEEEEEecCCccCCcceEehHHHHHHHHhcCceEEEEEEeccc--hhhHHHHHHHHh
Confidence 4689999999999999999999 5889987543321 13566888889999999986554433 558999999999
Q ss_pred cCCCeEEEEEcChhHHHHHHHHHHHcCccccCeEEEEcCccccccc-------------cCCccccccccceEEEEeccC
Q 043276 76 TMQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLR-------------TLEPSVTDSMQGVIGVRPYVP 142 (829)
Q Consensus 76 ~~~arViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t~~~~~~~~-------------~~~~~~~~~~~g~l~~~~~~~ 142 (829)
+ ++||||++++.+.+..++++|+++||+.++|+||..+.+..... .......+++++++++..+.+
T Consensus 201 ~-~~~vIi~~~~~~~~~~i~~qa~~~g~~~~~y~~i~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~v~~~~~~~~ 279 (399)
T cd06384 201 Q-NGRIVYICGPLETFLEIMLQAQREGLTPGDYVFFYLDVFGESLRVKSPRESYKQMNHSSWTVLKEAFKSVFVITYREP 279 (399)
T ss_pred h-cccEEEEeCCchHHHHHHHHHHHcCCCCCcEEEEEehhcccccccCCCCccccCCCCcccHHHHHHHhheEEeecCCC
Confidence 7 89999999999999999999999999999999999886543211 001223347889999988888
Q ss_pred CChhHHHHHHHHHHhhcccCCC-CCccccchhHHHHHHHHHHHHHHHHHhcccCccccCCCCCCCCCCCccccCCCChHH
Q 043276 143 KTKALENFRVRWKRKFLQENPS-LFDAELNIFGLLAYDATSALAVAVEKAGITGFGFDKTNVSSNATDLEAFGISQNGPK 221 (829)
Q Consensus 143 ~~~~~~~F~~~w~~~~~~~~~~-~~~~~~~~~~~~~YDAV~~~A~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~ 221 (829)
..+.+++|.++|++.+...+.. .+....+.+++++||||+++|.||+++..... .+.+|..
T Consensus 280 ~~~~~~~F~~~~~~~~~~~~~~~~~p~~~~~~aa~~YDav~l~a~Al~~~~~~~~------------------~~~~g~~ 341 (399)
T cd06384 280 ENPEYKEFQRELHARAKEDFGVELEPSLMNFIAGCFYDGVMLYAMALNETLAEGG------------------SQKDGLN 341 (399)
T ss_pred CCchHHHHHHHHHHHHhhhcCCCcCcchHhhhhhhhHHHHHHHHHHHHHHHhcCC------------------CCCCcHh
Confidence 8888999999998753322110 01112366899999999999999999843211 1234789
Q ss_pred HHHHHhccceecccccEEEe-cCccccceEEEEEc---c-CCcEEEEEecCC
Q 043276 222 LLQALSSIRFRGLTGDYIFV-DGQLQSSAFEIINV---N-NGARGVGFWSPE 268 (829)
Q Consensus 222 l~~~L~~~~f~G~tG~~~F~-~G~~~~~~y~I~n~---~-~g~~~VG~w~~~ 268 (829)
|.++|++++|.|+||.+.|+ +|++. ..|.++.+ + ++++.||+|+..
T Consensus 342 i~~~l~~~~f~GvtG~v~fd~~G~r~-~~~~~~~~~~~~~g~~~~v~~~~~~ 392 (399)
T cd06384 342 ITRKMQDRRFWGVTGLVSIDKNNDRD-IDFDLWAMTDHETGKYEVVAHYNGI 392 (399)
T ss_pred HHHHHhCceeecceeEEEECCCCCcc-cceEEEEeecCCCCeEEEEEEEcCC
Confidence 99999999999999999996 99985 67888544 4 449999999864
No 32
>cd06373 PBP1_NPR_like Ligand binding domain of natriuretic peptide receptor (NPR) family. Ligand binding domain of natriuretic peptide receptor (NPR) family which consists of three different subtypes: type A natriuretic peptide receptor (NPR-A, or GC-A), type B natriuretic peptide receptors (NPR-B, or GC-B), and type C natriuretic peptide receptor (NPR-C). There are three types of natriuretic peptide (NP) ligands specific to the receptors: atrial NP (ANP), brain or B-type NP (BNP), and C-type NP (CNP). The NP family is thought to have arisen through gene duplication during evolution and plays an essential role in cardiovascular and body fluid homeostasis. ANP and BNP bind mainly to NPR-A, while CNP binds specifically to NPR-B. Both NPR-A and NPR-B have guanylyl cyclase catalytic activity and produces intracellular secondary messenger cGMP in response to peptide-ligand binding. Consequently, the NPR-A activation results in vasodilation and inhibition of vascular smooth muscle cell proli
Probab=99.91 E-value=2.3e-23 Score=233.11 Aligned_cols=247 Identities=18% Similarity=0.240 Sum_probs=192.1
Q ss_pred CCCChHHHHHHHHHHHHHcCCcEEEEEEEeCccc----cchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhc
Q 043276 1 GALNDSSQVGAITAIIKAFGWREAVPIYVDNQYG----EELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFT 76 (829)
Q Consensus 1 t~psD~~q~~ai~~ll~~fgW~~V~iI~~dd~yG----~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~ 76 (829)
+.|+|..|+.++++++++|||++|++||.+++++ ....+.|.+++++.|+||+... +.......++..+|+++++
T Consensus 122 ~~p~~~~~~~a~~~~~~~~~w~~vaii~~~~~~~~~~~~~~~~~~~~~~~~~g~~v~~~~-~~~~~~~~d~~~~l~~ik~ 200 (396)
T cd06373 122 TGPSYTKLGEFVLALHEHFNWSRAALLYHDDKNDDRPCYFTLEGVYTVLKEENITVSDFP-FDEDKELDDYKELLRDISK 200 (396)
T ss_pred ccccHHHHHHHHHHHHHHcCCeEEEEEEECCCCCcchHHHHHHHHHHHHhhcCceeeEEe-ecCCccccCHHHHHHHHHh
Confidence 5789999999999999999999999999888774 5568899999999999998543 4433112578999999997
Q ss_pred CCCeEEEEEcChhHHHHHHHHHHHcCccccCeEEEEcCcccccc----ccC-------CccccccccceEEEEeccCCCh
Q 043276 77 MQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLL----RTL-------EPSVTDSMQGVIGVRPYVPKTK 145 (829)
Q Consensus 77 ~~arViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t~~~~~~~----~~~-------~~~~~~~~~g~l~~~~~~~~~~ 145 (829)
.. |+||++++.+.+..++++|+++||+..+||||..+.+.... ... .....+.++|++++....+..+
T Consensus 201 ~~-~vii~~~~~~~~~~~~~qa~~~g~~~~~yv~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~ 279 (396)
T cd06373 201 KG-RVVIMCASPDTVREIMLAAHRLGLTSGEYVFFNIDLFGSSLYGGGPWWWERGDEDDEKAKEAYQALMTITLREPDNP 279 (396)
T ss_pred cC-cEEEEecCHHHHHHHHHHHHHcCCCCCcEEEEEEccchhhhccCCCCcCCCCCcccHHHHHHHHHheEEecCCCCCh
Confidence 65 99999999999999999999999998999999976543211 000 1122345678888888888888
Q ss_pred hHHHHHHHHHHhhcccCC-CCCccccchhHHHHHHHHHHHHHHHHHhcccCccccCCCCCCCCCCCccccCCCChHHHHH
Q 043276 146 ALENFRVRWKRKFLQENP-SLFDAELNIFGLLAYDATSALAVAVEKAGITGFGFDKTNVSSNATDLEAFGISQNGPKLLQ 224 (829)
Q Consensus 146 ~~~~F~~~w~~~~~~~~~-~~~~~~~~~~~~~~YDAV~~~A~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~ 224 (829)
.+++|.++|++.....+. ..+...++.+++++||||+++|+||+++..+... +.+|..|.+
T Consensus 280 ~~~~F~~~~~~~~~~~~~~~~~~~~~~~~a~~~YDav~~~a~Al~~~~~~~~~------------------~~~~~~i~~ 341 (396)
T cd06373 280 EYKEFSLEVKERAKKKFNTTSDDSLVNFFAGAFYDAVLLYALALNETLAEGGD------------------PRDGTNITR 341 (396)
T ss_pred HHHHHHHHHHHHhhhcCCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHhccCC------------------CCChHHHHH
Confidence 899999999875322211 1122246678999999999999999998533210 124789999
Q ss_pred HHhccceecccccEEEe-cCccccceEEEEEcc---CC-cEEEEEecCC
Q 043276 225 ALSSIRFRGLTGDYIFV-DGQLQSSAFEIINVN---NG-ARGVGFWSPE 268 (829)
Q Consensus 225 ~L~~~~f~G~tG~~~F~-~G~~~~~~y~I~n~~---~g-~~~VG~w~~~ 268 (829)
+|++++|+|++|.+.|+ +|++. ..|.|+.+. +| ++.||+|++.
T Consensus 342 ~l~~~~f~G~tG~v~fd~~G~~~-~~~~v~~~~~~~~g~~~~~~~~~~~ 389 (396)
T cd06373 342 RMWNRTFEGITGNVSIDENGDRE-SDFSLWDMTDTETGTFEVVANYNGS 389 (396)
T ss_pred HhcCCceecccCceEeecCCccc-ceeeeeeccCCCCceEEEEeecccc
Confidence 99999999999999997 99985 789998774 44 8999999874
No 33
>cd06352 PBP1_NPR_GC_like Ligand-binding domain of membrane guanylyl-cyclase receptors. Ligand-binding domain of membrane guanylyl-cyclase receptors. Membrane guanylyl cyclases (GC) have a single membrane-spanning region and are activated by endogenous and exogenous peptides. This family can be divided into three major subfamilies: the natriuretic peptide receptors (NPRs), sensory organ-specific membrane GCs, and the enterotoxin/guanylin receptors. The binding of peptide ligands to the receptor results in the activation of the cytosolic catalytic domain. Three types of NPRs have been cloned from mammalian tissues: NPR-A/GC-A, NPR-B/ GC-B, and NPR-C. In addition, two of the GCs, GC-D and GC-G, appear to be pseudogenes in humans. Atrial natriuretic peptide (ANP) and brain natriuretic peptide (BNP) are produced in the heart, and both bind to the NPR-A. NPR-C, also termed the clearance receptor, binds each of the natriuretic peptides and can alter circulating levels of these peptides. The l
Probab=99.91 E-value=5.6e-23 Score=229.72 Aligned_cols=250 Identities=17% Similarity=0.234 Sum_probs=204.8
Q ss_pred CCCChHHHHHHHHHHHHHcCCcEEEEEEEeCc-cccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCC
Q 043276 1 GALNDSSQVGAITAIIKAFGWREAVPIYVDNQ-YGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQT 79 (829)
Q Consensus 1 t~psD~~q~~ai~~ll~~fgW~~V~iI~~dd~-yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~a 79 (829)
+.|++..|+.+++++++++||+++++++++++ ||....+.+.+++++.|+||+....++...+..++..++.++++.+
T Consensus 117 ~~~~~~~~~~a~~~~l~~~~~~~v~ii~~~~~~~g~~~~~~~~~~~~~~G~~v~~~~~~~~~~~~~d~~~~l~~i~~~~- 195 (389)
T cd06352 117 TLPPARKLGEAVLALLRWFNWHVAVVVYSDDSENCFFTLEALEAALREFNLTVSHVVFMEDNSGAEDLLEILQDIKRRS- 195 (389)
T ss_pred cCCcHHHHHHHHHHHHHHcCceEEEEEEecCCccHHHHHHHHHHHHHhcCCeEEEEEEecCCccchhHHHHHHHhhhcc-
Confidence 46899999999999999999999999998888 9999999999999999999999888876522457889999999877
Q ss_pred eEEEEEcChhHHHHHHHHHHHcCccccCeEEEEcCccccccc-----------cCCccccccccceEEEEeccCCChhHH
Q 043276 80 RVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLR-----------TLEPSVTDSMQGVIGVRPYVPKTKALE 148 (829)
Q Consensus 80 rViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t~~~~~~~~-----------~~~~~~~~~~~g~l~~~~~~~~~~~~~ 148 (829)
||||+++..+.+..++++++++||...+++||.++.+..... .......+.++|++++.+..+..+.++
T Consensus 196 ~vii~~~~~~~~~~~l~q~~~~g~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~ 275 (389)
T cd06352 196 RIIIMCGSSEDVRELLLAAHDLGLTSGDYVFILIDLFNYSLPYQNSYPWERGDGDDEKAKEAYDAVLTITLRPPDNPEYE 275 (389)
T ss_pred eEEEEECCHHHHHHHHHHHHHcCCCCCcEEEEEEehhccccccCCCCCcccCCcccHHHHHHHHhheEEEecCCCCchHH
Confidence 999999999999999999999999877899999887764421 111123456789999888877788999
Q ss_pred HHHHHHHHhhcccCCCC--CccccchhHHHHHHHHHHHHHHHHHhcccCccccCCCCCCCCCCCccccCCCChHHHHHHH
Q 043276 149 NFRVRWKRKFLQENPSL--FDAELNIFGLLAYDATSALAVAVEKAGITGFGFDKTNVSSNATDLEAFGISQNGPKLLQAL 226 (829)
Q Consensus 149 ~F~~~w~~~~~~~~~~~--~~~~~~~~~~~~YDAV~~~A~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~L 226 (829)
+|.++|+++++.....+ ....++.++..+|||||++|+|++++..+... +..+..+.+.|
T Consensus 276 ~f~~~~~~~~~~~~~~~~~~~~~~~~~a~~~YDav~~~a~Al~~~~~~~~~------------------~~~~~~v~~~l 337 (389)
T cd06352 276 EFSEEVKEAAKRPPFNTDAEPEQVSPYAGYLYDAVLLYAHALNETLAEGGD------------------YNGGLIITRRM 337 (389)
T ss_pred HHHHHHHHHHhcccCccCCCccccchhhhhHHHHHHHHHHHHHHHHHhCCC------------------CCchHHHHHHh
Confidence 99999998876421100 12245678999999999999999998654311 12467899999
Q ss_pred hccceecccccEEEe-cCccccceEEEEEcc-CC--cEEEEEecCCCC
Q 043276 227 SSIRFRGLTGDYIFV-DGQLQSSAFEIINVN-NG--ARGVGFWSPEKG 270 (829)
Q Consensus 227 ~~~~f~G~tG~~~F~-~G~~~~~~y~I~n~~-~g--~~~VG~w~~~~g 270 (829)
+++.|.|++|++.|+ +|++. +.|+|++++ ++ +..++.+.+.++
T Consensus 338 ~~~~f~g~~G~v~fd~~G~~~-~~~~v~~~~~~~~~~~~~~~~~~~~~ 384 (389)
T cd06352 338 WNRTFSGITGPVTIDENGDRE-GDYSLLDLDSTGGQLEVVYLYDTSSG 384 (389)
T ss_pred cCcEEEeeeeeEEEcCCCCee-eeEEEEEecCCCceEEEEEeccccce
Confidence 999999999999996 99986 799999999 43 888888876554
No 34
>cd06394 PBP1_iGluR_Kainate_KA1_2 N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the KA1 and KA2 subunits of Kainate receptor. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the KA1 and KA2 subunits of Kainate receptor. While this N-terminal domain belongs to the periplasmic-binding fold type I superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type II. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR. There are five types of kainate receptors, GluR5, GluR6, GluR7, KA1, and KA2, which are structurally similar to AMPA and NMDA subunits of ionotropic glutamate receptors. KA1 and KA2 subunits can only form functional receptors with one of the GluR5-7 subunits. Moreover, GluR5-7 can also form functional homomeric receptor channels act
Probab=99.91 E-value=3.9e-24 Score=229.90 Aligned_cols=214 Identities=20% Similarity=0.275 Sum_probs=164.1
Q ss_pred CCChHHHHHHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCC--CChhHHHHHHHHhhcCCC
Q 043276 2 ALNDSSQVGAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPL--ATDDQIEKELYKLFTMQT 79 (829)
Q Consensus 2 ~psD~~q~~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~--~~~~~~~~~l~~lk~~~a 79 (829)
.|++..|++||++|+++|||++|++||++++| +..|++.++..++ +...++.. .++.+++.+|++|+++++
T Consensus 115 ~P~~~~~~~Ai~dli~~~~W~~v~~iYe~d~~----l~~L~~~l~~~~~---~~~~i~~~~~~~~~d~~~~L~~ik~~~~ 187 (333)
T cd06394 115 HPSNEDISVAVAGILNSFNYPTASLICAKAEC----LLRLEELLRQFLI---SKETLSVRMLDDSRDPTPLLKEIRDDKT 187 (333)
T ss_pred cCCHHHHHHHHHHHHHhcCCCEEEEEEeCcHH----HHHHHHHHHhhcc---cCCceeeEEccCcccHHHHHHHHHhcCC
Confidence 58999999999999999999999999999987 5666666665433 12222221 134589999999999999
Q ss_pred eEEEEEcChhHHHHHHHHHHHcCccccCeEEEEcCccccccccCCccccccccceEEEEeccCCChhHHHHHHHHHHhhc
Q 043276 80 RVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLEPSVTDSMQGVIGVRPYVPKTKALENFRVRWKRKFL 159 (829)
Q Consensus 80 rViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t~~~~~~~~~~~~~~~~~~~g~l~~~~~~~~~~~~~~F~~~w~~~~~ 159 (829)
|+||++|+++.+..++++|+++||+..+|+||+|+.-....+... .......+.++++..++.+..++|.+.|++++.
T Consensus 188 ~~iVv~~~~~~a~~il~qa~~lGm~~~~y~~i~T~l~~~~~~L~~--~~~~~~niTgF~l~d~~~~~v~~f~~~~~~~~~ 265 (333)
T cd06394 188 ATIIIDANASMSHTILLKASELGMTSAFYKYILTTMDFPLLRLDS--IVDDRSNILGFSMFNQSHAFYQEFIRSLNQSWR 265 (333)
T ss_pred CEEEEECChHHHHHHHHHHHHcCCCCCceEEEEecCCcccccHHH--hhcCCcceEEEEeecCCcHHHHHHHHHHHHhhh
Confidence 999999999999999999999999999999999976554332221 112234478999999988999999999988764
Q ss_pred ccCCCCCccccchhHHHHHHHHHHHHHHHHHhcccCccccCCCCCCCCCCCccccCCCChHHHHHHHhccceecccccEE
Q 043276 160 QENPSLFDAELNIFGLLAYDATSALAVAVEKAGITGFGFDKTNVSSNATDLEAFGISQNGPKLLQALSSIRFRGLTGDYI 239 (829)
Q Consensus 160 ~~~~~~~~~~~~~~~~~~YDAV~~~A~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~L~~~~f~G~tG~~~ 239 (829)
+.....+......-++++||||+++ |+||++.
T Consensus 266 ~~~~~~~~~~~~~~~al~~D~v~~~------------------------------------------------glTg~i~ 297 (333)
T cd06394 266 ENCDHSPYTGPALSSALLFDAVYAV------------------------------------------------GLTGRIE 297 (333)
T ss_pred hhcccccCCCcccceeeecceEEEE------------------------------------------------eeeccee
Confidence 3211100001122455666666554 8999999
Q ss_pred Ee-cCccccceEEEEEcc-CCcEEEEEecCCCCcc
Q 043276 240 FV-DGQLQSSAFEIINVN-NGARGVGFWSPEKGLT 272 (829)
Q Consensus 240 F~-~G~~~~~~y~I~n~~-~g~~~VG~w~~~~g~~ 272 (829)
|+ +|.|.+-..+|+++. +|.++||+|++..|+.
T Consensus 298 f~~~g~R~~~~l~v~~l~~~g~~kig~W~~~~gl~ 332 (333)
T cd06394 298 FNSKGQRSNYTLKILQKTRSGFRQIGQWHSNETLS 332 (333)
T ss_pred cCCCCcCcccEEEEEEecCCcceEEEEEeCCCCcC
Confidence 96 899998888999999 9999999999988764
No 35
>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=99.91 E-value=2.9e-23 Score=228.53 Aligned_cols=226 Identities=44% Similarity=0.780 Sum_probs=192.5
Q ss_pred CCCChHHHHHHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCe
Q 043276 1 GALNDSSQVGAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTR 80 (829)
Q Consensus 1 t~psD~~q~~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~ar 80 (829)
+.|++..++.+++++++++||++|++||.+++||....+.+.+++++.|+||+....++...+..++..++.+|++++++
T Consensus 115 ~~p~~~~~~~a~~~~~~~~~~~~v~ii~~~~~~g~~~~~~~~~~~~~~g~~v~~~~~~~~~~~~~d~~~~l~~i~~~~~d 194 (350)
T cd06366 115 TTPSDSSQNPAIAALLKKFGWRRVATIYEDDDYGSGGLPDLVDALQEAGIEISYRAAFPPSANDDDITDALKKLKEKDSR 194 (350)
T ss_pred cccchHhHHHHHHHHHHHCCCcEEEEEEEcCcccchhHHHHHHHHHHcCCEEEEEeccCCCCChhHHHHHHHHHhcCCCe
Confidence 46889999999999999999999999999999999999999999999999999998887654356899999999999999
Q ss_pred EEEEEcChhHHHHHHHHHHHcCccccCeEEEEcCcccccc----ccCCccccccccceEEEEeccCC-ChhHHHHHHHHH
Q 043276 81 VFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLL----RTLEPSVTDSMQGVIGVRPYVPK-TKALENFRVRWK 155 (829)
Q Consensus 81 ViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t~~~~~~~----~~~~~~~~~~~~g~l~~~~~~~~-~~~~~~F~~~w~ 155 (829)
+||+++....+..++++|+++||...+|+||.++.+.... ..........++|++++.++.+. .+..++|.++|+
T Consensus 195 vvi~~~~~~~~~~~~~~a~~~g~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~gv~~~~~~~~~~~~~~~~f~~~~~ 274 (350)
T cd06366 195 VIVVHFSPDLARRVFCEAYKLGMMGKGYVWILTDWLSSNWWSSSDCTDEEMLEAMQGVIGVRSYVPNSSMTLQEFTSRWR 274 (350)
T ss_pred EEEEECChHHHHHHHHHHHHcCCcCCCEEEEECcchhhhhccCCCCChHHHHHhhceEEEEeecccccCccHHHHHHHHH
Confidence 9999999999999999999999987889999998766432 12222344678899999988887 788999999999
Q ss_pred HhhcccCCCCCccccchhHHHHHHHHHHHHHHHHHhcccCccccCCCCCCCCCCCccccCCCChHHHHHHHhccceeccc
Q 043276 156 RKFLQENPSLFDAELNIFGLLAYDATSALAVAVEKAGITGFGFDKTNVSSNATDLEAFGISQNGPKLLQALSSIRFRGLT 235 (829)
Q Consensus 156 ~~~~~~~~~~~~~~~~~~~~~~YDAV~~~A~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~L~~~~f~G~t 235 (829)
++++...+. ...++.++..+|||+++ +++|.|++
T Consensus 275 ~~~~~~~~~--~~~p~~~a~~~YDav~~--------------------------------------------~~~~~G~~ 308 (350)
T cd06366 275 KRFGNENPE--LTEPSIYALYAYDAVWA--------------------------------------------STNFNGLS 308 (350)
T ss_pred HHhcccCcC--cCCCCcccchhhhheee--------------------------------------------eceEEeee
Confidence 988753211 11356789999999998 12599999
Q ss_pred ccEEEe-cCccccceEEEEEcc-CCcEEEEEecCCCCcc
Q 043276 236 GDYIFV-DGQLQSSAFEIINVN-NGARGVGFWSPEKGLT 272 (829)
Q Consensus 236 G~~~F~-~G~~~~~~y~I~n~~-~g~~~VG~w~~~~g~~ 272 (829)
|++.|+ +|++....|+++++. +++++||+|++..|+.
T Consensus 309 G~v~fd~~~~~~~~~~~~~~~~~~~~~~vg~~~~~~~~~ 347 (350)
T cd06366 309 GPVQFDGGRRLASPAFEIINIIGKGYRKIGFWSSESGLS 347 (350)
T ss_pred eeEEEcCCCccCCcceEEEEecCCceEEEEEEeCCCCcc
Confidence 999996 899877899999999 7899999999887765
No 36
>cd06381 PBP1_iGluR_delta_like N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of an orphan family of delta receptors, GluRdelta1 and GluRdelta2. This CD represents the N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of an orphan family of delta receptors, GluRdelta1 and GluRdelta2. While this N-terminal domain belongs to the periplasmic-binding fold type I superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type II. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR. Although the delta receptors are a member of the ionotropic glutamate receptor family, they cannot be activated by AMPA, kainate, NMDA, glutamate, or any other ligands. Phylogenetic analysis shows that both GluRdelta1 and GluRalpha2 are more homologous to non-NMDA receptors. G
Probab=99.90 E-value=1.1e-22 Score=222.69 Aligned_cols=222 Identities=18% Similarity=0.223 Sum_probs=168.5
Q ss_pred HHHHHHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHh-----h--cCC
Q 043276 6 SSQVGAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKL-----F--TMQ 78 (829)
Q Consensus 6 ~~q~~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~l-----k--~~~ 78 (829)
..+..|+++++++|||++|+++|++++ |...++.+.+++++.|+.+.... ...+. ...+...++.+ + +.+
T Consensus 123 ~~~~~ai~~lv~~~~wkkvavly~~d~-g~~~l~~~~~~~~~~g~~v~~~~-~~~~~-~~~~~~l~~~~~~~~l~~~~~~ 199 (363)
T cd06381 123 VRLNDVMLRLVTEWRWQKFVYFYDNDY-DIRGLQEFLDQLSRQGIDVLLQK-VDLNI-SKMATALFTTMRCEELNRYRDT 199 (363)
T ss_pred HHHHHHHHHHHHhCCCeEEEEEEECCc-hHHHHHHHHHHHHhcCceEEEEe-ccccc-chhhhhhhhHHHHHHHHhhccc
Confidence 468899999999999999999997766 55556788888999998776543 22111 11233333322 2 456
Q ss_pred CeEEEEEcChhHHHHHHHHHHHcCccccCeEEEEcCccccccccCCccccccccceEEEEeccCCChhHH----HHHHHH
Q 043276 79 TRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLEPSVTDSMQGVIGVRPYVPKTKALE----NFRVRW 154 (829)
Q Consensus 79 arViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t~~~~~~~~~~~~~~~~~~~g~l~~~~~~~~~~~~~----~F~~~w 154 (829)
.++||++|+++.+..++++|.++||+..+|+||+++.|....... ........|++||++..+..+..+ +|...|
T Consensus 200 ~~~vIl~~~~~~~~~~l~~a~~~gm~~~~~~wi~~~~l~~~~~~l-~~~~~~~~nitgfrl~~~~~~~~~~~~~~~~~~~ 278 (363)
T cd06381 200 LRRALLLLSPNGAYTFIDASVETNLAIKDSHWFLINEEISDTEID-ELVRYAHGRMTVIRQTFSKEKTNQRCLRNNHRIS 278 (363)
T ss_pred ceEEEEEcCcHHHHHHHHHHHHcCCCcCceEEEEeccccccchhh-HHHhhcCccEEEEEEecCCcCchHHHHHHHHHHH
Confidence 778899999999999999999999999999999999998643222 235567899999999988777666 455567
Q ss_pred HHhhcccCCCCCccccchhHHHHHHHHHHHHHHHHHhcccCccccCCCCCCCCCCCccccCCCChHHHHHHHhccceecc
Q 043276 155 KRKFLQENPSLFDAELNIFGLLAYDATSALAVAVEKAGITGFGFDKTNVSSNATDLEAFGISQNGPKLLQALSSIRFRGL 234 (829)
Q Consensus 155 ~~~~~~~~~~~~~~~~~~~~~~~YDAV~~~A~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~L~~~~f~G~ 234 (829)
+...... ++ ....+...++++|||||++ +++|++++|+|+
T Consensus 279 ~~~~~~~-~~-~~~~~~~~~al~yDaV~~~--------------------------------------~~~~~~~~~~GL 318 (363)
T cd06381 279 SLLCDPK-DG-YLQMLEISNLYIYDSVLLL--------------------------------------LETIKKGPITGL 318 (363)
T ss_pred HhhcCCC-CC-CCCChhHHHHHHHHHHHHH--------------------------------------HHHHHhcCccCc
Confidence 6432222 21 1124567899999999999 356788899999
Q ss_pred cccEEEe-cCccccceEEEEEcc-CC-----cEEEEEecCCCCc
Q 043276 235 TGDYIFV-DGQLQSSAFEIINVN-NG-----ARGVGFWSPEKGL 271 (829)
Q Consensus 235 tG~~~F~-~G~~~~~~y~I~n~~-~g-----~~~VG~w~~~~g~ 271 (829)
||++.|+ +|.+.+..++|+.+. +| .++||+|++..|+
T Consensus 319 TG~i~F~~~g~r~~~~l~i~~~~~~~~~~~~~~~~~~w~~~~~~ 362 (363)
T cd06381 319 TGKLEFNEGGDNSNVQFEILGTGYSETLGKDGRWLATWNPSKGL 362 (363)
T ss_pred ceeEEeCCCCCccccEEEEEEeccCCccccceEEeeeccCCCCC
Confidence 9999996 999999999999999 65 7889999987764
No 37
>PRK10797 glutamate and aspartate transporter subunit; Provisional
Probab=99.88 E-value=2.7e-21 Score=206.61 Aligned_cols=224 Identities=19% Similarity=0.261 Sum_probs=187.9
Q ss_pred CCceEEEecccccCccceEEEeecCCCCCceEEEeeHHHHHHHHH----HCCC-cccEEEEecCCCCCCCCCChhHHHHh
Q 043276 306 NEKKLRVGVPVKKGFSDFVKVTIDPKTQETSVVGYSIDVFKAVIE----ELPY-AVAYDFVPYAQPDGTSSGSYNDLIYQ 380 (829)
Q Consensus 306 ~~~~lrv~v~~~~~~~p~~~~~~~~~~~~~~~~G~~idll~~ia~----~l~f-~~~~~~~~~~~~~g~~ng~~~~li~~ 380 (829)
..+.|+||+. +.|+||.+.+ +++++.||++||+++|++ ++|. .+++++++. +|..++..
T Consensus 38 ~~g~L~Vg~~--~~~pP~~f~~-----~~g~~~G~didl~~~ia~~l~~~lg~~~~~~~~v~~---------~~~~~i~~ 101 (302)
T PRK10797 38 KNGVIVVGHR--ESSVPFSYYD-----NQQKVVGYSQDYSNAIVEAVKKKLNKPDLQVKLIPI---------TSQNRIPL 101 (302)
T ss_pred hCCeEEEEEc--CCCCCcceEC-----CCCCEeeecHHHHHHHHHHHHHhhCCCCceEEEEEc---------ChHhHHHH
Confidence 3677999988 6788998864 356899999998777765 6764 467888885 47889999
Q ss_pred HhcCcccEEEeccccccccceeccccccccccceEEEEEccCCCCCCceeeeccCCHhHHHHHHHHHHHHHHHHHhhhcc
Q 043276 381 VFLGEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMIVPIKDSKKRNAWVFLQPLTWDLWVTSGCFFIFIGFVVWVLEHR 460 (829)
Q Consensus 381 l~~g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv~~~~~~~~~~~~fl~PF~~~vW~~i~~~~~~~~~v~~~~~~~ 460 (829)
|..|++|++++++++|++|.+.++||.||..++..+++++.+ .
T Consensus 102 L~~G~~Di~~~~~~~t~eR~~~~~fS~Py~~~~~~lv~r~~~--~----------------------------------- 144 (302)
T PRK10797 102 LQNGTFDFECGSTTNNLERQKQAAFSDTIFVVGTRLLTKKGG--D----------------------------------- 144 (302)
T ss_pred HHCCCccEEecCCccCcchhhcceecccEeeccEEEEEECCC--C-----------------------------------
Confidence 999999999999999999999999999999999999998542 1
Q ss_pred cCCCCCCCccCccchhHHHHHHHhhhcCccccccchhHHHHHHHHHHHHHHHHHhHHHHHHHhhcccCCCCCCCHHHHHh
Q 043276 461 VNEDFRGPARHQVGTSFWFSFSTMVFSQRERVISNLARFVVIVWCFVVLILIQSYTASLTSLLTVDQLQPTITDVNLLIK 540 (829)
Q Consensus 461 ~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~s~~~R~v~~~w~~~~lil~~~YtA~L~s~Lt~~~~~~~I~s~~dL~~ 540 (829)
|++++||
T Consensus 145 -----------------------------------------------------------------------i~sl~dL-- 151 (302)
T PRK10797 145 -----------------------------------------------------------------------IKDFADL-- 151 (302)
T ss_pred -----------------------------------------------------------------------CCChHHc--
Confidence 6889999
Q ss_pred CCCcEEEEeCchHHHHHHhcC---CCccceeecCChHHHHHHHhcCCcCCceeEEEcchhHHHHHHhc--CCCceEEeCc
Q 043276 541 RGDNVGYQKGSFVLGILKQLG---FDERKLVVYNSHEECDELFQKGSANGGIAAAFDEIPYAKLLIGQ--HCSKYTMVEP 615 (829)
Q Consensus 541 ~~~~vg~~~~s~~~~~l~~~~---~~~~~~~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~--~c~~l~~v~~ 615 (829)
.|++||+..|+....++++.. .+..+++.+.+.++.+++|..|+ +|+++.+...+.+.+.+ ..+.+.++++
T Consensus 152 ~Gk~V~v~~gs~~~~~l~~~~~~~~~~~~i~~~~~~~~~l~~L~~Gr----vDa~i~d~~~~~~~~~~~~~~~~l~i~~~ 227 (302)
T PRK10797 152 KGKAVVVTSGTTSEVLLNKLNEEQKMNMRIISAKDHGDSFRTLESGR----AVAFMMDDALLAGERAKAKKPDNWEIVGK 227 (302)
T ss_pred CCCEEEEeCCCcHHHHHHHHhhhcCCceEEEEeCCHHHHHHHHHcCC----ceEEEccHHHHHHHHHcCCCCcceEECCc
Confidence 588999999999888886532 22356788899999999999999 99999998777664443 2335778888
Q ss_pred ccccCCceeeecCCCC-chhhHHHHHHhhhccChhHHHHHHHccC
Q 043276 616 TFKTAGFGFAFPLHSP-LVHDVSKAILNVTEGDKMKEIEDAWFKK 659 (829)
Q Consensus 616 ~~~~~~~~~~~~k~sp-l~~~in~~il~l~e~G~~~~~~~~w~~~ 659 (829)
.+...+++++++|+++ +++.+|.+|.++.++|.+++|.++|+..
T Consensus 228 ~~~~~~~~~a~~k~~~~L~~~in~~L~~l~~~G~l~~i~~kw~~~ 272 (302)
T PRK10797 228 PQSQEAYGCMLRKDDPQFKKLMDDTIAQAQTSGEAEKWFDKWFKN 272 (302)
T ss_pred cCCcCceeEEEeCCCHHHHHHHHHHHHHHHhCchHHHHHHHHcCC
Confidence 7777889999999988 9999999999999999999999999974
No 38
>PRK09495 glnH glutamine ABC transporter periplasmic protein; Reviewed
Probab=99.88 E-value=2.8e-21 Score=201.58 Aligned_cols=220 Identities=24% Similarity=0.387 Sum_probs=187.8
Q ss_pred CceEEEecccccCccceEEEeecCCCCCceEEEeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcc
Q 043276 307 EKKLRVGVPVKKGFSDFVKVTIDPKTQETSVVGYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEF 386 (829)
Q Consensus 307 ~~~lrv~v~~~~~~~p~~~~~~~~~~~~~~~~G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~ 386 (829)
.++|+||+. ++|+||.+.+ ++++.|+++||++++++++|. ++++++. +|.+++..|.+|++
T Consensus 24 ~~~l~v~~~--~~~~P~~~~~------~g~~~G~~vdl~~~ia~~lg~--~~~~~~~---------~~~~~~~~l~~G~v 84 (247)
T PRK09495 24 DKKLVVATD--TAFVPFEFKQ------GDKYVGFDIDLWAAIAKELKL--DYTLKPM---------DFSGIIPALQTKNV 84 (247)
T ss_pred CCeEEEEeC--CCCCCeeecC------CCceEEEeHHHHHHHHHHhCC--ceEEEeC---------CHHHHHHHHhCCCc
Confidence 568999976 5678888742 567899999999999999996 4555553 59999999999999
Q ss_pred cEEEeccccccccceeccccccccccceEEEEEccCCCCCCceeeeccCCHhHHHHHHHHHHHHHHHHHhhhcccCCCCC
Q 043276 387 DAVVGDTTIVFNRSNYVDFTLPYTESGVSMIVPIKDSKKRNAWVFLQPLTWDLWVTSGCFFIFIGFVVWVLEHRVNEDFR 466 (829)
Q Consensus 387 Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv~~~~~~~~~~~~fl~PF~~~vW~~i~~~~~~~~~v~~~~~~~~~~~~~ 466 (829)
|+++++++.+++|.+.++||.||+.+++.+++++...
T Consensus 85 Di~~~~~~~t~~R~~~~~fs~p~~~~~~~~~~~~~~~------------------------------------------- 121 (247)
T PRK09495 85 DLALAGITITDERKKAIDFSDGYYKSGLLVMVKANNN------------------------------------------- 121 (247)
T ss_pred CEEEecCccCHHHHhhccccchheecceEEEEECCCC-------------------------------------------
Confidence 9998889999999999999999999999999985432
Q ss_pred CCccCccchhHHHHHHHhhhcCccccccchhHHHHHHHHHHHHHHHHHhHHHHHHHhhcccCCCCCCCHHHHHhCCCcEE
Q 043276 467 GPARHQVGTSFWFSFSTMVFSQRERVISNLARFVVIVWCFVVLILIQSYTASLTSLLTVDQLQPTITDVNLLIKRGDNVG 546 (829)
Q Consensus 467 ~~~~~~~~~~~~~~~~~l~~~~~~~~~s~~~R~v~~~w~~~~lil~~~YtA~L~s~Lt~~~~~~~I~s~~dL~~~~~~vg 546 (829)
++++++|| .+++||
T Consensus 122 ----------------------------------------------------------------~~~~~~dL--~g~~I~ 135 (247)
T PRK09495 122 ----------------------------------------------------------------DIKSVKDL--DGKVVA 135 (247)
T ss_pred ----------------------------------------------------------------CCCChHHh--CCCEEE
Confidence 16889999 588999
Q ss_pred EEeCchHHHHHHhcCCCccceeecCChHHHHHHHhcCCcCCceeEEEcchhHHHHHHhcC-CCceEEeCcccccCCceee
Q 043276 547 YQKGSFVLGILKQLGFDERKLVVYNSHEECDELFQKGSANGGIAAAFDEIPYAKLLIGQH-CSKYTMVEPTFKTAGFGFA 625 (829)
Q Consensus 547 ~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~~-c~~l~~v~~~~~~~~~~~~ 625 (829)
+..|+....++++. .+..+++.+++.++.+.+|.+|+ +|+++.+...+.+++++. ...+..++......+++++
T Consensus 136 v~~g~~~~~~l~~~-~~~~~i~~~~~~~~~~~~L~~gr----vDa~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a 210 (247)
T PRK09495 136 VKSGTGSVDYAKAN-IKTKDLRQFPNIDNAYLELGTGR----ADAVLHDTPNILYFIKTAGNGQFKAVGDSLEAQQYGIA 210 (247)
T ss_pred EecCchHHHHHHhc-CCCCceEEcCCHHHHHHHHHcCc----eeEEEeChHHHHHHHHhCCCCceEEecCcccccceEEE
Confidence 99999888888764 55667888899999999999999 999999988888887764 3356677766677789999
Q ss_pred ecCCCCchhhHHHHHHhhhccChhHHHHHHHccC
Q 043276 626 FPLHSPLVHDVSKAILNVTEGDKMKEIEDAWFKK 659 (829)
Q Consensus 626 ~~k~spl~~~in~~il~l~e~G~~~~~~~~w~~~ 659 (829)
++|++.+++.+|++|..+.++|.++++.+||+..
T Consensus 211 ~~~~~~l~~~~n~al~~~~~~g~~~~i~~k~~~~ 244 (247)
T PRK09495 211 FPKGSELREKVNGALKTLKENGTYAEIYKKWFGT 244 (247)
T ss_pred EcCcHHHHHHHHHHHHHHHHCCcHHHHHHHHcCC
Confidence 9999999999999999999999999999999964
No 39
>cd06382 PBP1_iGluR_Kainate N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the kainate receptors. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the kainate receptors, non-NMDA ionotropic receptors which respond to the neurotransmitter glutamate. While this N-terminal domain belongs to the periplasmic-binding fold type I superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type II. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR. Kainate receptors have five subunits, GluR5, GluR6, GluR7, KA1, and KA2, which are structurally similar to AMPA and NMDA subunits of ionotropic glutamate receptors. KA1 and KA2 subunits can only form functional receptors with one of the GluR5-7 subunits. Moreover, GluR5-7 can also form functional homomeri
Probab=99.88 E-value=1.2e-21 Score=213.64 Aligned_cols=213 Identities=20% Similarity=0.274 Sum_probs=171.8
Q ss_pred CCCChHHHHHHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCc---eeeeEEecCCCCChhHHHHHHHHhhcC
Q 043276 1 GALNDSSQVGAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDT---RVPYRSVISPLATDDQIEKELYKLFTM 77 (829)
Q Consensus 1 t~psD~~q~~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi---~I~~~~~i~~~~~~~~~~~~l~~lk~~ 77 (829)
+.|++..|+.+++++++++||++|++||++++++.. +.+.+++.+. .|.. ..++.. . +++.+|.+|+++
T Consensus 109 ~~p~~~~~~~a~~~~~~~~~w~~vavl~~~~~~~~~----l~~~~~~~~~~g~~v~~-~~~~~~--~-d~~~~l~~i~~~ 180 (327)
T cd06382 109 LYPSNADLSRAYADIVKSFNWKSFTIIYESAEGLLR----LQELLQAFGISGITITV-RQLDDD--L-DYRPLLKEIKNS 180 (327)
T ss_pred eCCCHHHHHHHHHHHHHhcCCcEEEEEecChHHHHH----HHHHHHhhccCCCeEEE-EEccCC--c-cHHHHHHHHHhc
Confidence 468999999999999999999999999998886544 4455555554 4444 345544 3 899999999999
Q ss_pred CCeEEEEEcChhHHHHHHHHHHHcCccccCeEEEEcCccccccccCCccccccccceEEEEeccCCChhHHHHHHHHHHh
Q 043276 78 QTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLEPSVTDSMQGVIGVRPYVPKTKALENFRVRWKRK 157 (829)
Q Consensus 78 ~arViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t~~~~~~~~~~~~~~~~~~~g~l~~~~~~~~~~~~~~F~~~w~~~ 157 (829)
++++||+++..+.+..++++|+++||....|+||+++......+... ......++++++++.++++.+++|.++|+++
T Consensus 181 ~~d~vv~~~~~~~~~~~~~qa~~~g~~~~~~~~i~~~~~~~~~~l~~--~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~ 258 (327)
T cd06382 181 GDNRIIIDCSADILIELLKQAQQVGMMSEYYHYIITNLDLHTLDLED--YRYSGVNITGFRLVDPDSPEVKEVIRSLELS 258 (327)
T ss_pred CceEEEEECCHHHHHHHHHHHHHhCccccceEEEEecCCccccchhh--hccCceeEEEEEEecCCchhHHHHHHHHHhh
Confidence 99999999999999999999999999988999999876554432211 2223447788888888889999999999999
Q ss_pred hcccCCCCCccccchhHHHHHHHHHHHHHHHHHhcccCccccCCCCCCCCCCCccccCCCChHHHHHHHhccceeccccc
Q 043276 158 FLQENPSLFDAELNIFGLLAYDATSALAVAVEKAGITGFGFDKTNVSSNATDLEAFGISQNGPKLLQALSSIRFRGLTGD 237 (829)
Q Consensus 158 ~~~~~~~~~~~~~~~~~~~~YDAV~~~A~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~L~~~~f~G~tG~ 237 (829)
++...+......++.+++.+|||++++ |+||.
T Consensus 259 ~~~~~~~~~~~~p~~~~a~~yDav~~~------------------------------------------------g~tG~ 290 (327)
T cd06382 259 WDEGCRILPSTGVTTESALMYDAVYLF------------------------------------------------GLTGR 290 (327)
T ss_pred cccccccCCCCCcchhhhhhhceEEEe------------------------------------------------ecccc
Confidence 976433222334677899999998877 89999
Q ss_pred EEEe-cCccccceEEEEEcc-CCcEEEEEecCCCCc
Q 043276 238 YIFV-DGQLQSSAFEIINVN-NGARGVGFWSPEKGL 271 (829)
Q Consensus 238 ~~F~-~G~~~~~~y~I~n~~-~g~~~VG~w~~~~g~ 271 (829)
++|+ +|+|.+..|+|+|+. +|+++||+|++..|+
T Consensus 291 v~f~~~g~r~~~~~~~~~~~~~~~~~vg~w~~~~~~ 326 (327)
T cd06382 291 IEFDSSGQRSNFTLDVIELTESGLRKVGTWNSSEGL 326 (327)
T ss_pred eeeCCCCCEeeeEEEEEeccccCceEEEEECCCCCc
Confidence 9997 999999999999999 889999999987764
No 40
>cd06383 PBP1_iGluR_AMPA_Like N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of uncharacterized AMPA-like receptors. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of uncharacterized AMPA-like receptors. While this N-terminal domain belongs to the periplasmic-binding fold type I superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type II. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR. AMPA receptors consist of four types of subunits (GluR1, GluR2, GluR3, and GluR4) which combine to form a tetramer and play an important roles in mediating the rapid excitatory synaptic current.
Probab=99.87 E-value=1.1e-21 Score=215.08 Aligned_cols=239 Identities=15% Similarity=0.143 Sum_probs=160.2
Q ss_pred CCCChHHHHHHHHHHHHHcCCcEEEEEEEeCccccchHHHHHH-HHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCC
Q 043276 1 GALNDSSQVGAITAIIKAFGWREAVPIYVDNQYGEELIPSLTD-ALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQT 79 (829)
Q Consensus 1 t~psD~~q~~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~-~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~a 79 (829)
|.|+|..|++||++|+++|||+||++||++++++....+.+.. .....+.|+. +.. ..++.+.|++|+++++
T Consensus 113 ~~Ps~~~~~~Ai~dlI~~f~W~~v~iIYddd~gl~~~l~~~l~~~~~~~~~~v~-----~~~--~~~~~~~Lk~lk~~~~ 185 (368)
T cd06383 113 LMPPADDIVEAIRDIVSYYNITNAAILYDDDFVMDHKYKSLLQNWPTRHVITII-----NSI--IDEVREQIKRLRNLDI 185 (368)
T ss_pred EeCChHHHHHHHHHHHHHCCCcEEEEEEEcCchhhHHHHHHHHhHHhcCCEEEE-----ecc--chhHHHHHHHHHhCCC
Confidence 5799999999999999999999999999666644333333333 3334445543 111 3468899999999888
Q ss_pred -eEEEEEcChhHHHHHHHHHHHcCccccCeEEEEcCccccccccCCccccccccceEEEEeccCCChhHHHHHHHHHHhh
Q 043276 80 -RVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLEPSVTDSMQGVIGVRPYVPKTKALENFRVRWKRKF 158 (829)
Q Consensus 80 -rViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t~~~~~~~~~~~~~~~~~~~g~l~~~~~~~~~~~~~~F~~~w~~~~ 158 (829)
||||+|..++.+..+|++|.++||++.+|+||+++......+... ....-.++.|+++........+.+..+|...
T Consensus 186 ~rIIi~~s~~~~~~~il~qA~~lgm~~~~y~wilt~ld~~~~dl~~--~~~~~~Nitgfrl~~~~~~~~~~~~~~~~~~- 262 (368)
T cd06383 186 KNIFILGSTEEIIRYVLDQALAEGFMGRKYAWFLGNPDLGIYDDLS--CQLRNASIFVTRPMMDYQSSVRGALLRTDEP- 262 (368)
T ss_pred eEEEEEeCCHHHHHHHHHHHHHcCCcCCceEEEEcCCCchhhhhhh--hccccCcEEEeeccccchhhhccceeeccCC-
Confidence 555555556999999999999999999999999987554433221 2223357889998766555557777766221
Q ss_pred cccCCCCCccccchhHHHHHHHHHHHHHHHHHhcccCccccCCCCCCCCCCCcccc---CC-CChHHHHHHHhccceecc
Q 043276 159 LQENPSLFDAELNIFGLLAYDATSALAVAVEKAGITGFGFDKTNVSSNATDLEAFG---IS-QNGPKLLQALSSIRFRGL 234 (829)
Q Consensus 159 ~~~~~~~~~~~~~~~~~~~YDAV~~~A~Al~~~~~~~~~~~~~~~~~~~~~~~~~~---~~-~~g~~l~~~L~~~~f~G~ 234 (829)
..+......+..-++++||||+++|.|++++........ ...+....|.... +| ..|..+.++|+.++|+|+
T Consensus 263 --~~~~~~~~~~~~~~aL~~Dav~~~~~a~~~l~~~~~~~~--~~~~~~~~~~g~~~~~~w~~~g~~~~~~~k~~~~~gl 338 (368)
T cd06383 263 --TLRPVFYFEWAFRLFLAYDAVLAVGEWPRRMRKKRVEDG--STGTSVLPGFGISPESPLMTLQSSPFNGSSEIKFEML 338 (368)
T ss_pred --ccCchhHHHHHHHHHHHHHHHHHhccccchhheeeccCC--CcCccccCCCCCCcccchhhcccccccCccceeEeee
Confidence 101001112344689999999999999998732111100 0000111232211 23 456699999999999999
Q ss_pred cccEEEe-cCccccceEEEEEc
Q 043276 235 TGDYIFV-DGQLQSSAFEIINV 255 (829)
Q Consensus 235 tG~~~F~-~G~~~~~~y~I~n~ 255 (829)
||++.|+ +|.|. +|++..|
T Consensus 339 tG~i~f~~~g~R~--~~~l~~~ 358 (368)
T cd06383 339 AGRVAIDEGSSVS--TKTIGSW 358 (368)
T ss_pred cCeEEEecCceee--eeeeeeE
Confidence 9999996 89884 5665444
No 41
>PRK11260 cystine transporter subunit; Provisional
Probab=99.86 E-value=1.6e-20 Score=198.03 Aligned_cols=225 Identities=20% Similarity=0.332 Sum_probs=191.3
Q ss_pred CCCceEEEecccccCccceEEEeecCCCCCceEEEeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcC
Q 043276 305 TNEKKLRVGVPVKKGFSDFVKVTIDPKTQETSVVGYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLG 384 (829)
Q Consensus 305 ~~~~~lrv~v~~~~~~~p~~~~~~~~~~~~~~~~G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g 384 (829)
...+.++||+. ..++||.+.+ .++++.|+.+|+++.+++++|.+ +++++. .|.+++.+|.+|
T Consensus 38 ~~~~~l~v~~~--~~~~P~~~~~-----~~g~~~G~~~dl~~~i~~~lg~~--~e~~~~---------~~~~~~~~l~~G 99 (266)
T PRK11260 38 KERGTLLVGLE--GTYPPFSFQG-----EDGKLTGFEVEFAEALAKHLGVK--ASLKPT---------KWDGMLASLDSK 99 (266)
T ss_pred hcCCeEEEEeC--CCcCCceEEC-----CCCCEEEehHHHHHHHHHHHCCe--EEEEeC---------CHHHHHHHHhcC
Confidence 34678999976 5678887754 35789999999999999999974 555553 499999999999
Q ss_pred cccEEEeccccccccceeccccccccccceEEEEEccCCCCCCceeeeccCCHhHHHHHHHHHHHHHHHHHhhhcccCCC
Q 043276 385 EFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMIVPIKDSKKRNAWVFLQPLTWDLWVTSGCFFIFIGFVVWVLEHRVNED 464 (829)
Q Consensus 385 ~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv~~~~~~~~~~~~fl~PF~~~vW~~i~~~~~~~~~v~~~~~~~~~~~ 464 (829)
++|+++++++.+++|.+.+.||.||...++.+++++.+...
T Consensus 100 ~~D~~~~~~~~~~~r~~~~~fs~p~~~~~~~~~~~~~~~~~--------------------------------------- 140 (266)
T PRK11260 100 RIDVVINQVTISDERKKKYDFSTPYTVSGIQALVKKGNEGT--------------------------------------- 140 (266)
T ss_pred CCCEEEeccccCHHHHhccccCCceeecceEEEEEcCCcCC---------------------------------------
Confidence 99999988999999999999999999999999988654322
Q ss_pred CCCCccCccchhHHHHHHHhhhcCccccccchhHHHHHHHHHHHHHHHHHhHHHHHHHhhcccCCCCCCCHHHHHhCCCc
Q 043276 465 FRGPARHQVGTSFWFSFSTMVFSQRERVISNLARFVVIVWCFVVLILIQSYTASLTSLLTVDQLQPTITDVNLLIKRGDN 544 (829)
Q Consensus 465 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~s~~~R~v~~~w~~~~lil~~~YtA~L~s~Lt~~~~~~~I~s~~dL~~~~~~ 544 (829)
+++++|| ++++
T Consensus 141 -------------------------------------------------------------------~~~~~dL--~g~~ 151 (266)
T PRK11260 141 -------------------------------------------------------------------IKTAADL--KGKK 151 (266)
T ss_pred -------------------------------------------------------------------CCCHHHc--CCCE
Confidence 6889999 5889
Q ss_pred EEEEeCchHHHHHHhcCCCccceeecCChHHHHHHHhcCCcCCceeEEEcchhHHHHHHhcCCCceEEeCcccccCCcee
Q 043276 545 VGYQKGSFVLGILKQLGFDERKLVVYNSHEECDELFQKGSANGGIAAAFDEIPYAKLLIGQHCSKYTMVEPTFKTAGFGF 624 (829)
Q Consensus 545 vg~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~~c~~l~~v~~~~~~~~~~~ 624 (829)
+|+..|+....++++. ++..++..+++..+++++|.+|+ +|+++.+...+.+++++....+.+....+...++++
T Consensus 152 Igv~~G~~~~~~l~~~-~~~~~i~~~~~~~~~l~~L~~Gr----vD~~i~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 226 (266)
T PRK11260 152 VGVGLGTNYEQWLRQN-VQGVDVRTYDDDPTKYQDLRVGR----IDAILVDRLAALDLVKKTNDTLAVAGEAFSRQESGV 226 (266)
T ss_pred EEEecCCcHHHHHHHh-CCCCceEecCCHHHHHHHHHcCC----CCEEEechHHHHHHHHhCCCcceecCCccccCceEE
Confidence 9999999888888763 66677888999999999999999 999999998888888776544555566677788999
Q ss_pred eecCCCC-chhhHHHHHHhhhccChhHHHHHHHccCC
Q 043276 625 AFPLHSP-LVHDVSKAILNVTEGDKMKEIEDAWFKKH 660 (829)
Q Consensus 625 ~~~k~sp-l~~~in~~il~l~e~G~~~~~~~~w~~~~ 660 (829)
+++|+++ |++.||++|.++.++|.++++.+||+.+.
T Consensus 227 ~v~~~~~~l~~~ln~~l~~~~~~g~~~~i~~k~~~~~ 263 (266)
T PRK11260 227 ALRKGNPDLLKAVNQAIAEMQKDGTLKALSEKWFGAD 263 (266)
T ss_pred EEeCCCHHHHHHHHHHHHHHHhCCcHHHHHHHhcCCc
Confidence 9999988 99999999999999999999999999753
No 42
>cd06377 PBP1_iGluR_NMDA_NR3 N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the NR3 subunit of NMDA receptor family. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the NR3 subunit of NMDA receptor family. The ionotropic N-methyl-d-asparate (NMDA) subtype of glutamate receptor serves critical functions in neuronal development, functioning, and degeneration in the mammalian central nervous system. The functional NMDA receptor is a heterotetramer composed of two NR1 and two NR2 (A, B, C, and D) or of NR3 (A and B) subunits. The receptor controls a cation channel that is highly permeable to monovalent ions and calcium and exhibits voltage-dependent inhibition by magnesium. Dual agonists, glutamate and glycine, are required for efficient activation of the NMDA receptor. Among NMDA receptor subtypes, the NR2B subunit containing receptors appear particularly important for pain perception; thus NR2B-selective antagonists may be useful in
Probab=99.86 E-value=5.9e-20 Score=197.66 Aligned_cols=233 Identities=17% Similarity=0.214 Sum_probs=159.3
Q ss_pred CCChHHHHHHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCC--ceeeeEEecCCC-CChhHH-HHHHHHhhcC
Q 043276 2 ALNDSSQVGAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAID--TRVPYRSVISPL-ATDDQI-EKELYKLFTM 77 (829)
Q Consensus 2 ~psD~~q~~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~g--i~I~~~~~i~~~-~~~~~~-~~~l~~lk~~ 77 (829)
.|+-+.|+.|++++|++|||++|++||+.++... ..+.+.+.....+ ..|..+. ++.. .+..+. +..|+.|++.
T Consensus 132 ~P~~~~l~~a~~~ll~~~~W~~f~~iy~~~~gl~-~lq~l~~~~~~~~~~~~i~v~~-~~~~~~d~~~~~~~~L~~i~~~ 209 (382)
T cd06377 132 ASPLSTLLDVLLSVLQRNGWEDVSLVLCRERDPT-GLLLLWTNHARFHLGSVLNLSR-NDPSTADLLDFLRAQLELLKDP 209 (382)
T ss_pred cCCHHHHHHHHHHHHHHCCCcEEEEEEecCcCHH-HHHHHHHHhcccccCceEEEEe-ccCccCChhHHHHHHHHHhhcc
Confidence 6888999999999999999999999998777433 3333333333323 2333332 2211 123344 8899999999
Q ss_pred C-CeEEEEEcChhHHHHHHHHHHHcCccccCeEEEEcCccccccccCCccccccccceEEEEeccCCChhHHHHHHHHHH
Q 043276 78 Q-TRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLEPSVTDSMQGVIGVRPYVPKTKALENFRVRWKR 156 (829)
Q Consensus 78 ~-arViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t~~~~~~~~~~~~~~~~~~~g~l~~~~~~~~~~~~~~F~~~w~~ 156 (829)
. .++||++|+.+.+..+|.++.+ +|+||+++... ++.. .....--|.++. .+
T Consensus 210 ~~~~~ill~cs~e~~~~il~~~~~------~y~wIv~~~~~--le~~--~~~g~nigLl~~-----------------~~ 262 (382)
T cd06377 210 PGPAVVLFGCDVARARRVLELTPP------GPHWILGDPLP--PEAL--RTEGLPPGLLAH-----------------GE 262 (382)
T ss_pred cCceEEEEECCHHHHHHHHHhhcc------ceEEEEcCCcC--hhhc--cCCCCCceEEEE-----------------ee
Confidence 9 9999999999999999977754 59999997221 1111 111222233321 10
Q ss_pred hhcccCCCCCccccchhHHHHHHHHHHHHHHHHHhcccCc--cccCCCCCCCCCCCccc--c-CCCChHHHHHHHhccce
Q 043276 157 KFLQENPSLFDAELNIFGLLAYDATSALAVAVEKAGITGF--GFDKTNVSSNATDLEAF--G-ISQNGPKLLQALSSIRF 231 (829)
Q Consensus 157 ~~~~~~~~~~~~~~~~~~~~~YDAV~~~A~Al~~~~~~~~--~~~~~~~~~~~~~~~~~--~-~~~~g~~l~~~L~~~~f 231 (829)
. ......+++||||+++|.|++.+..... .... ...+|... + .|..|..|.++|++++|
T Consensus 263 ---~--------~~~~l~ali~DAV~lvA~a~~~l~~~~~~~~l~~-----~~~~C~~~~~~~~W~~G~~l~~~Lknv~~ 326 (382)
T cd06377 263 ---T--------TQPPLEAYVQDALELVARAVGSATLVQPELALIP-----ATVNCMDLPTKGNESSGQYLARFLANTSF 326 (382)
T ss_pred ---c--------ccccHHHHHHHHHHHHHHHHHHhhhcccccccCC-----CCCCcccCCCCCCCCchHHHHHHHHhCcc
Confidence 0 0012378999999999999998732111 1111 11356433 4 78999999999999999
Q ss_pred ecccccEEEecCcc--ccceEEEEEcc---CC---cEEEEEecCCCCcccccCCCccccCCccceecC
Q 043276 232 RGLTGDYIFVDGQL--QSSAFEIINVN---NG---ARGVGFWSPEKGLTQKLSSNSTTKSKLRPIIWP 291 (829)
Q Consensus 232 ~G~tG~~~F~~G~~--~~~~y~I~n~~---~g---~~~VG~w~~~~g~~~~l~~~~~~~~~~~~i~Wp 291 (829)
+|+||.+.|+.|.+ .+..++|++++ +| |++||+|++...+ ..+.+.||
T Consensus 327 eGlTG~I~F~~g~R~~~~~~l~I~~L~~~~~G~~~W~kVG~W~~~~~~------------~~~~~~wp 382 (382)
T cd06377 327 DGRTGPVWVTGSSQVHSSRHFKVWSLRRDPVGQPTWTTVGSWQGGRKI------------VMDQGLWP 382 (382)
T ss_pred cccceeEEEccCeeecccceEEEEEeccccCCCccceEEEEecCCCce------------ecccCCCC
Confidence 99999999987777 67889999998 45 6999999986222 34677886
No 43
>cd06368 PBP1_iGluR_non_NMDA_like N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the non-NMDA (N-methyl-d-asparate) subtypes of ionotropic glutamate receptors. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the non-NMDA (N-methyl-d-asparate) subtypes of ionotropic glutamate receptors. While this N-terminal domain belongs to the periplasmic-binding fold type I superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type II. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR. Glutamate mediates the majority of excitatory synaptic transmission in the central nervous system via two broad classes of ionotropic receptors, characterized by their response to glutamate agonists: N-methyl-d -aspartate (NMDA) and non-NMDA receptors. NMDA receptors
Probab=99.86 E-value=1.4e-20 Score=204.87 Aligned_cols=214 Identities=27% Similarity=0.353 Sum_probs=172.1
Q ss_pred CCChHHHHHHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeE
Q 043276 2 ALNDSSQVGAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRV 81 (829)
Q Consensus 2 ~psD~~q~~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arV 81 (829)
.|++..|+.++++++++|||++|++||++++++ ..++.+.+++++.|++|+.....+ . .++++.+|.+|+++++++
T Consensus 108 ~~~~~~~~~a~~~~~~~~~w~~vaii~~~~~~~-~~l~~~~~~~~~~g~~v~~~~~~~-~--~~d~~~~l~~i~~~~~d~ 183 (324)
T cd06368 108 YPSMRDLSDALLDLIKYFGWRKFVYIYDSDEGL-LRLQELLDALSPKGIQVTVRRLDD-D--TDMYRPLLKEIKREKERR 183 (324)
T ss_pred cCCHHHHHHHHHHHHHhcCCCEEEEEECCcHhH-HHHHHHHHhhccCCceEEEEEecC-C--chHHHHHHHHHhhccCce
Confidence 467779999999999999999999999776654 455677777888899998765433 2 227999999999999999
Q ss_pred EEEEcChhHHHHHHHHHHHcCccccCeEEEEcCccccccccCCccccccccceEEEEeccCCChhHHHHHHHHHHhhccc
Q 043276 82 FILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLEPSVTDSMQGVIGVRPYVPKTKALENFRVRWKRKFLQE 161 (829)
Q Consensus 82 iIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t~~~~~~~~~~~~~~~~~~~g~l~~~~~~~~~~~~~~F~~~w~~~~~~~ 161 (829)
||++++.+++..++++|+++||+..+|+||+++.-....+. ........++.++....+.++..++|.++|++.++..
T Consensus 184 Vi~~~~~~~~~~i~~qa~~~g~~~~~~~~i~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~ 261 (324)
T cd06368 184 IILDCSPERLKEFLEQAVEVGMMSEYYHYILTNLDFHTLDL--ELFRYGGVNITGFRLVDPDNPEVQKFIQRWERSDHRI 261 (324)
T ss_pred EEEECCHHHHHHHHHHHHHhccccCCcEEEEccCCccccch--hhhhcCCceEEEEEEecCCChHHHHHHHHHHhccccc
Confidence 99999999999999999999998889999998754322211 1122234467787777788899999999999998764
Q ss_pred CCCCCccccchhHHHHHHHHHHHHHHHHHhcccCccccCCCCCCCCCCCccccCCCChHHHHHHHhccceecccccEEEe
Q 043276 162 NPSLFDAELNIFGLLAYDATSALAVAVEKAGITGFGFDKTNVSSNATDLEAFGISQNGPKLLQALSSIRFRGLTGDYIFV 241 (829)
Q Consensus 162 ~~~~~~~~~~~~~~~~YDAV~~~A~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~L~~~~f~G~tG~~~F~ 241 (829)
.+......+..+++.+||||+++ ||++.|+
T Consensus 262 ~~~~~~~~p~~~aa~~yDav~~~--------------------------------------------------tg~~~f~ 291 (324)
T cd06368 262 CPGSGLKPIKTESALTYDAVLLF--------------------------------------------------TGRIQFD 291 (324)
T ss_pred cCCCCCCCcchhhHhhhcEEEEe--------------------------------------------------eeeeEeC
Confidence 33222235678999999998876 7889996
Q ss_pred -cCccccceEEEEEcc-CCcEEEEEecCCCCc
Q 043276 242 -DGQLQSSAFEIINVN-NGARGVGFWSPEKGL 271 (829)
Q Consensus 242 -~G~~~~~~y~I~n~~-~g~~~VG~w~~~~g~ 271 (829)
+|++.+..++|+++. +|+++||+|++..++
T Consensus 292 ~~g~~~~~~~~i~~~~~~~~~~~g~W~~~~~~ 323 (324)
T cd06368 292 ENGQRSNFTLDILELKEGGLRKVGTWNPEDGL 323 (324)
T ss_pred CCCcCcceEEEEEEEcCCCceEEEEECCCCCC
Confidence 899999999999999 899999999987664
No 44
>PF00497 SBP_bac_3: Bacterial extracellular solute-binding proteins, family 3; InterPro: IPR001638 Bacterial high affinity transport systems are involved in active transport of solutes across the cytoplasmic membrane. The protein components of these traffic systems include one or two transmembrane protein components, one or two membrane-associated ATP-binding proteins (ABC transporters; see IPR003439 from INTERPRO) and a high affinity periplasmic solute-binding protein. The latter are thought to bind the substrate in the vicinity of the inner membrane, and to transfer it to a complex of inner membrane proteins for concentration into the cytoplasm. In Gram-positive bacteria which are surrounded by a single membrane and have therefore no periplasmic region, the equivalent proteins are bound to the membrane via an N-terminal lipid anchor. These homologue proteins do not play an integral role in the transport process per se, but probably serve as receptors to trigger or initiate translocation of the solute throught the membrane by binding to external sites of the integral membrane proteins of the efflux system. In addition, at least some solute-binding proteins function in the initiation of sensory transduction pathways. On the basis of sequence similarities, the vast majority of these solute-binding proteins can be grouped [] into eight families or clusters, which generally correlate with the nature of the solute bound. Family 3 groups together specific amino acids and opine-binding periplasmic proteins and a periplasmic homologue with catalytic activity.; GO: 0005215 transporter activity, 0006810 transport, 0030288 outer membrane-bounded periplasmic space; PDB: 3N26_A 3QAX_A 3I6V_A 2VHA_B 2IA4_B 2Q89_A 2Q88_A 2YJP_C 1II5_A 1IIW_A ....
Probab=99.85 E-value=7.5e-21 Score=194.97 Aligned_cols=223 Identities=25% Similarity=0.395 Sum_probs=182.9
Q ss_pred EEEecccccCccceEEEeecCCCCCceEEEeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccEE
Q 043276 310 LRVGVPVKKGFSDFVKVTIDPKTQETSVVGYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDAV 389 (829)
Q Consensus 310 lrv~v~~~~~~~p~~~~~~~~~~~~~~~~G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di~ 389 (829)
||||+. +.++||.+.+ .+++..|+++||++++++++|++++ ++.. +|.+++.+|.+|++|++
T Consensus 1 l~V~~~--~~~~P~~~~~-----~~~~~~G~~~dl~~~i~~~~g~~~~--~~~~---------~~~~~~~~l~~g~~D~~ 62 (225)
T PF00497_consen 1 LRVGVD--EDYPPFSYID-----EDGEPSGIDVDLLRAIAKRLGIKIE--FVPM---------PWSRLLEMLENGKADII 62 (225)
T ss_dssp EEEEEE--SEBTTTBEEE-----TTSEEESHHHHHHHHHHHHHTCEEE--EEEE---------EGGGHHHHHHTTSSSEE
T ss_pred CEEEEc--CCCCCeEEEC-----CCCCEEEEhHHHHHHHHhhcccccc--eeec---------ccccccccccccccccc
Confidence 688885 4677888876 3788999999999999999998544 4443 48999999999999999
Q ss_pred EeccccccccceeccccccccccceEEEEEccCCCCCCceeeeccCCHhHHHHHHHHHHHHHHHHHhhhcccCCCCCCCc
Q 043276 390 VGDTTIVFNRSNYVDFTLPYTESGVSMIVPIKDSKKRNAWVFLQPLTWDLWVTSGCFFIFIGFVVWVLEHRVNEDFRGPA 469 (829)
Q Consensus 390 ~~~~~it~~R~~~vdft~p~~~~~~~~vv~~~~~~~~~~~~fl~PF~~~vW~~i~~~~~~~~~v~~~~~~~~~~~~~~~~ 469 (829)
+++++.+++|.+.++||.||+....++++++.+...
T Consensus 63 ~~~~~~~~~r~~~~~~s~p~~~~~~~~~~~~~~~~~-------------------------------------------- 98 (225)
T PF00497_consen 63 IGGLSITPERAKKFDFSDPYYSSPYVLVVRKGDAPP-------------------------------------------- 98 (225)
T ss_dssp ESSEB-BHHHHTTEEEESESEEEEEEEEEETTSTCS--------------------------------------------
T ss_pred cccccccccccccccccccccchhheeeeccccccc--------------------------------------------
Confidence 999999999999999999999999999999643211
Q ss_pred cCccchhHHHHHHHhhhcCccccccchhHHHHHHHHHHHHHHHHHhHHHHHHHhhcccCCCCCCCHHHHHhCCCcEEEEe
Q 043276 470 RHQVGTSFWFSFSTMVFSQRERVISNLARFVVIVWCFVVLILIQSYTASLTSLLTVDQLQPTITDVNLLIKRGDNVGYQK 549 (829)
Q Consensus 470 ~~~~~~~~~~~~~~l~~~~~~~~~s~~~R~v~~~w~~~~lil~~~YtA~L~s~Lt~~~~~~~I~s~~dL~~~~~~vg~~~ 549 (829)
...+++++|| .+.++|+..
T Consensus 99 -----------------------------------------------------------~~~~~~~~dl--~~~~i~~~~ 117 (225)
T PF00497_consen 99 -----------------------------------------------------------IKTIKSLDDL--KGKRIGVVR 117 (225)
T ss_dssp -----------------------------------------------------------TSSHSSGGGG--TTSEEEEET
T ss_pred -----------------------------------------------------------cccccchhhh--cCccccccc
Confidence 0125777899 577999999
Q ss_pred CchHHHHHHhcCCCccceeecCChHHHHHHHhcCCcCCceeEEEcchhHHHHHHhcCCC-ceEEeCcccccCCceeeecC
Q 043276 550 GSFVLGILKQLGFDERKLVVYNSHEECDELFQKGSANGGIAAAFDEIPYAKLLIGQHCS-KYTMVEPTFKTAGFGFAFPL 628 (829)
Q Consensus 550 ~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~~c~-~l~~v~~~~~~~~~~~~~~k 628 (829)
|+....++++......+++.+.+.++++++|.+|+ +|+++.+...+.+++++... ............++++++.+
T Consensus 118 g~~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~g~----~d~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 193 (225)
T PF00497_consen 118 GSSYADYLKQQYPSNINIVEVDSPEEALEALLSGR----IDAFIVDESTAEYLLKRHPLENIVVIPPPISPSPVYFAVRK 193 (225)
T ss_dssp TSHHHHHHHHHTHHTSEEEEESSHHHHHHHHHTTS----SSEEEEEHHHHHHHHHHTTTCEEEEEEEEEEEEEEEEEEET
T ss_pred chhHHHHhhhhccchhhhcccccHHHHHHHHhcCC----eeeeeccchhhhhhhhhcccccccccccccccceeEEeecc
Confidence 99988888764222557778999999999999999 99999999999999988743 22222455566677788777
Q ss_pred CCC-chhhHHHHHHhhhccChhHHHHHHHccC
Q 043276 629 HSP-LVHDVSKAILNVTEGDKMKEIEDAWFKK 659 (829)
Q Consensus 629 ~sp-l~~~in~~il~l~e~G~~~~~~~~w~~~ 659 (829)
+.+ |++.||++|.++.++|.++++.+||+++
T Consensus 194 ~~~~l~~~~n~~i~~l~~~G~~~~i~~ky~g~ 225 (225)
T PF00497_consen 194 KNPELLEIFNKAIRELKQSGEIQKILKKYLGD 225 (225)
T ss_dssp TTHHHHHHHHHHHHHHHHTTHHHHHHHHHHSS
T ss_pred cccHHHHHHHHHHHHHHhCcHHHHHHHHHcCC
Confidence 655 9999999999999999999999999963
No 45
>PRK11917 bifunctional adhesin/ABC transporter aspartate/glutamate-binding protein; Reviewed
Probab=99.84 E-value=1.2e-19 Score=189.95 Aligned_cols=219 Identities=14% Similarity=0.221 Sum_probs=179.8
Q ss_pred CCCceEEEecccccCccceEEEeecCCCCCceEEEeeHHHHHHHHHHC-CCcccEEEEecCCCCCCCCCChhHHHHhHhc
Q 043276 305 TNEKKLRVGVPVKKGFSDFVKVTIDPKTQETSVVGYSIDVFKAVIEEL-PYAVAYDFVPYAQPDGTSSGSYNDLIYQVFL 383 (829)
Q Consensus 305 ~~~~~lrv~v~~~~~~~p~~~~~~~~~~~~~~~~G~~idll~~ia~~l-~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~ 383 (829)
...++|+||+. ++++||.+.+. .++++.||++||++++++++ |..+++++++. +|...+.+|.+
T Consensus 35 ~~~g~l~vg~~--~~~pP~~~~~~----~~g~~~G~~vdl~~~ia~~llg~~~~~~~~~~---------~~~~~~~~l~~ 99 (259)
T PRK11917 35 KSKGQLIVGVK--NDVPHYALLDQ----ATGEIKGFEIDVAKLLAKSILGDDKKIKLVAV---------NAKTRGPLLDN 99 (259)
T ss_pred HhCCEEEEEEC--CCCCCceeeeC----CCCceeEeeHHHHHHHHHHhcCCCccEEEEEc---------ChhhHHHHHHC
Confidence 34789999998 67889987541 35789999999999999994 86667777765 46777789999
Q ss_pred CcccEEEeccccccccceeccccccccccceEEEEEccCCCCCCceeeeccCCHhHHHHHHHHHHHHHHHHHhhhcccCC
Q 043276 384 GEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMIVPIKDSKKRNAWVFLQPLTWDLWVTSGCFFIFIGFVVWVLEHRVNE 463 (829)
Q Consensus 384 g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv~~~~~~~~~~~~fl~PF~~~vW~~i~~~~~~~~~v~~~~~~~~~~ 463 (829)
|++|++++++++|++|.+.++||.||+.++..+++++.+ .
T Consensus 100 g~~D~~~~~~~~t~eR~~~~~fs~py~~~~~~lvv~~~~--~-------------------------------------- 139 (259)
T PRK11917 100 GSVDAVIATFTITPERKRIYNFSEPYYQDAIGLLVLKEK--N-------------------------------------- 139 (259)
T ss_pred CCccEEEecccCChhhhheeeeccCceeeceEEEEECCC--C--------------------------------------
Confidence 999999999999999999999999999999999999553 1
Q ss_pred CCCCCccCccchhHHHHHHHhhhcCccccccchhHHHHHHHHHHHHHHHHHhHHHHHHHhhcccCCCCCCCHHHHHhCCC
Q 043276 464 DFRGPARHQVGTSFWFSFSTMVFSQRERVISNLARFVVIVWCFVVLILIQSYTASLTSLLTVDQLQPTITDVNLLIKRGD 543 (829)
Q Consensus 464 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~s~~~R~v~~~w~~~~lil~~~YtA~L~s~Lt~~~~~~~I~s~~dL~~~~~ 543 (829)
+++++|| .|+
T Consensus 140 --------------------------------------------------------------------~~s~~dL--~g~ 149 (259)
T PRK11917 140 --------------------------------------------------------------------YKSLADM--KGA 149 (259)
T ss_pred --------------------------------------------------------------------CCCHHHh--CCC
Confidence 5889999 588
Q ss_pred cEEEEeCchHHHHHHhc---CCCccceeecCChHHHHHHHhcCCcCCceeEEEcchhHHHHHHhcCCCceEEeCcccccC
Q 043276 544 NVGYQKGSFVLGILKQL---GFDERKLVVYNSHEECDELFQKGSANGGIAAAFDEIPYAKLLIGQHCSKYTMVEPTFKTA 620 (829)
Q Consensus 544 ~vg~~~~s~~~~~l~~~---~~~~~~~~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~~c~~l~~v~~~~~~~ 620 (829)
+||+..|+.....+.+. .....++..+++..+.+++|..|+ +|+++.+...+.++..+. ..++++.+...
T Consensus 150 ~V~v~~gs~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~l~~Gr----vDa~~~d~~~~~~~~~~~---~~~~~~~~~~~ 222 (259)
T PRK11917 150 NIGVAQAATTKKAIGEAAKKIGIDVKFSEFPDYPSIKAALDAKR----VDAFSVDKSILLGYVDDK---SEILPDSFEPQ 222 (259)
T ss_pred eEEEecCCcHHHHHHHhhHhcCCceeEEecCCHHHHHHHHHcCC----CcEEEecHHHHHHhhhcC---CeecCCcCCCC
Confidence 99999999877665432 111235667889999999999999 999999988776665542 35667777788
Q ss_pred CceeeecCCCC-chhhHHHHHHhhhccChhHHHHHHHc
Q 043276 621 GFGFAFPLHSP-LVHDVSKAILNVTEGDKMKEIEDAWF 657 (829)
Q Consensus 621 ~~~~~~~k~sp-l~~~in~~il~l~e~G~~~~~~~~w~ 657 (829)
+++++++|+++ +.+.+|++|.++.. .+++|.+||-
T Consensus 223 ~~~~a~~k~~~~l~~~ln~~l~~~~~--~~~~i~~kw~ 258 (259)
T PRK11917 223 SYGIVTKKDDPAFAKYVDDFVKEHKN--EIDALAKKWG 258 (259)
T ss_pred ceEEEEeCCCHHHHHHHHHHHHHHHH--HHHHHHHHhC
Confidence 89999999988 99999999999864 7999999994
No 46
>PRK15007 putative ABC transporter arginine-biding protein; Provisional
Probab=99.84 E-value=1.2e-19 Score=188.96 Aligned_cols=217 Identities=21% Similarity=0.372 Sum_probs=179.8
Q ss_pred CceEEEecccccCccceEEEeecCCCCCceEEEeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcc
Q 043276 307 EKKLRVGVPVKKGFSDFVKVTIDPKTQETSVVGYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEF 386 (829)
Q Consensus 307 ~~~lrv~v~~~~~~~p~~~~~~~~~~~~~~~~G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~ 386 (829)
.++||||+. +.|+||.+.+ .++++.|+++|+++++++++|.+ ++++.. .|..++..+.+|++
T Consensus 20 ~~~l~v~~~--~~~~P~~~~~-----~~g~~~G~~~dl~~~i~~~lg~~--~~~~~~---------~~~~~~~~l~~g~~ 81 (243)
T PRK15007 20 AETIRFATE--ASYPPFESID-----ANNQIVGFDVDLAQALCKEIDAT--CTFSNQ---------AFDSLIPSLKFRRV 81 (243)
T ss_pred CCcEEEEeC--CCCCCceeeC-----CCCCEEeeeHHHHHHHHHHhCCc--EEEEeC---------CHHHHhHHHhCCCc
Confidence 568999987 5678888765 36789999999999999999975 445442 59999999999999
Q ss_pred cEEEeccccccccceeccccccccccceEEEEEccCCCCCCceeeeccCCHhHHHHHHHHHHHHHHHHHhhhcccCCCCC
Q 043276 387 DAVVGDTTIVFNRSNYVDFTLPYTESGVSMIVPIKDSKKRNAWVFLQPLTWDLWVTSGCFFIFIGFVVWVLEHRVNEDFR 466 (829)
Q Consensus 387 Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv~~~~~~~~~~~~fl~PF~~~vW~~i~~~~~~~~~v~~~~~~~~~~~~~ 466 (829)
|+++++++.+++|.+.++||.||+..+..++.+...
T Consensus 82 D~~~~~~~~~~~r~~~~~fs~p~~~~~~~~v~~~~~-------------------------------------------- 117 (243)
T PRK15007 82 EAVMAGMDITPEREKQVLFTTPYYDNSALFVGQQGK-------------------------------------------- 117 (243)
T ss_pred CEEEEcCccCHHHhcccceecCccccceEEEEeCCC--------------------------------------------
Confidence 999888889999999999999999988877766331
Q ss_pred CCccCccchhHHHHHHHhhhcCccccccchhHHHHHHHHHHHHHHHHHhHHHHHHHhhcccCCCCCCCHHHHHhCCCcEE
Q 043276 467 GPARHQVGTSFWFSFSTMVFSQRERVISNLARFVVIVWCFVVLILIQSYTASLTSLLTVDQLQPTITDVNLLIKRGDNVG 546 (829)
Q Consensus 467 ~~~~~~~~~~~~~~~~~l~~~~~~~~~s~~~R~v~~~w~~~~lil~~~YtA~L~s~Lt~~~~~~~I~s~~dL~~~~~~vg 546 (829)
+++++|| ++++||
T Consensus 118 -----------------------------------------------------------------~~~~~dL--~g~~Ig 130 (243)
T PRK15007 118 -----------------------------------------------------------------YTSVDQL--KGKKVG 130 (243)
T ss_pred -----------------------------------------------------------------CCCHHHh--CCCeEE
Confidence 4778999 588999
Q ss_pred EEeCchHHHHHHhcCCCccceeecCChHHHHHHHhcCCcCCceeEEEcchhHHHHHHhcCCCceEEeCcc-----cccCC
Q 043276 547 YQKGSFVLGILKQLGFDERKLVVYNSHEECDELFQKGSANGGIAAAFDEIPYAKLLIGQHCSKYTMVEPT-----FKTAG 621 (829)
Q Consensus 547 ~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~~c~~l~~v~~~-----~~~~~ 621 (829)
+..|+...+++++. .+..+.+.+++.++.+++|.+|+ +|+++.+...+.+++++... +..++.. +...+
T Consensus 131 v~~g~~~~~~l~~~-~~~~~~~~~~~~~~~~~~L~~gr----vDa~i~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~ 204 (243)
T PRK15007 131 VQNGTTHQKFIMDK-HPEITTVPYDSYQNAKLDLQNGR----IDAVFGDTAVVTEWLKDNPK-LAAVGDKVTDKDYFGTG 204 (243)
T ss_pred EecCcHHHHHHHHh-CCCCeEEEcCCHHHHHHHHHcCC----CCEEEeCHHHHHHHHhcCCC-ceeecCcccccccCCcc
Confidence 99999888888763 55667778889999999999999 99999999888888877653 4444322 22345
Q ss_pred ceeeecCCCC-chhhHHHHHHhhhccChhHHHHHHHcc
Q 043276 622 FGFAFPLHSP-LVHDVSKAILNVTEGDKMKEIEDAWFK 658 (829)
Q Consensus 622 ~~~~~~k~sp-l~~~in~~il~l~e~G~~~~~~~~w~~ 658 (829)
++|+++++.+ |++.||++|..+.++|.++++.+||+.
T Consensus 205 ~~~~~~~~~~~l~~~ln~~l~~l~~~g~~~~i~~~w~~ 242 (243)
T PRK15007 205 LGIAVRQGNTELQQKLNTALEKVKKDGTYETIYNKWFQ 242 (243)
T ss_pred eEEEEeCCCHHHHHHHHHHHHHHHhCCcHHHHHHHhcC
Confidence 7899998776 999999999999999999999999984
No 47
>PRK15010 ABC transporter lysine/arginine/ornithine binding periplasmic protein; Provisional
Probab=99.83 E-value=2.7e-19 Score=188.07 Aligned_cols=222 Identities=16% Similarity=0.276 Sum_probs=177.4
Q ss_pred CCceEEEecccccCccceEEEeecCCCCCceEEEeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCc
Q 043276 306 NEKKLRVGVPVKKGFSDFVKVTIDPKTQETSVVGYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGE 385 (829)
Q Consensus 306 ~~~~lrv~v~~~~~~~p~~~~~~~~~~~~~~~~G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~ 385 (829)
..++|+||+. +.|+||.+.+ +++++.|+++||++++++++|.+ +++++. .|+.++.++..|+
T Consensus 24 ~~~~l~v~~~--~~~pPf~~~~-----~~g~~~G~~vdl~~~ia~~lg~~--~~~~~~---------~~~~~~~~l~~g~ 85 (260)
T PRK15010 24 LPETVRIGTD--TTYAPFSSKD-----AKGDFVGFDIDLGNEMCKRMQVK--CTWVAS---------DFDALIPSLKAKK 85 (260)
T ss_pred cCCeEEEEec--CCcCCceeEC-----CCCCEEeeeHHHHHHHHHHhCCc--eEEEeC---------CHHHHHHHHHCCC
Confidence 3578999987 5678898864 35789999999999999999965 555553 5999999999999
Q ss_pred ccEEEeccccccccceeccccccccccceEEEEEccCCCCCCceeeeccCCHhHHHHHHHHHHHHHHHHHhhhcccCCCC
Q 043276 386 FDAVVGDTTIVFNRSNYVDFTLPYTESGVSMIVPIKDSKKRNAWVFLQPLTWDLWVTSGCFFIFIGFVVWVLEHRVNEDF 465 (829)
Q Consensus 386 ~Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv~~~~~~~~~~~~fl~PF~~~vW~~i~~~~~~~~~v~~~~~~~~~~~~ 465 (829)
+|++++++..|++|.+.++||.||+.+..++++++....
T Consensus 86 ~Di~~~~~~~t~eR~~~~~fs~p~~~~~~~~~~~~~~~~----------------------------------------- 124 (260)
T PRK15010 86 IDAIISSLSITDKRQQEIAFSDKLYAADSRLIAAKGSPI----------------------------------------- 124 (260)
T ss_pred CCEEEecCcCCHHHHhhcccccceEeccEEEEEECCCCC-----------------------------------------
Confidence 999998999999999999999999999999999865432
Q ss_pred CCCccCccchhHHHHHHHhhhcCccccccchhHHHHHHHHHHHHHHHHHhHHHHHHHhhcccCCCCCCCHHHHHhCCCcE
Q 043276 466 RGPARHQVGTSFWFSFSTMVFSQRERVISNLARFVVIVWCFVVLILIQSYTASLTSLLTVDQLQPTITDVNLLIKRGDNV 545 (829)
Q Consensus 466 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~s~~~R~v~~~w~~~~lil~~~YtA~L~s~Lt~~~~~~~I~s~~dL~~~~~~v 545 (829)
..+++|| +|++|
T Consensus 125 ------------------------------------------------------------------~~~~~dl--~g~~I 136 (260)
T PRK15010 125 ------------------------------------------------------------------QPTLDSL--KGKHV 136 (260)
T ss_pred ------------------------------------------------------------------CCChhHc--CCCEE
Confidence 2368899 58899
Q ss_pred EEEeCchHHHHHHhcC-CCccceeecCChHHHHHHHhcCCcCCceeEEEcchhHHHH-HHhcC-CCceEEeCccc-----
Q 043276 546 GYQKGSFVLGILKQLG-FDERKLVVYNSHEECDELFQKGSANGGIAAAFDEIPYAKL-LIGQH-CSKYTMVEPTF----- 617 (829)
Q Consensus 546 g~~~~s~~~~~l~~~~-~~~~~~~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~-~~~~~-c~~l~~v~~~~----- 617 (829)
|+..|+....++.... ....+++.+.+.++++++|.+|+ +|+++.+...+.+ +.++. ...+...+..+
T Consensus 137 gv~~gs~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~gr----iDa~i~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 212 (260)
T PRK15010 137 GVLQGSTQEAYANETWRSKGVDVVAYANQDLVYSDLAAGR----LDAALQDEVAASEGFLKQPAGKDFAFAGPSVKDKKY 212 (260)
T ss_pred EEecCchHHHHHHHhcccCCceEEecCCHHHHHHHHHcCC----ccEEEeCcHHHHHHHHhCCCCCceEEecCccccccc
Confidence 9999998877775421 12245667888899999999999 9999999877654 34432 33455554332
Q ss_pred ccCCceeeecCCCC-chhhHHHHHHhhhccChhHHHHHHHcc
Q 043276 618 KTAGFGFAFPLHSP-LVHDVSKAILNVTEGDKMKEIEDAWFK 658 (829)
Q Consensus 618 ~~~~~~~~~~k~sp-l~~~in~~il~l~e~G~~~~~~~~w~~ 658 (829)
...+++++++++.+ |++.+|++|.++.++|.++++.+||++
T Consensus 213 ~~~~~~~a~~~~~~~L~~~ln~~l~~l~~~G~~~~i~~ky~~ 254 (260)
T PRK15010 213 FGDGTGVGLRKDDAELTAAFNKALGELRQDGTYDKMAKKYFD 254 (260)
T ss_pred cCCceEEEEeCCCHHHHHHHHHHHHHHHhCCcHHHHHHHhcC
Confidence 22345789999876 999999999999999999999999995
No 48
>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=1.8e-19 Score=190.91 Aligned_cols=226 Identities=18% Similarity=0.188 Sum_probs=182.2
Q ss_pred CCCCceEEEecccccCccceEEEeecCCCCCceEEEeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhc
Q 043276 304 PTNEKKLRVGVPVKKGFSDFVKVTIDPKTQETSVVGYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFL 383 (829)
Q Consensus 304 p~~~~~lrv~v~~~~~~~p~~~~~~~~~~~~~~~~G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~ 383 (829)
....++|+||+. +|+||.+.+ .++++.|+++||++++++++|.+. +++.. ..|+.++..+.+
T Consensus 29 i~~~~~l~v~~~---~~pP~~~~~-----~~g~~~G~~~dl~~~i~~~lg~~~-~~~~~---------~~w~~~~~~l~~ 90 (275)
T TIGR02995 29 LKEQGFARIAIA---NEPPFTYVG-----ADGKVSGAAPDVARAIFKRLGIAD-VNASI---------TEYGALIPGLQA 90 (275)
T ss_pred HHhCCcEEEEcc---CCCCceeEC-----CCCceecchHHHHHHHHHHhCCCc-eeecc---------CCHHHHHHHHHC
Confidence 345788999986 467788754 267889999999999999999641 22322 169999999999
Q ss_pred CcccEEEeccccccccceeccccccccccceEEEEEccCCCCCCceeeeccCCHhHHHHHHHHHHHHHHHHHhhhcccCC
Q 043276 384 GEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMIVPIKDSKKRNAWVFLQPLTWDLWVTSGCFFIFIGFVVWVLEHRVNE 463 (829)
Q Consensus 384 g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv~~~~~~~~~~~~fl~PF~~~vW~~i~~~~~~~~~v~~~~~~~~~~ 463 (829)
|++|++++++++|++|...++||.||..+++++++++.....
T Consensus 91 G~~Di~~~~~~~t~eR~~~~~fs~py~~~~~~~~~~~~~~~~-------------------------------------- 132 (275)
T TIGR02995 91 GRFDAIAAGLFIKPERCKQVAFTQPILCDAEALLVKKGNPKG-------------------------------------- 132 (275)
T ss_pred CCcCEEeecccCCHHHHhccccccceeecceeEEEECCCCCC--------------------------------------
Confidence 999999888999999999999999999999999998654321
Q ss_pred CCCCCccCccchhHHHHHHHhhhcCccccccchhHHHHHHHHHHHHHHHHHhHHHHHHHhhcccCCCCCCCHHHHHh-CC
Q 043276 464 DFRGPARHQVGTSFWFSFSTMVFSQRERVISNLARFVVIVWCFVVLILIQSYTASLTSLLTVDQLQPTITDVNLLIK-RG 542 (829)
Q Consensus 464 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~s~~~R~v~~~w~~~~lil~~~YtA~L~s~Lt~~~~~~~I~s~~dL~~-~~ 542 (829)
+++++||.. .+
T Consensus 133 --------------------------------------------------------------------i~~~~dl~~~~g 144 (275)
T TIGR02995 133 --------------------------------------------------------------------LKSYKDIAKNPD 144 (275)
T ss_pred --------------------------------------------------------------------CCCHHHhccCCC
Confidence 578889853 26
Q ss_pred CcEEEEeCchHHHHHHhcCCCccceeecCChHHHHHHHhcCCcCCceeEEEcchhHHHHHHhcCC-CceEEeCcc---cc
Q 043276 543 DNVGYQKGSFVLGILKQLGFDERKLVVYNSHEECDELFQKGSANGGIAAAFDEIPYAKLLIGQHC-SKYTMVEPT---FK 618 (829)
Q Consensus 543 ~~vg~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~~c-~~l~~v~~~---~~ 618 (829)
.+||+..|+...+++++.+++..+++.+++.++.+++|.+|+ +|+++.+...+.+++++.- ..+..+.+. ..
T Consensus 145 ~~Igv~~g~~~~~~l~~~~~~~~~i~~~~~~~~~i~~L~~gr----vDa~i~d~~~~~~~~~~~~~~~~~~~~~~~~~~~ 220 (275)
T TIGR02995 145 AKIAAPGGGTEEKLAREAGVKREQIIVVPDGQSGLKMVQDGR----ADAYSLTVLTINDLASKAGDPNVEVLAPFKDAPV 220 (275)
T ss_pred ceEEEeCCcHHHHHHHHcCCChhhEEEeCCHHHHHHHHHcCC----CCEEecChHHHHHHHHhCCCCCceeecCccCCcc
Confidence 799999999998899876666667888999999999999999 9999999998888887642 134433221 11
Q ss_pred cCCceeeecCCCC-chhhHHHHHHhhhccChhHHHHHHHc
Q 043276 619 TAGFGFAFPLHSP-LVHDVSKAILNVTEGDKMKEIEDAWF 657 (829)
Q Consensus 619 ~~~~~~~~~k~sp-l~~~in~~il~l~e~G~~~~~~~~w~ 657 (829)
...++|+++++++ |++.||++|.++.++|.+++|.++|-
T Consensus 221 ~~~~~~~~~~~~~~l~~~~n~~l~~~~~sG~~~~i~~ky~ 260 (275)
T TIGR02995 221 RYYGGAAFRPEDKELRDAFNVELAKLKESGEFAKIIAPYG 260 (275)
T ss_pred ccceeEEECCCCHHHHHHHHHHHHHHHhChHHHHHHHHhC
Confidence 1233788888776 99999999999999999999999994
No 49
>TIGR01096 3A0103s03R lysine-arginine-ornithine-binding periplasmic protein.
Probab=99.83 E-value=3.6e-19 Score=186.15 Aligned_cols=218 Identities=22% Similarity=0.413 Sum_probs=183.2
Q ss_pred ceEEEecccccCccceEEEeecCCCCCceEEEeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCccc
Q 043276 308 KKLRVGVPVKKGFSDFVKVTIDPKTQETSVVGYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFD 387 (829)
Q Consensus 308 ~~lrv~v~~~~~~~p~~~~~~~~~~~~~~~~G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~D 387 (829)
++|+||+. ..|+||.+.+ .+++++|+++|+++++++++|. ++++++. +|..++.+|.+|++|
T Consensus 24 ~~l~v~~~--~~~~P~~~~~-----~~g~~~G~~~dl~~~i~~~lg~--~~~~~~~---------~~~~~~~~l~~G~~D 85 (250)
T TIGR01096 24 GSVRIGTE--TGYPPFESKD-----ANGKLVGFDVDLAKALCKRMKA--KCKFVEQ---------NFDGLIPSLKAKKVD 85 (250)
T ss_pred CeEEEEEC--CCCCCceEEC-----CCCCEEeehHHHHHHHHHHhCC--eEEEEeC---------CHHHHHHHHhCCCcC
Confidence 78999985 5678888764 3678999999999999999996 5566653 599999999999999
Q ss_pred EEEeccccccccceeccccccccccceEEEEEccCCCCCCceeeeccCCHhHHHHHHHHHHHHHHHHHhhhcccCCCCCC
Q 043276 388 AVVGDTTIVFNRSNYVDFTLPYTESGVSMIVPIKDSKKRNAWVFLQPLTWDLWVTSGCFFIFIGFVVWVLEHRVNEDFRG 467 (829)
Q Consensus 388 i~~~~~~it~~R~~~vdft~p~~~~~~~~vv~~~~~~~~~~~~fl~PF~~~vW~~i~~~~~~~~~v~~~~~~~~~~~~~~ 467 (829)
+++++++.+.+|.+.+.||.||+.++..++++.....
T Consensus 86 ~~~~~~~~~~~r~~~~~~s~p~~~~~~~~~~~~~~~~------------------------------------------- 122 (250)
T TIGR01096 86 AIMATMSITPKRQKQIDFSDPYYATGQGFVVKKGSDL------------------------------------------- 122 (250)
T ss_pred EEEecCccCHHHhhccccccchhcCCeEEEEECCCCc-------------------------------------------
Confidence 9988888999999999999999999999999865422
Q ss_pred CccCccchhHHHHHHHhhhcCccccccchhHHHHHHHHHHHHHHHHHhHHHHHHHhhcccCCCCCCCHHHHHhCCCcEEE
Q 043276 468 PARHQVGTSFWFSFSTMVFSQRERVISNLARFVVIVWCFVVLILIQSYTASLTSLLTVDQLQPTITDVNLLIKRGDNVGY 547 (829)
Q Consensus 468 ~~~~~~~~~~~~~~~~l~~~~~~~~~s~~~R~v~~~w~~~~lil~~~YtA~L~s~Lt~~~~~~~I~s~~dL~~~~~~vg~ 547 (829)
+.+++|| .++++|+
T Consensus 123 ----------------------------------------------------------------~~~~~dl--~g~~i~~ 136 (250)
T TIGR01096 123 ----------------------------------------------------------------AKTLEDL--DGKTVGV 136 (250)
T ss_pred ----------------------------------------------------------------CCChHHc--CCCEEEE
Confidence 3678899 4889999
Q ss_pred EeCchHHHHHHhcCCC-ccceeecCChHHHHHHHhcCCcCCceeEEEcchhHHHHHHhcCC--CceEEeCccccc-----
Q 043276 548 QKGSFVLGILKQLGFD-ERKLVVYNSHEECDELFQKGSANGGIAAAFDEIPYAKLLIGQHC--SKYTMVEPTFKT----- 619 (829)
Q Consensus 548 ~~~s~~~~~l~~~~~~-~~~~~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~~c--~~l~~v~~~~~~----- 619 (829)
..|+....++.+. ++ ..++..+.+.++++++|.+|+ +|+++.+...+.+++++.. +++.+++..+..
T Consensus 137 ~~g~~~~~~l~~~-~~~~~~~~~~~s~~~~~~~L~~g~----vD~~v~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~ 211 (250)
T TIGR01096 137 QSGTTHEQYLKDY-FKPGVDIVEYDSYDNANMDLKAGR----IDAVFTDASVLAEGFLKPPNGKDFKFVGPSVTDEKYFG 211 (250)
T ss_pred ecCchHHHHHHHh-ccCCcEEEEcCCHHHHHHHHHcCC----CCEEEeCHHHHHHHHHhCCCCCceEEeccccccccccC
Confidence 9999888888764 33 456778899999999999999 9999999999998887753 246666554332
Q ss_pred CCceeeecCCCC-chhhHHHHHHhhhccChhHHHHHHHc
Q 043276 620 AGFGFAFPLHSP-LVHDVSKAILNVTEGDKMKEIEDAWF 657 (829)
Q Consensus 620 ~~~~~~~~k~sp-l~~~in~~il~l~e~G~~~~~~~~w~ 657 (829)
..++++++++++ |+..||++|.++.++|.++.|.+||+
T Consensus 212 ~~~~~~~~~~~~~l~~~ln~~l~~l~~~g~~~~i~~kw~ 250 (250)
T TIGR01096 212 DGYGIGLRKGDTELKAAFNKALAAIRADGTYQKISKKWF 250 (250)
T ss_pred CceEEEEeCCCHHHHHHHHHHHHHHHHCCcHHHHHHhhC
Confidence 247899999887 99999999999999999999999996
No 50
>PRK15437 histidine ABC transporter substrate-binding protein HisJ; Provisional
Probab=99.81 E-value=1.7e-18 Score=181.88 Aligned_cols=222 Identities=19% Similarity=0.301 Sum_probs=175.7
Q ss_pred CceEEEecccccCccceEEEeecCCCCCceEEEeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcc
Q 043276 307 EKKLRVGVPVKKGFSDFVKVTIDPKTQETSVVGYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEF 386 (829)
Q Consensus 307 ~~~lrv~v~~~~~~~p~~~~~~~~~~~~~~~~G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~ 386 (829)
.++|++|+. +.|+||.+.+ .++++.|+++||++++++++|.++ +++.. .|+.++.++.+|++
T Consensus 25 ~~~l~v~~~--~~~~P~~~~~-----~~g~~~G~~vdi~~~ia~~lg~~i--~~~~~---------pw~~~~~~l~~g~~ 86 (259)
T PRK15437 25 PQNIRIGTD--PTYAPFESKN-----SQGELVGFDIDLAKELCKRINTQC--TFVEN---------PLDALIPSLKAKKI 86 (259)
T ss_pred CCeEEEEeC--CCCCCcceeC-----CCCCEEeeeHHHHHHHHHHcCCce--EEEeC---------CHHHHHHHHHCCCC
Confidence 478999976 5577888764 367899999999999999999754 44443 49999999999999
Q ss_pred cEEEeccccccccceeccccccccccceEEEEEccCCCCCCceeeeccCCHhHHHHHHHHHHHHHHHHHhhhcccCCCCC
Q 043276 387 DAVVGDTTIVFNRSNYVDFTLPYTESGVSMIVPIKDSKKRNAWVFLQPLTWDLWVTSGCFFIFIGFVVWVLEHRVNEDFR 466 (829)
Q Consensus 387 Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv~~~~~~~~~~~~fl~PF~~~vW~~i~~~~~~~~~v~~~~~~~~~~~~~ 466 (829)
|+++++++.|++|...++||.||..++.++++++....
T Consensus 87 D~~~~~~~~t~eR~~~~~fs~p~~~~~~~~~~~~~~~~------------------------------------------ 124 (259)
T PRK15437 87 DAIMSSLSITEKRQQEIAFTDKLYAADSRLVVAKNSDI------------------------------------------ 124 (259)
T ss_pred CEEEecCCCCHHHhhhccccchhhcCceEEEEECCCCC------------------------------------------
Confidence 99999999999999999999999999999999865422
Q ss_pred CCccCccchhHHHHHHHhhhcCccccccchhHHHHHHHHHHHHHHHHHhHHHHHHHhhcccCCCCCCCHHHHHhCCCcEE
Q 043276 467 GPARHQVGTSFWFSFSTMVFSQRERVISNLARFVVIVWCFVVLILIQSYTASLTSLLTVDQLQPTITDVNLLIKRGDNVG 546 (829)
Q Consensus 467 ~~~~~~~~~~~~~~~~~l~~~~~~~~~s~~~R~v~~~w~~~~lil~~~YtA~L~s~Lt~~~~~~~I~s~~dL~~~~~~vg 546 (829)
..+++|| ++++||
T Consensus 125 -----------------------------------------------------------------~~~~~dl--~g~~Ig 137 (259)
T PRK15437 125 -----------------------------------------------------------------QPTVESL--KGKRVG 137 (259)
T ss_pred -----------------------------------------------------------------CCChHHh--CCCEEE
Confidence 2468898 588999
Q ss_pred EEeCchHHHHHHhcCC-CccceeecCChHHHHHHHhcCCcCCceeEEEcchhHHHH-HHhcC-CCceEEeCc-----ccc
Q 043276 547 YQKGSFVLGILKQLGF-DERKLVVYNSHEECDELFQKGSANGGIAAAFDEIPYAKL-LIGQH-CSKYTMVEP-----TFK 618 (829)
Q Consensus 547 ~~~~s~~~~~l~~~~~-~~~~~~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~-~~~~~-c~~l~~v~~-----~~~ 618 (829)
+..|+....++++... ...+++.+.+.++.+++|.+|+ +|+++.+...+.+ ++.+. -..+.+.+. .+.
T Consensus 138 v~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~L~~gr----vD~~v~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~ 213 (259)
T PRK15437 138 VLQGTTQETFGNEHWAPKGIEIVSYQGQDNIYSDLTAGR----IDAAFQDEVAASEGFLKQPVGKDYKFGGPSVKDEKLF 213 (259)
T ss_pred EecCcHHHHHHHhhccccCceEEecCCHHHHHHHHHcCC----ccEEEechHHHHHHHHhCCCCCceEEecCcccccccc
Confidence 9999988888765322 1245778888899999999999 9999988866643 33332 222433322 222
Q ss_pred cCCceeeecCCCC-chhhHHHHHHhhhccChhHHHHHHHccC
Q 043276 619 TAGFGFAFPLHSP-LVHDVSKAILNVTEGDKMKEIEDAWFKK 659 (829)
Q Consensus 619 ~~~~~~~~~k~sp-l~~~in~~il~l~e~G~~~~~~~~w~~~ 659 (829)
..+++++++++.+ |++.+|++|.++..+|.++++.+||++.
T Consensus 214 ~~~~~ia~~~~~~~l~~~~n~~l~~~~~~G~~~~i~~k~~~~ 255 (259)
T PRK15437 214 GVGTGMGLRKEDNELREALNKAFAEMRADGTYEKLAKKYFDF 255 (259)
T ss_pred CcceEEEEeCCCHHHHHHHHHHHHHHHHCCcHHHHHHHhcCC
Confidence 3346788887766 9999999999999999999999999963
No 51
>cd06342 PBP1_ABC_LIVBP_like Type I periplasmic ligand-binding domain of ABC (Atpase Binding Cassette)-type active transport systems that are involved in the transport of all three branched chain aliphatic amino acids (leucine, isoleucine and valine). This subgroup includes the type I periplasmic ligand-binding domain of ABC (Atpase Binding Cassette)-type active transport systems that are involved in the transport of all three branched chain aliphatic amino acids (leucine, isoleucine and valine). This subgroup also includes a leucine-specific binding protein (or LivK), which is very similar in sequence and structure to leucine-isoleucine-valine binding protein (LIVBP). ABC-type active transport systems are transmembrane proteins that function in the transport of diverse sets of substrates across extra- and intracellular membranes, including carbohydrates, amino acids, inorganic ions, dipeptides and oligopeptides, metabolic products, lipids and sterols, and heme, to name a few.
Probab=99.80 E-value=2.9e-18 Score=187.51 Aligned_cols=217 Identities=24% Similarity=0.307 Sum_probs=180.4
Q ss_pred CCCChHHHHHHHHHHH-HHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCC
Q 043276 1 GALNDSSQVGAITAII-KAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQT 79 (829)
Q Consensus 1 t~psD~~q~~ai~~ll-~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~a 79 (829)
+.|++..|+.++++++ ++++|++|++|+.+++||+...+.+.+.+++.|++|.....++.+ ..++...+.++++.++
T Consensus 114 ~~~~~~~~~~~~~~~~~~~~~~~~v~~v~~~~~~g~~~~~~~~~~~~~~g~~v~~~~~~~~~--~~d~~~~l~~i~~~~~ 191 (334)
T cd06342 114 VVARDDQQGPAAAKYAVETLKAKKVAIIDDKTAYGQGLADEFKKALKAAGGKVVAREGTTDG--ATDFSAILTKIKAANP 191 (334)
T ss_pred ccCCcHHHHHHHHHHHHHhcCCCEEEEEeCCcchhhHHHHHHHHHHHHcCCEEEEEecCCCC--CccHHHHHHHHHhcCC
Confidence 4688999999999976 689999999999999999999999999999999999998888765 4579999999999999
Q ss_pred eEEEEEcChhHHHHHHHHHHHcCccccCeEEEEcCccccccccCCccccccccceEEEEeccC--CChhHHHHHHHHHHh
Q 043276 80 RVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLEPSVTDSMQGVIGVRPYVP--KTKALENFRVRWKRK 157 (829)
Q Consensus 80 rViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t~~~~~~~~~~~~~~~~~~~g~l~~~~~~~--~~~~~~~F~~~w~~~ 157 (829)
++||+.+..+.+..+++++++.|+ ...||.++++... .. .......++|++...++.+ ..+..++|.++|+++
T Consensus 192 ~~vi~~~~~~~~~~~~~~~~~~g~---~~~~~~~~~~~~~-~~-~~~~~~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~ 266 (334)
T cd06342 192 DAVFFGGYYPEAGPLVRQMRQLGL---KAPFMGGDGLCDP-EF-IKIAGDAAEGTYATFPGGPLEKMPAGKAFVARYKAK 266 (334)
T ss_pred CEEEEcCcchhHHHHHHHHHHcCC---CCcEEecCccCCH-HH-HHHhhHhhCCcEEEecCCCCCCChHHHHHHHHHHHH
Confidence 999999999999999999999997 3567877665421 11 1112345788887766655 467889999999887
Q ss_pred hcccCCCCCccccchhHHHHHHHHHHHHHHHHHhcccCccccCCCCCCCCCCCccccCCCChHHHHHHHhccceeccccc
Q 043276 158 FLQENPSLFDAELNIFGLLAYDATSALAVAVEKAGITGFGFDKTNVSSNATDLEAFGISQNGPKLLQALSSIRFRGLTGD 237 (829)
Q Consensus 158 ~~~~~~~~~~~~~~~~~~~~YDAV~~~A~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~L~~~~f~G~tG~ 237 (829)
++. .++.++..+||+++++++|++++... .+..+.++|++.+|+|++|+
T Consensus 267 ~~~--------~~~~~~~~~yda~~~~~~al~~~~~~-----------------------~~~~v~~~l~~~~~~g~~g~ 315 (334)
T cd06342 267 FGD--------PPGAYAPYAYDAANVLAEAIKKAGST-----------------------DPAKVADALRKVDFDGVTGK 315 (334)
T ss_pred hCC--------CCchhHHHHHHHHHHHHHHHHHhCCC-----------------------CHHHHHHHHHhCCCCCccee
Confidence 754 24668899999999999999987311 26789999999999999999
Q ss_pred EEEe-cCccccceEEEEEc
Q 043276 238 YIFV-DGQLQSSAFEIINV 255 (829)
Q Consensus 238 ~~F~-~G~~~~~~y~I~n~ 255 (829)
+.|+ +|++.+..|+|++|
T Consensus 316 i~f~~~g~~~~~~~~~~~~ 334 (334)
T cd06342 316 ISFDAKGDLKGAAVTVYQV 334 (334)
T ss_pred eEECCCCCcccCcEEEEeC
Confidence 9996 99998899999986
No 52
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=99.78 E-value=9.9e-18 Score=213.83 Aligned_cols=217 Identities=16% Similarity=0.224 Sum_probs=181.1
Q ss_pred CceEEEecccccCccceEEEeecCCCCCceEEEeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcc
Q 043276 307 EKKLRVGVPVKKGFSDFVKVTIDPKTQETSVVGYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEF 386 (829)
Q Consensus 307 ~~~lrv~v~~~~~~~p~~~~~~~~~~~~~~~~G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~ 386 (829)
.++++||+. +.|+||.+.+ .++++.||++|++++|++++|. ++++++.. .|..++..|.+|++
T Consensus 301 ~~~l~v~~~--~~~pP~~~~d-----~~g~~~G~~~Dll~~i~~~~g~--~~~~v~~~--------~~~~~~~~l~~g~~ 363 (1197)
T PRK09959 301 HPDLKVLEN--PYSPPYSMTD-----ENGSVRGVMGDILNIITLQTGL--NFSPITVS--------HNIHAGTQLNPGGW 363 (1197)
T ss_pred CCceEEEcC--CCCCCeeEEC-----CCCcEeeehHHHHHHHHHHHCC--eEEEEecC--------CHHHHHHHHHCCCc
Confidence 567999877 7889999976 3689999999999999999995 67777764 68889999999999
Q ss_pred cEEEeccccccccceeccccccccccceEEEEEccCCCCCCceeeeccCCHhHHHHHHHHHHHHHHHHHhhhcccCCCCC
Q 043276 387 DAVVGDTTIVFNRSNYVDFTLPYTESGVSMIVPIKDSKKRNAWVFLQPLTWDLWVTSGCFFIFIGFVVWVLEHRVNEDFR 466 (829)
Q Consensus 387 Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv~~~~~~~~~~~~fl~PF~~~vW~~i~~~~~~~~~v~~~~~~~~~~~~~ 466 (829)
|++. +++.|++|.+.++||.||+.+++++++++....
T Consensus 364 D~i~-~~~~t~~r~~~~~fs~py~~~~~~~v~~~~~~~------------------------------------------ 400 (1197)
T PRK09959 364 DIIP-GAIYSEDRENNVLFAEAFITTPYVFVMQKAPDS------------------------------------------ 400 (1197)
T ss_pred eEee-cccCCccccccceeccccccCCEEEEEecCCCC------------------------------------------
Confidence 9876 556899999999999999999999998744211
Q ss_pred CCccCccchhHHHHHHHhhhcCccccccchhHHHHHHHHHHHHHHHHHhHHHHHHHhhcccCCCCCCCHHHHHhCCCcEE
Q 043276 467 GPARHQVGTSFWFSFSTMVFSQRERVISNLARFVVIVWCFVVLILIQSYTASLTSLLTVDQLQPTITDVNLLIKRGDNVG 546 (829)
Q Consensus 467 ~~~~~~~~~~~~~~~~~l~~~~~~~~~s~~~R~v~~~w~~~~lil~~~YtA~L~s~Lt~~~~~~~I~s~~dL~~~~~~vg 546 (829)
+. ++. .|++||
T Consensus 401 -----------------------------------------------------------------~~---~~~-~g~~va 411 (1197)
T PRK09959 401 -----------------------------------------------------------------EQ---TLK-KGMKVA 411 (1197)
T ss_pred -----------------------------------------------------------------cc---ccc-cCCEEE
Confidence 12 222 588999
Q ss_pred EEeCchHHHHHHhcCCCccceeecCChHHHHHHHhcCCcCCceeEEEcchhHHHHHHhcCC-Cc-eEEeCcccccCCcee
Q 043276 547 YQKGSFVLGILKQLGFDERKLVVYNSHEECDELFQKGSANGGIAAAFDEIPYAKLLIGQHC-SK-YTMVEPTFKTAGFGF 624 (829)
Q Consensus 547 ~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~~c-~~-l~~v~~~~~~~~~~~ 624 (829)
++.|+...+++++. ++..+++.|++.++++++|.+|+ +||++.+...+.|+++++. .. +....+.+....++|
T Consensus 412 v~~g~~~~~~~~~~-~p~~~~~~~~~~~~~l~av~~G~----~Da~i~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~ 486 (1197)
T PRK09959 412 IPYYYELHSQLKEM-YPEVEWIKVDNASAAFHKVKEGE----LDALVATQLNSRYMIDHYYPNELYHFLIPGVPNASLSF 486 (1197)
T ss_pred EeCCcchHHHHHHH-CCCcEEEEcCCHHHHHHHHHcCC----CCEEehhhHHHHHHHHhcccccceeeecCCCCchheEE
Confidence 99999888888764 67778999999999999999999 9999999999999988752 22 333444455667899
Q ss_pred eecCCCC-chhhHHHHHHhhhccChhHHHHHHHcc
Q 043276 625 AFPLHSP-LVHDVSKAILNVTEGDKMKEIEDAWFK 658 (829)
Q Consensus 625 ~~~k~sp-l~~~in~~il~l~e~G~~~~~~~~w~~ 658 (829)
+++|+.| |++.+|++|..+.++ .++++.+||+.
T Consensus 487 av~k~~~~L~~~lnk~l~~i~~~-~~~~i~~kW~~ 520 (1197)
T PRK09959 487 AFPRGEPELKDIINKALNAIPPS-EVLRLTEKWIK 520 (1197)
T ss_pred eeCCCCHHHHHHHHHHHHhCCHH-HHHHHHhhccc
Confidence 9999988 999999999999998 78899999995
No 53
>cd06350 PBP1_GPCR_family_C_like Ligand-binding domain of membrane-bound glutamate receptors that mediate excitatory transmission on the cellular surface through initial binding of glutamate and are categorized into ionotropic glutamate receptors (iGluRs) and metabotropic glutamate receptors (mGluRs). Ligand-binding domain of membrane-bound glutamate receptors that mediate excitatory transmission on the cellular surface through initial binding of glutamate and are categorized into ionotropic glutamate receptors (iGluRs) and metabotropic glutamate receptors (mGluRs). The metabotropic glutamate receptors (mGluR) are key receptors in the modulation of excitatory synaptic transmission in the central nervous system. The mGluRs are coupled to G proteins and are thus distinct from the iGluRs which internally contain ligand-gated ion channels. The mGluR structure is divided into three regions: the extracellular region, the seven-spanning transmembrane region and the cytoplasmic region. The extr
Probab=99.78 E-value=3.8e-18 Score=187.75 Aligned_cols=195 Identities=28% Similarity=0.502 Sum_probs=160.6
Q ss_pred CCCChHHHHHHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCe
Q 043276 1 GALNDSSQVGAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTR 80 (829)
Q Consensus 1 t~psD~~q~~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~ar 80 (829)
+.|+|..|+.+++++++++||++|++|+++++||....+.|.+.+++.|+||+..+.++......++...+++|+++++|
T Consensus 140 ~~p~~~~~~~a~~~~~~~~~~~~v~~l~~~~~~g~~~~~~~~~~~~~~gi~v~~~~~~~~~~~~~d~~~~l~~l~~~~~~ 219 (348)
T cd06350 140 TVPSDTSQALAIVALLKHFGWTWVGLVYSDDDYGRSGLSDLEEELEKNGICIAFVEAIPPSSTEEDIKRILKKLKSSTAR 219 (348)
T ss_pred ecCCcHHHHHHHHHHHHHCCCeEEEEEEecchhHHHHHHHHHHHHHHCCCcEEEEEEccCCCcHHHHHHHHHHHHhCCCc
Confidence 57999999999999999999999999999999999999999999999999999998888664456899999999999999
Q ss_pred EEEEEcChhHHHHHHHHHHHcCccccCeEEEEcCccccccccCCccccccccceEEEEeccCCChhHHHHHHHHHHhhcc
Q 043276 81 VFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLEPSVTDSMQGVIGVRPYVPKTKALENFRVRWKRKFLQ 160 (829)
Q Consensus 81 ViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t~~~~~~~~~~~~~~~~~~~g~l~~~~~~~~~~~~~~F~~~w~~~~~~ 160 (829)
+||+++....+..++++|+++|| .+..|+.+++|....... ....+.++|++++..+.+.......|.++|++
T Consensus 220 vvv~~~~~~~~~~~~~~a~~~g~--~~~~~i~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~~~~~f~~~~~~---- 292 (348)
T cd06350 220 VIVVFGDEDDALRLFCEAYKLGM--TGKYWIISTDWDTSTCLL-LFTLDAFQGVLGFSGHAPRSGEIPGFKDFLRK---- 292 (348)
T ss_pred EEEEEeCcHHHHHHHHHHHHhCC--CCeEEEEEccccCccccc-cCCcceeeeEEEEEEEeecCCcCCChHHHHHH----
Confidence 99999999999999999999998 345566777776432111 22346688999888877654445556655554
Q ss_pred cCCCCCccccchhHHHHHHHHHHHHHHHHHhcccCccccCCCCCCCCCCCccccCCCChHHHHHHHhccceecccccEEE
Q 043276 161 ENPSLFDAELNIFGLLAYDATSALAVAVEKAGITGFGFDKTNVSSNATDLEAFGISQNGPKLLQALSSIRFRGLTGDYIF 240 (829)
Q Consensus 161 ~~~~~~~~~~~~~~~~~YDAV~~~A~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~L~~~~f~G~tG~~~F 240 (829)
+++++|||||+ .+.|
T Consensus 293 ------------~~~~~YDav~~-----------------------------------------------------~v~f 307 (348)
T cd06350 293 ------------YAYNVYDAVYA-----------------------------------------------------EVKF 307 (348)
T ss_pred ------------HHHHHHhheeE-----------------------------------------------------EEEe
Confidence 67889999998 5677
Q ss_pred e-cCccccceEEEEEcc-C----CcEEEEEecCC
Q 043276 241 V-DGQLQSSAFEIINVN-N----GARGVGFWSPE 268 (829)
Q Consensus 241 ~-~G~~~~~~y~I~n~~-~----g~~~VG~w~~~ 268 (829)
+ +||+. ..|+|++++ . ++++||.|.+.
T Consensus 308 ~~~gd~~-~~~~i~~~~~~~~~~~~~~vg~~~~~ 340 (348)
T cd06350 308 DENGDRL-ASYDIINWQIFPGGGGFVKVGFWDPQ 340 (348)
T ss_pred cCCCCcc-cceeEEEEEEcCCcEEEEEEEEEcCC
Confidence 5 89985 789999997 2 38999999874
No 54
>PRK10859 membrane-bound lytic transglycosylase F; Provisional
Probab=99.77 E-value=6.4e-18 Score=192.23 Aligned_cols=222 Identities=16% Similarity=0.181 Sum_probs=175.8
Q ss_pred CCCceEEEecccccCccceEEEeecCCCCCceEEEeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcC
Q 043276 305 TNEKKLRVGVPVKKGFSDFVKVTIDPKTQETSVVGYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLG 384 (829)
Q Consensus 305 ~~~~~lrv~v~~~~~~~p~~~~~~~~~~~~~~~~G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g 384 (829)
...++||||+.. + |+.+... ++...||++||++++++++|.++ +++... +|++++..|.+|
T Consensus 40 ~~~g~LrVg~~~-~---P~~~~~~-----~~~~~G~~~DLl~~ia~~LGv~~--e~v~~~--------~~~~ll~aL~~G 100 (482)
T PRK10859 40 QERGELRVGTIN-S---PLTYYIG-----NDGPTGFEYELAKRFADYLGVKL--EIKVRD--------NISQLFDALDKG 100 (482)
T ss_pred HhCCEEEEEEec-C---CCeeEec-----CCCcccHHHHHHHHHHHHhCCcE--EEEecC--------CHHHHHHHHhCC
Confidence 457889999973 2 3333321 23349999999999999999754 554432 799999999999
Q ss_pred cccEEEeccccccccceeccccccccccceEEEEEccCCCCCCceeeeccCCHhHHHHHHHHHHHHHHHHHhhhcccCCC
Q 043276 385 EFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMIVPIKDSKKRNAWVFLQPLTWDLWVTSGCFFIFIGFVVWVLEHRVNED 464 (829)
Q Consensus 385 ~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv~~~~~~~~~~~~fl~PF~~~vW~~i~~~~~~~~~v~~~~~~~~~~~ 464 (829)
++|++++++++|++|.+.++||.||+....++++++....
T Consensus 101 ~iDi~~~~lt~T~eR~~~~~FS~Py~~~~~~lv~r~~~~~---------------------------------------- 140 (482)
T PRK10859 101 KADLAAAGLTYTPERLKQFRFGPPYYSVSQQLVYRKGQPR---------------------------------------- 140 (482)
T ss_pred CCCEEeccCcCChhhhccCcccCCceeeeEEEEEeCCCCC----------------------------------------
Confidence 9999988999999999999999999999999999855421
Q ss_pred CCCCccCccchhHHHHHHHhhhcCccccccchhHHHHHHHHHHHHHHHHHhHHHHHHHhhcccCCCCCCCHHHHHhCCCc
Q 043276 465 FRGPARHQVGTSFWFSFSTMVFSQRERVISNLARFVVIVWCFVVLILIQSYTASLTSLLTVDQLQPTITDVNLLIKRGDN 544 (829)
Q Consensus 465 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~s~~~R~v~~~w~~~~lil~~~YtA~L~s~Lt~~~~~~~I~s~~dL~~~~~~ 544 (829)
+++++|| +|++
T Consensus 141 -------------------------------------------------------------------i~~l~dL--~Gk~ 151 (482)
T PRK10859 141 -------------------------------------------------------------------PRSLGDL--KGGT 151 (482)
T ss_pred -------------------------------------------------------------------CCCHHHh--CCCe
Confidence 6889999 5889
Q ss_pred EEEEeCchHHHHHHhcC--CCccce--eecCChHHHHHHHhcCCcCCceeEEEcchhHHHHHHhcCCCceEEeCcccccC
Q 043276 545 VGYQKGSFVLGILKQLG--FDERKL--VVYNSHEECDELFQKGSANGGIAAAFDEIPYAKLLIGQHCSKYTMVEPTFKTA 620 (829)
Q Consensus 545 vg~~~~s~~~~~l~~~~--~~~~~~--~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~~c~~l~~v~~~~~~~ 620 (829)
||+..|+.....+++.. ++...+ ..+.+.++++++|.+|+ +|+++.+...+.+....+. .+.+........
T Consensus 152 I~V~~gS~~~~~L~~l~~~~p~i~~~~~~~~s~~e~l~aL~~G~----iDa~v~d~~~~~~~~~~~p-~l~v~~~l~~~~ 226 (482)
T PRK10859 152 LTVAAGSSHVETLQELKKKYPELSWEESDDKDSEELLEQVAEGK----IDYTIADSVEISLNQRYHP-ELAVAFDLTDEQ 226 (482)
T ss_pred EEEECCCcHHHHHHHHHHhCCCceEEecCCCCHHHHHHHHHCCC----CCEEEECcHHHHHHHHhCC-CceeeeecCCCc
Confidence 99999998888776432 233333 34568899999999999 9999999877765544444 355554444556
Q ss_pred CceeeecCC-CC-chhhHHHHHHhhhccChhHHHHHHHccC
Q 043276 621 GFGFAFPLH-SP-LVHDVSKAILNVTEGDKMKEIEDAWFKK 659 (829)
Q Consensus 621 ~~~~~~~k~-sp-l~~~in~~il~l~e~G~~~~~~~~w~~~ 659 (829)
+++++++|+ .+ |+..+|++|.++.++|.++++.+||+..
T Consensus 227 ~~~~av~k~~~~~L~~~ln~~L~~i~~~G~l~~L~~kyfg~ 267 (482)
T PRK10859 227 PVAWALPPSGDDSLYAALLDFFNQIKEDGTLARLEEKYFGH 267 (482)
T ss_pred eeEEEEeCCCCHHHHHHHHHHHHHhhcCCHHHHHHHHHhhh
Confidence 789999994 55 9999999999999999999999999975
No 55
>cd06351 PBP1_iGluR_N_LIVBP_like N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the NMDA, AMPA, and kainate receptor subtypes of ionotropic glutamate receptors (iGluRs). N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the NMDA, AMPA, and kainate receptor subtypes of ionotropic glutamate receptors (iGluRs). While this N-terminal domain belongs to the periplasmic-binding fold type I superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type II. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR. Glutamate mediates the majority of excitatory synaptic transmission in the central nervous system via two broad classes of ionotropic receptors characterized by their response to glutamate agonists: N-methyl-aspartate (NMDA) and non-NMDA receptors
Probab=99.76 E-value=1.8e-17 Score=180.72 Aligned_cols=207 Identities=24% Similarity=0.325 Sum_probs=157.1
Q ss_pred CCCChHHHHHHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCC-
Q 043276 1 GALNDSSQVGAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQT- 79 (829)
Q Consensus 1 t~psD~~q~~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~a- 79 (829)
+.|++..|++++++++++|+|++|++||++++++.. ++.+.+.....+.++... .+... .++++..+.+++++++
T Consensus 112 ~~p~~~~~~~a~~~~l~~~~w~~v~iiy~~~~~~~~-l~~~~~~~~~~~~~v~~~-~~~~~--~~~~~~~l~~l~~~~~~ 187 (328)
T cd06351 112 LYPSLEDLADALLDLLEYYNWTKFAIIYDSDEGLSR-LQELLDESGIKGIQVTVR-RLDLD--DDNYRQLLKELKRSESR 187 (328)
T ss_pred ecCCHHHHHHHHHHHHHHcCCcEEEEEEeCchHHHH-HHHHHHhhcccCceEEEE-EecCC--chhHHHHHHHHhhcccc
Confidence 468999999999999999999999999998885543 344444444445566654 33333 2278899999999988
Q ss_pred eEEEEEcChhHHHHHHHHHHHcCccccCeEEEEcCccccccccCCccccccccceEEEEeccCCChhHHHHHHHHHHhhc
Q 043276 80 RVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLEPSVTDSMQGVIGVRPYVPKTKALENFRVRWKRKFL 159 (829)
Q Consensus 80 rViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t~~~~~~~~~~~~~~~~~~~g~l~~~~~~~~~~~~~~F~~~w~~~~~ 159 (829)
+||++++..+.+..++++|.++||+..+|+||+++......+. ........|++|++...+..+...+|..+|..
T Consensus 188 ~vil~~~~~~~~~~~l~~a~~~gm~~~~~~~i~~~~~~~~~d~--~~~~~~~~~i~g~~~~~~~~~~~~~~~~~~~~--- 262 (328)
T cd06351 188 RIILDCSSEEEAKEILEQAVELGMMGYGYHWILTNLDLSDIDL--EPFQYGPANITGFRLVDPDSPDVSQFLQRWLE--- 262 (328)
T ss_pred eEEEECCcHHHHHHHHHHHHHhccccCCcEEEEecCCccccch--hhhccCCcceEEEEEeCCCchHHHHHHHhhhh---
Confidence 7777666669999999999999999999999999876654332 23455679999999999999999999999922
Q ss_pred ccCCCCCccccchhHHHHHHHHHHHHHHHHHhcccCccccCCCCCCCCCCCccccCCCChHHHHHHHhccceecccccEE
Q 043276 160 QENPSLFDAELNIFGLLAYDATSALAVAVEKAGITGFGFDKTNVSSNATDLEAFGISQNGPKLLQALSSIRFRGLTGDYI 239 (829)
Q Consensus 160 ~~~~~~~~~~~~~~~~~~YDAV~~~A~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~L~~~~f~G~tG~~~ 239 (829)
..+......+...+..+||+++++ ||.+.
T Consensus 263 -~~~~~~~~~~~~~~~~~~d~~~~~--------------------------------------------------tg~i~ 291 (328)
T cd06351 263 -ESPGVNLRAPIYDAALLYDAVLLL--------------------------------------------------TGTVS 291 (328)
T ss_pred -ccCCCCcCccchhhHhhhcEEEEE--------------------------------------------------EeeEE
Confidence 222222223344555666654333 89999
Q ss_pred Ee-cCccccceEEEEEcc--CCcEEEEEecC
Q 043276 240 FV-DGQLQSSAFEIINVN--NGARGVGFWSP 267 (829)
Q Consensus 240 F~-~G~~~~~~y~I~n~~--~g~~~VG~w~~ 267 (829)
|+ +|++.+..++|+++. .++++||.|+.
T Consensus 292 f~~~g~r~~~~l~i~~l~~~~~~~~vg~W~~ 322 (328)
T cd06351 292 FDEDGVRSNFTLDIIELNRSRGWRKVGTWNG 322 (328)
T ss_pred ECCCCcccceEEEEEEecCCCCceEEEEecC
Confidence 96 899999999999998 67999999994
No 56
>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=99.74 E-value=5.5e-19 Score=168.80 Aligned_cols=107 Identities=32% Similarity=0.625 Sum_probs=81.7
Q ss_pred CHhHHHHHHHHHHHHHHHHHhhhcccCCCCCC-------CccCccchhHHHHHHHhhhcC-ccccccchhHHHHHHHHHH
Q 043276 436 TWDLWVTSGCFFIFIGFVVWVLEHRVNEDFRG-------PARHQVGTSFWFSFSTMVFSQ-RERVISNLARFVVIVWCFV 507 (829)
Q Consensus 436 ~~~vW~~i~~~~~~~~~v~~~~~~~~~~~~~~-------~~~~~~~~~~~~~~~~l~~~~-~~~~~s~~~R~v~~~w~~~ 507 (829)
++++|++++++++++++++|++++..+.+++. ....++.+++|+.+++++.++ ...|++.++|++.++|+++
T Consensus 1 s~~vW~~il~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~~~~~~s~s~Ril~~~w~l~ 80 (148)
T PF00060_consen 1 SWSVWLLILLSILLVSLVLWLFERFSPYEWRKNQSSPPRRWRFSLSNSFWYTFGTLLQQGSSIRPRSWSGRILLAFWWLF 80 (148)
T ss_dssp -HHHHHHHHHHHHHHHTTGGGT------------------HHHHHHHHHHHCCCCCHHHHH------HHHHHHHHHHHHH
T ss_pred CHhHHHHHHHHHHHHHHHHHHHHHHhhhhhccccccccccCcccHHHHHHHHHHhhccccccccccchHHHHHHHHHHHH
Confidence 57899999999999999999999987777665 223467889999999999765 5678999999999999999
Q ss_pred HHHHHHHhHHHHHHHhhcccCCCCCCCHHHHHhCC
Q 043276 508 VLILIQSYTASLTSLLTVDQLQPTITDVNLLIKRG 542 (829)
Q Consensus 508 ~lil~~~YtA~L~s~Lt~~~~~~~I~s~~dL~~~~ 542 (829)
+++++++|||+|+|+||.++++++|+|++||.+++
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 57
>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=6.9e-17 Score=168.05 Aligned_cols=210 Identities=15% Similarity=0.090 Sum_probs=156.5
Q ss_pred eEEEecccccCccceEEEeecCCCCCceEEEeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHH---HhHhcCc
Q 043276 309 KLRVGVPVKKGFSDFVKVTIDPKTQETSVVGYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLI---YQVFLGE 385 (829)
Q Consensus 309 ~lrv~v~~~~~~~p~~~~~~~~~~~~~~~~G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li---~~l~~g~ 385 (829)
+||||+. +.|+||.+.+ + .||++||+++|+++||++ +++++. .|++++ ..|.+|+
T Consensus 1 ~l~vg~~--~~~pPf~~~~-------~--~Gfdvdl~~~ia~~lg~~--~~~~~~---------~~~~~~~~~~~L~~g~ 58 (246)
T TIGR03870 1 TLRVCAA--TKEAPYSTKD-------G--SGFENKIAAALAAAMGRK--VVFVWL---------AKPAIYLVRDGLDKKL 58 (246)
T ss_pred CeEEEeC--CCCCCCccCC-------C--CcchHHHHHHHHHHhCCC--eEEEEe---------ccchhhHHHHHHhcCC
Confidence 4789987 7899999842 1 699999999999999975 455553 477766 6999999
Q ss_pred ccEEEeccccccccceeccccccccccceEEEEEccCCCCCCceeeeccCCHhHHHHHHHHHHHHHHHHHhhhcccCCCC
Q 043276 386 FDAVVGDTTIVFNRSNYVDFTLPYTESGVSMIVPIKDSKKRNAWVFLQPLTWDLWVTSGCFFIFIGFVVWVLEHRVNEDF 465 (829)
Q Consensus 386 ~Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv~~~~~~~~~~~~fl~PF~~~vW~~i~~~~~~~~~v~~~~~~~~~~~~ 465 (829)
+|+++ +++++++| ++||.||+.++.++++++.+...
T Consensus 59 ~Dii~-~~~~t~~r---~~fS~PY~~~~~~~v~~k~~~~~---------------------------------------- 94 (246)
T TIGR03870 59 CDVVL-GLDTGDPR---VLTTKPYYRSSYVFLTRKDRNLD---------------------------------------- 94 (246)
T ss_pred ccEEE-eCCCChHH---HhcccCcEEeeeEEEEeCCCCCC----------------------------------------
Confidence 99998 58888877 78999999999999999664321
Q ss_pred CCCccCccchhHHHHHHHhhhcCccccccchhHHHHHHHHHHHHHHHHHhHHHHHHHhhcccCCCCCCCHHHHHhCCC-c
Q 043276 466 RGPARHQVGTSFWFSFSTMVFSQRERVISNLARFVVIVWCFVVLILIQSYTASLTSLLTVDQLQPTITDVNLLIKRGD-N 544 (829)
Q Consensus 466 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~s~~~R~v~~~w~~~~lil~~~YtA~L~s~Lt~~~~~~~I~s~~dL~~~~~-~ 544 (829)
+++++|+.-.|+ +
T Consensus 95 ------------------------------------------------------------------~~~~~d~~L~g~~~ 108 (246)
T TIGR03870 95 ------------------------------------------------------------------IKSWNDPRLKKVSK 108 (246)
T ss_pred ------------------------------------------------------------------CCCccchhhccCce
Confidence 567765222587 9
Q ss_pred EEEEeCchHHHHHHhcCCC------ccceeecC---------ChHHHHHHHhcCCcCCceeEEEcchhHHHHHHhcCCCc
Q 043276 545 VGYQKGSFVLGILKQLGFD------ERKLVVYN---------SHEECDELFQKGSANGGIAAAFDEIPYAKLLIGQHCSK 609 (829)
Q Consensus 545 vg~~~~s~~~~~l~~~~~~------~~~~~~~~---------~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~~c~~ 609 (829)
+|++.|+..+.++++.... ...+..++ +..+.+++|..|+ +||++.+...+.+++.+.-..
T Consensus 109 vgv~~gs~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~aL~~Gr----vDa~i~~~~~~~~~~~~~~~~ 184 (246)
T TIGR03870 109 IGVIFGSPAETMLKQIGRYEDNFAYLYSLVNFKSPRNQYTQIDPRKLVSEVATGK----ADLAVAFAPEVARYVKASPEP 184 (246)
T ss_pred EEEecCChHHHHHHhcCccccccccccccccccCcccccccCCHHHHHHHHHcCC----CCEEEeeHHhHHHHHHhCCCC
Confidence 9999999999988764210 01122222 3578899999999 999999877777777653222
Q ss_pred eE--EeCccc-------c--cCCceeeecCCCC-chhhHHHHHHhhhccChhHHHHHHH
Q 043276 610 YT--MVEPTF-------K--TAGFGFAFPLHSP-LVHDVSKAILNVTEGDKMKEIEDAW 656 (829)
Q Consensus 610 l~--~v~~~~-------~--~~~~~~~~~k~sp-l~~~in~~il~l~e~G~~~~~~~~w 656 (829)
+. .+++.. . ..+++++++|+.+ |++.||++|.++. |.+++|..+|
T Consensus 185 ~~~~~~~~~~~~~~~~~~~~~~~~~iav~k~~~~L~~~in~aL~~l~--~~~~~i~~~y 241 (246)
T TIGR03870 185 LRMTVIPDDATRSDGAKIPMQYDQSMGVRKDDTALLAEIDAALAKAK--PRIDAILKEE 241 (246)
T ss_pred ceEEeccccccccCCCCcceeeEEEEEEccCCHHHHHHHHHHHHHhH--HHHHHHHHHc
Confidence 32 233221 0 1135899999998 9999999999998 4899999888
No 58
>cd06338 PBP1_ABC_ligand_binding_like_5 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT); however their ligand specificity has not been determined experimentally.
Probab=99.72 E-value=2.2e-16 Score=173.55 Aligned_cols=217 Identities=18% Similarity=0.245 Sum_probs=171.3
Q ss_pred CCCChHHHHHHHHHHHHHcC--CcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCC
Q 043276 1 GALNDSSQVGAITAIIKAFG--WREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQ 78 (829)
Q Consensus 1 t~psD~~q~~ai~~ll~~fg--W~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~ 78 (829)
+.|++..++.++++++++++ |+++++|+.+++||+...+.+.+.+++.|++|.....++.+ ..+++.++.+|++.+
T Consensus 119 ~~~~~~~~~~~~~~~~~~~~~~~~~v~~v~~~~~~g~~~~~~~~~~~~~~g~~v~~~~~~~~~--~~d~~~~v~~l~~~~ 196 (345)
T cd06338 119 TLPPASQYAKSLLEMLVALDPRPKKVAILYADDPFSQDVAEGAREKAEAAGLEVVYDETYPPG--TADLSPLISKAKAAG 196 (345)
T ss_pred ecCchHHHHHHHHHHHHhcCCCCceEEEEecCCcccHHHHHHHHHHHHHcCCEEEEEeccCCC--ccchHHHHHHHHhcC
Confidence 46889999999999999998 99999999999999999999999999999999987777755 347999999999999
Q ss_pred CeEEEEEcChhHHHHHHHHHHHcCccccCeEEEEcCccccccccCCccccccccceEEEEeccCC-------ChhHHHHH
Q 043276 79 TRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLEPSVTDSMQGVIGVRPYVPK-------TKALENFR 151 (829)
Q Consensus 79 arViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t~~~~~~~~~~~~~~~~~~~g~l~~~~~~~~-------~~~~~~F~ 151 (829)
+++||+++....+..+++++++.|+.. ..++ .+.++... ... .......+|+++...+.+. .+..++|.
T Consensus 197 ~d~i~~~~~~~~~~~~~~~~~~~g~~~-~~~~-~~~~~~~~-~~~-~~~g~~~~g~~~~~~~~~~~~~~~~~~~~~~~f~ 272 (345)
T cd06338 197 PDAVVVAGHFPDAVLLVRQMKELGYNP-KALY-MTVGPAFP-AFV-KALGADAEGVFGPTQWTPALDYKDDLFPSAAEFA 272 (345)
T ss_pred CCEEEECCcchhHHHHHHHHHHcCCCC-CEEE-EecCCCcH-HHH-HHHhhhhCceeecceeccCcccccccCccHHHHH
Confidence 999999999999999999999999743 2332 23332211 010 1122345787776555443 36789999
Q ss_pred HHHHHhhcccCCCCCccccchhHHHHHHHHHHHHHHHHHhcccCccccCCCCCCCCCCCccccCCCChHHHHHHHhccce
Q 043276 152 VRWKRKFLQENPSLFDAELNIFGLLAYDATSALAVAVEKAGITGFGFDKTNVSSNATDLEAFGISQNGPKLLQALSSIRF 231 (829)
Q Consensus 152 ~~w~~~~~~~~~~~~~~~~~~~~~~~YDAV~~~A~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~L~~~~f 231 (829)
++|+++|+. .++.++..+|||++++++|+++++.. ++..+.++|++++|
T Consensus 273 ~~~~~~~~~--------~p~~~~~~~y~a~~~~~~a~~~ag~~-----------------------~~~~v~~al~~~~~ 321 (345)
T cd06338 273 AAYKEKYGK--------APDYHAAGAYAAGQVLQEAVERAGSL-----------------------DPAAVRDALASNDF 321 (345)
T ss_pred HHHHHHhCC--------CCCcccHHHHHHHHHHHHHHHHhCCC-----------------------CHHHHHHHHHhCCC
Confidence 999998865 24557889999999999999987532 15789999999999
Q ss_pred ecccccEEEe-cCccccceEEEEEc
Q 043276 232 RGLTGDYIFV-DGQLQSSAFEIINV 255 (829)
Q Consensus 232 ~G~tG~~~F~-~G~~~~~~y~I~n~ 255 (829)
.|++|++.|+ +|++. ..+-|++|
T Consensus 322 ~~~~G~~~f~~~~~~~-~~~~~~~~ 345 (345)
T cd06338 322 DTFYGPIKFDETGQNN-HPMTVVQW 345 (345)
T ss_pred cccccCeeECCCCCcC-CCceeeeC
Confidence 9999999996 89975 45556554
No 59
>PRK15404 leucine ABC transporter subunit substrate-binding protein LivK; Provisional
Probab=99.72 E-value=3.1e-16 Score=173.25 Aligned_cols=220 Identities=20% Similarity=0.225 Sum_probs=176.6
Q ss_pred CCCChHHHHHHHHHHH-HHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCC
Q 043276 1 GALNDSSQVGAITAII-KAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQT 79 (829)
Q Consensus 1 t~psD~~q~~ai~~ll-~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~a 79 (829)
+.++|..|+.++++++ +.++|++|++|+.|++||+...+.+.+.+++.|.+|+....++.+ ..|+..++.++++.++
T Consensus 140 ~~~~~~~~~~~~~~~~~~~~~~k~va~i~~d~~~g~~~~~~~~~~~~~~G~~v~~~~~~~~g--~~D~~~~v~~l~~~~~ 217 (369)
T PRK15404 140 TIGLDSDQGPTAAKYILEKVKPKRIAVLHDKQQYGEGLARSVKDGLKKAGANVVFFEGITAG--DKDFSALIAKLKKENV 217 (369)
T ss_pred CCCCcHHHHHHHHHHHHHhcCCCEEEEEeCCCchhHHHHHHHHHHHHHcCCEEEEEEeeCCC--CCchHHHHHHHHhcCC
Confidence 3578889999999966 678999999999999999999999999999999999988888766 4579999999999999
Q ss_pred eEEEEEcChhHHHHHHHHHHHcCccccCeEEEEcCccccccccCCccccccccceEEEEec-cCCChhHHHHHHHHHHhh
Q 043276 80 RVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLEPSVTDSMQGVIGVRPY-VPKTKALENFRVRWKRKF 158 (829)
Q Consensus 80 rViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t~~~~~~~~~~~~~~~~~~~g~l~~~~~-~~~~~~~~~F~~~w~~~~ 158 (829)
++|++.+....+..++++++++|+. ..|+.++++... .. .....+..+|+++..+. ....+..++|.+.|++++
T Consensus 218 d~v~~~~~~~~~~~~~k~~~~~G~~---~~~i~~~~~~~~-~~-~~~~~~~~~Gv~~~~~~~~~~~~~~~~f~~~~~~~~ 292 (369)
T PRK15404 218 DFVYYGGYHPEMGQILRQAREAGLK---TQFMGPEGVGNK-SL-SNIAGPASEGMLVTLPKRYDQDPANKAIVDAFKAKK 292 (369)
T ss_pred CEEEECCCchHHHHHHHHHHHCCCC---CeEEecCcCCCH-HH-HHhhhhhhcCcEEEccCCCccChhHHHHHHHHHHhc
Confidence 9998888778888999999999963 357776544321 11 11123457888765443 334577889999998875
Q ss_pred cccCCCCCccccchhHHHHHHHHHHHHHHHHHhcccCccccCCCCCCCCCCCccccCCCChHHHHHHHhccceecccccE
Q 043276 159 LQENPSLFDAELNIFGLLAYDATSALAVAVEKAGITGFGFDKTNVSSNATDLEAFGISQNGPKLLQALSSIRFRGLTGDY 238 (829)
Q Consensus 159 ~~~~~~~~~~~~~~~~~~~YDAV~~~A~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~L~~~~f~G~tG~~ 238 (829)
+. .++.++..+||++++++.|+++++.. ++..|.++|++..|.|++|++
T Consensus 293 ~~--------~~~~~~~~~Y~~~~~l~~Al~~aG~~-----------------------~~~~l~~al~~~~~~~~~G~~ 341 (369)
T PRK15404 293 QD--------PSGPFVWTTYAAVQSLAAGINRAGSD-----------------------DPAKVAKYLKANTFDTVIGPL 341 (369)
T ss_pred CC--------CCccchHHHHHHHHHHHHHHHhhCCC-----------------------CHHHHHHHHHhCCCCcceEee
Confidence 32 24457788999999999999987532 157899999999999999999
Q ss_pred EEe-cCccccceEEEEEcc-CC
Q 043276 239 IFV-DGQLQSSAFEIINVN-NG 258 (829)
Q Consensus 239 ~F~-~G~~~~~~y~I~n~~-~g 258 (829)
.|+ +|+.....|.|++|+ +|
T Consensus 342 ~~~~~g~~~~~~~~i~~~~~~~ 363 (369)
T PRK15404 342 SWDEKGDLKGFEFGVFEWHADG 363 (369)
T ss_pred EECCCCCcccCCEEEEEEEcCC
Confidence 996 898877899999988 64
No 60
>COG0834 HisJ ABC-type amino acid transport/signal transduction systems, periplasmic component/domain [Amino acid transport and metabolism / Signal transduction mechanisms]
Probab=99.71 E-value=6.4e-16 Score=163.93 Aligned_cols=226 Identities=25% Similarity=0.366 Sum_probs=181.3
Q ss_pred CCceEEEecccccCccceEEEeecCCCCC-ceEEEeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcC
Q 043276 306 NEKKLRVGVPVKKGFSDFVKVTIDPKTQE-TSVVGYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLG 384 (829)
Q Consensus 306 ~~~~lrv~v~~~~~~~p~~~~~~~~~~~~-~~~~G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g 384 (829)
..+.++|++... ..+||.+.+. . +++.||++|+++++++.++.....+++.. .|++++..|..|
T Consensus 32 ~~~~~~v~~~~~-~~~p~~~~~~-----~~~~~~G~dvdl~~~ia~~l~~~~~~~~~~~---------~~~~~~~~l~~g 96 (275)
T COG0834 32 ARGKLRVGTEAT-YAPPFEFLDA-----KGGKLVGFDVDLAKAIAKRLGGDKKVEFVPV---------AWDGLIPALKAG 96 (275)
T ss_pred hcCeEEEEecCC-CCCCcccccC-----CCCeEEeeeHHHHHHHHHHhCCcceeEEecc---------chhhhhHHHhcC
Confidence 467788888732 2347887652 3 59999999999999999886433444443 699999999999
Q ss_pred cccEEEeccccccccceeccccccccccceEEEEEccCCCCCCceeeeccCCHhHHHHHHHHHHHHHHHHHhhhcccCCC
Q 043276 385 EFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMIVPIKDSKKRNAWVFLQPLTWDLWVTSGCFFIFIGFVVWVLEHRVNED 464 (829)
Q Consensus 385 ~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv~~~~~~~~~~~~fl~PF~~~vW~~i~~~~~~~~~v~~~~~~~~~~~ 464 (829)
++|++++++++|++|.+.++||.||+.++..+++++.....
T Consensus 97 ~~D~~~~~~~~t~er~~~~~fs~py~~~~~~~~~~~~~~~~--------------------------------------- 137 (275)
T COG0834 97 KVDIIIAGMTITPERKKKVDFSDPYYYSGQVLLVKKDSDIG--------------------------------------- 137 (275)
T ss_pred CcCEEEeccccCHHHhccccccccccccCeEEEEECCCCcC---------------------------------------
Confidence 99999999999999999999999999999999999665432
Q ss_pred CCCCccCccchhHHHHHHHhhhcCccccccchhHHHHHHHHHHHHHHHHHhHHHHHHHhhcccCCCCCCCHHHHHhCCCc
Q 043276 465 FRGPARHQVGTSFWFSFSTMVFSQRERVISNLARFVVIVWCFVVLILIQSYTASLTSLLTVDQLQPTITDVNLLIKRGDN 544 (829)
Q Consensus 465 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~s~~~R~v~~~w~~~~lil~~~YtA~L~s~Lt~~~~~~~I~s~~dL~~~~~~ 544 (829)
+.+++|| .|++
T Consensus 138 -------------------------------------------------------------------~~~~~DL--~gk~ 148 (275)
T COG0834 138 -------------------------------------------------------------------IKSLEDL--KGKK 148 (275)
T ss_pred -------------------------------------------------------------------cCCHHHh--CCCE
Confidence 5789999 4899
Q ss_pred EEEEeCch--HHHHHHhcCCCccceeecCChHHHHHHHhcCCcCCceeEEEcchhHHHHH--HhcCCCceEEeCccccc-
Q 043276 545 VGYQKGSF--VLGILKQLGFDERKLVVYNSHEECDELFQKGSANGGIAAAFDEIPYAKLL--IGQHCSKYTMVEPTFKT- 619 (829)
Q Consensus 545 vg~~~~s~--~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~--~~~~c~~l~~v~~~~~~- 619 (829)
+|++.|++ ....... ..+...++.+++..+.+.+|..|+ +|+++.+...+.++ ..+..............
T Consensus 149 v~v~~gt~~~~~~~~~~-~~~~~~~~~~~~~~~~~~al~~Gr----~Da~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~ 223 (275)
T COG0834 149 VGVQLGTTDEAEEKAKK-PGPNAKIVAYDSNAEALLALKNGR----ADAVVSDSAVLAGLKLLKKNPGLYVLLVFPGLSV 223 (275)
T ss_pred EEEEcCcchhHHHHHhh-ccCCceEEeeCCHHHHHHHHHcCC----ccEEEcchHhhhhhhhhhcCCCCceeeeccCCCc
Confidence 99999998 4444443 244567889999999999999999 99999999998884 43333222233333333
Q ss_pred CCceeeecCC--CCchhhHHHHHHhhhccChhHHHHHHHccC
Q 043276 620 AGFGFAFPLH--SPLVHDVSKAILNVTEGDKMKEIEDAWFKK 659 (829)
Q Consensus 620 ~~~~~~~~k~--spl~~~in~~il~l~e~G~~~~~~~~w~~~ 659 (829)
.+++++++|+ ..+++.+|++|.++.++|.++++.++|+..
T Consensus 224 ~~~~~~~~~~~~~~l~~~in~~l~~l~~~G~~~~i~~kw~~~ 265 (275)
T COG0834 224 EYLGIALRKGDDPELLEAVNKALKELKADGTLQKISDKWFGP 265 (275)
T ss_pred ceeEEEeccCCcHHHHHHHHHHHHHHHhCccHHHHHHHhcCc
Confidence 6899999999 469999999999999999999999999963
No 61
>cd06346 PBP1_ABC_ligand_binding_like_11 Type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine/isoleucine/valine binding protein (LIVBP); however its ligand specificity has not been determined experimentally.
Probab=99.70 E-value=2.2e-16 Score=170.76 Aligned_cols=194 Identities=24% Similarity=0.334 Sum_probs=160.0
Q ss_pred CCCChHHHHHHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCe
Q 043276 1 GALNDSSQVGAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTR 80 (829)
Q Consensus 1 t~psD~~q~~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~ar 80 (829)
+.|+|..|+.+++++++++||++|++||.|++||+...+.+++.+++.|++|+....++.. ..++..++.+|++.+++
T Consensus 117 ~~~~~~~~~~~l~~~~~~~~~~~vail~~~~~~g~~~~~~~~~~~~~~G~~vv~~~~~~~~--~~d~~~~v~~l~~~~pd 194 (312)
T cd06346 117 TAPSDALQGQALAQLAAERGYKSVATTYINNDYGVGLADAFTKAFEALGGTVTNVVAHEEG--KSSYSSEVAAAAAGGPD 194 (312)
T ss_pred ecCCcHHHHHHHHHHHHHcCCCeEEEEEccCchhhHHHHHHHHHHHHcCCEEEEEEeeCCC--CCCHHHHHHHHHhcCCC
Confidence 4689999999999999999999999999999999999999999999999999998888866 45899999999999999
Q ss_pred EEEEEcChhHHHHHHHHHHHcCccccCeEEEEcCccccccccCCccccccccceEEEEeccCCChhHHHHHHHHHHhhcc
Q 043276 81 VFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLEPSVTDSMQGVIGVRPYVPKTKALENFRVRWKRKFLQ 160 (829)
Q Consensus 81 ViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t~~~~~~~~~~~~~~~~~~~g~l~~~~~~~~~~~~~~F~~~w~~~~~~ 160 (829)
+|++.+....+..++++++++|+ ...|+.++++... ..........++|+++..+..+ .+..++|.++|+++|+.
T Consensus 195 ~v~~~~~~~~~~~~~~~~~~~G~---~~~~~~~~~~~~~-~~~~~~~~~~~~g~~~~~~~~~-~~~~~~f~~~~~~~~g~ 269 (312)
T cd06346 195 ALVVIGYPETGSGILRSAYEQGL---FDKFLLTDGMKSD-SFLPADGGYILAGSYGTSPGAG-GPGLEAFTSAYKAAYGE 269 (312)
T ss_pred EEEEecccchHHHHHHHHHHcCC---CCceEeeccccCh-HHHHhhhHHHhCCcEEccCCCC-chhHHHHHHHHHHHhCC
Confidence 99999999999999999999997 3447777665431 1111112245788887765444 37889999999999865
Q ss_pred cCCCCCccccchhHHHHHHHHHHHHHHHHHhcccCccccCCCCCCCCCCCccccCCCChHHHHHHHhccceecccccEEE
Q 043276 161 ENPSLFDAELNIFGLLAYDATSALAVAVEKAGITGFGFDKTNVSSNATDLEAFGISQNGPKLLQALSSIRFRGLTGDYIF 240 (829)
Q Consensus 161 ~~~~~~~~~~~~~~~~~YDAV~~~A~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~L~~~~f~G~tG~~~F 240 (829)
.++.++..+||+++++++| |.|++|++.|
T Consensus 270 --------~p~~~~~~~Yd~~~~l~~A-------------------------------------------~~g~~g~~~f 298 (312)
T cd06346 270 --------SPSAFADQSYDAAALLALA-------------------------------------------YQGASGVVDF 298 (312)
T ss_pred --------CCCccchhhHHHHHHHHHH-------------------------------------------hCCCccceee
Confidence 3567889999999999987 5688999999
Q ss_pred e-cCccccceEEEE
Q 043276 241 V-DGQLQSSAFEII 253 (829)
Q Consensus 241 ~-~G~~~~~~y~I~ 253 (829)
+ +|++. ..|+-+
T Consensus 299 ~~~g~~~-~~~~~~ 311 (312)
T cd06346 299 DENGDVA-GSYDEW 311 (312)
T ss_pred CCCCCcc-cceeee
Confidence 6 89975 477643
No 62
>cd06345 PBP1_ABC_ligand_binding_like_10 Type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine/isoleucine/valine binding protein (LIVBP); however its ligand specificity has not been determined experimentally.
Probab=99.70 E-value=4.4e-16 Score=170.99 Aligned_cols=209 Identities=21% Similarity=0.213 Sum_probs=166.0
Q ss_pred CCCChHHHHHHHHHHHHH-----cCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhh
Q 043276 1 GALNDSSQVGAITAIIKA-----FGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLF 75 (829)
Q Consensus 1 t~psD~~q~~ai~~ll~~-----fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk 75 (829)
+.|++..++.++++++.+ +||++|++|+.+++||....+.+.+.+++.|++|+....++.. ..++..++.+|+
T Consensus 119 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~va~l~~~~~~g~~~~~~~~~~~~~~G~~vv~~~~~~~~--~~d~~~~v~~l~ 196 (344)
T cd06345 119 AGPTNSSYAQSVADALKETLVDKHGFKTAAIVAEDAAWGKGIDAGIKALLPEAGLEVVSVERFSPD--TTDFTPILQQIK 196 (344)
T ss_pred cCCCcHHHHHHHHHHHHHhhcccCCCceEEEEecCchhhhHHHHHHHHHHHHcCCeEEEEEecCCC--CCchHHHHHHHH
Confidence 468888899999998876 8999999999999999999999999999999999988887765 447999999999
Q ss_pred cCCCeEEEEEcChhHHHHHHHHHHHcCccccCeEEEEcCccccccccCCccccccccceEEEEecc----CCChhHHHHH
Q 043276 76 TMQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLEPSVTDSMQGVIGVRPYV----PKTKALENFR 151 (829)
Q Consensus 76 ~~~arViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t~~~~~~~~~~~~~~~~~~~g~l~~~~~~----~~~~~~~~F~ 151 (829)
+.++++|++.+....+..+++++.+.|+.. . ++..+.+....... ......++|+++..... ..++..++|.
T Consensus 197 ~~~~d~v~~~~~~~~~~~~~~~~~~~g~~~-~--~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~ 272 (344)
T cd06345 197 AADPDVIIAGFSGNVGVLFTQQWAEQKVPI-P--TIGISVEGNSPAFW-KATNGAGNYVITAESGAPGVEAITDKTVPFT 272 (344)
T ss_pred hcCCCEEEEeecCchHHHHHHHHHHcCCCC-c--eEEecCCcCCHHHH-HhhchhcceEEeecccccCccCCCHHHHHHH
Confidence 999999999999989999999999999632 2 33333222111111 11223456666544333 2467789999
Q ss_pred HHHHHhhcccCCCCCccccchhHHHHHHHHHHHHHHHHHhcccCccccCCCCCCCCCCCccccCCCChHHHHHHHhccce
Q 043276 152 VRWKRKFLQENPSLFDAELNIFGLLAYDATSALAVAVEKAGITGFGFDKTNVSSNATDLEAFGISQNGPKLLQALSSIRF 231 (829)
Q Consensus 152 ~~w~~~~~~~~~~~~~~~~~~~~~~~YDAV~~~A~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~L~~~~f 231 (829)
++|+++|+. .++.++..+||+++++++|+++++.. .+..+.++|++++|
T Consensus 273 ~~y~~~~g~--------~p~~~~~~~yda~~~l~~A~~~ag~~-----------------------~~~~i~~al~~~~~ 321 (344)
T cd06345 273 EAYEAKFGG--------PPNYMGASTYDSIYILAEAIERAGST-----------------------DGDALVEALEKTDF 321 (344)
T ss_pred HHHHHHhCC--------CCcccchHHHHHHHHHHHHHHHhcCC-----------------------CHHHHHHHHHhCCC
Confidence 999988865 36678889999999999999987532 25789999999999
Q ss_pred ecccccEEEe-cCccc
Q 043276 232 RGLTGDYIFV-DGQLQ 246 (829)
Q Consensus 232 ~G~tG~~~F~-~G~~~ 246 (829)
.|++|.+.|+ +||+.
T Consensus 322 ~g~~G~i~f~~~g~~~ 337 (344)
T cd06345 322 VGTAGRIQFYGDDSAF 337 (344)
T ss_pred cCCceeEEECCCCCcC
Confidence 9999999996 99985
No 63
>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=99.69 E-value=3.3e-16 Score=165.35 Aligned_cols=230 Identities=13% Similarity=0.178 Sum_probs=164.2
Q ss_pred CceEEEecccccCccceEEEeecCCCCCceEEEeeHHHHHHHHHHC-CCcccEEEEecCCCCCCCCCChhHHHHhHhcCc
Q 043276 307 EKKLRVGVPVKKGFSDFVKVTIDPKTQETSVVGYSIDVFKAVIEEL-PYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGE 385 (829)
Q Consensus 307 ~~~lrv~v~~~~~~~p~~~~~~~~~~~~~~~~G~~idll~~ia~~l-~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~ 385 (829)
.++|+++.. +|+||.+.+ +++...|+..++++++++++ ++. +++... .|++++..| .|+
T Consensus 17 ~~~l~~~~~---~~pPf~~~~-----~~~~~~G~~~~i~~~i~~~~~~~~--~~~~~~---------pw~r~l~~l-~~~ 76 (268)
T TIGR02285 17 KEAITWIVN---DFPPFFIFS-----GPSKGRGVFDVILQEIRRALPQYE--HRFVRV---------SFARSLKEL-QGK 76 (268)
T ss_pred cceeEEEec---ccCCeeEeC-----CCCCCCChHHHHHHHHHHHcCCCc--eeEEEC---------CHHHHHHHH-hcC
Confidence 468888765 677888764 34677999999999999998 764 444443 599999999 788
Q ss_pred ccEEEeccccccccceeccccccccc-cceEEEEEccCCCCCCceeeeccCCHhHHHHHHHHHHHHHHHHHhhhcccCCC
Q 043276 386 FDAVVGDTTIVFNRSNYVDFTLPYTE-SGVSMIVPIKDSKKRNAWVFLQPLTWDLWVTSGCFFIFIGFVVWVLEHRVNED 464 (829)
Q Consensus 386 ~Di~~~~~~it~~R~~~vdft~p~~~-~~~~~vv~~~~~~~~~~~~fl~PF~~~vW~~i~~~~~~~~~v~~~~~~~~~~~ 464 (829)
.|+++.++++|++|.+.++||.||.. ...++++++..... .
T Consensus 77 ~d~~~~~~~~t~eR~~~~~Fs~P~~~~~~~~~~~~~~~~~~--~------------------------------------ 118 (268)
T TIGR02285 77 GGVCTVNLLRTPEREKFLIFSDPTLRALPVGLVLRKELTAG--V------------------------------------ 118 (268)
T ss_pred CCeEEeeccCCcchhhceeecCCccccCCceEEEccchhhh--c------------------------------------
Confidence 88777789999999999999999975 57888888653221 0
Q ss_pred CCCCccCccchhHHHHHHHhhhcCccccccchhHHHHHHHHHHHHHHHHHhHHHHHHHhhcccCCCCCCCHHHHH-hCCC
Q 043276 465 FRGPARHQVGTSFWFSFSTMVFSQRERVISNLARFVVIVWCFVVLILIQSYTASLTSLLTVDQLQPTITDVNLLI-KRGD 543 (829)
Q Consensus 465 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~s~~~R~v~~~w~~~~lil~~~YtA~L~s~Lt~~~~~~~I~s~~dL~-~~~~ 543 (829)
..+.....++.+|. .+|+
T Consensus 119 -------------------------------------------------------------~~~~d~~~~~~~l~~l~g~ 137 (268)
T TIGR02285 119 -------------------------------------------------------------RDEQDGDVDLKKLLASKKK 137 (268)
T ss_pred -------------------------------------------------------------cccCCCCccHHHHhcCCCe
Confidence 00000001233332 1467
Q ss_pred cEEEEeCchH----HHHHHhcCCCc-cceeecCChHHHHHHHhcCCcCCceeEEEcchhHHHHHHhcC---CCceEEeCc
Q 043276 544 NVGYQKGSFV----LGILKQLGFDE-RKLVVYNSHEECDELFQKGSANGGIAAAFDEIPYAKLLIGQH---CSKYTMVEP 615 (829)
Q Consensus 544 ~vg~~~~s~~----~~~l~~~~~~~-~~~~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~~---c~~l~~v~~ 615 (829)
++|++.|+.. ..++++..... .++..+.+.++.+++|..|+ +|+++.+...+.+++++. ...+...+.
T Consensus 138 ~vgv~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~Gr----vD~~v~d~~~~~~~~~~~~~~~~~~~~~~~ 213 (268)
T TIGR02285 138 RLGVIASRSYGQQIDDILSDSGYQHNTRIIGNAAMGNLFKMLEKGR----VNYTLAYPPEKTYYEELNNGALPPLKFLPV 213 (268)
T ss_pred EEEEecceeccHHHHHHHHhCCcccceeeeccchHHHHHHHHHcCC----ccEEEeCcHHHHHHHHhccCCcCCeeEeec
Confidence 8999887654 34444433221 23455677788999999999 999999999999888753 223444432
Q ss_pred cc--ccCCceeeecCCC---CchhhHHHHHHhhhccChhHHHHHHHccC
Q 043276 616 TF--KTAGFGFAFPLHS---PLVHDVSKAILNVTEGDKMKEIEDAWFKK 659 (829)
Q Consensus 616 ~~--~~~~~~~~~~k~s---pl~~~in~~il~l~e~G~~~~~~~~w~~~ 659 (829)
.. ...+++++++|+. .+++.||++|.+|.++|.++++.+||++.
T Consensus 214 ~~~~~~~~~~i~~~k~~~~~~l~~~in~~L~~l~~dG~~~~i~~k~~~~ 262 (268)
T TIGR02285 214 AGMPAHISVWVACPKTEWGRKVIADIDQALSELNVDPKYYKYFDRWLSP 262 (268)
T ss_pred CCCccceEEEEEeCCCHHHHHHHHHHHHHHHHHhhCHHHHHHHHHhCCH
Confidence 11 2235789999974 39999999999999999999999999964
No 64
>KOG1055 consensus GABA-B ion channel receptor subunit GABABR1 and related subunits, G-protein coupled receptor superfamily [Inorganic ion transport and metabolism; Amino acid transport and metabolism; Signal transduction mechanisms]
Probab=99.68 E-value=6.3e-17 Score=178.85 Aligned_cols=255 Identities=16% Similarity=0.245 Sum_probs=188.7
Q ss_pred CCCChHHHHHHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCe
Q 043276 1 GALNDSSQVGAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTR 80 (829)
Q Consensus 1 t~psD~~q~~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~ar 80 (829)
|.||+..+...+.+++++|+|+.|+.++.++.....-...|...+.+.+++|+.++.+.. +....++++++..+|
T Consensus 161 t~PS~~~~np~rl~l~~~~~w~rvgt~~q~e~~f~~~~~dl~~~~~~~~ieiv~~qsf~~-----dp~~~vk~l~~~D~R 235 (865)
T KOG1055|consen 161 THPSANAHNPTRIKLLKKFGWKRVATLQQTEEVFSSTLNDLEARLKEAGIEIVFRQSFSS-----DPADSVKNLKRQDAR 235 (865)
T ss_pred cCCccccCCcceeeechhcCcceeeeeeeehhhhcchHHHHHHhhhccccEEEEeecccc-----CHHHHHhhccccchh
Confidence 579999999999999999999999999999999999999999999999999998877643 344578899999999
Q ss_pred EEEEEcChhHHHHHHHHHHHcCccccCeEEEEcCccccc-----cc---cCCccccccccceEEEEecc--CC------C
Q 043276 81 VFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNL-----LR---TLEPSVTDSMQGVIGVRPYV--PK------T 144 (829)
Q Consensus 81 ViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t~~~~~~-----~~---~~~~~~~~~~~g~l~~~~~~--~~------~ 144 (829)
+|+...+...|+.++++|++.+|.+..|+|++..+.... .+ +.-.++..+++|.+++.... +. .
T Consensus 236 iI~g~f~~~~Arkv~C~~Y~~~myg~ky~w~~~g~y~d~w~ev~~~~~~ctveem~~A~eg~~s~e~~pl~~~~~~tisg 315 (865)
T KOG1055|consen 236 IIVGLFYETEARKVFCEAYKERLYGRKYVWFLIGWYADNWWEITHPSENCTVEEMTEAAEGHITTEFVMLSPANITTISG 315 (865)
T ss_pred heeccchHhhhhHHHHhhchhhcccceeEEEEEEeeccchhhccCchhhhhHHHHHHHHhhheeeeeeccccccceeecc
Confidence 999999999999999999999999999999986543211 11 11234567788887765422 11 1
Q ss_pred hhHHHHHHHHHHhhcccCCCCCccccchhHHHHHHHHHHHHHHHHHhcccCccccCCCCCCCCCCCccccCCCChHHHHH
Q 043276 145 KALENFRVRWKRKFLQENPSLFDAELNIFGLLAYDATSALAVAVEKAGITGFGFDKTNVSSNATDLEAFGISQNGPKLLQ 224 (829)
Q Consensus 145 ~~~~~F~~~w~~~~~~~~~~~~~~~~~~~~~~~YDAV~~~A~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~ 224 (829)
-.-..|+..+..+.+... +......++.++|||||++|+|++++...... ...+. .+. ++.....+.+|++
T Consensus 316 ~T~~~~l~~~~~~r~~~~---~~~~~~~~~~~ayd~Iwa~ala~n~t~e~l~~---~~~~l--~~f-~y~~k~i~d~i~e 386 (865)
T KOG1055|consen 316 MTAQEFLEELTKYRKRHP---EETGGFQEAPLAYDAIWALALALNKTMEGLGR---SHVRL--EDF-NYNNKTIADQIYE 386 (865)
T ss_pred chhHHHHHHHHhhhcccc---ccccCcccCchHHHHHHHHHHHHHHHHhcCCc---cceec--ccc-chhhhHHHHHHHH
Confidence 123455555444333210 11234567889999999999999998654321 10000 011 1111234678999
Q ss_pred HHhccceecccccEEEecCccccceEEEEEcc-CCcEEEEEecCCCC
Q 043276 225 ALSSIRFRGLTGDYIFVDGQLQSSAFEIINVN-NGARGVGFWSPEKG 270 (829)
Q Consensus 225 ~L~~~~f~G~tG~~~F~~G~~~~~~y~I~n~~-~g~~~VG~w~~~~g 270 (829)
+|.+++|.|++|.+.|.+|++. +.-.|-+++ +.++++|+|+....
T Consensus 387 amn~tsF~GvsG~V~F~~geR~-a~t~ieQ~qdg~y~k~g~Yds~~D 432 (865)
T KOG1055|consen 387 AMNSTSFEGVSGHVVFSNGERM-ALTLIEQFQDGKYKKIGYYDSTKD 432 (865)
T ss_pred HhhcccccccccceEecchhhH-HHHHHHHHhCCceEeecccccccc
Confidence 9999999999999999779986 677788888 44999999987554
No 65
>cd06348 PBP1_ABC_ligand_binding_like_13 Type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine/isoleucine/valine binding protein (LIVBP); however its ligand specificity has not been determined experimentally.
Probab=99.68 E-value=1.7e-15 Score=166.45 Aligned_cols=220 Identities=18% Similarity=0.302 Sum_probs=166.7
Q ss_pred CChH-HHHHHHHHHHHHc-CCcEEEEEEEeCc-cccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCC
Q 043276 3 LNDS-SQVGAITAIIKAF-GWREAVPIYVDNQ-YGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQT 79 (829)
Q Consensus 3 psD~-~q~~ai~~ll~~f-gW~~V~iI~~dd~-yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~a 79 (829)
+++. .+..++..+++++ ||++|++||.+++ ||+.....+++.+++.|++|+....++.. ..++..++.+|+++++
T Consensus 116 ~~~~~~~~~~~~~~~~~~~~~~~v~~l~~~~~~~g~~~~~~~~~~~~~~g~~v~~~~~~~~~--~~d~~~~v~~i~~~~~ 193 (344)
T cd06348 116 APEAVVAPAAIAAALKLNPGIKRVAVFYAQDDAFSVSETEIFQKALRDQGLNLVTVQTFQTG--DTDFQAQITAVLNSKP 193 (344)
T ss_pred CcHHHHHHHHHHHHHHHhcCCeEEEEEEeCCchHHHHHHHHHHHHHHHcCCEEEEEEeeCCC--CCCHHHHHHHHHhcCC
Confidence 3443 4445666778888 9999999997655 99999999999999999999988888765 4589999999999999
Q ss_pred eEEEEEcChhHHHHHHHHHHHcCccccCeEEEEcCccccccccCCccccccccceEEEEeccC--CChhHHHHHHHHHHh
Q 043276 80 RVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLEPSVTDSMQGVIGVRPYVP--KTKALENFRVRWKRK 157 (829)
Q Consensus 80 rViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t~~~~~~~~~~~~~~~~~~~g~l~~~~~~~--~~~~~~~F~~~w~~~ 157 (829)
++|++.+....+..+++++.+.|+.. .|+.++++... ... ....+..+|+++..++.+ ..+..++|.+.|+++
T Consensus 194 d~vi~~~~~~~~~~~~~~~~~~g~~~---~~~~~~~~~~~-~~~-~~~g~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~ 268 (344)
T cd06348 194 DLIVISALAADGGNLVRQLRELGYNG---LIVGGNGFNTP-NVF-PVCQAACDGVLVAQAYSPENDTPVNRDFVEAYKKK 268 (344)
T ss_pred CEEEECCcchhHHHHHHHHHHcCCCC---ceeccccccCH-HHH-HhhhHhhcCeEEEeeccCCCCCHHHHHHHHHHHHH
Confidence 99999999999999999999999732 35555544321 111 123355678877665543 446789999999988
Q ss_pred hcccCCCCCccccchhHHHHHHHHHHHHHHHHHhcccCccccCCCCCCCCCCCccccCCCChHHHHHHHhccceeccccc
Q 043276 158 FLQENPSLFDAELNIFGLLAYDATSALAVAVEKAGITGFGFDKTNVSSNATDLEAFGISQNGPKLLQALSSIRFRGLTGD 237 (829)
Q Consensus 158 ~~~~~~~~~~~~~~~~~~~~YDAV~~~A~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~L~~~~f~G~tG~ 237 (829)
++. .++.++..+|||++++++|+++++.+... .++. ....+..|.++|++++|.|++|.
T Consensus 269 ~g~--------~p~~~~~~~yda~~~~~~A~~~a~~~~~~----------~~~~---~~~~~~~l~~~l~~~~~~g~~G~ 327 (344)
T cd06348 269 YGK--------APPQFSAQAFDAVQVVAEALKRLNQKQKL----------AELP---LPELRTALNAALLSGQYDTPLGE 327 (344)
T ss_pred HCC--------CccHHHHHHHHHHHHHHHHHHHhcCCCcc----------ccch---hhhHHHHHHHHHhccCCccceee
Confidence 864 35668889999999999999998754210 0010 01125678899999999999999
Q ss_pred EEEe-cCccccceE
Q 043276 238 YIFV-DGQLQSSAF 250 (829)
Q Consensus 238 ~~F~-~G~~~~~~y 250 (829)
+.|+ +|++....|
T Consensus 328 v~f~~~g~~~~~~~ 341 (344)
T cd06348 328 ISFTPDGEVLQKAF 341 (344)
T ss_pred eEECCCCCcccCce
Confidence 9996 898765444
No 66
>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=99.68 E-value=1.6e-15 Score=156.67 Aligned_cols=212 Identities=16% Similarity=0.118 Sum_probs=159.4
Q ss_pred eEEEecccccCccceEEEeecCCCCCceEEEeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccE
Q 043276 309 KLRVGVPVKKGFSDFVKVTIDPKTQETSVVGYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDA 388 (829)
Q Consensus 309 ~lrv~v~~~~~~~p~~~~~~~~~~~~~~~~G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di 388 (829)
+||||+. +.|+||.+. +..||++||++++++++|.++++++.+. .+..++..+..|++|+
T Consensus 1 ~l~v~~~--~~~~P~~~~---------~~~G~~~el~~~i~~~~g~~i~~~~~~~---------~~~~~~~~l~~g~~Di 60 (232)
T TIGR03871 1 ALRVCAD--PNNLPFSNE---------KGEGFENKIAQLLADDLGLPLEYTWFPQ---------RRGFVRNTLNAGRCDV 60 (232)
T ss_pred CeEEEeC--CCCCCccCC---------CCCchHHHHHHHHHHHcCCceEEEecCc---------chhhHHHHHhcCCccE
Confidence 4788877 678888752 2369999999999999998766655442 2444677899999999
Q ss_pred EEeccccccccceeccccccccccceEEEEEccCCCCCCceeeeccCCHhHHHHHHHHHHHHHHHHHhhhcccCCCCCCC
Q 043276 389 VVGDTTIVFNRSNYVDFTLPYTESGVSMIVPIKDSKKRNAWVFLQPLTWDLWVTSGCFFIFIGFVVWVLEHRVNEDFRGP 468 (829)
Q Consensus 389 ~~~~~~it~~R~~~vdft~p~~~~~~~~vv~~~~~~~~~~~~fl~PF~~~vW~~i~~~~~~~~~v~~~~~~~~~~~~~~~ 468 (829)
+++ +++|.+.++||.||...+.+++++..+...
T Consensus 61 ~~~----~~~r~~~~~fs~py~~~~~~lv~~~~~~~~------------------------------------------- 93 (232)
T TIGR03871 61 VIG----VPAGYEMVLTTRPYYRSTYVFVTRKDSLLD------------------------------------------- 93 (232)
T ss_pred EEe----ccCccccccccCCcEeeeEEEEEeCCCccc-------------------------------------------
Confidence 875 477888999999999999999998664221
Q ss_pred ccCccchhHHHHHHHhhhcCccccccchhHHHHHHHHHHHHHHHHHhHHHHHHHhhcccCCCCCCCHHHHHhCCCcEEEE
Q 043276 469 ARHQVGTSFWFSFSTMVFSQRERVISNLARFVVIVWCFVVLILIQSYTASLTSLLTVDQLQPTITDVNLLIKRGDNVGYQ 548 (829)
Q Consensus 469 ~~~~~~~~~~~~~~~l~~~~~~~~~s~~~R~v~~~w~~~~lil~~~YtA~L~s~Lt~~~~~~~I~s~~dL~~~~~~vg~~ 548 (829)
+++++|+...+++||+.
T Consensus 94 ---------------------------------------------------------------~~~~~d~~l~g~~V~v~ 110 (232)
T TIGR03871 94 ---------------------------------------------------------------VKSLDDPRLKKLRIGVF 110 (232)
T ss_pred ---------------------------------------------------------------ccchhhhhhcCCeEEEE
Confidence 67888832257899999
Q ss_pred eCchHHHHHHhcCCCccceee---------cCChHHHHHHHhcCCcCCceeEEEcchhHHHHHHhcCCCceEEeCcc---
Q 043276 549 KGSFVLGILKQLGFDERKLVV---------YNSHEECDELFQKGSANGGIAAAFDEIPYAKLLIGQHCSKYTMVEPT--- 616 (829)
Q Consensus 549 ~~s~~~~~l~~~~~~~~~~~~---------~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~~c~~l~~v~~~--- 616 (829)
.|+....++++.+... ++.. ..+..+.+.+|..|+ +|+++.+...+.+++++....+.+....
T Consensus 111 ~g~~~~~~l~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~l~~G~----~Da~i~~~~~~~~~~~~~~~~~~~~~~~~~~ 185 (232)
T TIGR03871 111 AGTPPAHWLARHGLVE-NVVGYSLFGDYRPESPPGRMVEDLAAGE----IDVAIVWGPIAGYFAKQAGPPLVVVPLLPED 185 (232)
T ss_pred cCChHHHHHHhcCccc-ccccccccccccccCCHHHHHHHHHcCC----cCEEEeccHHHHHHHHhCCCCceeeccccCC
Confidence 9999988887644321 2221 236789999999999 9999999888888777542234443321
Q ss_pred ---cccCCceeeecCCCC-chhhHHHHHHhhhccChhHHHHHHHc
Q 043276 617 ---FKTAGFGFAFPLHSP-LVHDVSKAILNVTEGDKMKEIEDAWF 657 (829)
Q Consensus 617 ---~~~~~~~~~~~k~sp-l~~~in~~il~l~e~G~~~~~~~~w~ 657 (829)
....+++|+++++.+ |+..||++|.++. |.+++|.+||.
T Consensus 186 ~~~~~~~~~~~~~~~~~~~l~~~~n~~l~~~~--~~~~~i~~kyg 228 (232)
T TIGR03871 186 GGIPFDYRIAMGVRKGDKAWKDELNAVLDRRQ--AEIDAILREYG 228 (232)
T ss_pred CCCCccceEEEEEecCCHHHHHHHHHHHHHHH--HHHHHHHHHcC
Confidence 123356888999877 9999999999985 47899999995
No 67
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=99.67 E-value=8.4e-16 Score=196.19 Aligned_cols=222 Identities=14% Similarity=0.124 Sum_probs=184.4
Q ss_pred CCceEEEecccccCccceEEEeecCCCCCceEEEeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCc
Q 043276 306 NEKKLRVGVPVKKGFSDFVKVTIDPKTQETSVVGYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGE 385 (829)
Q Consensus 306 ~~~~lrv~v~~~~~~~p~~~~~~~~~~~~~~~~G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~ 385 (829)
..++++||+. ++++|+.+... .++++.||.+|+++.|++++|. +++++++. +|++++.+|.+|+
T Consensus 54 ~~~~l~vgv~--~~~~p~~~~~~----~~g~~~G~~~D~l~~ia~~lG~--~~e~v~~~--------~~~~~l~~l~~g~ 117 (1197)
T PRK09959 54 SKKNLVIAVH--KSQTATLLHTD----SQQRVRGINADYLNLLKRALNI--KLTLREYA--------DHQKAMDALEEGE 117 (1197)
T ss_pred hCCeEEEEec--CCCCCCceeec----CCCccceecHHHHHHHHHhcCC--ceEEEeCC--------CHHHHHHHHHcCC
Confidence 4678999987 55555444321 3688999999999999999995 77788764 7999999999999
Q ss_pred ccEEEeccccccccceeccccccccccceEEEEEccCCCCCCceeeeccCCHhHHHHHHHHHHHHHHHHHhhhcccCCCC
Q 043276 386 FDAVVGDTTIVFNRSNYVDFTLPYTESGVSMIVPIKDSKKRNAWVFLQPLTWDLWVTSGCFFIFIGFVVWVLEHRVNEDF 465 (829)
Q Consensus 386 ~Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv~~~~~~~~~~~~fl~PF~~~vW~~i~~~~~~~~~v~~~~~~~~~~~~ 465 (829)
+|++++.++.+++|.+.++||.||+.+..++++++...
T Consensus 118 iDl~~~~~~~~~~r~~~~~fs~py~~~~~~~v~~~~~~------------------------------------------ 155 (1197)
T PRK09959 118 VDIVLSHLVASPPLNDDIAATKPLIITFPALVTTLHDS------------------------------------------ 155 (1197)
T ss_pred CcEecCccccccccccchhcCCCccCCCceEEEeCCCC------------------------------------------
Confidence 99998889999999999999999999999999986532
Q ss_pred CCCccCccchhHHHHHHHhhhcCccccccchhHHHHHHHHHHHHHHHHHhHHHHHHHhhcccCCCCCCCHHHHHhCCCcE
Q 043276 466 RGPARHQVGTSFWFSFSTMVFSQRERVISNLARFVVIVWCFVVLILIQSYTASLTSLLTVDQLQPTITDVNLLIKRGDNV 545 (829)
Q Consensus 466 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~s~~~R~v~~~w~~~~lil~~~YtA~L~s~Lt~~~~~~~I~s~~dL~~~~~~v 545 (829)
+++++|+ .++++
T Consensus 156 ------------------------------------------------------------------~~~~~~l--~~~~i 167 (1197)
T PRK09959 156 ------------------------------------------------------------------MRPLTSS--KPVNI 167 (1197)
T ss_pred ------------------------------------------------------------------CCCcccc--cCeEE
Confidence 4667777 47789
Q ss_pred EEEeCchHHHHHHhcCCCccceeecCChHHHHHHHhcCCcCCceeEEEcchhHHHHHHhcCC-CceEEeCc-ccccCCce
Q 043276 546 GYQKGSFVLGILKQLGFDERKLVVYNSHEECDELFQKGSANGGIAAAFDEIPYAKLLIGQHC-SKYTMVEP-TFKTAGFG 623 (829)
Q Consensus 546 g~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~~c-~~l~~v~~-~~~~~~~~ 623 (829)
+++.|+....++++. ++..+++.|++..+++++|..|+ +||++.+...+.|+++++. ..+.+++. .......+
T Consensus 168 ~~~~g~~~~~~~~~~-~p~~~i~~~~s~~~al~av~~G~----~Da~i~~~~~~~~~i~~~~~~~l~~~~~~~~~~~~~~ 242 (1197)
T PRK09959 168 ARVANYPPDEVIHQS-FPKATIISFTNLYQALASVSAGQ----NDYFIGSNIITSSMISRYFTHSLNVVKYYNSPRQYNF 242 (1197)
T ss_pred EEeCCCCCHHHHHHh-CCCCEEEeCCCHHHHHHHHHcCC----CCEEEccHHHHHHHHhcccccceEEEeeccCCCCcee
Confidence 999999888888774 78889999999999999999999 9999999999999988752 23444432 22234467
Q ss_pred eeecCCCC-chhhHHHHHHhhhccChhHHHHHHHccC
Q 043276 624 FAFPLHSP-LVHDVSKAILNVTEGDKMKEIEDAWFKK 659 (829)
Q Consensus 624 ~~~~k~sp-l~~~in~~il~l~e~G~~~~~~~~w~~~ 659 (829)
++++|+.| |...||++|..+.++|.. .+.+||+..
T Consensus 243 ~~~~~~~~~L~~~lnkal~~i~~~~~~-~i~~kW~~~ 278 (1197)
T PRK09959 243 FLTRKESVILNEVLNRFVDALTNEVRY-EVSQNWLDT 278 (1197)
T ss_pred EEEcCCcHHHHHHHHHHHHhCCHHHHH-HHHHhccCC
Confidence 88999988 899999999999999887 899999964
No 68
>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=99.66 E-value=8e-15 Score=148.45 Aligned_cols=214 Identities=29% Similarity=0.461 Sum_probs=176.6
Q ss_pred EEEecccccCccceEEEeecCCCCCceEEEeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccEE
Q 043276 310 LRVGVPVKKGFSDFVKVTIDPKTQETSVVGYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDAV 389 (829)
Q Consensus 310 lrv~v~~~~~~~p~~~~~~~~~~~~~~~~G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di~ 389 (829)
|+||+. +.++||.+.+ +++++.|++.|+++.+++++|. ++++++. .|.+++.+|.+|++|++
T Consensus 1 l~i~~~--~~~~p~~~~~-----~~g~~~G~~~~~~~~~~~~~g~--~~~~~~~---------~~~~~~~~l~~g~~D~~ 62 (218)
T cd00134 1 LTVGTA--GTYPPFSFRD-----ANGELTGFDVDLAKAIAKELGV--KVKFVEV---------DWDGLITALKSGKVDLI 62 (218)
T ss_pred CEEecC--CCCCCeeEEC-----CCCCEEeeeHHHHHHHHHHhCC--eEEEEeC---------CHHHHHHHHhcCCcCEE
Confidence 578887 6777888764 4788999999999999999995 5566654 38999999999999999
Q ss_pred EeccccccccceeccccccccccceEEEEEccCCCCCCceeeeccCCHhHHHHHHHHHHHHHHHHHhhhcccCCCCCCCc
Q 043276 390 VGDTTIVFNRSNYVDFTLPYTESGVSMIVPIKDSKKRNAWVFLQPLTWDLWVTSGCFFIFIGFVVWVLEHRVNEDFRGPA 469 (829)
Q Consensus 390 ~~~~~it~~R~~~vdft~p~~~~~~~~vv~~~~~~~~~~~~fl~PF~~~vW~~i~~~~~~~~~v~~~~~~~~~~~~~~~~ 469 (829)
++....+.+|...+.|+.|+.....++++++...
T Consensus 63 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---------------------------------------------- 96 (218)
T cd00134 63 AAGMTITPERAKQVDFSDPYYKSGQVILVKKGSP---------------------------------------------- 96 (218)
T ss_pred eecCcCCHHHHhhccCcccceeccEEEEEECCCC----------------------------------------------
Confidence 9877788899999999999999999999995542
Q ss_pred cCccchhHHHHHHHhhhcCccccccchhHHHHHHHHHHHHHHHHHhHHHHHHHhhcccCCCCCCCHHHHHhCCCcEEEEe
Q 043276 470 RHQVGTSFWFSFSTMVFSQRERVISNLARFVVIVWCFVVLILIQSYTASLTSLLTVDQLQPTITDVNLLIKRGDNVGYQK 549 (829)
Q Consensus 470 ~~~~~~~~~~~~~~l~~~~~~~~~s~~~R~v~~~w~~~~lil~~~YtA~L~s~Lt~~~~~~~I~s~~dL~~~~~~vg~~~ 549 (829)
+.+++|| .|+++++..
T Consensus 97 --------------------------------------------------------------~~~~~dl--~g~~i~~~~ 112 (218)
T cd00134 97 --------------------------------------------------------------IKSVKDL--KGKKVAVQK 112 (218)
T ss_pred --------------------------------------------------------------CCChHHh--CCCEEEEEc
Confidence 3579999 588999998
Q ss_pred CchHHHHHHhcCCCccceeecCChHHHHHHHhcCCcCCceeEEEcchhHHHHHHhcC-CCceEEeCcc--cccCCceeee
Q 043276 550 GSFVLGILKQLGFDERKLVVYNSHEECDELFQKGSANGGIAAAFDEIPYAKLLIGQH-CSKYTMVEPT--FKTAGFGFAF 626 (829)
Q Consensus 550 ~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~~-c~~l~~v~~~--~~~~~~~~~~ 626 (829)
|+....++.+. .....+..+.+.++.+++|.+|+ +|+++.+.....++.++. + .+.++... .....++++.
T Consensus 113 ~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~l~~g~----~d~~~~~~~~~~~~~~~~~~-~l~~~~~~~~~~~~~~~~~~ 186 (218)
T cd00134 113 GSTAEKYLKKA-LPEAKVVSYDDNAEALAALENGR----ADAVIVDEIALAALLKKHPP-ELKIVGPSIDLEPLGFGVAV 186 (218)
T ss_pred CchHHHHHHHh-CCcccEEEeCCHHHHHHHHHcCC----ccEEEeccHHHHHHHHhcCC-CcEEeccccCCCccceEEEE
Confidence 88877777764 33456778889999999999999 999999998888877765 4 36666553 4445567777
Q ss_pred cCCCC-chhhHHHHHHhhhccChhHHHHHHHc
Q 043276 627 PLHSP-LVHDVSKAILNVTEGDKMKEIEDAWF 657 (829)
Q Consensus 627 ~k~sp-l~~~in~~il~l~e~G~~~~~~~~w~ 657 (829)
.++++ +...++++|..+.++|.++.+.+||+
T Consensus 187 ~~~~~~l~~~~~~~l~~~~~~g~~~~i~~~~~ 218 (218)
T cd00134 187 GKDNKELLDAVNKALKELRADGELKKISKKWF 218 (218)
T ss_pred cCCCHHHHHHHHHHHHHHHhCccHHHHHHhhC
Confidence 77774 99999999999999999999999996
No 69
>cd06347 PBP1_ABC_ligand_binding_like_12 Type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine/isoleucine/valine binding protein (LIVBP); however its ligand specificity has not been determined experimentally.
Probab=99.65 E-value=4.8e-15 Score=162.03 Aligned_cols=209 Identities=22% Similarity=0.289 Sum_probs=167.1
Q ss_pred CCChHHHHHHHHHHH-HHcCCcEEEEEEEeC-ccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCC
Q 043276 2 ALNDSSQVGAITAII-KAFGWREAVPIYVDN-QYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQT 79 (829)
Q Consensus 2 ~psD~~q~~ai~~ll-~~fgW~~V~iI~~dd-~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~a 79 (829)
+|++..|+.++++++ ++++|++|++||.++ +|+....+.+.+++++.|+||+....++.+ ..++...+.++++.++
T Consensus 115 ~~~~~~~~~~~~~~~~~~~~~~~v~ii~~~~~~~~~~~~~~~~~~~~~~g~~v~~~~~~~~~--~~d~~~~~~~~~~~~~ 192 (334)
T cd06347 115 CFIDPFQGTVMAKFATENLKAKKAAVLYDNSSDYSKGLAKAFKEAFKKLGGEIVAEETFNAG--DTDFSAQLTKIKAKNP 192 (334)
T ss_pred eCCcHHHHHHHHHHHHHhcCCcEEEEEEeCCCchhHHHHHHHHHHHHHcCCEEEEEEEecCC--CCcHHHHHHHHHhcCC
Confidence 467888999999987 778999999999875 899999999999999999999988887765 3478899999999999
Q ss_pred eEEEEEcChhHHHHHHHHHHHcCccccCeEEEEcCccccccccCCccccccccceEEEEeccC--CChhHHHHHHHHHHh
Q 043276 80 RVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLEPSVTDSMQGVIGVRPYVP--KTKALENFRVRWKRK 157 (829)
Q Consensus 80 rViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t~~~~~~~~~~~~~~~~~~~g~l~~~~~~~--~~~~~~~F~~~w~~~ 157 (829)
++|++.+..+....+++++++.|+ ...|+.++.|..... ........+|++...++.+ ..+..+.|.+.|++.
T Consensus 193 d~i~~~~~~~~~~~~~~~~~~~g~---~~~i~~~~~~~~~~~--~~~~~~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~ 267 (334)
T cd06347 193 DVIFLPGYYTEVGLIAKQARELGI---KVPILGGDGWDSPKL--EEAGGAAAEGVYFTTHFSADDPTPKAKKFVKAYKAK 267 (334)
T ss_pred CEEEEcCchhhHHHHHHHHHHcCC---CCcEEecccccCHHH--HHHHHHHhCCcEEecccCCCCCCHHHHHHHHHHHHH
Confidence 999999999999999999999996 346888887764321 1112345778777666544 357789999999887
Q ss_pred hcccCCCCCccccchhHHHHHHHHHHHHHHHHHhcccCccccCCCCCCCCCCCccccCCCChHHHHHHHhcc-ceecccc
Q 043276 158 FLQENPSLFDAELNIFGLLAYDATSALAVAVEKAGITGFGFDKTNVSSNATDLEAFGISQNGPKLLQALSSI-RFRGLTG 236 (829)
Q Consensus 158 ~~~~~~~~~~~~~~~~~~~~YDAV~~~A~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~L~~~-~f~G~tG 236 (829)
++. .++.++..+|||+++++.|+++++.. .+..+.+.|.+. .|+|++|
T Consensus 268 ~~~--------~~~~~~~~~yda~~~~~~Al~~ag~~-----------------------~~~~v~~~l~~~~~~~g~~G 316 (334)
T cd06347 268 YGK--------EPDAFAALGYDAYYLLADAIERAGST-----------------------DPEAIRDALAKTKDFDGVTG 316 (334)
T ss_pred HCC--------CcchhHHHHHHHHHHHHHHHHHhCCC-----------------------CHHHHHHHHHhCCCccccee
Confidence 753 35678889999999999999986421 257788888754 6999999
Q ss_pred cEEEe-cCccccc
Q 043276 237 DYIFV-DGQLQSS 248 (829)
Q Consensus 237 ~~~F~-~G~~~~~ 248 (829)
.+.|+ +|+....
T Consensus 317 ~v~f~~~g~~~~~ 329 (334)
T cd06347 317 KITIDENGNPVKS 329 (334)
T ss_pred eeEECCCCCcCCC
Confidence 99996 7887643
No 70
>cd06360 PBP1_alkylbenzenes_like Type I periplasmic binding component of active transport systems that are predicted be involved in anaerobic biodegradation of alkylbenzenes such as toluene and ethylbenzene. This group includes the type I periplasmic binding component of active transport systems that are predicted be involved in anaerobic biodegradation of alkylbenzenes such as toluene and ethylbenzene; their substrate specificity is not well characterized, however.
Probab=99.64 E-value=1.1e-14 Score=159.42 Aligned_cols=215 Identities=14% Similarity=0.220 Sum_probs=172.8
Q ss_pred CCChHHHHHHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeE
Q 043276 2 ALNDSSQVGAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRV 81 (829)
Q Consensus 2 ~psD~~q~~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arV 81 (829)
.+++..++..+++++...+|++|++++.++.||+...+.+.+.+++.|+++.....++.. ..++..++.++++.++++
T Consensus 115 ~~~~~~~~~~~~~~l~~~~~~~v~~l~~~~~~g~~~~~~~~~~~~~~G~~v~~~~~~~~~--~~d~~~~v~~~~~~~pd~ 192 (336)
T cd06360 115 SFSNAQWAAPMGKYAADDGYKKVVTVAWDYAFGYEVVEGFKEAFTEAGGKIVKELWVPFG--TSDFASYLAQIPDDVPDA 192 (336)
T ss_pred eCchHHHHHHHHHHHHHcCCCeEEEEeccchhhHHHHHHHHHHHHHcCCEEEEEEecCCC--CcchHHHHHHHHhcCCCE
Confidence 567888999999999989999999999999999999999999999999999887777655 458999999999999999
Q ss_pred EEEEcChhHHHHHHHHHHHcCccccCeEEEEcCccccccccCCccccccccceEEEEeccC--CChhHHHHHHHHHHhhc
Q 043276 82 FILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLEPSVTDSMQGVIGVRPYVP--KTKALENFRVRWKRKFL 159 (829)
Q Consensus 82 iIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t~~~~~~~~~~~~~~~~~~~g~l~~~~~~~--~~~~~~~F~~~w~~~~~ 159 (829)
|++.+....+..+++++.+.|+.. +..|+.++++.... . .....+.++|++...++.+ +.+..+.|.+.|+++++
T Consensus 193 v~~~~~~~~~~~~~~~~~~~g~~~-~~~~~~~~~~~~~~-~-~~~~g~~~~g~~~~~~~~~~~~~~~~~~f~~~y~~~~~ 269 (336)
T cd06360 193 VFVFFAGGDAIKFVKQYDAAGLKA-KIPLIGSGFLTDGT-T-LGAAGEAAEGVITALHYADTLDNPANQAFVKAYRAAYP 269 (336)
T ss_pred EEEecccccHHHHHHHHHHcCCcc-CCeEEecccccCHH-H-HHhhHhhhcCceeccccCCCCCCHHHHHHHHHHHHHhC
Confidence 999988999999999999999632 34566665543211 1 1123355788877666544 46788999999999886
Q ss_pred ccCCCCCccccchhHHHHHHHHHHHHHHHHHhcccCccccCCCCCCCCCCCccccCCCChHHHHHHHhccceecccccEE
Q 043276 160 QENPSLFDAELNIFGLLAYDATSALAVAVEKAGITGFGFDKTNVSSNATDLEAFGISQNGPKLLQALSSIRFRGLTGDYI 239 (829)
Q Consensus 160 ~~~~~~~~~~~~~~~~~~YDAV~~~A~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~L~~~~f~G~tG~~~ 239 (829)
. .++.++..+||++++++.|+++++... ..+..+.++|++..|.|..|.+.
T Consensus 270 ~--------~~~~~~~~~yda~~~~~~A~~~a~~~~---------------------~~~~~v~~al~~~~~~~~~g~~~ 320 (336)
T cd06360 270 D--------TPSVYAVQGYDAGQALILALEAVGGDL---------------------SDGQALIAAMAAAKIDSPRGPFT 320 (336)
T ss_pred C--------CccHHHHHHHHHHHHHHHHHHHhCCCC---------------------CCHHHHHHHHhcCCccCCCcceE
Confidence 4 367789999999999999999985321 02567999999999999999999
Q ss_pred Ee-cCccccceE
Q 043276 240 FV-DGQLQSSAF 250 (829)
Q Consensus 240 F~-~G~~~~~~y 250 (829)
|+ +|+...+.|
T Consensus 321 f~~~~~~~~~~~ 332 (336)
T cd06360 321 LDKAHNPIQDNY 332 (336)
T ss_pred ECCCCCcccceE
Confidence 96 888765443
No 71
>smart00062 PBPb Bacterial periplasmic substrate-binding proteins. bacterial proteins, eukaryotic ones are in PBPe
Probab=99.64 E-value=1.1e-14 Score=147.22 Aligned_cols=216 Identities=29% Similarity=0.516 Sum_probs=179.0
Q ss_pred eEEEecccccCccceEEEeecCCCCCceEEEeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccE
Q 043276 309 KLRVGVPVKKGFSDFVKVTIDPKTQETSVVGYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDA 388 (829)
Q Consensus 309 ~lrv~v~~~~~~~p~~~~~~~~~~~~~~~~G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di 388 (829)
+|+||+. +.++||...+ .++...|+.+|+++.+.+++|. ++++.+. .|..++.++.+|++|+
T Consensus 1 ~l~v~~~--~~~~p~~~~~-----~~g~~~G~~~~~~~~~~~~~g~--~~~~~~~---------~~~~~~~~l~~g~~D~ 62 (219)
T smart00062 1 TLRVGTN--GDYPPFSFAD-----EDGELTGFDVDLAKAIAKELGL--KVEFVEV---------SFDNLLTALKSGKIDV 62 (219)
T ss_pred CEEEEec--CCCCCcEEEC-----CCCCcccchHHHHHHHHHHhCC--eEEEEec---------cHHHHHHHHHCCcccE
Confidence 4789987 6778888754 3667999999999999999985 5555553 4899999999999999
Q ss_pred EEeccccccccceeccccccccccceEEEEEccCCCCCCceeeeccCCHhHHHHHHHHHHHHHHHHHhhhcccCCCCCCC
Q 043276 389 VVGDTTIVFNRSNYVDFTLPYTESGVSMIVPIKDSKKRNAWVFLQPLTWDLWVTSGCFFIFIGFVVWVLEHRVNEDFRGP 468 (829)
Q Consensus 389 ~~~~~~it~~R~~~vdft~p~~~~~~~~vv~~~~~~~~~~~~fl~PF~~~vW~~i~~~~~~~~~v~~~~~~~~~~~~~~~ 468 (829)
+++....+.+|...+.|+.|+...+..+++++...
T Consensus 63 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--------------------------------------------- 97 (219)
T smart00062 63 VAAGMTITPERAKQVDFSDPYYKSGQVILVRKDSP--------------------------------------------- 97 (219)
T ss_pred EeccccCCHHHHhheeeccceeeceeEEEEecCCC---------------------------------------------
Confidence 99877778888888999999999999999885431
Q ss_pred ccCccchhHHHHHHHhhhcCccccccchhHHHHHHHHHHHHHHHHHhHHHHHHHhhcccCCCCCCCHHHHHhCCCcEEEE
Q 043276 469 ARHQVGTSFWFSFSTMVFSQRERVISNLARFVVIVWCFVVLILIQSYTASLTSLLTVDQLQPTITDVNLLIKRGDNVGYQ 548 (829)
Q Consensus 469 ~~~~~~~~~~~~~~~l~~~~~~~~~s~~~R~v~~~w~~~~lil~~~YtA~L~s~Lt~~~~~~~I~s~~dL~~~~~~vg~~ 548 (829)
+.+++|| .|+++++.
T Consensus 98 ---------------------------------------------------------------~~~~~dL--~g~~i~~~ 112 (219)
T smart00062 98 ---------------------------------------------------------------IKSLEDL--KGKKVAVV 112 (219)
T ss_pred ---------------------------------------------------------------CCChHHh--CCCEEEEe
Confidence 5889999 58899999
Q ss_pred eCchHHHHHHhcCCCccceeecCChHHHHHHHhcCCcCCceeEEEcchhHHHHHHhcCC-CceEEeCccccc-CCceeee
Q 043276 549 KGSFVLGILKQLGFDERKLVVYNSHEECDELFQKGSANGGIAAAFDEIPYAKLLIGQHC-SKYTMVEPTFKT-AGFGFAF 626 (829)
Q Consensus 549 ~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~~c-~~l~~v~~~~~~-~~~~~~~ 626 (829)
.|+....++... .+..++..+.+..+.+.+|.+|+ +|+++...+.+.+...+.- ..+.++...... ..+++++
T Consensus 113 ~g~~~~~~~~~~-~~~~~~~~~~~~~~~~~~l~~g~----~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 187 (219)
T smart00062 113 AGTTGEELLKKL-YPEAKIVSYDSQAEALAALKAGR----ADAAVADAPALAALVKQHGLPELKIVGDPLDTPEGYAFAV 187 (219)
T ss_pred cCccHHHHHHHh-CCCceEEEcCCHHHHHHHhhcCc----ccEEEeccHHHHHHHHhcCCCceeeccCCCCCCcceEEEE
Confidence 998888888765 34456778888899999999999 9999999988888776651 246666655544 7889999
Q ss_pred cCCCC-chhhHHHHHHhhhccChhHHHHHHHc
Q 043276 627 PLHSP-LVHDVSKAILNVTEGDKMKEIEDAWF 657 (829)
Q Consensus 627 ~k~sp-l~~~in~~il~l~e~G~~~~~~~~w~ 657 (829)
+++++ +.+.++++|..+.++|.++++.++|+
T Consensus 188 ~~~~~~~~~~~~~~l~~~~~~~~~~~i~~~~~ 219 (219)
T smart00062 188 RKGDPELLDKINKALKELKADGTLKKIYEKWF 219 (219)
T ss_pred ECCCHHHHHHHHHHHHHHHhCchHHHHHhccC
Confidence 99987 99999999999999999999999985
No 72
>cd06340 PBP1_ABC_ligand_binding_like_6 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine-isoleucine-valine-binding protein (LIVBP); however their ligand specificity has not been determined experimentally.
Probab=99.63 E-value=9.3e-15 Score=160.57 Aligned_cols=211 Identities=15% Similarity=0.160 Sum_probs=165.4
Q ss_pred CCCChHHHHHHHHHHHHHcC------CcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHh
Q 043276 1 GALNDSSQVGAITAIIKAFG------WREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKL 74 (829)
Q Consensus 1 t~psD~~q~~ai~~ll~~fg------W~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~l 74 (829)
+.|++..|+.++++++.+++ |++|++|+.|++||....+.+.+.+++.|++|+..+.++.. ..++..++.+|
T Consensus 118 ~~p~~~~~~~~~~~~l~~~~~~~~~~~~~v~~l~~~~~~g~~~~~~~~~~~~~~G~~vv~~~~~~~~--~~d~~~~i~~l 195 (347)
T cd06340 118 ITPHDGMFTRDMFDFLKDLNEKTGKPLKTVALVHEDTEFGTSVAEAIKKFAKERGFEIVEDISYPAN--ARDLTSEVLKL 195 (347)
T ss_pred cCCChHHHHHHHHHHHHHhhHhcCCCCceEEEEecCchHhHHHHHHHHHHHHHcCCEEEEeeccCCC--CcchHHHHHHH
Confidence 46899999999999998874 59999999999999999999999999999999988888765 45899999999
Q ss_pred hcCCCeEEEEEcChhHHHHHHHHHHHcCccccCeEEEEcCccccccccCCccccccccceEEEEeccCC-ChhHHHHHHH
Q 043276 75 FTMQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLEPSVTDSMQGVIGVRPYVPK-TKALENFRVR 153 (829)
Q Consensus 75 k~~~arViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t~~~~~~~~~~~~~~~~~~~g~l~~~~~~~~-~~~~~~F~~~ 153 (829)
++.++++|++.+....+..+++++++.|+.. ..++...++.... .. .....+..+|++...++.+. .+..+.|.++
T Consensus 196 ~~~~~d~v~~~~~~~~~~~~~~~~~~~G~~~-~~~~~~~~~~~~~-~~-~~~~g~~~~g~~~~~~~~~~~~~~~~~f~~~ 272 (347)
T cd06340 196 KAANPDAILPASYTNDAILLVRTMKEQRVEP-KAVYSVGGGAEDP-SF-VKALGKDAEGILTRNEWSDPKDPMAKDLNKR 272 (347)
T ss_pred HhcCCCEEEEcccchhHHHHHHHHHHcCCCC-cEEEecCCCcCcH-HH-HHHhhHhhheEEeccccCCCCChHHHHHHHH
Confidence 9999999999999999999999999999742 2333222222211 11 11123456888887766553 6788899999
Q ss_pred HHHhhcccCCCCCccccchhHHHHHHHHHHHHHHHHHhcccCccccCCCCCCCCCCCccccCCCChHHHH--HHHhccce
Q 043276 154 WKRKFLQENPSLFDAELNIFGLLAYDATSALAVAVEKAGITGFGFDKTNVSSNATDLEAFGISQNGPKLL--QALSSIRF 231 (829)
Q Consensus 154 w~~~~~~~~~~~~~~~~~~~~~~~YDAV~~~A~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~--~~L~~~~f 231 (829)
|++.++. .++.++...||+++++++|+++++..+ +..+. ..|+...+
T Consensus 273 y~~~~~~--------~~~~~~~~~Y~a~~~l~~A~~~ag~~~-----------------------~~~v~~~~~~~~~~~ 321 (347)
T cd06340 273 FKARFGV--------DLSGNSARAYTAVLVIADALERAGSAD-----------------------PEKIRDLAALASTSG 321 (347)
T ss_pred HHHHhCC--------CCChHHHHHHHHHHHHHHHHHHhcCCC-----------------------HHHHHHHHHhccCCc
Confidence 9998864 356789999999999999999986422 45666 47777776
Q ss_pred e---cccccEEEe-cCcccc
Q 043276 232 R---GLTGDYIFV-DGQLQS 247 (829)
Q Consensus 232 ~---G~tG~~~F~-~G~~~~ 247 (829)
. +..|.+.|+ +|+..+
T Consensus 322 ~~~~~~~g~~~f~~~g~~~~ 341 (347)
T cd06340 322 EDLIMPYGPIKFDAKGQNTN 341 (347)
T ss_pred cccccCCCCeeECCCCCccc
Confidence 5 467899996 999754
No 73
>cd06355 PBP1_FmdD_like Periplasmic component (FmdD) of an active transport system for short-chain amides and urea (FmdDEF). This group includes the periplasmic component (FmdD) of an active transport system for short-chain amides and urea (FmdDEF), found in Methylophilus methylotrophus, and its homologs from other bacteria. FmdD, a type I periplasmic binding protein, is induced by short-chain amides and urea and repressed by excess ammonia, while FmdE and FmdF are hydrophobic transmembrane proteins. FmdDEF is predicted to be an ATP-dependent transporter and closely resembles the periplasmic binding protein and the two transmembrane proteins present in various hydrophobic amino acid-binding transport systems.
Probab=99.61 E-value=5e-14 Score=154.78 Aligned_cols=222 Identities=16% Similarity=0.126 Sum_probs=168.6
Q ss_pred CCChHHHHHHHHHHHH-HcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCe
Q 043276 2 ALNDSSQVGAITAIIK-AFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTR 80 (829)
Q Consensus 2 ~psD~~q~~ai~~ll~-~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~ar 80 (829)
.+++..++.++++.+. ..|+++|++|+.|++||....+.+.+.+++.|++|+....++.+ ..|+..++.++++.+++
T Consensus 113 ~~~~~~~~~~~~~~~~~~~g~k~vaii~~d~~~g~~~~~~~~~~~~~~G~~vv~~~~~~~~--~~D~~~~v~~l~~~~pd 190 (348)
T cd06355 113 GAAPNQQIIPAVDWLMSNKGGKRFYLVGSDYVYPRTANKILKAQLESLGGEVVGEEYLPLG--HTDFQSIINKIKAAKPD 190 (348)
T ss_pred CCChHHhHHHHHHHHHhccCCCeEEEECCcchHHHHHHHHHHHHHHHcCCeEEeeEEecCC--hhhHHHHHHHHHHhCCC
Confidence 4567778888888775 56899999999999999999999999999999999998888765 56899999999999999
Q ss_pred EEEEEcChhHHHHHHHHHHHcCccccCeEEEEcCccccccccCCccccccccceEEEEec--cCCChhHHHHHHHHHHhh
Q 043276 81 VFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLEPSVTDSMQGVIGVRPY--VPKTKALENFRVRWKRKF 158 (829)
Q Consensus 81 ViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t~~~~~~~~~~~~~~~~~~~g~l~~~~~--~~~~~~~~~F~~~w~~~~ 158 (829)
+|++......+..+++++++.|+......++.+ ++... .......+.+.|+++...+ ..+.+..+.|.+.++++|
T Consensus 191 ~v~~~~~~~~~~~~~~~~~~~G~~~~~~~~~~~-~~~~~--~~~~~g~~~~~g~~~~~~~~~~~~~~~~~~f~~~y~~~~ 267 (348)
T cd06355 191 VVVSTVNGDSNVAFFKQLKAAGITASKVPVLSF-SVAEE--ELRGIGPENLAGHYAAWNYFQSVDTPENKKFVAAFKARY 267 (348)
T ss_pred EEEEeccCCchHHHHHHHHHcCCCccCCeeEEc-cccHH--HHhhcChHhhcCCEEeccchhhcCCHHHHHHHHHHHHHc
Confidence 999999988999999999999975433445543 32211 1111112346677664432 235677889999999887
Q ss_pred cccCCCCCccccchhHHHHHHHHHHHHHHHHHhcccCccccCCCCCCCCCCCccccCCCChHHHHHHHhccceecccccE
Q 043276 159 LQENPSLFDAELNIFGLLAYDATSALAVAVEKAGITGFGFDKTNVSSNATDLEAFGISQNGPKLLQALSSIRFRGLTGDY 238 (829)
Q Consensus 159 ~~~~~~~~~~~~~~~~~~~YDAV~~~A~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~L~~~~f~G~tG~~ 238 (829)
+... .++.++..+|||+++++.|+++++..+ +..|.++|++..|.+..|.+
T Consensus 268 g~~~------~~~~~a~~~Y~a~~~~~~Al~~ag~~~-----------------------~~~i~~aL~~~~~~~~~g~~ 318 (348)
T cd06355 268 GQDR------VTNDPMEAAYIGVYLWKQAVEKAGSFD-----------------------VDKVRAALPGQSFDAPEGPV 318 (348)
T ss_pred CCCC------CCCcHHHHHHHHHHHHHHHHHHhCCCC-----------------------HHHHHHHhccCcccCCCcce
Confidence 6421 234567889999999999999985321 57899999999999999999
Q ss_pred EEe--cCccccceEEEEEcc-CC
Q 043276 239 IFV--DGQLQSSAFEIINVN-NG 258 (829)
Q Consensus 239 ~F~--~G~~~~~~y~I~n~~-~g 258 (829)
.|+ +++.. ..+.|..++ +|
T Consensus 319 ~f~~~~~~~~-~~~~i~~~~~~g 340 (348)
T cd06355 319 TVDPANHHLW-KPVRIGRIQADG 340 (348)
T ss_pred EeecCCCeee-eeeEEEEEcCCC
Confidence 995 44442 455566665 44
No 74
>cd06344 PBP1_ABC_ligand_binding_like_9 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. Members of this group are sequence-similar to members of the family of ABC-type hydrophobic amino acid transporters, such as leucine/isoleucine/valine binding protein (LIVBP); however their ligand specificity has not been determined experimentally.
Probab=99.60 E-value=2.3e-14 Score=156.57 Aligned_cols=210 Identities=18% Similarity=0.189 Sum_probs=162.8
Q ss_pred CCCChHHHHHHHHHHHHHcC-CcEEEEEEEeCc-cccchHHHHHHHHHh-CCceeeeEEecCCCCChhHHHHHHHHhhcC
Q 043276 1 GALNDSSQVGAITAIIKAFG-WREAVPIYVDNQ-YGEELIPSLTDALQA-IDTRVPYRSVISPLATDDQIEKELYKLFTM 77 (829)
Q Consensus 1 t~psD~~q~~ai~~ll~~fg-W~~V~iI~~dd~-yG~~~~~~l~~~l~~-~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~ 77 (829)
+.|++..++.++++++++++ |++|++||.|++ ||+...+.+.+.+++ .|.+|.....++. .+.++..++.++++.
T Consensus 113 ~~~~~~~~~~~~~~~~~~~~~~~~v~~i~~~~~~~g~~~~~~~~~~~~~~~g~~v~~~~~~~~--~~~~~~~~v~~i~~~ 190 (332)
T cd06344 113 TVPSNAVAARALAKYLKKKNKIKKVAIFYNSTSPYSQSLKQEFTSALLERGGGIVVTPCDLSS--PDFNANTAVSQAINN 190 (332)
T ss_pred eCCCcHHHHHHHHHHHHhhcCCCeEEEEeCCCchHhHHHHHHHHHHHHHhcCCeeeeeccCCC--CCCCHHHHHHHHHhc
Confidence 46889999999999998876 999999998876 999999999999999 5999876544432 344678899999999
Q ss_pred CCeEEEEEcChhHHHHHHHHHHHcCccccCeEEEEcCccccccccCCccccccccceEEEEeccCCChhHHHHHHHHHHh
Q 043276 78 QTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLEPSVTDSMQGVIGVRPYVPKTKALENFRVRWKRK 157 (829)
Q Consensus 78 ~arViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t~~~~~~~~~~~~~~~~~~~g~l~~~~~~~~~~~~~~F~~~w~~~ 157 (829)
++++|++.+.......+++++.+.|. ...|+.++++... +... .....++|+++..++.+..+..++|.+.|+++
T Consensus 191 ~~d~v~~~~~~~~~~~~~~~~~~~~~---~~~i~~~~~~~~~-~~~~-~~~~~~~G~~~~~~~~~~~~~~~~f~~~~~~~ 265 (332)
T cd06344 191 GATVLVLFPDTDTLDKALEVAKANKG---RLTLLGGDSLYTP-DTLL-DGGKDLEGLVLAVPWHPLASPNSPFAKLAQQL 265 (332)
T ss_pred CCCEEEEeCChhHHHHHHHHHHhcCC---CceEEecccccCH-HHHH-hchhhhcCeEEEEecccccccchHHHHHHHHH
Confidence 99999999988888888999888762 3445555555432 1111 12345788888888777777789999999998
Q ss_pred hcccCCCCCccccchhHHHHHHHHHHHHHHHHHhcccCccccCCCCCCCCCCCccccCCCChHHHH-HHHhccceecccc
Q 043276 158 FLQENPSLFDAELNIFGLLAYDATSALAVAVEKAGITGFGFDKTNVSSNATDLEAFGISQNGPKLL-QALSSIRFRGLTG 236 (829)
Q Consensus 158 ~~~~~~~~~~~~~~~~~~~~YDAV~~~A~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~-~~L~~~~f~G~tG 236 (829)
++. .++.++..+||+++++++|+++++..+ +..+. ..+.+..|.|..|
T Consensus 266 ~~~--------~~~~~a~~~Yda~~~l~~A~~~ag~~~-----------------------~~~~~~~~~~~~~~~g~~g 314 (332)
T cd06344 266 WGG--------DVSWRTATAYDATKALIAALSQGPTRE-----------------------GVQQVELSLRNFSVQGATG 314 (332)
T ss_pred hcC--------CchHHHHhHHHHHHHHHHHHHhCCChh-----------------------hhhhhhhhcccccccCCCc
Confidence 865 356789999999999999999875332 22233 5667778999999
Q ss_pred cEEEe-cCccccc
Q 043276 237 DYIFV-DGQLQSS 248 (829)
Q Consensus 237 ~~~F~-~G~~~~~ 248 (829)
++.|+ +||+...
T Consensus 315 ~i~f~~~g~~~~~ 327 (332)
T cd06344 315 KIKFLPSGDRNGQ 327 (332)
T ss_pred eeEeCCCCcccCc
Confidence 99996 9998643
No 75
>cd06330 PBP1_Arsenic_SBP_like Periplasmic solute-binding domain of active transport proteins. Periplasmic solute-binding domain of active transport proteins found in bacteria and Archaea that is predicted to be involved in the efflux of toxic compounds. Members of this subgroup include proteins from Herminiimonas arsenicoxydans, which is resistant to arsenic and various heavy metals such as cadmium and zinc. Moreover, they show significant sequence similarity to the cluster of AmiC and active transport systems for short-chain amides and urea (FmdDEF), and thus are likely to exhibit a ligand-binding mode similar to that of the amide sensor protein AmiC from Pseudomonas aeruginosa.
Probab=99.59 E-value=2.3e-14 Score=157.57 Aligned_cols=209 Identities=21% Similarity=0.167 Sum_probs=160.7
Q ss_pred CCCChHHHHHHHHHHHHHcC--CcEEEEEEEeCccccchHHHHHHHHHhCCce--eeeEEecCCCCChhHHHHHHHHhhc
Q 043276 1 GALNDSSQVGAITAIIKAFG--WREAVPIYVDNQYGEELIPSLTDALQAIDTR--VPYRSVISPLATDDQIEKELYKLFT 76 (829)
Q Consensus 1 t~psD~~q~~ai~~ll~~fg--W~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~--I~~~~~i~~~~~~~~~~~~l~~lk~ 76 (829)
+.|++..|..++++++++++ |++|++|+.|++||....+.+.+.+++.|++ +.....++.. ..++..++.+|++
T Consensus 116 ~~~~~~~~~~~~~~~~~~~~~~~~~v~~l~~~~~~g~~~~~~~~~~~~~~g~~~~~v~~~~~~~~--~~d~~~~v~~i~~ 193 (346)
T cd06330 116 TRNSTIMDAVAGALYAAKLDKKAKTWATINPDYAYGQDAWADFKAALKRLRPDVEVVSEQWPKLG--APDYGSEITALLA 193 (346)
T ss_pred ecCChHHHHHHHHHHHHHhCcCccEEEEECCchHHHHHHHHHHHHHHHHhCCCCeecccccCCCC--CcccHHHHHHHHh
Confidence 46889999999999998874 9999999999999999999999999998655 4433333333 4588999999999
Q ss_pred CCCeEEEEEcChhHHHHHHHHHHHcCccccCeEEEEcCccccccccCCccccccccceEEEEe--ccC--CChhHHHHHH
Q 043276 77 MQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLEPSVTDSMQGVIGVRP--YVP--KTKALENFRV 152 (829)
Q Consensus 77 ~~arViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t~~~~~~~~~~~~~~~~~~~g~l~~~~--~~~--~~~~~~~F~~ 152 (829)
.++++|++++.......+++++++.|+.. +..|+.+++....+. .......+|++.... ... ..+..+.|.+
T Consensus 194 ~~~d~ii~~~~~~~~~~~~~~~~~~g~~~-~~~~~~~~~~~~~~~---~~~~~~~~g~~~~~~~~~~~~~~~~~~~~f~~ 269 (346)
T cd06330 194 AKPDAIFSSLWGGDLVTFVRQANARGLFD-GTTVVLTLTGAPELA---PLGDEMPEGVIIGGRGPYFIPPDTPENKAFVD 269 (346)
T ss_pred cCCCEEEEecccccHHHHHHHHHhcCccc-CceEEeeccchhhhh---hhhcccCCceEEeccccCCCCCCChHHHHHHH
Confidence 99999999999899999999999999743 667887765443211 112344567654332 111 4678899999
Q ss_pred HHHHhhcccCCCCCccccchhHHHHHHHHHHHHHHHHHhcccCccccCCCCCCCCCCCccccCCCChHHHHHHHhcccee
Q 043276 153 RWKRKFLQENPSLFDAELNIFGLLAYDATSALAVAVEKAGITGFGFDKTNVSSNATDLEAFGISQNGPKLLQALSSIRFR 232 (829)
Q Consensus 153 ~w~~~~~~~~~~~~~~~~~~~~~~~YDAV~~~A~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~L~~~~f~ 232 (829)
+|+++++. .++.++..+||++.+++.|+++++..... . ....+.++|++++|.
T Consensus 270 ~~~~~~g~--------~p~~~~~~~y~a~~~l~~a~~~a~~~~~~------------------~-~~~~v~~al~~~~~~ 322 (346)
T cd06330 270 AYQEKYGD--------YPTYGAYGAYQAVMALAAAVEKAGATDGG------------------A-PPEQIAAALEGLSFE 322 (346)
T ss_pred HHHHHHCC--------CCChHHHHHHHHHHHHHHHHHHhcCCCCC------------------C-cHHHHHHHHcCCCcc
Confidence 99998863 35567889999999999999998643210 0 015699999999999
Q ss_pred cccccEEEec
Q 043276 233 GLTGDYIFVD 242 (829)
Q Consensus 233 G~tG~~~F~~ 242 (829)
|+.|.+.|+.
T Consensus 323 ~~~G~~~f~~ 332 (346)
T cd06330 323 TPGGPITMRA 332 (346)
T ss_pred CCCCceeeec
Confidence 9999999963
No 76
>cd06329 PBP1_SBP_like_3 Periplasmic solute-binding domain of active transport proteins. Periplasmic solute-binding domain of active transport proteins found in bacteria and Archaea. Members of this group are initial receptors in the process of active transport across cellular membrane, but their substrate specificities are not known in detail. However, they closely resemble the group of AmiC and active transport systems for short-chain amides and urea (FmdDEF), and thus are likely to exhibit a ligand-binding mode similar to that of the amide sensor protein AmiC from Pseudomonas aeruginosa. Moreover, this binding domain has high sequence identity to the family of hydrophobic amino acid transporters (HAAT), and thus it may also be involved in transport of amino acids.
Probab=99.59 E-value=5e-14 Score=154.49 Aligned_cols=207 Identities=18% Similarity=0.144 Sum_probs=164.7
Q ss_pred CCCChHHHHHHHHHHHHHcC-CcEEEEEEEeCccccchHHHHHHHHHh--CCceeeeEEecCCCCChhHHHHHHHHhhcC
Q 043276 1 GALNDSSQVGAITAIIKAFG-WREAVPIYVDNQYGEELIPSLTDALQA--IDTRVPYRSVISPLATDDQIEKELYKLFTM 77 (829)
Q Consensus 1 t~psD~~q~~ai~~ll~~fg-W~~V~iI~~dd~yG~~~~~~l~~~l~~--~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~ 77 (829)
+.|++..|+.++++++...+ |++|++|+.|+.||+...+.+.+.+++ .|++|+....++.+. ..++..++.++++.
T Consensus 122 ~~~~~~~~~~~l~~~~~~~~~~k~v~i~~~~~~~g~~~~~~~~~~~~~~~~G~~vv~~~~~~~~~-~~d~~~~i~~l~~~ 200 (342)
T cd06329 122 TDANTDMKMEALASYIKKQPDGKKVYLINQDYSWGQDVAAAFKAMLAAKRPDIQIVGEDLHPLGK-VKDFSPYVAKIKAS 200 (342)
T ss_pred ecCChHHHHHHHHHHHHhcccCceEEEEeCChHHHHHHHHHHHHHHHhhcCCcEEeceeccCCCC-CCchHHHHHHHHHc
Confidence 46899999999999998776 999999999999999999999999999 999999877777653 15789999999999
Q ss_pred CCeEEEEEcChhHHHHHHHHHHHcCccccCeEEEEcCccccccccCCccccccccceEEEEeccC--CChhHHHHHHHHH
Q 043276 78 QTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLEPSVTDSMQGVIGVRPYVP--KTKALENFRVRWK 155 (829)
Q Consensus 78 ~arViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t~~~~~~~~~~~~~~~~~~~g~l~~~~~~~--~~~~~~~F~~~w~ 155 (829)
++++|++......+..+++++++.|+.. .|+....+... ......+..+|++....+.+ .++..++|.++|+
T Consensus 201 ~~d~v~~~~~~~~~~~~~~~~~~~g~~~---~~~~~~~~~~~---~~~~~g~~~~g~~~~~~~~~~~~~~~~~~f~~~~~ 274 (342)
T cd06329 201 GADTVITGNWGNDLLLLVKQAADAGLKL---PFYTPYLDQPG---NPAALGEAGLGLVVAVAYWHPNDTPANRAFVEAFK 274 (342)
T ss_pred CCCEEEEcccCchHHHHHHHHHHcCCCc---eEEeccccchh---HHHhhcccccceEEeeeccCCCCCHHHHHHHHHHH
Confidence 9999999988888999999999999732 34544433221 11123345678776655433 3678899999999
Q ss_pred HhhcccCCCCCccccchhHHHHHHHHHHHHHHHHHhcccCccccCCCCCCCCCCCccccCCCChHHHHHHHhccceeccc
Q 043276 156 RKFLQENPSLFDAELNIFGLLAYDATSALAVAVEKAGITGFGFDKTNVSSNATDLEAFGISQNGPKLLQALSSIRFRGLT 235 (829)
Q Consensus 156 ~~~~~~~~~~~~~~~~~~~~~~YDAV~~~A~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~L~~~~f~G~t 235 (829)
+.++. .++.++..+||++++++.|+++++.. ++..+.++|++++|+|..
T Consensus 275 ~~~~~--------~~~~~~~~~y~~~~~~~~a~~~ag~~-----------------------~~~~v~~al~~~~~~~~~ 323 (342)
T cd06329 275 AKYGR--------VPDYYEGQAYNGIQMLADAIEKAGST-----------------------DPEAVAKALEGMEVDTPV 323 (342)
T ss_pred HHhCC--------CCCchHHHHHHHHHHHHHHHHHhCCC-----------------------CHHHHHHHHhCCccccCC
Confidence 88764 35668889999999999999986432 157899999999999999
Q ss_pred ccEEEe--cCcc
Q 043276 236 GDYIFV--DGQL 245 (829)
Q Consensus 236 G~~~F~--~G~~ 245 (829)
|.+.|+ +.+.
T Consensus 324 g~~~~~~~~~~~ 335 (342)
T cd06329 324 GPVTMRASDHQA 335 (342)
T ss_pred CCeEEcccCcch
Confidence 999995 4443
No 77
>cd06336 PBP1_ABC_ligand_binding_like_3 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. This group includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. Members of this group are sequence-similar to members of the family of ABC-type hydrophobic amino acid transporters (HAAT), such as leucine-isoleucine-valine-binding protein (LIVBP); however their ligand specificity has not been determined experimentally.
Probab=99.59 E-value=3e-14 Score=156.57 Aligned_cols=214 Identities=18% Similarity=0.172 Sum_probs=165.3
Q ss_pred CCCChHHHHHHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCe
Q 043276 1 GALNDSSQVGAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTR 80 (829)
Q Consensus 1 t~psD~~q~~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~ar 80 (829)
+.|++..++.+++++++..+|++|++|+.|++||+...+.+.+.+++.|++|+....++.+ ..|+...+.+|++++++
T Consensus 118 ~~~~~~~~~~~~~~~~~~~~~~~v~il~~d~~~g~~~~~~~~~~l~~~G~~vv~~~~~~~~--~~D~s~~i~~i~~~~~d 195 (347)
T cd06336 118 VPPIYNVYGVPFLAYAKKPGGKKVALLGPNDAYGQPWVAAYKAAWEAAGGKVVSEEPYDPG--TTDFSPIVTKLLAEKPD 195 (347)
T ss_pred ecCCchhHHHHHHHHHhhcCCceEEEEccCCchhHHHHHHHHHHHHHcCCEEeeecccCCC--CcchHHHHHHHHhcCCC
Confidence 4688999999999999889999999999999999999999999999999999988888765 45899999999999999
Q ss_pred EEEEEcChh-HHHHHHHHHHHcCccccCeEEEEcCccccccccCCccccccccceEEEEeccC----CChhHHHHHHHHH
Q 043276 81 VFILHMLPS-LGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLEPSVTDSMQGVIGVRPYVP----KTKALENFRVRWK 155 (829)
Q Consensus 81 ViIv~~~~~-~~~~i~~~a~~~gm~~~~~vwI~t~~~~~~~~~~~~~~~~~~~g~l~~~~~~~----~~~~~~~F~~~w~ 155 (829)
+|++++... .+..++++++++|+... ..++....... .......+.++|++...+..+ ..+..++|.++|+
T Consensus 196 ~v~~~~~~~~~~~~~~~~~~~~g~~~~-~~~~~~~~~~~---~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~f~~~~~ 271 (347)
T cd06336 196 VIFLGGPSPAPAALVIKQARELGFKGG-FLSCTGDKYDE---LLVATGADFMEGVYFQFPDVDDPALAFPRAKAFVEEYK 271 (347)
T ss_pred EEEEcCCCchHHHHHHHHHHHcCCCcc-EEeccCCCchH---HHHHhcHHhhCceEEEeecccccccCCHHHHHHHHHHH
Confidence 999999988 99999999999997432 22222212111 011112345788888776654 4677889999999
Q ss_pred HhhcccCCCCCccccchhHHHHHHHHHHHHHHHHHhcccCccccCCCCCCCCCCCccccCCCChHHHHHHHh-------c
Q 043276 156 RKFLQENPSLFDAELNIFGLLAYDATSALAVAVEKAGITGFGFDKTNVSSNATDLEAFGISQNGPKLLQALS-------S 228 (829)
Q Consensus 156 ~~~~~~~~~~~~~~~~~~~~~~YDAV~~~A~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~L~-------~ 228 (829)
++++. .++.++..+||++.+++.|+++++..+. ...+...++ .
T Consensus 272 ~~~~~--------~p~~~~~~~y~~~~~~~~Al~~ag~~~~----------------------~~~~~~~~~~~~~~~~~ 321 (347)
T cd06336 272 KRYGE--------PPNSEAAVSYDAVYILKAAMEAAGSVDD----------------------TAAVAALAAMLGVGKPA 321 (347)
T ss_pred HHHCC--------CCcHHHHHHHHHHHHHHHHHHhcCCCCc----------------------HHHHHHHhhccCCCcCc
Confidence 98865 2567889999999999999999764321 122222232 3
Q ss_pred cceecccccEEEe-cCccccceE
Q 043276 229 IRFRGLTGDYIFV-DGQLQSSAF 250 (829)
Q Consensus 229 ~~f~G~tG~~~F~-~G~~~~~~y 250 (829)
..|.+..|.+.|+ +||...+.+
T Consensus 322 ~~~~~~~g~~~~~~~~~~~~~~~ 344 (347)
T cd06336 322 FGYARWWGKELFGVNGALVGPWP 344 (347)
T ss_pred cccccccccccccCCCccccCcc
Confidence 5688999999996 999865443
No 78
>cd06369 PBP1_GC_C_enterotoxin_receptor Ligand-binding domain of the membrane guanylyl cyclase C. Ligand-binding domain of the membrane guanylyl cyclase C (GC-C or StaR). StaR is a key receptor for the STa (Escherichia coli Heat Stable enterotoxin), a potent stimulant of intestinal chloride and bicarbonate secretion that cause acute secretory diarrhea. The catalytic domain of the STa/guanylin receptor type membrane GC is highly similar to those of the natriuretic peptide receptor (NPR) type and sensory organ-specific type membrane GCs (GC-D, GC-E and GC-F). The GC-C receptor is mainly expressed in the intestine of most vertebrates, but is also found in the kidney and other organs. Moreover, GC-C is activated by guanylin and uroguanylin, endogenous peptide ligands synthesized in the intestine and kidney. Consequently, the receptor activation results in increased cGMP levels and phosphorylation of the CFTR chloride channel and secretion.
Probab=99.59 E-value=1.1e-13 Score=145.26 Aligned_cols=226 Identities=12% Similarity=0.141 Sum_probs=164.1
Q ss_pred CCChHHHHHHHHHHH------HHcCCcEEEEEEEeCccc---cchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHH
Q 043276 2 ALNDSSQVGAITAII------KAFGWREAVPIYVDNQYG---EELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELY 72 (829)
Q Consensus 2 ~psD~~q~~ai~~ll------~~fgW~~V~iI~~dd~yG---~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~ 72 (829)
.|+-...+..+.++. ++++|+..- ||.+++-- ---+.+|....+..+..+.+...... ++++.+.++
T Consensus 128 ~pparK~~~~~~~f~~~~~~~~~~~W~~ay-vyk~~~~~edCf~~i~al~a~~~~f~~~~~~~~~l~~---~~~~~~il~ 203 (380)
T cd06369 128 LPPARKISDFFVDFWKEKNFPKKPKWETAY-VYKKQENTEDCFWYINALEAGVAYFSSALKFKELLRT---EEELQKLLT 203 (380)
T ss_pred CchHHHHHHHHHHHHhcccccCCCCCceeE-EEcCCCCccceeeEhHhhhhhhhhhhhcccceeeecC---chhHHHHHH
Confidence 356666777788888 599998554 89776432 23366666666666666665555432 357777887
Q ss_pred HhhcCCCeEEEEEcChhHHHHHHHHHHHcCccccCeEEEEcCccccccccCCccccccccceEEEEeccCCChhHHHHHH
Q 043276 73 KLFTMQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLEPSVTDSMQGVIGVRPYVPKTKALENFRV 152 (829)
Q Consensus 73 ~lk~~~arViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t~~~~~~~~~~~~~~~~~~~g~l~~~~~~~~~~~~~~F~~ 152 (829)
.++ .++||||+|++++..+.++.. ++...+|++|..|.+..... .+....++++.++.+++..|+.+..+++
T Consensus 204 ~~~-~~sRIiImCG~p~~ir~lm~~----~~~~gDYVf~~IDlF~~sy~-~d~~a~~amqsVLvIT~~~p~~~~~~~~-- 275 (380)
T cd06369 204 DKN-RKSNVIIMCGTPEDIVNLKGD----RAVAEDIVIILIDLFNDVYY-ENTTSPPYMRNVLVLTLPPRNSTNNSSF-- 275 (380)
T ss_pred Hhc-cCccEEEEeCCHHHHHHHHhc----CccCCCEEEEEEecccchhc-cCcchHHHHhceEEEecCCCCCcccccC--
Confidence 765 788999999999999999886 33346999999997754321 2234567899999999888766544331
Q ss_pred HHHHhhcccCCCCCccccc-hhHHHHHHHHHHHHHHHHHhcccCccccCCCCCCCCCCCccccCCCChHHHHHHHhccce
Q 043276 153 RWKRKFLQENPSLFDAELN-IFGLLAYDATSALAVAVEKAGITGFGFDKTNVSSNATDLEAFGISQNGPKLLQALSSIRF 231 (829)
Q Consensus 153 ~w~~~~~~~~~~~~~~~~~-~~~~~~YDAV~~~A~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~L~~~~f 231 (829)
..+ +..+. .|++..||||.++|+||++....... ..+..+.+.++|.+|
T Consensus 276 ---~~f--------n~~l~~~~aa~fyDaVLLYa~AL~EtL~~G~~-------------------~~~~~I~~~m~NrTF 325 (380)
T cd06369 276 ---TTD--------NSLLKDDYVAAYHDGVLLFGHVLKKFLESQEG-------------------VQTFSFINEFRNISF 325 (380)
T ss_pred ---CCC--------CcchHHHHHHHHHHHHHHHHHHHHHHHHhCCC-------------------CCcHHHHHHHhCcce
Confidence 011 11222 79999999999999999998765421 124778999999999
Q ss_pred ecccccEEEe-cCccccceEEEEEcc---CCcEEEEEecCCCC
Q 043276 232 RGLTGDYIFV-DGQLQSSAFEIINVN---NGARGVGFWSPEKG 270 (829)
Q Consensus 232 ~G~tG~~~F~-~G~~~~~~y~I~n~~---~g~~~VG~w~~~~g 270 (829)
.|++|.+.+| |||+. .+|.++-+. ++++.||+|+....
T Consensus 326 ~GitG~V~IDeNGDRd-~dfsLl~ms~~tg~y~vV~~y~t~~n 367 (380)
T cd06369 326 EGAGGPYTLDEYGDRD-VNFTLLYTSTDTSKYKVLFEFDTSTN 367 (380)
T ss_pred ecCCCceEeCCCCCcc-CceEEEEeeCCCCCeEEEEEEECCCC
Confidence 9999999997 99995 899999887 44999999987444
No 79
>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=99.58 E-value=1.5e-14 Score=154.83 Aligned_cols=116 Identities=30% Similarity=0.475 Sum_probs=107.9
Q ss_pred CCCChHHHHHHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCe
Q 043276 1 GALNDSSQVGAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTR 80 (829)
Q Consensus 1 t~psD~~q~~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~ar 80 (829)
+.|++..|++++++++++|||++|+++|++++||....+.|++.+++.|+|+.....++.. ..++...+.++++.++|
T Consensus 120 ~~p~~~~~~~a~~~~l~~~~w~~v~~v~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~--~~~~~~~l~~l~~~~~~ 197 (298)
T cd06269 120 TVPSDSSQAQAIVDLLKHFGWTWVGLVYSDDDYGRRLLELLEEELEKNGICVAFVESIPDG--SEDIRRLLKELKSSTAR 197 (298)
T ss_pred cCCCcHHHHHHHHHHHHHCCCeEEEEEEecchhhHHHHHHHHHHHHHCCeeEEEEEEcCCC--HHHHHHHHHHHHhcCCc
Confidence 5789999999999999999999999999999999999999999999999999998887755 36888999999999999
Q ss_pred EEEEEcChhHHHHHHHHHHHcCccccCeEEEEcCccccc
Q 043276 81 VFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNL 119 (829)
Q Consensus 81 ViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t~~~~~~ 119 (829)
|||+++..+.+..++++|.++||+ .+++||+++.|...
T Consensus 198 viv~~~~~~~~~~~l~~a~~~g~~-~~~~~i~~~~~~~~ 235 (298)
T cd06269 198 VIVVFSSEEDALRLLEEAVELGMM-TGYHWIITDLWLTS 235 (298)
T ss_pred EEEEEechHHHHHHHHHHHHcCCC-CCeEEEEEChhhcc
Confidence 999999999999999999999998 89999999998754
No 80
>cd06331 PBP1_AmiC_like Type I periplasmic components of amide-binding protein (AmiC) and the active transport system for short-chain and urea (FmdDEF). This group includes the type I periplasmic components of amide-binding protein (AmiC) and the active transport system for short-chain and urea (FmdDEF), found in bacteria and Archaea. AmiC controls expression of the amidase operon by a ligand-triggered conformational switch. In the absence of ligand or presence of butyramide (repressor), AmiC (the ligand sensor and negative regulator) adopts an open conformation and inhibits the transcription antitermination function of AmiR by direct protein-protein interaction. In the presence of inducing ligands such as acetamide, AmiC adopts a closed conformation which disrupts a silencing AmiC-AmiR complex and the expression of amidase and other genes of the operon is induced. FmdDEF is predicted to be an ATP-dependent transporter and closely resembles the periplasmic binding protein and the two t
Probab=99.57 E-value=9e-14 Score=151.92 Aligned_cols=209 Identities=16% Similarity=0.161 Sum_probs=164.7
Q ss_pred CCChHHHHHHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeE
Q 043276 2 ALNDSSQVGAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRV 81 (829)
Q Consensus 2 ~psD~~q~~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arV 81 (829)
.|++..++.++++.+..-+|++|++|+.|+.||+...+.+.+.+++.|.+|+....++.. ..|+..++.++++.++++
T Consensus 113 ~~~~~~~~~~~~~~~~~~~~~~v~il~~d~~~g~~~~~~~~~~~~~~G~~vv~~~~~~~~--~~d~~~~v~~~~~~~~d~ 190 (333)
T cd06331 113 GATPNQQLLPLIPYLMEKYGKRFYLIGSDYVWPRESNRIARALLEELGGEVVGEEYLPLG--TSDFGSVIEKIKAAGPDV 190 (333)
T ss_pred cCChHHhHHHHHHHHHHhcCCeEEEECCCchhHHHHHHHHHHHHHHcCCEEEEEEEecCC--cccHHHHHHHHHHcCCCE
Confidence 567788899999987655699999999999999999999999999999999988888865 458999999999999999
Q ss_pred EEEEcChhHHHHHHHHHHHcCccccCeEEEEcCccccccccCCccccccccceEEEEeccC--CChhHHHHHHHHHHhhc
Q 043276 82 FILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLEPSVTDSMQGVIGVRPYVP--KTKALENFRVRWKRKFL 159 (829)
Q Consensus 82 iIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t~~~~~~~~~~~~~~~~~~~g~l~~~~~~~--~~~~~~~F~~~w~~~~~ 159 (829)
|++++....+..+++++.+.|+.... +++.+..+... . .........+|+++..++.+ +.+..+.|.++|+++++
T Consensus 191 v~~~~~~~~~~~~~~~~~~~g~~~~~-~~~~~~~~~~~-~-~~~~~~~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~~ 267 (333)
T cd06331 191 VLSTLVGDSNVAFYRQFAAAGLDADR-IPILSLTLDEN-E-LAAIGAEAAEGHYSAASYFQSLDTPENKAFVARYRARYG 267 (333)
T ss_pred EEEecCCCChHHHHHHHHHcCCCcCC-CeeEEcccchh-h-hhccChhhhCCcEeechhhhhcCChhHHHHHHHHHHHcC
Confidence 99999999999999999999975323 44444333321 1 11112234678887766543 45678899999988775
Q ss_pred ccCCCCCccccchhHHHHHHHHHHHHHHHHHhcccCccccCCCCCCCCCCCccccCCCChHHHHHHHhccceecccccEE
Q 043276 160 QENPSLFDAELNIFGLLAYDATSALAVAVEKAGITGFGFDKTNVSSNATDLEAFGISQNGPKLLQALSSIRFRGLTGDYI 239 (829)
Q Consensus 160 ~~~~~~~~~~~~~~~~~~YDAV~~~A~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~L~~~~f~G~tG~~~ 239 (829)
... .++.++..+|||+++++.|+++++.. ++..|.++|++++|+|++|.+.
T Consensus 268 ~~~------~~~~~~~~~yda~~~~~~A~~~ag~~-----------------------~~~~l~~al~~~~~~~~~G~i~ 318 (333)
T cd06331 268 DDA------VINSPAEAAYEAVYLWAAAVEKAGST-----------------------DPEAVRAALEGVSFDAPQGPVR 318 (333)
T ss_pred CCc------CCCchhHHHHHHHHHHHHHHHHcCCC-----------------------CHHHHHHHhhcCcccCCCCceE
Confidence 420 25678899999999999999986421 2678999999999999999999
Q ss_pred Ee-cCc
Q 043276 240 FV-DGQ 244 (829)
Q Consensus 240 F~-~G~ 244 (829)
|+ ++.
T Consensus 319 f~~~~~ 324 (333)
T cd06331 319 IDPDNH 324 (333)
T ss_pred ecCCCC
Confidence 95 444
No 81
>cd06327 PBP1_SBP_like_1 Periplasmic solute-binding domain of active transport proteins that belong to the type I periplasmic binding fold protein family. Periplasmic solute-binding domain of active transport proteins that belong to the type I periplasmic binding fold protein family. Solute binding proteins are the primary specific receptors that initiate uptake of a broad range of solutes, including amino acids, peptides and inorganic ions. The members are predicted to have a similar function to an active transport system for short chain amides and urea by sequence comparison and phylogenetic analysis. Moreover, this binding domain has high sequence identity to the family of hydrophobic amino acid transporters (HAAT), and thus may also be involved in transport of amino acids.
Probab=99.57 E-value=9e-14 Score=151.98 Aligned_cols=211 Identities=16% Similarity=0.118 Sum_probs=166.4
Q ss_pred CCCChHHHHHHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCe
Q 043276 1 GALNDSSQVGAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTR 80 (829)
Q Consensus 1 t~psD~~q~~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~ar 80 (829)
+.+++..|+.++++++...++++|++++.|++||+...+.+++.+++.|++|+....++.. ..++..++.++++.+++
T Consensus 115 ~~~~~~~~~~~~~~~~~~~~~~~v~~i~~~~~~g~~~~~~~~~~~~~~G~~vv~~~~~~~~--~~d~~~~v~~l~~~~~d 192 (334)
T cd06327 115 WAYDTYMLANGTAPALVKAGGKKWFFLTADYAFGHSLERDARKVVKANGGKVVGSVRHPLG--TSDFSSYLLQAQASGAD 192 (334)
T ss_pred ccCChHHHHHHHHHHHHHhcCCeEEEEecchHHhHHHHHHHHHHHHhcCCEEcCcccCCCC--CccHHHHHHHHHhCCCC
Confidence 4678999999999988766799999999999999999999999999999999988888765 45899999999999999
Q ss_pred EEEEEcChhHHHHHHHHHHHcCccccCeEEEEcCccccccccCCccccccccceEEEEeccC--CChhHHHHHHHHHHhh
Q 043276 81 VFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLEPSVTDSMQGVIGVRPYVP--KTKALENFRVRWKRKF 158 (829)
Q Consensus 81 ViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t~~~~~~~~~~~~~~~~~~~g~l~~~~~~~--~~~~~~~F~~~w~~~~ 158 (829)
+|++.+....+..+++++++.|+. .+..|+.+..+.... .....+.++|++...++.+ +.+..++|.+.|++++
T Consensus 193 ~v~~~~~~~~~~~~~~~~~~~g~~-~~~~~~~~~~~~~~~---~~~~~~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~ 268 (334)
T cd06327 193 VLVLANAGADTVNAIKQAAEFGLT-KGQKLAGLLLFLTDV---HSLGLDAAQGLYLTTAWYWDLPNDETRAFVKRFQAKY 268 (334)
T ss_pred EEEEeccchhHHHHHHHHHHhCCc-cCCcEEEecccHHHH---HhhchhhhcCeEEeeeccccCCCHHHHHHHHHHHHHH
Confidence 999999999999999999999974 233333322222111 1112245788877766543 3677889999999988
Q ss_pred cccCCCCCccccchhHHHHHHHHHHHHHHHHHhcccCccccCCCCCCCCCCCccccCCCChHHHHHHHhccc-eeccccc
Q 043276 159 LQENPSLFDAELNIFGLLAYDATSALAVAVEKAGITGFGFDKTNVSSNATDLEAFGISQNGPKLLQALSSIR-FRGLTGD 237 (829)
Q Consensus 159 ~~~~~~~~~~~~~~~~~~~YDAV~~~A~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~L~~~~-f~G~tG~ 237 (829)
+. .++.++..+||++++++.|+++++..+ +..+.++|++++ +++..|.
T Consensus 269 g~--------~p~~~~~~~Y~~~~~~~~A~~~ag~~~-----------------------~~~v~~al~~~~~~~~~~g~ 317 (334)
T cd06327 269 GK--------MPSMVQAGAYSAVLHYLKAVEAAGTDD-----------------------ADKVVAKMKETPIYDLFAGN 317 (334)
T ss_pred Cc--------CCCcHHHHHHHHHHHHHHHHHHHCCCC-----------------------hHHHHHhccccceeccCCCC
Confidence 65 255688899999999999999986432 456899999875 6888999
Q ss_pred EEE-e-cCccccc
Q 043276 238 YIF-V-DGQLQSS 248 (829)
Q Consensus 238 ~~F-~-~G~~~~~ 248 (829)
+.| + +|+...+
T Consensus 318 ~~~~~~~~~~~~~ 330 (334)
T cd06327 318 GYIRACDHQMVHD 330 (334)
T ss_pred ceeeccccchhcc
Confidence 999 4 6776433
No 82
>PF13458 Peripla_BP_6: Periplasmic binding protein; PDB: 4EVS_A 4EY3_A 4EYG_B 4EYK_A 3H5L_B 3TD9_A 3EAF_A 1Z18_A 1Z17_A 2LIV_A ....
Probab=99.57 E-value=2.7e-13 Score=148.85 Aligned_cols=221 Identities=25% Similarity=0.399 Sum_probs=175.4
Q ss_pred CCChHHHHHHHHHHH-HHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCe
Q 043276 2 ALNDSSQVGAITAII-KAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTR 80 (829)
Q Consensus 2 ~psD~~q~~ai~~ll-~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~ar 80 (829)
.|++..++.++++.+ +++|.++|++|+.+++||+...+.+.+.+++.|+.|+....++.+ ..++...+.++++.+++
T Consensus 115 ~~~~~~~~~~~~~~~~~~~g~~~v~iv~~~~~~g~~~~~~~~~~~~~~G~~vv~~~~~~~~--~~d~~~~~~~l~~~~~d 192 (343)
T PF13458_consen 115 SPSDSQQAAALAEYLAKKLGAKKVAIVYPDDPYGRSLAEAFRKALEAAGGKVVGEIRYPPG--DTDFSALVQQLKSAGPD 192 (343)
T ss_dssp S--HHHHHHHHHHHHHHTTTTSEEEEEEESSHHHHHHHHHHHHHHHHTTCEEEEEEEE-TT--SSHHHHHHHHHHHTTTS
T ss_pred eccccHHHHHHHHHHHHHcCCcEEEEEecCchhhhHHHHHHHHHHhhcCceeccceecccc--cccchHHHHHHhhcCCC
Confidence 578899999999975 669999999999999999999999999999999999888888766 35899999999999999
Q ss_pred EEEEEcChhHHHHHHHHHHHcCccccCeEEEEcCc-cccccccCCccccccccceEEEEeccC--CChhHHHHHHHHHHh
Q 043276 81 VFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDG-MTNLLRTLEPSVTDSMQGVIGVRPYVP--KTKALENFRVRWKRK 157 (829)
Q Consensus 81 ViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t~~-~~~~~~~~~~~~~~~~~g~l~~~~~~~--~~~~~~~F~~~w~~~ 157 (829)
+|++++....+..+++++.+.|.... .+++...+ +...+.. .....++|+++..++.+ ..+..++|.++|++.
T Consensus 193 ~v~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~l~~---~~~~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~ 268 (343)
T PF13458_consen 193 VVVLAGDPADAAAFLRQLRQLGLKPP-RIPLFGTSLDDASLQQ---LGGDALEGVYIVSPWFPDPDSPAVKQFQERYRAA 268 (343)
T ss_dssp EEEEESTHHHHHHHHHHHHHTTGCSC-TEEEEEGGGSSHHHHH---HHGGGGTTEEEEESGGGTGGSHHHHHHHHHHHHH
T ss_pred EEEEeccchhHHHHHHHHHhhccccc-cceeeccccCcHHHHH---hhhhhccCceeecccCCCCCCHHHHHHHHHHHHH
Confidence 99999999999999999999996432 24444333 2222111 12245788888877665 467889999999999
Q ss_pred hcccCCCCCccccchhHHHHHHHHHHHHHHHHHhcccCccccCCCCCCCCCCCccccCCCChHHHHHHHhccceeccccc
Q 043276 158 FLQENPSLFDAELNIFGLLAYDATSALAVAVEKAGITGFGFDKTNVSSNATDLEAFGISQNGPKLLQALSSIRFRGLTGD 237 (829)
Q Consensus 158 ~~~~~~~~~~~~~~~~~~~~YDAV~~~A~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~L~~~~f~G~tG~ 237 (829)
++... .++.++..+||++.+++.|+++++.. ++..+.++|++++|+|+.|.
T Consensus 269 ~~~~~------~~~~~~~~~yda~~~~~~al~~~g~~-----------------------~~~~v~~al~~~~~~g~~g~ 319 (343)
T PF13458_consen 269 YGEEP------PPSLYAAQGYDAARLLAQALERAGSL-----------------------DREAVREALESLKYDGLFGP 319 (343)
T ss_dssp HSSTG------GTCHHHHHHHHHHHHHHHHHHHHTSH-----------------------HHHHHHHHHHTSEEEETTEE
T ss_pred cCCCC------CCchhHHHHHHHHHHHHHHHHHhCCC-----------------------CHHHHHHHHHhCCCcccccc
Confidence 87620 26778999999999999999997421 26789999999999999999
Q ss_pred EEEe--cCccccceEEEEEcc-CC
Q 043276 238 YIFV--DGQLQSSAFEIINVN-NG 258 (829)
Q Consensus 238 ~~F~--~G~~~~~~y~I~n~~-~g 258 (829)
+.|+ +++. ...+.|++++ +|
T Consensus 320 ~~~~~~~~~~-~~~~~i~~v~~~G 342 (343)
T PF13458_consen 320 ISFDPPDHQA-NKPVYIVQVKSDG 342 (343)
T ss_dssp EEEETTTSBE-EEEEEEEEEETTT
T ss_pred eEEeCCCCcc-ccCeEEEEEecCC
Confidence 9984 6665 4678888876 54
No 83
>cd06332 PBP1_aromatic_compounds_like Type I periplasmic binding proteins of active transport systems that are predicted to be involved in transport of aromatic compounds such as 2-nitrobenzoic acid and alkylbenzenes. This group includes the type I periplasmic binding proteins of active transport systems that are predicted to be involved in transport of aromatic compounds such as 2-nitrobenzoic acid and alkylbenzenes; their substrate specificities are not well characterized, however. Members also exhibit close similarity to active transport systems for short chain amides and/or urea found in bacteria and archaea.
Probab=99.55 E-value=1.9e-13 Score=149.36 Aligned_cols=210 Identities=16% Similarity=0.222 Sum_probs=163.4
Q ss_pred CCChHHHHHHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeE
Q 043276 2 ALNDSSQVGAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRV 81 (829)
Q Consensus 2 ~psD~~q~~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arV 81 (829)
.|++..++..+++++...||+++++|+.++.||+...+.+.+.++ ..+.....++.. ..++..++.++++.++++
T Consensus 115 ~~~~~~~~~~~~~~l~~~g~~~v~il~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~--~~d~~~~i~~l~~~~~d~ 189 (333)
T cd06332 115 SWQNDQVHEAMGKYAADKGYKKVVIIAPDYAAGKDAVAGFKRTFK---GEVVEEVYTPLG--QLDFSAELAQIRAAKPDA 189 (333)
T ss_pred eCChHHhHHHHHHHHHHhCCceEEEEecCcchhHHHHHHHHHhhc---EEEeeEEecCCC--CcchHHHHHHHHhcCCCE
Confidence 578899999999999999999999999999999999999998887 355545455544 346888899999999999
Q ss_pred EEEEcChhHHHHHHHHHHHcCccccCeEEEEcCccccccccCCccccccccceEEEEeccC--CChhHHHHHHHHHHhhc
Q 043276 82 FILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLEPSVTDSMQGVIGVRPYVP--KTKALENFRVRWKRKFL 159 (829)
Q Consensus 82 iIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t~~~~~~~~~~~~~~~~~~~g~l~~~~~~~--~~~~~~~F~~~w~~~~~ 159 (829)
|++......+..++++++++|+.. ...++.++.+... ... ......++|+++..++.+ ..+..++|.+.|+++++
T Consensus 190 i~~~~~~~~~~~~~~~~~~~g~~~-~~~~~~~~~~~~~-~~~-~~~~~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~~ 266 (333)
T cd06332 190 VFVFLPGGMAVNFVKQYDQAGLKK-KIPLYGPGFLTDQ-DTL-PAQGDAAVGVLTALHWAPDLDNPANKRFVAAYKAAYG 266 (333)
T ss_pred EEEecccchHHHHHHHHHHcCccc-CCceeccCCCCCH-HHH-HhhchhhcCeeeeeccCCCCCCHHHHHHHHHHHHHhC
Confidence 999888788999999999999632 3456666555432 111 123355778887766654 35778999999999886
Q ss_pred ccCCCCCccccchhHHHHHHHHHHHHHHHHHhcccCccccCCCCCCCCCCCccccCCCChHHHHHHHhccceecccccEE
Q 043276 160 QENPSLFDAELNIFGLLAYDATSALAVAVEKAGITGFGFDKTNVSSNATDLEAFGISQNGPKLLQALSSIRFRGLTGDYI 239 (829)
Q Consensus 160 ~~~~~~~~~~~~~~~~~~YDAV~~~A~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~L~~~~f~G~tG~~~ 239 (829)
. .++.++..+||++++++.|+++++... ..+..+.++|+++.|.|++|.+.
T Consensus 267 ~--------~~~~~~~~~yda~~~~~~a~~~ag~~~---------------------~~~~~v~~al~~~~~~~~~g~i~ 317 (333)
T cd06332 267 R--------VPSVYAAQGYDAAQLLDAALRAVGGDL---------------------SDKDALRAALRAADFDSPRGPFK 317 (333)
T ss_pred C--------CCcHHHHHHHHHHHHHHHHHHHhcCCC---------------------CCHHHHHHHHhcCceecCcccee
Confidence 4 356788999999999999999975321 11467999999999999999999
Q ss_pred Ee-cCccccc
Q 043276 240 FV-DGQLQSS 248 (829)
Q Consensus 240 F~-~G~~~~~ 248 (829)
|+ +|+...+
T Consensus 318 f~~~~~~~~~ 327 (333)
T cd06332 318 FNPNHNPIQD 327 (333)
T ss_pred ECCCCCcccc
Confidence 96 8887543
No 84
>cd06359 PBP1_Nba_like Type I periplasmic binding component of active transport systems that are predicted to be involved in 2-nitrobenzoic acid degradation pathway. This group includes the type I periplasmic binding component of active transport systems that are predicted to be involved in 2-nitrobenzoic acid degradation pathway; their substrate specificities are not well characterized.
Probab=99.55 E-value=2.2e-13 Score=148.91 Aligned_cols=214 Identities=17% Similarity=0.241 Sum_probs=163.7
Q ss_pred CCChHHHHHHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeE
Q 043276 2 ALNDSSQVGAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRV 81 (829)
Q Consensus 2 ~psD~~q~~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arV 81 (829)
.|++..|..+++++++..||++|++++.|++||+...+.+.+.++ ..+.....++.. ..|+..++.+++++++++
T Consensus 115 ~~~~~~~~~~~~~~~~~~g~~~vail~~~~~~g~~~~~~~~~~~~---~~v~~~~~~~~~--~~d~~~~i~~l~~~~pd~ 189 (333)
T cd06359 115 SWQNDQVHEAMGKYAQDKGYKRVFLIAPNYQAGKDALAGFKRTFK---GEVVGEVYTKLG--QLDFSAELAQIRAAKPDA 189 (333)
T ss_pred eCChHhhHHHHHHHHHHhCCCeEEEEecCchhhHHHHHHHHHHhC---ceeeeeecCCCC--CcchHHHHHHHHhCCCCE
Confidence 578889999999999989999999999999999999998888774 345544444433 458999999999999999
Q ss_pred EEEEcChhHHHHHHHHHHHcCccccCeEEEEcCccccccccCCccccccccceEEEEeccC--CChhHHHHHHHHHHhhc
Q 043276 82 FILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLEPSVTDSMQGVIGVRPYVP--KTKALENFRVRWKRKFL 159 (829)
Q Consensus 82 iIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t~~~~~~~~~~~~~~~~~~~g~l~~~~~~~--~~~~~~~F~~~w~~~~~ 159 (829)
|++......+..+++++++.|+.. ...++.++.+... +.. ....+.++|+++..++.+ .++..++|.+.|+++++
T Consensus 190 v~~~~~~~~~~~~~~~~~~~G~~~-~~~~~~~~~~~~~-~~~-~~~g~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~~ 266 (333)
T cd06359 190 VFVFLPGGMGVNFVKQYRQAGLKK-DIPLYSPGFSDEE-DTL-PAVGDAALGLYNTAQWAPDLDNPANKKFVADFEKKYG 266 (333)
T ss_pred EEEEccCccHHHHHHHHHHcCccc-CCeeeccCcccCH-HHH-HhcchhhcCeeeccccCCCCCCHHHHHHHHHHHHHhC
Confidence 999888888899999999999742 3445555444321 111 123355688887766554 46788999999999885
Q ss_pred ccCCCCCccccchhHHHHHHHHHHHHHHHHHhcccCccccCCCCCCCCCCCccccCCCChHHHHHHHhccceecccccEE
Q 043276 160 QENPSLFDAELNIFGLLAYDATSALAVAVEKAGITGFGFDKTNVSSNATDLEAFGISQNGPKLLQALSSIRFRGLTGDYI 239 (829)
Q Consensus 160 ~~~~~~~~~~~~~~~~~~YDAV~~~A~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~L~~~~f~G~tG~~~ 239 (829)
. .++.++..+||++++++.|+++++... .++..+.+.|.+..|.|++|.+.
T Consensus 267 ~--------~~~~~~~~~yda~~~~~~A~~~ag~~~---------------------~~~~~v~~al~~~~~~~~~G~~~ 317 (333)
T cd06359 267 R--------LPTLYAAQAYDAAQLLDSAVRKVGGNL---------------------SDKDALRAALRAADFKSVRGAFR 317 (333)
T ss_pred C--------CCcHHHHHHHHHHHHHHHHHHHhcCCC---------------------CCHHHHHHHHhcCccccCccceE
Confidence 4 367788999999999999999975321 02578999999999999999999
Q ss_pred Ee-cCccccceEEEE
Q 043276 240 FV-DGQLQSSAFEII 253 (829)
Q Consensus 240 F~-~G~~~~~~y~I~ 253 (829)
|+ +|+... ...|+
T Consensus 318 ~~~~~~~~~-~~~~~ 331 (333)
T cd06359 318 FGTNHFPIQ-DFYLR 331 (333)
T ss_pred ECCCCCcce-eEEEE
Confidence 96 777643 34443
No 85
>TIGR03407 urea_ABC_UrtA urea ABC transporter, urea binding protein. Members of this protein family are ABC transporter substrate-binding proteins associated with urea transport and metabolism. This protein is found in a conserved five-gene transport operon typically found adjacent to urease genes. It was shown in Cyanobacteria that disruption leads to the loss of high-affinity urea transport activity. Members of this protein family tend to have the twin-arginine signal for Sec-independent transport across the plasma membrane.
Probab=99.54 E-value=7.6e-13 Score=145.98 Aligned_cols=211 Identities=15% Similarity=0.104 Sum_probs=159.3
Q ss_pred CCCChHHHHHHHHHHHHH-cCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCC
Q 043276 1 GALNDSSQVGAITAIIKA-FGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQT 79 (829)
Q Consensus 1 t~psD~~q~~ai~~ll~~-fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~a 79 (829)
+.+++..|+.++++.+.. .|.++|++|+.|++||+...+.+++.+++.|+.|+....++.+ ..|+..++.+|++.++
T Consensus 113 ~~~~~~~~~~~~~~~~~~~~g~k~v~~l~~d~~~g~~~~~~~~~~~~~~G~~vv~~~~~~~~--~~D~s~~v~~l~~~~p 190 (359)
T TIGR03407 113 TGAAPNQQIIPAVDYLLSKKGAKRFFLLGSDYVFPRTANKIIKAYLKSLGGTVVGEDYTPLG--HTDFQTIINKIKAFKP 190 (359)
T ss_pred cCCChHHHHHHHHHHHHhccCCceEEEecCccHHHHHHHHHHHHHHHHcCCEEEeeEEecCC--hHhHHHHHHHHHHhCC
Confidence 357888899999887755 6999999999999999999999999999999999988887765 5689999999999999
Q ss_pred eEEEEEcChhHHHHHHHHHHHcCccccCeEEEEcCccccccccCCccccccccceEEEEec--cCCChhHHHHHHHHHHh
Q 043276 80 RVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLEPSVTDSMQGVIGVRPY--VPKTKALENFRVRWKRK 157 (829)
Q Consensus 80 rViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t~~~~~~~~~~~~~~~~~~~g~l~~~~~--~~~~~~~~~F~~~w~~~ 157 (829)
++|++......+..+++++++.|+......++.+....... .....+.++|+++...+ ....+..+.|.+.+++.
T Consensus 191 Dav~~~~~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~~~---~~~g~~~~~G~~~~~~~~~~~~~~~~~~f~~~~~~~ 267 (359)
T TIGR03407 191 DVVFNTLNGDSNVAFFKQLKNAGITAKDVPVVSFSVAEEEI---RGIGPENLVGHLAAWNYFQSVDTPANKKFVKAFKAK 267 (359)
T ss_pred CEEEEeccCCCHHHHHHHHHHcCCCccCCcEEEeecCHHHH---hhcChHhhCCeEEeccchhcCCCHHHHHHHHHHHHH
Confidence 99988877777889999999999743222333332221111 11112346777654322 23567788999999888
Q ss_pred hcccCCCCCccccchhHHHHHHHHHHHHHHHHHhcccCccccCCCCCCCCCCCccccCCCChHHHHHHHhccceeccccc
Q 043276 158 FLQENPSLFDAELNIFGLLAYDATSALAVAVEKAGITGFGFDKTNVSSNATDLEAFGISQNGPKLLQALSSIRFRGLTGD 237 (829)
Q Consensus 158 ~~~~~~~~~~~~~~~~~~~~YDAV~~~A~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~L~~~~f~G~tG~ 237 (829)
++... .+..++...|||+.+++.|+++++.. ++..+.+.|..++|.+..|.
T Consensus 268 ~~~~~------~~~~~~~~~y~a~~~~~~A~~~ag~~-----------------------~~~~i~~al~~~~~~~~~G~ 318 (359)
T TIGR03407 268 YGDDR------VTNDPMEAAYLGVYLWKAAVEKAGSF-----------------------DVDAVRDAAIGIEFDAPEGK 318 (359)
T ss_pred cCCCC------CCCcHHHHHHHHHHHHHHHHHHhCCC-----------------------CHHHHHHHhcCCcccCCCcc
Confidence 75421 12345667899999999999997532 15789999999999999999
Q ss_pred EEEe--cCcc
Q 043276 238 YIFV--DGQL 245 (829)
Q Consensus 238 ~~F~--~G~~ 245 (829)
+.|+ +++.
T Consensus 319 i~f~~~~~~~ 328 (359)
T TIGR03407 319 VKVDGKNHHL 328 (359)
T ss_pred EEEeCCCCee
Confidence 9995 4443
No 86
>TIGR03669 urea_ABC_arch urea ABC transporter, substrate-binding protein, archaeal type. Members of this protein family are identified as the substrate-binding protein of a urea ABC transport system by similarity to a known urea transporter from Corynebacterium glutamicum, operon structure, proximity of its operons to urease (urea-utilization protein) operons, and by Partial Phylogenetic Profiling vs. urea utilization.
Probab=99.54 E-value=6.1e-13 Score=146.85 Aligned_cols=229 Identities=15% Similarity=0.149 Sum_probs=169.1
Q ss_pred CCCChHHHHHHHHHHHH-HcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCC
Q 043276 1 GALNDSSQVGAITAIIK-AFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQT 79 (829)
Q Consensus 1 t~psD~~q~~ai~~ll~-~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~a 79 (829)
+.|++..|+.++++++. ..+ ++|++|+.|++||+.....+.+.+++.|+.|+....++.+ ..|+..++.+|+++++
T Consensus 113 ~~~~~~~~~~~~~~~~~~~~g-~~va~l~~d~~~g~~~~~~~~~~~~~~G~~vv~~~~~~~g--~~Df~~~l~~i~~~~p 189 (374)
T TIGR03669 113 VGATARQQLGTVVPYMVEEYG-KKIYTIAADYNFGQLSADWVRVIAKENGAEVVGEEFIPLS--VSQFSSTIQNIQKADP 189 (374)
T ss_pred cCCChHHHHHHHHHHHHHcCC-CeEEEEcCCcHHHHHHHHHHHHHHHHcCCeEEeEEecCCC--cchHHHHHHHHHHcCC
Confidence 35778889999999875 567 5799999999999999999999999999999988888766 4589999999999999
Q ss_pred eEEEEEcChhHHHHHHHHHHHcCccccCeEEEEcCccccccccCCccccccccceEEEEeccC--CChhHHHHHHHHHHh
Q 043276 80 RVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLEPSVTDSMQGVIGVRPYVP--KTKALENFRVRWKRK 157 (829)
Q Consensus 80 rViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t~~~~~~~~~~~~~~~~~~~g~l~~~~~~~--~~~~~~~F~~~w~~~ 157 (829)
++|++.........++++++++|+..+ ++............. .......|+++...+.+ ..+..++|.+.|+++
T Consensus 190 D~V~~~~~g~~~~~~~kq~~~~G~~~~---~~~~~~~~~~~~~~~-~~~~~~~g~~~~~~~~~~~~~~~~~~F~~~y~~~ 265 (374)
T TIGR03669 190 DFVMSMLVGANHASFYEQAASANLNLP---MGTSTAMAQGYEHKR-FEPPALKDVYAGVNYMEEIDTPENEAFVERFYAK 265 (374)
T ss_pred CEEEEcCcCCcHHHHHHHHHHcCCCCc---ccchhhhhhhhhhhh-cCchhhCCcEEeeeccccCCCHHHHHHHHHHHHH
Confidence 999998888888899999999997432 222221211101000 11134567665554443 467889999999998
Q ss_pred hcccCCCCCccccchhHHHHHHHHHHHHHHHHHhcccCccccCCCCCCCCCCCccccCCCChHHHHHHHhc-cceecccc
Q 043276 158 FLQENPSLFDAELNIFGLLAYDATSALAVAVEKAGITGFGFDKTNVSSNATDLEAFGISQNGPKLLQALSS-IRFRGLTG 236 (829)
Q Consensus 158 ~~~~~~~~~~~~~~~~~~~~YDAV~~~A~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~L~~-~~f~G~tG 236 (829)
|+.. | .++.++..+|||+++++.|++++++.+ +..+.++|++ ..|.|..|
T Consensus 266 ~g~~-p-----~~~~~a~~~Yda~~~l~~Ai~~AGs~d-----------------------~~av~~aL~~~~~~~~~~G 316 (374)
T TIGR03669 266 FPDA-P-----YINQEAENNYFSVYMYKQAVEEAGTTD-----------------------QDAVRDVLESGVEMDAPEG 316 (374)
T ss_pred cCCC-C-----CCChHHHHHHHHHHHHHHHHHHhCCCC-----------------------HHHHHHHHHcCCeEECCCc
Confidence 8642 1 235678889999999999999986432 5789999986 67999999
Q ss_pred cEEEe-c-CccccceEEEEEcc-CC-cEEEEEec
Q 043276 237 DYIFV-D-GQLQSSAFEIINVN-NG-ARGVGFWS 266 (829)
Q Consensus 237 ~~~F~-~-G~~~~~~y~I~n~~-~g-~~~VG~w~ 266 (829)
.+.|+ + ++. ...+.|..+. +| ...+..|.
T Consensus 317 ~i~fd~~~~~~-~~~~~v~~~~~~~~~~~~~~~~ 349 (374)
T TIGR03669 317 KVCIDGATHHM-SHTMRLARADADHNITFVKEQE 349 (374)
T ss_pred cEEEcCCCCee-eeeeEEEEEcCCCCEEEEEecC
Confidence 99996 3 444 2455566666 43 44454554
No 87
>cd06349 PBP1_ABC_ligand_binding_like_14 Type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in the uptake of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine/isoleucine/valine binding protein (LIVBP); however its ligand specificity has not been determined experimentally.
Probab=99.53 E-value=4.3e-13 Score=147.03 Aligned_cols=217 Identities=18% Similarity=0.265 Sum_probs=164.7
Q ss_pred CCCChHHHHHHHHHHH-HHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCC
Q 043276 1 GALNDSSQVGAITAII-KAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQT 79 (829)
Q Consensus 1 t~psD~~q~~ai~~ll-~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~a 79 (829)
+.|++..++.++++++ +++||++|++|+.|++||....+.+.+++++.|+||+....++.. ..+++..+.+++.+++
T Consensus 114 ~~~~~~~~~~~~~~~~~~~~~~~~v~ii~~~~~~g~~~~~~~~~~~~~~g~~v~~~~~~~~~--~~d~~~~v~~l~~~~~ 191 (340)
T cd06349 114 NSTSQAIEAPLLADYAVKDLGFKKVAILSVNTDWGRTSADIFVKAAEKLGGQVVAHEEYVPG--EKDFRPTITRLRDANP 191 (340)
T ss_pred ccCCcHHHHHHHHHHHHHHcCCcEEEEEecCChHhHHHHHHHHHHHHHcCCEEEEEEEeCCC--CCcHHHHHHHHHhcCC
Confidence 3577888999999986 788999999999999999999999999999999999988777765 4479999999999999
Q ss_pred eEEEEEcChhHHHHHHHHHHHcCccccCeEEEEcCccccccccCCccccccccceEEEEeccC--CChhHHHHHHHHHHh
Q 043276 80 RVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLEPSVTDSMQGVIGVRPYVP--KTKALENFRVRWKRK 157 (829)
Q Consensus 80 rViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t~~~~~~~~~~~~~~~~~~~g~l~~~~~~~--~~~~~~~F~~~w~~~ 157 (829)
++|++.+....+..+++++.+.|+.. -++.+..+... .... .....++|++...++.+ ..+..++|.+.|+++
T Consensus 192 d~v~~~~~~~~~~~~~~~~~~~g~~~---~~~~~~~~~~~-~~~~-~~~~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~ 266 (340)
T cd06349 192 DAIILISYYNDGAPIARQARAVGLDI---PVVASSSVYSP-KFIE-LGGDAVEGVYTPTAFFPGDPRPEVQSFVSAYEAK 266 (340)
T ss_pred CEEEEccccchHHHHHHHHHHcCCCC---cEEccCCcCCH-HHHH-HhHHHhCCcEEecccCCCCCCHHHHHHHHHHHHH
Confidence 99999999999999999999999742 24444333211 1111 12235678877666554 356788999999887
Q ss_pred hcccCCCCCccccchhHHHHHHHHHHHHHHHHHhcccCccccCCCCCCCCCCCccccCCCChHHHHHH-Hhccceecccc
Q 043276 158 FLQENPSLFDAELNIFGLLAYDATSALAVAVEKAGITGFGFDKTNVSSNATDLEAFGISQNGPKLLQA-LSSIRFRGLTG 236 (829)
Q Consensus 158 ~~~~~~~~~~~~~~~~~~~~YDAV~~~A~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~-L~~~~f~G~tG 236 (829)
++. .++.++..+||++.+++.|+++++... ...+... +.+..+.|.+|
T Consensus 267 ~~~--------~p~~~~~~~y~~~~~~~~a~~~ag~~~-----------------------~~~~~~~~~~~~~~~~~~g 315 (340)
T cd06349 267 YGA--------QPDAFAAQAYDAVGILAAAVRRAGTDR-----------------------RAARDGFAKAEDVYSGVTG 315 (340)
T ss_pred HCC--------CcchhhhhHHHHHHHHHHHHHHhCCCC-----------------------HHHHHHHHHhccCcccceE
Confidence 764 356788999999999999999975322 1222222 24556889999
Q ss_pred cEEEe-c-CccccceEEEEEcc
Q 043276 237 DYIFV-D-GQLQSSAFEIINVN 256 (829)
Q Consensus 237 ~~~F~-~-G~~~~~~y~I~n~~ 256 (829)
.+.|+ + ++.. ..|-++.++
T Consensus 316 ~i~~~~~~~~~~-~~~~~~~~~ 336 (340)
T cd06349 316 STKFDPNTRRVI-KRFVPLVVR 336 (340)
T ss_pred eEEECCCCCCcc-CceEEEEEe
Confidence 99995 4 6654 467666654
No 88
>cd06343 PBP1_ABC_ligand_binding_like_8 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine/isoleucine/valine binding protein (LIVBP); however its ligand specificity has not been determined experimentally.
Probab=99.53 E-value=6.2e-13 Score=147.16 Aligned_cols=221 Identities=14% Similarity=0.241 Sum_probs=166.4
Q ss_pred CCChHHHHHHHHHH-HHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCe
Q 043276 2 ALNDSSQVGAITAI-IKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTR 80 (829)
Q Consensus 2 ~psD~~q~~ai~~l-l~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~ar 80 (829)
.|++..|+.++++. ++++||++|++|+.+++||+...+.+.+.+++.|+||+....++.. ..++...+.++++.+++
T Consensus 124 ~~~~~~~~~~~~~~~~~~~g~~~v~ii~~~~~~g~~~~~~~~~~~~~~G~~vv~~~~~~~~--~~d~~~~v~~i~~~~~d 201 (362)
T cd06343 124 QPSYQDEARIYAKYLVEEKPNAKIAVLYQNDDFGKDYLKGLKDGLGDAGLEIVAETSYEVT--EPDFDSQVAKLKAAGAD 201 (362)
T ss_pred CCChHHHHHHHHHHHHHhCCCceEEEEEeccHHHHHHHHHHHHHHHHcCCeEEEEeeecCC--CccHHHHHHHHHhcCCC
Confidence 58888999999996 4789999999999999999999999999999999999988888765 45799999999999999
Q ss_pred EEEEEcChhHHHHHHHHHHHcCccccCeEEEEcCccccccccCCccccccccceEEEEecc-------CCChhHHHHHHH
Q 043276 81 VFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLEPSVTDSMQGVIGVRPYV-------PKTKALENFRVR 153 (829)
Q Consensus 81 ViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t~~~~~~~~~~~~~~~~~~~g~l~~~~~~-------~~~~~~~~F~~~ 153 (829)
+|++.+....+..+++++++.|+.. .++.++++............+.++|+++...+. ...+..++|.+.
T Consensus 202 ~v~~~~~~~~~~~~~~~~~~~g~~~---~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~p~~~~~~~~~~f~~~ 278 (362)
T cd06343 202 VVVLATTPKFAAQAIRKAAELGWKP---TFLLSSVSASVASVLKPAGLEAAEGVIAAAYLKDPTDPAWADDPGVKEFIAF 278 (362)
T ss_pred EEEEEcCcHHHHHHHHHHHHcCCCc---eEEEEecccccHHHHHHhhhHhhCceEEEEEecCCCccccccCHHHHHHHHH
Confidence 9999999999999999999999642 356665544221101111224567777655432 246778889988
Q ss_pred HHHhhcccCCCCCccccchhHHHHHHHHHHHHHHHHHhcccCccccCCCCCCCCCCCccccCCCChHHHHHHHhccce--
Q 043276 154 WKRKFLQENPSLFDAELNIFGLLAYDATSALAVAVEKAGITGFGFDKTNVSSNATDLEAFGISQNGPKLLQALSSIRF-- 231 (829)
Q Consensus 154 w~~~~~~~~~~~~~~~~~~~~~~~YDAV~~~A~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~L~~~~f-- 231 (829)
+++.++.. ..++.++...||++.++++|+++++.. .++..+.++|.++++
T Consensus 279 ~~~~~~~~------~~~~~~~~~~y~a~~~~~~a~~~ag~~----------------------~~~~~v~~aL~~~~~~~ 330 (362)
T cd06343 279 YKKYFPEG------DPPDTYAVYGYAAAETLVKVLKQAGDD----------------------LTRENIMKQAESLKDVL 330 (362)
T ss_pred HHHhcCCC------CCCchhhhHHHHHHHHHHHHHHHhCCC----------------------CCHHHHHHHHHhCCCCC
Confidence 88877542 125678899999999999999997521 125789999999987
Q ss_pred -ecc-cccEEEe--cCccccceEEEEEcc
Q 043276 232 -RGL-TGDYIFV--DGQLQSSAFEIINVN 256 (829)
Q Consensus 232 -~G~-tG~~~F~--~G~~~~~~y~I~n~~ 256 (829)
.+. .|++.|+ +++. ...+.|..++
T Consensus 331 ~~~~~~~~~~~~~~~~~~-~~~~~i~~~~ 358 (362)
T cd06343 331 PDLLPGIRINTSPDDHLP-IEQMQLMRFE 358 (362)
T ss_pred ccccCccceecCcccccc-ceeEEEEEEe
Confidence 333 3477884 3333 3455566554
No 89
>cd06357 PBP1_AmiC Periplasmic binding domain of amidase (AmiC) that belongs to the type I periplasmic binding fold protein family. This group includes the periplasmic binding domain of amidase (AmiC) that belongs to the type I periplasmic binding fold protein family. AmiC controls expression of the amidase operon by the ligand-triggered conformational switch. In the absence of ligand or presence of butyramide (repressor), AmiC (the ligand sensor and negative regulator) adopts an open conformation and inhibits the transcription antitermination function of AmiR by direct protein-protein interaction. In the presence of inducing ligands such as acetamide, AmiC adopts a closed conformation which disrupts a silencing AmiC-AmiR complex and the expression of amidase and other genes of the operon are induced.
Probab=99.52 E-value=1.3e-12 Score=144.17 Aligned_cols=221 Identities=15% Similarity=0.139 Sum_probs=164.7
Q ss_pred CChHHHHHHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEE
Q 043276 3 LNDSSQVGAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVF 82 (829)
Q Consensus 3 psD~~q~~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arVi 82 (829)
+++..+..++++++..-+=++|++|+.|++||......+.+.+++.|++|+....++.+....|+..++.+++++++++|
T Consensus 114 ~~~~~~~~~~~~~~~~~~~~~v~~i~~d~~~g~~~~~~~~~~~~~~G~~vv~~~~~~~~~~~~d~s~~v~~l~~~~pd~V 193 (360)
T cd06357 114 AAPNQNSVPLADYLLRHYGKRVFLVGSNYIYPYESNRIMRDLLEQRGGEVLGERYLPLGASDEDFARIVEEIREAQPDFI 193 (360)
T ss_pred CCcHHHHHHHHHHHHhcCCcEEEEECCCCcchHHHHHHHHHHHHHcCCEEEEEEEecCCCchhhHHHHHHHHHHcCCCEE
Confidence 44455677898887544448999999999999999999999999999999876556655446689999999999999999
Q ss_pred EEEcChhHHHHHHHHHHHcCccccCeEEEEcCccccccccCCccccccccceEEEEeccC--CChhHHHHHHHHHHhhcc
Q 043276 83 ILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLEPSVTDSMQGVIGVRPYVP--KTKALENFRVRWKRKFLQ 160 (829)
Q Consensus 83 Iv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t~~~~~~~~~~~~~~~~~~~g~l~~~~~~~--~~~~~~~F~~~w~~~~~~ 160 (829)
++.+....+..++++++++|+.. ..+.+.+...... . ......+.++|+++..++.+ ..+..+.|.+.|+++|+.
T Consensus 194 ~~~~~~~~~~~~~~~~~~~G~~~-~~~~~~~~~~~~~-~-~~~~~g~~~~g~~~~~~~~~~~~~p~~~~f~~~~~~~~g~ 270 (360)
T cd06357 194 FSTLVGQSSYAFYRAYAAAGFDP-ARMPIASLTTSEA-E-VAAMGAEAAAGHITAAPYFSSIDTPANRAFVARYRARFGE 270 (360)
T ss_pred EEeCCCCChHHHHHHHHHcCCCc-cCceeEEeeccHH-H-HhhcchHhhCCcEEecccccccCChhHHHHHHHHHHHcCC
Confidence 99999999999999999999743 2334444332211 1 11112356788888766533 467889999999998864
Q ss_pred cCCCCCccccchhHHHHHHHHHHHHHHHHHhcccCccccCCCCCCCCCCCccccCCCChHHHHHHHhccceecccccEEE
Q 043276 161 ENPSLFDAELNIFGLLAYDATSALAVAVEKAGITGFGFDKTNVSSNATDLEAFGISQNGPKLLQALSSIRFRGLTGDYIF 240 (829)
Q Consensus 161 ~~~~~~~~~~~~~~~~~YDAV~~~A~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~L~~~~f~G~tG~~~F 240 (829)
.. .++.++...||+++++++|+++++..+ +..+.++|.+++|.|..|.+.|
T Consensus 271 ~~------~~~~~~~~~yda~~~l~~Al~~ag~~~-----------------------~~~v~~aL~~~~~~~~~g~~~f 321 (360)
T cd06357 271 DA------PVSACAEAAYFQVHLFARALQRAGSDD-----------------------PEDVLAALLGFSFDAPQGPVRI 321 (360)
T ss_pred CC------CCCcHHHHHHHHHHHHHHHHHHcCCCC-----------------------HHHHHHHhccCcccCCCcceEE
Confidence 21 245688899999999999999875321 5679999999999999999999
Q ss_pred e-cCccccceEEEEEc
Q 043276 241 V-DGQLQSSAFEIINV 255 (829)
Q Consensus 241 ~-~G~~~~~~y~I~n~ 255 (829)
+ .++.......+..+
T Consensus 322 ~~~~~~~~~~~~~~~~ 337 (360)
T cd06357 322 DPDNNHTYLWPRIARV 337 (360)
T ss_pred eCCCCeeeeeeEEEEE
Confidence 6 44322223334444
No 90
>cd06358 PBP1_NHase Type I periplasmic-binding protein of the nitrile hydratase (NHase) system that selectively converts nitriles to corresponding amides. This group includes the type I periplasmic-binding protein of the nitrile hydratase (NHase) system that selectively converts nitriles to corresponding amides, which are subsequently converted by amidases to yield free carboxylic acids and ammonia. NHases from bacteria and fungi have been purified and characterized. In Rhodococcus sp., the nitrile hydratase operon consists of six genes encoding NHase regulator 2, NHase regulator 1, amidase, NHase alpha subunit, NHase beta subunit, and NHase activator. The operon produces a constitutive hydratase that has a broad substrate spectrum: aliphatic and aromatic nitriles, mononitriles and dinitriles, hydroxynitriles and amino-nitriles, and a constitutive amidase of equally low substrate specificity. NHases are metalloenzymes containing either cobalt or iron, and therefore can be classified int
Probab=99.52 E-value=4.9e-13 Score=146.07 Aligned_cols=209 Identities=17% Similarity=0.202 Sum_probs=161.2
Q ss_pred CCChHHHHHHHHHHH-HHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCe
Q 043276 2 ALNDSSQVGAITAII-KAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTR 80 (829)
Q Consensus 2 ~psD~~q~~ai~~ll-~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~ar 80 (829)
.+++..++.++++.+ +..||++|++++.|++||+...+.+.+.+++.|+.|+....++.+ ..|+...+.++++.+++
T Consensus 112 ~~~~~~~~~~~~~~~~~~~g~~~v~i~~~~~~~g~~~~~~~~~~~~~~G~~v~~~~~~~~~--~~d~~~~v~~l~~~~pd 189 (333)
T cd06358 112 GETPEQQLAPAIPWLAEEKGARRWYLIGNDYVWPRGSLAAAKRYIAELGGEVVGEEYVPLG--TTDFTSVLERIAASGAD 189 (333)
T ss_pred CCCcHHHHHHHHHHHHHhcCCCeEEEEeccchhhHHHHHHHHHHHHHcCCEEeeeeeecCC--hHHHHHHHHHHHHcCCC
Confidence 456777877777665 678999999999999999999999999999999999988888765 56899999999999999
Q ss_pred EEEEEcChhHHHHHHHHHHHcCccccCeEEEE-cCccccccccCCccccccccceEEEEeccC--CChhHHHHHHHHHHh
Q 043276 81 VFILHMLPSLGSRIFEKANEIGLMNKGCVWIM-TDGMTNLLRTLEPSVTDSMQGVIGVRPYVP--KTKALENFRVRWKRK 157 (829)
Q Consensus 81 ViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~-t~~~~~~~~~~~~~~~~~~~g~l~~~~~~~--~~~~~~~F~~~w~~~ 157 (829)
+|++.+....+..+++++++.|+... |+. +..+.... ........++|++....+.+ ..+..++|.+.|+++
T Consensus 190 ~v~~~~~~~~~~~~~~~~~~~G~~~~---~~~~~~~~~~~~--~~~~~~~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~ 264 (333)
T cd06358 190 AVLSTLVGQDAVAFNRQFAAAGLRDR---ILRLSPLMDENM--LLASGAEAAEGLYSSSGYFASLQTPANAAFLARYRAR 264 (333)
T ss_pred EEEEeCCCCchHHHHHHHHHcCCCcc---CceeecccCHHH--HHhcChHhhCCcEEeccchhhcCCHHHHHHHHHHHHH
Confidence 99998888888899999999997542 232 22232211 11112234677776654433 567889999999998
Q ss_pred hcccCCCCCccccchhHHHHHHHHHHHHHHHHHhcccCccccCCCCCCCCCCCccccCCCChHHHHHHHhccceeccccc
Q 043276 158 FLQENPSLFDAELNIFGLLAYDATSALAVAVEKAGITGFGFDKTNVSSNATDLEAFGISQNGPKLLQALSSIRFRGLTGD 237 (829)
Q Consensus 158 ~~~~~~~~~~~~~~~~~~~~YDAV~~~A~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~L~~~~f~G~tG~ 237 (829)
|+... ..++.++..+||++.+++.|+++++.. ++..|.+.|++++|.|.+|.
T Consensus 265 ~g~~~-----~~~~~~~~~~yda~~~~~~A~~~ag~~-----------------------~~~~v~~al~~~~~~~~~G~ 316 (333)
T cd06358 265 FGDDA-----PPLNSLSESCYEAVHALAAAAERAGSL-----------------------DPEALIAALEDVSYDGPRGT 316 (333)
T ss_pred cCCCC-----CCCChHHHHHHHHHHHHHHHHHHhCCC-----------------------CHHHHHHHhccCeeeCCCcc
Confidence 86531 135678889999999999999986421 25789999999999999999
Q ss_pred EEEe-cCcc
Q 043276 238 YIFV-DGQL 245 (829)
Q Consensus 238 ~~F~-~G~~ 245 (829)
+.|+ ++..
T Consensus 317 ~~~~~~~~~ 325 (333)
T cd06358 317 VTMRGRHAR 325 (333)
T ss_pred eEEcccccc
Confidence 9996 5543
No 91
>COG0683 LivK ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]
Probab=99.51 E-value=6.4e-13 Score=146.65 Aligned_cols=221 Identities=23% Similarity=0.229 Sum_probs=168.7
Q ss_pred CCCChHHHHHHHHHHH-HHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCC
Q 043276 1 GALNDSSQVGAITAII-KAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQT 79 (829)
Q Consensus 1 t~psD~~q~~ai~~ll-~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~a 79 (829)
|+|+|..|+.++++++ +.++.++|++|+.|+.||++..+.+++.+++.|..+...+.+.+..+ ++..++.++++.++
T Consensus 127 ~~~~~~~q~~~~~~~l~~~~~~k~v~ii~~~~~yg~~~~~~~~~~l~~~G~~~~~~~~~~~~~~--~~~~~v~~i~~~~~ 204 (366)
T COG0683 127 TGPTDNQQAAAAADYLVKKGGKKRVAIIGDDYAYGEGLADAFKAALKALGGEVVVEEVYAPGDT--DFSALVAKIKAAGP 204 (366)
T ss_pred ecCChHHHHHHHHHHHHHhcCCcEEEEEeCCCCcchhHHHHHHHHHHhCCCeEEEEEeeCCCCC--ChHHHHHHHHhcCC
Confidence 5789999999999988 57777899999999999999999999999999998666667666533 49999999999999
Q ss_pred eEEEEEcChhHHHHHHHHHHHcCccccCeEEEEcCccccccccCCccccccccc--eEEEEecc-CCChhHHHHHHHHHH
Q 043276 80 RVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLEPSVTDSMQG--VIGVRPYV-PKTKALENFRVRWKR 156 (829)
Q Consensus 80 rViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t~~~~~~~~~~~~~~~~~~~g--~l~~~~~~-~~~~~~~~F~~~w~~ 156 (829)
++|++.+..+.+..+++++++.|+.. ..+++.+.+........ .....+ .+...... ...|..+.|.++|++
T Consensus 205 d~v~~~~~~~~~~~~~r~~~~~G~~~-~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~p~~~~f~~~~~~ 279 (366)
T COG0683 205 DAVLVGGYGPDAALFLRQAREQGLKA-KLIGGDGAGTAEFEEIA----GAGGAGAGLLATAYSTPDDSPANKKFVEAYKA 279 (366)
T ss_pred CEEEECCCCccchHHHHHHHHcCCCC-ccccccccCchhhhhhc----ccCccccEEEEecccccccCcchHHHHHHHHH
Confidence 99999999999999999999999632 23333332221111111 111222 23222222 245567779999999
Q ss_pred hhcccCCCCCccccchhHHHHHHHHHHHHHHHHHhcccCccccCCCCCCCCCCCccccCCCChHHHHHHHhccc-eeccc
Q 043276 157 KFLQENPSLFDAELNIFGLLAYDATSALAVAVEKAGITGFGFDKTNVSSNATDLEAFGISQNGPKLLQALSSIR-FRGLT 235 (829)
Q Consensus 157 ~~~~~~~~~~~~~~~~~~~~~YDAV~~~A~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~L~~~~-f~G~t 235 (829)
+++.. ..++.++..+|||+++++.|+++++. .. +...+.++|.... +.+.+
T Consensus 280 ~~g~~------~~~~~~~~~~y~a~~~~~~ai~~a~~-~~---------------------d~~~v~~al~~~~~~~~~~ 331 (366)
T COG0683 280 KYGDP------AAPSYFAAAAYDAVKLLAKAIEKAGK-SS---------------------DREAVAEALKGGKFFDTAG 331 (366)
T ss_pred HhCCC------CCcccchHHHHHHHHHHHHHHHHHhc-CC---------------------CHHHHHHHHhhCCCCccCC
Confidence 98721 13566889999999999999999863 10 1467999999887 78999
Q ss_pred ccEEEe-cCccccceEEEEEcc
Q 043276 236 GDYIFV-DGQLQSSAFEIINVN 256 (829)
Q Consensus 236 G~~~F~-~G~~~~~~y~I~n~~ 256 (829)
|.+.|+ +|++....|.|..|+
T Consensus 332 G~v~~~~~~~~~~~~~~i~~~~ 353 (366)
T COG0683 332 GPVTFDEKGDRGSKPVYVGQVQ 353 (366)
T ss_pred cceeECCCCCcCCCceEEEEEE
Confidence 999997 899888888888887
No 92
>cd06328 PBP1_SBP_like_2 Periplasmic solute-binding domain of active transport proteins found in gram-negative and gram-positive bacteria. Periplasmic solute-binding domain of active transport proteins found in gram-negative and gram-positive bacteria. Members of this group are initial receptors in the process of active transport across cellular membrane, but their substrate specificities are not known in detail. However, they closely resemble the group of AmiC and active transport systems for short-chain amides and urea (FmdDEF), and thus are likely to exhibit a ligand-binding mode similar to that of the amide sensor protein AmiC from Pseudomonas aeruginosa. Moreover, this binding domain has high sequence identity to the family of hydrophobic amino acid transporters (HAAT), and thus it may also be involved in transport of amino acids.
Probab=99.48 E-value=1.7e-12 Score=141.81 Aligned_cols=210 Identities=16% Similarity=0.166 Sum_probs=157.1
Q ss_pred CCChHHHHHHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeE
Q 043276 2 ALNDSSQVGAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRV 81 (829)
Q Consensus 2 ~psD~~q~~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arV 81 (829)
.+++..++.++++.+... +++|++|+.|++||++..+.+.+.+++.|++|+....++.+ ..|+..++.+|+++++++
T Consensus 118 ~~~~~~~~~~~~~~~~~~-~~~v~~i~~~~~~g~~~~~~~~~~~~~~G~~vv~~~~~~~~--~~d~~~~v~~l~~~~pd~ 194 (333)
T cd06328 118 GRNSSQDAIAAAAALGKP-GKKIATLAQDYAFGRDGVAAFKAALEKLGAAIVTEEYAPTD--TTDFTPYAQRLLDALKKV 194 (333)
T ss_pred cCChHHHHHHHHHHHHhc-CCeEEEEecCccccHHHHHHHHHHHHhCCCEEeeeeeCCCC--CcchHHHHHHHHhcCCCE
Confidence 467778888888877655 89999999999999999999999999999999998888765 458999999999999999
Q ss_pred EEEEcChh-HHHHHHHHHHHcCccccCeEEEEcCccccccccCCccccccccceEEEEecc-CCChhHHHHHHHHHHhhc
Q 043276 82 FILHMLPS-LGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLEPSVTDSMQGVIGVRPYV-PKTKALENFRVRWKRKFL 159 (829)
Q Consensus 82 iIv~~~~~-~~~~i~~~a~~~gm~~~~~vwI~t~~~~~~~~~~~~~~~~~~~g~l~~~~~~-~~~~~~~~F~~~w~~~~~ 159 (829)
|++..... .+..+++++.+.|... . ............ ........+|++...... +.++..+.|.+.|+++++
T Consensus 195 V~~~~~~~~~~~~~~~~~~~~g~~~--~-~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~y~~~~g 269 (333)
T cd06328 195 LFVIWAGAGGPWPKLQQMGVLGYGI--E-ITLAGDILANLT--MYKAGPGMSGASYYYHYFLPKNPVNDWLVEEHKARFG 269 (333)
T ss_pred EEEEecCchhHHHHHHHhhhhcCCC--e-EEecccccCccc--cccccccccceeeeecCCCCCCHHHHHHHHHHHHHhC
Confidence 87765444 6777788888777421 1 222222221111 111233456666554443 667888899999999876
Q ss_pred ccCCCCCccccchhHHHHHHHHHHHHHHHHHhcccCccccCCCCCCCCCCCccccCCCChHHHHHHHhccceecccccEE
Q 043276 160 QENPSLFDAELNIFGLLAYDATSALAVAVEKAGITGFGFDKTNVSSNATDLEAFGISQNGPKLLQALSSIRFRGLTGDYI 239 (829)
Q Consensus 160 ~~~~~~~~~~~~~~~~~~YDAV~~~A~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~L~~~~f~G~tG~~~ 239 (829)
. .++.++...||++.+++.|+++++.. ++..+.++|++.+|.+..|.+.
T Consensus 270 ~--------~p~~~~~~~y~a~~~l~~Ai~~ag~~-----------------------~~~~v~~aL~~~~~~~~~g~~~ 318 (333)
T cd06328 270 S--------PPDLFTAGGMSAAIAVVEALEETGDT-----------------------DTEALIAAMEGMSFETPKGTMT 318 (333)
T ss_pred C--------CcchhhHHHHHHHHHHHHHHHHhCCC-----------------------CHHHHHHHHhCCeeecCCCceE
Confidence 4 36778999999999999999997621 1577999999999999999999
Q ss_pred Ee--cCccccceE
Q 043276 240 FV--DGQLQSSAF 250 (829)
Q Consensus 240 F~--~G~~~~~~y 250 (829)
|+ +++...+.|
T Consensus 319 f~~~~~~~~~~~~ 331 (333)
T cd06328 319 FRKEDHQALQPMY 331 (333)
T ss_pred ECcccchhhhccc
Confidence 95 555443333
No 93
>cd06335 PBP1_ABC_ligand_binding_like_2 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. Members of this group are sequence-similar to members of the family of ABC-type hydrophobic amino acid transporters, such as leucine-isoleucine-valine-binding protein (LIVBP); however their ligand specificity has not been determined experimentally.
Probab=99.45 E-value=3.6e-12 Score=140.05 Aligned_cols=206 Identities=20% Similarity=0.253 Sum_probs=154.0
Q ss_pred CCCChHHHHHHHHHHH-HHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCC
Q 043276 1 GALNDSSQVGAITAII-KAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQT 79 (829)
Q Consensus 1 t~psD~~q~~ai~~ll-~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~a 79 (829)
+.++|..|+.++++++ ++.+|++|+++|.+++||+...+.+.+.+++.|++|+....++.+ ..++...+.+|++.++
T Consensus 117 ~~~~~~~~~~~~a~~~~~~~~~~~v~ii~~~~~~g~~~~~~~~~~~~~~G~~v~~~~~~~~~--~~d~s~~i~~i~~~~~ 194 (347)
T cd06335 117 VSADDSIQAPFLVDEAVKRGGFKKVALLLDNTGWGRSNRKDLTAALAARGLKPVAVEWFNWG--DKDMTAQLLRAKAAGA 194 (347)
T ss_pred eccChHHHHHHHHHHHHHhcCCCeEEEEeccCchhhhHHHHHHHHHHHcCCeeEEEeeecCC--CccHHHHHHHHHhCCC
Confidence 3578889999999976 667799999999999999999999999999999999988888765 4479999999999999
Q ss_pred eEEEEEcChhHHHHHHHHHHHcCccccCeEEEEcCccccccccCCccccccccceEEEEecc---CCChhHHHHHHHHHH
Q 043276 80 RVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLEPSVTDSMQGVIGVRPYV---PKTKALENFRVRWKR 156 (829)
Q Consensus 80 rViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t~~~~~~~~~~~~~~~~~~~g~l~~~~~~---~~~~~~~~F~~~w~~ 156 (829)
++|++.+....+..+++++++.|+. +.+++.+......... .......|++....+. +..+..++|.+.|++
T Consensus 195 d~v~~~~~~~~~~~~~~~~~~~g~~----~~~~~~~~~~~~~~~~-~~g~~~~g~~~~~~~~~~~~~~~~~~~f~~~~~~ 269 (347)
T cd06335 195 DAIIIVGNGPEGAQIANGMAKLGWK----VPIISHWGLSGGNFIE-GAGPAANDALMIQTFIFEPPSNPKAKAFLAAYHK 269 (347)
T ss_pred CEEEEEecChHHHHHHHHHHHcCCC----CcEecccCCcCchhhh-ccchhhcCcEEEEeeccccCCCHHHHHHHHHHHH
Confidence 9999999999999999999999963 2333321111111111 1224467776654432 256788999999999
Q ss_pred hhcccCCCCCccccchhHHHHHHHHHHHHHHHHHhcccCccccCCCCCCCCCCCccccCCCChHHHHHHHhcc--ceecc
Q 043276 157 KFLQENPSLFDAELNIFGLLAYDATSALAVAVEKAGITGFGFDKTNVSSNATDLEAFGISQNGPKLLQALSSI--RFRGL 234 (829)
Q Consensus 157 ~~~~~~~~~~~~~~~~~~~~~YDAV~~~A~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~L~~~--~f~G~ 234 (829)
+++..... ...++.++..+||+++++++|+++++... +..+.+.|.+. .+.|+
T Consensus 270 ~~~~~~~~--~~~~~~~~~~aYd~~~~l~~A~~~ag~~~-----------------------~~~v~~al~~~~~~~~G~ 324 (347)
T cd06335 270 KYPEKKPA--DIPAPVGAAHAYDAVHLLAAAIKQAGSTD-----------------------GRAIKRALENLKKPVEGL 324 (347)
T ss_pred HhCCCccc--ccCcchhHHHHHHHHHHHHHHHHHhcCCC-----------------------HHHHHHHHHhccCCceee
Confidence 88653100 01234567789999999999999975321 35677888765 47788
Q ss_pred cccE
Q 043276 235 TGDY 238 (829)
Q Consensus 235 tG~~ 238 (829)
.|..
T Consensus 325 ~~~~ 328 (347)
T cd06335 325 VKTY 328 (347)
T ss_pred eccc
Confidence 7755
No 94
>cd06356 PBP1_Amide_Urea_BP_like Periplasmic component (FmdD) of an active transport system for short-chain amides and urea (FmdDEF). This group includes the type I periplasmic-binding proteins that are predicted to have a function similar to that of an active transport system for short chain amides and/or urea in bacteria and Archaea, by sequence comparison and phylogenetic analysis.
Probab=99.41 E-value=8.6e-12 Score=136.24 Aligned_cols=210 Identities=15% Similarity=0.172 Sum_probs=157.6
Q ss_pred CCChHHHHHHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeE
Q 043276 2 ALNDSSQVGAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRV 81 (829)
Q Consensus 2 ~psD~~q~~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arV 81 (829)
.+++..++.++++.+...+=++|++|+.|++||......+.+.+++.|+.++....++.+ ..|++.++.+|+..++++
T Consensus 113 ~~~~~~~~~~~~~~~~~~~~~~vail~~d~~~g~~~~~~~~~~~~~~G~~vv~~~~~~~~--~~d~~~~v~~l~~~~pd~ 190 (334)
T cd06356 113 GATPAQQFSTLVPYMMEKYGKKVYTIAADYNFGQISAEWVRKIVEENGGEVVGEEFIPLD--VSDFGSTIQKIQAAKPDF 190 (334)
T ss_pred CCCcHHHHHHHHHHHHHccCCeEEEECCCchhhHHHHHHHHHHHHHcCCEEEeeeecCCC--chhHHHHHHHHHhcCCCE
Confidence 467788999999988654337899999999999999999999999999999988888766 458999999999999999
Q ss_pred EEEEcChhHHHHHHHHHHHcCccccCeEEEEcCcccc-ccccCCccccccccceEEEEeccC--CChhHHHHHHHHHHhh
Q 043276 82 FILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTN-LLRTLEPSVTDSMQGVIGVRPYVP--KTKALENFRVRWKRKF 158 (829)
Q Consensus 82 iIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t~~~~~-~~~~~~~~~~~~~~g~l~~~~~~~--~~~~~~~F~~~w~~~~ 158 (829)
|++.........+++++++.|+ . . +-+.+..+.. .... .......++|+++...+.+ ..+..+.|.+.|++++
T Consensus 191 v~~~~~~~~~~~~~~~~~~~G~-~-~-~~~~~~~~~~~~~~~-~~~~~~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~ 266 (334)
T cd06356 191 VMSILVGANHLSFYRQWAAAGL-G-N-IPMASSTLGAQGYEH-KRLKPPALKDMYATANYIEELDTPANKAFVERFRAKF 266 (334)
T ss_pred EEEeccCCcHHHHHHHHHHcCC-c-c-CceeeeecccchhHH-hccCchhcCCeEEecchhhhcCCHHHHHHHHHHHHHc
Confidence 9998888888999999999997 1 1 1122222211 1000 0011244677776655433 3567889999999988
Q ss_pred cccCCCCCccccchhHHHHHHHHHHHHHHHHHhcccCccccCCCCCCCCCCCccccCCCChHHHHHHHhc-cceeccccc
Q 043276 159 LQENPSLFDAELNIFGLLAYDATSALAVAVEKAGITGFGFDKTNVSSNATDLEAFGISQNGPKLLQALSS-IRFRGLTGD 237 (829)
Q Consensus 159 ~~~~~~~~~~~~~~~~~~~YDAV~~~A~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~L~~-~~f~G~tG~ 237 (829)
+.. | .++.++..+||++.+++.|+++++.. ++..|.++|+. ..|+|..|.
T Consensus 267 ~~~-p-----~~~~~~~~~y~a~~~~~~A~~~ag~~-----------------------~~~~v~~aL~~~~~~~~~~g~ 317 (334)
T cd06356 267 PDA-P-----YINEEAENNYEAIYLYKEAVEKAGTT-----------------------DRDAVIEALESGLVCDGPEGK 317 (334)
T ss_pred CCC-C-----CCCchhHHHHHHHHHHHHHHHHHCCC-----------------------CHHHHHHHHHhCCceeCCCce
Confidence 642 1 12457889999999999999997532 15779999996 579999999
Q ss_pred EEEe--cCccc
Q 043276 238 YIFV--DGQLQ 246 (829)
Q Consensus 238 ~~F~--~G~~~ 246 (829)
+.|+ +++..
T Consensus 318 ~~~~~~~h~~~ 328 (334)
T cd06356 318 VCIDGKTHHTS 328 (334)
T ss_pred EEEecCCCcee
Confidence 9996 44443
No 95
>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=99.38 E-value=5.7e-12 Score=137.66 Aligned_cols=201 Identities=16% Similarity=0.155 Sum_probs=150.5
Q ss_pred CCChHHHHHHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcC----
Q 043276 2 ALNDSSQVGAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTM---- 77 (829)
Q Consensus 2 ~psD~~q~~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~---- 77 (829)
.+++..|+.++++.+...|+++|++|+.+++||.+..+.|.+.+++.|++|+....++.+ ..++..++.+|+..
T Consensus 105 ~~~~~~~~~~~~~~~~~~g~k~vaii~~~~~~g~~~~~~f~~~~~~~G~~vv~~~~~~~~--~~d~~~~i~~i~~~~~~~ 182 (336)
T cd06339 105 GLSPEDEARRAAEYARSQGKRRPLVLAPDGAYGQRVADAFRQAWQQLGGTVVAIESYDPS--PTDLSDAIRRLLGVDDSE 182 (336)
T ss_pred cCChHHHHHHHHHHHHhcCccceEEEecCChHHHHHHHHHHHHHHHcCCceeeeEecCCC--HHHHHHHHHHHhccccch
Confidence 568889999999999878999999999999999999999999999999999988888765 56899999999987
Q ss_pred -----------------CCeEEEEEcChh-HHHHHHHHHHHcCccccCeEEEEcCccccccccCCccccccccceEEEEe
Q 043276 78 -----------------QTRVFILHMLPS-LGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLEPSVTDSMQGVIGVRP 139 (829)
Q Consensus 78 -----------------~arViIv~~~~~-~~~~i~~~a~~~gm~~~~~vwI~t~~~~~~~~~~~~~~~~~~~g~l~~~~ 139 (829)
++++|++.+.+. .+..+..++...+....+-.++.+++|.... ... ......+|++...+
T Consensus 183 ~~~~~~~~~~~~~~~~~~~d~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~-~~~-~~g~~~~g~~~~~~ 260 (336)
T cd06339 183 QRIAQLKSLESEPRRRQDIDAIDAVALPDGEARLIKPQLLFYYGVPGDVPLYGTSRWYSGT-PAP-LRDPDLNGAWFADP 260 (336)
T ss_pred hhhhhhhhcccCccccCCCCcEEEEecChhhhhhhcchhhhhccCcCCCCEEEeccccCCC-CCc-ccCcccCCcEEeCC
Confidence 899999888876 6667777776655211244678888777431 111 22345677765544
Q ss_pred ccCCChhHHHHHHHHHHhhcccCCCCCcccc-chhHHHHHHHHHHHHHHHHHhcccCccccCCCCCCCCCCCccccCCCC
Q 043276 140 YVPKTKALENFRVRWKRKFLQENPSLFDAEL-NIFGLLAYDATSALAVAVEKAGITGFGFDKTNVSSNATDLEAFGISQN 218 (829)
Q Consensus 140 ~~~~~~~~~~F~~~w~~~~~~~~~~~~~~~~-~~~~~~~YDAV~~~A~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 218 (829)
... ...+|.+.|+++|+. .+ +.++..+|||+.+++.|+++...+
T Consensus 261 ~~~---~~~~f~~~y~~~~~~--------~p~~~~~a~~YDa~~l~~~~~~~~~~~------------------------ 305 (336)
T cd06339 261 PWL---LDANFELRYRAAYGW--------PPLSRLAALGYDAYALAAALAQLGQGD------------------------ 305 (336)
T ss_pred Ccc---cCcchhhhHHHHhcC--------CCCchHHHHHHhHHHHHHHHHHccccc------------------------
Confidence 222 223788888888765 35 779999999999999877664311
Q ss_pred hHHHHHHH-hccceecccccEEEe-cCccc
Q 043276 219 GPKLLQAL-SSIRFRGLTGDYIFV-DGQLQ 246 (829)
Q Consensus 219 g~~l~~~L-~~~~f~G~tG~~~F~-~G~~~ 246 (829)
. +| +...|.|++|.+.|+ +|+..
T Consensus 306 ~-----al~~~~~~~g~~G~~~f~~~g~~~ 330 (336)
T cd06339 306 A-----ALTPGAGFSGVTGVLRLDPDGVIE 330 (336)
T ss_pred c-----ccCCCCccccCcceEEECCCCeEE
Confidence 0 22 223699999999996 88863
No 96
>cd06334 PBP1_ABC_ligand_binding_like_1 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. Members of this group are sequence-similar to members of the family of ABC-type hydrophobic amino acid transporters, such as leucine-isoleucine-valine-binding protein (LIVBP); however their ligand specificity has not been determined experimentally.
Probab=99.35 E-value=2.4e-11 Score=133.39 Aligned_cols=222 Identities=14% Similarity=0.074 Sum_probs=161.6
Q ss_pred CCCChHHHHHHHHHHHHHcC-----CcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhh
Q 043276 1 GALNDSSQVGAITAIIKAFG-----WREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLF 75 (829)
Q Consensus 1 t~psD~~q~~ai~~ll~~fg-----W~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk 75 (829)
+.|++..|+.++++++...+ .++|++|+.|++||+...+.+.+.+++.|++|+....++.+ ..|+..++.+++
T Consensus 115 ~~~~~~~~~~~l~~~~~~~~~~~~~~~kvaiv~~~~~~g~~~~~~~~~~~~~~G~~vv~~~~~~~~--~~D~~~~v~~i~ 192 (351)
T cd06334 115 VGPTYSDQARALVQYIAEQEGGKLKGKKIALVYHDSPFGKEPIEALKALAEKLGFEVVLEPVPPPG--PNDQKAQWLQIR 192 (351)
T ss_pred CCCCHHHHHHHHHHHHHHhcccCCCCCeEEEEeCCCccchhhHHHHHHHHHHcCCeeeeeccCCCC--cccHHHHHHHHH
Confidence 46889999999999987655 69999999999999999999999999999999988888766 458999999999
Q ss_pred cCCCeEEEEEcChhHHHHHHHHHHHcCccccCeEEEEcCccccccccCCccccccccceEEEEeccC--CChhHHHHHHH
Q 043276 76 TMQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLEPSVTDSMQGVIGVRPYVP--KTKALENFRVR 153 (829)
Q Consensus 76 ~~~arViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t~~~~~~~~~~~~~~~~~~~g~l~~~~~~~--~~~~~~~F~~~ 153 (829)
+.++++|++.+....+..++++++++|+. -.|+.+.+ ....... .......+|+++..++.+ .+|..+.|.+.
T Consensus 193 ~~~pd~V~~~~~~~~~~~~~~~~~~~G~~---~~~~~~~~-~~~~~~~-~~~g~~~~g~~~~~~~~~~~~~p~~~~f~~~ 267 (351)
T cd06334 193 RSGPDYVILWGWGVMNPVAIKEAKRVGLD---DKFIGNWW-SGDEEDV-KPAGDAAKGYKGVTPFAGGADDPVGKEIVKE 267 (351)
T ss_pred HcCCCEEEEecccchHHHHHHHHHHcCCC---ceEEEeec-cCcHHHH-HHhhhhhcCcEEeecccCCCCchHHHHHHHH
Confidence 99999999999999999999999999962 23554432 2111111 123345678777665543 56888999999
Q ss_pred HHHhhcccCCCCCccccchhHHHHHHHHHHHHHHHHHhcccCccccCCCCCCCCCCCccccCCCChHHHHHHHhccceec
Q 043276 154 WKRKFLQENPSLFDAELNIFGLLAYDATSALAVAVEKAGITGFGFDKTNVSSNATDLEAFGISQNGPKLLQALSSIRFRG 233 (829)
Q Consensus 154 w~~~~~~~~~~~~~~~~~~~~~~~YDAV~~~A~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~L~~~~f~G 233 (829)
++++++.. +. .+..++.++...|||+++++.||++++...... ..........-...++.+.+....|
T Consensus 268 ~~~~~~~~-~~-~~~~~~~~~~~gy~a~~~l~~Al~~ag~~~~~~----------~~~~~~~~~~~~~~~~~~~~~~~~g 335 (351)
T cd06334 268 VYDKGKGS-GN-DKEIGSVYYNRGVVNAMIMVEAIRRAQEKGGET----------TIAGEEQLENLKLDAARLEELGAEG 335 (351)
T ss_pred HHHccCCC-CC-cccccccHHHHHHHHHHHHHHHHHHHHHhcCCC----------CCcHHHHHHhhhhhhhhhhhcCccc
Confidence 99887532 10 012345688999999999999999997664210 0000000000012345666777888
Q ss_pred ccccEEEe
Q 043276 234 LTGDYIFV 241 (829)
Q Consensus 234 ~tG~~~F~ 241 (829)
+.|++.|.
T Consensus 336 ~~~~~~~~ 343 (351)
T cd06334 336 LGPPVSVS 343 (351)
T ss_pred ccCCceec
Confidence 99999884
No 97
>cd06337 PBP1_ABC_ligand_binding_like_4 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. Members of this group are sequence-similar to members of the family of ABC-type hydrophobic amino acid transporters, such as leucine-isoleucine-valine-binding protein (LIVBP); however their ligand specificity has not been determined experimentally.
Probab=99.35 E-value=1.8e-11 Score=135.10 Aligned_cols=203 Identities=10% Similarity=0.107 Sum_probs=148.7
Q ss_pred CChHHHHHHHHHHHHHcC-CcEEEEEEEeCccccchHHHHH---HHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCC
Q 043276 3 LNDSSQVGAITAIIKAFG-WREAVPIYVDNQYGEELIPSLT---DALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQ 78 (829)
Q Consensus 3 psD~~q~~ai~~ll~~fg-W~~V~iI~~dd~yG~~~~~~l~---~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~ 78 (829)
+++..+..+++++++..+ +++|++++.|++||....+.+. +++++.|+.|+..+.++.+ ..|+..++.+||+++
T Consensus 126 ~~~~~~~~~~~~~~~~~~~~k~v~ii~~~~~~g~~~~~~~~~~~~~~~~~G~~vv~~~~~~~~--~~D~~~~v~~ik~a~ 203 (357)
T cd06337 126 WGAEDVVATYVGMWKQLETNKKVGILYPNDPDGNAFADPVIGLPAALADAGYKLVDPGRFEPG--TDDFSSQINAFKREG 203 (357)
T ss_pred CCHHHHHHHHHHHHHhCCCCceEEEEeecCchhHHHHHhhhcccHHHHhCCcEEecccccCCC--CCcHHHHHHHHHhcC
Confidence 345567788888888888 9999999999999998777665 5677899999988888776 448999999999999
Q ss_pred CeEEEEEcChhHHHHHHHHHHHcCccccCeEEEEcCccccccccCCccccccccceEEEEeccCC--------ChhHHHH
Q 043276 79 TRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLEPSVTDSMQGVIGVRPYVPK--------TKALENF 150 (829)
Q Consensus 79 arViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t~~~~~~~~~~~~~~~~~~~g~l~~~~~~~~--------~~~~~~F 150 (829)
+++|++.+..+.+..++++++++|... .+...+.+... ..... ......+|++....+.+. ++..++|
T Consensus 204 pD~v~~~~~~~~~~~~~~~~~~~G~~~--~~~~~~~~~~~-~~~~~-~~g~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~ 279 (357)
T cd06337 204 VDIVTGFAIPPDFATFWRQAAQAGFKP--KIVTIAKALLF-PEDVE-ALGDRGDGMSTEVWWSPSHPFRSSLTGQSAAEL 279 (357)
T ss_pred CCEEEeCCCccHHHHHHHHHHHCCCCC--CeEEEeccccC-HHHHH-HhhhhhcCccccceeccCCCcccccCCccHHHH
Confidence 999999999999999999999999632 22222222211 11111 111234566544332222 2457899
Q ss_pred HHHHHHhhcccCCCCCccccchhHHHHHHHHHHHHHHHHHhcccCccccCCCCCCCCCCCccccCCCChHHHHHHHhccc
Q 043276 151 RVRWKRKFLQENPSLFDAELNIFGLLAYDATSALAVAVEKAGITGFGFDKTNVSSNATDLEAFGISQNGPKLLQALSSIR 230 (829)
Q Consensus 151 ~~~w~~~~~~~~~~~~~~~~~~~~~~~YDAV~~~A~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~L~~~~ 230 (829)
.++|+++++.. +.....++||++.+++.|++++++.. ++..|.++|++.+
T Consensus 280 ~~~y~~~~g~~--------~~~~~~~~~~~~~~l~~Ai~~Ags~~----------------------d~~~v~~aL~~~~ 329 (357)
T cd06337 280 ADAYEAATGRQ--------WTQPLGYAHALFEVGVKALVRADDPD----------------------DPAAVADAIATLK 329 (357)
T ss_pred HHHHHHHhCCC--------ccCcchHHHHHHHHHHHHHHHcCCCC----------------------CHHHHHHHHHcCC
Confidence 99999888652 33345679999999999999975421 1567999999999
Q ss_pred eecccccEEEe
Q 043276 231 FRGLTGDYIFV 241 (829)
Q Consensus 231 f~G~tG~~~F~ 241 (829)
|.++.|++.|+
T Consensus 330 ~~~~~G~~~f~ 340 (357)
T cd06337 330 LDTVVGPVDFG 340 (357)
T ss_pred cccceeeeecC
Confidence 99999999995
No 98
>smart00079 PBPe Eukaryotic homologues of bacterial periplasmic substrate binding proteins. Prokaryotic homologues are represented by a separate alignment: PBPb
Probab=99.32 E-value=1.4e-11 Score=115.25 Aligned_cols=122 Identities=32% Similarity=0.486 Sum_probs=105.5
Q ss_pred CCCCHHHHHhC-CCcEEEEeCchHHHHHHhcCCCc----------cceeecCChHHHHHHHhcCCcCCceeEEEcchhHH
Q 043276 531 TITDVNLLIKR-GDNVGYQKGSFVLGILKQLGFDE----------RKLVVYNSHEECDELFQKGSANGGIAAAFDEIPYA 599 (829)
Q Consensus 531 ~I~s~~dL~~~-~~~vg~~~~s~~~~~l~~~~~~~----------~~~~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~ 599 (829)
+|++++||..+ ++++|++.|++.+.++++..... .+++.+++..+++.+|..|+ ||++.+.+.+
T Consensus 1 ~i~~~~dl~~~~~~~vgv~~gs~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~-----da~v~d~~~~ 75 (134)
T smart00079 1 PITSVEDLAKQTKIEYGTIRGSSTLAFFKRSGNPEYSRMWNYMSASPSVFVKSYAEGVQRVRVSN-----YAFLMESTYL 75 (134)
T ss_pred CCCChHHHhhCCCccceEecCchHHHHHHhCCChHHHHHHHHHHhCCCCCCCCHHHHHHHHHcCC-----CEEEeehHhH
Confidence 47899999643 26899999999999998753321 25677889999999999887 7899999999
Q ss_pred HHHHhcCCCceEEeCcccccCCceeeecCCCCchhhHHHHHHhhhccChhHHHHHHHcc
Q 043276 600 KLLIGQHCSKYTMVEPTFKTAGFGFAFPLHSPLVHDVSKAILNVTEGDKMKEIEDAWFK 658 (829)
Q Consensus 600 ~~~~~~~c~~l~~v~~~~~~~~~~~~~~k~spl~~~in~~il~l~e~G~~~~~~~~w~~ 658 (829)
.++.++.|+ +.+++..+...+++++++||++|++.+|.+|.++.++|.++++.++|+.
T Consensus 76 ~~~~~~~~~-~~~~~~~~~~~~~~ia~~k~~~l~~~vn~~l~~l~~~G~~~~l~~kw~~ 133 (134)
T smart00079 76 DYELSQNCD-LMTVGENFGRKGYGIAFPKGSPLRDDLSRAILKLSESGELQKLENKWWK 133 (134)
T ss_pred HHHHhCCCC-eEEcCcccCCCceEEEecCCCHHHHHHHHHHHHHHhcCcHHHHHHhhcc
Confidence 999888885 8888888888899999999999999999999999999999999999985
No 99
>COG4623 Predicted soluble lytic transglycosylase fused to an ABC-type amino acid-binding protein [Cell envelope biogenesis, outer membrane]
Probab=99.31 E-value=2.5e-11 Score=124.33 Aligned_cols=223 Identities=14% Similarity=0.117 Sum_probs=178.2
Q ss_pred CCCceEEEecccccCccceEEEeecCCCCCceEEEeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcC
Q 043276 305 TNEKKLRVGVPVKKGFSDFVKVTIDPKTQETSVVGYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLG 384 (829)
Q Consensus 305 ~~~~~lrv~v~~~~~~~p~~~~~~~~~~~~~~~~G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g 384 (829)
..++.|||++.++|- .+.. +++...|++.++.+++++.|| |+++..+.. +-+.|+.+|.+|
T Consensus 20 q~rGvLrV~tinsp~----sy~~-----~~~~p~G~eYelak~Fa~yLg--V~Lki~~~~--------n~dqLf~aL~ng 80 (473)
T COG4623 20 QARGVLRVSTINSPL----SYFE-----DKGGPTGLEYELAKAFADYLG--VKLKIIPAD--------NIDQLFDALDNG 80 (473)
T ss_pred HhcCeEEEEeecCcc----ceec-----cCCCccchhHHHHHHHHHHhC--CeEEEEecC--------CHHHHHHHHhCC
Confidence 457899999986643 3322 356677999999999999999 466777754 679999999999
Q ss_pred cccEEEeccccccccceeccccccccccceEEEEEccCCCCCCceeeeccCCHhHHHHHHHHHHHHHHHHHhhhcccCCC
Q 043276 385 EFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMIVPIKDSKKRNAWVFLQPLTWDLWVTSGCFFIFIGFVVWVLEHRVNED 464 (829)
Q Consensus 385 ~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv~~~~~~~~~~~~fl~PF~~~vW~~i~~~~~~~~~v~~~~~~~~~~~ 464 (829)
++|++.+++...++|.+.+.....|....+.+|.++.+.+
T Consensus 81 ~~DL~Aagl~~~~~~l~~~~~gP~y~svs~qlVyRkG~~R---------------------------------------- 120 (473)
T COG4623 81 NADLAAAGLLYNSERLKNFQPGPTYYSVSQQLVYRKGQYR---------------------------------------- 120 (473)
T ss_pred CcceecccccCChhHhcccCCCCceecccHHHHhhcCCCC----------------------------------------
Confidence 9999999999999999999988889999999998877654
Q ss_pred CCCCccCccchhHHHHHHHhhhcCccccccchhHHHHHHHHHHHHHHHHHhHHHHHHHhhcccCCCCCCCHHHHHhCCCc
Q 043276 465 FRGPARHQVGTSFWFSFSTMVFSQRERVISNLARFVVIVWCFVVLILIQSYTASLTSLLTVDQLQPTITDVNLLIKRGDN 544 (829)
Q Consensus 465 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~s~~~R~v~~~w~~~~lil~~~YtA~L~s~Lt~~~~~~~I~s~~dL~~~~~~ 544 (829)
.+++++|. +..
T Consensus 121 -------------------------------------------------------------------p~~l~~L~--g~~ 131 (473)
T COG4623 121 -------------------------------------------------------------------PRSLGQLK--GRQ 131 (473)
T ss_pred -------------------------------------------------------------------CCCHHHcc--Cce
Confidence 37899994 777
Q ss_pred EEEEeCchHHHHHHh---cCCCcccee--ecCChHHHHHHHhcCCcCCceeEEEcchhHHHHHHhcCCCceEEeCccccc
Q 043276 545 VGYQKGSFVLGILKQ---LGFDERKLV--VYNSHEECDELFQKGSANGGIAAAFDEIPYAKLLIGQHCSKYTMVEPTFKT 619 (829)
Q Consensus 545 vg~~~~s~~~~~l~~---~~~~~~~~~--~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~~c~~l~~v~~~~~~ 619 (829)
+.+..|+...+.++. ..+|..... .-...++.++.+..|+ ++..+.++..+..+..-+.+ +.+.-+.-..
T Consensus 132 i~v~~gs~~~~~l~~lk~~kyP~l~~k~d~~~~~~dLle~v~~Gk----ldytiads~~is~~q~i~P~-laVafd~tde 206 (473)
T COG4623 132 ITVAKGSAHVEDLKLLKETKYPELIWKVDDKLGVEDLLEMVAEGK----LDYTIADSVEISLFQRVHPE-LAVAFDLTDE 206 (473)
T ss_pred eeccCCcHHHHHHHHHHHhhcchhhhhhcccccHHHHHHHHhcCC----cceeeeccHHHHHHHHhCcc-ceeeeecccc
Confidence 888999887766643 334443222 2236789999999999 99999999888887766664 5555555555
Q ss_pred CCceeeecCC--CCchhhHHHHHHhhhccChhHHHHHHHccCC
Q 043276 620 AGFGFAFPLH--SPLVHDVSKAILNVTEGDKMKEIEDAWFKKH 660 (829)
Q Consensus 620 ~~~~~~~~k~--spl~~~in~~il~l~e~G~~~~~~~~w~~~~ 660 (829)
.+.++++|.+ +.|...++..+..+.|.|.++.+++||++.-
T Consensus 207 ~~v~Wy~~~~dd~tL~a~ll~F~~~~~e~g~larleeky~gH~ 249 (473)
T COG4623 207 QPVAWYLPRDDDSTLSAALLDFLNEAKEDGLLARLEEKYLGHG 249 (473)
T ss_pred cCceeeccCCchHHHHHHHHHHHHHhhcchHHHHHHHHHhccc
Confidence 8899999986 4499999999999999999999999999754
No 100
>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=99.23 E-value=6.1e-11 Score=126.80 Aligned_cols=174 Identities=22% Similarity=0.284 Sum_probs=132.1
Q ss_pred CCCChHHHHHHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCe
Q 043276 1 GALNDSSQVGAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTR 80 (829)
Q Consensus 1 t~psD~~q~~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~ar 80 (829)
+.|++..++.+++++++++||++|++++.++.+|....+.+.+.+++.|+++.....++.. .+++...+.++++.+++
T Consensus 116 ~~~~~~~~~~~~~~~l~~~~~~~v~iv~~~~~~~~~~~~~~~~~~~~~g~~i~~~~~~~~~--~~~~~~~~~~l~~~~~~ 193 (299)
T cd04509 116 TGPSDEQQAEALADYIKEYNWKKVAILYDDDSYGRGLLEAFKAAFKKKGGTVVGEEYYPLG--TTDFTSLLQKLKAAKPD 193 (299)
T ss_pred ecCCcHHHHHHHHHHHHHcCCcEEEEEecCchHHHHHHHHHHHHHHHcCCEEEEEecCCCC--CccHHHHHHHHHhcCCC
Confidence 3578889999999999999999999999999999999999999999999999876666544 24677888888888899
Q ss_pred EEEEEcChhHHHHHHHHHHHcCccccCeEEEEcCccccccccCCccccccccceEEEEeccCCChhHH-HHHHHHHHhhc
Q 043276 81 VFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLEPSVTDSMQGVIGVRPYVPKTKALE-NFRVRWKRKFL 159 (829)
Q Consensus 81 ViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t~~~~~~~~~~~~~~~~~~~g~l~~~~~~~~~~~~~-~F~~~w~~~~~ 159 (829)
+|++++....+..+++++++.|+. .++.||..+.+...... ....+.++|+++..+..+..+... .+...|+..+.
T Consensus 194 ~v~~~~~~~~~~~~~~~~~~~g~~-~~~~~i~~~~~~~~~~~--~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~ 270 (299)
T cd04509 194 VIVLCGSGEDAATILKQAAEAGLT-GGYPILGITLGLSDVLL--EAGGEAAEGVLTGTPYFPGDPPPESFFFVRAAAREK 270 (299)
T ss_pred EEEEcccchHHHHHHHHHHHcCCC-CCCcEEecccccCHHHH--HHhHHhhcCcEEeeccCCCCCChHHHHHHhHHHHHH
Confidence 999999889999999999999987 78999999887643221 123456788888877665443322 22221222222
Q ss_pred ccCCCCCccccchhHHHHHHHHHH
Q 043276 160 QENPSLFDAELNIFGLLAYDATSA 183 (829)
Q Consensus 160 ~~~~~~~~~~~~~~~~~~YDAV~~ 183 (829)
... ...++.++.++|||+++
T Consensus 271 ~~~----~~~~~~~~~~~yda~~~ 290 (299)
T cd04509 271 KKY----EDQPDYFAALAYDAVLL 290 (299)
T ss_pred HHh----CCCCChhhhhhcceeee
Confidence 111 11467789999999988
No 101
>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=99.23 E-value=3.8e-10 Score=123.49 Aligned_cols=207 Identities=16% Similarity=0.164 Sum_probs=151.0
Q ss_pred CCChHHHHHHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeE
Q 043276 2 ALNDSSQVGAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRV 81 (829)
Q Consensus 2 ~psD~~q~~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arV 81 (829)
.+++..++.++++++.+.||++|++|+.++.||....+.+.+++++.|+++.....++.. ..++...+.++++.++++
T Consensus 117 ~~~~~~~~~~~~~~l~~~g~~~v~~l~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~~~~~--~~d~~~~~~~l~~~~~da 194 (336)
T cd06326 117 RASYADEIAAIVRHLVTLGLKRIAVFYQDDAFGKDGLAGVEKALAARGLKPVATASYERN--TADVAAAVAQLAAARPQA 194 (336)
T ss_pred CCChHHHHHHHHHHHHHhCCceEEEEEecCcchHHHHHHHHHHHHHcCCCeEEEEeecCC--cccHHHHHHHHHhcCCCE
Confidence 567888999999999999999999999999999999999999999999998777666654 347888999999888999
Q ss_pred EEEEcChhHHHHHHHHHHHcCccccCeEEEEcCccccccccCCccccccccceEEEE--ec--cCCChhHHHHHHHHHHh
Q 043276 82 FILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLEPSVTDSMQGVIGVR--PY--VPKTKALENFRVRWKRK 157 (829)
Q Consensus 82 iIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t~~~~~~~~~~~~~~~~~~~g~l~~~--~~--~~~~~~~~~F~~~w~~~ 157 (829)
|++......+..+++++++.|+.. ..++ ...+.. .. .........+|++... +. ....+..+.|.+.|++.
T Consensus 195 v~~~~~~~~a~~~i~~~~~~G~~~-~~~~--~~~~~~-~~-~~~~~g~~~~g~~~~~~~~~~~~~~~~~~~~f~~~~~~~ 269 (336)
T cd06326 195 VIMVGAYKAAAAFIRALRKAGGGA-QFYN--LSFVGA-DA-LARLLGEYARGVIVTQVVPNPWSRTLPIVREYQAAMKAY 269 (336)
T ss_pred EEEEcCcHHHHHHHHHHHhcCCCC-cEEE--EeccCH-HH-HHHHhhhhhcceEEEEEecCccccCCHHHHHHHHHHHhh
Confidence 999988888999999999999732 1222 222211 11 1111223456766432 22 22356788898888887
Q ss_pred hcccCCCCCccccchhHHHHHHHHHHHHHHHHHhcccCccccCCCCCCCCCCCccccCCCChHHHHHHHhccceecccc-
Q 043276 158 FLQENPSLFDAELNIFGLLAYDATSALAVAVEKAGITGFGFDKTNVSSNATDLEAFGISQNGPKLLQALSSIRFRGLTG- 236 (829)
Q Consensus 158 ~~~~~~~~~~~~~~~~~~~~YDAV~~~A~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~L~~~~f~G~tG- 236 (829)
+... +++.++..+||++++++.|+++++... ++..+.++|++++..+..|
T Consensus 270 ~~~~-------~~~~~~~~~y~~~~~~~~a~~~~g~~~----------------------~~~~v~~al~~~~~~~~~g~ 320 (336)
T cd06326 270 GPGA-------PPSYVSLEGYIAAKVLVEALRRAGPDP----------------------TRESLLAALEAMGKFDLGGF 320 (336)
T ss_pred CCCC-------CCCeeeehhHHHHHHHHHHHHHcCCCC----------------------CHHHHHHHHHhcCCCCCCCe
Confidence 6531 345677889999999999999865321 2578999999987644444
Q ss_pred cEEEecCc
Q 043276 237 DYIFVDGQ 244 (829)
Q Consensus 237 ~~~F~~G~ 244 (829)
.+.|..+|
T Consensus 321 ~~~~~~~~ 328 (336)
T cd06326 321 RLDFSPGN 328 (336)
T ss_pred EEecCccc
Confidence 77785443
No 102
>PF13433 Peripla_BP_5: Periplasmic binding protein domain; PDB: 1QNL_A 1QO0_A 1PEA_A.
Probab=99.16 E-value=1.8e-09 Score=114.36 Aligned_cols=201 Identities=16% Similarity=0.143 Sum_probs=145.3
Q ss_pred HHHHHHHH-HHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEE
Q 043276 7 SQVGAITA-IIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILH 85 (829)
Q Consensus 7 ~q~~ai~~-ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~ 85 (829)
.|..-+++ ++++||-+++-+|.+|..|++..-..+++.+++.|+.|....-+|.+ .+++...+.+|++.++++|+-.
T Consensus 119 Q~~~pl~~~~~~~~G~~r~~lvGSdYv~pre~Nri~r~~l~~~GgevvgE~Y~plg--~td~~~ii~~I~~~~Pd~V~st 196 (363)
T PF13433_consen 119 QQLLPLIDYLLENFGAKRFYLVGSDYVYPRESNRIIRDLLEARGGEVVGERYLPLG--ATDFDPIIAEIKAAKPDFVFST 196 (363)
T ss_dssp GTHHHHHHHHHHHS--SEEEEEEESSHHHHHHHHHHHHHHHHTT-EEEEEEEE-S---HHHHHHHHHHHHHHT-SEEEEE
T ss_pred hhHHHHHHHHHhccCCceEEEecCCccchHHHHHHHHHHHHHcCCEEEEEEEecCC--chhHHHHHHHHHhhCCCEEEEe
Confidence 44455555 55999999999999999999999999999999999999998888877 5799999999999999999999
Q ss_pred cChhHHHHHHHHHHHcCccccCeEEEEcCccccccccCCccccccccceEEEEeccC--CChhHHHHHHHHHHhhcccCC
Q 043276 86 MLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLEPSVTDSMQGVIGVRPYVP--KTKALENFRVRWKRKFLQENP 163 (829)
Q Consensus 86 ~~~~~~~~i~~~a~~~gm~~~~~vwI~t~~~~~~~~~~~~~~~~~~~g~l~~~~~~~--~~~~~~~F~~~w~~~~~~~~~ 163 (829)
.-.+....|+++.++.|+. ++..-|++...+... . ..-..+...|.++..++.. ++|..+.|+++|+++|+...
T Consensus 197 lvG~s~~aF~r~~~~aG~~-~~~~Pi~S~~~~E~E-~-~~~g~~~~~Gh~~~~~YFqsidtp~N~~Fv~~~~~~~g~~~- 272 (363)
T PF13433_consen 197 LVGDSNVAFYRAYAAAGLD-PERIPIASLSTSEAE-L-AAMGAEAAAGHYTSAPYFQSIDTPENQAFVARFRARYGDDR- 272 (363)
T ss_dssp --TTCHHHHHHHHHHHH-S-SS---EEESS--HHH-H-TTS-HHHHTT-EEEES--TT-SSHHHHHHHHHHHTTS-TT--
T ss_pred CcCCcHHHHHHHHHHcCCC-cccCeEEEEecCHHH-H-hhcChhhcCCcEEeehhhhhCCcHHHHHHHHHHHHHhCCCC-
Confidence 8889999999999999974 456777776655321 1 1112346788888877654 57899999999999987631
Q ss_pred CCCccccchhHHHHHHHHHHHHHHHHHhcccCccccCCCCCCCCCCCccccCCCChHHHHHHHhccceecccccEEEe
Q 043276 164 SLFDAELNIFGLLAYDATSALAVAVEKAGITGFGFDKTNVSSNATDLEAFGISQNGPKLLQALSSIRFRGLTGDYIFV 241 (829)
Q Consensus 164 ~~~~~~~~~~~~~~YDAV~~~A~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~L~~~~f~G~tG~~~F~ 241 (829)
.++...-.+|-+|+++|.|++++++.+ ..+++++|...+|+...|.+.++
T Consensus 273 -----v~s~~~eaaY~~v~l~a~Av~~ags~d-----------------------~~~vr~al~g~~~~aP~G~v~id 322 (363)
T PF13433_consen 273 -----VTSDPMEAAYFQVHLWAQAVEKAGSDD-----------------------PEAVREALAGQSFDAPQGRVRID 322 (363)
T ss_dssp --------HHHHHHHHHHHHHHHHHHHHTS-------------------------HHHHHHHHTT--EEETTEEEEE-
T ss_pred -----CCCcHHHHHHHHHHHHHHHHHHhCCCC-----------------------HHHHHHHhcCCeecCCCcceEEc
Confidence 245556679999999999999996543 57899999999999999999886
No 103
>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=99.08 E-value=1.7e-09 Score=117.90 Aligned_cols=194 Identities=14% Similarity=0.127 Sum_probs=133.6
Q ss_pred CCCChHHHHHHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCCh--hHHHHHHHHhhcCC
Q 043276 1 GALNDSSQVGAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATD--DQIEKELYKLFTMQ 78 (829)
Q Consensus 1 t~psD~~q~~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~--~~~~~~l~~lk~~~ 78 (829)
+.|++..|+.++++.+..-|.++|++|+.|++||....+.+.+.+++.|++|+..+.++...+. .++.......+.++
T Consensus 108 ~~~~~~~~~~ala~~~~~~g~kkvaii~~~~~~g~~~~~~~~~~~~~~G~~vv~~~~~~~~~~~~~~d~s~~~~~~~~s~ 187 (347)
T TIGR03863 108 TLPSRAMLADALAQYLAAKRWRRILLIQGPLPADALYADAFRRSAKRFGAKIVAERPFTFSGDPRRTDQSEVPLFTQGAD 187 (347)
T ss_pred ecCChHhHHHHHHHHHHHcCCCEEEEEeCCCcccHHHHHHHHHHHHHCCCEEEEeEEeccCCchhhhhcccCceeecCCC
Confidence 4689999999999999777999999999999999999999999999999999988888754321 13332222233478
Q ss_pred CeEEEEEcChhHHHHHHHHHHHcCccccCeEEEEcCccccccccCCccccccccceEEEEec-cCCChhHHHHHHHHHHh
Q 043276 79 TRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLEPSVTDSMQGVIGVRPY-VPKTKALENFRVRWKRK 157 (829)
Q Consensus 79 arViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t~~~~~~~~~~~~~~~~~~~g~l~~~~~-~~~~~~~~~F~~~w~~~ 157 (829)
+++|++.....+....+... .++ .... ....|+.....+ ....+..++|.++|+++
T Consensus 188 pDvv~~~~~~~~~~~~~~~~----------~~~-~~~~------------~g~~G~~~~~~~~~~~~~~~~~f~~~f~~~ 244 (347)
T TIGR03863 188 YDVVVVADEAGEFARYLPYA----------TWL-PRPV------------AGSAGLVPTAWHRAWERWGATQLQSRFEKL 244 (347)
T ss_pred CCEEEEecchhhHhhhcccc----------ccc-cccc------------ccccCccccccCCcccchhHHHHHHHHHHH
Confidence 99998865443221110000 000 0000 011222211111 12345678999999998
Q ss_pred hcccCCCCCccccchhHHHHHHHHHHHHHHHHHhcccCccccCCCCCCCCCCCccccCCCChHHHHHHHhccce--eccc
Q 043276 158 FLQENPSLFDAELNIFGLLAYDATSALAVAVEKAGITGFGFDKTNVSSNATDLEAFGISQNGPKLLQALSSIRF--RGLT 235 (829)
Q Consensus 158 ~~~~~~~~~~~~~~~~~~~~YDAV~~~A~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~l~~~L~~~~f--~G~t 235 (829)
|+. .++.+++.+||||++++.|++++++.+ +..+.++|++..+ .+..
T Consensus 245 ~g~--------~p~~~~a~aY~av~~~a~Ai~~AGs~d-----------------------~~aV~~aL~~~~~~~~~~~ 293 (347)
T TIGR03863 245 AGR--------PMTELDYAAWLAVRAVGEAVTRTRSAD-----------------------PATLRDYLLSDEFELAGFK 293 (347)
T ss_pred hCC--------CCChHHHHHHHHHHHHHHHHHHhcCCC-----------------------HHHHHHHHcCCCceecccC
Confidence 865 356678889999999999999997543 6889999998877 4677
Q ss_pred c-cEEE-e-cCccccc
Q 043276 236 G-DYIF-V-DGQLQSS 248 (829)
Q Consensus 236 G-~~~F-~-~G~~~~~ 248 (829)
| ++.| . |++...+
T Consensus 294 g~~~~~R~~Dhq~~~~ 309 (347)
T TIGR03863 294 GRPLSFRPWDGQLRQP 309 (347)
T ss_pred CCcceeeCCCcccccc
Confidence 7 5888 4 8887643
No 104
>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=99.07 E-value=4.4e-09 Score=115.37 Aligned_cols=203 Identities=17% Similarity=0.116 Sum_probs=149.8
Q ss_pred CCChHHHHHHHHHHHHHcCCcEEEEEEEeCc-cccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCe
Q 043276 2 ALNDSSQVGAITAIIKAFGWREAVPIYVDNQ-YGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTR 80 (829)
Q Consensus 2 ~psD~~q~~ai~~ll~~fgW~~V~iI~~dd~-yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~ar 80 (829)
.+++..++.++++++..-|-+++++|+.++. ||+.....+.+++++.|+.+.....++.. ..++...+.++++.+++
T Consensus 113 ~~~~~~~~~~~~~~l~~~g~~~~~~i~~~~~~~g~~~~~~~~~~~~~~G~~v~~~~~~~~~--~~d~~~~~~~i~~~~pd 190 (341)
T cd06341 113 SGGTPASLTTWGDFAKDQGGTRAVALVTALSAAVSAAAALLARSLAAAGVSVAGIVVITAT--APDPTPQAQQAAAAGAD 190 (341)
T ss_pred cCCCcchhHHHHHHHHHcCCcEEEEEEeCCcHHHHHHHHHHHHHHHHcCCccccccccCCC--CCCHHHHHHHHHhcCCC
Confidence 4567778899999998889999999987766 99999999999999999998876666554 34788899999989999
Q ss_pred EEEEEcChhHHHHHHHHHHHcCccccCeEEEEcCccccccccCCccccccccceEEEEeccC---CChhHHHHHHHHHHh
Q 043276 81 VFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLEPSVTDSMQGVIGVRPYVP---KTKALENFRVRWKRK 157 (829)
Q Consensus 81 ViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t~~~~~~~~~~~~~~~~~~~g~l~~~~~~~---~~~~~~~F~~~w~~~ 157 (829)
+|++......+..+++++++.|+..+ ..+........ .. .......+|++....+.+ ..|..+.|.+.+++.
T Consensus 191 aV~~~~~~~~a~~~~~~~~~~G~~~~--~~~~~~~~~~~--~~-~~~g~~~~g~~~~~~~~~~~~~~p~~~~~~~~~~~~ 265 (341)
T cd06341 191 AIITVLDAAVCASVLKAVRAAGLTPK--VVLSGTCYDPA--LL-AAPGPALAGVYIAVFYRPFESGTPAVALYLAAMARY 265 (341)
T ss_pred EEEEecChHHHHHHHHHHHHcCCCCC--EEEecCCCCHH--HH-HhcCcccCceEEEeeeccccCCCHHHHHHHHHHHHh
Confidence 99999888899999999999997443 22222222211 11 123356788887766554 467788888766543
Q ss_pred hcccCCCCCccccchhHHHHHHHHHHHHHHHHHhcccCccccCCCCCCCCCCCccccCCCChHH-HHHHHhccceecccc
Q 043276 158 FLQENPSLFDAELNIFGLLAYDATSALAVAVEKAGITGFGFDKTNVSSNATDLEAFGISQNGPK-LLQALSSIRFRGLTG 236 (829)
Q Consensus 158 ~~~~~~~~~~~~~~~~~~~~YDAV~~~A~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~-l~~~L~~~~f~G~tG 236 (829)
... + ...++.++..+||++++++.|+++++... .+.. +.++|+++++....|
T Consensus 266 ~~~-~----~~~~~~~~~~~yda~~~~~~a~~~ag~~~----------------------~~~~~v~~al~~~~~~~~~g 318 (341)
T cd06341 266 APQ-L----DPPEQGFALIGYIAADLFLRGLSGAGGCP----------------------TRASQFLRALRAVTDYDAGG 318 (341)
T ss_pred CCC-C----CCCcchHHHHHHHHHHHHHHHHHhcCCCC----------------------ChHHHHHHHhhcCCCCCCCC
Confidence 322 1 11467789999999999999999985321 1455 999999987655545
Q ss_pred cE
Q 043276 237 DY 238 (829)
Q Consensus 237 ~~ 238 (829)
-.
T Consensus 319 ~~ 320 (341)
T cd06341 319 LT 320 (341)
T ss_pred cc
Confidence 33
No 105
>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=99.05 E-value=2.9e-09 Score=115.17 Aligned_cols=170 Identities=21% Similarity=0.213 Sum_probs=127.9
Q ss_pred CCChHHHHHHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeE
Q 043276 2 ALNDSSQVGAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRV 81 (829)
Q Consensus 2 ~psD~~q~~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arV 81 (829)
.+++..++.++++.+...||++|++++.++++|....+.+.+.+++.|+++.....++.. ..++...+.++++.++++
T Consensus 114 ~~~~~~~~~~~~~~l~~~g~~~vail~~~~~~~~~~~~~~~~~~~~~G~~v~~~~~~~~~--~~d~~~~~~~l~~~~pda 191 (312)
T cd06333 114 PQNDRLMAEAILADMKKRGVKTVAFIGFSDAYGESGLKELKALAPKYGIEVVADERYGRT--DTSVTAQLLKIRAARPDA 191 (312)
T ss_pred CCCcHHHHHHHHHHHHHcCCCEEEEEecCcHHHHHHHHHHHHHHHHcCCEEEEEEeeCCC--CcCHHHHHHHHHhCCCCE
Confidence 478889999999999999999999999999999999999999999999999877667644 336778888888888999
Q ss_pred EEEEcChhHHHHHHHHHHHcCccccCeEEEEcCccccccccCCccccccccceEEEEe------ccC----CChhHHHHH
Q 043276 82 FILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLEPSVTDSMQGVIGVRP------YVP----KTKALENFR 151 (829)
Q Consensus 82 iIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t~~~~~~~~~~~~~~~~~~~g~l~~~~------~~~----~~~~~~~F~ 151 (829)
|++......+..+++++++.|+.. .++ .++++.. .+.. .......+|++.... ..| ..+..++|.
T Consensus 192 Ii~~~~~~~~~~~~~~l~~~g~~~--p~~-~~~~~~~-~~~~-~~~g~~~~g~~~~~~~~~~~~~~p~~~~~~~~~~~f~ 266 (312)
T cd06333 192 VLIWGSGTPAALPAKNLRERGYKG--PIY-QTHGVAS-PDFL-RLAGKAAEGAILPAGPVLVADQLPDSDPQKKVALDFV 266 (312)
T ss_pred EEEecCCcHHHHHHHHHHHcCCCC--CEE-eecCcCc-HHHH-HHhhHhhcCcEeecccceeeeeCCCCCcchHHHHHHH
Confidence 999887777888999999999632 333 3333332 1111 112345677765431 122 235688999
Q ss_pred HHHHHhhcccCCCCCccccchhHHHHHHHHHHHH
Q 043276 152 VRWKRKFLQENPSLFDAELNIFGLLAYDATSALA 185 (829)
Q Consensus 152 ~~w~~~~~~~~~~~~~~~~~~~~~~~YDAV~~~A 185 (829)
++++++|+.. .++.++...|||+++++
T Consensus 267 ~~~~~~~g~~-------~~~~~~~~~Yda~~~~~ 293 (312)
T cd06333 267 KAYEAKYGAG-------SVSTFGGHAYDALLLLA 293 (312)
T ss_pred HHHHHHhCCC-------CCCchhHHHHHHHHHHH
Confidence 9999888652 25678999999999999
No 106
>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=98.98 E-value=8.3e-09 Score=110.20 Aligned_cols=169 Identities=24% Similarity=0.329 Sum_probs=132.8
Q ss_pred CCChHHHHHHHHHHHHHcC-CcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCe
Q 043276 2 ALNDSSQVGAITAIIKAFG-WREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTR 80 (829)
Q Consensus 2 ~psD~~q~~ai~~ll~~fg-W~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~ar 80 (829)
.|++..++.++++++...+ |++|++|+.++++|....+.+.+++++.|++|.....++.. ..++...+.++++.+++
T Consensus 115 ~~~~~~~~~~~~~~~~~~~~~~~i~~v~~~~~~~~~~~~~~~~~~~~~g~~i~~~~~~~~~--~~~~~~~~~~l~~~~~~ 192 (298)
T cd06268 115 APSDAQQAAALADYLAEKGKVKKVAIIYDDYAYGRGLAAAFREALKKLGGEVVAEETYPPG--ATDFSPLIAKLKAAGPD 192 (298)
T ss_pred ccCcHHHHHHHHHHHHHhcCCCEEEEEEcCCchhHHHHHHHHHHHHHcCCEEEEEeccCCC--CccHHHHHHHHHhcCCC
Confidence 5788889999999998888 99999999999999999999999999999998877666544 24678888999888889
Q ss_pred EEEEEcChhHHHHHHHHHHHcCccccCeEEEEcCccccccccCCccccccccceEEEEeccCCC--hhHHHHH-HHHHHh
Q 043276 81 VFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNLLRTLEPSVTDSMQGVIGVRPYVPKT--KALENFR-VRWKRK 157 (829)
Q Consensus 81 ViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t~~~~~~~~~~~~~~~~~~~g~l~~~~~~~~~--~~~~~F~-~~w~~~ 157 (829)
+|++++....+..+++++++.|+ +..|+.++.+...... ....+..+|+++..++.+.. +....|. ..|++.
T Consensus 193 ~vi~~~~~~~~~~~~~~~~~~g~---~~~~~~~~~~~~~~~~--~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~ 267 (298)
T cd06268 193 AVFLAGYGGDAALFLKQAREAGL---KVPIVGGDGAAAPALL--ELAGDAAEGVLGTTPYAPDDDDPAAAAFFQKAFKAK 267 (298)
T ss_pred EEEEccccchHHHHHHHHHHcCC---CCcEEecCccCCHHHH--HhhhHhhCCcEEeccCCCCCCChhhhHHHHHHHHHH
Confidence 99999888899999999999986 5678888877643221 12234568888877765432 3344454 666666
Q ss_pred hcccCCCCCccccchhHHHHHHHHHHHH
Q 043276 158 FLQENPSLFDAELNIFGLLAYDATSALA 185 (829)
Q Consensus 158 ~~~~~~~~~~~~~~~~~~~~YDAV~~~A 185 (829)
++. .++.++...||++++++
T Consensus 268 ~~~--------~~~~~~~~~y~~~~~~~ 287 (298)
T cd06268 268 YGR--------PPDSYAAAAYDAVRLLA 287 (298)
T ss_pred hCC--------CcccchHHHHHHHHHHc
Confidence 544 46778999999999998
No 107
>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=98.89 E-value=2.5e-08 Score=104.40 Aligned_cols=199 Identities=19% Similarity=0.179 Sum_probs=140.3
Q ss_pred CceEEEecccccCccceEEEeecCCCCCceEEEeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcc
Q 043276 307 EKKLRVGVPVKKGFSDFVKVTIDPKTQETSVVGYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEF 386 (829)
Q Consensus 307 ~~~lrv~v~~~~~~~p~~~~~~~~~~~~~~~~G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~ 386 (829)
.++|+||+. +.+.|+. +.+...++.+.+++++|.++ +++... +|+.++..+..|++
T Consensus 31 ~~~l~vg~~--~~~~~~~------------~~~~~~~l~~~l~~~~g~~v--~~~~~~--------~~~~~~~~l~~g~~ 86 (254)
T TIGR01098 31 PKELNFGIL--PGENASN------------LTRRWEPLADYLEKKLGIKV--QLFVAT--------DYSAVIEAMRFGRV 86 (254)
T ss_pred CCceEEEEC--CCCCHHH------------HHHHHHHHHHHHHHHhCCcE--EEEeCC--------CHHHHHHHHHcCCc
Confidence 467999987 5544332 23446799999999998754 554432 69999999999999
Q ss_pred cEEEecccccc---ccceecccccccccc------ceEEEEEccCCCCCCceeeeccCCHhHHHHHHHHHHHHHHHHHhh
Q 043276 387 DAVVGDTTIVF---NRSNYVDFTLPYTES------GVSMIVPIKDSKKRNAWVFLQPLTWDLWVTSGCFFIFIGFVVWVL 457 (829)
Q Consensus 387 Di~~~~~~it~---~R~~~vdft~p~~~~------~~~~vv~~~~~~~~~~~~fl~PF~~~vW~~i~~~~~~~~~v~~~~ 457 (829)
|+++.+..... +|....+|+.||... ...+++++..
T Consensus 87 Di~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lvv~~d~----------------------------------- 131 (254)
T TIGR01098 87 DIAWFGPSSYVLAHYRANAEVFALTAVSTDGSPGYYSVIIVKADS----------------------------------- 131 (254)
T ss_pred cEEEECcHHHHHHHHhcCCceEEeeccccCCCCceEEEEEEECCC-----------------------------------
Confidence 99986654333 566667888886643 2466666432
Q ss_pred hcccCCCCCCCccCccchhHHHHHHHhhhcCccccccchhHHHHHHHHHHHHHHHHHhHHHHHHHhhcccCCCCCCCHHH
Q 043276 458 EHRVNEDFRGPARHQVGTSFWFSFSTMVFSQRERVISNLARFVVIVWCFVVLILIQSYTASLTSLLTVDQLQPTITDVNL 537 (829)
Q Consensus 458 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~s~~~R~v~~~w~~~~lil~~~YtA~L~s~Lt~~~~~~~I~s~~d 537 (829)
+|++++|
T Consensus 132 -------------------------------------------------------------------------~i~~~~d 138 (254)
T TIGR01098 132 -------------------------------------------------------------------------PIKSLKD 138 (254)
T ss_pred -------------------------------------------------------------------------CCCChHH
Confidence 1689999
Q ss_pred HHhCCCcEEEEe-CchH-----HHHHHh-cCCCc----cceeecCChHHHHHHHhcCCcCCceeEEEcchhHHHHHHhcC
Q 043276 538 LIKRGDNVGYQK-GSFV-----LGILKQ-LGFDE----RKLVVYNSHEECDELFQKGSANGGIAAAFDEIPYAKLLIGQH 606 (829)
Q Consensus 538 L~~~~~~vg~~~-~s~~-----~~~l~~-~~~~~----~~~~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~~ 606 (829)
| +|+++++.. ++.. ..++.+ .+.+. ..+....+..+.+++|..|+ +|+++.+.+.+..+..+.
T Consensus 139 L--~gk~I~~~~~~s~~~~~~~~~~l~~~~~~~~~~~~~~i~~~~~~~~~~~al~~G~----~Da~~~~~~~~~~~~~~~ 212 (254)
T TIGR01098 139 L--KGKTFAFGDPASTSGYLVPRYQLKKEGGLDADGFFSEVVFSGSHDASALAVANGK----VDAATNNSSAIGRLKKRG 212 (254)
T ss_pred h--cCCEEEeeCCCCccchHhHHHHHHHhcCCChHHhhhheeecCchHHHHHHHHcCC----CCeEEecHHHHHHHHHhC
Confidence 9 488999864 3321 233433 22221 34555566788999999999 999999988887776654
Q ss_pred C---CceEEeCcccccCCceeeecCC-CC-chhhHHHHHHhh
Q 043276 607 C---SKYTMVEPTFKTAGFGFAFPLH-SP-LVHDVSKAILNV 643 (829)
Q Consensus 607 c---~~l~~v~~~~~~~~~~~~~~k~-sp-l~~~in~~il~l 643 (829)
. ..+.+++......+++++++|+ .+ +++.+|++|+.+
T Consensus 213 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~~l~~~ 254 (254)
T TIGR01098 213 PSDMKKVRVIWKSPLIPNDPIAVRKDLPPELKEKIRDAFLTL 254 (254)
T ss_pred ccchhheEEEEecCCCCCCCEEEECCCCHHHHHHHHHHHhhC
Confidence 2 2577787666666789999999 55 999999999764
No 108
>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=98.84 E-value=7.1e-10 Score=86.73 Aligned_cols=61 Identities=30% Similarity=0.480 Sum_probs=43.6
Q ss_pred ceEEEeec--CCCCCceEEEeeHHHHHHHHHHCCCcccEEEEecCCCCCC--CCCChhHHHHhHhc
Q 043276 322 DFVKVTID--PKTQETSVVGYSIDVFKAVIEELPYAVAYDFVPYAQPDGT--SSGSYNDLIYQVFL 383 (829)
Q Consensus 322 p~~~~~~~--~~~~~~~~~G~~idll~~ia~~l~f~~~~~~~~~~~~~g~--~ng~~~~li~~l~~ 383 (829)
||++.+++ ..+++.++.|||+||+++||+.|||++++..++.+ ..|. +||+|+||+++|.+
T Consensus 1 Pfvm~~~~~~~~~g~~~~eGyciDll~~la~~l~F~y~i~~~~Dg-~yG~~~~~g~W~GmiGeli~ 65 (65)
T PF10613_consen 1 PFVMLKEDGENLTGNDRYEGYCIDLLEELAEELNFTYEIYLVPDG-KYGSKNPNGSWNGMIGELIR 65 (65)
T ss_dssp TTBEE-TTSSGSBGGGGEESHHHHHHHHHHHHHT-EEEEEE-TTS---EEBETTSEBEHHHHHHHT
T ss_pred CeEEEecCCcccCCCccEEEEHHHHHHHHHHHcCCeEEEEECCCC-CCcCcCCCCcCcCHHHHhcC
Confidence 56676554 45678999999999999999999996555544322 3332 68999999999874
No 109
>PRK00489 hisG ATP phosphoribosyltransferase; Reviewed
Probab=98.82 E-value=3.1e-08 Score=104.99 Aligned_cols=164 Identities=13% Similarity=0.137 Sum_probs=132.7
Q ss_pred ChhHHHHhHhcCcccEEEeccccccccceecccccc--ccccceEEEEEccCCCCCCceeeeccCCHhHHHHHHHHHHHH
Q 043276 373 SYNDLIYQVFLGEFDAVVGDTTIVFNRSNYVDFTLP--YTESGVSMIVPIKDSKKRNAWVFLQPLTWDLWVTSGCFFIFI 450 (829)
Q Consensus 373 ~~~~li~~l~~g~~Di~~~~~~it~~R~~~vdft~p--~~~~~~~~vv~~~~~~~~~~~~fl~PF~~~vW~~i~~~~~~~ 450 (829)
.|.+++..|..|++|+++++..++.+|.+.++|+.| |....+++++|....
T Consensus 52 ~~~~i~~~L~sG~vDlgi~g~~~~~er~~~v~~~~~l~~~~~~lvvvvp~~~~--------------------------- 104 (287)
T PRK00489 52 RPDDIPGYVADGVVDLGITGEDLLEESGADVEELLDLGFGKCRLVLAVPEDSD--------------------------- 104 (287)
T ss_pred CcHHHHHHHHcCCCCEEEcchHHHHHCCCCceEeeeccCCceEEEEEEECCCC---------------------------
Confidence 689999999999999999999999999999999988 677778888884421
Q ss_pred HHHHHhhhcccCCCCCCCccCccchhHHHHHHHhhhcCccccccchhHHHHHHHHHHHHHHHHHhHHHHHHHhhcccCCC
Q 043276 451 GFVVWVLEHRVNEDFRGPARHQVGTSFWFSFSTMVFSQRERVISNLARFVVIVWCFVVLILIQSYTASLTSLLTVDQLQP 530 (829)
Q Consensus 451 ~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~s~~~R~v~~~w~~~~lil~~~YtA~L~s~Lt~~~~~~ 530 (829)
T Consensus 105 -------------------------------------------------------------------------------- 104 (287)
T PRK00489 105 -------------------------------------------------------------------------------- 104 (287)
T ss_pred --------------------------------------------------------------------------------
Confidence
Q ss_pred CCCCHHHHHhCCCcEEEEeCchHHHHHHhcCCCccceeecCChHHHHHHHhcCCcCCceeEEEcchhHHHHHHhcCCCce
Q 043276 531 TITDVNLLIKRGDNVGYQKGSFVLGILKQLGFDERKLVVYNSHEECDELFQKGSANGGIAAAFDEIPYAKLLIGQHCSKY 610 (829)
Q Consensus 531 ~I~s~~dL~~~~~~vg~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~~c~~l 610 (829)
|++++|| .|+++++..+.....++++.+. ..+++.+.+..+. ++..|. +|++++.......+.+. .+
T Consensus 105 -i~sl~DL--~Gk~ia~~~~~~~~~~l~~~gi-~~~iv~~~gs~ea--a~~~G~----aDaivd~~~~~~~l~~~---~L 171 (287)
T PRK00489 105 -WQGVEDL--AGKRIATSYPNLTRRYLAEKGI-DAEVVELSGAVEV--APRLGL----ADAIVDVVSTGTTLRAN---GL 171 (287)
T ss_pred -CCChHHh--CCCEEEEcCcHHHHHHHHHcCC-ceEEEECCCchhh--hhcCCc----ccEEEeeHHHHHHHHHC---CC
Confidence 6889999 5889999888888999988766 3456667655554 566688 99999887777776653 36
Q ss_pred EEeCcccccCCceeeecC--CCC-chhhHHHHHHhhhccChhHHHHHHHccC
Q 043276 611 TMVEPTFKTAGFGFAFPL--HSP-LVHDVSKAILNVTEGDKMKEIEDAWFKK 659 (829)
Q Consensus 611 ~~v~~~~~~~~~~~~~~k--~sp-l~~~in~~il~l~e~G~~~~~~~~w~~~ 659 (829)
.++ +.+.....+++.+| .+| ....++.++.++ .|.+..+.+|||..
T Consensus 172 ~~v-~~~~~~~~~li~~k~~~~~~~~~~i~~~l~~l--~g~l~a~~~k~~~~ 220 (287)
T PRK00489 172 KIV-EVILRSEAVLIARKGWLDPEKQEKIDQLLTRL--QGVLRARESKYLMM 220 (287)
T ss_pred EEE-EeeeeeeEEEEEcccccChhHHHHHHHHHHHH--HHHHHhhceEEEEE
Confidence 666 46566678999999 666 788899999999 59999999999963
No 110
>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=98.13 E-value=6.7e-05 Score=80.07 Aligned_cols=115 Identities=21% Similarity=0.194 Sum_probs=74.7
Q ss_pred CCCHHHHHhCCCcEEEE-eCchHH-----HHH-HhcCCCcc---ceeecC-ChHHHHHHHhcCCcCCceeEEEcchhHHH
Q 043276 532 ITDVNLLIKRGDNVGYQ-KGSFVL-----GIL-KQLGFDER---KLVVYN-SHEECDELFQKGSANGGIAAAFDEIPYAK 600 (829)
Q Consensus 532 I~s~~dL~~~~~~vg~~-~~s~~~-----~~l-~~~~~~~~---~~~~~~-~~~~~~~~l~~g~~~~g~~a~~~~~~~~~ 600 (829)
|++++|| .|+++|+. .++... ..+ +..+.... ..+.+. +..+.+.+|..|+ +|+++.+...+.
T Consensus 127 i~sl~DL--~Gk~v~~~~~~s~~~~~~~~~~l~~~~g~~~~~~~~~v~~~~~~~~~~~al~~G~----vDa~~~~~~~~~ 200 (288)
T TIGR03431 127 IKSLEDL--KGKTFGFVDPNSTSGFLVPSYYLFKKNGIKPKEYFKKVTFSGSHEAAILAVANGT----VDAATTNDENLD 200 (288)
T ss_pred CCcHHHh--CCCEEEeeCCCcchhhHHHHHHHHHhcCCChHHhHHhheecCchHHHHHHHHcCC----CCeEeccHHHHH
Confidence 7899999 58899986 333221 122 33333221 123444 6788999999999 999998887777
Q ss_pred HHHhcCC----CceEEeCcccccCCceeeecCCC-C-chhhHHHHHHhhhccChhHHH
Q 043276 601 LLIGQHC----SKYTMVEPTFKTAGFGFAFPLHS-P-LVHDVSKAILNVTEGDKMKEI 652 (829)
Q Consensus 601 ~~~~~~c----~~l~~v~~~~~~~~~~~~~~k~s-p-l~~~in~~il~l~e~G~~~~~ 652 (829)
.+..+.. ..+.++...-.....+++++++- + +.+.++++|..+.+++...++
T Consensus 201 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~l~~~~~~~~~~~~ 258 (288)
T TIGR03431 201 RMIRKGQPDAMEDLRIIWKSPLIPNGPIVYRKDLPADLKAKIRKAFLNYHKTDKACFE 258 (288)
T ss_pred HHHHcCCCCchhheEEEEEcCCCCCCcEEEeCCCCHHHHHHHHHHHHhcCCCcHHHHH
Confidence 7665321 12444332111224578889984 3 999999999999999665543
No 111
>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=97.74 E-value=0.00028 Score=73.29 Aligned_cols=116 Identities=19% Similarity=0.206 Sum_probs=89.5
Q ss_pred CCChHHHHHHHHHHHHHcCCcEEEEEEEeC-ccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcC-CC
Q 043276 2 ALNDSSQVGAITAIIKAFGWREAVPIYVDN-QYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTM-QT 79 (829)
Q Consensus 2 ~psD~~q~~ai~~ll~~fgW~~V~iI~~dd-~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~-~a 79 (829)
.+++..++.++++++.+++|+++++|+.+. .++......+.+++++.|.++......+.. .+.++......+++. ++
T Consensus 105 ~~~~~~~~~~~~~~l~~~~~~~i~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~l~~~~~~ 183 (269)
T cd01391 105 GPDNEQAGEAAAEYLAEKGWKRVALIYGDDGAYGRERLEGFKAALKKAGIEVVAIEYGDLD-TEKGFQALLQLLKAAPKP 183 (269)
T ss_pred cCCcHHHHHHHHHHHHHhCCceEEEEecCCcchhhHHHHHHHHHHHhcCcEEEeccccCCC-ccccHHHHHHHHhcCCCC
Confidence 577888999999999999999999999877 677788899999999998776544333322 223566666667665 68
Q ss_pred eEEEEEcChhHHHHHHHHHHHcCccccCeEEEEcCccccc
Q 043276 80 RVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDGMTNL 119 (829)
Q Consensus 80 rViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t~~~~~~ 119 (829)
++|++++. ..+..+++++.+.|+...++.|+..+.+...
T Consensus 184 ~~i~~~~~-~~a~~~~~~~~~~g~~~~~~~ii~~~~~~~~ 222 (269)
T cd01391 184 DAIFACND-EMAAGALKAAREAGLTPGDISIIGFDGSPAA 222 (269)
T ss_pred CEEEEcCc-hHHHHHHHHHHHcCCCCCCCEEEeccccccc
Confidence 88888877 8899999999999986456777777766543
No 112
>PRK11553 alkanesulfonate transporter substrate-binding subunit; Provisional
Probab=97.46 E-value=0.0016 Score=70.45 Aligned_cols=69 Identities=28% Similarity=0.368 Sum_probs=48.3
Q ss_pred CCCHHHHHhCCCcEEEEeCchHHHHH----HhcCCCccce-eecCChHHHHHHHhcCCcCCceeEEEcchhHHHHHHhcC
Q 043276 532 ITDVNLLIKRGDNVGYQKGSFVLGIL----KQLGFDERKL-VVYNSHEECDELFQKGSANGGIAAAFDEIPYAKLLIGQH 606 (829)
Q Consensus 532 I~s~~dL~~~~~~vg~~~~s~~~~~l----~~~~~~~~~~-~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~~ 606 (829)
|++++|| .|+++++..++..+.++ ++.+++...+ ..+.+..+...+|..|+ +|+++...++......+.
T Consensus 121 i~s~~dL--~Gk~I~~~~gs~~~~~l~~~l~~~g~~~~dv~~v~~~~~~~~~al~~G~----vDa~~~~ep~~~~~~~~~ 194 (314)
T PRK11553 121 IKTVADL--KGHKVAFQKGSSSHNLLLRALRKAGLKFTDIQPTYLTPADARAAFQQGN----VDAWAIWDPYYSAALLQG 194 (314)
T ss_pred CCCHHHh--CCCEEeecCCCcHHHHHHHHHHHcCCCHHHeEEEecChHHHHHHHHcCC----CCEEEEcCcHHHHHHhcC
Confidence 6889999 48889998887665544 4445543333 23446677889999999 999988777766655543
No 113
>PF12974 Phosphonate-bd: ABC transporter, phosphonate, periplasmic substrate-binding protein ; PDB: 3N5L_B 3QUJ_C 3P7I_A 3QK6_A 3S4U_A.
Probab=97.25 E-value=0.003 Score=65.49 Aligned_cols=119 Identities=23% Similarity=0.231 Sum_probs=74.3
Q ss_pred CCCHHHHHhCCCcEEEEeCchH------HHHH-HhcCCCcc---ceeecCChHHHHHHHhcCCcCCceeEEEcchhHHHH
Q 043276 532 ITDVNLLIKRGDNVGYQKGSFV------LGIL-KQLGFDER---KLVVYNSHEECDELFQKGSANGGIAAAFDEIPYAKL 601 (829)
Q Consensus 532 I~s~~dL~~~~~~vg~~~~s~~------~~~l-~~~~~~~~---~~~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~ 601 (829)
|++++|| .|+++++...+.. ...| ++.+++.. ..+...+.+..+++|.+|+ +|+.+......+.
T Consensus 97 i~~l~dL--~Gk~v~~~~~~s~sg~l~~~~~L~~~~Gl~~~~~~~~~~~~~~~~~~~~l~~G~----~Da~~~~~~~~~~ 170 (243)
T PF12974_consen 97 ITSLADL--KGKRVAFPDPSSTSGYLIPRYELLREAGLDPGDDFKQVFVGSHDAVLEALLNGK----ADAAAIPSDAFER 170 (243)
T ss_dssp --SHHHH--GGSEEEEE-TT-TTTTHHHHHHTCCCCT--HHHHSSEEEEE-HHHHHHHHHTTS----SSEEEEEHHHHHH
T ss_pred CCChhhc--CCCEEEEecCCccHHHHHHHHHHHHHcCCChhHceeEEEeCCHHHHHHHHHcCC----ccEEEEechhHHH
Confidence 7899999 5889998655422 2234 45555431 3345568888999999999 8988888777776
Q ss_pred HHhcC---CCceEEeCcccccCCceeeecCCCC--chhhHHHHHHhhhccChhHHHHHHH
Q 043276 602 LIGQH---CSKYTMVEPTFKTAGFGFAFPLHSP--LVHDVSKAILNVTEGDKMKEIEDAW 656 (829)
Q Consensus 602 ~~~~~---c~~l~~v~~~~~~~~~~~~~~k~sp--l~~~in~~il~l~e~G~~~~~~~~w 656 (829)
+.... .+.++++...-......++..++-| .++.|-.+++.+..+-.-..+.+.+
T Consensus 171 ~~~~~~~~~~~~rvl~~s~~~p~~~~~~~~~~~~~~~~~l~~al~~~~~~~~~~~~l~~~ 230 (243)
T PF12974_consen 171 LEAEGPDIPSQLRVLWTSPPYPNWPLVASPDLPPELRQRLRDALLSLSKDPEGKAILDAF 230 (243)
T ss_dssp HHHH-HHHHTTEEEEEEEEEEE--EEEEETTS-HHHHHHHHHHHHHTTSSHHHHHHHHHT
T ss_pred HHHccCcccccEEEEEEeCCCCCcEEEEeCCCCHHHHHHHHHHHHcCCCChhhHHHHHhc
Confidence 66542 3457776543223345677777755 8999999999999864444444443
No 114
>TIGR01729 taurine_ABC_bnd taurine ABC transporter, periplasmic binding protein. This model identifies a cluster of ABC transporter periplasmic substrate binding proteins, apparently specific for taurine. Transport systems for taurine (NH2-CH2-CH2-SO3H), sulfonates, and sulfate esters import sulfur when sulfate levels are low. The most closely related proteins outside this family are putative aliphatic sulfonate binding proteins (TIGR01728).
Probab=96.33 E-value=0.026 Score=60.47 Aligned_cols=68 Identities=25% Similarity=0.212 Sum_probs=47.8
Q ss_pred CCCHHHHHhCCCcEEEEeCchHHH----HHHhcCCCccceeec-CChHHHHHHHhcCCcCCceeEEEcchhHHHHHHhc
Q 043276 532 ITDVNLLIKRGDNVGYQKGSFVLG----ILKQLGFDERKLVVY-NSHEECDELFQKGSANGGIAAAFDEIPYAKLLIGQ 605 (829)
Q Consensus 532 I~s~~dL~~~~~~vg~~~~s~~~~----~l~~~~~~~~~~~~~-~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~ 605 (829)
|++++|| .|++||+..++..+. +|+..+++...+..+ -...+...+|..|+ +||++...++...+.++
T Consensus 92 I~s~~DL--kGK~Igv~~~s~~~~~l~~~L~~~Gl~~~dv~~v~~~~~~~~~al~~G~----vDa~~~~~p~~~~~~~~ 164 (300)
T TIGR01729 92 IEKPEDL--KGKNVAVPFVSTTHYSLLAALKHWKTDPREVNILNLKPPQIVAAWQRGD----IDAAYVWPPALSELLKS 164 (300)
T ss_pred CCChhHc--CCCEEEeCCCCcHHHHHHHHHHHcCCChhheEEEecCcHHHHHHHHcCC----cCEEEEecHHHHHHHhc
Confidence 7899999 599999987765443 445555544333222 24567899999999 99998888877655544
No 115
>PF13379 NMT1_2: NMT1-like family; PDB: 2G29_A 3UN6_A 2I4C_A 2I49_A 2I4B_A 2I48_A 3QSL_A.
Probab=96.26 E-value=0.016 Score=60.37 Aligned_cols=71 Identities=28% Similarity=0.280 Sum_probs=48.8
Q ss_pred CCCHHHHHh-----CCCcEEE-EeCchHH----HHHHhcCCCc---cceeecCChHHHHHHHhcCCcCCceeEEEcchhH
Q 043276 532 ITDVNLLIK-----RGDNVGY-QKGSFVL----GILKQLGFDE---RKLVVYNSHEECDELFQKGSANGGIAAAFDEIPY 598 (829)
Q Consensus 532 I~s~~dL~~-----~~~~vg~-~~~s~~~----~~l~~~~~~~---~~~~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~ 598 (829)
+++++||.+ .|+++++ ..++... .+|++.+++. .+++.++. .+...++..|+ +|++....++
T Consensus 106 ~~~~~dl~~~~~~~kGk~i~~~~~gs~~~~~l~~~l~~~Gl~~~~dv~~~~~~~-~~~~~al~~g~----iDa~~~~eP~ 180 (252)
T PF13379_consen 106 IKSLADLIKKRKAQKGKKIAVPFPGSTHDMLLRYLLKKAGLDPKDDVTLVNVPP-PEMVAALRAGE----IDAAVLWEPF 180 (252)
T ss_dssp TCCGHHHHHTCCSCSTEEEEESSTTSHHHHHHHHHHHHTT--TTTSSEEEE--G-HHHHHHHHTTS-----SEEEEETTH
T ss_pred ccCHHHHHhhhcccCCcEEEEcCCCCHHHHHHHHHHHhCCCCcccceEEEecCH-HHHHHHHhCCC----cCEEEecCCH
Confidence 789999954 5778998 4555433 3445566655 45555555 89999999999 9999999998
Q ss_pred HHHHHhcCC
Q 043276 599 AKLLIGQHC 607 (829)
Q Consensus 599 ~~~~~~~~c 607 (829)
......+.-
T Consensus 181 ~~~~~~~g~ 189 (252)
T PF13379_consen 181 ASQAEAKGI 189 (252)
T ss_dssp HHHHHHTTS
T ss_pred HHHHHhccC
Confidence 887776653
No 116
>TIGR03427 ABC_peri_uca ABC transporter periplasmic binding protein, urea carboxylase region. Members of this family are ABC transporter periplasmic binding proteins associated with the urea carboxylase/allophanate hydrolase pathway, an alternative to urease for urea degradation. The protein is restricted to bacteria with the pathway, with its gene close to the urea carboxylase and allophanate hydrolase genes. The substrate for this transporter therefore is likely to be urea or a compound from which urea is easily derived.
Probab=96.22 E-value=0.033 Score=60.20 Aligned_cols=67 Identities=19% Similarity=0.200 Sum_probs=49.2
Q ss_pred CCCHHHHHhCCCcEEEEeCchHHHH----HHhcCCCccc--eeecCChHHHHHHHhcCCcCCceeEEEcchhHHHHHHhc
Q 043276 532 ITDVNLLIKRGDNVGYQKGSFVLGI----LKQLGFDERK--LVVYNSHEECDELFQKGSANGGIAAAFDEIPYAKLLIGQ 605 (829)
Q Consensus 532 I~s~~dL~~~~~~vg~~~~s~~~~~----l~~~~~~~~~--~~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~ 605 (829)
|++++|| .|++||+..++..+-+ |++.+++... ++.. ...+...++.+|+ +||+....++......+
T Consensus 98 i~svaDL--KGKkIav~~gs~~~~ll~~aL~~aGL~~~DV~~v~~-~~~d~~aAl~~G~----VDAa~~~eP~~s~~~~~ 170 (328)
T TIGR03427 98 GKSLADL--KGQKVNLVELSVSHYLLARALESVGLSEKDVKVVNT-SDADIVAAFITKD----VTAVVTWNPQLSEIKAQ 170 (328)
T ss_pred CCCHHHc--CCCEEeccCCChHHHHHHHHHHHcCCCHHHeEEEeC-ChHHHHHHHhcCC----CcEEEEcCchHHHHHhC
Confidence 6899999 5999999988776533 4456665433 3333 4567889999999 99998888886655544
No 117
>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=96.03 E-value=0.08 Score=52.49 Aligned_cols=180 Identities=16% Similarity=0.133 Sum_probs=112.4
Q ss_pred eeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccEEEeccccccccceeccccccccccceEEEEE
Q 043276 340 YSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMIVP 419 (829)
Q Consensus 340 ~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv~ 419 (829)
+-.+++..+.++.+ .+++++.. ++...++..|.+|++|++++....... .+. ..|+....++++++
T Consensus 20 ~l~~~l~~~~~~~P-~i~i~~~~---------~~~~~~~~~l~~g~~Dl~i~~~~~~~~---~~~-~~~l~~~~~~~~~~ 85 (209)
T PF03466_consen 20 LLPPLLAEFRERHP-NIRIEIRE---------GDSDELIEALRSGELDLAITFGPPPPP---GLE-SEPLGEEPLVLVVS 85 (209)
T ss_dssp THHHHHHHHHHHST-TEEEEEEE---------ESHHHHHHHHHTTSSSEEEESSSSSST---TEE-EEEEEEEEEEEEEE
T ss_pred HHHHHHHHHHHHCC-CcEEEEEe---------ccchhhhHHHhcccccEEEEEeecccc---ccc-cccccceeeeeeee
Confidence 45678899989887 46666655 256899999999999999876554222 222 46788888999998
Q ss_pred ccCCCCCCceeeeccCCHhHHHHHHHHHHHHHHHHHhhhcccCCCCCCCccCccchhHHHHHHHhhhcCccccccchhHH
Q 043276 420 IKDSKKRNAWVFLQPLTWDLWVTSGCFFIFIGFVVWVLEHRVNEDFRGPARHQVGTSFWFSFSTMVFSQRERVISNLARF 499 (829)
Q Consensus 420 ~~~~~~~~~~~fl~PF~~~vW~~i~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~s~~~R~ 499 (829)
...+..
T Consensus 86 ~~~pl~-------------------------------------------------------------------------- 91 (209)
T PF03466_consen 86 PDHPLA-------------------------------------------------------------------------- 91 (209)
T ss_dssp TTSGGG--------------------------------------------------------------------------
T ss_pred cccccc--------------------------------------------------------------------------
Confidence 553221
Q ss_pred HHHHHHHHHHHHHHHhHHHHHHHhhcccCCCCCCCHHHHHhCCCcEEEEe-CchHHH----HHHhcCCCccceeecCChH
Q 043276 500 VVIVWCFVVLILIQSYTASLTSLLTVDQLQPTITDVNLLIKRGDNVGYQK-GSFVLG----ILKQLGFDERKLVVYNSHE 574 (829)
Q Consensus 500 v~~~w~~~~lil~~~YtA~L~s~Lt~~~~~~~I~s~~dL~~~~~~vg~~~-~s~~~~----~l~~~~~~~~~~~~~~~~~ 574 (829)
+ ..++ +++||. +.++.... +..... ++++.+........+++.+
T Consensus 92 ---------------------------~-~~~i-~~~dL~--~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 140 (209)
T PF03466_consen 92 ---------------------------Q-KKPI-TLEDLA--DYPLILLSPGSPYRDQLDRWLREHGFSPNIVIEVDSFE 140 (209)
T ss_dssp ---------------------------T-TSSS-SGGGGT--TSEEEEESTTTSHHHHHHHHHHHTTEEEEEEEEESSHH
T ss_pred ---------------------------c-cccc-hhhhhh--hccccccccccccccccccccccccccccccccccchh
Confidence 0 1113 789995 45544433 333333 3444555554556778999
Q ss_pred HHHHHHhcCCcCCceeEEEcchhHHHHHHhcCCCceEEeCc-ccccCCceeeecCCCCchhhHHHHHHhhh
Q 043276 575 ECDELFQKGSANGGIAAAFDEIPYAKLLIGQHCSKYTMVEP-TFKTAGFGFAFPLHSPLVHDVSKAILNVT 644 (829)
Q Consensus 575 ~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~~c~~l~~v~~-~~~~~~~~~~~~k~spl~~~in~~il~l~ 644 (829)
.....+..|. .-+++-+.....+....... ...+.+ .+. ..++++.+++.+....+...+..+.
T Consensus 141 ~~~~~v~~g~----gi~~~p~~~~~~~~~~~~l~-~~~~~~~~~~-~~~~l~~~~~~~~~~~~~~~~~~l~ 205 (209)
T PF03466_consen 141 SILSLVASGD----GIAILPDSLAQDELESGELV-FLPLPDPPLP-RPIYLVWRKDRPLSPAIQWFIDLLR 205 (209)
T ss_dssp HHHHHHHTTS----EBEEEEHHHHHHHHHCTTEE-EEEESSSTEE-EEEEEEEETTGTTHHHHHHHHHHHH
T ss_pred hhcccccccc----ceeecCcccccccccCCCEE-EEECCCCCCc-eEEEEEEECCCCCCHHHHHHHHHHH
Confidence 9999999988 56665554333333222221 123344 444 7788888888776666666555544
No 118
>PF04348 LppC: LppC putative lipoprotein; InterPro: IPR007443 This entry includes several bacterial outer membrane antigens, whose molecular function is unknown.; PDB: 3CKM_A.
Probab=95.86 E-value=0.083 Score=61.03 Aligned_cols=128 Identities=14% Similarity=0.117 Sum_probs=75.0
Q ss_pred ChHHHHHHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEE
Q 043276 4 NDSSQVGAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFI 83 (829)
Q Consensus 4 sD~~q~~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViI 83 (829)
+-+..+..+|+.+..-|++...||+.++++|+...+.|.+..++.|..+.-...+.. ..++...+..-.+...+.|+
T Consensus 328 spEdEA~q~A~~a~~~g~~~alvl~p~~~~g~R~~~aF~~~W~~~gg~~~~~~~~~~---~~~~~~~i~~r~r~d~D~if 404 (536)
T PF04348_consen 328 SPEDEARQAAQKAFQDGYRRALVLAPQNAWGQRMAEAFNQQWQALGGQVAEVSYYGS---PADLQAAIQPRRRQDIDAIF 404 (536)
T ss_dssp -HHHHHHHHHHHHHHTT--S-EEEEESSHHHHHHHHHHHHHHHHHHSS--EEEEESS---TTHHHHHHHHS--TT--EEE
T ss_pred CcHHHHHHHHHHHHhcCCCCEEEEcCCChHHHHHHHHHHHHHHHcCCCceeeEecCC---HHHHHHHHhhcCCCCCCEEE
Confidence 345678889999988999999999999999999999999999998887765555542 34677777755556789999
Q ss_pred EEcChhHHHHHHHHHHHcCccccCeEEEE-cC-ccccccccCCccccccccceEEEEec
Q 043276 84 LHMLPSLGSRIFEKANEIGLMNKGCVWIM-TD-GMTNLLRTLEPSVTDSMQGVIGVRPY 140 (829)
Q Consensus 84 v~~~~~~~~~i~~~a~~~gm~~~~~vwI~-t~-~~~~~~~~~~~~~~~~~~g~l~~~~~ 140 (829)
+.+.+++++.|--...-.. .+-+-|. |+ ...+. .+......++|+......
T Consensus 405 l~a~~~~ar~ikP~l~~~~---a~~lPvyatS~~~~g~---~~~~~~~dL~gv~f~d~P 457 (536)
T PF04348_consen 405 LVANPEQARLIKPQLDFHF---AGDLPVYATSRSYSGS---PNPSQDRDLNGVRFSDMP 457 (536)
T ss_dssp E---HHHHHHHHHHHTT-T----TT-EEEE-GGG--HH---T-HHHHHHTTT-EEEE-G
T ss_pred EeCCHHHHHHHhhhccccc---CCCCCEEEeccccCCC---CCcchhhhhcCCEEeccc
Confidence 9999888877654433211 1222222 22 22221 122334568898777643
No 119
>COG3221 PhnD ABC-type phosphate/phosphonate transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=95.81 E-value=0.2 Score=53.01 Aligned_cols=110 Identities=17% Similarity=0.212 Sum_probs=73.9
Q ss_pred CCCCCHHHHHhCCCcEEEEeCchHHH------HHHhcC-CCcc---ceeecCC-hHHHHHHHhcCCcCCceeEEEcchhH
Q 043276 530 PTITDVNLLIKRGDNVGYQKGSFVLG------ILKQLG-FDER---KLVVYNS-HEECDELFQKGSANGGIAAAFDEIPY 598 (829)
Q Consensus 530 ~~I~s~~dL~~~~~~vg~~~~s~~~~------~l~~~~-~~~~---~~~~~~~-~~~~~~~l~~g~~~~g~~a~~~~~~~ 598 (829)
++|++++|| .|+++++..-++... +|.+.+ .+.. .-+.+.. .+..+.+|.+|+ +|+.......
T Consensus 134 s~i~sl~dl--kgk~~af~d~~StSG~l~P~~~L~~~g~~d~~~~f~~v~~~G~H~~a~~aV~nG~----vDva~~~~~~ 207 (299)
T COG3221 134 SPIKSLEDL--KGKRFAFGDPDSTSGYLFPLYYLAKEGGIDPDKFFGEVIFSGGHDAAVLAVANGQ----VDVAAVNSSA 207 (299)
T ss_pred CCcchHHHh--cCCeEeccCCCcchhhHhHHHHHHHhcCCChhhhhceeeccChHHHHHHHHHcCC----ceEEeccHHH
Confidence 348999999 599999865543333 333333 2211 1223343 788899999999 8988777766
Q ss_pred HHHHHhcCC----CceEEeCcccccCCceeeecCCCC--chhhHHHHHHhhhc
Q 043276 599 AKLLIGQHC----SKYTMVEPTFKTAGFGFAFPLHSP--LVHDVSKAILNVTE 645 (829)
Q Consensus 599 ~~~~~~~~c----~~l~~v~~~~~~~~~~~~~~k~sp--l~~~in~~il~l~e 645 (829)
...+..... +++.++...-......++++++-| +++.|..+++.+.+
T Consensus 208 ~~~~~~~~~~~~~~~l~vi~~S~~iP~~pi~vr~~L~~~~k~kl~~af~~l~~ 260 (299)
T COG3221 208 RGLLKKAAPEGVAEKLRVIWKSPLIPNDPIAVRSDLPADLKEKLRDAFLDLAK 260 (299)
T ss_pred HhhhhhcccccchhhceEEEecCCCCCCCEEEeCCCCHHHHHHHHHHHHhcCc
Confidence 666555442 357777554344455677888766 99999999999986
No 120
>TIGR02122 TRAP_TAXI TRAP transporter solute receptor, TAXI family. This family is one of at least three major families of extracytoplasmic solute receptor (ESR) for TRAP (Tripartite ATP-independent Periplasmic Transporter) transporters. The others are the DctP (TIGR00787) and SmoM (pfam03480) families. These transporters are secondary (driven by an ion gradient) but composed of three polypeptides, although in some species the 4-TM and 12-TM integral membrane proteins are fused. Substrates for this transporter family are not fully characterized but, besides C4 dicarboxylates, may include mannitol and other compounds.
Probab=95.69 E-value=0.057 Score=58.40 Aligned_cols=58 Identities=29% Similarity=0.310 Sum_probs=39.6
Q ss_pred CCCHHHHHhCCCcEEEEeC-chH----HHHHHhcCCCccc--eeecCChHHHHHHHhcCCcCCceeEEEcc
Q 043276 532 ITDVNLLIKRGDNVGYQKG-SFV----LGILKQLGFDERK--LVVYNSHEECDELFQKGSANGGIAAAFDE 595 (829)
Q Consensus 532 I~s~~dL~~~~~~vg~~~~-s~~----~~~l~~~~~~~~~--~~~~~~~~~~~~~l~~g~~~~g~~a~~~~ 595 (829)
+++++||. ++++++... +.. ..+++..+..... .+.+.+..+...+|..|+ +|+++..
T Consensus 133 i~sl~dL~--gk~v~~~~~~s~~~~~~~~~l~~~G~~~~~~~~v~~~~~~~~~~al~~G~----vDa~~~~ 197 (320)
T TIGR02122 133 IKTVADLK--GKRVAVGAPGSGTELNARAVLKAAGLTYDDVKKVEYLGYAEAADALKDGK----IDAAFYT 197 (320)
T ss_pred CCcHHHcC--CCEEecCCCCcchHHHHHHHHHHcCCCHHHccchhcCCHHHHHHHHHCCC----ccEEEEe
Confidence 68899995 777776433 322 3345555554332 246677888999999999 9998877
No 121
>cd05466 PBP2_LTTR_substrate The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily. This model and hierarchy represent the the substrate-binding domain of the LysR-type transcriptional regulators that form the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA bin
Probab=95.63 E-value=0.62 Score=44.76 Aligned_cols=69 Identities=17% Similarity=0.255 Sum_probs=47.4
Q ss_pred EeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccEEEeccccccccceeccccccccccceEEEE
Q 043276 339 GYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMIV 418 (829)
Q Consensus 339 G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv 418 (829)
.+..++++.+.++.+ ++++++... ...+++..|.+|++|++++..... ...++ ..++....+++++
T Consensus 13 ~~l~~~i~~~~~~~p-~i~i~~~~~---------~~~~~~~~l~~g~~D~~i~~~~~~---~~~~~-~~~l~~~~~~~~~ 78 (197)
T cd05466 13 YLLPPLLAAFRQRYP-GVELSLVEG---------GSSELLEALLEGELDLAIVALPVD---DPGLE-SEPLFEEPLVLVV 78 (197)
T ss_pred HHhHHHHHHHHHHCC-CCEEEEEEC---------ChHHHHHHHHcCCceEEEEcCCCC---CCcce-EeeeeccceEEEe
Confidence 355677888888776 466666553 357899999999999998654432 22333 3566677888887
Q ss_pred Ecc
Q 043276 419 PIK 421 (829)
Q Consensus 419 ~~~ 421 (829)
+..
T Consensus 79 ~~~ 81 (197)
T cd05466 79 PPD 81 (197)
T ss_pred cCC
Confidence 744
No 122
>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=95.55 E-value=0.088 Score=53.25 Aligned_cols=56 Identities=27% Similarity=0.422 Sum_probs=39.0
Q ss_pred CCCHHHHHhCCCcEEEEeCchHH----HHHHhcCCCccceeecC-ChHHHHHHHhcCCcCCceeEEE
Q 043276 532 ITDVNLLIKRGDNVGYQKGSFVL----GILKQLGFDERKLVVYN-SHEECDELFQKGSANGGIAAAF 593 (829)
Q Consensus 532 I~s~~dL~~~~~~vg~~~~s~~~----~~l~~~~~~~~~~~~~~-~~~~~~~~l~~g~~~~g~~a~~ 593 (829)
|++++|| .|++||+..++... .+|++.+++...+..+. +..+...+|.+|+ +||++
T Consensus 85 i~~~~DL--kGK~i~v~~~s~~~~~~~~~l~~~g~~~~~v~~v~~~~~~~~~al~~g~----vDa~~ 145 (216)
T PF09084_consen 85 IKSPADL--KGKKIGVSRGSSSEYFLRALLKKNGIDPDDVKIVNLGPPELAQALLSGQ----VDAAI 145 (216)
T ss_dssp -SSGGGG--TTSEEEESTTSHHHHHHHHHHHHTTT-GGGSEEEES-HHHHHHHHHTTS----SSEEE
T ss_pred CCCHHHh--CCCEEEEecCcchhHHHHHHHHHhccccccceeeeeehhhhhhhhhcCC----CCEEE
Confidence 7999999 49999998876443 44556666555554433 3566777999999 89888
No 123
>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=95.39 E-value=0.54 Score=46.10 Aligned_cols=69 Identities=16% Similarity=0.074 Sum_probs=47.7
Q ss_pred EeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccEEEeccccccccceeccccccccccceEEEE
Q 043276 339 GYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMIV 418 (829)
Q Consensus 339 G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv 418 (829)
.+-.+++..+.++.+ .+++++.. ++.+++...|.+|++|+++...... ...+. +.|.....+++++
T Consensus 13 ~~l~~~l~~~~~~~P-~v~v~i~~---------~~~~~~~~~l~~g~~D~~i~~~~~~---~~~l~-~~~l~~~~~~~v~ 78 (201)
T cd08459 13 YFLPRLLAALREVAP-GVRIETVR---------LPVDELEEALESGEIDLAIGYLPDL---GAGFF-QQRLFRERYVCLV 78 (201)
T ss_pred HHHHHHHHHHHHHCC-CCeEEEEe---------cCccCHHHHhhCCCceEEEEcCCCC---cccce-EEEeecCceEEEE
Confidence 445678888888876 35666554 2457889999999999998543221 22233 4688888888888
Q ss_pred Ecc
Q 043276 419 PIK 421 (829)
Q Consensus 419 ~~~ 421 (829)
+..
T Consensus 79 ~~~ 81 (201)
T cd08459 79 RKD 81 (201)
T ss_pred cCC
Confidence 744
No 124
>TIGR01728 SsuA_fam ABC transporter, substrate-binding protein, aliphatic sulfonates family. Members of this family are substrate-binding periplasmic proteins of ABC transporters. This subfamily includes SsuA, a member of a transporter operon needed to obtain sulfur from aliphatic sulfonates. Related proteins outside the scope of this model include taurine (NH2-CH2-CH2-S03H) binding proteins, the probable sulfate ester binding protein AtsR, and the probable aromatic sulfonate binding protein AsfC. All these families make sulfur available when Cys and sulfate levels are low. Please note that phylogenetic analysis by neighbor-joining suggests that a number of sequences belonging to this family have been excluded because of scoring lower than taurine-binding proteins.
Probab=95.27 E-value=0.25 Score=52.26 Aligned_cols=68 Identities=21% Similarity=0.282 Sum_probs=47.1
Q ss_pred CCCHHHHHhCCCcEEEEeCchHHH----HHHhcCCCcccee-ecCChHHHHHHHhcCCcCCceeEEEcchhHHHHHHhc
Q 043276 532 ITDVNLLIKRGDNVGYQKGSFVLG----ILKQLGFDERKLV-VYNSHEECDELFQKGSANGGIAAAFDEIPYAKLLIGQ 605 (829)
Q Consensus 532 I~s~~dL~~~~~~vg~~~~s~~~~----~l~~~~~~~~~~~-~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~ 605 (829)
|++++||. |+++++..++.... ++++.+.+...+. .+.+..+..+++.+|+ +++++...++...+..+
T Consensus 93 i~s~~dL~--Gk~i~~~~~~~~~~~~~~~l~~~G~~~~~v~~~~~~~~~~~~al~~g~----vda~~~~~p~~~~~~~~ 165 (288)
T TIGR01728 93 IRTVADLK--GKRIAVPKGGSGHDLLLRALLKAGLSGDDVTILYLGPSDARAAFAAGQ----VDAWAIWEPWGSALVEE 165 (288)
T ss_pred CCCHHHcC--CCEEEecCCccHHHHHHHHHHHcCCCccceeEEecCcHHHHHHHHCCC----CCEEEeccchHhHHhhc
Confidence 78999994 88999877764433 3444555443332 2345678889999999 89998887777665544
No 125
>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=95.25 E-value=0.16 Score=42.15 Aligned_cols=56 Identities=20% Similarity=0.328 Sum_probs=48.3
Q ss_pred ccCccchhHHHHHHHhhhcC-c-cccccchhHHHHHHHHHHHHHHHHHhHHHHHHHhh
Q 043276 469 ARHQVGTSFWFSFSTMVFSQ-R-ERVISNLARFVVIVWCFVVLILIQSYTASLTSLLT 524 (829)
Q Consensus 469 ~~~~~~~~~~~~~~~l~~~~-~-~~~~s~~~R~v~~~w~~~~lil~~~YtA~L~s~Lt 524 (829)
...++.+++|+++.++...| + ..|.+..+|++.+++.+.++.+.+...+.+++.++
T Consensus 21 ~~~~~~da~yfs~~t~tTvGyGDi~p~t~~gr~~~~~~~~~G~~~~~~~~~~~~~~l~ 78 (79)
T PF07885_consen 21 EKWSFIDALYFSFVTITTVGYGDIVPQTPAGRIFTIIYMLIGIFLFALFLSVLASVLT 78 (79)
T ss_dssp STTSHHHHHHHHHHHHTT---SSSSTSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred ccCCHHHHHHHHHHHHhcccCCCccCCccchHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 35678899999999999877 3 47889999999999999999999999999999886
No 126
>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=95.24 E-value=1.4 Score=42.69 Aligned_cols=70 Identities=16% Similarity=0.200 Sum_probs=47.4
Q ss_pred EEeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccEEEeccccccccceeccccccccccceEEE
Q 043276 338 VGYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMI 417 (829)
Q Consensus 338 ~G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~v 417 (829)
..+-.+++..+.++.+ .+++++.. ++..+++..|.+|++|+++.... .....+. ..+.....++++
T Consensus 12 ~~~l~~~l~~~~~~~P-~i~l~i~~---------~~~~~~~~~l~~g~~Dl~i~~~~---~~~~~~~-~~~l~~~~~~~v 77 (193)
T cd08442 12 AVRLPPLLAAYHARYP-KVDLSLST---------GTTGALIQAVLEGRLDGAFVAGP---VEHPRLE-QEPVFQEELVLV 77 (193)
T ss_pred hhhhHHHHHHHHHHCC-CceEEEEe---------CCcHHHHHHHHCCCccEEEEeCC---CCCCCcE-EEEeecCcEEEE
Confidence 3456788999998887 35666654 24678999999999999985322 1222222 456677778888
Q ss_pred EEcc
Q 043276 418 VPIK 421 (829)
Q Consensus 418 v~~~ 421 (829)
++..
T Consensus 78 ~~~~ 81 (193)
T cd08442 78 SPKG 81 (193)
T ss_pred ecCC
Confidence 7744
No 127
>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=95.04 E-value=1.3 Score=43.61 Aligned_cols=72 Identities=14% Similarity=0.132 Sum_probs=48.4
Q ss_pred EeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccEEEeccccccccceeccccccccccceEEEE
Q 043276 339 GYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMIV 418 (829)
Q Consensus 339 G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv 418 (829)
.+-.+++..+.++.+ .+++++.. ++..+++..|.+|++|++++.......-...+. +.+..+...++++
T Consensus 13 ~~l~~~l~~~~~~~P-~v~i~~~~---------~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~~~-~~~l~~~~~~~~~ 81 (202)
T cd08468 13 AVMPRLMARLEELAP-SVRLNLVH---------AEQKLPLDALLAGEIDFALGYSHDDGAEPRLIE-ERDWWEDTYVVIA 81 (202)
T ss_pred HHhHHHHHHHHhhCC-CCEEEEEE---------CChHhHHHHHHCCCccEEEecccccccCCCCEE-EEEEecCcEEEEE
Confidence 456788999988886 35666654 356899999999999999864322100012233 3567777888888
Q ss_pred Ecc
Q 043276 419 PIK 421 (829)
Q Consensus 419 ~~~ 421 (829)
+..
T Consensus 82 ~~~ 84 (202)
T cd08468 82 SRD 84 (202)
T ss_pred eCC
Confidence 744
No 128
>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=94.92 E-value=1.5 Score=42.75 Aligned_cols=72 Identities=17% Similarity=0.169 Sum_probs=47.5
Q ss_pred EEeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccEEEeccccccccceeccccccccccceEEE
Q 043276 338 VGYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMI 417 (829)
Q Consensus 338 ~G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~v 417 (829)
..+-.+++..+.++.+ .+++++.. ++...+..+|.+|++|++++..... .....+. +.+.....++++
T Consensus 12 ~~~l~~~l~~~~~~~P-~i~l~i~~---------~~~~~~~~~l~~g~~Dl~i~~~~~~-~~~~~~~-~~~l~~~~~~~v 79 (201)
T cd08418 12 HTLMPAVINRFKEQFP-DVQISIYE---------GQLSSLLPELRDGRLDFAIGTLPDE-MYLKELI-SEPLFESDFVVV 79 (201)
T ss_pred HhhhHHHHHHHHHHCC-CceEEEEe---------CcHHHHHHHHHcCCCcEEEEecCCC-CCCccee-EEeecCCceEEE
Confidence 3455678888888876 46666654 2568899999999999998643211 1112233 356677788888
Q ss_pred EEcc
Q 043276 418 VPIK 421 (829)
Q Consensus 418 v~~~ 421 (829)
++..
T Consensus 80 ~~~~ 83 (201)
T cd08418 80 ARKD 83 (201)
T ss_pred eCCC
Confidence 7743
No 129
>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=94.86 E-value=1.7 Score=43.02 Aligned_cols=72 Identities=14% Similarity=0.190 Sum_probs=49.0
Q ss_pred EEeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccEEEeccccccccceeccccccccccceEEE
Q 043276 338 VGYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMI 417 (829)
Q Consensus 338 ~G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~v 417 (829)
..+-.+++..+.++.+ .+++++.... +.++++..|.+|++|++++..... ...++ ..|+.+...+++
T Consensus 12 ~~~~~~~l~~~~~~~P-~~~v~~~~~~--------~~~~l~~~L~~g~lDl~i~~~~~~---~~~l~-~~~l~~~~~~lv 78 (203)
T cd08463 12 ALFLPELVARFRREAP-GARLEIHPLG--------PDFDYERALASGELDLVIGNWPEP---PEHLH-LSPLFSDEIVCL 78 (203)
T ss_pred HHHhHHHHHHHHHHCC-CCEEEEEeCC--------cchhHHHHHhcCCeeEEEeccccC---CCCcE-EeEeecCceEEE
Confidence 3566789999998887 3566665421 457899999999999998642221 12233 367778888888
Q ss_pred EEccC
Q 043276 418 VPIKD 422 (829)
Q Consensus 418 v~~~~ 422 (829)
++...
T Consensus 79 ~~~~h 83 (203)
T cd08463 79 MRADH 83 (203)
T ss_pred EeCCC
Confidence 87543
No 130
>cd08438 PBP2_CidR The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains the type 2 periplasmic binding fold. This CD includes the substrate binding domain of CidR which positively up-regulates the expression of cidABC operon in the presence of acetic acid produced by the metabolism of excess glucose. The CidR affects the control of murein hydrolase activity by enhancing cidABC expression in the presence of acetic acid. Thus, up-regulation of cidABC expression results in increased murein hydrolase activity. This substrate binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate
Probab=94.68 E-value=2.2 Score=41.28 Aligned_cols=69 Identities=14% Similarity=0.189 Sum_probs=48.0
Q ss_pred EeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccEEEeccccccccceeccccccccccceEEEE
Q 043276 339 GYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMIV 418 (829)
Q Consensus 339 G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv 418 (829)
.+..+++..+.++.+ .+++++.. ++..+++..|.+|++|+++...... ...+. ..++.+..+++++
T Consensus 13 ~~l~~~l~~~~~~~p-~v~i~i~~---------~~~~~~~~~L~~~~~Dl~i~~~~~~---~~~~~-~~~l~~~~~~~v~ 78 (197)
T cd08438 13 LLFAPLLAAFRQRYP-NIELELVE---------YGGKKVEQAVLNGELDVGITVLPVD---EEEFD-SQPLCNEPLVAVL 78 (197)
T ss_pred hhcHHHHHHHHHHCc-CeEEEEEE---------cCcHHHHHHHHcCCCCEEEEecccc---cCCce-eEEeccccEEEEe
Confidence 456788999998886 45666654 2468899999999999998643322 12232 3567778888888
Q ss_pred Ecc
Q 043276 419 PIK 421 (829)
Q Consensus 419 ~~~ 421 (829)
+..
T Consensus 79 ~~~ 81 (197)
T cd08438 79 PRG 81 (197)
T ss_pred cCC
Confidence 744
No 131
>cd08421 PBP2_LTTR_like_1 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold. LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functi
Probab=94.42 E-value=2.8 Score=40.62 Aligned_cols=69 Identities=17% Similarity=0.271 Sum_probs=47.3
Q ss_pred EeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccEEEeccccccccceeccccccccccceEEEE
Q 043276 339 GYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMIV 418 (829)
Q Consensus 339 G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv 418 (829)
.+-.+++..+.++.+ .+++++.. ++..+++.+|.+|++|+++..... ....+. ..++....+++++
T Consensus 13 ~~l~~~l~~~~~~~P-~i~i~~~~---------~~~~~~~~~l~~~~~D~~i~~~~~---~~~~~~-~~~l~~~~~~~v~ 78 (198)
T cd08421 13 EFLPEDLASFLAAHP-DVRIDLEE---------RLSADIVRAVAEGRADLGIVAGNV---DAAGLE-TRPYRTDRLVVVV 78 (198)
T ss_pred hhhHHHHHHHHHHCC-CceEEEEe---------cCcHHHHHHHhcCCceEEEEecCC---CCCCcE-EEEeecCcEEEEe
Confidence 345678888888876 45666554 246889999999999999854322 223333 4677788888888
Q ss_pred Ecc
Q 043276 419 PIK 421 (829)
Q Consensus 419 ~~~ 421 (829)
++.
T Consensus 79 ~~~ 81 (198)
T cd08421 79 PRD 81 (198)
T ss_pred CCC
Confidence 744
No 132
>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=3.4 Score=39.76 Aligned_cols=70 Identities=17% Similarity=0.168 Sum_probs=47.9
Q ss_pred EEeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccEEEeccccccccceeccccccccccceEEE
Q 043276 338 VGYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMI 417 (829)
Q Consensus 338 ~G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~v 417 (829)
..+-.+++..+.++.+ .+++++.. ++..++...|.+|++|+++..... ....+. +.++....++++
T Consensus 12 ~~~l~~~l~~~~~~~p-~v~i~i~~---------~~~~~~~~~l~~g~~D~~i~~~~~---~~~~~~-~~~l~~~~~~~~ 77 (197)
T cd08440 12 ATLLPPVLAAFRRRHP-GIRVRLRD---------VSAEQVIEAVRSGEVDFGIGSEPE---ADPDLE-FEPLLRDPFVLV 77 (197)
T ss_pred hhHHHHHHHHHHHhCC-CcEEEEEe---------CChHHHHHHHHcCCccEEEEeCCC---CCCCee-EEEeecccEEEE
Confidence 3556788899988876 45666554 246889999999999999864322 112222 356777888888
Q ss_pred EEcc
Q 043276 418 VPIK 421 (829)
Q Consensus 418 v~~~ 421 (829)
++..
T Consensus 78 ~~~~ 81 (197)
T cd08440 78 CPKD 81 (197)
T ss_pred ecCC
Confidence 8744
No 133
>PRK11480 tauA taurine transporter substrate binding subunit; Provisional
Probab=94.21 E-value=0.29 Score=52.94 Aligned_cols=66 Identities=21% Similarity=0.217 Sum_probs=46.5
Q ss_pred CCCHHHHHhCCCcEEEEeCchHH----HHHHhcCCCccceeecC-ChHHHHHHHhcCCcCCceeEEEcchhHHHHHH
Q 043276 532 ITDVNLLIKRGDNVGYQKGSFVL----GILKQLGFDERKLVVYN-SHEECDELFQKGSANGGIAAAFDEIPYAKLLI 603 (829)
Q Consensus 532 I~s~~dL~~~~~~vg~~~~s~~~----~~l~~~~~~~~~~~~~~-~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~ 603 (829)
|++++|| .|++||+..++..+ .+|++.+.+...+..+. ...+...++.+|+ +||++...++.....
T Consensus 114 I~s~~DL--kGK~Iav~~~s~~~~~l~~~L~~~Gl~~~dv~~v~~~~~~~~~Al~~G~----VDAa~~~~p~~~~~~ 184 (320)
T PRK11480 114 ISKPEDL--IGKRIAVPFISTTHYSLLAALKHWGIKPGQVEIVNLQPPAIIAAWQRGD----IDGAYVWAPAVNALE 184 (320)
T ss_pred CCChHHc--CCCEEecCCCCchHHHHHHHHHHcCCCHhheEEEECCcHHHHHHHHcCC----cCEEEEcchHHHHHH
Confidence 8999999 59999997765433 34566666554443332 4567889999999 999887777654443
No 134
>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=94.20 E-value=4 Score=39.62 Aligned_cols=69 Identities=16% Similarity=0.166 Sum_probs=46.5
Q ss_pred EeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccEEEeccccccccceeccccccccccceEEEE
Q 043276 339 GYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMIV 418 (829)
Q Consensus 339 G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv 418 (829)
.+-.+++..+.++.+ ++++++... +-.++...|.+|++|+++..... ....+ -+.++....+++++
T Consensus 13 ~~l~~~l~~~~~~~P-~i~i~~~~~---------~~~~~~~~l~~~~~D~~i~~~~~---~~~~~-~~~~l~~~~~~~~~ 78 (198)
T cd08433 13 VLAVPLLRAVRRRYP-GIRLRIVEG---------LSGHLLEWLLNGRLDLALLYGPP---PIPGL-STEPLLEEDLFLVG 78 (198)
T ss_pred hcchHHHHHHHHHCC-CcEEEEEec---------CcHHHHHHHhCCCCcEEEEeCCC---CCCCe-eEEEeccccEEEEe
Confidence 455678888888876 456666542 34788999999999999853221 11222 24677778888887
Q ss_pred Ecc
Q 043276 419 PIK 421 (829)
Q Consensus 419 ~~~ 421 (829)
+..
T Consensus 79 ~~~ 81 (198)
T cd08433 79 PAD 81 (198)
T ss_pred cCC
Confidence 744
No 135
>cd08412 PBP2_PAO1_like The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator PAO1-like, a member of the type 2 periplasmic binding fold protein superfamily. This family includes the C-terminal substrate domain of a putative LysR-type transcriptional regulator from the plant pathogen Pseudomonas aeruginosa PAO1and its closely related homologs. The LysR-type transcriptional regulators (LTTRs) are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controll
Probab=94.18 E-value=2.9 Score=40.49 Aligned_cols=70 Identities=17% Similarity=0.164 Sum_probs=48.9
Q ss_pred EEeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccEEEeccccccccceeccccccccccceEEE
Q 043276 338 VGYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMI 417 (829)
Q Consensus 338 ~G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~v 417 (829)
..+-.+++..+.++.+ ++++++.. ++..+++.+|.+|++|+++..... ....+. +.|+....++++
T Consensus 12 ~~~l~~~l~~~~~~~P-~i~l~i~~---------~~~~~~~~~l~~~~~D~~i~~~~~---~~~~~~-~~~l~~~~~~~~ 77 (198)
T cd08412 12 PYYLPGLLRRFREAYP-GVEVRVVE---------GNQEELEEGLRSGELDLALTYDLD---LPEDIA-FEPLARLPPYVW 77 (198)
T ss_pred hhhhHHHHHHHHHHCC-CcEEEEEE---------CCHHHHHHHHHcCCCcEEEEcCCC---CCcccc-eeeeeccceEEE
Confidence 4566789999999887 45666654 256789999999999999853221 122332 477888888888
Q ss_pred EEcc
Q 043276 418 VPIK 421 (829)
Q Consensus 418 v~~~ 421 (829)
++..
T Consensus 78 ~~~~ 81 (198)
T cd08412 78 LPAD 81 (198)
T ss_pred ecCC
Confidence 7744
No 136
>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=94.08 E-value=2.4 Score=41.23 Aligned_cols=69 Identities=16% Similarity=0.139 Sum_probs=46.6
Q ss_pred EeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccEEEeccccccccceeccccccccccceEEEE
Q 043276 339 GYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMIV 418 (829)
Q Consensus 339 G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv 418 (829)
.+-.+++..+.++.+ ++++++... +.+.+...|.+|++|+++..... ....+. +.++....+++++
T Consensus 13 ~~l~~~l~~f~~~~P-~v~i~i~~~---------~~~~~~~~l~~~~~Di~i~~~~~---~~~~~~-~~~l~~~~~~lv~ 78 (198)
T cd08461 13 AILPPLLAALRQEAP-GVRVAIRDL---------ESDNLEAQLERGEVDLALTTPEY---APDGLR-SRPLFEERYVCVT 78 (198)
T ss_pred HHhHHHHHHHHHHCC-CcEEEEeeC---------CcccHHHHHhcCCCcEEEecCcc---CCccce-eeeeecCcEEEEE
Confidence 456788888888876 456665432 34678999999999999853221 122232 5677788888888
Q ss_pred Ecc
Q 043276 419 PIK 421 (829)
Q Consensus 419 ~~~ 421 (829)
+..
T Consensus 79 ~~~ 81 (198)
T cd08461 79 RRG 81 (198)
T ss_pred cCC
Confidence 744
No 137
>PRK11151 DNA-binding transcriptional regulator OxyR; Provisional
Probab=94.00 E-value=2.4 Score=45.39 Aligned_cols=69 Identities=10% Similarity=0.098 Sum_probs=47.9
Q ss_pred EeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccEEEeccccccccceeccccccccccceEEEE
Q 043276 339 GYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMIV 418 (829)
Q Consensus 339 G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv 418 (829)
++-..++..+.+..+ .+++++.. ++-+++++.|.+|++|+++........ .+ .+.|+....+++++
T Consensus 104 ~~~~~~l~~~~~~~P-~v~i~~~~---------~~~~~~~~~l~~g~~Dl~i~~~~~~~~---~l-~~~~l~~~~~~~~~ 169 (305)
T PRK11151 104 YLLPHIIPMLHQTFP-KLEMYLHE---------AQTHQLLAQLDSGKLDCAILALVKESE---AF-IEVPLFDEPMLLAV 169 (305)
T ss_pred HHHHHHHHHHHHHCC-CcEEEEEe---------CCHHHHHHHHHcCCccEEEEecCCCCC---Ce-EEEEeccCcEEEEe
Confidence 345577888888776 35666554 245889999999999999964322222 22 35788888999988
Q ss_pred Ecc
Q 043276 419 PIK 421 (829)
Q Consensus 419 ~~~ 421 (829)
++.
T Consensus 170 ~~~ 172 (305)
T PRK11151 170 YED 172 (305)
T ss_pred cCC
Confidence 744
No 138
>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=93.97 E-value=1.9 Score=42.04 Aligned_cols=69 Identities=16% Similarity=0.119 Sum_probs=47.3
Q ss_pred EeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccEEEeccccccccceeccccccccccceEEEE
Q 043276 339 GYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMIV 418 (829)
Q Consensus 339 G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv 418 (829)
.+-.+++..+.++.+ .+++++.. ++...+..+|.+|++|+++.... .....+. +.|+....+++++
T Consensus 13 ~~l~~~l~~f~~~~P-~v~l~~~~---------~~~~~~~~~l~~g~~Dl~i~~~~---~~~~~~~-~~~l~~~~~~lv~ 78 (200)
T cd08466 13 LLLPRLLARLKQLAP-NISLRESP---------SSEEDLFEDLRLQEVDLVIDYVP---FRDPSFK-SELLFEDELVCVA 78 (200)
T ss_pred HHHHHHHHHHHHHCC-CCEEEEec---------CchHhHHHHHHcCCccEEEeccc---CCCCCce-eeeecccceEEEE
Confidence 445678888888876 45665543 35678999999999999985322 1122232 4577788888888
Q ss_pred Ecc
Q 043276 419 PIK 421 (829)
Q Consensus 419 ~~~ 421 (829)
+..
T Consensus 79 ~~~ 81 (200)
T cd08466 79 RKD 81 (200)
T ss_pred eCC
Confidence 744
No 139
>PRK12679 cbl transcriptional regulator Cbl; Reviewed
Probab=93.96 E-value=3.2 Score=44.70 Aligned_cols=209 Identities=13% Similarity=0.130 Sum_probs=128.0
Q ss_pred CceEEEecccccCccceEEEeecCCCCCceEEEeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcc
Q 043276 307 EKKLRVGVPVKKGFSDFVKVTIDPKTQETSVVGYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEF 386 (829)
Q Consensus 307 ~~~lrv~v~~~~~~~p~~~~~~~~~~~~~~~~G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~ 386 (829)
.+.+|||++ +.+ ...+-.+++..+.++.+ .+++++.. ++.+.++.+|.+|++
T Consensus 92 ~g~lrIg~~--~~~----------------~~~~l~~~l~~f~~~~P-~i~l~l~~---------~~~~~~~~~L~~g~~ 143 (316)
T PRK12679 92 SGVLTIATT--HTQ----------------ARYSLPEVIKAFRELFP-EVRLELIQ---------GTPQEIATLLQNGEA 143 (316)
T ss_pred CceEEEEec--hHh----------------hhcchHHHHHHHHHHCC-CeEEEEec---------CCHHHHHHHHHcCCC
Confidence 467999987 221 23456778888888876 35555543 256789999999999
Q ss_pred cEEEeccccccccceeccccccccccceEEEEEccCCCCCCceeeeccCCHhHHHHHHHHHHHHHHHHHhhhcccCCCCC
Q 043276 387 DAVVGDTTIVFNRSNYVDFTLPYTESGVSMIVPIKDSKKRNAWVFLQPLTWDLWVTSGCFFIFIGFVVWVLEHRVNEDFR 466 (829)
Q Consensus 387 Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv~~~~~~~~~~~~fl~PF~~~vW~~i~~~~~~~~~v~~~~~~~~~~~~~ 466 (829)
|+++...... . ...+. +.++.....+++++...+..
T Consensus 144 Dl~i~~~~~~-~-~~~l~-~~~l~~~~~~~v~~~~hpl~----------------------------------------- 179 (316)
T PRK12679 144 DIGIASERLS-N-DPQLV-AFPWFRWHHSLLVPHDHPLT----------------------------------------- 179 (316)
T ss_pred CEEEecccCC-C-CCCce-EEEccCCcEEEEecCCCccc-----------------------------------------
Confidence 9998533211 1 12233 35778888888887543221
Q ss_pred CCccCccchhHHHHHHHhhhcCccccccchhHHHHHHHHHHHHHHHHHhHHHHHHHhhcccCCCCCCCHHHHHhCCCcEE
Q 043276 467 GPARHQVGTSFWFSFSTMVFSQRERVISNLARFVVIVWCFVVLILIQSYTASLTSLLTVDQLQPTITDVNLLIKRGDNVG 546 (829)
Q Consensus 467 ~~~~~~~~~~~~~~~~~l~~~~~~~~~s~~~R~v~~~w~~~~lil~~~YtA~L~s~Lt~~~~~~~I~s~~dL~~~~~~vg 546 (829)
....-+++||.+.. -+.
T Consensus 180 --------------------------------------------------------------~~~~i~~~~L~~~~-~i~ 196 (316)
T PRK12679 180 --------------------------------------------------------------QITPLTLESIAKWP-LIT 196 (316)
T ss_pred --------------------------------------------------------------cCCCCCHHHHhCCC-eEE
Confidence 00123688886322 233
Q ss_pred EEeCch----HHHHHHhcCCCccceeecCChHHHHHHHhcCCcCCceeEEEcchhHHHHHHhcCCCceEEeC--cccccC
Q 043276 547 YQKGSF----VLGILKQLGFDERKLVVYNSHEECDELFQKGSANGGIAAAFDEIPYAKLLIGQHCSKYTMVE--PTFKTA 620 (829)
Q Consensus 547 ~~~~s~----~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~~c~~l~~v~--~~~~~~ 620 (829)
...+.. ...++...+.........++.+...+++..|. .-+++-... ... . +.. .+..+. ......
T Consensus 197 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~g~----Gi~~lp~~~-~~~-~-~~~-~L~~~~~~~~~~~~ 268 (316)
T PRK12679 197 YRQGITGRSRIDDAFARKGLLADIVLSAQDSDVIKTYVALGL----GIGLVAEQS-SGE-Q-EES-NLIRLDTRHLFDAN 268 (316)
T ss_pred ecCCCcHHHHHHHHHHHcCCCceEEEEeccHHHHHHHHHcCC----cEEEecccc-ccc-c-cCC-cEEEEECcccCCCc
Confidence 444433 33445555554444556678888889999887 445554432 222 1 122 244332 233445
Q ss_pred CceeeecCCCCchhhHHHHHHhhhccChhHHHHHHHcc
Q 043276 621 GFGFAFPLHSPLVHDVSKAILNVTEGDKMKEIEDAWFK 658 (829)
Q Consensus 621 ~~~~~~~k~spl~~~in~~il~l~e~G~~~~~~~~w~~ 658 (829)
.++++.+|+.++...+...+..+.+.=-.+.+.++-+.
T Consensus 269 ~~~l~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~ 306 (316)
T PRK12679 269 TVWLGLKRGQLQRNYVWRFLELCNAGLSVEDIKRQVME 306 (316)
T ss_pred eEEEEEeCCchhhHHHHHHHHHHhcccCHHHHHHHHhh
Confidence 78899999988888888888777766667777777664
No 140
>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=93.92 E-value=2.8 Score=40.82 Aligned_cols=69 Identities=14% Similarity=0.158 Sum_probs=45.9
Q ss_pred EeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccEEEeccccccccceeccccccccccceEEEE
Q 043276 339 GYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMIV 418 (829)
Q Consensus 339 G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv 418 (829)
.+-.+++..+.++.+ ++++++.. ++..+++..|.+|++|+++...... ...+. ..++.+..+++++
T Consensus 14 ~~l~~~l~~~~~~~P-~i~i~i~~---------~~~~~~~~~l~~~~~Dl~i~~~~~~---~~~~~-~~~l~~~~~~~v~ 79 (200)
T cd08411 14 YLLPRLLPALRQAYP-KLRLYLRE---------DQTERLLEKLRSGELDAALLALPVD---EPGLE-EEPLFDEPFLLAV 79 (200)
T ss_pred hhhHHHHHHHHHHCC-CcEEEEEe---------CcHHHHHHHHHcCCccEEEEeccCC---CCCce-EEEeeccceEEEe
Confidence 356678888888876 35565554 2568899999999999998532211 12222 3566777788887
Q ss_pred Ecc
Q 043276 419 PIK 421 (829)
Q Consensus 419 ~~~ 421 (829)
+..
T Consensus 80 ~~~ 82 (200)
T cd08411 80 PKD 82 (200)
T ss_pred cCC
Confidence 743
No 141
>cd08415 PBP2_LysR_opines_like The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the catabolism of opines and that of related regulators, contains the type 2 periplasmic binding fold. This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulators, OccR and NocR, involved in the catabolism of opines and that of LysR for lysine biosynthesis which clustered together in phylogenetic trees. Opines, such as octopine and nopaline, are low molecular weight compounds found in plant crown gall tumors that are produced by the parasitic bacterium Agrobacterium. There are at least 30 different opines identified so far. Opines are utilized by tumor-colonizing bacteria as a source of carbon, nitrogen, and energy. NocR and OccR belong to the family of LysR-type transcriptional regulators that positively regulates the catabolism of nopaline and octopine, respectively. Both nopaline and octopalin are arginine derivatives. In Agrobacterium tumefa
Probab=93.77 E-value=3.7 Score=39.69 Aligned_cols=70 Identities=11% Similarity=0.095 Sum_probs=48.7
Q ss_pred EEeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccEEEeccccccccceeccccccccccceEEE
Q 043276 338 VGYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMI 417 (829)
Q Consensus 338 ~G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~v 417 (829)
..+-.+++..+.+..+ .+++++.. +...++..+|.+|++|+++...... ...+ .+.|+....++++
T Consensus 12 ~~~l~~~l~~~~~~~P-~i~l~i~~---------~~~~~~~~~l~~~~~Dl~i~~~~~~---~~~~-~~~~l~~~~~~~v 77 (196)
T cd08415 12 LSLLPRAIARFRARHP-DVRISLHT---------LSSSTVVEAVLSGQADLGLASLPLD---HPGL-ESEPLASGRAVCV 77 (196)
T ss_pred ccccHHHHHHHHHHCC-CcEEEEEe---------cchHHHHHHHHcCCccEEEEeCCCC---CCcc-eeeeecccceEEE
Confidence 3556789999988876 45666654 2467899999999999998643222 1222 3567778888888
Q ss_pred EEcc
Q 043276 418 VPIK 421 (829)
Q Consensus 418 v~~~ 421 (829)
++..
T Consensus 78 ~~~~ 81 (196)
T cd08415 78 LPPG 81 (196)
T ss_pred EcCC
Confidence 8743
No 142
>TIGR00363 lipoprotein, YaeC family. This family of putative lipoproteins contains a consensus site for lipoprotein signal sequence cleavage. Included in this family is the E. coli hypothetical protein yaeC. About half of the proteins between the noise and trusted cutoffs contain the consensus lipoprotein signature and may belong to this family.
Probab=93.75 E-value=2.2 Score=44.41 Aligned_cols=120 Identities=16% Similarity=0.124 Sum_probs=66.7
Q ss_pred CCCCHHHHHhCCCcEEEEeCchHHH----HHHhcCCC------------------ccceeecC-ChHHHHHHHhcCCcCC
Q 043276 531 TITDVNLLIKRGDNVGYQKGSFVLG----ILKQLGFD------------------ERKLVVYN-SHEECDELFQKGSANG 587 (829)
Q Consensus 531 ~I~s~~dL~~~~~~vg~~~~s~~~~----~l~~~~~~------------------~~~~~~~~-~~~~~~~~l~~g~~~~ 587 (829)
.+++++||. .|.+|++..+..... .|++.++- +..+...+ ...+...++..|.
T Consensus 107 ~~~sl~dlk-~G~~IAip~d~~n~~raL~~L~~aGLi~l~~~~~~~~t~~DI~~n~~~v~~vel~~~~~~~al~~g~--- 182 (258)
T TIGR00363 107 KIKNVNELQ-DGAKVAVPNDPTNLGRALLLLQKQGLIKLKDGNGLLPTVLDIVENPKKLNITELETSQLPRALDDPK--- 182 (258)
T ss_pred CCCCHHHcC-CCCEEEEeCCcchHHHHHHHHHHcCCceecCCCCCcCChhhhhcCCCCCEEEEcCHHHHHHHhhccc---
Confidence 489999994 488999986643332 35665552 22222222 3455778898888
Q ss_pred ceeEEEcchhHHHHHHhcCC-CceEEeCcccccCCceeeecCCCCchhhHHHHHHhhhccChhHHHHHHH
Q 043276 588 GIAAAFDEIPYAKLLIGQHC-SKYTMVEPTFKTAGFGFAFPLHSPLVHDVSKAILNVTEGDKMKEIEDAW 656 (829)
Q Consensus 588 g~~a~~~~~~~~~~~~~~~c-~~l~~v~~~~~~~~~~~~~~k~spl~~~in~~il~l~e~G~~~~~~~~w 656 (829)
+|+++...+++.-.-...- +.+ .....-...-..++++.+.-=.+.+.+.+..++....-+.|.++|
T Consensus 183 -vDaa~v~~~~~~~agl~~~~~~i-~~e~~~~~~~n~l~~r~~~~~~~~~~~lv~~~~s~~v~~~i~~~~ 250 (258)
T TIGR00363 183 -VDLAVINTTYAGQVGLNPQDDGV-FVEDKDSPYVNIIVSREDNKDAENVKDFIQSYQSEEVYQAAQKHF 250 (258)
T ss_pred -ccEEEEChHHHHHcCCCcCcCce-eecCCCCCeeEEEEEcCCccCCHHHHHHHHHHcCHHHHHHHHHHc
Confidence 9998888776554322211 112 121111112235566655334456666666666655555555553
No 143
>PRK12684 transcriptional regulator CysB-like protein; Reviewed
Probab=93.68 E-value=2.8 Score=45.07 Aligned_cols=207 Identities=11% Similarity=0.044 Sum_probs=121.0
Q ss_pred CceEEEecccccCccceEEEeecCCCCCceEEEeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcc
Q 043276 307 EKKLRVGVPVKKGFSDFVKVTIDPKTQETSVVGYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEF 386 (829)
Q Consensus 307 ~~~lrv~v~~~~~~~p~~~~~~~~~~~~~~~~G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~ 386 (829)
.+.++||+. +.+ ...+-.+++..+.++.+ .+++++.. ++...++..|.+|++
T Consensus 92 ~g~l~Ig~~--~~~----------------~~~~l~~~l~~~~~~~p-~i~l~~~~---------~~~~~~~~~L~~g~~ 143 (313)
T PRK12684 92 QGNLTIATT--HTQ----------------ARYALPAAIKEFKKRYP-KVRLSILQ---------GSPTQIAEMVLHGQA 143 (313)
T ss_pred CCeEEEEec--hHH----------------HHHHhHHHHHHHHHHCC-CceEEEEe---------CChHHHHHHHHCCCc
Confidence 567999987 221 12345678888888876 35666554 256889999999999
Q ss_pred cEEEeccccccccceeccccccccccceEEEEEccCCCCCCceeeeccCCHhHHHHHHHHHHHHHHHHHhhhcccCCCCC
Q 043276 387 DAVVGDTTIVFNRSNYVDFTLPYTESGVSMIVPIKDSKKRNAWVFLQPLTWDLWVTSGCFFIFIGFVVWVLEHRVNEDFR 466 (829)
Q Consensus 387 Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv~~~~~~~~~~~~fl~PF~~~vW~~i~~~~~~~~~v~~~~~~~~~~~~~ 466 (829)
|+++..-..... ..++ ..|+.....+++++...+..
T Consensus 144 D~~i~~~~~~~~--~~l~-~~~l~~~~~~~v~~~~~pl~----------------------------------------- 179 (313)
T PRK12684 144 DLAIATEAIADY--KELV-SLPCYQWNHCVVVPPDHPLL----------------------------------------- 179 (313)
T ss_pred CEEEeecCCCCC--CCce-EEEeccceEEEEeCCCCccc-----------------------------------------
Confidence 999853211111 1222 46777778888877443211
Q ss_pred CCccCccchhHHHHHHHhhhcCccccccchhHHHHHHHHHHHHHHHHHhHHHHHHHhhcccCCCCCCCHHHHHhCCCcEE
Q 043276 467 GPARHQVGTSFWFSFSTMVFSQRERVISNLARFVVIVWCFVVLILIQSYTASLTSLLTVDQLQPTITDVNLLIKRGDNVG 546 (829)
Q Consensus 467 ~~~~~~~~~~~~~~~~~l~~~~~~~~~s~~~R~v~~~w~~~~lil~~~YtA~L~s~Lt~~~~~~~I~s~~dL~~~~~~vg 546 (829)
...--+++||.+.. -+.
T Consensus 180 --------------------------------------------------------------~~~~i~~~dL~~~~-~i~ 196 (313)
T PRK12684 180 --------------------------------------------------------------ERKPLTLEDLAQYP-LIT 196 (313)
T ss_pred --------------------------------------------------------------cCCCcCHHHHhcCC-cEe
Confidence 00124678886332 344
Q ss_pred EEeCchH----HHHHHhcCCCccceeecCChHHHHHHHhcCCcCCceeEEEcchhHHHHHHhcCCCceEEe--CcccccC
Q 043276 547 YQKGSFV----LGILKQLGFDERKLVVYNSHEECDELFQKGSANGGIAAAFDEIPYAKLLIGQHCSKYTMV--EPTFKTA 620 (829)
Q Consensus 547 ~~~~s~~----~~~l~~~~~~~~~~~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~~c~~l~~v--~~~~~~~ 620 (829)
+..++.. ..++...+.........++.+...+++..|. ..+++.+. ...... . ..+..+ .......
T Consensus 197 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~----Gv~~lp~~-~~~~~~-~--~~l~~~~i~~~~~~~ 268 (313)
T PRK12684 197 YDFAFAGRSKINKAFALRGLKPDIVLEAIDADVIKTYVELGL----GVGIVADM-AFDPER-D--RNLRAIDAGHLFGSS 268 (313)
T ss_pred cCCCCcHHHHHHHHHHHcCCCCCeEEEeCCHHHHHHHHHhCC----ceEEeehh-hccccc-c--CCeEEEECCCCCcce
Confidence 4444433 3345445555444566778888899999887 34555442 222221 1 124433 2233345
Q ss_pred CceeeecCCCCchhhHHHHHHhhhccChhHHHHHHHc
Q 043276 621 GFGFAFPLHSPLVHDVSKAILNVTEGDKMKEIEDAWF 657 (829)
Q Consensus 621 ~~~~~~~k~spl~~~in~~il~l~e~G~~~~~~~~w~ 657 (829)
.++++.+|+.++...+...+..+.+. +..++..+-+
T Consensus 269 ~~~l~~~~~~~~~~~~~~f~~~l~~~-~~~~~~~~~~ 304 (313)
T PRK12684 269 TTRLGLRRGAYLRGYVYTFIELFAPT-LNRKLVEQAL 304 (313)
T ss_pred eEEEEEECCCcCCHHHHHHHHHHHHH-hCHHHHHHHh
Confidence 67899999988777666666655543 4455555544
No 144
>PRK11233 nitrogen assimilation transcriptional regulator; Provisional
Probab=93.64 E-value=2.9 Score=44.78 Aligned_cols=69 Identities=14% Similarity=0.177 Sum_probs=45.0
Q ss_pred EeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccEEEeccccccccceeccccccccccceEEEE
Q 043276 339 GYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMIV 418 (829)
Q Consensus 339 G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv 418 (829)
.+..+++..+.++.+ .+++.+.. +....+...|.+|++|+++..-... ...++ ..|+.+..+++++
T Consensus 105 ~~~~~~l~~~~~~~p-~i~l~~~~---------~~~~~~~~~l~~g~~Di~i~~~~~~---~~~~~-~~~l~~~~~~lv~ 170 (305)
T PRK11233 105 SLTMPLLQAVRAEFP-GIVLYLHE---------NSGATLNEKLMNGQLDMAVIYEHSP---VAGLS-SQPLLKEDLFLVG 170 (305)
T ss_pred HHHHHHHHHHHHHCC-CcEEEEEE---------CCcHHHHHHHHCCCCCEEEEcCCcC---CCCcE-EEEEeeeeEEEEE
Confidence 344568888888875 45555544 2457889999999999998532211 12232 4577778887777
Q ss_pred Ecc
Q 043276 419 PIK 421 (829)
Q Consensus 419 ~~~ 421 (829)
+..
T Consensus 171 ~~~ 173 (305)
T PRK11233 171 TQD 173 (305)
T ss_pred cCc
Confidence 643
No 145
>CHL00180 rbcR LysR transcriptional regulator; Provisional
Probab=93.63 E-value=4 Score=43.66 Aligned_cols=87 Identities=14% Similarity=0.209 Sum_probs=56.2
Q ss_pred CceEEEecccccCccceEEEeecCCCCCceEEEeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcc
Q 043276 307 EKKLRVGVPVKKGFSDFVKVTIDPKTQETSVVGYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEF 386 (829)
Q Consensus 307 ~~~lrv~v~~~~~~~p~~~~~~~~~~~~~~~~G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~ 386 (829)
.+.+|||+. +.. ...+-.+++..+.+..+ .+++++.. +....++..|.+|++
T Consensus 94 ~g~l~ig~~--~~~----------------~~~~~~~~l~~~~~~~P-~v~i~~~~---------~~~~~~~~~l~~g~~ 145 (305)
T CHL00180 94 RGTLIIGAS--QTT----------------GTYLMPRLIGLFRQRYP-QINVQLQV---------HSTRRIAWNVANGQI 145 (305)
T ss_pred CceEEEEEc--Ccc----------------hHhHHHHHHHHHHHHCC-CceEEEEe---------CCHHHHHHHHHcCCc
Confidence 467999987 221 12345678888888876 35666543 246889999999999
Q ss_pred cEEEeccccccccceeccccccccccceEEEEEccC
Q 043276 387 DAVVGDTTIVFNRSNYVDFTLPYTESGVSMIVPIKD 422 (829)
Q Consensus 387 Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv~~~~ 422 (829)
|+++..-.........+ ...++....++++++...
T Consensus 146 Dl~i~~~~~~~~~~~~~-~~~~l~~~~~~~v~~~~~ 180 (305)
T CHL00180 146 DIAIVGGEVPTELKKIL-EITPYVEDELALIIPKSH 180 (305)
T ss_pred cEEEEcCccCcccccce-eEEEeccCcEEEEECCCC
Confidence 99986322221111122 256788888888888543
No 146
>cd08426 PBP2_LTTR_like_5 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold. LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functi
Probab=93.63 E-value=4.7 Score=39.11 Aligned_cols=69 Identities=14% Similarity=0.113 Sum_probs=46.5
Q ss_pred EeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccEEEeccccccccceeccccccccccceEEEE
Q 043276 339 GYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMIV 418 (829)
Q Consensus 339 G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv 418 (829)
++-.+++..+.++.+ .+++++.. ++..+++.+|.+|++|+++....... ..+. +.++....+++++
T Consensus 13 ~~l~~~l~~~~~~~P-~i~l~i~~---------~~~~~~~~~l~~~~~D~~i~~~~~~~---~~~~-~~~l~~~~~~~v~ 78 (199)
T cd08426 13 ELLPSLIARFRQRYP-GVFFTVDV---------ASTADVLEAVLSGEADIGLAFSPPPE---PGIR-VHSRQPAPIGAVV 78 (199)
T ss_pred HHHHHHHHHHHHhCC-CeEEEEEe---------CCcHHHHHHHHCCCccEEEecCCCCC---CCeE-EEeeccCcEEEEe
Confidence 445678888888876 35555543 24578999999999999985432221 2232 4677788888888
Q ss_pred Ecc
Q 043276 419 PIK 421 (829)
Q Consensus 419 ~~~ 421 (829)
+..
T Consensus 79 ~~~ 81 (199)
T cd08426 79 PPG 81 (199)
T ss_pred cCC
Confidence 744
No 147
>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=93.41 E-value=4.4 Score=38.92 Aligned_cols=69 Identities=20% Similarity=0.381 Sum_probs=46.0
Q ss_pred EeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccEEEeccccccccceeccccccccccceEEEE
Q 043276 339 GYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMIV 418 (829)
Q Consensus 339 G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv 418 (829)
.+-..++..+.++.+ .+++++.. +....++.++.+|++|+++..... ....+. ..++....+++++
T Consensus 13 ~~l~~~l~~~~~~~P-~i~i~i~~---------~~~~~~~~~l~~~~~Dl~i~~~~~---~~~~l~-~~~l~~~~~~~v~ 78 (195)
T cd08434 13 SLVPDLIRAFRKEYP-NVTFELHQ---------GSTDELLDDLKNGELDLALCSPVP---DEPDIE-WIPLFTEELVLVV 78 (195)
T ss_pred hhhHHHHHHHHHhCC-CeEEEEec---------CcHHHHHHHHHcCCccEEEEccCC---CCCCee-EEEeecceEEEEe
Confidence 455677888888875 34555543 245788999999999999854322 222333 3567778888887
Q ss_pred Ecc
Q 043276 419 PIK 421 (829)
Q Consensus 419 ~~~ 421 (829)
+..
T Consensus 79 ~~~ 81 (195)
T cd08434 79 PKD 81 (195)
T ss_pred cCC
Confidence 744
No 148
>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=93.37 E-value=3.6 Score=40.00 Aligned_cols=69 Identities=20% Similarity=0.209 Sum_probs=46.6
Q ss_pred EeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccEEEeccccccccceeccccccccccceEEEE
Q 043276 339 GYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMIV 418 (829)
Q Consensus 339 G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv 418 (829)
.+-.+++..+.++.+ ++++++.. ++.+.+...|.+|++|+++.... .....+. ..|+....+++++
T Consensus 13 ~~~~~~i~~~~~~~P-~i~l~~~~---------~~~~~~~~~l~~g~~D~~i~~~~---~~~~~~~-~~~l~~~~~~~v~ 78 (200)
T cd08417 13 LLLPPLLARLRQEAP-GVRLRFVP---------LDRDDLEEALESGEIDLAIGVFP---ELPPGLR-SQPLFEDRFVCVA 78 (200)
T ss_pred HHHHHHHHHHHhhCC-CeEEEecc---------CCHHHHHHHHHcCCCCEEEeecc---cCCCccc-hhhhhcCceEEEe
Confidence 345677888888876 34555443 35688999999999999985432 2222232 4678888888888
Q ss_pred Ecc
Q 043276 419 PIK 421 (829)
Q Consensus 419 ~~~ 421 (829)
+..
T Consensus 79 ~~~ 81 (200)
T cd08417 79 RKD 81 (200)
T ss_pred cCC
Confidence 744
No 149
>PRK11242 DNA-binding transcriptional regulator CynR; Provisional
Probab=93.27 E-value=3.5 Score=43.75 Aligned_cols=69 Identities=12% Similarity=0.067 Sum_probs=47.8
Q ss_pred EeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccEEEeccccccccceeccccccccccceEEEE
Q 043276 339 GYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMIV 418 (829)
Q Consensus 339 G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv 418 (829)
.+-.+++..+.++.+ .+++++.. +....++..|.+|++|+++..... ....+ .+.++....+++++
T Consensus 104 ~~l~~~l~~~~~~~p-~~~i~~~~---------~~~~~~~~~l~~g~~Dl~i~~~~~---~~~~l-~~~~l~~~~~~~~~ 169 (296)
T PRK11242 104 YLIGPLIDAFHARYP-GITLTIRE---------MSQERIEALLADDELDVGIAFAPV---HSPEI-EAQPLFTETLALVV 169 (296)
T ss_pred hhhHHHHHHHHHHCC-CCEEEEEe---------CCHHHHHHHHHCCCCcEEEEecCC---CCcce-eEEEeeeccEEEEE
Confidence 455678888888876 45665543 246889999999999999854322 22223 24677788888888
Q ss_pred Ecc
Q 043276 419 PIK 421 (829)
Q Consensus 419 ~~~ 421 (829)
+..
T Consensus 170 ~~~ 172 (296)
T PRK11242 170 GRH 172 (296)
T ss_pred cCC
Confidence 854
No 150
>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=93.01 E-value=5.6 Score=38.57 Aligned_cols=68 Identities=21% Similarity=0.288 Sum_probs=45.3
Q ss_pred eeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccEEEeccccccccceeccccccccccceEEEEE
Q 043276 340 YSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMIVP 419 (829)
Q Consensus 340 ~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv~ 419 (829)
+-..++..+.++.+ .+++++.. ++...+...|.+|++|+++..-... ...+. ..++....++++++
T Consensus 14 ~~~~~l~~~~~~~P-~i~i~i~~---------~~~~~~~~~l~~g~~Dl~i~~~~~~---~~~~~-~~~l~~~~~~~~~~ 79 (198)
T cd08441 14 WLMPVLDQFRERWP-DVELDLSS---------GFHFDPLPALLRGELDLVITSDPLP---LPGIA-YEPLFDYEVVLVVA 79 (198)
T ss_pred hhHHHHHHHHHhCC-CeEEEEEe---------CCchhHHHHHHcCCceEEEecCCcC---CCCcE-EEEccCCcEEEEEc
Confidence 45678888888887 35565544 2467899999999999998532221 12232 35677777777777
Q ss_pred cc
Q 043276 420 IK 421 (829)
Q Consensus 420 ~~ 421 (829)
..
T Consensus 80 ~~ 81 (198)
T cd08441 80 PD 81 (198)
T ss_pred CC
Confidence 43
No 151
>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=92.77 E-value=7.1 Score=37.73 Aligned_cols=71 Identities=11% Similarity=0.166 Sum_probs=47.1
Q ss_pred EeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccEEEeccccccccceeccccccccccceEEEE
Q 043276 339 GYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMIV 418 (829)
Q Consensus 339 G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv 418 (829)
.+-.+++..+.+..+ ++++++.. ++..+++.+|.+|++|+++..... ..+...+. ..|+....+++++
T Consensus 13 ~~l~~~l~~~~~~~P-~v~i~i~~---------~~~~~~~~~l~~~~~Dl~i~~~~~-~~~~~~~~-~~~l~~~~~~~~~ 80 (201)
T cd08435 13 VLLPPAIARLLARHP-RLTVRVVE---------GTSDELLEGLRAGELDLAIGRLAD-DEQPPDLA-SEELADEPLVVVA 80 (201)
T ss_pred HHHHHHHHHHHHHCC-CeEEEEEe---------CCHHHHHHHHHcCCccEEEEecCc-ccCCCCcE-EEEcccCcEEEEE
Confidence 345678888888876 45666543 246889999999999999853221 11122232 4577888888888
Q ss_pred Ecc
Q 043276 419 PIK 421 (829)
Q Consensus 419 ~~~ 421 (829)
+..
T Consensus 81 ~~~ 83 (201)
T cd08435 81 RPG 83 (201)
T ss_pred eCC
Confidence 744
No 152
>PRK09791 putative DNA-binding transcriptional regulator; Provisional
Probab=92.72 E-value=3.4 Score=44.10 Aligned_cols=85 Identities=13% Similarity=0.154 Sum_probs=56.8
Q ss_pred CceEEEecccccCccceEEEeecCCCCCceEEEeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcc
Q 043276 307 EKKLRVGVPVKKGFSDFVKVTIDPKTQETSVVGYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEF 386 (829)
Q Consensus 307 ~~~lrv~v~~~~~~~p~~~~~~~~~~~~~~~~G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~ 386 (829)
.+.++||++ +.+ ...+-.+++..+.++.+ .+++++.. ++..+++.+|.+|++
T Consensus 94 ~g~l~I~~~--~~~----------------~~~~l~~~l~~~~~~~p-~i~~~~~~---------~~~~~~~~~l~~g~~ 145 (302)
T PRK09791 94 AGQINIGMG--ASI----------------ARSLMPAVISRFHQQHP-QVKVRIME---------GQLVSMINELRQGEL 145 (302)
T ss_pred ceEEEEEec--hHH----------------HHhhhHHHHHHHHHHCC-CeEEEEEe---------CChHHHHHHHHCCCc
Confidence 578999988 211 23455678888888877 45665543 256899999999999
Q ss_pred cEEEeccccccccceeccccccccccceEEEEEcc
Q 043276 387 DAVVGDTTIVFNRSNYVDFTLPYTESGVSMIVPIK 421 (829)
Q Consensus 387 Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv~~~ 421 (829)
|+++....... ....+.+ .|+....++++++..
T Consensus 146 Di~i~~~~~~~-~~~~~~~-~~l~~~~~~l~~~~~ 178 (302)
T PRK09791 146 DFTINTYYQGP-YDHEFTF-EKLLEKQFAVFCRPG 178 (302)
T ss_pred cEEEEecCCcc-cccceeE-EEeccceEEEEEcCC
Confidence 99985321111 1123443 688888888888844
No 153
>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=92.68 E-value=4.9 Score=38.99 Aligned_cols=69 Identities=14% Similarity=0.076 Sum_probs=45.9
Q ss_pred EeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccEEEeccccccccceeccccccccccceEEEE
Q 043276 339 GYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMIV 418 (829)
Q Consensus 339 G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv 418 (829)
++-..++..+.++.+ ++++++.. +....++..|.+|++|+++..... . ...+. ..++....+++++
T Consensus 13 ~~l~~~l~~~~~~~P-~v~l~i~~---------~~~~~~~~~l~~g~~D~~i~~~~~--~-~~~~~-~~~l~~~~~~~v~ 78 (200)
T cd08464 13 WLAPPLLAALRAEAP-GVRLVFRQ---------VDPFNVGDMLDRGEIDLAIGVFGE--L-PAWLK-REVLYTEGYACLF 78 (200)
T ss_pred HHHHHHHHHHHHHCC-CcEEEEec---------CCcccHHHHHhcCcccEEEecCCC--C-cccce-eeeecccceEEEE
Confidence 455678888888876 45666554 245788899999999999853221 1 22232 4577777887777
Q ss_pred Ecc
Q 043276 419 PIK 421 (829)
Q Consensus 419 ~~~ 421 (829)
+..
T Consensus 79 ~~~ 81 (200)
T cd08464 79 DPQ 81 (200)
T ss_pred eCC
Confidence 643
No 154
>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=92.64 E-value=9.4 Score=36.70 Aligned_cols=69 Identities=13% Similarity=0.151 Sum_probs=46.3
Q ss_pred EeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccEEEeccccccccceeccccccccccceEEEE
Q 043276 339 GYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMIV 418 (829)
Q Consensus 339 G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv 418 (829)
.+..+++..+.++.+ ++++++.. +....++.+|.+|++|+++....... ..+ ...++....+++++
T Consensus 12 ~~l~~~l~~~~~~~P-~i~l~i~~---------~~~~~~~~~l~~g~~Dl~i~~~~~~~---~~~-~~~~l~~~~~~~~~ 77 (197)
T cd08419 12 YFAPRLLGAFCRRHP-GVEVSLRV---------GNREQVLERLADNEDDLAIMGRPPED---LDL-VAEPFLDNPLVVIA 77 (197)
T ss_pred hHhhHHHHHHHHHCC-CceEEEEE---------CCHHHHHHHHhcCCccEEEecCCCCC---CCe-EEEEeccCCEEEEe
Confidence 355678888888876 35666554 24678899999999999985432211 112 24677778888888
Q ss_pred Ecc
Q 043276 419 PIK 421 (829)
Q Consensus 419 ~~~ 421 (829)
+..
T Consensus 78 ~~~ 80 (197)
T cd08419 78 PPD 80 (197)
T ss_pred cCC
Confidence 744
No 155
>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=92.56 E-value=8.2 Score=37.14 Aligned_cols=70 Identities=14% Similarity=0.176 Sum_probs=47.0
Q ss_pred EEeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccEEEeccccccccceeccccccccccceEEE
Q 043276 338 VGYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMI 417 (829)
Q Consensus 338 ~G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~v 417 (829)
..+-.+++..+.++.+ .+++++... .-..++.+|.+|++|+++...... ...+. +.++....+.++
T Consensus 12 ~~~l~~~l~~~~~~~P-~~~l~~~~~---------~~~~~~~~l~~g~~D~~i~~~~~~---~~~~~-~~~l~~~~~~~v 77 (201)
T cd08420 12 EYLLPRLLARFRKRYP-EVRVSLTIG---------NTEEIAERVLDGEIDLGLVEGPVD---HPDLI-VEPFAEDELVLV 77 (201)
T ss_pred hhhhHHHHHHHHHHCC-CceEEEEeC---------CcHHHHHHHHCCCccEEEecCCCC---CcceE-EEeecCccEEEE
Confidence 3455688888888876 356665542 357889999999999998643322 12222 367777888888
Q ss_pred EEcc
Q 043276 418 VPIK 421 (829)
Q Consensus 418 v~~~ 421 (829)
++..
T Consensus 78 ~~~~ 81 (201)
T cd08420 78 VPPD 81 (201)
T ss_pred ecCC
Confidence 7744
No 156
>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=92.55 E-value=4.4 Score=39.58 Aligned_cols=69 Identities=19% Similarity=0.195 Sum_probs=47.1
Q ss_pred EEeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccEEEeccccccccceeccccccccccceEEE
Q 043276 338 VGYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMI 417 (829)
Q Consensus 338 ~G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~v 417 (829)
..+-.+++..+.++.+ .++++... ++. .++..|.+|++|++++.... ....+. ..|+.+..++++
T Consensus 12 ~~~l~~~l~~~~~~~P-~v~v~l~~---------~~~-~~~~~l~~g~~D~~i~~~~~---~~~~~~-~~~l~~~~~~~v 76 (200)
T cd08460 12 AAFGPALLAAVAAEAP-GVRLRFVP---------ESD-KDVDALREGRIDLEIGVLGP---TGPEIR-VQTLFRDRFVGV 76 (200)
T ss_pred HHHHHHHHHHHHHHCC-CCEEEEec---------Cch-hHHHHHHCCCccEEEecCCC---CCcchh-eeeeeccceEEE
Confidence 3566788888888876 45666543 234 78899999999999863322 122343 467788888888
Q ss_pred EEcc
Q 043276 418 VPIK 421 (829)
Q Consensus 418 v~~~ 421 (829)
++..
T Consensus 77 ~~~~ 80 (200)
T cd08460 77 VRAG 80 (200)
T ss_pred EeCC
Confidence 8744
No 157
>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=92.33 E-value=6.1 Score=38.57 Aligned_cols=67 Identities=19% Similarity=0.221 Sum_probs=44.2
Q ss_pred eeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccEEEeccccccccceeccccccccccceEEEEE
Q 043276 340 YSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMIVP 419 (829)
Q Consensus 340 ~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv~ 419 (829)
+-..++..+.++.+ .++++... ++. +++..|.+|++|++++.-... ...+. ..|+....++++++
T Consensus 14 ~l~~~i~~~~~~~P-~i~l~i~~---------~~~-~~~~~l~~g~~D~~i~~~~~~---~~~~~-~~~l~~~~~~~v~~ 78 (200)
T cd08462 14 LLPPVIERVAREAP-GVRFELLP---------PDD-QPHELLERGEVDLLIAPERFM---SDGHP-SEPLFEEEFVCVVW 78 (200)
T ss_pred HHHHHHHHHHHHCC-CCEEEEec---------CCh-hHHHHHhcCCeeEEEecCCCC---CCCce-eeeeeccceEEEEc
Confidence 34567788888776 35555543 234 899999999999998632221 12233 44777788888877
Q ss_pred cc
Q 043276 420 IK 421 (829)
Q Consensus 420 ~~ 421 (829)
..
T Consensus 79 ~~ 80 (200)
T cd08462 79 AD 80 (200)
T ss_pred CC
Confidence 44
No 158
>cd08465 PBP2_ToxR The C-terminal substrate binding domain of LysR-type transcriptional regulator ToxR regulates the expression of the toxoflavin biosynthesis genes; contains the type 2 periplasmic bindinig fold. In soil bacterium Burkholderia glumae, ToxR regulates the toxABCDE and toxFGHI operons in the presence of toxoflavin as a coinducer. Additionally, the expression of both operons requires a transcriptional activator, ToxJ, whose expression is regulated by the TofI or TofR quorum-sensing system. The biosynthesis of toxoflavin is suggested to be synthesized in a pathway common to the synthesis of riboflavin. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After
Probab=92.21 E-value=2.7 Score=41.20 Aligned_cols=69 Identities=14% Similarity=0.112 Sum_probs=47.1
Q ss_pred EeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccEEEeccccccccceeccccccccccceEEEE
Q 043276 339 GYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMIV 418 (829)
Q Consensus 339 G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv 418 (829)
++-.+++..+.++.+ .++++... ++..+++.+|.+|++|++++..... ...++. .+.....+++++
T Consensus 13 ~~l~~~l~~f~~~~P-~i~l~i~~---------~~~~~~~~~L~~g~~Dl~i~~~~~~---~~~~~~-~~l~~~~~~lv~ 78 (200)
T cd08465 13 LVLPALMRQLRAEAP-GIDLAVSQ---------ASREAMLAQVADGEIDLALGVFPEL---PEELHA-ETLFEERFVCLA 78 (200)
T ss_pred HhhhHHHHHHHHHCC-CcEEEEec---------CChHhHHHHHHCCCccEEEeccccC---CcCeeE-EEeeeccEEEEE
Confidence 556678888888876 45665554 3578999999999999998533221 122333 467777788888
Q ss_pred Ecc
Q 043276 419 PIK 421 (829)
Q Consensus 419 ~~~ 421 (829)
+..
T Consensus 79 ~~~ 81 (200)
T cd08465 79 DRA 81 (200)
T ss_pred eCC
Confidence 744
No 159
>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=92.13 E-value=6 Score=42.08 Aligned_cols=85 Identities=18% Similarity=0.214 Sum_probs=56.3
Q ss_pred CceEEEecccccCccceEEEeecCCCCCceEEEeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcc
Q 043276 307 EKKLRVGVPVKKGFSDFVKVTIDPKTQETSVVGYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEF 386 (829)
Q Consensus 307 ~~~lrv~v~~~~~~~p~~~~~~~~~~~~~~~~G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~ 386 (829)
.+.++||++ +.+ ...+-.+++..+.++.+ .+++.+.. ++...++.+|.+|++
T Consensus 92 ~~~l~I~~~--~~~----------------~~~~~~~~l~~~~~~~P-~~~i~~~~---------~~~~~~~~~l~~g~~ 143 (300)
T TIGR02424 92 GPTVRIGAL--PTV----------------AARLMPEVVKRFLARAP-RLRVRIMT---------GPNAYLLDQLRVGAL 143 (300)
T ss_pred CceEEEecc--cHH----------------HHhhhHHHHHHHHHhCC-CcEEEEEe---------CchHHHHHHHHCCCC
Confidence 578999987 221 12345678888888887 45666654 246789999999999
Q ss_pred cEEEeccccccccceeccccccccccceEEEEEcc
Q 043276 387 DAVVGDTTIVFNRSNYVDFTLPYTESGVSMIVPIK 421 (829)
Q Consensus 387 Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv~~~ 421 (829)
|++++..... .....+. ..|......+++++..
T Consensus 144 D~~i~~~~~~-~~~~~~~-~~~l~~~~~~~~~~~~ 176 (300)
T TIGR02424 144 DLVVGRLGAP-ETMQGLS-FEHLYNEPVVFVVRAG 176 (300)
T ss_pred CEEEEecCCc-cccccee-eeeecCCceEEEEcCC
Confidence 9999643321 1122232 3577788888888744
No 160
>PRK12682 transcriptional regulator CysB-like protein; Reviewed
Probab=92.00 E-value=6.9 Score=41.88 Aligned_cols=84 Identities=20% Similarity=0.229 Sum_probs=55.3
Q ss_pred CceEEEecccccCccceEEEeecCCCCCceEEEeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcc
Q 043276 307 EKKLRVGVPVKKGFSDFVKVTIDPKTQETSVVGYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEF 386 (829)
Q Consensus 307 ~~~lrv~v~~~~~~~p~~~~~~~~~~~~~~~~G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~ 386 (829)
.+.++||++ +.+ ...+-.+++..+.++.+ .+++++.. ++.+.++..|.+|++
T Consensus 92 ~g~l~Ig~~--~~~----------------~~~~l~~~l~~~~~~~P-~i~i~i~~---------~~~~~~~~~l~~g~~ 143 (309)
T PRK12682 92 SGTLTIATT--HTQ----------------ARYVLPRVVAAFRKRYP-KVNLSLHQ---------GSPDEIARMVISGEA 143 (309)
T ss_pred CCeEEEeeC--chH----------------HHHHHHHHHHHHHHhCC-CeEEEEec---------CCHHHHHHHHHcCCc
Confidence 467999987 221 12455678888888876 35555543 245789999999999
Q ss_pred cEEEeccccccccceeccccccccccceEEEEEcc
Q 043276 387 DAVVGDTTIVFNRSNYVDFTLPYTESGVSMIVPIK 421 (829)
Q Consensus 387 Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv~~~ 421 (829)
|++++.-... ....++ +.|+.....+++++..
T Consensus 144 D~~i~~~~~~--~~~~l~-~~~l~~~~~~~~~~~~ 175 (309)
T PRK12682 144 DIGIATESLA--DDPDLA-TLPCYDWQHAVIVPPD 175 (309)
T ss_pred cEEEecCccc--CCCcce-EEEeeeeeEEEEecCC
Confidence 9998642211 112333 4578888888888754
No 161
>cd08425 PBP2_CynR The C-terminal substrate-binding domain of the LysR-type transcriptional regulator CynR, contains the type 2 periplasmic binding fold. CynR is a LysR-like transcriptional regulator of the cyn operon, which encodes genes that allow cyanate to be used as a sole source of nitrogen. The operon includes three genes in the following order: cynT (cyanate permease), cynS (cyanase), and cynX (a protein of unknown function). CynR negatively regulates its own expression independently of cyanate. CynR binds to DNA and induces bending of DNA in the presence or absence of cyanate, but the amount of bending is decreased by cyanate. The CynR of LysR-type transcriptional regulator family is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding
Probab=91.97 E-value=6.7 Score=37.95 Aligned_cols=69 Identities=10% Similarity=0.108 Sum_probs=47.0
Q ss_pred EeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccEEEeccccccccceeccccccccccceEEEE
Q 043276 339 GYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMIV 418 (829)
Q Consensus 339 G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv 418 (829)
.+-..++..+.++.+ ++++++... ...++...|.+|++|+++...... ...+. ..++....+++++
T Consensus 14 ~~l~~~l~~~~~~~P-~v~i~i~~~---------~~~~~~~~l~~g~~Dl~i~~~~~~---~~~~~-~~~l~~~~~~~v~ 79 (197)
T cd08425 14 YLIGPLIDRFHARYP-GIALSLREM---------PQERIEAALADDRLDLGIAFAPVR---SPDID-AQPLFDERLALVV 79 (197)
T ss_pred hhhHHHHHHHHHHCC-CcEEEEEEC---------cHHHHHHHHHcCCccEEEEecCCC---CCCcE-EEEeccccEEEEe
Confidence 345688888888876 466666542 457889999999999998533221 22232 3667778888888
Q ss_pred Ecc
Q 043276 419 PIK 421 (829)
Q Consensus 419 ~~~ 421 (829)
+..
T Consensus 80 ~~~ 82 (197)
T cd08425 80 GAT 82 (197)
T ss_pred cCC
Confidence 744
No 162
>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=91.88 E-value=12 Score=36.23 Aligned_cols=70 Identities=14% Similarity=0.156 Sum_probs=46.1
Q ss_pred EEeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccEEEeccccccccceeccccccccccceEEE
Q 043276 338 VGYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMI 417 (829)
Q Consensus 338 ~G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~v 417 (829)
..+-.+++..+.++.+ .+++++... .-.++...|.+|++|+++...... ...+. ..++.+..++++
T Consensus 12 ~~~l~~~l~~~~~~~P-~i~l~~~~~---------~~~~~~~~l~~~~~Dl~i~~~~~~---~~~~~-~~~l~~~~~~~~ 77 (196)
T cd08457 12 NGFLPRFLAAFLRLRP-NLHLSLMGL---------SSSQVLEAVASGRADLGIADGPLE---ERQGF-LIETRSLPAVVA 77 (196)
T ss_pred ccccHHHHHHHHHHCC-CeEEEEEec---------CcHHHHHHHHcCCccEEEeccCCC---CCCcE-EEEeccCCeEEE
Confidence 3456788999998887 456665542 346788999999999998543221 22222 356677777777
Q ss_pred EEcc
Q 043276 418 VPIK 421 (829)
Q Consensus 418 v~~~ 421 (829)
++..
T Consensus 78 ~~~~ 81 (196)
T cd08457 78 VPMG 81 (196)
T ss_pred eeCC
Confidence 7743
No 163
>PRK10341 DNA-binding transcriptional activator TdcA; Provisional
Probab=91.87 E-value=6.1 Score=42.39 Aligned_cols=70 Identities=13% Similarity=0.225 Sum_probs=47.8
Q ss_pred eeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccEEEeccccccccceeccccccccccceEEEEE
Q 043276 340 YSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMIVP 419 (829)
Q Consensus 340 ~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv~ 419 (829)
+-.+++..+.+..+ .+++++.. +...+++..|.+|++|+++....... ....+ ...|+.+..++++++
T Consensus 111 ~l~~~l~~~~~~~p-~v~i~~~~---------~~~~~~~~~l~~g~~Dl~i~~~~~~~-~~~~l-~~~~l~~~~~~lv~~ 178 (312)
T PRK10341 111 FMSDMINKFKEVFP-KAQVSMYE---------AQLSSFLPAIRDGRLDFAIGTLSNEM-KLQDL-HVEPLFESEFVLVAS 178 (312)
T ss_pred hHHHHHHHHHHhCC-CCEEEEEe---------CCHHHHHHHHHcCCCcEEEecCCccc-ccCCe-eEEEEecccEEEEEc
Confidence 44588888888876 35666654 25689999999999999985432111 11222 246788888888887
Q ss_pred cc
Q 043276 420 IK 421 (829)
Q Consensus 420 ~~ 421 (829)
..
T Consensus 179 ~~ 180 (312)
T PRK10341 179 KS 180 (312)
T ss_pred CC
Confidence 44
No 164
>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=91.87 E-value=6.5 Score=38.30 Aligned_cols=71 Identities=21% Similarity=0.203 Sum_probs=48.2
Q ss_pred EEeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccEEEeccccccccceeccccccccccceEEE
Q 043276 338 VGYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMI 417 (829)
Q Consensus 338 ~G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~v 417 (829)
..+-.+++..+.++.+ .+++++.. +....++..|.+|++|+++...... ....+. +.+.....++++
T Consensus 12 ~~~l~~~l~~~~~~~P-~i~v~~~~---------~~~~~~~~~l~~g~~D~~i~~~~~~--~~~~~~-~~~l~~~~~~~v 78 (198)
T cd08413 12 RYVLPPVIAAFRKRYP-KVKLSLHQ---------GTPSQIAEMVLKGEADIAIATEALD--DHPDLV-TLPCYRWNHCVI 78 (198)
T ss_pred hhhccHHHHHHHHhCC-ceEEEEEe---------CCHHHHHHHHHcCCCCEEEEccCCC--CCCCcE-EEEeeeeeEEEE
Confidence 3455688899999887 35666554 2568899999999999998532211 112233 467778888888
Q ss_pred EEcc
Q 043276 418 VPIK 421 (829)
Q Consensus 418 v~~~ 421 (829)
++..
T Consensus 79 ~~~~ 82 (198)
T cd08413 79 VPPG 82 (198)
T ss_pred ecCC
Confidence 8744
No 165
>cd08429 PBP2_NhaR The C-terminal substrate binding domain of LysR-type transcriptional activator of the nhaA gene, encoding Na+/H+ antiporter, contains the type 2 periplasmic binding fold. NhaR is a positive regulator of the LysR family and is known to be an activator of the nhaA gene encoding a Na(+)/H(+) antiporter. In Escherichia coli, NhaA is the vital antiporter that protects against high sodium stress, and it is essential for growth in high sodium levels, while NhaB becomes essential only if NhaA is not available. The nhaA gene of nhaAR operon is induced by monovalent cations. The nhaR of the operon activates nhaAR, as well as the osmC transcription which is induced at elevated osmolarity. OsmC is transcribed from the two overlapping promoters (osmCp1 and osmP2) and that NhaR is shown to activate only the expression of osmCp1. NhaR also activates the transcription of the pgaABCD operon which is required for production of the biofilm adhesion, poly-beta-1,6-N-acetyl-d-glucosamine
Probab=91.77 E-value=12 Score=37.01 Aligned_cols=71 Identities=14% Similarity=0.204 Sum_probs=45.7
Q ss_pred EeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccEEEeccccccccceeccccccccccceEEEE
Q 043276 339 GYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMIV 418 (829)
Q Consensus 339 G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv 418 (829)
.+-.+++..+.++.+ .++++... ++...++..|.+|++|+++........-...+ ...|+.+..+++++
T Consensus 13 ~~l~~~l~~f~~~~P-~v~l~i~~---------~~~~~~~~~L~~~~~D~~i~~~~~~~~~~~~~-~~~~l~~~~~~~~~ 81 (204)
T cd08429 13 SIAYRLLEPAMDLHE-PIRLVCRE---------GKLEQLLADLALHRLDMVLADRPMPSSLDVKG-YSHRLGECGVSFFA 81 (204)
T ss_pred HHHHHHHHHHHHhCC-CcEEEEEe---------CCHHHHHHHHHcCCccEEEecCCCccccchhe-eeccccccceEEEe
Confidence 455778888888876 45665554 36889999999999999985332111100111 13577777777766
Q ss_pred Ec
Q 043276 419 PI 420 (829)
Q Consensus 419 ~~ 420 (829)
+.
T Consensus 82 ~~ 83 (204)
T cd08429 82 AP 83 (204)
T ss_pred cC
Confidence 53
No 166
>PRK12683 transcriptional regulator CysB-like protein; Reviewed
Probab=91.77 E-value=6.8 Score=42.00 Aligned_cols=197 Identities=12% Similarity=0.064 Sum_probs=114.7
Q ss_pred CceEEEecccccCccceEEEeecCCCCCceEEEeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcc
Q 043276 307 EKKLRVGVPVKKGFSDFVKVTIDPKTQETSVVGYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEF 386 (829)
Q Consensus 307 ~~~lrv~v~~~~~~~p~~~~~~~~~~~~~~~~G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~ 386 (829)
.+.++||++ +.+ ...+-..++..+.++.+ .+++++.. +++++++..|.+|++
T Consensus 92 ~g~l~Ig~~--~~~----------------~~~~l~~~i~~f~~~~P-~i~l~~~~---------~~~~~~~~~L~~~~~ 143 (309)
T PRK12683 92 SGHLTVATT--HTQ----------------ARYALPKVVRQFKEVFP-KVHLALRQ---------GSPQEIAEMLLNGEA 143 (309)
T ss_pred CceEEEEec--cch----------------HHHHHHHHHHHHHHHCC-CceEEEEe---------CCHHHHHHHHHcCCc
Confidence 467999987 221 12344568888888876 35555544 368999999999999
Q ss_pred cEEEeccccccccceeccccccccccceEEEEEccCCCCCCceeeeccCCHhHHHHHHHHHHHHHHHHHhhhcccCCCCC
Q 043276 387 DAVVGDTTIVFNRSNYVDFTLPYTESGVSMIVPIKDSKKRNAWVFLQPLTWDLWVTSGCFFIFIGFVVWVLEHRVNEDFR 466 (829)
Q Consensus 387 Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv~~~~~~~~~~~~fl~PF~~~vW~~i~~~~~~~~~v~~~~~~~~~~~~~ 466 (829)
|+++...... ....+.+ .|+....++++++...+..
T Consensus 144 D~~i~~~~~~--~~~~l~~-~~l~~~~~~~v~~~~hpl~----------------------------------------- 179 (309)
T PRK12683 144 DIGIATEALD--REPDLVS-FPYYSWHHVVVVPKGHPLT----------------------------------------- 179 (309)
T ss_pred cEEEecCCCC--CCCCceE-EEcccCeEEEEecCCCCcc-----------------------------------------
Confidence 9998532111 1122333 4677778888877443221
Q ss_pred CCccCccchhHHHHHHHhhhcCccccccchhHHHHHHHHHHHHHHHHHhHHHHHHHhhcccCCCCCCCHHHHHhCCCcEE
Q 043276 467 GPARHQVGTSFWFSFSTMVFSQRERVISNLARFVVIVWCFVVLILIQSYTASLTSLLTVDQLQPTITDVNLLIKRGDNVG 546 (829)
Q Consensus 467 ~~~~~~~~~~~~~~~~~l~~~~~~~~~s~~~R~v~~~w~~~~lil~~~YtA~L~s~Lt~~~~~~~I~s~~dL~~~~~~vg 546 (829)
...--+++||.+.. -+.
T Consensus 180 --------------------------------------------------------------~~~~~~~~~L~~~~-~i~ 196 (309)
T PRK12683 180 --------------------------------------------------------------GRENLTLEAIAEYP-IIT 196 (309)
T ss_pred --------------------------------------------------------------cCCccCHHHHhcCC-eEe
Confidence 00124688886322 344
Q ss_pred EEeCchH----HHHHHhcCCCccceeecCChHHHHHHHhcCCcCCceeEEEcchhHHHHHHhcCCCceEEeC--cccccC
Q 043276 547 YQKGSFV----LGILKQLGFDERKLVVYNSHEECDELFQKGSANGGIAAAFDEIPYAKLLIGQHCSKYTMVE--PTFKTA 620 (829)
Q Consensus 547 ~~~~s~~----~~~l~~~~~~~~~~~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~~c~~l~~v~--~~~~~~ 620 (829)
...++.. ..++.+.+.........++.+...+.+..|. .-+++... ..... ... .+..+. +.....
T Consensus 197 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~----Gi~~lp~~-~~~~~--~~~-~l~~~~~~~~~~~~ 268 (309)
T PRK12683 197 YDQGFTGRSRIDQAFAEAGLVPDIVLTALDADVIKTYVELGM----GVGIVAAM-AYDPQ--RDT-GLVALDTDHLFEAN 268 (309)
T ss_pred ccCCCcHHHHHHHHHHHCCCCceeEEEeccHHHHHHHHHhCC----CeEEeehh-hcccc--CCC-ceEEEeCCCCcccc
Confidence 4444432 3345555555444556778888888898887 44444332 22211 112 244443 223345
Q ss_pred CceeeecCCCCchhhHHHHHHhhhcc
Q 043276 621 GFGFAFPLHSPLVHDVSKAILNVTEG 646 (829)
Q Consensus 621 ~~~~~~~k~spl~~~in~~il~l~e~ 646 (829)
.++++.+|+.++.......+..+.+.
T Consensus 269 ~~~l~~~~~~~~~~~~~~fi~~l~~~ 294 (309)
T PRK12683 269 TTRVGLRRGAYLRGYAYRFIELFAPH 294 (309)
T ss_pred eEEEEEECCCcCCHHHHHHHHHHHhh
Confidence 68899999988777766666555544
No 167
>PRK12680 transcriptional regulator CysB-like protein; Reviewed
Probab=91.77 E-value=6.5 Score=42.61 Aligned_cols=84 Identities=11% Similarity=0.012 Sum_probs=56.9
Q ss_pred CceEEEecccccCccceEEEeecCCCCCceEEEeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcc
Q 043276 307 EKKLRVGVPVKKGFSDFVKVTIDPKTQETSVVGYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEF 386 (829)
Q Consensus 307 ~~~lrv~v~~~~~~~p~~~~~~~~~~~~~~~~G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~ 386 (829)
.+.+|||+. +.+ ...+-.+++..+.++.+ .+++++.. +..++++.+|.+|++
T Consensus 92 ~g~lrIg~~--~~~----------------~~~~l~~~l~~f~~~~P-~v~i~l~~---------~~~~~~~~~l~~g~~ 143 (327)
T PRK12680 92 QGQLTLTTT--HTQ----------------ARFVLPPAVAQIKQAYP-QVSVHLQQ---------AAESAALDLLGQGDA 143 (327)
T ss_pred ceEEEEEec--chh----------------HHHhhHHHHHHHHHHCC-CcEEEEEe---------CChHHHHHHHHCCCC
Confidence 567999988 221 13355688999999887 45666654 346899999999999
Q ss_pred cEEEeccccccccceeccccccccccceEEEEEcc
Q 043276 387 DAVVGDTTIVFNRSNYVDFTLPYTESGVSMIVPIK 421 (829)
Q Consensus 387 Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv~~~ 421 (829)
|+++....... ..... ..|+.....+++++..
T Consensus 144 Dl~i~~~~~~~--~~~~~-~~~l~~~~~~l~~~~~ 175 (327)
T PRK12680 144 DIAIVSTAGGE--PSAGI-AVPLYRWRRLVVVPRG 175 (327)
T ss_pred cEEEEecCCCC--CCcce-EEEeeccceEEEEeCC
Confidence 99985321111 11222 4688888888888844
No 168
>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=91.64 E-value=11 Score=36.20 Aligned_cols=71 Identities=20% Similarity=0.266 Sum_probs=47.4
Q ss_pred EEeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccEEEeccccccccceeccccccccccceEEE
Q 043276 338 VGYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMI 417 (829)
Q Consensus 338 ~G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~v 417 (829)
..+-.+++..+.++.+ .+++++.. ++...++.+|.+|++|+++....... ...+. ..++.+..++++
T Consensus 12 ~~~l~~~l~~~~~~~P-~v~l~~~~---------~~~~~~~~~l~~g~~Dl~i~~~~~~~--~~~l~-~~~l~~~~~~~~ 78 (199)
T cd08430 12 YSFLPPILERFRAQHP-QVEIKLHT---------GDPADAIDKVLNGEADIAIAARPDKL--PARLA-FLPLATSPLVFI 78 (199)
T ss_pred eeeccHHHHHHHHHCC-CceEEEEe---------CCHHHHHHHHHCCCCCEEEEecCCCC--CcccE-EEeeccceEEEE
Confidence 3556788999999987 45666654 25788999999999999985322111 11232 356677777777
Q ss_pred EEcc
Q 043276 418 VPIK 421 (829)
Q Consensus 418 v~~~ 421 (829)
++..
T Consensus 79 ~~~~ 82 (199)
T cd08430 79 APNI 82 (199)
T ss_pred EeCC
Confidence 7643
No 169
>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=91.63 E-value=12 Score=35.85 Aligned_cols=70 Identities=13% Similarity=0.097 Sum_probs=46.9
Q ss_pred EeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccEEEeccccccccceeccccccccccceEEEE
Q 043276 339 GYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMIV 418 (829)
Q Consensus 339 G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv 418 (829)
.+-.+++..+.++.+ ++++++.. ++..++...|.+|++|+++..... .....+. ..++....+++++
T Consensus 13 ~~l~~~l~~~~~~~P-~v~i~i~~---------~~~~~~~~~l~~~~~Dl~i~~~~~--~~~~~~~-~~~l~~~~~~~~~ 79 (194)
T cd08436 13 VDLPELLARFHRRHP-GVDIRLRQ---------AGSDDLLAAVREGRLDLAFVGLPE--RRPPGLA-SRELAREPLVAVV 79 (194)
T ss_pred HHHHHHHHHHHHHCC-CcEEEEec---------CCHHHHHHHHHcCCccEEEEecCC--CCCCCcE-EEEeecceEEEEe
Confidence 456778888888876 45666654 246789999999999999864332 1222232 3566777778777
Q ss_pred Ecc
Q 043276 419 PIK 421 (829)
Q Consensus 419 ~~~ 421 (829)
+..
T Consensus 80 ~~~ 82 (194)
T cd08436 80 APD 82 (194)
T ss_pred cCC
Confidence 744
No 170
>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=91.60 E-value=0.39 Score=50.12 Aligned_cols=104 Identities=13% Similarity=0.110 Sum_probs=65.9
Q ss_pred CCCCCHHHHHhCCCcEEEEeCchHHHHHHhcCCCccceeecCChHHHHHHHhcCCcCCceeEEEcchhHHHHH-HhcCCC
Q 043276 530 PTITDVNLLIKRGDNVGYQKGSFVLGILKQLGFDERKLVVYNSHEECDELFQKGSANGGIAAAFDEIPYAKLL-IGQHCS 608 (829)
Q Consensus 530 ~~I~s~~dL~~~~~~vg~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~-~~~~c~ 608 (829)
.+|++++|| +|+++.+..++.....++..+.. .+ ..+..|...+|.+|. +|+++........+ +....+
T Consensus 126 ~~i~s~~Dl--~G~kir~~~~~~~~~~~~~~Ga~---~v-~~~~~e~~~aL~~G~----vDg~~~~~~~~~~~~~~ev~~ 195 (257)
T TIGR00787 126 KPITKPEDL--KGLKIRIPNSPMNEAQFKALGAN---PE-PMAFSEVYTALQTGV----VDGQENPLSNVYSSKFYEVQK 195 (257)
T ss_pred CccCChHHh--CCCEEecCCCHHHHHHHHHcCCc---cc-ccCHHHHHHHHHcCC----cccccCCHHHHhhcchhhhcc
Confidence 468999999 59999988777777888886542 22 456788999999999 99987664433221 111233
Q ss_pred ceEEeCcccccCCceeeecCC--CCchhhHHHHHHhhhc
Q 043276 609 KYTMVEPTFKTAGFGFAFPLH--SPLVHDVSKAILNVTE 645 (829)
Q Consensus 609 ~l~~v~~~~~~~~~~~~~~k~--spl~~~in~~il~l~e 645 (829)
.++..+ .......+.+.++ ..|-+....+|....+
T Consensus 196 y~~~~~--~~~~~~~~~~n~~~~~~L~~e~q~~i~~a~~ 232 (257)
T TIGR00787 196 YLSMTN--HGYLGYLVVVNKAFWKSLPPDLQAVVKEAAK 232 (257)
T ss_pred hheecC--CcccceEEEEeHHHHhcCCHHHHHHHHHHHH
Confidence 233222 2234556777776 2365666666655433
No 171
>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=91.53 E-value=9.9 Score=36.89 Aligned_cols=69 Identities=14% Similarity=0.143 Sum_probs=45.9
Q ss_pred EeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccEEEeccccccccceeccccccccccceEEEE
Q 043276 339 GYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMIV 418 (829)
Q Consensus 339 G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv 418 (829)
.+-.+++..+.++.+ .+++++.. ++..++...|.+|++|+++....... ..+. +.++.+...++++
T Consensus 13 ~~l~~~l~~f~~~~P-~v~i~~~~---------~~~~~~~~~l~~g~~Dl~i~~~~~~~---~~~~-~~~l~~~~~~~v~ 78 (196)
T cd08458 13 SFMSGVIQTFIADRP-DVSVYLDT---------VPSQTVLELVSLQHYDLGISILAGDY---PGLT-TEPVPSFRAVCLL 78 (196)
T ss_pred hhhHHHHHHHHHHCC-CcEEEEec---------cChHHHHHHHHcCCCCEEEEeccCCC---CCce-EEEeccCceEEEe
Confidence 345678889988887 35665543 24577899999999999986432211 1222 3567777788887
Q ss_pred Ecc
Q 043276 419 PIK 421 (829)
Q Consensus 419 ~~~ 421 (829)
+..
T Consensus 79 ~~~ 81 (196)
T cd08458 79 PPG 81 (196)
T ss_pred cCC
Confidence 743
No 172
>PRK11482 putative DNA-binding transcriptional regulator; Provisional
Probab=91.47 E-value=7.3 Score=41.97 Aligned_cols=81 Identities=7% Similarity=0.092 Sum_probs=54.0
Q ss_pred CceEEEecccccCccceEEEeecCCCCCceEEEeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcc
Q 043276 307 EKKLRVGVPVKKGFSDFVKVTIDPKTQETSVVGYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEF 386 (829)
Q Consensus 307 ~~~lrv~v~~~~~~~p~~~~~~~~~~~~~~~~G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~ 386 (829)
.+.++||+. +.. ...+-..++..+.+..+ +++++.. ..++++..|.+|++
T Consensus 116 ~~~l~Ig~~--~~~----------------~~~~l~~~l~~f~~~~P-~i~i~~~-----------~~~~~~~~l~~g~~ 165 (317)
T PRK11482 116 QRTITIATT--PSV----------------GALVMPVIYQAIKTHYP-QLLLRNI-----------PISDAENQLSQFQT 165 (317)
T ss_pred CceEEEEec--HHH----------------HHHHHHHHHHHHHHHCC-CCEEEEe-----------cchhHHHHHHCCCc
Confidence 467999988 221 12356678888888876 3444321 34678999999999
Q ss_pred cEEEeccccccccceeccccccccccceEEEEEcc
Q 043276 387 DAVVGDTTIVFNRSNYVDFTLPYTESGVSMIVPIK 421 (829)
Q Consensus 387 Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv~~~ 421 (829)
|++++..... ...+. +.|+....++++++..
T Consensus 166 Dl~i~~~~~~---~~~~~-~~~l~~~~~~lv~~~~ 196 (317)
T PRK11482 166 DLIIDTHSCS---NRTIQ-HHVLFTDNVVLVCRQG 196 (317)
T ss_pred CEEEeccCCC---CCceE-EEEEecCcEEEEEeCC
Confidence 9998644322 23343 3678888888888744
No 173
>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=91.46 E-value=7.5 Score=37.49 Aligned_cols=70 Identities=10% Similarity=0.016 Sum_probs=47.2
Q ss_pred EEeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccEEEeccccccccceeccccccccccceEEE
Q 043276 338 VGYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMI 417 (829)
Q Consensus 338 ~G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~v 417 (829)
..+-.+++..+.++.+ .+++++.. +....++.+|.+|++|+++...... ...+. +.+.....++++
T Consensus 12 ~~~l~~~l~~~~~~~P-~i~~~i~~---------~~~~~~~~~l~~g~~Dl~i~~~~~~---~~~~~-~~~l~~~~~~~~ 77 (196)
T cd08456 12 QSFLPRAIKAFLQRHP-DVTISIHT---------RDSPTVEQWLSAQQCDLGLVSTLHE---PPGIE-RERLLRIDGVCV 77 (196)
T ss_pred HhhHHHHHHHHHHHCC-CcEEEEEe---------CCHHHHHHHHHcCCccEEEEecCCC---CCCee-EEEeeccCeEEE
Confidence 3456788899999886 46666654 2467889999999999998532221 12222 456777788777
Q ss_pred EEcc
Q 043276 418 VPIK 421 (829)
Q Consensus 418 v~~~ 421 (829)
++..
T Consensus 78 ~~~~ 81 (196)
T cd08456 78 LPPG 81 (196)
T ss_pred ecCC
Confidence 7643
No 174
>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=91.35 E-value=13 Score=36.06 Aligned_cols=71 Identities=20% Similarity=0.229 Sum_probs=48.2
Q ss_pred EEeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccEEEeccccccccceeccccccccccceEEE
Q 043276 338 VGYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMI 417 (829)
Q Consensus 338 ~G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~v 417 (829)
.++-.+++..+.++.+ .+++++.. ++...+++.|.+|++|+++..-.. .....+. +.++....++++
T Consensus 12 ~~~l~~~l~~~~~~~P-~v~l~i~~---------~~~~~~~~~l~~g~~Dl~i~~~~~--~~~~~~~-~~~l~~~~~~~~ 78 (198)
T cd08444 12 RYALPWVVQAFKEQFP-NVHLVLHQ---------GSPEEIASMLANGQADIGIATEAL--ENHPELV-SFPYYDWHHHII 78 (198)
T ss_pred hhhhhHHHHHHHHHCC-CeEEEEEe---------CCHHHHHHHHHCCCccEEEecccc--CCCcCcE-EeeccccceeEE
Confidence 3566788999999876 45666554 256789999999999999853211 1112232 467777888888
Q ss_pred EEcc
Q 043276 418 VPIK 421 (829)
Q Consensus 418 v~~~ 421 (829)
++..
T Consensus 79 ~~~~ 82 (198)
T cd08444 79 VPVG 82 (198)
T ss_pred ecCC
Confidence 8744
No 175
>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=91.28 E-value=12 Score=36.49 Aligned_cols=71 Identities=21% Similarity=0.199 Sum_probs=47.9
Q ss_pred EEeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccEEEeccccccccceeccccccccccceEEE
Q 043276 338 VGYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMI 417 (829)
Q Consensus 338 ~G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~v 417 (829)
..+-.+++..+.++.+ .+++++.. ++...++..|.+|++|+++..... .....+. +.++....++++
T Consensus 12 ~~~l~~~l~~f~~~~P-~~~i~i~~---------~~~~~~~~~l~~g~~Dl~i~~~~~--~~~~~~~-~~~l~~~~~~~v 78 (198)
T cd08443 12 RYVLPPVIKGFIERYP-RVSLQMHQ---------GSPTQIAEMVSKGLVDFAIATEAL--HDYDDLI-TLPCYHWNRCVV 78 (198)
T ss_pred eeECcHHHHHHHHHCC-CeEEEEEe---------CCHHHHHHHHHCCCccEEEEeccc--cccCCce-EeeeeeceEEEE
Confidence 4567789999988876 35555543 356789999999999999853221 1112233 467777788888
Q ss_pred EEcc
Q 043276 418 VPIK 421 (829)
Q Consensus 418 v~~~ 421 (829)
++..
T Consensus 79 ~~~~ 82 (198)
T cd08443 79 VKRD 82 (198)
T ss_pred EcCC
Confidence 7744
No 176
>PRK10837 putative DNA-binding transcriptional regulator; Provisional
Probab=91.10 E-value=13 Score=39.18 Aligned_cols=83 Identities=13% Similarity=0.099 Sum_probs=53.2
Q ss_pred CceEEEecccccCccceEEEeecCCCCCceEEEeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcc
Q 043276 307 EKKLRVGVPVKKGFSDFVKVTIDPKTQETSVVGYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEF 386 (829)
Q Consensus 307 ~~~lrv~v~~~~~~~p~~~~~~~~~~~~~~~~G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~ 386 (829)
.+.++||++ +.+ ...+-.+++..+.++.+ .+++++.. +...+++..|.+|++
T Consensus 88 ~g~l~i~~~--~~~----------------~~~~~~~~l~~~~~~~P-~i~i~v~~---------~~~~~~~~~l~~g~~ 139 (290)
T PRK10837 88 NGALRIYAS--STI----------------GNYILPAMIARYRRDYP-QLPLELSV---------GNSQDVINAVLDFRV 139 (290)
T ss_pred CCeEEEEec--chh----------------HhhhhHHHHHHHHHHCC-CceEEEEE---------CCHHHHHHHHHhCCc
Confidence 467999987 221 12345678888888876 35666544 246789999999999
Q ss_pred cEEEeccccccccceeccccccccccceEEEEEcc
Q 043276 387 DAVVGDTTIVFNRSNYVDFTLPYTESGVSMIVPIK 421 (829)
Q Consensus 387 Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv~~~ 421 (829)
|+++...... ...+. ..|+....++++++..
T Consensus 140 Di~i~~~~~~---~~~~~-~~~l~~~~~~lv~~~~ 170 (290)
T PRK10837 140 DIGLIEGPCH---SPELI-SEPWLEDELVVFAAPD 170 (290)
T ss_pred eEEEecCCCC---CCcee-EEEeecceEEEEEcCC
Confidence 9998532211 11222 3566677777777743
No 177
>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=91.10 E-value=2.3 Score=43.93 Aligned_cols=100 Identities=10% Similarity=0.037 Sum_probs=66.2
Q ss_pred CChHHHHHHHHHHHHHc--CCcEEEEEEEeCc--cccchHHHHHHHHHhCC-ceeeeEEecCCCCChhHHHHHHHHhhcC
Q 043276 3 LNDSSQVGAITAIIKAF--GWREAVPIYVDNQ--YGEELIPSLTDALQAID-TRVPYRSVISPLATDDQIEKELYKLFTM 77 (829)
Q Consensus 3 psD~~q~~ai~~ll~~f--gW~~V~iI~~dd~--yG~~~~~~l~~~l~~~g-i~I~~~~~i~~~~~~~~~~~~l~~lk~~ 77 (829)
+++...+..+++.+... |-+++++|+..++ ++....+.+.+++++.+ .++..... ...+..+....+.++.+.
T Consensus 101 ~d~~~~~~~~~~~l~~~~~g~~~i~~i~~~~~~~~~~~r~~gf~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~ 178 (267)
T cd01536 101 TDNYEAGRLAGEYLAKLLGGKGKVAIIEGPPGSSNAQERVKGFRDALKEYPDIEIVAVQD--GNWDREKALQAMEDLLQA 178 (267)
T ss_pred cCHHHHHHHHHHHHHHHhCCCceEEEEEcccccchHHHHHHHHHHHHHhCCCcEEEEEec--CCCcHHHHHHHHHHHHHh
Confidence 34555567778877666 8899999986553 67777888999999884 66543322 222334455666666544
Q ss_pred CCeE-EEEEcChhHHHHHHHHHHHcCcc
Q 043276 78 QTRV-FILHMLPSLGSRIFEKANEIGLM 104 (829)
Q Consensus 78 ~arV-iIv~~~~~~~~~i~~~a~~~gm~ 104 (829)
..++ +|++++...+..+++.+++.|+.
T Consensus 179 ~~~~~~i~~~~d~~a~~~~~~l~~~g~~ 206 (267)
T cd01536 179 NPDIDAIFAANDSMALGAVAALKAAGRK 206 (267)
T ss_pred CCCccEEEEecCCchHHHHHHHHhcCCC
Confidence 4333 34445556778899999999864
No 178
>PRK12681 cysB transcriptional regulator CysB; Reviewed
Probab=90.95 E-value=5.9 Score=42.86 Aligned_cols=84 Identities=19% Similarity=0.192 Sum_probs=54.1
Q ss_pred CceEEEecccccCccceEEEeecCCCCCceEEEeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcc
Q 043276 307 EKKLRVGVPVKKGFSDFVKVTIDPKTQETSVVGYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEF 386 (829)
Q Consensus 307 ~~~lrv~v~~~~~~~p~~~~~~~~~~~~~~~~G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~ 386 (829)
.+.++||++ +.+ ...+-.+++..+.++.+ ++++++.. ++.++++..|.+|++
T Consensus 92 ~g~l~Ig~~--~~~----------------~~~~l~~~l~~f~~~~P-~i~i~i~~---------~~~~~~~~~L~~g~i 143 (324)
T PRK12681 92 KGSLYIATT--HTQ----------------ARYALPPVIKGFIERYP-RVSLHMHQ---------GSPTQIAEAAAKGNA 143 (324)
T ss_pred CCeEEEEec--hhH----------------HHHhhHHHHHHHHHHCC-CcEEEEEe---------CCHHHHHHHHHcCCC
Confidence 578999987 221 12345677888888876 45665544 357899999999999
Q ss_pred cEEEeccccccccceeccccccccccceEEEEEcc
Q 043276 387 DAVVGDTTIVFNRSNYVDFTLPYTESGVSMIVPIK 421 (829)
Q Consensus 387 Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv~~~ 421 (829)
|+++..... .....+. ..|+.....+++++..
T Consensus 144 Dl~i~~~~~--~~~~~l~-~~~l~~~~~~~v~~~~ 175 (324)
T PRK12681 144 DFAIATEAL--HLYDDLI-MLPCYHWNRSVVVPPD 175 (324)
T ss_pred CEEEecCcc--cCCCCeE-EEEeccceeEEEeCCC
Confidence 999853211 1112232 3566677777777643
No 179
>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=90.67 E-value=1.8 Score=44.56 Aligned_cols=107 Identities=10% Similarity=0.032 Sum_probs=70.9
Q ss_pred CChHHHHHHHHHHHHHcCCcEEEEEEEeCc--cccchHHHHHHHHHhCC-ceeeeEEecCCCCChhHHHHHHHHhhcCCC
Q 043276 3 LNDSSQVGAITAIIKAFGWREAVPIYVDNQ--YGEELIPSLTDALQAID-TRVPYRSVISPLATDDQIEKELYKLFTMQT 79 (829)
Q Consensus 3 psD~~q~~ai~~ll~~fgW~~V~iI~~dd~--yG~~~~~~l~~~l~~~g-i~I~~~~~i~~~~~~~~~~~~l~~lk~~~a 79 (829)
.++...+..+++.+...|-++|++|..+++ ++....+.+.+.+++.| ..+..... ...+.++....+.++.+...
T Consensus 100 ~d~~~~~~~~~~~l~~~g~~~i~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~l~~~~ 177 (264)
T cd01537 100 SDNEQAGYLAGEHLAEKGHRRIALLAGPLGSSTARERVAGFKDALKEAGPIEIVLVQE--GDWDAEKGYQAAEELLTAHP 177 (264)
T ss_pred cCcHHHHHHHHHHHHHhcCCcEEEEECCCCCCcHHHHHHHHHHHHHHcCCcChhhhcc--CCCCHHHHHHHHHHHHhcCC
Confidence 456677788888888889999999986654 55667888999998887 44332222 12234456667777766554
Q ss_pred --eEEEEEcChhHHHHHHHHHHHcCccccCeEEEE
Q 043276 80 --RVFILHMLPSLGSRIFEKANEIGLMNKGCVWIM 112 (829)
Q Consensus 80 --rViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~ 112 (829)
.+++ +++...+..+++++.+.|+..++.+-|+
T Consensus 178 ~~~~i~-~~~~~~a~~~~~~~~~~g~~i~~~i~i~ 211 (264)
T cd01537 178 DPTAIF-AANDDMALGALRALREAGLRVPDDISVI 211 (264)
T ss_pred CCCEEE-EcCcHHHHHHHHHHHHhCCCCCCCeEEE
Confidence 4444 3344567778899999987544445444
No 180
>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=90.61 E-value=14 Score=35.44 Aligned_cols=71 Identities=20% Similarity=0.277 Sum_probs=46.7
Q ss_pred EeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccEEEeccccccccceeccccccccccceEEEE
Q 043276 339 GYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMIV 418 (829)
Q Consensus 339 G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv 418 (829)
.+-.+++..+.+..+ ++++++.. ++.+.++..|.+|++|+++..-... .....+ .+.++....+++++
T Consensus 13 ~~l~~~l~~~~~~~P-~i~l~~~~---------~~~~~~~~~l~~g~~Dl~i~~~~~~-~~~~~~-~~~~l~~~~~~~v~ 80 (195)
T cd08427 13 GLLPRALARLRRRHP-DLEVHIVP---------GLSAELLARVDAGELDAAIVVEPPF-PLPKDL-VWTPLVREPLVLIA 80 (195)
T ss_pred HHhHHHHHHHHHHCC-CceEEEEe---------CCcHHHHHHHHCCCCCEEEEcCCCC-ccccCc-eEEEcccCcEEEEE
Confidence 455678888888876 35665554 2468899999999999998532211 101223 24567778888887
Q ss_pred Ecc
Q 043276 419 PIK 421 (829)
Q Consensus 419 ~~~ 421 (829)
+..
T Consensus 81 ~~~ 83 (195)
T cd08427 81 PAE 83 (195)
T ss_pred CCC
Confidence 744
No 181
>cd08451 PBP2_BudR The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is responsible for activation of the expression of the butanediol operon genes; contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of BudR regulator, which is responsible for induction of the butanediol formation pathway under fermentative growth conditions. Three enzymes are involved in the production of 1 mol of 2,3 butanediol from the condensation of 2 mol of pyruvate with acetolactate and acetoin as intermediates: acetolactate synthetase, acetolactate decarboxylase, and acetoin reductase. In Klebsiella terrigena, BudR regulates the expression of the budABC operon genes, encoding these three enzymes of the butanediol pathway. In many bacterial species, the use of this pathway can prevent intracellular acidification by diverting metabolism from acid production to the formation of neutral compounds (acetoin and butanediol). This substra
Probab=90.53 E-value=17 Score=34.97 Aligned_cols=69 Identities=16% Similarity=0.195 Sum_probs=47.1
Q ss_pred eeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccEEEeccccccccceeccccccccccceEEEEE
Q 043276 340 YSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMIVP 419 (829)
Q Consensus 340 ~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv~ 419 (829)
+-.++++.+.++.+ .+++++.. ++..++...|.+|++|+++...... ....+ .+.++....++++++
T Consensus 15 ~l~~~l~~~~~~~P-~i~l~i~~---------~~~~~~~~~l~~g~~Dl~i~~~~~~--~~~~~-~~~~l~~~~~~~v~~ 81 (199)
T cd08451 15 LVPGLIRRFREAYP-DVELTLEE---------ANTAELLEALREGRLDAAFVRPPVA--RSDGL-VLELLLEEPMLVALP 81 (199)
T ss_pred ccHHHHHHHHHHCC-CcEEEEec---------CChHHHHHHHHCCCccEEEEecCCC--CCCce-eEEEeecccEEEEec
Confidence 56778999999887 35565554 2467899999999999998543221 11222 246777888888887
Q ss_pred cc
Q 043276 420 IK 421 (829)
Q Consensus 420 ~~ 421 (829)
..
T Consensus 82 ~~ 83 (199)
T cd08451 82 AG 83 (199)
T ss_pred CC
Confidence 44
No 182
>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=90.49 E-value=12 Score=36.07 Aligned_cols=71 Identities=15% Similarity=0.148 Sum_probs=48.0
Q ss_pred EeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccEEEeccccccccceeccccccccccceEEEE
Q 043276 339 GYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMIV 418 (829)
Q Consensus 339 G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv 418 (829)
.+-.+++..+.++.+ .+++++.. +....++..|.+|++|+++.... .......++ ..++.+..+++++
T Consensus 13 ~~l~~~l~~~~~~~P-~v~i~~~~---------~~~~~~~~~l~~g~~Dl~i~~~~-~~~~~~~l~-~~~l~~~~~~~~~ 80 (198)
T cd08437 13 YYFPKLAKDLIKTGL-MIQIDTYE---------GGSAELLEQLLQGDLDIALLGSL-TPLENSALH-SKIIKTQHFMIIV 80 (198)
T ss_pred HHhHHHHHHHHHhCC-ceEEEEEE---------cCHHHHHHHHHcCCCCEEEecCC-CCCCcccce-EEEeecceEEEEe
Confidence 355678888888887 46666654 24688999999999999985321 111223343 4577778888887
Q ss_pred Ecc
Q 043276 419 PIK 421 (829)
Q Consensus 419 ~~~ 421 (829)
+..
T Consensus 81 ~~~ 83 (198)
T cd08437 81 SKD 83 (198)
T ss_pred cCC
Confidence 744
No 183
>PRK11063 metQ DL-methionine transporter substrate-binding subunit; Provisional
Probab=90.26 E-value=8.2 Score=40.50 Aligned_cols=118 Identities=14% Similarity=0.092 Sum_probs=61.3
Q ss_pred CCCCHHHHHhCCCcEEEEeCc-hHH---HHHHhcCC------------------Cc--cceeecCChHHHHHHHhcCCcC
Q 043276 531 TITDVNLLIKRGDNVGYQKGS-FVL---GILKQLGF------------------DE--RKLVVYNSHEECDELFQKGSAN 586 (829)
Q Consensus 531 ~I~s~~dL~~~~~~vg~~~~s-~~~---~~l~~~~~------------------~~--~~~~~~~~~~~~~~~l~~g~~~ 586 (829)
.|+|++||. .|++|++..+. ... .+|++.++ .+ .+++.. ...+...++..|+
T Consensus 120 ~i~si~DL~-~Gk~IAip~d~~n~~r~L~lL~~~Gli~l~~~~~~~~t~~di~~n~~~v~~v~~-~~~~~~~al~~g~-- 195 (271)
T PRK11063 120 KIKSLDELQ-DGSQVAVPNDPTNLGRSLLLLQKVGLIKLKDGVGLLPTVLDIVENPKNLKIVEL-EAPQLPRSLDDAQ-- 195 (271)
T ss_pred CCCCHHHhc-CCCEEEecCCCccHHHHHHHHHHCCCEEecCCCCCCCCHHHHhcCCCCCEEEEC-cHHHHHHhccccc--
Confidence 389999994 58899987532 222 23454443 11 122222 3456778888888
Q ss_pred CceeEEEcchhHHHHHHhcC-CCceEEeCcccccCCceeeecCCCCchhhHHHHHHhhhccChhHHHHHH
Q 043276 587 GGIAAAFDEIPYAKLLIGQH-CSKYTMVEPTFKTAGFGFAFPLHSPLVHDVSKAILNVTEGDKMKEIEDA 655 (829)
Q Consensus 587 ~g~~a~~~~~~~~~~~~~~~-c~~l~~v~~~~~~~~~~~~~~k~spl~~~in~~il~l~e~G~~~~~~~~ 655 (829)
+|+++...+++...-... -+.+ .....-...-..+++++..-=-+.+.+.+.-++....-+.++++
T Consensus 196 --vDaa~i~~~~a~~a~~~~~~~~l-~~e~~~~~~~~~~~v~~~~~~~~~~~~l~~a~~s~~v~~~i~~~ 262 (271)
T PRK11063 196 --IALAVINTTYASQIGLTPAKDGI-FVEDKDSPYVNLIVAREDNKDAENVKKFVQAYQSDEVYEAANKV 262 (271)
T ss_pred --ccEEEEChHHHHHcCCCCCCCee-EECCCCCCeEEEEEECCcccCCHHHHHHHHHHcCHHHHHHHHHH
Confidence 999988887766532222 1222 22221111123556665533334455555444444444445444
No 184
>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=90.20 E-value=13 Score=36.84 Aligned_cols=69 Identities=16% Similarity=0.125 Sum_probs=47.1
Q ss_pred EeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccEEEeccccccccceeccccccccccceEEEE
Q 043276 339 GYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMIV 418 (829)
Q Consensus 339 G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv 418 (829)
.+..+++..+.++.+ .+++++.. ++...+...|.+|++|++++.... ....+. ..|......++++
T Consensus 13 ~~l~~~l~~f~~~~P-~v~l~i~~---------~~~~~~~~~l~~g~~Di~i~~~~~---~~~~l~-~~~l~~~~~~~v~ 78 (221)
T cd08469 13 VLLPALVRRLETEAP-GIDLRIRP---------VTRLDLAEQLDLGRIDLVIGIFEQ---IPPRFR-RRTLFDEDEVWVM 78 (221)
T ss_pred HHHHHHHHHHHHHCC-CcEEEEee---------CChhhHHHHHHCCCccEEEecCCC---CCccce-eeeeeccceEEEE
Confidence 345678888888776 45666654 246789999999999999864321 123343 4677788888888
Q ss_pred Ecc
Q 043276 419 PIK 421 (829)
Q Consensus 419 ~~~ 421 (829)
+..
T Consensus 79 ~~~ 81 (221)
T cd08469 79 RKD 81 (221)
T ss_pred eCC
Confidence 744
No 185
>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=90.14 E-value=18 Score=35.15 Aligned_cols=69 Identities=13% Similarity=0.107 Sum_probs=46.8
Q ss_pred EeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccEEEeccccccccceeccccccccccceEEEE
Q 043276 339 GYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMIV 418 (829)
Q Consensus 339 G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv 418 (829)
.+-.+++..+.++.+ .+++++.. +...+++..|.+|++|+++..... . ...+. ..+.....+++++
T Consensus 13 ~~l~~~l~~~~~~~P-~i~l~~~~---------~~~~~~~~~l~~g~~D~~i~~~~~--~-~~~~~-~~~l~~~~~~~v~ 78 (200)
T cd08467 13 ALLPRLAPRLRERAP-GLDLRLCP---------IGDDLAERGLEQGTIDLAVGRFAV--P-PDGLV-VRRLYDDGFACLV 78 (200)
T ss_pred HHHHHHHHHHHhhCC-CCEEEEec---------CCcccHHHHhhCCCcCEEEecCCC--C-Cccce-eEEeeeccEEEEE
Confidence 455788888888877 45666554 245688999999999999853211 1 12233 3577788888888
Q ss_pred Ecc
Q 043276 419 PIK 421 (829)
Q Consensus 419 ~~~ 421 (829)
+..
T Consensus 79 ~~~ 81 (200)
T cd08467 79 RHG 81 (200)
T ss_pred cCC
Confidence 743
No 186
>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=90.09 E-value=15 Score=35.44 Aligned_cols=72 Identities=21% Similarity=0.265 Sum_probs=47.2
Q ss_pred EEeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccEEEeccccccccceeccccccccccceEEE
Q 043276 338 VGYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMI 417 (829)
Q Consensus 338 ~G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~v 417 (829)
.++-.+++..+.++.+ ++++++.. +....+...|.+|++|+++..... ......+. +.++....++++
T Consensus 12 ~~~l~~~l~~~~~~~P-~i~l~i~~---------~~~~~~~~~l~~~~~Dl~i~~~~~-~~~~~~l~-~~~l~~~~~~~v 79 (199)
T cd08416 12 VNTVPRIIMGLKLRRP-ELDIELTL---------GSNKDLLKKLKDGELDAILVATPE-GLNDPDFE-VVPLFEDDIFLA 79 (199)
T ss_pred HhhhHHHHHHHHHhCC-CeEEEEEE---------cCcHHHHHHHhCCCCCEEEEecCC-cCCCCCeE-EEEeecceEEEE
Confidence 3456788888888886 35665554 245778999999999999864321 00112222 456777788888
Q ss_pred EEcc
Q 043276 418 VPIK 421 (829)
Q Consensus 418 v~~~ 421 (829)
++..
T Consensus 80 ~~~~ 83 (199)
T cd08416 80 VPAT 83 (199)
T ss_pred ECCC
Confidence 8744
No 187
>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=89.95 E-value=16 Score=35.02 Aligned_cols=71 Identities=10% Similarity=-0.007 Sum_probs=46.9
Q ss_pred EeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccEEEeccccccccceeccccccccccceEEEE
Q 043276 339 GYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMIV 418 (829)
Q Consensus 339 G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv 418 (829)
.+-..++..+.++.+ .+++++.. +...+++..|.+|++|++++...... +...+. ..++....+++++
T Consensus 13 ~~l~~~l~~~~~~~P-~i~i~~~~---------~~~~~~~~~l~~~~~Dl~i~~~~~~~-~~~~~~-~~~l~~~~~~~v~ 80 (197)
T cd08449 13 GGLGPALRRFKRQYP-NVTVRFHE---------LSPEAQKAALLSKRIDLGFVRFADTL-NDPPLA-SELLWREPMVVAL 80 (197)
T ss_pred hhHHHHHHHHHHHCC-CeEEEEEE---------CCHHHHHHHHhCCCccEEEecccccC-CCCCce-EEEEEEeeEEEEe
Confidence 456788888888876 45666554 25688999999999999985432210 112222 3567777777777
Q ss_pred Ecc
Q 043276 419 PIK 421 (829)
Q Consensus 419 ~~~ 421 (829)
+..
T Consensus 81 ~~~ 83 (197)
T cd08449 81 PEE 83 (197)
T ss_pred cCC
Confidence 743
No 188
>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=89.85 E-value=16 Score=35.16 Aligned_cols=69 Identities=12% Similarity=0.100 Sum_probs=47.0
Q ss_pred EeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccEEEeccccccccceeccccccccccceEEEE
Q 043276 339 GYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMIV 418 (829)
Q Consensus 339 G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv 418 (829)
++-.+++..+.++.+ .+++++.. +.+..+..+|.+|++|+++..... ....+. +.++....+++++
T Consensus 14 ~~l~~~i~~~~~~~P-~v~l~i~~---------~~~~~~~~~l~~~~~Dl~i~~~~~---~~~~~~-~~~l~~~~~~~v~ 79 (198)
T cd08446 14 DTVPRLLRAFLTARP-DVTVSLHN---------MTKDEQIEALRAGRIHIGFGRFYP---VEPDIA-VENVAQERLYLAV 79 (198)
T ss_pred HHHHHHHHHHHHHCC-CeEEEEee---------CCHHHHHHHHHCCCccEEEEecCC---CCCCce-eEEeeeccEEEEE
Confidence 355788888888877 45666554 357889999999999999853222 112222 4567778888888
Q ss_pred Ecc
Q 043276 419 PIK 421 (829)
Q Consensus 419 ~~~ 421 (829)
+..
T Consensus 80 ~~~ 82 (198)
T cd08446 80 PKS 82 (198)
T ss_pred eCC
Confidence 744
No 189
>PRK11013 DNA-binding transcriptional regulator LysR; Provisional
Probab=89.80 E-value=11 Score=40.20 Aligned_cols=69 Identities=12% Similarity=0.077 Sum_probs=44.4
Q ss_pred EeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccEEEeccccccccceeccccccccccceEEEE
Q 043276 339 GYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMIV 418 (829)
Q Consensus 339 G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv 418 (829)
.+-.+++..+.+..+ ++++++... +-.++...|.+|++|+++...... ...+. ..++......+++
T Consensus 107 ~~l~~~l~~~~~~~P-~v~i~i~~~---------~~~~~~~~l~~~~~Dl~i~~~~~~---~~~~~-~~~l~~~~~~~~~ 172 (309)
T PRK11013 107 SLLPGLCQPFLARYP-DVSLNIVPQ---------ESPLLEEWLSAQRHDLGLTETLHT---PAGTE-RTELLTLDEVCVL 172 (309)
T ss_pred hhHHHHHHHHHHHCC-CCeEEEEeC---------CHHHHHHHHHcCCCCEEEEcCCCC---CCCce-eeeecceeEEEEE
Confidence 356788888888876 466666553 346788999999999998543211 11222 3455566666777
Q ss_pred Ecc
Q 043276 419 PIK 421 (829)
Q Consensus 419 ~~~ 421 (829)
+..
T Consensus 173 ~~~ 175 (309)
T PRK11013 173 PAG 175 (309)
T ss_pred cCC
Confidence 644
No 190
>PRK09508 leuO leucine transcriptional activator; Reviewed
Probab=89.70 E-value=7.3 Score=41.84 Aligned_cols=69 Identities=9% Similarity=0.144 Sum_probs=48.3
Q ss_pred EeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccEEEeccccccccceeccccccccccceEEEE
Q 043276 339 GYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMIV 418 (829)
Q Consensus 339 G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv 418 (829)
++-.+++..+.++.+ .+++++.. ++...++..|.+|++|+++..... ....+.+ .++....+++++
T Consensus 125 ~~l~~~l~~f~~~~P-~i~l~i~~---------~~~~~~~~~l~~g~~Di~i~~~~~---~~~~l~~-~~l~~~~~~lv~ 190 (314)
T PRK09508 125 RLTSQIYNRIEQIAP-NIHVVFKS---------SLNQNIEHQLRYQETEFVISYEEF---DRPEFTS-VPLFKDELVLVA 190 (314)
T ss_pred HHHHHHHHHHHHhCC-CcEEEEEe---------CcchhHHHHHhcCCccEEEecCCC---Cccccce-eeeecCceEEEE
Confidence 466788999999887 35666654 245789999999999999864322 1223333 467778888888
Q ss_pred Ecc
Q 043276 419 PIK 421 (829)
Q Consensus 419 ~~~ 421 (829)
+..
T Consensus 191 ~~~ 193 (314)
T PRK09508 191 SKN 193 (314)
T ss_pred cCC
Confidence 744
No 191
>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=89.20 E-value=3.1 Score=42.79 Aligned_cols=109 Identities=10% Similarity=0.061 Sum_probs=68.7
Q ss_pred ChHHHHHHHHHHHHHcCCcEEEEEEEeCc--cccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCC--C
Q 043276 4 NDSSQVGAITAIIKAFGWREAVPIYVDNQ--YGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQ--T 79 (829)
Q Consensus 4 sD~~q~~ai~~ll~~fgW~~V~iI~~dd~--yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~--a 79 (829)
++...+..+++.+..-|-+++++++.+.. ++....+.+.+.+++.+..+.....+....+.+.....+.++.+.. .
T Consensus 99 d~~~~g~~~~~~l~~~g~~~i~~i~~~~~~~~~~~r~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~ 178 (264)
T cd06267 99 DNRAGAYLAVEHLIELGHRRIAFIGGPPDLSTARERLEGYREALEEAGIPLDEELIVEGDFSEESGYEAARELLASGERP 178 (264)
T ss_pred ccHHHHHHHHHHHHHCCCceEEEecCCCccchHHHHHHHHHHHHHHcCCCCCcceEEecccchhhHHHHHHHHHhcCCCC
Confidence 44556667778777779999999986644 5666778888889888854332222222222334555666655444 4
Q ss_pred eEEEEEcChhHHHHHHHHHHHcCccccCeEEEEc
Q 043276 80 RVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMT 113 (829)
Q Consensus 80 rViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t 113 (829)
++|+ +.+...+..+..++++.|+..++.+-|.+
T Consensus 179 ~~i~-~~~~~~a~~~~~al~~~g~~~~~~i~i~~ 211 (264)
T cd06267 179 TAIF-AANDLMAIGALRALRELGLRVPEDVSVVG 211 (264)
T ss_pred cEEE-EcCcHHHHHHHHHHHHhCCCCCCceEEEe
Confidence 5544 44556677788888888875445555543
No 192
>PRK15421 DNA-binding transcriptional regulator MetR; Provisional
Probab=89.15 E-value=16 Score=39.22 Aligned_cols=68 Identities=16% Similarity=0.229 Sum_probs=45.8
Q ss_pred eeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccEEEeccccccccceeccccccccccceEEEEE
Q 043276 340 YSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMIVP 419 (829)
Q Consensus 340 ~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv~ 419 (829)
+-.+++..+.++.+ .+++++... .-.++...|.+|++|+++..-.. ....+.+ .++....++++++
T Consensus 103 ~l~~~l~~~~~~~P-~i~l~~~~~---------~~~~~~~~L~~g~~Dl~i~~~~~---~~~~~~~-~~l~~~~~~lv~~ 168 (317)
T PRK15421 103 WLTPALENFHKNWP-QVEMDFKSG---------VTFDPQPALQQGELDLVMTSDIL---PRSGLHY-SPMFDYEVRLVLA 168 (317)
T ss_pred HHHHHHHHHHHHCC-CceEEEEeC---------ccHHHHHHHHCCCcCEEEecCcc---cCCCceE-EEeccceEEEEEc
Confidence 34667888888876 456665442 34788999999999999854222 1223443 6777888888887
Q ss_pred cc
Q 043276 420 IK 421 (829)
Q Consensus 420 ~~ 421 (829)
..
T Consensus 169 ~~ 170 (317)
T PRK15421 169 PD 170 (317)
T ss_pred CC
Confidence 44
No 193
>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=88.99 E-value=11 Score=37.36 Aligned_cols=101 Identities=16% Similarity=0.119 Sum_probs=62.1
Q ss_pred CCCCHHHHHhCCCcEEE-EeCchHHHHHH----hcCCCccceeec----CChHHHHHHHhcCCcCCceeEEEcchhHHHH
Q 043276 531 TITDVNLLIKRGDNVGY-QKGSFVLGILK----QLGFDERKLVVY----NSHEECDELFQKGSANGGIAAAFDEIPYAKL 601 (829)
Q Consensus 531 ~I~s~~dL~~~~~~vg~-~~~s~~~~~l~----~~~~~~~~~~~~----~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~ 601 (829)
.|++++||.+.+.++.- ..||-.+.+|. +.+.+...+..| .+..+...++..|. .|+-+.-...+..
T Consensus 82 ~i~~~~dL~~~~~r~vnR~~GSGtR~l~d~~l~~~gi~~~~i~gy~~~~~th~~vA~aVa~G~----AD~G~g~~~~A~~ 157 (193)
T PF12727_consen 82 GITSLEDLADPGLRFVNRQPGSGTRILFDQLLAEEGIDPEDIPGYAQEANTHLAVAAAVASGK----ADAGIGIRAAAEE 157 (193)
T ss_pred cCCCHHHhccCCcEEEECCCCCHHHHHHHHHHHHcCCChhhCCCccccccChHHHHHHHHcCC----CCEEeehHHHHHh
Confidence 48999999766665443 56776666554 344554444444 46678889999999 7877765444331
Q ss_pred HHhcCCCceEEeCcccccCCceeeecCCCCchhhHHHHHHh
Q 043276 602 LIGQHCSKYTMVEPTFKTAGFGFAFPLHSPLVHDVSKAILN 642 (829)
Q Consensus 602 ~~~~~c~~l~~v~~~~~~~~~~~~~~k~spl~~~in~~il~ 642 (829)
+ ..- .|. ++....|-++++|..-..+.+.+.|.-
T Consensus 158 ~--~gL-~Fv----pl~~E~~dlv~~~~~~~~~~vq~ll~~ 191 (193)
T PF12727_consen 158 F--YGL-DFV----PLAEERYDLVIRREDLEDPAVQALLDF 191 (193)
T ss_pred h--cCC-CcE----EccccceEEEEEhhHcCCHHHHHHHHH
Confidence 1 111 132 233457778888876666666655543
No 194
>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=88.72 E-value=21 Score=34.65 Aligned_cols=70 Identities=14% Similarity=0.204 Sum_probs=47.3
Q ss_pred EEeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccEEEeccccccccceeccccccccccceEEE
Q 043276 338 VGYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMI 417 (829)
Q Consensus 338 ~G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~v 417 (829)
.++-.+++..+.++.+ .+++++.. ++..+++..|.+|++|++++..... ...+. +.|+....++++
T Consensus 13 ~~~l~~~l~~~~~~~P-~i~l~i~~---------~~~~~~~~~l~~~~~Dl~i~~~~~~---~~~~~-~~~l~~~~~~~v 78 (203)
T cd08445 13 YGLLPELIRRFRQAAP-DVEIELIE---------MTTVQQIEALKEGRIDVGFGRLRIE---DPAIR-RIVLREEPLVVA 78 (203)
T ss_pred HhHHHHHHHHHHHHCC-CeEEEEEe---------CChHHHHHHHHcCCCcEEEecCCCC---CCCce-eEEEEeccEEEE
Confidence 3566788888888876 35555543 2468899999999999998533221 12232 456777788888
Q ss_pred EEcc
Q 043276 418 VPIK 421 (829)
Q Consensus 418 v~~~ 421 (829)
++..
T Consensus 79 ~~~~ 82 (203)
T cd08445 79 LPAG 82 (203)
T ss_pred eeCC
Confidence 8743
No 195
>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=88.61 E-value=3.4 Score=42.78 Aligned_cols=107 Identities=10% Similarity=0.098 Sum_probs=67.2
Q ss_pred CChHHHHHHHHHHHHHcCCcEEEEEEEe---CccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHh-hcC-
Q 043276 3 LNDSSQVGAITAIIKAFGWREAVPIYVD---NQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKL-FTM- 77 (829)
Q Consensus 3 psD~~q~~ai~~ll~~fgW~~V~iI~~d---d~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~l-k~~- 77 (829)
.++...+..+++.+...|.+++++|..+ .+++....+.+.+++++.|+.+......+. +..+..+.+.++ ++.
T Consensus 98 ~d~~~~g~~~~~~l~~~g~~~i~~i~~~~~~~~~~~~r~~gf~~~l~~~~~~~~~~~~~~~--~~~~~~~~~~~~l~~~~ 175 (266)
T cd06282 98 VDNRAAARDVAQALAALGHRRIAMLAGRLAASDRARQRYAGYRAAMRAAGLAPLPPVEIPF--NTAALPSALLALLTAHP 175 (266)
T ss_pred eCcHHHHHHHHHHHHHcCcccEEEeccccccCchHHHHHHHHHHHHHHcCCCCCccccCCC--cHHHHHHHHHHHhcCCC
Confidence 3455667778888877899999999743 345666678889999999876433222221 222233444443 332
Q ss_pred CCeEEEEEcChhHHHHHHHHHHHcCccccCeEEEE
Q 043276 78 QTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIM 112 (829)
Q Consensus 78 ~arViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~ 112 (829)
..++|+ +++...+..+++.+++.|+..++.+-+.
T Consensus 176 ~~~ai~-~~~d~~a~g~~~al~~~g~~~p~di~v~ 209 (266)
T cd06282 176 APTAIF-CSNDLLALAVIRALRRLGLRVPDDLSVV 209 (266)
T ss_pred CCCEEE-ECCcHHHHHHHHHHHHcCCCCCCceEEE
Confidence 344444 4667778889999999997544444444
No 196
>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=88.31 E-value=9.7 Score=37.14 Aligned_cols=69 Identities=6% Similarity=0.056 Sum_probs=46.8
Q ss_pred EeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccEEEeccccccccceeccccccccccceEEEE
Q 043276 339 GYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMIV 418 (829)
Q Consensus 339 G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv 418 (829)
.+-.+++..+.++.+ +++++... ++...++..|.+|++|+++.... .. ...++ +.++....+.+++
T Consensus 14 ~~l~~~l~~f~~~~P-~v~i~i~~---------~~~~~l~~~l~~g~~D~~~~~~~--~~-~~~~~-~~~l~~~~~~lv~ 79 (198)
T cd08486 14 RSLPLLLRAFLTSTP-TATVSLTH---------MTKDEQVEGLLAGTIHVGFSRFF--PR-HPGIE-IVNIAQEDLYLAV 79 (198)
T ss_pred HHHHHHHHHHHHhCC-CeEEEEEE---------CCHHHHHHHHHcCCceEEEecCC--CC-CCceE-EEEEeeccEEEEe
Confidence 445678888888876 45665544 35789999999999999985321 11 12232 4567777888888
Q ss_pred Ecc
Q 043276 419 PIK 421 (829)
Q Consensus 419 ~~~ 421 (829)
+..
T Consensus 80 ~~~ 82 (198)
T cd08486 80 HRS 82 (198)
T ss_pred cCC
Confidence 744
No 197
>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=88.22 E-value=4 Score=42.37 Aligned_cols=107 Identities=15% Similarity=0.092 Sum_probs=66.2
Q ss_pred ChHHHHHHHHHHHHHcCCcEEEEEEEe---CccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcC--C
Q 043276 4 NDSSQVGAITAIIKAFGWREAVPIYVD---NQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTM--Q 78 (829)
Q Consensus 4 sD~~q~~ai~~ll~~fgW~~V~iI~~d---d~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~--~ 78 (829)
++...+..+++.+...|.++|++|... +.++......|.+++++.++.+.....+....+.++..+.+.++.+. .
T Consensus 99 d~~~~~~~~~~~l~~~g~~~i~~i~~~~~~~~~~~~r~~gf~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~ 178 (268)
T cd06273 99 DNREAGRLAARHLIALGHRRIAMIFGPTQGNDRARARRAGVRAALAEAGLELPELWQVEAPYSIADGRAALRQLLEQPPR 178 (268)
T ss_pred ChHHHHHHHHHHHHHCCCCeEEEEeccccCCccHHHHHHHHHHHHHHcCCCCCHHHeeeCCCcHHHHHHHHHHHHcCCCC
Confidence 445566777777766799999999743 23455667889999999886543222222222222333445555432 3
Q ss_pred CeEEEEEcChhHHHHHHHHHHHcCccccCeEEE
Q 043276 79 TRVFILHMLPSLGSRIFEKANEIGLMNKGCVWI 111 (829)
Q Consensus 79 arViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI 111 (829)
.++|+ +++...+..+++.+++.|+..++.+=|
T Consensus 179 ~~ai~-~~~~~~a~~~~~~l~~~g~~~p~~i~v 210 (268)
T cd06273 179 PTAVI-CGNDVLALGALYEARRLGLSVPEDLSI 210 (268)
T ss_pred CCEEE-EcChHHHHHHHHHHHHcCCCCCCceEE
Confidence 45544 466677888899999999755544433
No 198
>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=88.18 E-value=25 Score=33.65 Aligned_cols=69 Identities=10% Similarity=0.131 Sum_probs=46.4
Q ss_pred EeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccEEEeccccccccceeccccccccccceEEEE
Q 043276 339 GYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMIV 418 (829)
Q Consensus 339 G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv 418 (829)
.+..+++..+.++.+ .+++++.. ++..++...|.+|++|+++...... ...+. ..|+....+++++
T Consensus 13 ~~l~~~l~~~~~~~p-~i~i~i~~---------~~~~~~~~~l~~~~~Dl~i~~~~~~---~~~~~-~~~l~~~~~~~v~ 78 (197)
T cd08414 13 GLLPRLLRRFRARYP-DVELELRE---------MTTAEQLEALRAGRLDVGFVRPPPD---PPGLA-SRPLLREPLVVAL 78 (197)
T ss_pred HHHHHHHHHHHHHCC-CcEEEEec---------CChHHHHHHHHcCCccEEEEcCCCC---CCCee-EEEEeeccEEEEe
Confidence 345678888888876 35565543 2467899999999999998643222 22232 3677778888888
Q ss_pred Ecc
Q 043276 419 PIK 421 (829)
Q Consensus 419 ~~~ 421 (829)
+..
T Consensus 79 ~~~ 81 (197)
T cd08414 79 PAD 81 (197)
T ss_pred cCC
Confidence 744
No 199
>PRK11062 nhaR transcriptional activator NhaR; Provisional
Probab=87.94 E-value=23 Score=37.57 Aligned_cols=85 Identities=16% Similarity=0.205 Sum_probs=52.1
Q ss_pred CceEEEecccccCccceEEEeecCCCCCceEEEeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcc
Q 043276 307 EKKLRVGVPVKKGFSDFVKVTIDPKTQETSVVGYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEF 386 (829)
Q Consensus 307 ~~~lrv~v~~~~~~~p~~~~~~~~~~~~~~~~G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~ 386 (829)
.+.+|||++ +.+ ..++-.+++..+.++.+ .++++... ++...+...|.+|++
T Consensus 92 ~g~l~i~~~--~~~----------------~~~~l~~~l~~f~~~~P-~i~l~~~~---------~~~~~~~~~l~~g~~ 143 (296)
T PRK11062 92 NLLFDVGVA--DAL----------------SKRLVSRVLLTAVPEDE-SIHLRCFE---------STHEMLLEQLSQHKL 143 (296)
T ss_pred ceEEEEEec--chh----------------hHhhHHHHHHHHHhcCC-ceEEEEEe---------CCHHHHHHHHHcCCC
Confidence 457999987 221 13566778888877665 34554432 257889999999999
Q ss_pred cEEEeccccccccceeccccccccccceEEEEEc
Q 043276 387 DAVVGDTTIVFNRSNYVDFTLPYTESGVSMIVPI 420 (829)
Q Consensus 387 Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv~~ 420 (829)
|+++............+ ...|+.....+++++.
T Consensus 144 D~~i~~~~~~~~~~~~l-~~~~l~~~~~~~~~~~ 176 (296)
T PRK11062 144 DMILSDCPVDSTQQEGL-FSKKLGECGVSFFCTN 176 (296)
T ss_pred CEEEecCCCccccccch-hhhhhhccCcceEecC
Confidence 99985322111111222 2356677777666653
No 200
>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=87.88 E-value=22 Score=34.13 Aligned_cols=69 Identities=16% Similarity=0.206 Sum_probs=47.1
Q ss_pred EeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccEEEeccccccccceeccccccccccceEEEE
Q 043276 339 GYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMIV 418 (829)
Q Consensus 339 G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv 418 (829)
.+-.+++..+.++.+ .+++++.. ++..+++..|.+|++|+++...... ...+. +.++....+++++
T Consensus 13 ~~l~~~l~~~~~~~P-~i~l~i~~---------~~~~~~~~~l~~~~~Dl~i~~~~~~---~~~~~-~~~l~~~~~~~~~ 78 (196)
T cd08450 13 QWLPEVLPILREEHP-DLDVELSS---------LFSPQLAEALMRGKLDVAFMRPEIQ---SDGID-YQLLLKEPLIVVL 78 (196)
T ss_pred hhHHHHHHHHHhhCC-CcEEEEEe---------cChHHHHHHHhcCCccEEEEeCCCC---CCCcE-EEEEEccceEEEe
Confidence 456788888888887 45666654 2467899999999999998532211 12232 4667777888888
Q ss_pred Ecc
Q 043276 419 PIK 421 (829)
Q Consensus 419 ~~~ 421 (829)
+..
T Consensus 79 ~~~ 81 (196)
T cd08450 79 PAD 81 (196)
T ss_pred cCC
Confidence 744
No 201
>COG1910 Periplasmic molybdate-binding protein/domain [Inorganic ion transport and metabolism]
Probab=87.49 E-value=13 Score=36.83 Aligned_cols=104 Identities=13% Similarity=0.108 Sum_probs=63.0
Q ss_pred CCCHHHHHhCCCcEE-EEeCchHHHHH----HhcCCCccceeecC----ChHHHHHHHhcCCcCCceeEEEcchhHHHHH
Q 043276 532 ITDVNLLIKRGDNVG-YQKGSFVLGIL----KQLGFDERKLVVYN----SHEECDELFQKGSANGGIAAAFDEIPYAKLL 602 (829)
Q Consensus 532 I~s~~dL~~~~~~vg-~~~~s~~~~~l----~~~~~~~~~~~~~~----~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~ 602 (829)
|++++||.+.+.++. =.+||-.+.+| .+.+.....+.-|. +......++..|+ .|+-+.-. +.
T Consensus 89 i~~~edl~~~d~~fVNR~rGSGTR~LlD~~L~~~~~~~~~I~GY~~e~~th~avA~aVa~G~----AD~GvGlr----~~ 160 (223)
T COG1910 89 ISSLEDLLRKDLRFVNRNRGSGTRILLDELLGELNILPDSIKGYSDEATTHDAVASAVASGR----ADAGVGLR----HA 160 (223)
T ss_pred cccHHHHhhcCcEEEecCCCccHHHHHHHHHHHcCcCchhcCCccccccccHHHHHHHHcCC----CCccccHH----HH
Confidence 899999986654322 24666555444 34444455566554 4456678899999 78777644 33
Q ss_pred HhcCCCceEEeCcccccCCceeeecCCCCchhhHHHHHHhhhccC
Q 043276 603 IGQHCSKYTMVEPTFKTAGFGFAFPLHSPLVHDVSKAILNVTEGD 647 (829)
Q Consensus 603 ~~~~c~~l~~v~~~~~~~~~~~~~~k~spl~~~in~~il~l~e~G 647 (829)
..++.-+|. ++....|-|+.+|+.-=.+.+...+..|...+
T Consensus 161 A~~~gL~Fi----pl~~E~YD~virke~~~~~~vr~fi~~L~s~~ 201 (223)
T COG1910 161 AEKYGLDFI----PLGDEEYDFVIRKERLDKPVVRAFIKALKSEG 201 (223)
T ss_pred HHHcCCceE----EcccceEEEEEehhHccCHHHHHHHHHhcccc
Confidence 444432243 24456778899988555555555555555444
No 202
>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=87.10 E-value=29 Score=33.19 Aligned_cols=69 Identities=13% Similarity=0.089 Sum_probs=47.5
Q ss_pred EeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccEEEeccccccccceeccccccccccceEEEE
Q 043276 339 GYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMIV 418 (829)
Q Consensus 339 G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv 418 (829)
.+-.+++..+.++.+ .+++++.. ++..++...+.+|++|+++.... .....+. +.++....+++++
T Consensus 13 ~~l~~~l~~~~~~~P-~i~i~i~~---------~~~~~~~~~l~~~~~Di~i~~~~---~~~~~~~-~~~l~~~~~~~~~ 78 (197)
T cd08448 13 RGLPRILRAFRAEYP-GIEVALHE---------MSSAEQIEALLRGELDLGFVHSR---RLPAGLS-ARLLHREPFVCCL 78 (197)
T ss_pred HHHHHHHHHHHHHCC-CCeEEEEe---------CCHHHHHHHHHcCCcceEEEeCC---CCCcCce-EEEEecCcEEEEe
Confidence 456788888888886 45666654 35788999999999999885322 1222232 4677778888877
Q ss_pred Ecc
Q 043276 419 PIK 421 (829)
Q Consensus 419 ~~~ 421 (829)
+..
T Consensus 79 ~~~ 81 (197)
T cd08448 79 PAG 81 (197)
T ss_pred eCC
Confidence 743
No 203
>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=86.68 E-value=8.3 Score=39.18 Aligned_cols=193 Identities=16% Similarity=0.147 Sum_probs=110.6
Q ss_pred EEeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcC-cccEEEeccccccccc---eecc--ccccccc
Q 043276 338 VGYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLG-EFDAVVGDTTIVFNRS---NYVD--FTLPYTE 411 (829)
Q Consensus 338 ~G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g-~~Di~~~~~~it~~R~---~~vd--ft~p~~~ 411 (829)
.+..-++.+.+.++.|+++++.+. .-..++.+|..| ++|+.+.+-....++. ..++ -..|+..
T Consensus 10 ~~~~~~l~~~f~~~~g~~v~v~~~-----------~s~~~~~~l~~g~~~Dv~~~~~~~~~~~l~~~g~~~~~~~~~~~~ 78 (230)
T PF13531_consen 10 APALEELAEAFEKQPGIKVEVSFG-----------GSGELVRRLQAGKKPDVFIPASSEWLERLAAAGLVDPGSPAPLAR 78 (230)
T ss_dssp HHHHHHHHHHHHHHHCEEEEEEEE-----------CHHHHHHHHHTT-S-SEEEESSHHHHHHHHHTTTCSGGGEEEEEE
T ss_pred HHHHHHHHHHHHhccCCeEEEEEC-----------ChHHHHHHHhcCCCceEEEECCHHHHHHHHhcccccCCccccccc
Confidence 344567888887788765544443 246778888876 7999887643222222 2333 5678899
Q ss_pred cceEEEEEccCCCCCCceeeeccCCHhHHHHHHHHHHHHHHHHHhhhcccCCCCCCCccCccchhHHHHHHHhhhcCccc
Q 043276 412 SGVSMIVPIKDSKKRNAWVFLQPLTWDLWVTSGCFFIFIGFVVWVLEHRVNEDFRGPARHQVGTSFWFSFSTMVFSQRER 491 (829)
Q Consensus 412 ~~~~~vv~~~~~~~~~~~~fl~PF~~~vW~~i~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ 491 (829)
+.+++++++.....
T Consensus 79 ~~~vl~~~~~~~~~------------------------------------------------------------------ 92 (230)
T PF13531_consen 79 SPLVLAVPKGNPKG------------------------------------------------------------------ 92 (230)
T ss_dssp EEEEEEEETTSTTS------------------------------------------------------------------
T ss_pred CceEEEeccCcccc------------------------------------------------------------------
Confidence 99999999665322
Q ss_pred cccchhHHHHHHHHHHHHHHHHHhHHHHHHHhhcccCCCCCCCHHHHHhCCCcEEEEeCc------hHHHHHHhcC---C
Q 043276 492 VISNLARFVVIVWCFVVLILIQSYTASLTSLLTVDQLQPTITDVNLLIKRGDNVGYQKGS------FVLGILKQLG---F 562 (829)
Q Consensus 492 ~~s~~~R~v~~~w~~~~lil~~~YtA~L~s~Lt~~~~~~~I~s~~dL~~~~~~vg~~~~s------~~~~~l~~~~---~ 562 (829)
+.+++||.+.+.++++.... .....+.+.+ .
T Consensus 93 ----------------------------------------~~~~~dL~~~~~~i~~~dP~~s~~g~~~~~~l~~~g~~~~ 132 (230)
T PF13531_consen 93 ----------------------------------------IRSWADLAQPGLRIAIPDPSTSPSGLAALQVLAAAGGQEL 132 (230)
T ss_dssp ----------------------------------------TTCHHHHCSTT--EEEE-TTTTHHHHHHHHHHHHHTHCHH
T ss_pred ----------------------------------------cCCHHHHhhccCEEEecCcccChhhHHHHHHHHHcccHHH
Confidence 67788887666677776521 1222333322 0
Q ss_pred C---cccee-ecCChHHHHHHHhcCCcCCceeEEEcchhHHHHHHhcCCCceEEe--Cccccc--CCceeeecCCCCchh
Q 043276 563 D---ERKLV-VYNSHEECDELFQKGSANGGIAAAFDEIPYAKLLIGQHCSKYTMV--EPTFKT--AGFGFAFPLHSPLVH 634 (829)
Q Consensus 563 ~---~~~~~-~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~~c~~l~~v--~~~~~~--~~~~~~~~k~spl~~ 634 (829)
- ..++. ..++..+....+..|. +++.+.....+.+. ..-..+..+ ++.+.. ..+.+++-++++-.+
T Consensus 133 ~~~l~~~~~~~~~~~~~~~~~v~~g~----~d~~~~~~s~~~~~--~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~ 206 (230)
T PF13531_consen 133 LDALQKNIVQYVPSTSQVLSAVASGE----ADAGIVYESQAIFA--RQGDPLSYVYPPDGVNSPPIDYPIAILKNAPHPE 206 (230)
T ss_dssp HHHHHHTEEEEESSHHHHHHHHHTTS----SSEEEEEHHHHHHC--TSHTTEEEEE-STTTSSSEEEEEEEEBTTCTTHH
T ss_pred HHHHHHhCcccccchHHHHHHHHcCC----CcceeeHHHHHHHh--hcCCCeEEEECCchhcCCCEEEEEEEecCCCCHH
Confidence 0 11233 4566788888999998 88887665544221 221224333 444442 456778888877666
Q ss_pred hHHHHHHhhhccChhHHHHH
Q 043276 635 DVSKAILNVTEGDKMKEIED 654 (829)
Q Consensus 635 ~in~~il~l~e~G~~~~~~~ 654 (829)
.-...+..|... .-+++..
T Consensus 207 ~a~~f~~~L~s~-~~q~~l~ 225 (230)
T PF13531_consen 207 AARAFIDFLLSP-EGQQILA 225 (230)
T ss_dssp HHHHHHHHHTSH-HHHHHHH
T ss_pred HHHHHHHHHCCH-HHHHHHH
Confidence 655555555543 3344433
No 204
>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=85.99 E-value=33 Score=32.83 Aligned_cols=72 Identities=13% Similarity=0.127 Sum_probs=47.3
Q ss_pred EeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccEEEeccccc--cccceeccccccccccceEE
Q 043276 339 GYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDAVVGDTTIV--FNRSNYVDFTLPYTESGVSM 416 (829)
Q Consensus 339 G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di~~~~~~it--~~R~~~vdft~p~~~~~~~~ 416 (829)
.+-.+++..+.++.+ .+++++.. ++...++..|.+|++|+++...... ......+ .+.++....+++
T Consensus 13 ~~l~~~l~~~~~~~P-~i~i~~~~---------~~~~~~~~~l~~~~~Dl~i~~~~~~~~~~~~~~~-~~~~l~~~~~~~ 81 (200)
T cd08423 13 ALLPPALAALRARHP-GLEVRLRE---------AEPPESLDALRAGELDLAVVFDYPVTPPPDDPGL-TRVPLLDDPLDL 81 (200)
T ss_pred HhhhHHHHHHHHhCC-CCeEEEEe---------CCHHHHHHHHhcCCccEEEEeccccccCCCCCCc-EEEEeccCcEEE
Confidence 345678888888876 45666654 2457889999999999998532110 1122223 256777888888
Q ss_pred EEEcc
Q 043276 417 IVPIK 421 (829)
Q Consensus 417 vv~~~ 421 (829)
+++..
T Consensus 82 ~~~~~ 86 (200)
T cd08423 82 VLPAD 86 (200)
T ss_pred EecCC
Confidence 88744
No 205
>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=85.47 E-value=23 Score=35.49 Aligned_cols=70 Identities=6% Similarity=-0.044 Sum_probs=38.1
Q ss_pred ecCChHHHHHHHhcCCcCCceeEEEcchhHHHHHHhcCCCceEEeCcc-cccCCceeeecCCCCchhhHHHHHHhhh
Q 043276 569 VYNSHEECDELFQKGSANGGIAAAFDEIPYAKLLIGQHCSKYTMVEPT-FKTAGFGFAFPLHSPLVHDVSKAILNVT 644 (829)
Q Consensus 569 ~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~~c~~l~~v~~~-~~~~~~~~~~~k~spl~~~in~~il~l~ 644 (829)
...+..+..+.+.+|+ +++.+......... .... ....++.. .....+++++.|+++-.+.-.+.|..+.
T Consensus 134 ~~~~~~~~~~~~~~Ge----~~~~~~~~~~~~~~-~~~~-~~~~~P~~~~~~~~~~~ai~k~a~~~~~A~~fi~fl~ 204 (216)
T TIGR01256 134 YGEDVRQALQFVETGN----APAGIVALSDVIPS-KKVG-SVATFPEDLYKPIRYPAVIVKGGKNNAAAKAFIDYLK 204 (216)
T ss_pred ecCcHHHHHHHHHcCC----CCEEeeehhhhccc-CCcc-EEEEeCccccCCccccEEEEECCCChHHHHHHHHHHc
Confidence 3446677888999999 77776544322111 1122 12233332 2234568888898875554444444443
No 206
>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=85.41 E-value=7.9 Score=39.69 Aligned_cols=90 Identities=11% Similarity=0.098 Sum_probs=68.1
Q ss_pred HHHHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCC-------CChhHHHHHHHHhhcCCCe
Q 043276 8 QVGAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPL-------ATDDQIEKELYKLFTMQTR 80 (829)
Q Consensus 8 q~~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~-------~~~~~~~~~l~~lk~~~ar 80 (829)
-+.|+.+-++++|-++++++. .|-....+.+.+.+++.|+.|.....+... .+.+.+.+.+.++...+++
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 356888889999999999997 677788999999999999998776444331 1334566666666667889
Q ss_pred EEEEEcChhHHHHHHHHHHH
Q 043276 81 VFILHMLPSLGSRIFEKANE 100 (829)
Q Consensus 81 ViIv~~~~~~~~~i~~~a~~ 100 (829)
.|++.|..=....++.++.+
T Consensus 184 AifisCTnLrt~~vi~~lE~ 203 (239)
T TIGR02990 184 ALFLSCTALRAATCAQRIEQ 203 (239)
T ss_pred EEEEeCCCchhHHHHHHHHH
Confidence 98888877666677766644
No 207
>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=85.14 E-value=7.2 Score=41.31 Aligned_cols=102 Identities=14% Similarity=0.083 Sum_probs=62.5
Q ss_pred CCCCCHHHHHhCCCcEEEEeCchHHHHHHhcCCCccceeecCChHHHHHHHhcCCcCCceeEEEcchhHHHHHH-hcCCC
Q 043276 530 PTITDVNLLIKRGDNVGYQKGSFVLGILKQLGFDERKLVVYNSHEECDELFQKGSANGGIAAAFDEIPYAKLLI-GQHCS 608 (829)
Q Consensus 530 ~~I~s~~dL~~~~~~vg~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~-~~~c~ 608 (829)
.+|++++|| +|.++-+..+.....+++.+|... +. -...|...+|.+|. +|++..........- ...++
T Consensus 126 ~pi~s~~Dl--kG~kiR~~~~~~~~~~~~~lGa~p---v~-ip~~evy~aLq~G~----vDg~~~~~~~~~~~~~~ev~~ 195 (286)
T PF03480_consen 126 KPIRSPEDL--KGLKIRVPGSPVMSDFFEALGASP---VP-IPWSEVYQALQQGV----VDGAENSASSIYSLGLYEVAK 195 (286)
T ss_dssp S--SSGGGG--TTEEEEETSSHHHHHHHHHCTSEE---EE--TGGGHHHHHHTTS----SSEEEEEHHHHHHTTGGGTSS
T ss_pred cCCccHhhH--hhCeEEecCCHHHHHHHHHcCCee---ec-CcHHHHHHHHhcCC----cCeEecCHHHHHhcChhhhCC
Confidence 469999999 588888876677778888877643 22 24568999999999 999987766552221 22354
Q ss_pred ceEEeCcccccCCceeeecCCCC--chhhHHHHHHhh
Q 043276 609 KYTMVEPTFKTAGFGFAFPLHSP--LVHDVSKAILNV 643 (829)
Q Consensus 609 ~l~~v~~~~~~~~~~~~~~k~sp--l~~~in~~il~l 643 (829)
+..... +...++.+++.+..- |-+....+|...
T Consensus 196 -y~~~~~-~~~~~~~~~~n~~~w~~L~~e~q~~l~~~ 230 (286)
T PF03480_consen 196 -YFTDTN-HGWSPYAVIMNKDWWDSLPDEDQEALDDA 230 (286)
T ss_dssp -EEEEEE-EEEEEEEEEEEHHHHHHS-HHHHHHHHHH
T ss_pred -eeEeec-ccCcceEEEEcHHHHhcCCHHHHHHHHHH
Confidence 333222 444566677766522 444444444443
No 208
>PRK11074 putative DNA-binding transcriptional regulator; Provisional
Probab=85.11 E-value=32 Score=36.49 Aligned_cols=85 Identities=11% Similarity=0.065 Sum_probs=54.1
Q ss_pred CceEEEecccccCccceEEEeecCCCCCceEEEeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcc
Q 043276 307 EKKLRVGVPVKKGFSDFVKVTIDPKTQETSVVGYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEF 386 (829)
Q Consensus 307 ~~~lrv~v~~~~~~~p~~~~~~~~~~~~~~~~G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~ 386 (829)
.+.++||++ +.+ ...+..+++..+.++.+ .+++.+.. ++..+++..|.+|++
T Consensus 91 ~g~l~Ig~~--~~~----------------~~~~l~~~l~~~~~~~p-~i~i~i~~---------~~~~~~~~~l~~g~~ 142 (300)
T PRK11074 91 RGQLSIAVD--NIV----------------RPDRTRQLIVDFYRHFD-DVELIIRQ---------EVFNGVWDALADGRV 142 (300)
T ss_pred CceEEEEEc--Ccc----------------chhHHHHHHHHHHHhCC-CceEEEEe---------hhhhHHHHHHHCCCC
Confidence 578999987 221 12344678888888877 35555543 245789999999999
Q ss_pred cEEEeccccccccceeccccccccccceEEEEEcc
Q 043276 387 DAVVGDTTIVFNRSNYVDFTLPYTESGVSMIVPIK 421 (829)
Q Consensus 387 Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv~~~ 421 (829)
|++++..... .....+. ..++....+++++++.
T Consensus 143 Dl~i~~~~~~-~~~~~l~-~~~l~~~~~~~v~~~~ 175 (300)
T PRK11074 143 DIAIGATRAI-PVGGRFA-FRDMGMLSWACVVSSD 175 (300)
T ss_pred CEEEecCccC-Ccccccc-eeecccceEEEEEcCC
Confidence 9999633211 1112222 3567777788888744
No 209
>PRK11716 DNA-binding transcriptional regulator IlvY; Provisional
Probab=84.67 E-value=25 Score=36.36 Aligned_cols=70 Identities=20% Similarity=0.208 Sum_probs=45.9
Q ss_pred EeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccEEEeccccccccceeccccccccccceEEEE
Q 043276 339 GYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMIV 418 (829)
Q Consensus 339 G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv 418 (829)
.+..+++..+.++.+ .+++++.. +.-.+++..|.+|++|+++...... . ...+. ..++....+++++
T Consensus 80 ~~~~~~l~~~~~~~p-~i~l~i~~---------~~~~~~~~~l~~~~~D~~i~~~~~~-~-~~~~~-~~~l~~~~~~~v~ 146 (269)
T PRK11716 80 SHLPPILDRFRAEHP-LVEIKLTT---------GDAADAVEKVQSGEADLAIAAKPET-L-PASVA-FSPIDEIPLVLIA 146 (269)
T ss_pred HHHHHHHHHHHHHCC-CeEEEEEE---------CCHHHHHHHHHCCCccEEEEecCCC-C-CcceE-EEEcccceEEEEE
Confidence 355688899998886 35666554 2467899999999999998532211 1 11122 3566777777777
Q ss_pred Ecc
Q 043276 419 PIK 421 (829)
Q Consensus 419 ~~~ 421 (829)
+..
T Consensus 147 ~~~ 149 (269)
T PRK11716 147 PAL 149 (269)
T ss_pred cCC
Confidence 643
No 210
>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=84.18 E-value=41 Score=32.37 Aligned_cols=72 Identities=14% Similarity=0.140 Sum_probs=46.7
Q ss_pred EeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccEEEeccccccccceeccccccccccceEEEE
Q 043276 339 GYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMIV 418 (829)
Q Consensus 339 G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv 418 (829)
.+-.+++..+.++.+ .+++++.. +....+...|.+|++|+++............++ +.|.....+++++
T Consensus 13 ~~l~~~l~~~~~~~P-~i~l~i~~---------~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~~~~-~~~l~~~~~~~v~ 81 (200)
T cd08453 13 SVLPELVRRFREAYP-DVELQLRE---------ATSDVQLEALLAGEIDAGIVIPPPGASAPPALA-YRPLLSEPLVLAV 81 (200)
T ss_pred HHHHHHHHHHHHhCC-CceEEEEe---------CCHHHHHHHHHcCCCCEEEEecCcccCCCccee-EEEeeeCceEEEE
Confidence 355678888888876 35666554 246789999999999999853221110112222 4677778888888
Q ss_pred Ecc
Q 043276 419 PIK 421 (829)
Q Consensus 419 ~~~ 421 (829)
+..
T Consensus 82 ~~~ 84 (200)
T cd08453 82 PAA 84 (200)
T ss_pred ECC
Confidence 744
No 211
>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=84.09 E-value=42 Score=32.44 Aligned_cols=69 Identities=13% Similarity=0.003 Sum_probs=44.7
Q ss_pred EeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccEEEeccccccccceeccccccccccceEEEE
Q 043276 339 GYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMIV 418 (829)
Q Consensus 339 G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv 418 (829)
.+-.+++..+.++.+ .+++++.. ++-++++.+|.+|++|+++...... ...+. +.++....+.+++
T Consensus 14 ~~l~~~l~~~~~~~P-~i~l~~~~---------~~~~~~~~~l~~~~~D~~i~~~~~~---~~~l~-~~~l~~~~~~~~~ 79 (198)
T cd08485 14 HTLPLLLRQLLSVAP-SATVSLTQ---------MSKNRQIEALDAGTIDIGFGRFYPY---QEGVV-VRNVTNERLFLGA 79 (198)
T ss_pred HHHHHHHHHHHHhCC-CcEEEEEE---------CCHHHHHHHHHcCCccEEEecCCCC---CCCeE-EEEeeccceEEEe
Confidence 345678888888876 45666543 2457899999999999998642221 12232 3566677777666
Q ss_pred Ecc
Q 043276 419 PIK 421 (829)
Q Consensus 419 ~~~ 421 (829)
+..
T Consensus 80 ~~~ 82 (198)
T cd08485 80 QKS 82 (198)
T ss_pred CCC
Confidence 533
No 212
>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=83.57 E-value=5.6 Score=37.58 Aligned_cols=99 Identities=12% Similarity=0.090 Sum_probs=62.7
Q ss_pred HHHHHHcCCcEEEEEEEe--CccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHH-HHhhcCCCeEEEEEcChh
Q 043276 13 TAIIKAFGWREAVPIYVD--NQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKEL-YKLFTMQTRVFILHMLPS 89 (829)
Q Consensus 13 ~~ll~~fgW~~V~iI~~d--d~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l-~~lk~~~arViIv~~~~~ 89 (829)
++.+..-|-+.+++|... ..+.....+.+.+++++.|+............ ........ ..+++..+. .|++++..
T Consensus 1 ~~~L~~~G~r~i~~i~~~~~~~~~~~r~~gf~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~l~~~~pd-aii~~~~~ 78 (160)
T PF13377_consen 1 VDYLIERGHRRIAFIGGPPNSSVSRERLEGFREALKEHGIEFEELIFFSDDD-SEDAREAQLLWLRRLRPD-AIICSNDR 78 (160)
T ss_dssp HHHHHHTT-SSEEEEESSTTSHHHHHHHHHHHHHHHHTTSEEEGEEEEESSS-HHHHHHHHHHHHHTCSSS-EEEESSHH
T ss_pred ChHHHHCCCCeEEEEecCCCChhHHHHHHHHHHHHHHCCCCCCeeEeecCCc-chhHHHHHHHHHhcCCCc-EEEEcCHH
Confidence 356677899999999933 33345667788899999998765544433332 22222222 223333444 45557888
Q ss_pred HHHHHHHHHHHcCccccCeEEEEc
Q 043276 90 LGSRIFEKANEIGLMNKGCVWIMT 113 (829)
Q Consensus 90 ~~~~i~~~a~~~gm~~~~~vwI~t 113 (829)
.+..++..+.+.|+..++-+-|++
T Consensus 79 ~a~~~~~~l~~~g~~vP~di~vv~ 102 (160)
T PF13377_consen 79 LALGVLRALRELGIRVPQDISVVS 102 (160)
T ss_dssp HHHHHHHHHHHTTSCTTTTSEEEE
T ss_pred HHHHHHHHHHHcCCcccccccEEE
Confidence 999999999999986565555544
No 213
>PRK09860 putative alcohol dehydrogenase; Provisional
Probab=83.56 E-value=5.2 Score=44.39 Aligned_cols=79 Identities=10% Similarity=0.027 Sum_probs=61.6
Q ss_pred HHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcCh
Q 043276 10 GAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLP 88 (829)
Q Consensus 10 ~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~~ 88 (829)
..+.+.++.+|.+++.+++...-...+..+.+.+.|++.|+.+.....+.++++.+++.+....+++.++++||-.+..
T Consensus 20 ~~l~~~~~~~g~~~~livt~~~~~~~g~~~~v~~~L~~~~i~~~~f~~v~~np~~~~v~~~~~~~~~~~~D~IiaiGGG 98 (383)
T PRK09860 20 TDAMNMMADYGFTRTLIVTDNMLTKLGMAGDVQKALEERNIFSVIYDGTQPNPTTENVAAGLKLLKENNCDSVISLGGG 98 (383)
T ss_pred HHHHHHHHhcCCCEEEEEcCcchhhCccHHHHHHHHHHcCCeEEEeCCCCCCcCHHHHHHHHHHHHHcCCCEEEEeCCc
Confidence 4466778899999999988544444567889999999999876544455566777788888889999999999987654
No 214
>TIGR03339 phn_lysR aminoethylphosphonate catabolism associated LysR family transcriptional regulator. This group of sequences represents a number of related clades with numerous examples of members adjacent to operons for the degradation of 2-aminoethylphosphonate (AEP) in Pseudomonas, Ralstonia, Bordetella and Burkholderia species. These are transcriptional regulators of the LysR family which contain a helix-turn-helix (HTH) domain (pfam00126) and a periplasmic substrate-binding protein-like domain (pfam03466).
Probab=83.19 E-value=61 Score=33.62 Aligned_cols=68 Identities=12% Similarity=0.189 Sum_probs=45.7
Q ss_pred eeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccEEEeccccccccceeccccccccccceEEEEE
Q 043276 340 YSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMIVP 419 (829)
Q Consensus 340 ~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv~ 419 (829)
+-.+++..+.++.+ .+++++.. ++..+++..|.+|++|+++..-.... ..+. ..|+....++++++
T Consensus 98 ~~~~~l~~~~~~~p-~v~l~i~~---------~~~~~~~~~l~~g~~Dl~i~~~~~~~---~~~~-~~~l~~~~~~lv~s 163 (279)
T TIGR03339 98 YVLDLVARFRQRYP-GIEVSVRI---------GNSQEVLQALQSYRVDVAVSSEVVDD---PRLD-RVVLGNDPLVAVVH 163 (279)
T ss_pred HHHHHHHHHHHHCC-CcEEEEEE---------CCHHHHHHHHHcCCCcEEEEecccCC---CceE-EEEcCCceEEEEEC
Confidence 44577888888776 35566554 24678999999999999985333222 1222 36677788888887
Q ss_pred cc
Q 043276 420 IK 421 (829)
Q Consensus 420 ~~ 421 (829)
..
T Consensus 164 ~~ 165 (279)
T TIGR03339 164 RQ 165 (279)
T ss_pred CC
Confidence 44
No 215
>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=83.10 E-value=9.7 Score=39.41 Aligned_cols=110 Identities=14% Similarity=0.031 Sum_probs=66.0
Q ss_pred ChHHHHHHHHHHHHHcCCcEEEEEEEeCc---cccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCC-C
Q 043276 4 NDSSQVGAITAIIKAFGWREAVPIYVDNQ---YGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQ-T 79 (829)
Q Consensus 4 sD~~q~~ai~~ll~~fgW~~V~iI~~dd~---yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~-a 79 (829)
++...+..+++.+...|-+++++|..+.. ++....+.+.+++++.|+.+..........+.+...+.+.++.+.. .
T Consensus 99 d~~~~~~~~~~~l~~~g~~~i~~l~~~~~~~~~~~~r~~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~ 178 (268)
T cd06298 99 DYKKAAFEATELLIKNGHKKIAFISGPLEDSINGDERLAGYKEALSEANIEFDESLIFEGDYTYESGYELAEELLEDGKP 178 (268)
T ss_pred CcHHHHHHHHHHHHHcCCceEEEEeCCcccccchhHHHHHHHHHHHHcCCCCCHHHeEeCCCChhHHHHHHHHHhcCCCC
Confidence 33445566777776679999999974433 5666778889999998865432111111111222334445554433 4
Q ss_pred eEEEEEcChhHHHHHHHHHHHcCccccCe-EEEEcC
Q 043276 80 RVFILHMLPSLGSRIFEKANEIGLMNKGC-VWIMTD 114 (829)
Q Consensus 80 rViIv~~~~~~~~~i~~~a~~~gm~~~~~-vwI~t~ 114 (829)
.+|+ +++...+..+++.+++.|+..++. .++.-|
T Consensus 179 ~ai~-~~~d~~a~~~~~~l~~~g~~vp~di~vvg~d 213 (268)
T cd06298 179 TAAF-VTDDELAIGILNAAQDAGLKVPEDFEIIGFN 213 (268)
T ss_pred CEEE-EcCcHHHHHHHHHHHHcCCCCccceEEEeec
Confidence 4544 456666788999999999754443 444433
No 216
>PRK09906 DNA-binding transcriptional regulator HcaR; Provisional
Probab=82.49 E-value=52 Score=34.68 Aligned_cols=69 Identities=14% Similarity=0.180 Sum_probs=48.6
Q ss_pred EeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccEEEeccccccccceeccccccccccceEEEE
Q 043276 339 GYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMIV 418 (829)
Q Consensus 339 G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv 418 (829)
.+..+++..+.++.+ .+++.+... +..+++..|.+|++|+++..... ....++ +.|+....+++++
T Consensus 103 ~~l~~~~~~~~~~~p-~v~i~~~~~---------~~~~~~~~l~~~~~D~~i~~~~~---~~~~l~-~~~l~~~~~~~v~ 168 (296)
T PRK09906 103 NLLPKVLPMFRLRHP-DTLIELVSL---------ITTQQEEKLRRGELDVGFMRHPV---YSDEID-YLELLDEPLVVVL 168 (296)
T ss_pred hHHHHHHHHHHHHCC-CeEEEEEeC---------CcHHHHHHHHcCCeeEEEecCCC---CCCCce-EEEEecccEEEEe
Confidence 345678888888876 455555442 45889999999999999864432 223344 3688888999998
Q ss_pred Ecc
Q 043276 419 PIK 421 (829)
Q Consensus 419 ~~~ 421 (829)
+..
T Consensus 169 ~~~ 171 (296)
T PRK09906 169 PVD 171 (296)
T ss_pred cCC
Confidence 844
No 217
>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=82.39 E-value=8.9 Score=39.72 Aligned_cols=110 Identities=13% Similarity=0.025 Sum_probs=66.3
Q ss_pred CChHHHHHHHHHHHHHcCCcEEEEEEEeCc--cccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcC--C
Q 043276 3 LNDSSQVGAITAIIKAFGWREAVPIYVDNQ--YGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTM--Q 78 (829)
Q Consensus 3 psD~~q~~ai~~ll~~fgW~~V~iI~~dd~--yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~--~ 78 (829)
+++..-+..+++.+..-|-+++++|..+.. ....-.+.+.+.+++.|+.+..........+.......+.++.+. .
T Consensus 98 ~d~~~~~~~a~~~l~~~g~~~i~~l~~~~~~~~~~~R~~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~ 177 (269)
T cd06288 98 PDEEQGGYDATRHLLAAGHRRIAFINGEPWMLAAKDRLKGYRQALAEAGIPFDPDLVVHGDWSADDGYEAAAALLDLDDR 177 (269)
T ss_pred EccHHHHHHHHHHHHHcCCceEEEEeCCccchhHHHHHHHHHHHHHHcCCCCCHHHeEeCCCChHHHHHHHHHHHhCCCC
Confidence 345556677777776669999999975533 223456778888888886432111111111122333444554433 2
Q ss_pred CeEEEEEcChhHHHHHHHHHHHcCccccCeEEEEc
Q 043276 79 TRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMT 113 (829)
Q Consensus 79 arViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t 113 (829)
.++| ++.+...+..+++.+++.|+..++-+.|++
T Consensus 178 ~~ai-~~~~d~~a~~~~~~l~~~g~~vp~di~v~g 211 (269)
T cd06288 178 PTAI-FCGNDRMAMGAYQALLERGLRIPQDVSVVG 211 (269)
T ss_pred CCEE-EEeCcHHHHHHHHHHHHcCCCCcccceEEe
Confidence 4444 556667788899999999976555666654
No 218
>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=81.34 E-value=14 Score=38.23 Aligned_cols=103 Identities=14% Similarity=0.047 Sum_probs=60.7
Q ss_pred HHHHHHHHHHHHHcCCcEEEEEEEeCccc--cchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhc--CCCeE
Q 043276 6 SSQVGAITAIIKAFGWREAVPIYVDNQYG--EELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFT--MQTRV 81 (829)
Q Consensus 6 ~~q~~ai~~ll~~fgW~~V~iI~~dd~yG--~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~--~~arV 81 (829)
..-+..+++.+...|.+++++|..+..+. ......+.+++++.|+.+..........+.++-.+.+.++.+ ....+
T Consensus 103 ~~~g~~a~~~l~~~g~~~i~~i~~~~~~~~~~~R~~Gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~ 182 (270)
T cd01545 103 RAAAREMTRHLIDLGHRRIAFIAGPPDHRASAERLEGYRDALAEAGLPLDPELVAQGDFTFESGLEAAEALLALPDRPTA 182 (270)
T ss_pred HHHHHHHHHHHHHCCCceEEEEeCCCCchhHHHHHHHHHHHHHHcCCCCChhhEEeCCCChhhHHHHHHHHHhCCCCCCE
Confidence 33446677777777999999998655443 233567888888888765210111111111222234444433 23454
Q ss_pred EEEEcChhHHHHHHHHHHHcCccccCeE
Q 043276 82 FILHMLPSLGSRIFEKANEIGLMNKGCV 109 (829)
Q Consensus 82 iIv~~~~~~~~~i~~~a~~~gm~~~~~v 109 (829)
|+ +++...+..+++.+++.|...++.+
T Consensus 183 i~-~~~d~~a~~~~~~~~~~g~~~p~~i 209 (270)
T cd01545 183 IF-ASNDDMAAGVLAVAHRRGLRVPDDL 209 (270)
T ss_pred EE-EcCcHHHHHHHHHHHHcCCCCCCce
Confidence 44 5666788899999999997444433
No 219
>COG0725 ModA ABC-type molybdate transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=80.93 E-value=44 Score=34.75 Aligned_cols=114 Identities=16% Similarity=0.215 Sum_probs=64.6
Q ss_pred CCHHHHHhC-CCcEEE------EeCchHHHHHHhcCCC---ccceeecCChHHHHHHHhcCCcCCceeEEEcchhHHHHH
Q 043276 533 TDVNLLIKR-GDNVGY------QKGSFVLGILKQLGFD---ERKLVVYNSHEECDELFQKGSANGGIAAAFDEIPYAKLL 602 (829)
Q Consensus 533 ~s~~dL~~~-~~~vg~------~~~s~~~~~l~~~~~~---~~~~~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~ 602 (829)
..+++|.+. +.++++ ..|.+..+.|+..+.- ..+++.-.+.++.+..+..|. +|+.+.-...+...
T Consensus 125 ~~~~~l~~~~~~~lai~~p~~~P~G~ya~~~l~~~g~~~~~~~k~v~~~~v~~~l~~V~~G~----ad~g~vy~sd~~~~ 200 (258)
T COG0725 125 ESLEDLLERPDVRLAIGDPKTVPAGKYAKEALELLGLWYTLKDKLVLATNVRQALAYVETGE----ADAGFVYVSDALLS 200 (258)
T ss_pred ccHHHHhcCcCcEEEecCCCCCCchHHHHHHHHHhchhhhccccEEecCcHHHHHHHHHcCC----CCeEEEEEEhhhcc
Confidence 346777753 447776 3456777777764432 236677778889999999999 77655444322221
Q ss_pred HhcCCCceEEeCcccc-cCCceeeecCCCCc---hhhHHHHHHhhhccChhHHHHHHH
Q 043276 603 IGQHCSKYTMVEPTFK-TAGFGFAFPLHSPL---VHDVSKAILNVTEGDKMKEIEDAW 656 (829)
Q Consensus 603 ~~~~c~~l~~v~~~~~-~~~~~~~~~k~spl---~~~in~~il~l~e~G~~~~~~~~w 656 (829)
..-+.+..++.... ...|.+++.+++.- ...|-+.++. ..-+++.++|
T Consensus 201 --~~~~~~~~~~~~~~~Pi~y~iav~~~~~~~~~A~~f~~fl~s----~~a~~il~~~ 252 (258)
T COG0725 201 --KKVKIVGVFPEDLHSPIVYPIAVLKNAKNPELAKEFVDFLLS----PEAQEILEKY 252 (258)
T ss_pred --CCceEEEEcccccCCCeEEEEEEEcCCCCHHHHHHHHHHHhC----HHHHHHHHHc
Confidence 11212333443333 35677888887664 4444444433 2334455554
No 220
>COG0715 TauA ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]
Probab=80.82 E-value=7.1 Score=42.32 Aligned_cols=71 Identities=21% Similarity=0.200 Sum_probs=49.9
Q ss_pred CCCCHHHHHhCCCcEEEEeCch-HHH----HHHhcCCCcccee-ecCChHHHHHHHhcCCcCCceeEEEcchhHHHHHHh
Q 043276 531 TITDVNLLIKRGDNVGYQKGSF-VLG----ILKQLGFDERKLV-VYNSHEECDELFQKGSANGGIAAAFDEIPYAKLLIG 604 (829)
Q Consensus 531 ~I~s~~dL~~~~~~vg~~~~s~-~~~----~l~~~~~~~~~~~-~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~ 604 (829)
.|++++|| .|+++|+..++. ... .|.+.+.+...+. ..-.+.+...++..|+ +||+....++......
T Consensus 127 ~i~~~adl--kGk~vg~~~~~~~~~~~l~~~L~~~Gl~~~dv~~v~~~~~~~~~al~~g~----vda~~~~ep~~~~~~~ 200 (335)
T COG0715 127 GIKSVADL--KGKKVGVPFGGSTSDFLLRYALAKAGLDPDDVELVNLPPADAVAALAAGQ----VDAFVVWEPWNAAAEG 200 (335)
T ss_pred CcccccCC--CCceEEEeCCCchHHHHHHHHHHHcCCCcccceEEeeCcHHHHHHHhcCC----cceEEecCCchhhhhc
Confidence 37889999 599999988874 333 3345666555543 2234557888999999 9998888877766665
Q ss_pred cCC
Q 043276 605 QHC 607 (829)
Q Consensus 605 ~~c 607 (829)
+.-
T Consensus 201 ~~~ 203 (335)
T COG0715 201 EGG 203 (335)
T ss_pred cCC
Confidence 543
No 221
>COG1638 DctP TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]
Probab=80.64 E-value=24 Score=38.26 Aligned_cols=103 Identities=13% Similarity=0.187 Sum_probs=65.6
Q ss_pred CCCCHHHHHhCCCcEEEEeCchHHHHHHhcCCCccceeecCChHHHHHHHhcCCcCCceeEEEcchhHHHHHHhcCC---
Q 043276 531 TITDVNLLIKRGDNVGYQKGSFVLGILKQLGFDERKLVVYNSHEECDELFQKGSANGGIAAAFDEIPYAKLLIGQHC--- 607 (829)
Q Consensus 531 ~I~s~~dL~~~~~~vg~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~~c--- 607 (829)
+|.+.+|| +|.++=+.........++..+..+..+ ...|...+|..|. +|+.-.. ...++..+..
T Consensus 158 PI~~peDl--kGlkiRv~~s~~~~~~~~a~GA~P~pm----~f~Evy~aLqtGv----VDGqEnp--~~~i~~~k~~EVq 225 (332)
T COG1638 158 PIKTPEDL--KGLKIRVPQSPLLLAMFKALGANPTPM----PFAEVYTALQTGV----VDGQENP--LSNIYSAKLYEVQ 225 (332)
T ss_pred CCCChHHh--CCCeeecCCCHHHHHHHHHcCCCCCCC----CHHHHHHHHHcCC----cccccCC--HHHHhhccHHHHh
Confidence 79999999 598888888888888888877654332 4578999999999 8876444 3333333221
Q ss_pred CceEEeCcccccCCceeeecCCC--CchhhHHHHHHhhhccC
Q 043276 608 SKYTMVEPTFKTAGFGFAFPLHS--PLVHDVSKAILNVTEGD 647 (829)
Q Consensus 608 ~~l~~v~~~~~~~~~~~~~~k~s--pl~~~in~~il~l~e~G 647 (829)
+.++..+- ...++.+.+.+.. -|-+...++|++..+..
T Consensus 226 ky~t~tnH--~~~~~~~~~s~~~w~~L~~e~q~il~~aa~e~ 265 (332)
T COG1638 226 KYLTLTNH--IYLPLAVLVSKAFWDSLPEEDQTILLEAAKEA 265 (332)
T ss_pred HHhhhccc--cccceeeEEcHHHHhcCCHHHHHHHHHHHHHH
Confidence 11112221 2234556666653 37777777777765554
No 222
>PRK15454 ethanol dehydrogenase EutG; Provisional
Probab=80.62 E-value=8.2 Score=42.98 Aligned_cols=79 Identities=8% Similarity=-0.085 Sum_probs=61.1
Q ss_pred HHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcCh
Q 043276 10 GAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLP 88 (829)
Q Consensus 10 ~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~~ 88 (829)
+.+.++++.+|.+++.++....-...+..+.+.+.|++.|+.+.....+..+++.+.+.+.+...++.++++||-.+..
T Consensus 38 ~~l~~~~~~~g~~~~lvv~~~~~~~~g~~~~v~~~L~~~gi~~~~~~~v~~~P~~~~v~~~~~~~r~~~~D~IiavGGG 116 (395)
T PRK15454 38 SSCGQQAQTRGLKHLFVMADSFLHQAGMTAGLTRSLAVKGIAMTLWPCPVGEPCITDVCAAVAQLRESGCDGVIAFGGG 116 (395)
T ss_pred HHHHHHHHhcCCCEEEEEcCcchhhCccHHHHHHHHHHcCCeEEEECCCCCCcCHHHHHHHHHHHHhcCcCEEEEeCCh
Confidence 4566788899998888876544445577889999999999876544445556666778888888999999999998865
No 223
>PF14503 YhfZ_C: YhfZ C-terminal domain; PDB: 2OZZ_B.
Probab=80.62 E-value=2.4 Score=42.72 Aligned_cols=105 Identities=17% Similarity=0.183 Sum_probs=52.6
Q ss_pred CCCcEEEEeCchHHHHHHhcCCCccceeecC-ChHHHHHHHhcCCcCCceeEEEcchhHHHHHHhcCCCceEEeC--c-c
Q 043276 541 RGDNVGYQKGSFVLGILKQLGFDERKLVVYN-SHEECDELFQKGSANGGIAAAFDEIPYAKLLIGQHCSKYTMVE--P-T 616 (829)
Q Consensus 541 ~~~~vg~~~~s~~~~~l~~~~~~~~~~~~~~-~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~~c~~l~~v~--~-~ 616 (829)
.|.+||+-..|..+..|.+..+...++..++ +..+.++.+.+|. +||.+..... . ..+.- .+..+. . .
T Consensus 113 dGmRVGiD~~S~Dq~~LT~~~~~gk~Ve~Vei~Y~q~~~~l~~g~----IDA~IWN~d~--i-~~~~~-~l~~~~l~~~~ 184 (232)
T PF14503_consen 113 DGMRVGIDPSSIDQKILTEAEFEGKNVEFVEIPYNQLLELLRSGE----IDAAIWNYDE--I-EDKNF-GLKYVPLKDDP 184 (232)
T ss_dssp ---EEEE-TT-HHHHHHHHHHHTTS--EEEE--HHHHHHHHHHTS------EEEEE--H--H-CCHHC-TEEEEE--SSC
T ss_pred eeeEeecCCCCccHHHHHHHHhCCCceEEEEecHHHHHHHHHCCC----ccEEEECCcc--c-ccccC-CeeEEeCCchH
Confidence 3679999999998888866445444433333 4568999999999 9999988651 1 11112 233321 1 1
Q ss_pred --cccCCceeeecCCCC-chhhHHHHHHhhhccChhHHHHHHHc
Q 043276 617 --FKTAGFGFAFPLHSP-LVHDVSKAILNVTEGDKMKEIEDAWF 657 (829)
Q Consensus 617 --~~~~~~~~~~~k~sp-l~~~in~~il~l~e~G~~~~~~~~w~ 657 (829)
.....-.++++|+.+ +...+++ +.....+.++.++-.
T Consensus 185 ~~~~~seAVivi~~~~~~i~~ll~~----~id~~~vl~iQ~~V~ 224 (232)
T PF14503_consen 185 MSKDASEAVIVIRKDNEPIKALLRK----LIDVEKVLEIQKKVL 224 (232)
T ss_dssp HHHHTT-EEEEEETT-HHHHHHHHH----H--HHHHHHHHHHHH
T ss_pred HHHhcCeeEEEEeCCCHHHHHHHHH----hcCHHHHHHHHHHHH
Confidence 123445778888876 3333332 333345555666655
No 224
>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=80.03 E-value=17 Score=39.10 Aligned_cols=102 Identities=13% Similarity=0.053 Sum_probs=62.7
Q ss_pred HHHHHHHHHHHHcCCcEEEEEEEeC--c-cccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEE
Q 043276 7 SQVGAITAIIKAFGWREAVPIYVDN--Q-YGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFI 83 (829)
Q Consensus 7 ~q~~ai~~ll~~fgW~~V~iI~~dd--~-yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViI 83 (829)
.-+..+++.+...|.++++++.... . .+..-.+.|.+++++.|+.+.-........+.+.-...+.++.+....+ |
T Consensus 162 ~~~~~a~~~L~~~G~~~I~~i~g~~~~~~~~~~R~~Gf~~~l~~~g~~~~~~~~~~~~~~~~~~~~~~~~ll~~~p~a-i 240 (329)
T TIGR01481 162 QATKEAVGELIAKGHKSIAFVGGPLSDSINGEDRLEGYKEALNKAGIQFGEDLVCEGKYSYDAGYKAFAELKGSLPTA-V 240 (329)
T ss_pred HHHHHHHHHHHHCCCCeEEEEecCcccccchHHHHHHHHHHHHHcCCCCCcceEEecCCChHHHHHHHHHHhCCCCCE-E
Confidence 3345566777677999999996332 2 2355678888999999876542212211112223334455554444554 4
Q ss_pred EEcChhHHHHHHHHHHHcCccccCeE
Q 043276 84 LHMLPSLGSRIFEKANEIGLMNKGCV 109 (829)
Q Consensus 84 v~~~~~~~~~i~~~a~~~gm~~~~~v 109 (829)
++.+...|..+++.+++.|+..++-+
T Consensus 241 ~~~~d~~A~g~~~al~~~g~~vP~dv 266 (329)
T TIGR01481 241 FVASDEMAAGILNAAMDAGIKVPEDL 266 (329)
T ss_pred EEcCcHHHHHHHHHHHHcCCCCCCce
Confidence 45666788899999999997554433
No 225
>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=80.02 E-value=16 Score=37.76 Aligned_cols=108 Identities=12% Similarity=0.102 Sum_probs=64.1
Q ss_pred ChHHHHHHHHHHHHHcCCcEEEEEEEeCc--cccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcC-C-C
Q 043276 4 NDSSQVGAITAIIKAFGWREAVPIYVDNQ--YGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTM-Q-T 79 (829)
Q Consensus 4 sD~~q~~ai~~ll~~fgW~~V~iI~~dd~--yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~-~-a 79 (829)
++...+..+++.+...|-++++++..... .+....+.+.+++++.|+.+.....+....+.+...+.+.++.+. . .
T Consensus 103 d~~~~~~~a~~~l~~~g~~~i~~i~~~~~~~~~~~R~~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~ 182 (268)
T cd06271 103 DNEAAAYQAVRRLIALGHRRIALLNPPEDLTFAQHRRAGYRRALAEAGLPLDPALIVSGDMTEEGGYAAAAELLALPDRP 182 (268)
T ss_pred CcHHHHHHHHHHHHHcCCCcEEEecCccccchHHHHHHHHHHHHHHhCCCCCCceEEeCCCChHHHHHHHHHHHhCCCCC
Confidence 44455566777776779999999974433 334456788889998886542222222222222333445444332 2 3
Q ss_pred eEEEEEcChhHHHHHHHHHHHcCccccCeEEEE
Q 043276 80 RVFILHMLPSLGSRIFEKANEIGLMNKGCVWIM 112 (829)
Q Consensus 80 rViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~ 112 (829)
+ .|++.+...+..+++.+.+.|+..++.+-|.
T Consensus 183 ~-ai~~~~d~~a~g~~~al~~~g~~vp~~i~ii 214 (268)
T cd06271 183 T-AIVCSSELMALGVLAALAEAGLRPGRDVSVV 214 (268)
T ss_pred C-EEEEcCcHHHHHHHHHHHHhCCCCCcceeEE
Confidence 4 4444566677788999999997655555544
No 226
>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=79.95 E-value=8.4 Score=42.57 Aligned_cols=87 Identities=10% Similarity=0.003 Sum_probs=64.0
Q ss_pred HHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcCh-
Q 043276 10 GAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLP- 88 (829)
Q Consensus 10 ~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~~- 88 (829)
..+.++++.+|.+++.||+....+..+..+.+.+.|++.|+++.....+...++.+.+.+.+...++.++++||-.+..
T Consensus 13 ~~l~~~l~~~g~~~~liv~~~~~~~~~~~~~v~~~L~~~g~~~~~~~~v~~~p~~~~v~~~~~~~~~~~~d~IIaiGGGS 92 (370)
T cd08192 13 KELPAECAELGIKRPLIVTDPGLAALGLVARVLALLEDAGLAAALFDEVPPNPTEAAVEAGLAAYRAGGCDGVIAFGGGS 92 (370)
T ss_pred HHHHHHHHHcCCCeEEEEcCcchhhCccHHHHHHHHHHcCCeEEEeCCCCCCCCHHHHHHHHHHHHhcCCCEEEEeCCch
Confidence 3466778889999999988655544457888999999999887544445566667788888888888999999977653
Q ss_pred -hHHHHHHH
Q 043276 89 -SLGSRIFE 96 (829)
Q Consensus 89 -~~~~~i~~ 96 (829)
-++..++.
T Consensus 93 viD~aK~ia 101 (370)
T cd08192 93 ALDLAKAVA 101 (370)
T ss_pred HHHHHHHHH
Confidence 34444443
No 227
>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=79.92 E-value=8.3 Score=43.27 Aligned_cols=79 Identities=14% Similarity=0.046 Sum_probs=61.9
Q ss_pred HHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcCh
Q 043276 10 GAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLP 88 (829)
Q Consensus 10 ~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~~ 88 (829)
+.+.++++.+|.+++.||++..-+..+..+.+.+.|++.|+.+.....+...++.+.+.+.+...++.++++||-.+..
T Consensus 12 ~~l~~~l~~~g~~~vlivt~~~~~~~g~~~~v~~~L~~~gi~~~~f~~v~~~p~~~~v~~~~~~~~~~~~D~IIaiGGG 90 (414)
T cd08190 12 AEVGMDLKNLGARRVCLVTDPNLAQLPPVKVVLDSLEAAGINFEVYDDVRVEPTDESFKDAIAFAKKGQFDAFVAVGGG 90 (414)
T ss_pred HHHHHHHHHcCCCeEEEEECcchhhcchHHHHHHHHHHcCCcEEEeCCCCCCcCHHHHHHHHHHHHhcCCCEEEEeCCc
Confidence 4566778899999999998666555566799999999999877644445556667778888888888999999998764
No 228
>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=79.88 E-value=5.9 Score=43.71 Aligned_cols=89 Identities=12% Similarity=0.077 Sum_probs=68.4
Q ss_pred HHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcChh
Q 043276 10 GAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPS 89 (829)
Q Consensus 10 ~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~~~ 89 (829)
..+.+.++.+| ++.+|+...-...+..+.+.+.|++.|+.+.....+...++.+++.+.+..+++.++++||-.+...
T Consensus 12 ~~l~~~l~~~g--r~lvVt~~~~~~~~~~~~v~~~L~~~~i~~~~~~~~~~~p~~~~v~~~~~~~~~~~~D~IIaiGGGS 89 (366)
T PF00465_consen 12 EELGEELKRLG--RVLVVTDPSLSKSGLVDRVLDALEEAGIEVQVFDGVGPNPTLEDVDEAAEQARKFGADCIIAIGGGS 89 (366)
T ss_dssp GGHHHHHHCTT--EEEEEEEHHHHHHTHHHHHHHHHHHTTCEEEEEEEESSS-BHHHHHHHHHHHHHTTSSEEEEEESHH
T ss_pred HHHHHHHHhcC--CEEEEECchHHhCccHHHHHHHHhhCceEEEEEecCCCCCcHHHHHHHHHHHHhcCCCEEEEcCCCC
Confidence 34667788888 8888886644445589999999999999987777777777788999999999999999999998764
Q ss_pred --HHHHHHHHHHH
Q 043276 90 --LGSRIFEKANE 100 (829)
Q Consensus 90 --~~~~i~~~a~~ 100 (829)
++.+.+.....
T Consensus 90 ~~D~aK~va~~~~ 102 (366)
T PF00465_consen 90 VMDAAKAVALLLA 102 (366)
T ss_dssp HHHHHHHHHHHHT
T ss_pred cCcHHHHHHhhcc
Confidence 44455544443
No 229
>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=78.84 E-value=16 Score=37.70 Aligned_cols=104 Identities=11% Similarity=0.081 Sum_probs=61.5
Q ss_pred ChHHHHHHHHHHHHHcCCcEEEEEEEe--CccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcC--CC
Q 043276 4 NDSSQVGAITAIIKAFGWREAVPIYVD--NQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTM--QT 79 (829)
Q Consensus 4 sD~~q~~ai~~ll~~fgW~~V~iI~~d--d~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~--~a 79 (829)
++..-+..+++.+..-|.++++++..+ +..+....+.|.+++++.|+.+..........+.+.....+.++.+. ..
T Consensus 98 d~~~~g~~~~~~l~~~g~~~i~~l~~~~~~~~~~~r~~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~ 177 (267)
T cd06284 98 DNVAAARLAVDHLISLGHRRIALITGPRDNPLARDRLEGYRQALAEAGLPADEELIQEGDFSLESGYAAARRLLALPDRP 177 (267)
T ss_pred cccHHHHHHHHHHHHcCCceEEEEcCCccchhHHHHHHHHHHHHHHcCCCCCcceEEeCCCChHHHHHHHHHHHhCCCCC
Confidence 344555667777767799999999754 23455667888889998885432211111111222333444544332 23
Q ss_pred eEEEEEcChhHHHHHHHHHHHcCccccCe
Q 043276 80 RVFILHMLPSLGSRIFEKANEIGLMNKGC 108 (829)
Q Consensus 80 rViIv~~~~~~~~~i~~~a~~~gm~~~~~ 108 (829)
.+ |++++...+..+++..++.|+..++.
T Consensus 178 ~a-i~~~~~~~a~g~~~al~~~g~~~p~~ 205 (267)
T cd06284 178 TA-IFCFSDEMAIGAISALKELGLRVPED 205 (267)
T ss_pred cE-EEEcCcHHHHHHHHHHHHcCCCCccc
Confidence 44 44456666778889999988643333
No 230
>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=78.53 E-value=33 Score=35.53 Aligned_cols=103 Identities=6% Similarity=-0.088 Sum_probs=60.4
Q ss_pred HHHHHHHHHHHHc--CCcEEEEEEEeCccc--cchHHHHHHHHHhC-CceeeeEEecCCCCChhHHHHHHHHhhcCCCe-
Q 043276 7 SQVGAITAIIKAF--GWREAVPIYVDNQYG--EELIPSLTDALQAI-DTRVPYRSVISPLATDDQIEKELYKLFTMQTR- 80 (829)
Q Consensus 7 ~q~~ai~~ll~~f--gW~~V~iI~~dd~yG--~~~~~~l~~~l~~~-gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~ar- 80 (829)
.-+..+++.+... |.+++++|....++. ..-.+.+.+++++. |+.+... .....+.++-...+.++.+...+
T Consensus 107 ~~~~~~~~~l~~~~~g~~~i~~i~~~~~~~~~~~r~~gf~~a~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~l~~~~~~ 184 (273)
T cd06310 107 AAGKLAAEALAELLGKKGKVAVISFVPGSSTTDQREEGFLEGLKEYPGIEIVAT--QYSDSDYAKALDITEDLLTANPDL 184 (273)
T ss_pred HHHHHHHHHHHHHcCCCceEEEEeCCCCCccHHHHHHHHHHHHHhCCCcEEEec--ccCCcCHHHHHHHHHHHHHhCCCc
Confidence 3445667776555 899999997444432 33457788889888 7765321 11111222333344454433333
Q ss_pred EEEEEcChhHHHHHHHHHHHcCccccCeEEEE
Q 043276 81 VFILHMLPSLGSRIFEKANEIGLMNKGCVWIM 112 (829)
Q Consensus 81 ViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~ 112 (829)
..|++.+...+..+++.+++.|+. .+...+.
T Consensus 185 ~~i~~~~d~~a~g~~~~l~~~g~~-~di~vig 215 (273)
T cd06310 185 KGIFGANEGSAVGAARAVRQAGKA-GKVKVVG 215 (273)
T ss_pred eEEEecCchhHHHHHHHHHhcCCC-CCeEEEE
Confidence 345556677788899999999974 3434343
No 231
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=78.44 E-value=20 Score=38.53 Aligned_cols=105 Identities=9% Similarity=0.031 Sum_probs=64.3
Q ss_pred HHHHHHHHHHcCCcEEEEEEEeC--ccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCe-EEEEE
Q 043276 9 VGAITAIIKAFGWREAVPIYVDN--QYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTR-VFILH 85 (829)
Q Consensus 9 ~~ai~~ll~~fgW~~V~iI~~dd--~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~ar-ViIv~ 85 (829)
+..+++.+..-|-+++++|.... .....-.+.|.+++++.|+.+.....+....+.+...+.+.++.+...+ -.|++
T Consensus 162 ~~~a~~~L~~~G~~~I~~i~~~~~~~~~~~R~~Gf~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~ 241 (327)
T PRK10423 162 GDLATQYLIDKGYTRIACITGPLDKTPARLRLEGYRAAMKRAGLNIPDGYEVTGDFEFNGGFDAMQQLLALPLRPQAVFT 241 (327)
T ss_pred HHHHHHHHHHcCCCeEEEEeCCccccchHHHHHHHHHHHHHcCCCCCcceEEeCCCChHHHHHHHHHHhcCCCCCCEEEE
Confidence 56667777778999999996432 2334456788899999987653222222221222223344454433322 24566
Q ss_pred cChhHHHHHHHHHHHcCccccCeEEEEc
Q 043276 86 MLPSLGSRIFEKANEIGLMNKGCVWIMT 113 (829)
Q Consensus 86 ~~~~~~~~i~~~a~~~gm~~~~~vwI~t 113 (829)
++...+..++..+++.|+..++-+-|++
T Consensus 242 ~~d~~A~g~~~~l~~~g~~vP~dvsvig 269 (327)
T PRK10423 242 GNDAMAVGVYQALYQAGLSVPQDIAVIG 269 (327)
T ss_pred cCcHHHHHHHHHHHHcCCCCCCceEEEE
Confidence 6777788899999999976665555543
No 232
>PRK10624 L-1,2-propanediol oxidoreductase; Provisional
Probab=78.34 E-value=10 Score=42.05 Aligned_cols=79 Identities=16% Similarity=0.140 Sum_probs=60.0
Q ss_pred HHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcCh
Q 043276 10 GAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLP 88 (829)
Q Consensus 10 ~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~~ 88 (829)
..+.+.++.+|.+++.||+...-+-.+..+.+.+.|++.|+.+.....+..+++.+.+.+.+..+++.++++||-.+..
T Consensus 19 ~~l~~~~~~~g~~~~lvvtd~~~~~~g~~~~v~~~L~~~g~~~~~~~~v~~~p~~~~v~~~~~~~~~~~~D~IIaiGGG 97 (382)
T PRK10624 19 GALTDEVKRRGFKKALIVTDKTLVKCGVVAKVTDVLDAAGLAYEIYDGVKPNPTIEVVKEGVEVFKASGADYLIAIGGG 97 (382)
T ss_pred HHHHHHHHhcCCCEEEEEeCcchhhCcchHHHHHHHHHCCCeEEEeCCCCCCcCHHHHHHHHHHHHhcCCCEEEEeCCh
Confidence 4566788889999999988654444557888999999999876544445555566678888888888899999987654
No 233
>COG1454 EutG Alcohol dehydrogenase, class IV [Energy production and conversion]
Probab=78.17 E-value=11 Score=41.22 Aligned_cols=89 Identities=13% Similarity=0.048 Sum_probs=71.1
Q ss_pred HHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcChh
Q 043276 10 GAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPS 89 (829)
Q Consensus 10 ~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~~~ 89 (829)
+.+.+.++.+|++++-||.+..-...+..+.+.+.|++.|+.+.....+.++++.+.+.+-+..+++.+++.||-.+..+
T Consensus 18 ~~l~~~~~~~g~~r~liVTd~~~~~~g~~~~v~~~L~~~~i~~~if~~v~p~P~~~~v~~~~~~~~~~~~D~iIalGGGS 97 (377)
T COG1454 18 KELGEEVKRLGAKRALIVTDRGLAKLGLLDKVLDSLDAAGIEYEVFDEVEPEPTIETVEAGAEVAREFGPDTIIALGGGS 97 (377)
T ss_pred HHHHHHHHhcCCCceEEEECCccccchhHHHHHHHHHhcCCeEEEecCCCCCCCHHHHHHHHHHHHhcCCCEEEEeCCcc
Confidence 45677788999999999997777777899999999999998877666777777778888888999999999999987543
Q ss_pred --HHHHHHHHH
Q 043276 90 --LGSRIFEKA 98 (829)
Q Consensus 90 --~~~~i~~~a 98 (829)
++...+...
T Consensus 98 ~~D~AK~i~~~ 108 (377)
T COG1454 98 VIDAAKAIALL 108 (377)
T ss_pred HHHHHHHHHHH
Confidence 444444333
No 234
>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=78.15 E-value=11 Score=39.45 Aligned_cols=93 Identities=10% Similarity=0.089 Sum_probs=63.1
Q ss_pred hHHHHHHHHHHHHHc--CCcEEEEEEEeC-ccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeE
Q 043276 5 DSSQVGAITAIIKAF--GWREAVPIYVDN-QYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRV 81 (829)
Q Consensus 5 D~~q~~ai~~ll~~f--gW~~V~iI~~dd-~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arV 81 (829)
+...+..+++++... |.+++++++.+. .++....+.+.+++++.|+.+.... . . ..++..+.+.++.+. .++
T Consensus 113 ~~~~~~~~~~~l~~~~~g~~~i~~l~~~~~~~~~~r~~g~~~~~~~~g~~~~~~~-~-~--~~~~~~~~~~~~~~~-~da 187 (281)
T cd06325 113 DLVPVETQLELLKKLLPDAKTVGVLYNPSEANSVVQVKELKKAAAKLGIEVVEAT-V-S--SSNDVQQAAQSLAGK-VDA 187 (281)
T ss_pred cccchHHHHHHHHHHCCCCcEEEEEeCCCCccHHHHHHHHHHHHHhCCCEEEEEe-c-C--CHHHHHHHHHHhccc-CCE
Confidence 344556677777665 999999998554 3677778889999999998876532 2 1 234566667766543 355
Q ss_pred EEEEcChhHHHHHHHHHHHcCc
Q 043276 82 FILHMLPSLGSRIFEKANEIGL 103 (829)
Q Consensus 82 iIv~~~~~~~~~i~~~a~~~gm 103 (829)
|+ +.....+..++.++.+.|+
T Consensus 188 i~-~~~d~~a~~~~~~~~~~~~ 208 (281)
T cd06325 188 IY-VPTDNTVASAMEAVVKVAN 208 (281)
T ss_pred EE-EcCchhHHhHHHHHHHHHH
Confidence 44 4455677778888888774
No 235
>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=77.94 E-value=46 Score=34.98 Aligned_cols=111 Identities=13% Similarity=0.006 Sum_probs=75.1
Q ss_pred HHHHHHHHHHHcCCcE-EEEEEEeCccc--cchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeE-EE
Q 043276 8 QVGAITAIIKAFGWRE-AVPIYVDNQYG--EELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRV-FI 83 (829)
Q Consensus 8 q~~ai~~ll~~fgW~~-V~iI~~dd~yG--~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arV-iI 83 (829)
-+..+++.|...|-++ ++++..+.+.. ..-.+.+.+++++.|+++..........+.++-.+.+.++.+..+.+ .|
T Consensus 105 a~~~a~~~Li~~Gh~~~I~~i~~~~~~~~~~~R~~Gy~~Al~~~Gl~~~~~~i~~~~~~~~~g~~~~~~ll~~~p~idai 184 (279)
T PF00532_consen 105 AGYEATEYLIKKGHRRPIAFIGGPEDSSTSRERLQGYRDALKEAGLPIDEEWIFEGDFDYESGYEAARELLESHPDIDAI 184 (279)
T ss_dssp HHHHHHHHHHHTTCCSTEEEEEESTTTHHHHHHHHHHHHHHHHTTSCEEEEEEEESSSSHHHHHHHHHHHHHTSTT-SEE
T ss_pred HHHHHHHHHHhcccCCeEEEEecCcchHHHHHHHHHHHHHHHHcCCCCCcccccccCCCHHHHHHHHHHHHhhCCCCEEE
Confidence 3446667788889999 99998765543 45566789999999997665544433333333334555555444442 67
Q ss_pred EEcChhHHHHHHHHHHHcC-ccccCeEEEEcCcccc
Q 043276 84 LHMLPSLGSRIFEKANEIG-LMNKGCVWIMTDGMTN 118 (829)
Q Consensus 84 v~~~~~~~~~i~~~a~~~g-m~~~~~vwI~t~~~~~ 118 (829)
++++...|.-.++.+++.| ...++-+-+..++...
T Consensus 185 ~~~nd~~A~ga~~~l~~~gr~~ip~di~~~~~~v~g 220 (279)
T PF00532_consen 185 FCANDMMAIGAIRALRERGRLKIPEDIVSGFDSVVG 220 (279)
T ss_dssp EESSHHHHHHHHHHHHHTT-TCTTTEEEECSCCCGG
T ss_pred EEeCHHHHHHHHHHHHHcCCcccChhheeeeccchh
Confidence 7788888999999999999 7667666555554443
No 236
>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=77.63 E-value=29 Score=35.99 Aligned_cols=98 Identities=9% Similarity=-0.007 Sum_probs=59.2
Q ss_pred ChHHHHHHHHHHHHHc--CCcEEEEEEEeCcc--ccchHHHHHHHHHhC-CceeeeEEecCCCCChhHHHHHHHHhhcCC
Q 043276 4 NDSSQVGAITAIIKAF--GWREAVPIYVDNQY--GEELIPSLTDALQAI-DTRVPYRSVISPLATDDQIEKELYKLFTMQ 78 (829)
Q Consensus 4 sD~~q~~ai~~ll~~f--gW~~V~iI~~dd~y--G~~~~~~l~~~l~~~-gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~ 78 (829)
++..-+..+++.+... |.++++++....+. ...-.+.+.+++++. |+.+.... ....+.++....+.++.+..
T Consensus 103 d~~~~g~~~~~~l~~~~~g~~~i~~l~~~~~~~~~~~r~~g~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~l~~~ 180 (275)
T cd06320 103 DNKANGVRGAEWIIDKLAEGGKVAIIEGKAGAFAAEQRTEGFTEAIKKASGIEVVASQ--PADWDREKAYDVATTILQRN 180 (275)
T ss_pred CcHHHHHHHHHHHHHHhCCCceEEEEeCCCCCccHHHHHHHHHHHHhhCCCcEEEEec--CCCccHHHHHHHHHHHHHhC
Confidence 3344466777777554 89999999753332 234457788999998 88765322 11222233444555554444
Q ss_pred CeE-EEEEcChhHHHHHHHHHHHcCc
Q 043276 79 TRV-FILHMLPSLGSRIFEKANEIGL 103 (829)
Q Consensus 79 arV-iIv~~~~~~~~~i~~~a~~~gm 103 (829)
.++ .|++.+...+..+++.+++.|+
T Consensus 181 ~~~~ai~~~~d~~a~~~~~al~~~g~ 206 (275)
T cd06320 181 PDLKAIYCNNDTMALGVVEAVKNAGK 206 (275)
T ss_pred CCccEEEECCchhHHHHHHHHHhcCC
Confidence 444 3444455666678888889886
No 237
>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=77.51 E-value=11 Score=41.74 Aligned_cols=87 Identities=13% Similarity=0.063 Sum_probs=63.9
Q ss_pred HHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcChh
Q 043276 10 GAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPS 89 (829)
Q Consensus 10 ~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~~~ 89 (829)
+.+.++++.+|.+++.||+...-...+..+.+.+.|++.|+.+.....+...++.+.+.+.+..+++.++++||-.+...
T Consensus 15 ~~l~~~l~~~~~~~~livt~~~~~~~~~~~~v~~~L~~~~~~~~~~~~v~~~p~~~~v~~~~~~~~~~~~D~IIaiGGGs 94 (376)
T cd08193 15 ARLGELLAALGAKRVLVVTDPGILKAGLIDPLLASLEAAGIEVTVFDDVEADPPEAVVEAAVEAARAAGADGVIGFGGGS 94 (376)
T ss_pred HHHHHHHHHcCCCeEEEEcCcchhhCccHHHHHHHHHHcCCeEEEECCCCCCcCHHHHHHHHHHHHhcCCCEEEEeCCch
Confidence 44667788889999999885544445568889999999998765444555666677888888888889999999987643
Q ss_pred --HHHHHHH
Q 043276 90 --LGSRIFE 96 (829)
Q Consensus 90 --~~~~i~~ 96 (829)
++...+.
T Consensus 95 ~iD~aK~ia 103 (376)
T cd08193 95 SMDVAKLVA 103 (376)
T ss_pred HHHHHHHHH
Confidence 4444433
No 238
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=77.40 E-value=18 Score=39.31 Aligned_cols=108 Identities=14% Similarity=0.073 Sum_probs=63.9
Q ss_pred hHHHHHHHHHHHHHcCCcEEEEEEEeCc--cccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCe-E
Q 043276 5 DSSQVGAITAIIKAFGWREAVPIYVDNQ--YGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTR-V 81 (829)
Q Consensus 5 D~~q~~ai~~ll~~fgW~~V~iI~~dd~--yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~ar-V 81 (829)
+..-+..+++.+...|.+++++|..... ....-.+.|.+++++.|+.+..........+.+.-...+.++.+...+ -
T Consensus 160 n~~~~~~a~~~L~~~G~~~I~~i~~~~~~~~~~~R~~Gf~~al~~~gi~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ 239 (343)
T PRK10727 160 DRYGAWLATRHLIQQGHTRIGYLCSNHSISDAEDRLQGYYDALAESGIPANDRLVTFGEPDESGGEQAMTELLGRGRNFT 239 (343)
T ss_pred cHHHHHHHHHHHHHCCCccEEEEeCCccccchHHHHHHHHHHHHHCCCCCChhhEEeCCCChhHHHHHHHHHHhCCCCCC
Confidence 3344455566666679999999974433 234456788899999997543211111111222222334444333322 2
Q ss_pred EEEEcChhHHHHHHHHHHHcCccccCeEEEE
Q 043276 82 FILHMLPSLGSRIFEKANEIGLMNKGCVWIM 112 (829)
Q Consensus 82 iIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~ 112 (829)
.|++.+...|..++..+++.|+..++-+-|+
T Consensus 240 ai~~~nD~~A~g~~~al~~~G~~vP~disVi 270 (343)
T PRK10727 240 AVACYNDSMAAGAMGVLNDNGIDVPGEISLI 270 (343)
T ss_pred EEEEcCcHHHHHHHHHHHHcCCCCCcceeEE
Confidence 4556677788899999999998666555554
No 239
>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=77.35 E-value=16 Score=37.93 Aligned_cols=109 Identities=15% Similarity=0.050 Sum_probs=63.7
Q ss_pred ChHHHHHHHHHHHHHcCCcEEEEEEEeCc--cccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcC--CC
Q 043276 4 NDSSQVGAITAIIKAFGWREAVPIYVDNQ--YGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTM--QT 79 (829)
Q Consensus 4 sD~~q~~ai~~ll~~fgW~~V~iI~~dd~--yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~--~a 79 (829)
++...+..+++.+...|.+.+++|..+.. .+..-.+.|.+++++.|+.+.....+....+.+.....+.++.+. ..
T Consensus 108 d~~~~g~~~a~~l~~~g~~~i~~i~~~~~~~~~~~r~~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~ 187 (275)
T cd06295 108 DNVGGGRLATEHLLARGRRRIAFLGGPQDMPEGEERLEGYREALAEAGLPLDPRLVAPGDFTEESGRAAMRALLERGPDF 187 (275)
T ss_pred CcHHHHHHHHHHHHHCCCCeEEEEcCCCCcchhHHHHHHHHHHHHHcCCCCChhhEEeccCCHHHHHHHHHHHHhCCCCC
Confidence 44555677777887789999999975432 234456778888988885443221222222222333344444332 34
Q ss_pred eEEEEEcChhHHHHHHHHHHHcCccccCeEEEEc
Q 043276 80 RVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMT 113 (829)
Q Consensus 80 rViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t 113 (829)
+.|++ ++...+..++..+++.|+..++.+-|++
T Consensus 188 ~ai~~-~~~~~a~g~~~~l~~~g~~ip~~i~ii~ 220 (275)
T cd06295 188 DAVFA-ASDLMALGALRALREAGRRVPEDVAVVG 220 (275)
T ss_pred CEEEE-CCcHHHHHHHHHHHHhCCCCccceEEEe
Confidence 54444 4456677788888888875455555443
No 240
>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=77.07 E-value=12 Score=41.23 Aligned_cols=88 Identities=13% Similarity=0.036 Sum_probs=64.7
Q ss_pred HHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcCh-
Q 043276 10 GAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLP- 88 (829)
Q Consensus 10 ~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~~- 88 (829)
+.+.++++.+|.+++.+|+....+..+..+.+.+.|++.|+.+.....+....+.+++.+.+..+++.++++||-.+..
T Consensus 12 ~~l~~~l~~~~~~~~lvv~~~~~~~~~~~~~v~~~L~~~~~~~~~~~~~~~~p~~~~v~~~~~~~~~~~~d~IiaiGGGs 91 (370)
T cd08551 12 EKLGEEIKNLGGRKALIVTDPGLVKTGVLDKVIDSLKEAGIEVVIFDGVEPNPTLSNVDAAVAAYREEGCDGVIAVGGGS 91 (370)
T ss_pred HHHHHHHHHcCCCeEEEEeCcchhhCccHHHHHHHHHHcCCeEEEECCCCCCCCHHHHHHHHHHHHhcCCCEEEEeCCch
Confidence 4567778889999999998554444477888999999999876544445556667788888888888899999987754
Q ss_pred -hHHHHHHHH
Q 043276 89 -SLGSRIFEK 97 (829)
Q Consensus 89 -~~~~~i~~~ 97 (829)
-++.+++..
T Consensus 92 ~~D~AK~va~ 101 (370)
T cd08551 92 VLDTAKAIAL 101 (370)
T ss_pred HHHHHHHHHH
Confidence 344444433
No 241
>cd08447 PBP2_LTTR_aromatics_like_1 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to regulators involved in the catabolism of aromatic compounds, contains type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type regulator similar to CbnR which is involved in the regulation of chlorocatechol breakdown. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Ve
Probab=76.38 E-value=73 Score=30.39 Aligned_cols=69 Identities=17% Similarity=0.094 Sum_probs=45.6
Q ss_pred EEeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccEEEeccccccccceeccccccccccceEEE
Q 043276 338 VGYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMI 417 (829)
Q Consensus 338 ~G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~v 417 (829)
..+-.+++..+.++.+ ++++++.. ++.+.+..+|.+|++|+++.... .....+ .+.++....++++
T Consensus 12 ~~~l~~~l~~~~~~~P-~i~v~~~~---------~~~~~~~~~l~~g~~D~~i~~~~---~~~~~~-~~~~l~~~~~~~v 77 (198)
T cd08447 12 YSFLPRLLAAARAALP-DVDLVLRE---------MVTTDQIEALESGRIDLGLLRPP---FARPGL-ETRPLVREPLVAA 77 (198)
T ss_pred HHHHHHHHHHHHHHCC-CeEEEEEe---------CCHHHHHHHHHcCCceEEEecCC---CCCCCe-eEEEeecCceEEE
Confidence 3456788888888887 35555543 35788999999999999985321 111222 2356667777777
Q ss_pred EEc
Q 043276 418 VPI 420 (829)
Q Consensus 418 v~~ 420 (829)
++.
T Consensus 78 ~~~ 80 (198)
T cd08447 78 VPA 80 (198)
T ss_pred ecC
Confidence 764
No 242
>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=76.18 E-value=26 Score=36.34 Aligned_cols=101 Identities=9% Similarity=0.017 Sum_probs=58.9
Q ss_pred HHHHHHHHHHc------CCcEEEEEEEe--CccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCe
Q 043276 9 VGAITAIIKAF------GWREAVPIYVD--NQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTR 80 (829)
Q Consensus 9 ~~ai~~ll~~f------gW~~V~iI~~d--d~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~ar 80 (829)
+..+++++... |-++++++... ...+....+.+.+.+++.|+.+... ......+.+...+.+.++.+...+
T Consensus 107 g~~~~~~l~~~~~~~~~g~~~i~~i~~~~~~~~~~~r~~gf~~~l~~~~~~~~~~-~~~~~~~~~~~~~~~~~~l~~~~~ 185 (277)
T cd06319 107 AYDLGKFLAAAMKAQGWADGKVGMVAIPQKRKNGQKRTKGFKEAMKEAGCDLAGI-RQQKDFSYQETFDYTNDLLTANPD 185 (277)
T ss_pred HHHHHHHHHHHHHhhCCCCCcEEEEeccCCCccHHHHHHHHHHHHHhcCCceEee-ccCCCCCHHHHHHHHHHHHHhCCC
Confidence 44555555332 66899999743 2345666788899999998765422 111122223334445555443343
Q ss_pred E-EEEEcChhHHHHHHHHHHHcCccccCeEEEE
Q 043276 81 V-FILHMLPSLGSRIFEKANEIGLMNKGCVWIM 112 (829)
Q Consensus 81 V-iIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~ 112 (829)
. .|++.+...+..+++.+++.|+. +.+.|.
T Consensus 186 ~~ai~~~~d~~a~g~~~al~~~g~~--~di~vv 216 (277)
T cd06319 186 IRAIWLQGSDRYQGALDAIATAGKT--GKVLLI 216 (277)
T ss_pred CCEEEECCCccchHHHHHHHHcCCC--CCEEEE
Confidence 3 44455566677889999999974 344444
No 243
>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=76.17 E-value=29 Score=35.86 Aligned_cols=109 Identities=14% Similarity=0.031 Sum_probs=65.8
Q ss_pred CChHHHHHHHHHHHHHcCCcEEEEEEEeCcc--ccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhc--CC
Q 043276 3 LNDSSQVGAITAIIKAFGWREAVPIYVDNQY--GEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFT--MQ 78 (829)
Q Consensus 3 psD~~q~~ai~~ll~~fgW~~V~iI~~dd~y--G~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~--~~ 78 (829)
+++...+..+++.+..-|-+++++|..+... ...-.+.+.+++++.|..+..........+.+...+.+.++.+ ..
T Consensus 98 ~d~~~~~~~~~~~L~~~G~~~i~~i~~~~~~~~~~~R~~Gf~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~ 177 (269)
T cd06293 98 CDNEQGGRLATRHLARAGHRRIAFVGGPDALISARERYAGYREALAEAHIPEVPEYVCFGDYTREFGRAAAAQLLARGDP 177 (269)
T ss_pred ECCHHHHHHHHHHHHHCCCceEEEEecCcccccHHHHHHHHHHHHHHcCCCCChheEEecCCCHHHHHHHHHHHHcCCCC
Confidence 3455666777777777799999999744332 2344677888999888643211111111122233344444432 23
Q ss_pred CeEEEEEcChhHHHHHHHHHHHcCccccCeEEEE
Q 043276 79 TRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIM 112 (829)
Q Consensus 79 arViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~ 112 (829)
.+ .|++++...+..++..+.+.|...++.+-|.
T Consensus 178 ~~-ai~~~~d~~a~g~~~al~~~g~~vp~di~i~ 210 (269)
T cd06293 178 PT-AIFAASDEIAIGLLEVLRERGLSIPGDMSLV 210 (269)
T ss_pred CC-EEEEcCcHHHHHHHHHHHHcCCCCccceEEE
Confidence 44 4555667778889999999997655655555
No 244
>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=75.34 E-value=19 Score=37.02 Aligned_cols=109 Identities=7% Similarity=0.003 Sum_probs=64.5
Q ss_pred ChHHHHHHHHHHHHHcCCcEEEEEEEeCc--cccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCe-
Q 043276 4 NDSSQVGAITAIIKAFGWREAVPIYVDNQ--YGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTR- 80 (829)
Q Consensus 4 sD~~q~~ai~~ll~~fgW~~V~iI~~dd~--yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~ar- 80 (829)
++...+..+++.+..-|-++++++..... ....-...+.+++++.|+.+..........+.+.....+.++.+...+
T Consensus 94 d~~~~~~~~~~~l~~~g~~~i~~i~~~~~~~~~~~R~~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~ 173 (261)
T cd06272 94 DNEKAMELAVLYLAEKGHKKIAYIGDLSLDRRQRKRFKGFLETCDENGISISDSHIDVDGLSAEGGDNAAKKLLKESDLP 173 (261)
T ss_pred ChHHHHHHHHHHHHHcCchhEEEeecccccccHHHHHHHHHHHHHHcCCCCCHHHeeeCCCCHHHHHHHHHHHHcCCCCC
Confidence 44555677778777779999999975433 223345778888998886432211111111222333444554433322
Q ss_pred EEEEEcChhHHHHHHHHHHHcCccccCeEEEE
Q 043276 81 VFILHMLPSLGSRIFEKANEIGLMNKGCVWIM 112 (829)
Q Consensus 81 ViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~ 112 (829)
-.|++++...+..+++.+++.|+..++.+=|+
T Consensus 174 ~ai~~~~d~~a~~~~~~l~~~g~~vp~dv~vv 205 (261)
T cd06272 174 TAIICGSYDIALGVLSALNKQGISIPEDIEII 205 (261)
T ss_pred CEEEECCcHHHHHHHHHHHHhCCCCCCceEEE
Confidence 34556666778889999999997555544444
No 245
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=75.32 E-value=29 Score=37.55 Aligned_cols=103 Identities=8% Similarity=0.022 Sum_probs=61.0
Q ss_pred ChHHHHHHHHHHHHHcCCcEEEEEEEeCcc--ccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCe-
Q 043276 4 NDSSQVGAITAIIKAFGWREAVPIYVDNQY--GEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTR- 80 (829)
Q Consensus 4 sD~~q~~ai~~ll~~fgW~~V~iI~~dd~y--G~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~ar- 80 (829)
++...+..+++.|...|.+++++|...... ...-.+.+.+++++.|+.+.....+....+.+.....+.++.+...+
T Consensus 165 D~~~~~~~a~~~L~~~G~~~I~~i~g~~~~~~~~~R~~Gf~~al~~~g~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~ 244 (342)
T PRK10014 165 DNMQAAQLLTEHLIRNGHQRIAWLGGQSSSLTRAERVGGYCATLLKFGLPFHSEWVLECTSSQKQAAEAITALLRHNPTI 244 (342)
T ss_pred CCHHHHHHHHHHHHHCCCCEEEEEcCCcccccHHHHHHHHHHHHHHcCCCCCcceEecCCCChHHHHHHHHHHHcCCCCC
Confidence 344555667777877899999999643332 23345678889999887643222221111222233344444333322
Q ss_pred EEEEEcChhHHHHHHHHHHHcCcccc
Q 043276 81 VFILHMLPSLGSRIFEKANEIGLMNK 106 (829)
Q Consensus 81 ViIv~~~~~~~~~i~~~a~~~gm~~~ 106 (829)
-.|+|.+...|..++..+.+.|+..+
T Consensus 245 ~ai~~~nd~~A~g~~~~l~~~g~~vp 270 (342)
T PRK10014 245 SAVVCYNETIAMGAWFGLLRAGRQSG 270 (342)
T ss_pred CEEEECCcHHHHHHHHHHHHcCCCCC
Confidence 24556677788888999999987544
No 246
>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=75.26 E-value=23 Score=36.77 Aligned_cols=109 Identities=12% Similarity=0.058 Sum_probs=64.3
Q ss_pred ChHHHHHHHHHHHHHcCCcEEEEEEEeC--c------cccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhh
Q 043276 4 NDSSQVGAITAIIKAFGWREAVPIYVDN--Q------YGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLF 75 (829)
Q Consensus 4 sD~~q~~ai~~ll~~fgW~~V~iI~~dd--~------yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk 75 (829)
++..-+..+++.|... .+.+++|..+. . .+..-.+.+.+++++.|+.+.....+....+.++..+.+.++.
T Consensus 97 d~~~~g~~a~~~L~~~-~~~i~~i~~~~~~~~~~~~~~~~~R~~gf~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~l 175 (269)
T cd06297 97 DNRLGGRLAGAYLADF-PGRIGAITVEEEPDRAFRRTVFAERRAGFQQALKDAGRPFSPDLLAITDHSEEGGRLAMRHLL 175 (269)
T ss_pred CcHHHHHHHHHHHHHh-CCceEEEeCccccccccccccHHHHHHHHHHHHHHcCCCCChhhEEeCCCChhhHHHHHHHHH
Confidence 3344455555655444 79999986432 2 3445578888999998876532211211112223345556554
Q ss_pred cCCCe-EEEEEcChhHHHHHHHHHHHcCccccCeEEEEc
Q 043276 76 TMQTR-VFILHMLPSLGSRIFEKANEIGLMNKGCVWIMT 113 (829)
Q Consensus 76 ~~~ar-ViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t 113 (829)
+...+ -.|++++...+..+++.+++.|...++.+-|.+
T Consensus 176 ~~~~~~~ai~~~~d~~a~g~~~~l~~~g~~vP~di~vvg 214 (269)
T cd06297 176 EKASPPLAVFASADQQALGALQEAVELGLTVGEDVRVVG 214 (269)
T ss_pred cCCCCCcEEEEcCcHHHHHHHHHHHHcCCCCCCceEEEE
Confidence 43332 245555667888899999999976666665553
No 247
>PRK11041 DNA-binding transcriptional regulator CytR; Provisional
Probab=75.17 E-value=22 Score=37.70 Aligned_cols=108 Identities=12% Similarity=0.071 Sum_probs=64.7
Q ss_pred hHHHHHHHHHHHHHcCCcEEEEEEEeCcc--ccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCC--Ce
Q 043276 5 DSSQVGAITAIIKAFGWREAVPIYVDNQY--GEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQ--TR 80 (829)
Q Consensus 5 D~~q~~ai~~ll~~fgW~~V~iI~~dd~y--G~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~--ar 80 (829)
+..-+..+++.+...|-+++++|...... ...-.+.|.+.+++.|+.+.....+....+.+...+.+.++.+.. ..
T Consensus 136 n~~~g~~a~~~l~~~G~~~I~~l~~~~~~~~~~~R~~Gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ 215 (309)
T PRK11041 136 NLTAAFEAVNYLHELGHKRIACIAGPEEMPLCHYRLQGYVQALRRCGITVDPQYIARGDFTFEAGAKALKQLLDLPQPPT 215 (309)
T ss_pred cHHHHHHHHHHHHHcCCceEEEEeCCccccchHHHHHHHHHHHHHcCCCCCHHHeEeCCCCHHHHHHHHHHHHcCCCCCC
Confidence 34445556666766799999999744332 234567788889988876532111121222233344555554332 45
Q ss_pred EEEEEcChhHHHHHHHHHHHcCccccCeEEEEc
Q 043276 81 VFILHMLPSLGSRIFEKANEIGLMNKGCVWIMT 113 (829)
Q Consensus 81 ViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t 113 (829)
+|+ +++...+..++...++.|+..++-+.|++
T Consensus 216 ai~-~~~d~~a~gv~~al~~~g~~ip~di~vvg 247 (309)
T PRK11041 216 AVF-CHSDVMALGALSQAKRMGLRVPQDLSIIG 247 (309)
T ss_pred EEE-EcCcHHHHHHHHHHHHcCCCCCcceEEEE
Confidence 544 45666777888899999975555566554
No 248
>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=75.15 E-value=25 Score=36.32 Aligned_cols=105 Identities=15% Similarity=0.088 Sum_probs=62.4
Q ss_pred hHHHHHHHHHHHHHcCCcEEEEEEEeCc--cccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCe-E
Q 043276 5 DSSQVGAITAIIKAFGWREAVPIYVDNQ--YGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTR-V 81 (829)
Q Consensus 5 D~~q~~ai~~ll~~fgW~~V~iI~~dd~--yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~ar-V 81 (829)
+..-+..+++.+..-|-++++++..+.. .+..-.+.|.+.+++.|+.+.....+....+.+...+.+.++.+...+ .
T Consensus 98 ~~~ag~~a~~~L~~~g~~~i~~i~~~~~~~~~~~R~~Gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ 177 (265)
T cd06285 98 DVLGGRLATRHLLDLGHRRIAVLAGPDYASTARDRLAGFRAALAEAGIEVPPERIVYSGFDIEGGEAAAEKLLRSDSPPT 177 (265)
T ss_pred cHHHHHHHHHHHHHCCCccEEEEeCCcccccHHHHHHHHHHHHHHcCCCCChhhEEeCCCCHHHHHHHHHHHHcCCCCCC
Confidence 3344556667777779999999975433 234556778888888887653221111122222333445554433222 3
Q ss_pred EEEEcChhHHHHHHHHHHHcCccccCeE
Q 043276 82 FILHMLPSLGSRIFEKANEIGLMNKGCV 109 (829)
Q Consensus 82 iIv~~~~~~~~~i~~~a~~~gm~~~~~v 109 (829)
.|++++...+..+++.+++.|+..++-+
T Consensus 178 ai~~~~d~~a~g~~~~l~~~g~~~p~di 205 (265)
T cd06285 178 AIFAVNDFAAIGVMGAARDRGLRVPDDV 205 (265)
T ss_pred EEEEcCcHHHHHHHHHHHHcCCCCCcce
Confidence 4556677778889999999997544433
No 249
>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=74.83 E-value=30 Score=35.65 Aligned_cols=108 Identities=12% Similarity=0.058 Sum_probs=63.6
Q ss_pred ChHHHHHHHHHHHHHcCCcEEEEEEEeCc--cccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcC--CC
Q 043276 4 NDSSQVGAITAIIKAFGWREAVPIYVDNQ--YGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTM--QT 79 (829)
Q Consensus 4 sD~~q~~ai~~ll~~fgW~~V~iI~~dd~--yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~--~a 79 (829)
++...+..+++.+...|-+++++|..+.+ ........+.+++++.|.............+.+...+.+.++.+. ..
T Consensus 99 d~~~~~~~~~~~l~~~g~~~i~~i~~~~~~~~~~~r~~gf~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~ 178 (268)
T cd01575 99 SHAEAGRAMARHLLARGYRRIGFLGARMDDTRAQQRLEGFRAALRAAGLDPPLVVTTPEPSSFALGRELLAELLARWPDL 178 (268)
T ss_pred CcHHHHHHHHHHHHHCCCCcEEEecCCCCcccHHHHHHHHHHHHHHcCCCCCceeEeccCCCHHHHHHHHHHHHhCCCCC
Confidence 33455666777777779999999985532 334456778888888886432222222222222333445554333 34
Q ss_pred eEEEEEcChhHHHHHHHHHHHcCccccCeEEEE
Q 043276 80 RVFILHMLPSLGSRIFEKANEIGLMNKGCVWIM 112 (829)
Q Consensus 80 rViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~ 112 (829)
++ |++++...+..+++.+.+.|...++.+=|+
T Consensus 179 ~a-i~~~~d~~a~~~~~~l~~~g~~~p~di~vi 210 (268)
T cd01575 179 DA-VFCSNDDLALGALFECQRRGISVPEDIAIA 210 (268)
T ss_pred CE-EEECCcHHHHHHHHHHHHhCCCCCcceEEE
Confidence 44 445566677788999999887555544443
No 250
>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=74.73 E-value=82 Score=30.22 Aligned_cols=69 Identities=12% Similarity=0.131 Sum_probs=45.9
Q ss_pred EeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccEEEeccccccccceeccccccccccceEEEE
Q 043276 339 GYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMIV 418 (829)
Q Consensus 339 G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv 418 (829)
.+-.+++..+.++.+ +++++... +...++..+|.+|++|+++..- ......+. +.++....+.+++
T Consensus 13 ~~l~~~l~~~~~~~P-~v~i~i~~---------~~~~~~~~~l~~~~~Dl~i~~~---~~~~~~~~-~~~l~~~~~~lv~ 78 (197)
T cd08452 13 EFLPPIVREYRKKFP-SVKVELRE---------LSSPDQVEELLKGRIDIGFLHP---PIQHTALH-IETVQSSPCVLAL 78 (197)
T ss_pred hHHHHHHHHHHHHCC-CcEEEEEe---------cChHHHHHHHHCCCccEEEeeC---CCCCCCee-EEEeeeccEEEEE
Confidence 345678888888876 45666554 3568899999999999998532 11122233 3566777777777
Q ss_pred Ecc
Q 043276 419 PIK 421 (829)
Q Consensus 419 ~~~ 421 (829)
+..
T Consensus 79 ~~~ 81 (197)
T cd08452 79 PKQ 81 (197)
T ss_pred eCC
Confidence 743
No 251
>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=74.71 E-value=25 Score=36.15 Aligned_cols=108 Identities=13% Similarity=0.058 Sum_probs=64.9
Q ss_pred ChHHHHHHHHHHHHHcCCcEEEEEEEeC--ccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcC--CC
Q 043276 4 NDSSQVGAITAIIKAFGWREAVPIYVDN--QYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTM--QT 79 (829)
Q Consensus 4 sD~~q~~ai~~ll~~fgW~~V~iI~~dd--~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~--~a 79 (829)
++...+..+++.+...|-+++++|..+. .....-.+.|.+++++.|+.+.....+....+..+..+.+..+.+. ..
T Consensus 97 d~~~~~~~~~~~l~~~g~~~i~~i~~~~~~~~~~~R~~Gf~~~l~~~~~~~~~~~i~~~~~~~~~~~~~~~~~l~~~~~~ 176 (260)
T cd06286 97 DHYEAFYEALKYLIQKGYRKIAYCIGRKKSLNSQSRKKAYKDALEEYGLTPDEEWIFEGCFTIEDGERIGHQLLKMKDRP 176 (260)
T ss_pred CChHHHHHHHHHHHHCCCceEEEEcCCcccchhHHHHHHHHHHHHHcCCCCChHheEeCCCCHHHHHHHHHHHHcCCCCC
Confidence 4455566777878777999999997542 3334457788888999886543211111111222333344444433 33
Q ss_pred eEEEEEcChhHHHHHHHHHHHcCccccCeEEEE
Q 043276 80 RVFILHMLPSLGSRIFEKANEIGLMNKGCVWIM 112 (829)
Q Consensus 80 rViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~ 112 (829)
+ .|++++...+..++..+++.|+..++.+=|.
T Consensus 177 ~-ai~~~~d~~a~~~~~~l~~~g~~ip~di~v~ 208 (260)
T cd06286 177 D-AIFTGSDEVAAGIITEAKKQGIRVPEDLAII 208 (260)
T ss_pred C-EEEEcchHHHHHHHHHHHHcCCCCCcceEEE
Confidence 4 4556677778899999999997544444333
No 252
>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=74.66 E-value=14 Score=40.84 Aligned_cols=87 Identities=11% Similarity=0.060 Sum_probs=63.6
Q ss_pred HHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcCh-
Q 043276 10 GAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLP- 88 (829)
Q Consensus 10 ~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~~- 88 (829)
+.+.+.++.+|-+++.+|+...-+..+..+.+.+.|++.|+.+.....+..+.+.+.+.+.+..+++.++++||-.+..
T Consensus 15 ~~l~~~l~~~g~~~~lvvt~~~~~~~g~~~~v~~~L~~~g~~~~~~~~v~~~p~~~~v~~~~~~~~~~~~d~IIaiGGGS 94 (374)
T cd08189 15 AQLPAAISQLGVKKVLIVTDKGLVKLGLLDKVLEALEGAGIEYAVYDGVPPDPTIENVEAGLALYRENGCDAILAVGGGS 94 (374)
T ss_pred HHHHHHHHhcCCCeEEEEeCcchhhcccHHHHHHHHHhcCCeEEEeCCCCCCcCHHHHHHHHHHHHhcCCCEEEEeCCcc
Confidence 4466778888989998888555444456788999999999876544455556667778888888888999999987653
Q ss_pred -hHHHHHHH
Q 043276 89 -SLGSRIFE 96 (829)
Q Consensus 89 -~~~~~i~~ 96 (829)
-++...+.
T Consensus 95 ~~D~aK~ia 103 (374)
T cd08189 95 VIDCAKAIA 103 (374)
T ss_pred HHHHHHHHH
Confidence 34444443
No 253
>PLN02245 ATP phosphoribosyl transferase
Probab=74.58 E-value=18 Score=39.72 Aligned_cols=103 Identities=14% Similarity=0.058 Sum_probs=59.8
Q ss_pred CCCHHHHHh-------CCCcEEEEeCchHHHHHHhcCCCccceeecCChHHHHHHHhcCCcCCceeEEEcchhHHHHHHh
Q 043276 532 ITDVNLLIK-------RGDNVGYQKGSFVLGILKQLGFDERKLVVYNSHEECDELFQKGSANGGIAAAFDEIPYAKLLIG 604 (829)
Q Consensus 532 I~s~~dL~~-------~~~~vg~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~ 604 (829)
+++++||.. ..++|+...-...+.||++.+....+++...-.-|. +-..|- .|++++-.....-+.+
T Consensus 179 ~~s~~dL~g~~~~~~~~~~RIATkYp~ltr~ff~~~Gv~~v~Iv~l~GAvE~--AP~lGl----ADaIvDIVsTGtTLra 252 (403)
T PLN02245 179 INSLKELAQMPQWTEERPLRVVTGFTYLGPKFMKDNGFKHVTFSTADGALEA--APAMGI----ADAILDLVSSGTTLRE 252 (403)
T ss_pred cCCHHHhcccccccccCceEEEeCCHHHHHHHHHHcCCCeEEEEECcCceec--ccccCc----hhhhcchhccHHHHHH
Confidence 578888862 115888877778889999888755555554433333 334454 5666655444444333
Q ss_pred cCCCceEEeC-cccccCCceeeecCCCC-----chhhHHHHHHhh
Q 043276 605 QHCSKYTMVE-PTFKTAGFGFAFPLHSP-----LVHDVSKAILNV 643 (829)
Q Consensus 605 ~~c~~l~~v~-~~~~~~~~~~~~~k~sp-----l~~~in~~il~l 643 (829)
+ .|.+++ +.+....-.+...|++. -.+.++..+.+|
T Consensus 253 N---gLk~i~~~~Il~S~A~LIan~~sl~~~~~~~~~i~~ll~rl 294 (403)
T PLN02245 253 N---NLKEIEGGVVLESQAVLVASRRALLERKGALEVVHEILERL 294 (403)
T ss_pred C---CCEEccCceEEEEEEEEEEecchhhcchhHHHHHHHHHHHH
Confidence 3 366775 45555555666677754 222455444444
No 254
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=74.57 E-value=30 Score=37.58 Aligned_cols=103 Identities=10% Similarity=0.007 Sum_probs=62.7
Q ss_pred HHHHHHHHHHcCCcEEEEEEEeCc--cccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcC--CCeEEEE
Q 043276 9 VGAITAIIKAFGWREAVPIYVDNQ--YGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTM--QTRVFIL 84 (829)
Q Consensus 9 ~~ai~~ll~~fgW~~V~iI~~dd~--yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~--~arViIv 84 (829)
+..+++.|...|-+++++|....+ .+..-.+.|.+++++.|+.+..........+.+.-.+.+.++.+. ... .|+
T Consensus 164 ~~~a~~~L~~~G~~~I~~i~~~~~~~~~~~R~~Gf~~al~~~gi~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-ai~ 242 (346)
T PRK10401 164 ARMATRMLLNNGHQRIGYLSSSHGIEDDAMRRAGWMSALKEQGIIPPESWIGTGTPDMQGGEAAMVELLGRNLQLT-AVF 242 (346)
T ss_pred HHHHHHHHHHCCCCeEEEEeCCCcCcchHHHHHHHHHHHHHcCCCCChhheecCCCChHHHHHHHHHHHcCCCCCc-EEE
Confidence 445557777779999999964432 344557788899999997543221111111222222344444332 234 455
Q ss_pred EcChhHHHHHHHHHHHcCccccCeEEEE
Q 043276 85 HMLPSLGSRIFEKANEIGLMNKGCVWIM 112 (829)
Q Consensus 85 ~~~~~~~~~i~~~a~~~gm~~~~~vwI~ 112 (829)
+++...+..+++.+++.|+..++-+-|+
T Consensus 243 ~~nd~~A~g~~~al~~~G~~vP~disvi 270 (346)
T PRK10401 243 AYNDNMAAGALTALKDNGIAIPLHLSII 270 (346)
T ss_pred ECCcHHHHHHHHHHHHcCCCCCCceEEE
Confidence 6677788899999999998666555544
No 255
>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=74.44 E-value=19 Score=37.33 Aligned_cols=98 Identities=7% Similarity=-0.035 Sum_probs=61.6
Q ss_pred CChHHHHHHHHHHHHHc--CCcEEEEEEEe--CccccchHHHHHHHHHhCC-ceeeeEEecCCCCChhHHHHHHHHhhcC
Q 043276 3 LNDSSQVGAITAIIKAF--GWREAVPIYVD--NQYGEELIPSLTDALQAID-TRVPYRSVISPLATDDQIEKELYKLFTM 77 (829)
Q Consensus 3 psD~~q~~ai~~ll~~f--gW~~V~iI~~d--d~yG~~~~~~l~~~l~~~g-i~I~~~~~i~~~~~~~~~~~~l~~lk~~ 77 (829)
+++...+..+++.+... |=+++++|..+ ...+....+.+.+++++.+ +.+... .....+.++..+.+.++.+.
T Consensus 105 ~d~~~~g~~~~~~l~~~~~g~~~i~~i~~~~~~~~~~~R~~g~~~a~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~l~~ 182 (272)
T cd06300 105 EDQAEFGKQGAEWLVKELGGKGNVLVVRGLAGHPVDEDRYAGAKEVLKEYPGIKIVGE--VYGDWDQAVAQKAVADFLAS 182 (272)
T ss_pred CCHHHHHHHHHHHHHHHcCCCceEEEEECCCCCcchHHHHHHHHHHHHHCCCcEEEee--cCCCCCHHHHHHHHHHHHHh
Confidence 45556667777777554 88899999743 2344556677888898887 766432 22222334455666666554
Q ss_pred CCeE-EEEEcChhHHHHHHHHHHHcCc
Q 043276 78 QTRV-FILHMLPSLGSRIFEKANEIGL 103 (829)
Q Consensus 78 ~arV-iIv~~~~~~~~~i~~~a~~~gm 103 (829)
..++ .|++.+.. +..+++.+++.|+
T Consensus 183 ~~~~~~i~~~~d~-A~g~~~al~~~g~ 208 (272)
T cd06300 183 NPDVDGIWTQGGD-AVGAVQAFEQAGR 208 (272)
T ss_pred CCCcCEEEecCCC-cHHHHHHHHHcCC
Confidence 4333 33333444 8889999999996
No 256
>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=74.27 E-value=15 Score=40.55 Aligned_cols=79 Identities=15% Similarity=0.077 Sum_probs=61.4
Q ss_pred HHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcCh
Q 043276 10 GAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLP 88 (829)
Q Consensus 10 ~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~~ 88 (829)
+.+.++++.++-+++.+|+...-+..+..+.+.+.|++.|+.+.....+..+++.+.+.+.+..+++.++++||-.+..
T Consensus 12 ~~l~~~~~~~~~~r~livt~~~~~~~g~~~~v~~~L~~~gi~~~~~~~v~~~p~~~~v~~~~~~~~~~~~D~IIaiGGG 90 (375)
T cd08194 12 DETGAVLADLGGKRPLIVTDKVMVKLGLVDKLTDSLKKEGIESAIFDDVVSEPTDESVEEGVKLAKEGGCDVIIALGGG 90 (375)
T ss_pred HHHHHHHHHcCCCeEEEEcCcchhhcchHHHHHHHHHHCCCeEEEECCCCCCcCHHHHHHHHHHHHhcCCCEEEEeCCc
Confidence 4456677778889999998655554557888999999999887655556666677788888888888999999988764
No 257
>PLN03192 Voltage-dependent potassium channel; Provisional
Probab=74.24 E-value=8.8 Score=47.39 Aligned_cols=53 Identities=15% Similarity=0.249 Sum_probs=45.9
Q ss_pred cchhHHHHHHHhhhcC--ccccccchhHHHHHHHHHHHHHHHHHhHHHHHHHhhc
Q 043276 473 VGTSFWFSFSTMVFSQ--RERVISNLARFVVIVWCFVVLILIQSYTASLTSLLTV 525 (829)
Q Consensus 473 ~~~~~~~~~~~l~~~~--~~~~~s~~~R~v~~~w~~~~lil~~~YtA~L~s~Lt~ 525 (829)
...++|+++.++...| ...|.+...|++.++|+++++++.++..+++++++..
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 4458999999999766 3468999999999999999999999999999998754
No 258
>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=74.23 E-value=15 Score=40.77 Aligned_cols=79 Identities=13% Similarity=0.060 Sum_probs=59.6
Q ss_pred HHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcCh
Q 043276 10 GAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLP 88 (829)
Q Consensus 10 ~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~~ 88 (829)
+.+.+.++.+|-+++.||+...-.-.+..+.+.+.|++.|+.+.....+..+.+.+.+.+....+++.++++||-.+..
T Consensus 18 ~~l~~~l~~~g~~r~lvvt~~~~~~~g~~~~v~~~L~~~~i~~~~~~~v~~~p~~~~v~~~~~~~~~~~~D~IiaiGGG 96 (379)
T TIGR02638 18 EDIVDEVKRRGFKKALVVTDKDLIKFGVADKVTDLLDEAGIAYELFDEVKPNPTITVVKAGVAAFKASGADYLIAIGGG 96 (379)
T ss_pred HHHHHHHHhcCCCEEEEEcCcchhhccchHHHHHHHHHCCCeEEEECCCCCCcCHHHHHHHHHHHHhcCCCEEEEeCCh
Confidence 3466778889999999988554444457888999999999876544445555566778888888888999999988764
No 259
>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=74.20 E-value=43 Score=34.59 Aligned_cols=105 Identities=19% Similarity=0.126 Sum_probs=58.1
Q ss_pred hHHHHHHHHHHH-HHc-CCcEEEEEEEeCccc--cchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhh-c--C
Q 043276 5 DSSQVGAITAII-KAF-GWREAVPIYVDNQYG--EELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLF-T--M 77 (829)
Q Consensus 5 D~~q~~ai~~ll-~~f-gW~~V~iI~~dd~yG--~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk-~--~ 77 (829)
+...+..+++.+ +++ |-++|++++...+++ ..-.+.+.+++++.|..+..........+.++....+.++. + .
T Consensus 107 ~~~~g~~~~~~l~~~~~g~~~i~~l~~~~~~~~~~~r~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~ 186 (275)
T cd06317 107 DISQGERSAEAMCKALGGKGQIVVIAGQPGNGTAIERQKGFEDELAEVCPGVEVLDTQPADWDREKAQVAMEALITKFGD 186 (275)
T ss_pred HHHHHHHHHHHHHHHcCCCceEEEEecCCCCchHHHHHHHHHHHHHhhCCCCEEEeccCCCCCHHHHHHHHHHHHHhCCC
Confidence 334555555655 443 778999997644443 34457788899988643332222211112222223333332 2 2
Q ss_pred CCeEEEEEcChhHHHHHHHHHHHcCccccCeEEEE
Q 043276 78 QTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIM 112 (829)
Q Consensus 78 ~arViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~ 112 (829)
..+.|+ +++...+..+++.+++.|+. +.+-|.
T Consensus 187 ~~~ai~-~~~d~~a~g~~~~l~~~g~~--~dv~v~ 218 (275)
T cd06317 187 DIDGVY-AGDDNMARGALNAAKEAGLA--GGIVIV 218 (275)
T ss_pred CccEEE-ECCCcHHHHHHHHHHhcCCc--CCcEEE
Confidence 345555 45566688899999999964 344444
No 260
>PRK09861 cytoplasmic membrane lipoprotein-28; Provisional
Probab=74.03 E-value=91 Score=32.72 Aligned_cols=120 Identities=12% Similarity=0.102 Sum_probs=60.3
Q ss_pred CCCCHHHHHhCCCcEEEEeC--chHHH--HHHhcC---------CC---------ccceeec-CChHHHHHHHhcCCcCC
Q 043276 531 TITDVNLLIKRGDNVGYQKG--SFVLG--ILKQLG---------FD---------ERKLVVY-NSHEECDELFQKGSANG 587 (829)
Q Consensus 531 ~I~s~~dL~~~~~~vg~~~~--s~~~~--~l~~~~---------~~---------~~~~~~~-~~~~~~~~~l~~g~~~~ 587 (829)
.|++++||. .|.+|++..+ ...+. +|+..+ .. +.++... -...+...++..|.
T Consensus 121 ~iksl~DL~-~Ga~IAipnd~~n~~ral~lL~~agli~l~~~~g~~~t~~di~~np~~l~~ve~~~~q~~~al~dg~--- 196 (272)
T PRK09861 121 KIKTVAQIK-EGATVAIPNDPTNLGRALLLLQKEKLITLKEGKGLLPTALDITDNPRHLQIMELEGAQLPRVLDDPK--- 196 (272)
T ss_pred CCCCHHHcC-CCCEEEEeCCCccHHHHHHHHHHCCCEEEcCCCCCCCCHhHHhcCCCCCEEEEcCHHHhHhhccCcc---
Confidence 489999994 6889999863 22232 223322 11 0122211 13456777888887
Q ss_pred ceeEEEcchhHHHHHHhcCC-CceEEeCcccccCCceeeecCCCCchhhHHHHHHhhhccChhHHHHHHH
Q 043276 588 GIAAAFDEIPYAKLLIGQHC-SKYTMVEPTFKTAGFGFAFPLHSPLVHDVSKAILNVTEGDKMKEIEDAW 656 (829)
Q Consensus 588 g~~a~~~~~~~~~~~~~~~c-~~l~~v~~~~~~~~~~~~~~k~spl~~~in~~il~l~e~G~~~~~~~~w 656 (829)
+|+++...+++.-. .-.. ..-......-......++++.+..=.+.+.+.+..++....-+.|.++|
T Consensus 197 -vD~a~i~~~~~~~a-g~~~~~~~l~~e~~~~~~~n~~~~r~~~~~~~~~~~lv~~~~s~~v~~~i~~~~ 264 (272)
T PRK09861 197 -VDVAIISTTYIQQT-GLSPVHDSVFIEDKNSPYVNILVAREDNKNAENVKEFLQSYQSPEVAKAAETIF 264 (272)
T ss_pred -cCEEEEchhHHHHc-CCCcccceeEEcCCCCCeEEEEEEcCCccCCHHHHHHHHHHcCHHHHHHHHHHc
Confidence 88888777665431 1111 1111122111111224555554334455666666666555555555553
No 261
>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=73.98 E-value=36 Score=35.12 Aligned_cols=108 Identities=13% Similarity=0.044 Sum_probs=64.3
Q ss_pred ChHHHHHHHHHHHHHcCCcEEEEEEEeCcc--ccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCC--C
Q 043276 4 NDSSQVGAITAIIKAFGWREAVPIYVDNQY--GEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQ--T 79 (829)
Q Consensus 4 sD~~q~~ai~~ll~~fgW~~V~iI~~dd~y--G~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~--a 79 (829)
++..-+..+++.+...|-+++++|..+... ...-.+.|.+.+++.|+.+.....+....+.++..+.+.++.+.. .
T Consensus 99 d~~~~~~~~~~~l~~~g~~~i~~i~~~~~~~~~~~R~~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~ 178 (268)
T cd06270 99 DNEQGGYLATEHLIELGHRKIACITGPLTKEDARLRLQGYRDALAEAGIALDESLIIEGDFTEEGGYAAMQELLARGAPF 178 (268)
T ss_pred CcHHHHHHHHHHHHHCCCceEEEEeCCcccccHHHHHHHHHHHHHHcCCCCCcceEEECCCCHHHHHHHHHHHHhCCCCC
Confidence 445556677788877799999999754322 233456778888888876432212222222334445555554333 3
Q ss_pred eEEEEEcChhHHHHHHHHHHHcCccccCeEEEE
Q 043276 80 RVFILHMLPSLGSRIFEKANEIGLMNKGCVWIM 112 (829)
Q Consensus 80 rViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~ 112 (829)
+ .|++++...+..+++.+++.|+..++.+=|.
T Consensus 179 ~-ai~~~~d~~a~g~~~~l~~~g~~ip~di~v~ 210 (268)
T cd06270 179 T-AVFCANDEMAAGAISALREHGISVPQDVSII 210 (268)
T ss_pred C-EEEEcCcHHHHHHHHHHHHcCCCCCCceeEE
Confidence 4 4445556677788999999887555444333
No 262
>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=73.77 E-value=26 Score=36.20 Aligned_cols=108 Identities=12% Similarity=0.006 Sum_probs=63.2
Q ss_pred HHHHHHHHHHHHHcCCcEEEEEEEeCc--cccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCe-EE
Q 043276 6 SSQVGAITAIIKAFGWREAVPIYVDNQ--YGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTR-VF 82 (829)
Q Consensus 6 ~~q~~ai~~ll~~fgW~~V~iI~~dd~--yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~ar-Vi 82 (829)
...+..+++.+...|-+++++|....+ ....-.+.+.+.+++.|+.+..........+.....+.+.++.+...+ -.
T Consensus 102 ~~~~~~~~~~l~~~G~~~i~~i~~~~~~~~~~~r~~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~a 181 (269)
T cd06275 102 EEGGYLATRHLIELGHRRIGCITGPLEKAPAQQRLAGFRRAMAEAGLPVNPGWIVEGDFECEGGYEAMQRLLAQPKRPTA 181 (269)
T ss_pred HHHHHHHHHHHHHCCCceEEEEeCCCCCccHHHHHHHHHHHHHHcCCCCCHHHhccCCCChHHHHHHHHHHHcCCCCCcE
Confidence 344566677777779999999974322 223445778888888887653211111121222333445554433322 24
Q ss_pred EEEcChhHHHHHHHHHHHcCccccCeEEEEc
Q 043276 83 ILHMLPSLGSRIFEKANEIGLMNKGCVWIMT 113 (829)
Q Consensus 83 Iv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t 113 (829)
|++++...+..+++.+++.|...++.+-|++
T Consensus 182 i~~~~d~~a~g~~~~l~~~g~~vp~di~vvg 212 (269)
T cd06275 182 VFCGNDLMAMGALCAAQEAGLRVPQDLSIIG 212 (269)
T ss_pred EEECChHHHHHHHHHHHHcCCCCCcceEEEE
Confidence 5556677777888999998875555555543
No 263
>PF13685 Fe-ADH_2: Iron-containing alcohol dehydrogenase; PDB: 3CE9_C.
Probab=73.70 E-value=26 Score=36.14 Aligned_cols=100 Identities=16% Similarity=0.162 Sum_probs=59.4
Q ss_pred HHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcChhH
Q 043276 11 AITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSL 90 (829)
Q Consensus 11 ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~~~~ 90 (829)
-+.++++.++.+++.+|+..+-| .-.-+.+.+.|+..|+.+..........+.+.+.+...+++..+++++|-.+...-
T Consensus 9 ~l~~~l~~~~~~~~lvv~d~~t~-~~~g~~v~~~l~~~g~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~d~ii~vGgG~i 87 (250)
T PF13685_consen 9 KLPEILSELGLKKVLVVTDENTY-KAAGEKVEESLKSAGIEVAVIEEFVGDADEDEVEKLVEALRPKDADLIIGVGGGTI 87 (250)
T ss_dssp GHHHHHGGGT-SEEEEEEETTHH-HHHHHHHHHHHHTTT-EEEEEE-EE---BHHHHHHHHTTS--TT--EEEEEESHHH
T ss_pred HHHHHHHhcCCCcEEEEEcCCHH-HHHHHHHHHHHHHcCCeEEEEecCCCCCCHHHHHHHHHHhcccCCCEEEEeCCcHH
Confidence 35678888899999999855554 34456778889999988874433333445556667777777778889999888643
Q ss_pred HHHHHHHHHHcCccccCeEEEEcC
Q 043276 91 GSRIFEKANEIGLMNKGCVWIMTD 114 (829)
Q Consensus 91 ~~~i~~~a~~~gm~~~~~vwI~t~ 114 (829)
.=.-=..|.++|+ .|+=|-|.
T Consensus 88 ~D~~K~~A~~~~~---p~isVPTa 108 (250)
T PF13685_consen 88 IDIAKYAAFELGI---PFISVPTA 108 (250)
T ss_dssp HHHHHHHHHHHT-----EEEEES-
T ss_pred HHHHHHHHHhcCC---CEEEeccc
Confidence 3333334666663 57776664
No 264
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=73.52 E-value=24 Score=38.23 Aligned_cols=104 Identities=11% Similarity=0.086 Sum_probs=62.6
Q ss_pred HHHHHHHHHHHcCCcEEEEEEEe--CccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcC--CCeEEE
Q 043276 8 QVGAITAIIKAFGWREAVPIYVD--NQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTM--QTRVFI 83 (829)
Q Consensus 8 q~~ai~~ll~~fgW~~V~iI~~d--d~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~--~arViI 83 (829)
-+..+++.+...|-+++++|..+ +..+..-.+.|.+++++.|+.+..........+.++....+.++.+. ..++ |
T Consensus 165 ~g~~a~~~L~~~G~~~i~~i~~~~~~~~~~~R~~Gf~~~l~~~gi~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~a-i 243 (341)
T PRK10703 165 GGYLAGRYLIERGHRDIGVIPGPLERNTGAGRLAGFMKAMEEANIKVPEEWIVQGDFEPESGYEAMQQILSQKHRPTA-V 243 (341)
T ss_pred HHHHHHHHHHHCCCCcEEEEeCCccccchHHHHHHHHHHHHHcCCCCChHHeEeCCCCHHHHHHHHHHHHhCCCCCCE-E
Confidence 45666676666699999999643 22334456788889999887654321111122223334455554433 3344 4
Q ss_pred EEcChhHHHHHHHHHHHcCccccCeEEEE
Q 043276 84 LHMLPSLGSRIFEKANEIGLMNKGCVWIM 112 (829)
Q Consensus 84 v~~~~~~~~~i~~~a~~~gm~~~~~vwI~ 112 (829)
++++...+..++..+.+.|...++.+.|+
T Consensus 244 ~~~nd~~a~g~~~al~~~g~~ip~dv~vv 272 (341)
T PRK10703 244 FCGGDIMAMGAICAADEMGLRVPQDISVI 272 (341)
T ss_pred EECCcHHHHHHHHHHHHcCCCCCCceEEE
Confidence 45667777889999999997555555554
No 265
>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=73.23 E-value=29 Score=36.01 Aligned_cols=108 Identities=6% Similarity=-0.031 Sum_probs=63.8
Q ss_pred ChHHHHHHHHHHHHHcCCcEEEEEEEeCc-------cccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhc
Q 043276 4 NDSSQVGAITAIIKAFGWREAVPIYVDNQ-------YGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFT 76 (829)
Q Consensus 4 sD~~q~~ai~~ll~~fgW~~V~iI~~dd~-------yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~ 76 (829)
++...+..+++.+..-|-++++++..... +...-.+.+.+++.+.|.. .....+....+.......+.++.+
T Consensus 95 D~~~a~~~~~~~l~~~g~~~i~~i~~~~~~~~~~~~~~~~R~~gf~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~l~ 173 (270)
T cd01544 95 DFEQAVEKALDYLLELGHTRIGFIGGEEKTTDGHEYIEDPRETAFREYMKEKGLY-DPELIYIGDFTVESGYQLMKEALK 173 (270)
T ss_pred CHHHHHHHHHHHHHHcCCCcEEEECCCcccccccchhhhHHHHHHHHHHHHcCCC-ChheEeeCCCCHHHHHHHHHHHHh
Confidence 44555666777777789999999975433 2344577788889888842 110111111122223334444332
Q ss_pred C---C-CeEEEEEcChhHHHHHHHHHHHcCccccCeEEEEc
Q 043276 77 M---Q-TRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMT 113 (829)
Q Consensus 77 ~---~-arViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t 113 (829)
. . .+ .|++++...+..++..+++.|+..++-+-|.+
T Consensus 174 ~~~~~~~~-ai~~~~d~~a~g~~~~l~~~g~~vp~di~v~g 213 (270)
T cd01544 174 SLGDNLPT-AFFIASDPMAIGALRALQEAGIKVPEDVSVIS 213 (270)
T ss_pred ccCCCCCC-EEEEcCcHHHHHHHHHHHHcCCCCCCceEEEE
Confidence 2 2 33 45556777888899999999976555444443
No 266
>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=73.16 E-value=48 Score=31.54 Aligned_cols=98 Identities=8% Similarity=0.014 Sum_probs=50.3
Q ss_pred CCHHHHHhCCCcEEEEe-C-chHHHHHHhcCCCcc---ceeecCChHHHHHHHhcCCcCCceeEEEcchhHHHHHHhcCC
Q 043276 533 TDVNLLIKRGDNVGYQK-G-SFVLGILKQLGFDER---KLVVYNSHEECDELFQKGSANGGIAAAFDEIPYAKLLIGQHC 607 (829)
Q Consensus 533 ~s~~dL~~~~~~vg~~~-~-s~~~~~l~~~~~~~~---~~~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~~c 607 (829)
-+++||.. .++.... . .....++.+.+.... ....+++.+...+.+..|. .-+++.+.. +...... .
T Consensus 86 ~~~~dl~~--~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~----Gi~~~p~~~-~~~~~~~-~ 157 (194)
T cd08481 86 AAPADLAH--LPLLQQTTRPEAWRDWFEEVGLEVPTAYRGMRFEQFSMLAQAAVAGL----GVALLPRFL-IEEELAR-G 157 (194)
T ss_pred CcHHHHhh--CceEecCCCCcCHHHHHHHcCCCCCCccCceEeccHHHHHHHHHhCC----CeEEecHHH-HHHHHHC-C
Confidence 36788863 3332221 1 234455665554321 1234567888889998887 455555533 3322222 2
Q ss_pred CceEEe--CcccccCCceeeecCCCCchhhHHHH
Q 043276 608 SKYTMV--EPTFKTAGFGFAFPLHSPLVHDVSKA 639 (829)
Q Consensus 608 ~~l~~v--~~~~~~~~~~~~~~k~spl~~~in~~ 639 (829)
. +... .+......++++.+++.+....+...
T Consensus 158 ~-l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~ 190 (194)
T cd08481 158 R-LVVPFNLPLTSDKAYYLVYPEDKAESPPVQAF 190 (194)
T ss_pred C-EEeecCccccCCCeEEEEeCcccccCHHHHHH
Confidence 1 2222 22223457788888887655544443
No 267
>PRK03635 chromosome replication initiation inhibitor protein; Validated
Probab=73.11 E-value=98 Score=32.62 Aligned_cols=66 Identities=12% Similarity=0.027 Sum_probs=43.2
Q ss_pred eHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccEEEeccccccccceeccccccccccceEEEEEc
Q 043276 341 SIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMIVPI 420 (829)
Q Consensus 341 ~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv~~ 420 (829)
-..++..+.++ . .+++++... .-..++..+.+|++|+++..-.. ....+ .+.|+.+..++++++.
T Consensus 105 l~~~l~~f~~~-~-~i~i~l~~~---------~~~~~~~~l~~~~~d~~i~~~~~---~~~~l-~~~~l~~~~~~lv~~~ 169 (294)
T PRK03635 105 FLPALAPVLAR-S-GVLLDLVVE---------DQDHTAELLRRGEVVGAVTTEPQ---PVQGC-RVDPLGAMRYLAVASP 169 (294)
T ss_pred HHHHHHHHHhC-C-CcEEEEEec---------CcHHHHHHHhCCCceEEEeccCC---CCCCc-eeeecccceEEEEEcc
Confidence 34566777765 2 566666542 34678999999999999853221 12223 4578888888888874
Q ss_pred c
Q 043276 421 K 421 (829)
Q Consensus 421 ~ 421 (829)
.
T Consensus 170 ~ 170 (294)
T PRK03635 170 A 170 (294)
T ss_pred h
Confidence 3
No 268
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=72.20 E-value=48 Score=35.96 Aligned_cols=103 Identities=14% Similarity=0.069 Sum_probs=70.6
Q ss_pred ChHHHHHHHHHHHHHcCCcEEEEEEEe--CccccchHHHHHHHHHhCCcee-eeEEecCCCCChhHHHHHHHHhhcCCC-
Q 043276 4 NDSSQVGAITAIIKAFGWREAVPIYVD--NQYGEELIPSLTDALQAIDTRV-PYRSVISPLATDDQIEKELYKLFTMQT- 79 (829)
Q Consensus 4 sD~~q~~ai~~ll~~fgW~~V~iI~~d--d~yG~~~~~~l~~~l~~~gi~I-~~~~~i~~~~~~~~~~~~l~~lk~~~a- 79 (829)
++..-+..+++.+...|-+++++|... ...+..-.+.+.+++++.|+.. ..... ....+..+-.+.+.++.....
T Consensus 158 Dn~~~~~~a~~~L~~~G~~~i~~i~~~~~~~~~~~R~~Gf~~al~~~~~~~~~~~i~-~~~~~~~~g~~~~~~ll~~~~~ 236 (333)
T COG1609 158 DNFAGAYLATEHLIELGHRRIAFIGGPLDSSASRERLEGYRAALREAGLPINPEWIV-EGDFSEESGYEAAERLLARGEP 236 (333)
T ss_pred ChHHHHHHHHHHHHHCCCceEEEEeCCCccccHhHHHHHHHHHHHHCCCCCCcceEE-ecCCChHHHHHHHHHHHhcCCC
Confidence 455566778888999999999999965 4455667889999999999875 22111 111123344445555543332
Q ss_pred -eEEEEEcChhHHHHHHHHHHHcCccccC
Q 043276 80 -RVFILHMLPSLGSRIFEKANEIGLMNKG 107 (829)
Q Consensus 80 -rViIv~~~~~~~~~i~~~a~~~gm~~~~ 107 (829)
--.|+|++...|.-++..+++.|+..++
T Consensus 237 ~ptAif~~nD~~Alg~l~~~~~~g~~vP~ 265 (333)
T COG1609 237 RPTAIFCANDLMALGALRALRELGLRVPE 265 (333)
T ss_pred CCcEEEEcCcHHHHHHHHHHHHcCCCCCC
Confidence 2457778888999999999999976554
No 269
>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=71.30 E-value=31 Score=35.56 Aligned_cols=105 Identities=17% Similarity=0.094 Sum_probs=59.9
Q ss_pred HHHHHHHHHHHHHcCCcEEEEEEEeCcc--ccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeE-E
Q 043276 6 SSQVGAITAIIKAFGWREAVPIYVDNQY--GEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRV-F 82 (829)
Q Consensus 6 ~~q~~ai~~ll~~fgW~~V~iI~~dd~y--G~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arV-i 82 (829)
..-++.+++.+...|-++++++.....+ ...-.+.|.+++++.|+.+..........+.+...+.+.++.+...++ .
T Consensus 107 ~~~g~~~~~~l~~~g~~~i~~i~~~~~~~~~~~r~~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~a 186 (270)
T cd06294 107 IQAGYDATEYLIKLGHKKIAFVGGDLDLEVTQDRLQGYKQALEDHGIPDRNEVIISLDFSEEGGYKALKKLLEQHPRPTA 186 (270)
T ss_pred HHHHHHHHHHHHHcCCccEEEecCCcccHHHHHHHHHHHHHHHHcCCCCCcceEEecCCchHHHHHHHHHHHhCCCCCCE
Confidence 3444566676666699999999744332 233467888899988853221111111112223334454544333223 3
Q ss_pred EEEcChhHHHHHHHHHHHcCccccCeEE
Q 043276 83 ILHMLPSLGSRIFEKANEIGLMNKGCVW 110 (829)
Q Consensus 83 Iv~~~~~~~~~i~~~a~~~gm~~~~~vw 110 (829)
|++.+...+..++..+++.|+..++.+=
T Consensus 187 i~~~~d~~a~g~~~al~~~g~~iP~dv~ 214 (270)
T cd06294 187 IVATDDLLALGVLKVLNELGLKVPEDLS 214 (270)
T ss_pred EEECChHHHHHHHHHHHHcCCCCCcceE
Confidence 3345666888899999999976555443
No 270
>PRK09986 DNA-binding transcriptional activator XapR; Provisional
Probab=71.16 E-value=1.4e+02 Score=31.28 Aligned_cols=72 Identities=17% Similarity=0.112 Sum_probs=46.8
Q ss_pred EeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccEEEeccccccccceeccccccccccceEEEE
Q 043276 339 GYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMIV 418 (829)
Q Consensus 339 G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv 418 (829)
.+-.+++..+.++.+ .+++++... +-++++.+|.+|++|+++.... .......+.+ .|+....+++++
T Consensus 110 ~~l~~~l~~f~~~~p-~i~l~i~~~---------~~~~~~~~l~~g~~D~~i~~~~-~~~~~~~l~~-~~l~~~~~~~v~ 177 (294)
T PRK09986 110 GRLRPAMRHFLKENP-NVEWLLREL---------SPSMQMAALERRELDAGIWRMA-DLEPNPGFTS-RRLHESAFAVAV 177 (294)
T ss_pred HHHHHHHHHHHHhCC-CeEEEEEeC---------CHHHHHHHHHcCCCCEEEecCC-ccCCCCCeEE-EEeecccEEEEE
Confidence 345677888888876 355655432 3478899999999999984211 0112233443 677778888888
Q ss_pred EccC
Q 043276 419 PIKD 422 (829)
Q Consensus 419 ~~~~ 422 (829)
+...
T Consensus 178 ~~~~ 181 (294)
T PRK09986 178 PEEH 181 (294)
T ss_pred cCCC
Confidence 8553
No 271
>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=70.94 E-value=27 Score=36.10 Aligned_cols=109 Identities=16% Similarity=0.051 Sum_probs=61.5
Q ss_pred ChHHHHHHHHHHHHHcCCcEEEEEEEeCc--cccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCe-
Q 043276 4 NDSSQVGAITAIIKAFGWREAVPIYVDNQ--YGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTR- 80 (829)
Q Consensus 4 sD~~q~~ai~~ll~~fgW~~V~iI~~dd~--yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~ar- 80 (829)
++...+..+++.+..-|.++++++..... ......+.|.+++++.|+.+..........+.+.....+.++.+....
T Consensus 100 d~~~~~~~a~~~l~~~g~~~i~~i~~~~~~~~~~~r~~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~ 179 (270)
T cd06296 100 TNWAGGLAATEHLLELGHRRIGFITGPPDLLCSRARLDGYRAALAEAGIPVDPALVREGDFSTESGFRAAAELLALPERP 179 (270)
T ss_pred CcHHHHHHHHHHHHHcCCCcEEEEcCCCcchhHHHHHHHHHHHHHHcCCCCChHHheeCCCCHHHHHHHHHHHHhCCCCC
Confidence 34445666677776679999999964322 234556778888888876543211111111222333344444332222
Q ss_pred EEEEEcChhHHHHHHHHHHHcCccccCeEEEE
Q 043276 81 VFILHMLPSLGSRIFEKANEIGLMNKGCVWIM 112 (829)
Q Consensus 81 ViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~ 112 (829)
-.|++.+...+..+++...+.|...++.+-|+
T Consensus 180 ~ai~~~~d~~a~~~~~~l~~~g~~~p~~i~v~ 211 (270)
T cd06296 180 TAIFAGNDLMALGVYEAARERGLRIPEDLSVV 211 (270)
T ss_pred cEEEEcCcHHHHHHHHHHHHhCCCCCCceEEE
Confidence 24445566777788999999997544444333
No 272
>cd08188 Fe-ADH4 Iron-containing alcohol dehydrogenases-like. Iron-containing alcohol dehydrogenase-like. Alcohol dehydrogenase catalyzes the reduction of acetaldehyde to alcohol with NADP as cofactor. Its activity requires iron ions. The protein structure represents a dehydroquinate synthase-like fold and is belonged to the alcohol dehydrogenase-like superfamily. They are distinct from other alcohol dehydrogenases which contain different protein domains. Proteins of this family have not been characterized. Their specific function is unknown.
Probab=70.94 E-value=21 Score=39.52 Aligned_cols=79 Identities=10% Similarity=0.034 Sum_probs=59.0
Q ss_pred HHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcCh
Q 043276 10 GAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLP 88 (829)
Q Consensus 10 ~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~~ 88 (829)
..+.++++.+|-+++.||+...-...+..+.+.+.|++.|+.+.....+..+++.+++.+.+..+++.++++||-.+..
T Consensus 17 ~~l~~~l~~~g~~~~livt~~~~~~~~~~~~v~~~L~~~~~~~~~~~~v~~~p~~~~v~~~~~~~~~~~~d~IIaiGGG 95 (377)
T cd08188 17 KLAGRYARRLGAKKVLLVSDPGVIKAGWVDRVIESLEEAGLEYVVFSDVSPNPRDEEVMAGAELYLENGCDVIIAVGGG 95 (377)
T ss_pred HHHHHHHHHcCCCeEEEEeCcchhhCccHHHHHHHHHHcCCeEEEeCCCCCCCCHHHHHHHHHHHHhcCCCEEEEeCCc
Confidence 4566778889999999988544444456788999999988876544445555666678888888888899999988754
No 273
>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=70.67 E-value=37 Score=34.99 Aligned_cols=104 Identities=12% Similarity=-0.021 Sum_probs=60.0
Q ss_pred hHHHHHHHHHHHHHcCCcEEEEEEEeCc--cccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCC--Ce
Q 043276 5 DSSQVGAITAIIKAFGWREAVPIYVDNQ--YGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQ--TR 80 (829)
Q Consensus 5 D~~q~~ai~~ll~~fgW~~V~iI~~dd~--yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~--ar 80 (829)
+..-+..+++.+..-|-+.+++|..+.+ ......+.+.+.+++.|+.+.....+....+.+.....+.++.+.. .+
T Consensus 99 ~~~a~~~~~~~l~~~g~~~i~~i~~~~~~~~~~~r~~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ 178 (265)
T cd06290 99 NFQGGYLATQHLIDLGHRRIAHITGPRGHIDARDRLAGYRKALEEAGLEVQPDLIVQGDFEEESGLEAVEELLQRGPDFT 178 (265)
T ss_pred cHHHHHHHHHHHHHCCCCeEEEEeCccccchhhHHHHHHHHHHHHcCCCCCHHHEEecCCCHHHHHHHHHHHHcCCCCCC
Confidence 3444556666665569999999975422 2334567788888888765432111111111222233444444332 34
Q ss_pred EEEEEcChhHHHHHHHHHHHcCccccCeE
Q 043276 81 VFILHMLPSLGSRIFEKANEIGLMNKGCV 109 (829)
Q Consensus 81 ViIv~~~~~~~~~i~~~a~~~gm~~~~~v 109 (829)
.|++++...+..+++.+++.|+..++.+
T Consensus 179 -aii~~~~~~a~~~~~~l~~~g~~ip~di 206 (265)
T cd06290 179 -AIFAANDQTAYGARLALYRRGLRVPEDV 206 (265)
T ss_pred -EEEEcCcHHHHHHHHHHHHcCCCCCcce
Confidence 4555677788889999999997554443
No 274
>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=70.48 E-value=20 Score=39.73 Aligned_cols=86 Identities=7% Similarity=-0.036 Sum_probs=62.1
Q ss_pred HHHHHHHHHcCCcEEEEEEEeCc-cccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcCh
Q 043276 10 GAITAIIKAFGWREAVPIYVDNQ-YGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLP 88 (829)
Q Consensus 10 ~ai~~ll~~fgW~~V~iI~~dd~-yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~~ 88 (829)
.-+.++++.+| +++-||+.... ...+..+.+.+.|++.|+.+.....+..+++.+++.+....+++.++++||-.+..
T Consensus 15 ~~l~~~~~~~g-~r~livt~~~~~~~~g~~~~v~~~L~~~~~~~~~~~~v~~~p~~~~v~~~~~~~~~~~~D~IiavGGG 93 (380)
T cd08185 15 NELGEEALKPG-KKALIVTGNGSSKKTGYLDRVIELLKQAGVEVVVFDKVEPNPTTTTVMEGAALAREEGCDFVVGLGGG 93 (380)
T ss_pred HHHHHHHHhcC-CeEEEEeCCCchhhccHHHHHHHHHHHcCCeEEEeCCccCCCCHHHHHHHHHHHHHcCCCEEEEeCCc
Confidence 34566777788 88888885443 25677889999999999887644455666677778888888888899999977653
Q ss_pred --hHHHHHHH
Q 043276 89 --SLGSRIFE 96 (829)
Q Consensus 89 --~~~~~i~~ 96 (829)
-++...+.
T Consensus 94 S~iD~aK~ia 103 (380)
T cd08185 94 SSMDTAKAIA 103 (380)
T ss_pred cHHHHHHHHH
Confidence 24444443
No 275
>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=70.32 E-value=36 Score=35.24 Aligned_cols=109 Identities=14% Similarity=0.060 Sum_probs=63.8
Q ss_pred ChHHHHHHHHHHHHHcCCcEEEEEEEeCc--cccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeE
Q 043276 4 NDSSQVGAITAIIKAFGWREAVPIYVDNQ--YGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRV 81 (829)
Q Consensus 4 sD~~q~~ai~~ll~~fgW~~V~iI~~dd~--yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arV 81 (829)
++..-+..+++.+...|-+++++|....+ ....-.+.|.++++++|+.......+....+.+...+.+.++.+....+
T Consensus 105 d~~~~~~~~~~~l~~~g~~~i~~i~~~~~~~~~~~R~~gf~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~l~~~~~a 184 (273)
T cd06292 105 DDALAMRLAVRHLVALGHRRIGFASGPGRTVPRRRKIAGFRAALEEAGLEPPEALVARGMFSVEGGQAAAVELLGSGPTA 184 (273)
T ss_pred CcHHHHHHHHHHHHHCCCceEEEEeCCcccccHHHHHHHHHHHHHHcCCCCChhheEeCCCCHHHHHHHHHHHhcCCCCE
Confidence 34455666777777779999999864432 2344567888889888864321111111112222233344443333454
Q ss_pred EEEEcChhHHHHHHHHHHHcCccccCeEEEEc
Q 043276 82 FILHMLPSLGSRIFEKANEIGLMNKGCVWIMT 113 (829)
Q Consensus 82 iIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t 113 (829)
|++++...+..+++..++.|+..++.+-|++
T Consensus 185 -i~~~~d~~a~g~~~~l~~~g~~ip~di~ii~ 215 (273)
T cd06292 185 -IVAASDLMALGAIRAARRRGLRVPEDVSVVG 215 (273)
T ss_pred -EEEcCcHHHHHHHHHHHHcCCCCCcceEEEe
Confidence 4455667777888999999976556555554
No 276
>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=69.79 E-value=47 Score=34.10 Aligned_cols=109 Identities=11% Similarity=0.075 Sum_probs=62.7
Q ss_pred hHHHHHHHHHHHHHcCCcEEEEEEEeCc--cc-cchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeE
Q 043276 5 DSSQVGAITAIIKAFGWREAVPIYVDNQ--YG-EELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRV 81 (829)
Q Consensus 5 D~~q~~ai~~ll~~fgW~~V~iI~~dd~--yG-~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arV 81 (829)
+..-+..+++.+..-|-++++++..... .. ..-.+.+.+.+++.|+.+..........+.....+.+.++.++..++
T Consensus 100 ~~~~g~~~~~~l~~~g~~~i~~l~~~~~~~~~~~~r~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~ 179 (267)
T cd06283 100 NYEAAKEAVDHLIEKGYERILFVTEPLDEISPRMERYEGFKEALAEHGIGVNEELIEIDDEDADELDERLRQLLNKPKKK 179 (267)
T ss_pred cHHHHHHHHHHHHHcCCCcEEEEecCccccccHHHHHHHHHHHHHHcCCCCCcceeEecccchHHHHHHHHHHHcCCCCC
Confidence 3445566777777779999999974432 11 24467778888888753322111111112233445555654443222
Q ss_pred -EEEEcChhHHHHHHHHHHHcCccccCeEEEEc
Q 043276 82 -FILHMLPSLGSRIFEKANEIGLMNKGCVWIMT 113 (829)
Q Consensus 82 -iIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t 113 (829)
.|++++...+..++..+++.|+..++.+-|.+
T Consensus 180 ~ai~~~~d~~a~g~~~~l~~~g~~vp~di~v~g 212 (267)
T cd06283 180 TAIFAANGLILLEVLKALKELGIRIPEDVGLIG 212 (267)
T ss_pred CEEEEcCcHHHHHHHHHHHHcCCCCccceEEEE
Confidence 34444566777888999999975555555443
No 277
>PRK13348 chromosome replication initiation inhibitor protein; Provisional
Probab=69.12 E-value=1.5e+02 Score=31.01 Aligned_cols=64 Identities=9% Similarity=0.047 Sum_probs=40.7
Q ss_pred HHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccEEEeccccccccceeccccccccccceEEEEEcc
Q 043276 343 DVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMIVPIK 421 (829)
Q Consensus 343 dll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv~~~ 421 (829)
..+..+.++ + .+++++.. +..++++..|.+|++|+++..... ....+. +.|+....+.++++..
T Consensus 107 ~~l~~~~~~-~-~i~i~~~~---------~~~~~~~~~L~~~~~d~~i~~~~~---~~~~~~-~~~l~~~~~~~v~~~~ 170 (294)
T PRK13348 107 PALAAVLAG-E-RILLELIV---------DDQDHTFALLERGEVVGCVSTQPK---PMRGCL-AEPLGTMRYRCVASPA 170 (294)
T ss_pred HHHHHHHhC-C-CeEEEEEE---------cchHHHHHHHhcCCeEEEEecCCc---ccCCcc-cccccccceEEEEccc
Confidence 445555444 2 45555544 246889999999999998743222 223444 5778888888887633
No 278
>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=68.74 E-value=43 Score=34.43 Aligned_cols=96 Identities=6% Similarity=-0.019 Sum_probs=56.8
Q ss_pred HHHHHHHHHHHHHc--CCcEEEEEEEe--CccccchHHHHHHHHHhC-CceeeeEEecCCCCChhHHHHHHHHhhcCCCe
Q 043276 6 SSQVGAITAIIKAF--GWREAVPIYVD--NQYGEELIPSLTDALQAI-DTRVPYRSVISPLATDDQIEKELYKLFTMQTR 80 (829)
Q Consensus 6 ~~q~~ai~~ll~~f--gW~~V~iI~~d--d~yG~~~~~~l~~~l~~~-gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~ar 80 (829)
...+..+++.+... |-+++++++.+ ..++....+.+.++++++ |+.+..... ...+.++....+.++.+...+
T Consensus 104 ~~~~~~~~~~l~~~~~g~~~i~~l~~~~~~~~~~~r~~g~~~~l~~~~~~~~~~~~~--~~~~~~~~~~~~~~~l~~~~~ 181 (268)
T cd06323 104 VAGGKMAAEYLVKLLGGKGKVVELQGIPGASAARERGKGFHEVVDKYPGLKVVASQP--ADFDRAKGLNVMENILQAHPD 181 (268)
T ss_pred HHHHHHHHHHHHHHhCCCceEEEEeCCCCCccHHHHHHHHHHHHHhCCCcEEEeccc--CCCCHHHHHHHHHHHHHHCCC
Confidence 33456777777665 78999999853 334556678888889884 776542111 111222333344444333332
Q ss_pred E-EEEEcChhHHHHHHHHHHHcCc
Q 043276 81 V-FILHMLPSLGSRIFEKANEIGL 103 (829)
Q Consensus 81 V-iIv~~~~~~~~~i~~~a~~~gm 103 (829)
. .|++.+...+..++..+++.|+
T Consensus 182 ~~ai~~~~d~~a~~~~~~l~~~g~ 205 (268)
T cd06323 182 IKGVFAQNDEMALGAIEALKAAGK 205 (268)
T ss_pred cCEEEEcCCchHHHHHHHHHHcCC
Confidence 2 3445555666678888999886
No 279
>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=68.32 E-value=26 Score=38.50 Aligned_cols=78 Identities=10% Similarity=0.016 Sum_probs=58.3
Q ss_pred HHHHHHHHHcCCcEEEEEEEeCccc-cchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcCh
Q 043276 10 GAITAIIKAFGWREAVPIYVDNQYG-EELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLP 88 (829)
Q Consensus 10 ~ai~~ll~~fgW~~V~iI~~dd~yG-~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~~ 88 (829)
+-+.++++.+| +++-+|+....+- .+..+.+.+.|++.|+.+.....+..+++.+++.+....+++.++++||-.+..
T Consensus 15 ~~l~~~~~~~g-~r~lvVt~~~~~~~~g~~~~v~~~L~~~g~~~~~~~~v~~~p~~~~v~~~~~~~~~~~~D~IIavGGG 93 (357)
T cd08181 15 EKHGEELAALG-KRALIVTGKSSAKKNGSLDDVTKALEELGIEYEIFDEVEENPSLETIMEAVEIAKKFNADFVIGIGGG 93 (357)
T ss_pred HHHHHHHHHcC-CEEEEEeCCchHhhcCcHHHHHHHHHHcCCeEEEeCCCCCCcCHHHHHHHHHHHHhcCCCEEEEeCCc
Confidence 34556788888 8888887544433 356788999999999877644445556667778888888899999999998765
No 280
>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=68.10 E-value=26 Score=38.87 Aligned_cols=86 Identities=15% Similarity=0.067 Sum_probs=58.6
Q ss_pred HHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcChh
Q 043276 10 GAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPS 89 (829)
Q Consensus 10 ~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~~~ 89 (829)
.-+.++++.+| +++-||+...-+..+..+.+.+.|++.|+.+.....+....+..++.+.+...++.++++||-.+...
T Consensus 12 ~~l~~~~~~~g-~~~livt~~~~~~~~~~~~v~~~L~~~~~~~~~f~~v~~~~~~~~v~~~~~~~~~~~~D~IIaiGGGS 90 (386)
T cd08191 12 RQLPRLAARLG-SRALIVTDERMAGTPVFAELVQALAAAGVEVEVFDGVLPDLPRSELCDAASAAARAGPDVIIGLGGGS 90 (386)
T ss_pred HHHHHHHHHcC-CeEEEEECcchhhcchHHHHHHHHHHcCCeEEEECCCCCCcCHHHHHHHHHHHHhcCCCEEEEeCCch
Confidence 34667788899 88888884433334778889999999998765443443333455666777777788999999887642
Q ss_pred --HHHHHHH
Q 043276 90 --LGSRIFE 96 (829)
Q Consensus 90 --~~~~i~~ 96 (829)
++..++.
T Consensus 91 ~iD~aK~ia 99 (386)
T cd08191 91 CIDLAKIAG 99 (386)
T ss_pred HHHHHHHHH
Confidence 4444443
No 281
>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=67.53 E-value=41 Score=34.54 Aligned_cols=104 Identities=11% Similarity=0.064 Sum_probs=58.7
Q ss_pred ChHHHHHHHHHHHHHcCCcEEEEEEEeCc--cccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcC--CC
Q 043276 4 NDSSQVGAITAIIKAFGWREAVPIYVDNQ--YGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTM--QT 79 (829)
Q Consensus 4 sD~~q~~ai~~ll~~fgW~~V~iI~~dd~--yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~--~a 79 (829)
++...+..+++.+..-|-++|+++....+ ......+.|.+.+++.|..+.....+....+.+...+.+.++.+. ..
T Consensus 100 d~~~~~~~~~~~l~~~g~~~i~~l~~~~~~~~~~~r~~gf~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~ 179 (268)
T cd06289 100 DNAAGARLATEHLISLGHRRIAFIGGLEDSSTRRERLAGYRAALAEAGLPFDSELVVEGPPSRQGGAEAVAQLLDLPPRP 179 (268)
T ss_pred cchHHHHHHHHHHHHCCCCCEEEecCCccccchHHHHHHHHHHHHHcCCCCCchhEEecCcchhhHHHHHHHHHcCCCCC
Confidence 33445566667666668899998874332 345567888888888875332111112111222333444444333 33
Q ss_pred eEEEEEcChhHHHHHHHHHHHcCccccCe
Q 043276 80 RVFILHMLPSLGSRIFEKANEIGLMNKGC 108 (829)
Q Consensus 80 rViIv~~~~~~~~~i~~~a~~~gm~~~~~ 108 (829)
++| ++.+...+..+++.+++.|+..++.
T Consensus 180 ~~i-~~~~~~~a~~~~~al~~~g~~~p~d 207 (268)
T cd06289 180 TAI-VCFNDLVAFGAMSGLRRAGLTPGRD 207 (268)
T ss_pred CEE-EEcCcHHHHHHHHHHHHcCCCCCcc
Confidence 443 3445556777888888988754433
No 282
>PRK11119 proX glycine betaine transporter periplasmic subunit; Provisional
Probab=67.30 E-value=37 Score=36.76 Aligned_cols=63 Identities=13% Similarity=0.127 Sum_probs=43.3
Q ss_pred CCCCceEEEecccccCccceEEEeecCCCCCceEEEeeHHHHHHHHHHCCCcc-cEEEEecCCCCCCCCCChhHHHHhHh
Q 043276 304 PTNEKKLRVGVPVKKGFSDFVKVTIDPKTQETSVVGYSIDVFKAVIEELPYAV-AYDFVPYAQPDGTSSGSYNDLIYQVF 382 (829)
Q Consensus 304 p~~~~~lrv~v~~~~~~~p~~~~~~~~~~~~~~~~G~~idll~~ia~~l~f~~-~~~~~~~~~~~g~~ng~~~~li~~l~ 382 (829)
|+.++++++|++ +|.. .-+.-.+++.+.+.+||++ ++ ++.+ -.-+...|.
T Consensus 25 ~~~~~~V~~~~~---~W~~---------------~~~~t~v~~~iLe~~GY~V~e~--~~~~---------~~~~~~ala 75 (331)
T PRK11119 25 PGKGITVQPAQS---TIAE---------------ETFQTLLVSRALEKLGYDVNKP--KEVD---------YNVFYTSIA 75 (331)
T ss_pred CCCCeEEEEeec---CccH---------------HHHHHHHHHHHHHHcCCceeee--cccC---------cHHHHHHHH
Confidence 677899999887 3321 1234567888888899865 44 3322 367788899
Q ss_pred cCcccEEEecccc
Q 043276 383 LGEFDAVVGDTTI 395 (829)
Q Consensus 383 ~g~~Di~~~~~~i 395 (829)
+|.+|+.+.....
T Consensus 76 ~GdiDv~~~~W~P 88 (331)
T PRK11119 76 NGDATFTAVNWFP 88 (331)
T ss_pred cCCCeEehhhccc
Confidence 9999998865543
No 283
>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=66.97 E-value=1.2e+02 Score=28.86 Aligned_cols=71 Identities=15% Similarity=0.029 Sum_probs=46.6
Q ss_pred EEeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccEEEeccccccccceeccccccccccceEEE
Q 043276 338 VGYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMI 417 (829)
Q Consensus 338 ~G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~v 417 (829)
..+-.+++..+.++.+ ++++++... +.+.++.+|.+|++|+++....... ...+ .+.++....++++
T Consensus 12 ~~~l~~~l~~~~~~~P-~v~i~i~~~---------~~~~~~~~l~~g~~D~~i~~~~~~~--~~~~-~~~~l~~~~~~~v 78 (195)
T cd08431 12 LQPLYPLIAEFYQLNK-ATRIRLSEE---------VLGGTWDALASGRADLVIGATGELP--PGGV-KTRPLGEVEFVFA 78 (195)
T ss_pred hHHHHHHHHHHHHHCC-CCceEEEEe---------ccchHHHHHhCCCCCEEEEecCCCC--CCce-EEEecccceEEEE
Confidence 3456788999999887 356666542 3568899999999999985321111 1122 2456667777777
Q ss_pred EEcc
Q 043276 418 VPIK 421 (829)
Q Consensus 418 v~~~ 421 (829)
++..
T Consensus 79 ~~~~ 82 (195)
T cd08431 79 VAPN 82 (195)
T ss_pred EcCC
Confidence 7743
No 284
>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=66.75 E-value=79 Score=32.93 Aligned_cols=98 Identities=10% Similarity=0.075 Sum_probs=57.7
Q ss_pred hHHHHHHHHHHHHH--cCCcEEEEEEEeCc-cccchHHHHHHHHHhC-CceeeeEEecCCCCChhHHHHHHHHhhcCCCe
Q 043276 5 DSSQVGAITAIIKA--FGWREAVPIYVDNQ-YGEELIPSLTDALQAI-DTRVPYRSVISPLATDDQIEKELYKLFTMQTR 80 (829)
Q Consensus 5 D~~q~~ai~~ll~~--fgW~~V~iI~~dd~-yG~~~~~~l~~~l~~~-gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~ar 80 (829)
+..-+..+++.|.. .|.+++++|..... ....-.+.+.+++++. |+.+.. .+....+.+.-...+.++.+...+
T Consensus 113 ~~~~g~~~~~~L~~~~~g~~~i~~l~~~~~~~~~~R~~gf~~al~~~~~~~~~~--~~~~~~~~~~~~~~~~~~l~~~~~ 190 (280)
T cd06303 113 HAAGARLLADYFIKRYPNHARYAMLYFSPGYISTARGDTFIDCVHARNNWTLTS--EFYTDATRQKAYQATSDILSNNPD 190 (280)
T ss_pred HHHHHHHHHHHHHHhcCCCcEEEEEECCCCcchhHHHHHHHHHHHhCCCceEEE--eecCCCCHHHHHHHHHHHHHhCCC
Confidence 33344566676655 79999999964332 2334467788888887 665432 122222222333344444333222
Q ss_pred E-EEEEcChhHHHHHHHHHHHcCcc
Q 043276 81 V-FILHMLPSLGSRIFEKANEIGLM 104 (829)
Q Consensus 81 V-iIv~~~~~~~~~i~~~a~~~gm~ 104 (829)
+ .|++++...+..++..+++.|+.
T Consensus 191 ~~ai~~~nd~~A~g~l~al~~~G~~ 215 (280)
T cd06303 191 VDFIYACSTDIALGASDALKELGRE 215 (280)
T ss_pred CcEEEECCcHHHHHHHHHHHHcCCC
Confidence 2 45566777788899999999973
No 285
>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=65.31 E-value=69 Score=32.87 Aligned_cols=106 Identities=13% Similarity=0.020 Sum_probs=60.5
Q ss_pred HHHHHHHHHHHHHcCCcEEEEEEEeCc---cccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCe-E
Q 043276 6 SSQVGAITAIIKAFGWREAVPIYVDNQ---YGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTR-V 81 (829)
Q Consensus 6 ~~q~~ai~~ll~~fgW~~V~iI~~dd~---yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~ar-V 81 (829)
...+..+++.+...|.++++++....+ ....-.+.|.+++++.|+.+.... .....+..+..+.+.++.+...+ -
T Consensus 97 ~~~g~~~~~~l~~~g~~~i~~i~~~~~~~~~~~~r~~gf~~~l~~~~~~~~~~~-~~~~~~~~~~~~~~~~~l~~~~~~~ 175 (265)
T cd06291 97 YEGGRLAAEELIERGCKHIAHIGGPNNTVSPTNLRYEGFLDVLKENGLEVRIIE-IQENFDDAEKKEEIKELLEEYPDID 175 (265)
T ss_pred HHHHHHHHHHHHHcCCcEEEEEccCcccccchHHHHHHHHHHHHHcCCCCChhe-eeccccchHHHHHHHHHHhCCCCCC
Confidence 444566777776679999999964332 344556788899998887643221 11111111223344444333222 2
Q ss_pred EEEEcChhHHHHHHHHHHHcCccccCeEEEE
Q 043276 82 FILHMLPSLGSRIFEKANEIGLMNKGCVWIM 112 (829)
Q Consensus 82 iIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~ 112 (829)
.|++.+...+..+++...+.|...++.+=|+
T Consensus 176 ai~~~~d~~a~~~~~al~~~g~~vp~di~v~ 206 (265)
T cd06291 176 GIFASNDLTAILVLKEAQQRGIRVPEDLQII 206 (265)
T ss_pred EEEECChHHHHHHHHHHHHcCCCCCcceEEe
Confidence 3444455677788888999886544444443
No 286
>cd08170 GlyDH Glycerol dehydrogenases (GlyDH) catalyzes oxidation of glycerol to dihydroxyacetone in glycerol dissmilation. Glycerol dehydrogenases (GlyDH) is a key enzyme in the glycerol dissimilation pathway . In anaerobic conditions, many microorganisms utilize glycerol as a source of carbon through coupled oxidative and reductive pathways. One of the pathways involves the oxidation of glycerol to dihydroxyacetone with the reduction of NAD+ to NADH catalyzed by glycerol dehydrogenases. Dihydroxyacetone is then phosphorylated by dihydroxyacetone kinase and enters the glycolytic pathway for further degradation. The activity of GlyDH is zinc-dependent. The zinc ion plays a role in stabilizing an alkoxide intermediate at the active site.
Probab=65.21 E-value=26 Score=38.35 Aligned_cols=76 Identities=14% Similarity=0.064 Sum_probs=57.5
Q ss_pred HHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcCh
Q 043276 10 GAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLP 88 (829)
Q Consensus 10 ~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~~ 88 (829)
..+.++++.++ +++.||+....+. +..+.+.+.|++.|+.+.+. .+....+.+++.+.+..+++.++++||-.+..
T Consensus 12 ~~l~~~~~~~~-~r~livt~~~~~~-~~~~~v~~~L~~~~i~~~~~-~~~~~p~~~~v~~~~~~~~~~~~D~IIavGGG 87 (351)
T cd08170 12 DELGEYLARLG-KRALIIADEFVLD-LVGAKIEESLAAAGIDARFE-VFGGECTRAEIERLAEIARDNGADVVIGIGGG 87 (351)
T ss_pred HHHHHHHHHhC-CeEEEEECHHHHH-HHHHHHHHHHHhCCCeEEEE-EeCCcCCHHHHHHHHHHHhhcCCCEEEEecCc
Confidence 34566777777 8888888444443 78888999999999887654 45556666778888888888899999998765
No 287
>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=65.17 E-value=82 Score=32.26 Aligned_cols=107 Identities=11% Similarity=0.089 Sum_probs=64.1
Q ss_pred ChHHHHHHHHHHHHHcCCcEEEEEEEeCccc--cchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCC-Ce
Q 043276 4 NDSSQVGAITAIIKAFGWREAVPIYVDNQYG--EELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQ-TR 80 (829)
Q Consensus 4 sD~~q~~ai~~ll~~fgW~~V~iI~~dd~yG--~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~-ar 80 (829)
++..-+..+++.+...|-++|+++..+.... ..-.+.+.+++++.|+.+... +..+.+.+...+.+.++.+.. .+
T Consensus 99 d~~~~g~~~~~~l~~~g~~~i~~i~~~~~~~~~~~r~~gf~~~l~~~~~~~~~~--~~~~~~~~~~~~~~~~~l~~~~~~ 176 (264)
T cd01574 99 DQEGGARLATEHLLELGHRTIAHVAGPEEWLSARARLAGWRAALEAAGIAPPPV--LEGDWSAESGYRAGRELLREGDPT 176 (264)
T ss_pred CcHHHHHHHHHHHHHCCCCEEEEEecCCccchHHHHHHHHHHHHHHCCCCccee--eecCCCHHHHHHHHHHHHhCCCCc
Confidence 3445566777888778999999997543322 234566888888888765422 222222223334444444332 33
Q ss_pred EEEEEcChhHHHHHHHHHHHcCccccCeEEEEc
Q 043276 81 VFILHMLPSLGSRIFEKANEIGLMNKGCVWIMT 113 (829)
Q Consensus 81 ViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t 113 (829)
.|++++...+..++..+++.|...++.+-|++
T Consensus 177 -ai~~~~d~~a~g~~~~~~~~g~~ip~~i~ii~ 208 (264)
T cd01574 177 -AVFAANDQMALGVLRALHELGLRVPDDVSVVG 208 (264)
T ss_pred -EEEEcCcHHHHHHHHHHHHcCCCCccceEEec
Confidence 45556667788899999998864454444443
No 288
>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=65.06 E-value=28 Score=38.54 Aligned_cols=79 Identities=14% Similarity=0.090 Sum_probs=58.8
Q ss_pred HHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcCh
Q 043276 10 GAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLP 88 (829)
Q Consensus 10 ~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~~ 88 (829)
..+.+.++.+|-+++.+|+...-+-.+..+.+.+.|++.|+.+.....+...++.+.+.+....+++.++++||-.+..
T Consensus 17 ~~l~~~l~~~g~~~~lvv~~~~~~~~~~~~~v~~~L~~~~~~~~~f~~v~~~p~~~~v~~~~~~~~~~~~D~IIavGGG 95 (377)
T cd08176 17 KEIGDELKNLGFKKALIVTDKGLVKIGVVEKVTDVLDEAGIDYVIYDGVKPNPTITNVKDGLAVFKKEGCDFIISIGGG 95 (377)
T ss_pred HHHHHHHHHhCCCeEEEECCchHhhcCcHHHHHHHHHHcCCeEEEeCCCCCCCCHHHHHHHHHHHHhcCCCEEEEeCCc
Confidence 4456778888888888887444333367888999999999876544445556667778888888888899999987764
No 289
>PRK09526 lacI lac repressor; Reviewed
Probab=64.97 E-value=78 Score=34.11 Aligned_cols=106 Identities=8% Similarity=-0.025 Sum_probs=63.6
Q ss_pred hHHHHHHHHHHHHHcCCcEEEEEEEeCc--cccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCe-E
Q 043276 5 DSSQVGAITAIIKAFGWREAVPIYVDNQ--YGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTR-V 81 (829)
Q Consensus 5 D~~q~~ai~~ll~~fgW~~V~iI~~dd~--yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~ar-V 81 (829)
+..-+..+++.|...|-+++++|..... ....-.+.+.+++++.|+.+... +....+.+.-.+.+.++.+...+ -
T Consensus 165 ~~~~~~~a~~~L~~~G~~~I~~l~g~~~~~~~~~R~~Gf~~al~~~gi~~~~~--~~~~~~~~~~~~~~~~~l~~~~~~~ 242 (342)
T PRK09526 165 PEDGTRLGVEHLVELGHQRIALLAGPESSVSARLRLAGWLEYLTDYQLQPIAV--REGDWSAMSGYQQTLQMLREGPVPS 242 (342)
T ss_pred cHHHHHHHHHHHHHCCCCeEEEEeCCCccccHHHHHHHHHHHHHHcCCCcceE--EeCCCchHHHHHHHHHHhcCCCCCc
Confidence 3344466677777779999999974322 22344677888999988764322 11111222222334444333222 2
Q ss_pred EEEEcChhHHHHHHHHHHHcCccccCeEEEE
Q 043276 82 FILHMLPSLGSRIFEKANEIGLMNKGCVWIM 112 (829)
Q Consensus 82 iIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~ 112 (829)
.|++++...+..++..+++.|+..++-+-|+
T Consensus 243 ai~~~~d~~A~g~~~al~~~g~~vP~disvi 273 (342)
T PRK09526 243 AILVANDQMALGVLRALHESGLRVPGQISVI 273 (342)
T ss_pred EEEEcCcHHHHHHHHHHHHcCCCCCCceEEE
Confidence 4556677788899999999998666555444
No 290
>cd06305 PBP1_methylthioribose_binding_like Methylthioribose-binding protein-like of ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily. Methylthioribose-binding protein-like of ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding. The sugar-binding domain of the periplasmic proteins in this group is also homologous to the ligand-binding domain of eukaryotic receptors such as metabotropic glutamate receptor (mGluR), DNA-binding transcriptional repressors such as LacI and GalR.
Probab=64.82 E-value=65 Score=33.22 Aligned_cols=101 Identities=10% Similarity=-0.063 Sum_probs=56.3
Q ss_pred ChHHHHHHHHHHHHH--cCCcEEEEEEEe-CccccchHHHHHHHHHhCC-ceeeeEEecCCCCChhHHHHHHHHhhcCCC
Q 043276 4 NDSSQVGAITAIIKA--FGWREAVPIYVD-NQYGEELIPSLTDALQAID-TRVPYRSVISPLATDDQIEKELYKLFTMQT 79 (829)
Q Consensus 4 sD~~q~~ai~~ll~~--fgW~~V~iI~~d-d~yG~~~~~~l~~~l~~~g-i~I~~~~~i~~~~~~~~~~~~l~~lk~~~a 79 (829)
++...+..+++.+.. -|.++|+++... ..........+.+.+++.+ +.+..........+.+...+.+.++.+...
T Consensus 101 d~~~~g~~~~~~l~~~~~g~~~i~~i~~~~~~~~~~R~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~ 180 (273)
T cd06305 101 DDYSLARLSLDQLVKDLGGKGNVGYVNVAGFPPLDRRYDVWQAVLKAYPGIKEVAELGDVSNNTAQDAAAQVEAVLKKYP 180 (273)
T ss_pred chHHHHHHHHHHHHHHhCCCCCEEEEEccCCchHHHHHHHHHHHHHHCCCcEEecccccccccchhHHHHHHHHHHHHCC
Confidence 445556666776644 589999999743 1123334556777788777 544322111111112233344555433333
Q ss_pred eE---EEEEcChhHHHHHHHHHHHcCcc
Q 043276 80 RV---FILHMLPSLGSRIFEKANEIGLM 104 (829)
Q Consensus 80 rV---iIv~~~~~~~~~i~~~a~~~gm~ 104 (829)
++ .|++.+...+..++..+++.|..
T Consensus 181 ~~~~~ai~~~~d~~a~g~~~~l~~~g~~ 208 (273)
T cd06305 181 KGGIDAIWAAWDEFAKGAKQALDEAGRT 208 (273)
T ss_pred CcccCeEEEcChhhhHHHHHHHHHcCCC
Confidence 32 44555666777888888998863
No 291
>PRK10537 voltage-gated potassium channel; Provisional
Probab=64.74 E-value=28 Score=38.63 Aligned_cols=56 Identities=20% Similarity=0.273 Sum_probs=43.2
Q ss_pred CccCccchhHHHHHHHhhhcC--ccccccchhHHHHHHHHHHHHHHHHHhHHHHHHHh
Q 043276 468 PARHQVGTSFWFSFSTMVFSQ--RERVISNLARFVVIVWCFVVLILIQSYTASLTSLL 523 (829)
Q Consensus 468 ~~~~~~~~~~~~~~~~l~~~~--~~~~~s~~~R~v~~~w~~~~lil~~~YtA~L~s~L 523 (829)
+...++.+++||++.++...| ...|.+..+|++.+++.++++.+..+..+.++..+
T Consensus 164 ~~~~s~~dA~y~svvt~tTvGyGdi~p~t~~grl~~i~~ii~Gi~vf~~~is~i~~p~ 221 (393)
T PRK10537 164 PPIESLSTAFYFSIVTMSTVGYGDIVPVSESARLFTISVIILGITVFATSISAIFGPV 221 (393)
T ss_pred cCCCCHHHHHHhhheeeecccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 445689999999998888666 34678889999999999998877766555555433
No 292
>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=64.66 E-value=1.2e+02 Score=29.39 Aligned_cols=100 Identities=8% Similarity=-0.007 Sum_probs=63.1
Q ss_pred HHHHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhC--CceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEE
Q 043276 8 QVGAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAI--DTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILH 85 (829)
Q Consensus 8 q~~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~--gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~ 85 (829)
....+.+.+..-+| .+.++....+ ..+.+.+.|++. |+.|+....-+ .+.++..+.+..|++++++++++.
T Consensus 36 l~~~l~~~~~~~~~-~ifllG~~~~----~~~~~~~~l~~~yP~l~ivg~~~g~--f~~~~~~~i~~~I~~~~pdiv~vg 108 (172)
T PF03808_consen 36 LFPDLLRRAEQRGK-RIFLLGGSEE----VLEKAAANLRRRYPGLRIVGYHHGY--FDEEEEEAIINRINASGPDIVFVG 108 (172)
T ss_pred HHHHHHHHHHHcCC-eEEEEeCCHH----HHHHHHHHHHHHCCCeEEEEecCCC--CChhhHHHHHHHHHHcCCCEEEEE
Confidence 34455555555566 6666665544 345555556654 66666543322 244567788889999999999999
Q ss_pred cChhHHHHHHHHHHHcCccccCeEEEEcCccc
Q 043276 86 MLPSLGSRIFEKANEIGLMNKGCVWIMTDGMT 117 (829)
Q Consensus 86 ~~~~~~~~i~~~a~~~gm~~~~~vwI~t~~~~ 117 (829)
+..+.-..++.+.++.. ..-+||...+..
T Consensus 109 lG~PkQE~~~~~~~~~l---~~~v~i~vG~~~ 137 (172)
T PF03808_consen 109 LGAPKQERWIARHRQRL---PAGVIIGVGGAF 137 (172)
T ss_pred CCCCHHHHHHHHHHHHC---CCCEEEEECchh
Confidence 88776667766665543 223788776543
No 293
>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=64.22 E-value=31 Score=38.23 Aligned_cols=78 Identities=9% Similarity=0.102 Sum_probs=57.4
Q ss_pred HHHHHHHHHcCCcEEEEEEEeCcc-ccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcCh
Q 043276 10 GAITAIIKAFGWREAVPIYVDNQY-GEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLP 88 (829)
Q Consensus 10 ~ai~~ll~~fgW~~V~iI~~dd~y-G~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~~ 88 (829)
+.+.++++.++ +++.||.....+ ..+..+.+.+.|++.|+++.....+..+++.+.+.+.+..++..++++||-.+..
T Consensus 18 ~~l~~~~~~~~-~r~livt~~~~~~~~~~~~~v~~~L~~~g~~~~~~~~v~~~p~~~~v~~~~~~~~~~~~D~IIaiGGG 96 (382)
T cd08187 18 SELGKELKKYG-KKVLLVYGGGSIKKNGLYDRVIASLKEAGIEVVELGGVEPNPRLETVREGIELCKEEKVDFILAVGGG 96 (382)
T ss_pred HHHHHHHHHhC-CEEEEEeCCcHHHhcCcHHHHHHHHHHcCCeEEEECCccCCCCHHHHHHHHHHHHHcCCCEEEEeCCh
Confidence 34567777776 888888643333 2456788999999999887644455556666778888888888999999987754
No 294
>PRK10094 DNA-binding transcriptional activator AllS; Provisional
Probab=63.99 E-value=2e+02 Score=30.51 Aligned_cols=69 Identities=12% Similarity=0.177 Sum_probs=45.6
Q ss_pred eHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccEEEeccccccccceeccccccccccceEEEEEc
Q 043276 341 SIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMIVPI 420 (829)
Q Consensus 341 ~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv~~ 420 (829)
-.+++..+.++.+. +++++.. ++-.++...|.+|++|++++... .......+. ..++....++++++.
T Consensus 108 l~~~l~~~~~~~P~-i~l~l~~---------~~~~~~~~~l~~g~~D~~i~~~~-~~~~~~~l~-~~~l~~~~~~~v~~~ 175 (308)
T PRK10094 108 VAQLLAWLNERYPF-TQFHISR---------QIYMGVWDSLLYEGFSLAIGVTG-TEALANTFS-LDPLGSVQWRFVMAA 175 (308)
T ss_pred HHHHHHHHHHhCCC-cEEEEEe---------ehhhhHHHHHhCCCccEEEeccc-CccccCCee-EEEecceeEEEEECC
Confidence 45788889888874 5666654 24578889999999999985321 111122233 357777788888864
Q ss_pred c
Q 043276 421 K 421 (829)
Q Consensus 421 ~ 421 (829)
.
T Consensus 176 ~ 176 (308)
T PRK10094 176 D 176 (308)
T ss_pred C
Confidence 3
No 295
>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=63.89 E-value=56 Score=33.40 Aligned_cols=107 Identities=12% Similarity=0.080 Sum_probs=64.4
Q ss_pred ChHHHHHHHHHHHHHcCCcEEEEEEEe-Cc--cccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCC-C
Q 043276 4 NDSSQVGAITAIIKAFGWREAVPIYVD-NQ--YGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQ-T 79 (829)
Q Consensus 4 sD~~q~~ai~~ll~~fgW~~V~iI~~d-d~--yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~-a 79 (829)
++...+..+++.+..-|-++++++... ++ .+....+.+.+.+++.|..... ......+.....+.+.++.+.. .
T Consensus 97 d~~~~~~~~~~~l~~~g~~~i~~v~~~~~~~~~~~~r~~gf~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~l~~~~~ 174 (259)
T cd01542 97 DDYGAGYELGEYLAQQGHKNIAYLGVSESDIAVGILRKQGYLDALKEHGICPPN--IVETDFSYESAYEAAQELLEPQPP 174 (259)
T ss_pred CcHHHHHHHHHHHHHcCCCcEEEEcCCcccchhHHHHHHHHHHHHHHcCCChHH--eeeccCchhhHHHHHHHHhcCCCC
Confidence 445566778888877899999998633 22 2344567788889888861111 1111111223334444444333 3
Q ss_pred eEEEEEcChhHHHHHHHHHHHcCccccCeEEEEc
Q 043276 80 RVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMT 113 (829)
Q Consensus 80 rViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t 113 (829)
++ |++++...+..+++.+++.|+..++.+.|.+
T Consensus 175 ~~-i~~~~d~~a~g~~~~l~~~g~~vp~di~v~g 207 (259)
T cd01542 175 DA-IVCATDTIALGAMKYLQELGRRIPEDISVAG 207 (259)
T ss_pred CE-EEEcCcHHHHHHHHHHHHcCCCCCCceEEEe
Confidence 44 4444566778899999999986666677664
No 296
>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=63.72 E-value=1.4e+02 Score=28.45 Aligned_cols=64 Identities=6% Similarity=0.007 Sum_probs=40.1
Q ss_pred eHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccEEEeccccccccceeccccccccccceEEEEE
Q 043276 341 SIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMIVP 419 (829)
Q Consensus 341 ~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv~ 419 (829)
...++..+.++ + .+++++... +.+.+...|.+|++|+++..-. .....+ .+.++......++++
T Consensus 15 l~~~l~~f~~~-~-~v~l~l~~~---------~~~~~~~~l~~~~~D~~i~~~~---~~~~~~-~~~~l~~~~~~~~~~ 78 (195)
T cd08428 15 FLPALAPVLKR-E-RILLDLIVD---------DEDRTHDLLRDGEVVGCISTQA---QPMQGC-RSDYLGSMDYLLVAS 78 (195)
T ss_pred hHHHHHHHHhC-c-CeEEEEEeC---------CchhHHHHHHcCcceEEEEecC---CCCCCc-eeEEeeeeeEEEEEC
Confidence 44567777776 3 566666542 4578899999999998774321 111222 245666667776665
No 297
>PRK10677 modA molybdate transporter periplasmic protein; Provisional
Probab=62.99 E-value=1.1e+02 Score=31.69 Aligned_cols=70 Identities=16% Similarity=0.161 Sum_probs=40.4
Q ss_pred HHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCc-ccEEEeccccccccc---eec-ccc-ccccccceE
Q 043276 342 IDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGE-FDAVVGDTTIVFNRS---NYV-DFT-LPYTESGVS 415 (829)
Q Consensus 342 idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~-~Di~~~~~~it~~R~---~~v-dft-~p~~~~~~~ 415 (829)
-+|.+.+.++.|.++++++- .-..+..++.+|. +|+.+++-.-..++. ..+ ..+ .+|....++
T Consensus 42 ~~l~~~Fe~~~g~~v~~~~~-----------~Sg~l~~qi~~g~~~Dv~~~a~~~~~~~l~~~gl~~~~~~~~~a~n~lv 110 (257)
T PRK10677 42 QDIAAQYKKEKGVDVVSSFA-----------SSSTLARQIEQGAPADLFISADQKWMDYAVDKKAIDTATRYTLLGNSLV 110 (257)
T ss_pred HHHHHHHHhhhCCeEEEEec-----------ccHHHHHHHHcCCCCCEEEECCHHHHHHHHHCCCCCCcchheeecCEEE
Confidence 44566666666655444432 1236777888877 999887642222222 222 221 357778888
Q ss_pred EEEEccC
Q 043276 416 MIVPIKD 422 (829)
Q Consensus 416 ~vv~~~~ 422 (829)
+++++..
T Consensus 111 l~~~~~~ 117 (257)
T PRK10677 111 VVAPKAS 117 (257)
T ss_pred EEEECCC
Confidence 9988654
No 298
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=62.76 E-value=95 Score=33.18 Aligned_cols=106 Identities=10% Similarity=-0.016 Sum_probs=63.4
Q ss_pred ChHHHHHHHHHHHHHcCCcEEEEEEEeCc--cccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcC--CC
Q 043276 4 NDSSQVGAITAIIKAFGWREAVPIYVDNQ--YGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTM--QT 79 (829)
Q Consensus 4 sD~~q~~ai~~ll~~fgW~~V~iI~~dd~--yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~--~a 79 (829)
++...+..+++.|...|-+++++|....+ .+..-.+.|.+++++.|+.+... .....+.++-.+.+.++.+. ..
T Consensus 162 d~~~~~~~a~~~L~~~G~r~I~~i~~~~~~~~~~~R~~Gf~~al~~~g~~~~~~--~~~~~~~~~~~~~~~~~l~~~~~~ 239 (328)
T PRK11303 162 DDQDDAEMLAESLLKFPAESILLLGALPELSVSFEREQGFRQALKDDPREVHYL--YANSFEREAGAQLFEKWLETHPMP 239 (328)
T ss_pred CCHHHHHHHHHHHHHCCCCeEEEEeCccccccHHHHHHHHHHHHHHcCCCceEE--EeCCCChHHHHHHHHHHHcCCCCC
Confidence 34445556667676679999999975433 23445678888999988754322 11111222333344454433 23
Q ss_pred eEEEEEcChhHHHHHHHHHHHcCccccCeEEEE
Q 043276 80 RVFILHMLPSLGSRIFEKANEIGLMNKGCVWIM 112 (829)
Q Consensus 80 rViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~ 112 (829)
. .|++++...+..++..+.+.|+..++-+=|+
T Consensus 240 ~-ai~~~~d~~A~g~~~al~~~g~~vP~disv~ 271 (328)
T PRK11303 240 D-ALFTTSYTLLQGVLDVLLERPGELPSDLAIA 271 (328)
T ss_pred C-EEEEcCcHHHHHHHHHHHHcCCCCCCceEEE
Confidence 4 4555566678888999999997555544443
No 299
>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=62.16 E-value=60 Score=33.28 Aligned_cols=104 Identities=13% Similarity=0.091 Sum_probs=59.5
Q ss_pred HHHHHHHHHHcCCcEEEEEEEeCc--cccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEc
Q 043276 9 VGAITAIIKAFGWREAVPIYVDNQ--YGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHM 86 (829)
Q Consensus 9 ~~ai~~ll~~fgW~~V~iI~~dd~--yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~ 86 (829)
+..+++.+...|-++|++|..... ....-...+.+++++.|+.+..........+.+.....+.++.+...+ .|+++
T Consensus 104 ~~~~~~~l~~~g~~~I~~i~~~~~~~~~~~R~~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~-av~~~ 182 (265)
T cd06299 104 MTEAVSLLVALGHKKIGYISGPQDTSTGRERLEAFRQACASLGLEVNEDLVVLGGYSQESGYAGATKLLDQGAT-AIIAG 182 (265)
T ss_pred HHHHHHHHHHcCCCcEEEEeCCCCcccHHHHHHHHHHHHHHCCCCCChHhEEecCcchHHHHHHHHHHHcCCCC-EEEEc
Confidence 344556666679999999964332 223445678888888885432211111111122233444454433445 45556
Q ss_pred ChhHHHHHHHHHHHcCccccCeEEEEc
Q 043276 87 LPSLGSRIFEKANEIGLMNKGCVWIMT 113 (829)
Q Consensus 87 ~~~~~~~i~~~a~~~gm~~~~~vwI~t 113 (829)
+...+..++..+++.|+..++-+-|++
T Consensus 183 ~d~~a~gv~~al~~~g~~vp~dv~v~g 209 (265)
T cd06299 183 DSMMTIGAIRAIHDAGLVIGEDISLIG 209 (265)
T ss_pred CcHHHHHHHHHHHHhCCCCCcceeEEE
Confidence 666788888999999976555555554
No 300
>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=61.88 E-value=2.1e+02 Score=29.95 Aligned_cols=63 Identities=13% Similarity=0.058 Sum_probs=40.5
Q ss_pred HHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccEEEeccccccccceeccccccccccceEEEEEc
Q 043276 343 DVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMIVPI 420 (829)
Q Consensus 343 dll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv~~ 420 (829)
.++..+.++. .+++..... +-..++..|.+|++|+++...... ...+. +.|+.+...+++++.
T Consensus 107 ~~l~~~~~~~--~i~i~l~~~---------~~~~~~~~l~~g~~d~~i~~~~~~---~~~l~-~~~l~~~~~~~v~~~ 169 (292)
T TIGR03298 107 PALAPVLAQE--GVLLDLVVE---------DQDHTAELLRSGEVLGAVTTQAKP---VQGCR-VVPLGAMRYLAVASP 169 (292)
T ss_pred HHHHHHHhCC--CceEEEEeC---------cchhHHHHHhCCCceEEEecCCCC---CCCce-EEecCCceEEEEECc
Confidence 4566666653 455555442 346788999999999998543222 22333 467888888888764
No 301
>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=61.79 E-value=72 Score=33.29 Aligned_cols=106 Identities=16% Similarity=0.139 Sum_probs=62.2
Q ss_pred ChHHHHHHHHHHHHHcCCcEEEEEEEeC-------------------ccccchHHHHHHHHHhCCceeeeEEecCC-CCC
Q 043276 4 NDSSQVGAITAIIKAFGWREAVPIYVDN-------------------QYGEELIPSLTDALQAIDTRVPYRSVISP-LAT 63 (829)
Q Consensus 4 sD~~q~~ai~~ll~~fgW~~V~iI~~dd-------------------~yG~~~~~~l~~~l~~~gi~I~~~~~i~~-~~~ 63 (829)
++...+..+++.|...|-++++++..+. .......+.+.+++++.|+.+.....+.. ..+
T Consensus 99 d~~~~g~~~~~~L~~~g~~~i~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~R~~gf~~~~~~~~~~~~~~~~~~~~~~~ 178 (283)
T cd06279 99 DDRAAAREAARHLLDLGHRRIGILGLRLGRDRNTGRVTDERLASATFSVARERLEGYLEALEEAGIDISDVPIWEIPEND 178 (283)
T ss_pred CcHHHHHHHHHHHHHcCCCcEEEecCcccccccccccccccccccccccHHHHHHHHHHHHHHcCCCCChheEEecCCCc
Confidence 3445566677888778999999997532 11234467788888888865422111111 112
Q ss_pred hhHHHHHHHHhhcCCCe-EEEEEcChhHHHHHHHHHHHcCccccCeE
Q 043276 64 DDQIEKELYKLFTMQTR-VFILHMLPSLGSRIFEKANEIGLMNKGCV 109 (829)
Q Consensus 64 ~~~~~~~l~~lk~~~ar-ViIv~~~~~~~~~i~~~a~~~gm~~~~~v 109 (829)
.+...+.+.++.++..+ -.|++++...+..+++.+++.|+..++.+
T Consensus 179 ~~~~~~~~~~~l~~~~~~~ai~~~~d~~a~gv~~al~~~g~~ip~di 225 (283)
T cd06279 179 RASGEEAARELLDASPRPTAILCMSDVLALGALQVARELGLRVPEDL 225 (283)
T ss_pred hHHHHHHHHHHHcCCCCCcEEEECCcHHHHHHHHHHHHcCCCCCCce
Confidence 23344455555433322 23555666777889999999997544433
No 302
>PRK11139 DNA-binding transcriptional activator GcvA; Provisional
Probab=61.71 E-value=2e+02 Score=30.17 Aligned_cols=101 Identities=10% Similarity=0.013 Sum_probs=51.1
Q ss_pred CCHHHHHhCCCcE-EEEeCchHHHHHHhcCCC---ccceeecCChHHHHHHHhcCCcCCceeEEEcchhHHHHHHhcCCC
Q 043276 533 TDVNLLIKRGDNV-GYQKGSFVLGILKQLGFD---ERKLVVYNSHEECDELFQKGSANGGIAAAFDEIPYAKLLIGQHCS 608 (829)
Q Consensus 533 ~s~~dL~~~~~~v-g~~~~s~~~~~l~~~~~~---~~~~~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~~c~ 608 (829)
-+++||. +.++ ....+.....++...+.. ......+++.+...+++..|. .-+++.+. ..........
T Consensus 181 i~~~dL~--~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~----gi~~lp~~-~~~~~~~~~~- 252 (297)
T PRK11139 181 KTPEDLA--RHTLLHDDSREDWRAWFRAAGLDDLNVQQGPIFSHSSMALQAAIHGQ----GVALGNRV-LAQPEIEAGR- 252 (297)
T ss_pred CCHHHhh--cCceEeecCcccHHHHHHHhCCCCcCcccceeeCCHHHHHHHHHhCC----CeEecchh-hhHHHHHCCc-
Confidence 4688886 3333 333333445566554442 111235677777788888876 44454433 3333333322
Q ss_pred ceEEeCccc-ccCCceeeecCCCCchhhHHHHHH
Q 043276 609 KYTMVEPTF-KTAGFGFAFPLHSPLVHDVSKAIL 641 (829)
Q Consensus 609 ~l~~v~~~~-~~~~~~~~~~k~spl~~~in~~il 641 (829)
....+.+.. ....+.++.+|+.+....+...+.
T Consensus 253 l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~f~~ 286 (297)
T PRK11139 253 LVCPFDTVLPSPNAFYLVCPDSQAELPKVAAFRQ 286 (297)
T ss_pred eecccccCcCCCccEEEEeccccccChhHHHHHH
Confidence 011222222 235678888887665555544443
No 303
>PRK14498 putative molybdopterin biosynthesis protein MoeA/LysR substrate binding-domain-containing protein; Provisional
Probab=61.67 E-value=57 Score=38.95 Aligned_cols=67 Identities=12% Similarity=0.132 Sum_probs=47.6
Q ss_pred cCCcEEEEEEEeCcc---------c---cchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEc
Q 043276 19 FGWREAVPIYVDNQY---------G---EELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHM 86 (829)
Q Consensus 19 fgW~~V~iI~~dd~y---------G---~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~ 86 (829)
|.--+|+||.+.|+- | ......|...+++.|..+.....++++ .+.+.+.+.+..+ ++++||..+
T Consensus 184 ~~~prv~vi~tG~El~~~~~~~~~g~i~dsn~~~l~~~l~~~g~~~~~~~~v~Dd--~~~i~~~l~~~~~-~~D~iIttG 260 (633)
T PRK14498 184 YKKPRVGIISTGDELVEPGEPLKPGKIYDVNSYTLAAAVEEAGGEPVRYGIVPDD--EEELEAALRKALK-ECDLVLLSG 260 (633)
T ss_pred ecCcEEEEEecCccccCCCCCCCCCEEEEChHHHHHHHHHHCCCEEEEEEEeCCC--HHHHHHHHHHHHh-cCCEEEECC
Confidence 334577888776552 2 245678888899999988877777654 4567777777654 789999987
Q ss_pred Ch
Q 043276 87 LP 88 (829)
Q Consensus 87 ~~ 88 (829)
..
T Consensus 261 G~ 262 (633)
T PRK14498 261 GT 262 (633)
T ss_pred CC
Confidence 65
No 304
>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=61.58 E-value=20 Score=36.80 Aligned_cols=78 Identities=15% Similarity=0.184 Sum_probs=57.4
Q ss_pred EEEEE--EeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEc-ChhHHHHHHHHHHH
Q 043276 24 AVPIY--VDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHM-LPSLGSRIFEKANE 100 (829)
Q Consensus 24 V~iI~--~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~-~~~~~~~i~~~a~~ 100 (829)
|++|. .++.|.......+.+++++.|..+... .+...+.....+.+.++.+.+++.||+.. .++....++.++.+
T Consensus 1 I~vi~~~~~~~~~~~~~~g~~~~a~~~g~~~~~~--~~~~~d~~~q~~~i~~~i~~~~d~Iiv~~~~~~~~~~~l~~~~~ 78 (257)
T PF13407_consen 1 IGVIVPSMDNPFWQQVIKGAKAAAKELGYEVEIV--FDAQNDPEEQIEQIEQAISQGVDGIIVSPVDPDSLAPFLEKAKA 78 (257)
T ss_dssp EEEEESSSSSHHHHHHHHHHHHHHHHHTCEEEEE--EESTTTHHHHHHHHHHHHHTTESEEEEESSSTTTTHHHHHHHHH
T ss_pred cEEEeCCCCCHHHHHHHHHHHHHHHHcCCEEEEe--CCCCCCHHHHHHHHHHHHHhcCCEEEecCCCHHHHHHHHHHHhh
Confidence 34554 456688888999999999999887765 23333444555677777778899888874 55677789999999
Q ss_pred cCc
Q 043276 101 IGL 103 (829)
Q Consensus 101 ~gm 103 (829)
.|+
T Consensus 79 ~gI 81 (257)
T PF13407_consen 79 AGI 81 (257)
T ss_dssp TTS
T ss_pred cCc
Confidence 885
No 305
>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=61.51 E-value=98 Score=32.15 Aligned_cols=107 Identities=9% Similarity=-0.003 Sum_probs=64.4
Q ss_pred HHHHHHHHHHHHHcCCcEEEEEEEeC--ccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCC-eEE
Q 043276 6 SSQVGAITAIIKAFGWREAVPIYVDN--QYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQT-RVF 82 (829)
Q Consensus 6 ~~q~~ai~~ll~~fgW~~V~iI~~dd--~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~a-rVi 82 (829)
..-+..+++.+...|-+++++|.... ..+..-...+.+++++.|+..... .+....+.++-.+.+.++.+... --.
T Consensus 103 ~~~~~~a~~~L~~~G~~~I~~i~~~~~~~~~~~R~~gf~~a~~~~g~~~~~~-~~~~~~~~~~~~~~~~~~l~~~~~~~a 181 (269)
T cd06287 103 AATARMLLEHLRAQGARQIALIVGSARRNSYLEAEAAYRAFAAEHGMPPVVL-RVDEAGGEEAGYAACAQLLAQHPDLDA 181 (269)
T ss_pred HHHHHHHHHHHHHcCCCcEEEEeCCcccccHHHHHHHHHHHHHHcCCCccee-EecCCCChHHHHHHHHHHHhCCCCCCE
Confidence 34445666777777999999996432 233445677888899888753321 11111122233344445433322 134
Q ss_pred EEEcChhHHHHHHHHHHHcCccccCeEEEEc
Q 043276 83 ILHMLPSLGSRIFEKANEIGLMNKGCVWIMT 113 (829)
Q Consensus 83 Iv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t 113 (829)
|++.+...+..++..+++.|+..++-+=|++
T Consensus 182 i~~~~d~~A~gvl~al~~~gl~vP~dvsvig 212 (269)
T cd06287 182 LCVPVDAFAVGAVRAATELGRAVPDQLRVVT 212 (269)
T ss_pred EEEcCcHHHHHHHHHHHHcCCCCCCceEEEe
Confidence 5566778888999999999986666555443
No 306
>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=61.30 E-value=77 Score=33.93 Aligned_cols=102 Identities=8% Similarity=0.012 Sum_probs=60.9
Q ss_pred HHHHHHHHHHHHcCCcEEEEEEEeCc--cccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcC-C--CeE
Q 043276 7 SQVGAITAIIKAFGWREAVPIYVDNQ--YGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTM-Q--TRV 81 (829)
Q Consensus 7 ~q~~ai~~ll~~fgW~~V~iI~~dd~--yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~-~--arV 81 (829)
.-+..+++.+...|.+++++|....+ ....-.+.+.+++++.|+.+... +....+.+.-.+.+.++.+. . ..
T Consensus 164 ~~~~~~~~~L~~~G~~~I~~i~~~~~~~~~~~R~~Gf~~al~~~~~~~~~~--~~~~~~~~~~~~~~~~ll~~~~~~~~- 240 (327)
T TIGR02417 164 DAAAELIERLLSQHADEFWYLGAQPELSVSRDRLAGFRQALKQATLEVEWV--YGGNYSRESGYQMFAKLCARLGRLPQ- 240 (327)
T ss_pred HHHHHHHHHHHHCCCCeEEEEeCcccchhHHHHHHHHHHHHHHcCCChHhE--EeCCCChHHHHHHHHHHHhcCCCCCc-
Confidence 33445556666679999999974433 23445677888899888753221 11111222233444454432 2 34
Q ss_pred EEEEcChhHHHHHHHHHHHcCccccCeEEEE
Q 043276 82 FILHMLPSLGSRIFEKANEIGLMNKGCVWIM 112 (829)
Q Consensus 82 iIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~ 112 (829)
.|+|.+...+..+++.+++.| ..++.+-|+
T Consensus 241 Ai~~~~D~~A~g~~~al~~~g-~vP~dvsvi 270 (327)
T TIGR02417 241 ALFTTSYTLLEGVLDYMLERP-LLDSQLHLA 270 (327)
T ss_pred EEEEcCcHHHHHHHHHHHHcC-CCCCcceEE
Confidence 455566778888999999999 666555544
No 307
>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=61.11 E-value=1.2e+02 Score=31.50 Aligned_cols=99 Identities=6% Similarity=-0.071 Sum_probs=59.1
Q ss_pred CChHHHHHHHHHHHHHc--CCcEEEEEEEeCcc--ccchHHHHHHHHHhCC-ceeeeEEecCCCCChhHHHHHHHHhhcC
Q 043276 3 LNDSSQVGAITAIIKAF--GWREAVPIYVDNQY--GEELIPSLTDALQAID-TRVPYRSVISPLATDDQIEKELYKLFTM 77 (829)
Q Consensus 3 psD~~q~~ai~~ll~~f--gW~~V~iI~~dd~y--G~~~~~~l~~~l~~~g-i~I~~~~~i~~~~~~~~~~~~l~~lk~~ 77 (829)
+++..-+..+++.+... |.++++++..+... ...-.+.+.+.+++.+ ..+.. ......+.+...+.+.++.+.
T Consensus 103 ~d~~~~g~~~~~~l~~~~~g~~~i~~l~g~~~~~~~~~R~~gf~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~l~~ 180 (272)
T cd06313 103 PDNYFMGASVAQALCNAMGGKGKIAMLQGALGHTGAQGRAQGFNDVIKKYPDIEVVD--EQPANWDVSKAARIWETWLTK 180 (272)
T ss_pred CCcHHHHHHHHHHHHHHcCCCceEEEEECCCCCcchhHHHHHHHHHHHhCCCCEEEe--ccCCCCCHHHHHHHHHHHHHh
Confidence 34445566777777555 89999999754332 2345778888888875 55432 112222222333445554333
Q ss_pred CCe-EEEEEcChhHHHHHHHHHHHcCc
Q 043276 78 QTR-VFILHMLPSLGSRIFEKANEIGL 103 (829)
Q Consensus 78 ~ar-ViIv~~~~~~~~~i~~~a~~~gm 103 (829)
..+ -.|++.+...+..+++.+++.|+
T Consensus 181 ~~~~~ai~~~nd~~a~g~~~al~~~g~ 207 (272)
T cd06313 181 YPQLDGAFCHNDSMALAAYQIMKAAGR 207 (272)
T ss_pred CCCCCEEEECCCcHHHHHHHHHHHcCC
Confidence 222 24555667777888899999986
No 308
>PF01634 HisG: ATP phosphoribosyltransferase; InterPro: IPR013820 ATP phosphoribosyltransferase (2.4.2.17 from EC) is the enzyme that catalyzes the first step in the biosynthesis of histidine in bacteria, fungi and plants as shown below. It is a member of the larger phosphoribosyltransferase superfamily of enzymes which catalyse the condensation of 5-phospho-alpha-D-ribose 1-diphosphate with nitrogenous bases in the presence of divalent metal ions []. ATP + 5-phospho-alpha-D-ribose 1-diphosphate = 1-(5-phospho-D-ribosyl)-ATP + diphosphate Histidine biosynthesis is an energetically expensive process and ATP phosphoribosyltransferase activity is subject to control at several levels. Transcriptional regulation is based primarily on nutrient conditions and determines the amount of enzyme present in the cell, while feedback inihibition rapidly modulates activity in response to cellular conditions. The enzyme has been shown to be inhibited by 1-(5-phospho-D-ribosyl)-ATP, histidine, ppGpp (a signal associated with adverse environmental conditions) and ADP and AMP (which reflect the overall energy status of the cell). As this pathway of histidine biosynthesis is present only in prokayrotes, plants and fungi, this enzyme is a promising target for the development of novel antimicrobial compounds and herbicides. ATP phosphoribosyltransferase is found in two distinct forms: a long form containing two catalytic domains and a C-terminal regulatory domain, and a short form in which the regulatory domain is missing. The long form is catalytically competent, but in organisms with the short form, a histidyl-tRNA synthetase paralogue, HisZ, is required for enzyme activity []. This entry represents the catalytic region of this enzyme. The structures of the long form enzymes from Escherichia coli (P60757 from SWISSPROT) and Mycobacterium tuberculosis (P60759 from SWISSPROT) have been determined [, ]. The enzyme itself exists in equilibrium between an active dimeric form, an inactive hexameric form and higher aggregates. Interconversion between the various forms is largely reversible and is influenced by the binding of the natural substrates and inhibitors of the enzyme. The two catalytic domains are linked by a two-stranded beta-sheet and togther form a "periplasmic binding protein fold". A crevice between these domains contains the active site. The C-terminal domain is not directly involved in catalysis but appears to be involved the formation of hexamers, induced by the binding of inhibitors such as histidine to the enzyme, thus regulating activity.; GO: 0003879 ATP phosphoribosyltransferase activity, 0000105 histidine biosynthetic process, 0005737 cytoplasm; PDB: 1VE4_A 2VD3_B 1NH7_A 1NH8_A 1Z7N_G 1Z7M_E 1O64_A 1O63_A 1USY_F 1Q1K_A ....
Probab=60.96 E-value=16 Score=34.98 Aligned_cols=100 Identities=12% Similarity=0.075 Sum_probs=56.3
Q ss_pred CCCHHHHHhCCCcEEEEeCchHHHHHHhcCCCccceeecCChHHHHHHHhcCCcCCceeEEEcchhHHHHHHhcCCCceE
Q 043276 532 ITDVNLLIKRGDNVGYQKGSFVLGILKQLGFDERKLVVYNSHEECDELFQKGSANGGIAAAFDEIPYAKLLIGQHCSKYT 611 (829)
Q Consensus 532 I~s~~dL~~~~~~vg~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~~c~~l~ 611 (829)
+.+++||.. +.+|+...-...+.||++.+.+-.-+....+.| .. ...|- .|++++-.....-+.++ +|.
T Consensus 58 ~~~~~~l~~-~~rIATkyp~l~~~yf~~~g~~~~ii~l~GsvE-~a--p~~gl----AD~IvDiv~TG~TLr~N---gL~ 126 (163)
T PF01634_consen 58 YKSVEDLKA-GLRIATKYPNLTRRYFAEKGINVEIIKLSGSVE-LA--PPLGL----ADAIVDIVETGTTLRAN---GLK 126 (163)
T ss_dssp GCCGGGGSS-TEEEEES-HHHHHHHHHHCT-EEEEEE-SS-TT-HH--HHTTS----SSEEEEEESSSHHHHHT---TEE
T ss_pred CCCHHHhcc-CCEEEECCHHHHHHHHHHcCCcEEEEEccCCcc-cc--CCCCC----CCEEEEeccCcHHHHHC---CCE
Confidence 477888842 678988777788899998776433333344444 33 34455 78887766555444444 356
Q ss_pred EeCcccccCCceeeecCCCC--chhhHHHHHHhh
Q 043276 612 MVEPTFKTAGFGFAFPLHSP--LVHDVSKAILNV 643 (829)
Q Consensus 612 ~v~~~~~~~~~~~~~~k~sp--l~~~in~~il~l 643 (829)
.++..+. ....+...|.+. -.+.+++.+.+|
T Consensus 127 ~i~~i~~-s~a~LI~n~~~~~~k~~~i~~l~~~l 159 (163)
T PF01634_consen 127 EIETILE-SSARLIANKASLKEKEEKIDELVTRL 159 (163)
T ss_dssp EEEEEEE-EEEEEEEEHHHHHHCHHHHHHHHHHH
T ss_pred EeEEEEE-EEEEEEEcCccchhhHHHHHHHHHHH
Confidence 6655444 444555555543 223455555554
No 309
>KOG3857 consensus Alcohol dehydrogenase, class IV [Energy production and conversion]
Probab=60.91 E-value=38 Score=35.91 Aligned_cols=77 Identities=16% Similarity=0.075 Sum_probs=63.8
Q ss_pred HHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcCh
Q 043276 12 ITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLP 88 (829)
Q Consensus 12 i~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~~ 88 (829)
+++-++..|.+++-+|.+-+---....+..++.|+++||.+.........++...+...+.-.|+...+.+|-.+..
T Consensus 61 vg~dikn~gaKk~llvTDkni~~~~~~~~a~~~L~~~~I~~~vyD~v~~ePtv~s~~~alefak~~~fDs~vaiGGG 137 (465)
T KOG3857|consen 61 VGDDIKNLGAKKTLLVTDKNIAKLGLVKVAQDSLEENGINVEVYDKVQPEPTVGSVTAALEFAKKKNFDSFVAIGGG 137 (465)
T ss_pred HHHHHHhcCccceEEeeCCChhhcccHHHHHHHHHHcCCceEEecCccCCCchhhHHHHHHHHHhcccceEEEEcCc
Confidence 44567899999999999777777788899999999999998876666667777788999988888888888877654
No 310
>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=60.75 E-value=38 Score=37.57 Aligned_cols=87 Identities=14% Similarity=0.077 Sum_probs=60.4
Q ss_pred HHHHHHHHHc---CCcEEEEEEEeCccc-cchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEE
Q 043276 10 GAITAIIKAF---GWREAVPIYVDNQYG-EELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILH 85 (829)
Q Consensus 10 ~ai~~ll~~f---gW~~V~iI~~dd~yG-~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~ 85 (829)
+.+.++++.+ |.+++.+|+....+. .+..+.+.+.|++.|+.+.....+.++.+.+.+.+.+..+++.++++||-.
T Consensus 12 ~~l~~~l~~~~~~g~kr~livtd~~~~~~~g~~~~v~~~L~~~gi~~~~f~~v~~~p~~~~v~~~~~~~~~~~~D~IIai 91 (383)
T cd08186 12 EKIGEILKDLKSKGISKVLLVTGKSAYKKSGAWDKVEPALDEHGIEYVLYNKVTPNPTVDQVDEAAKLGREFGAQAVIAI 91 (383)
T ss_pred HHHHHHHHHhcccCCCEEEEEcCccHHhhcChHHHHHHHHHHcCCeEEEeCCCCCCCCHHHHHHHHHHHHHcCCCEEEEe
Confidence 3455667776 888998887444333 355788999999999876544445556666778888888888899999987
Q ss_pred cCh--hHHHHHHH
Q 043276 86 MLP--SLGSRIFE 96 (829)
Q Consensus 86 ~~~--~~~~~i~~ 96 (829)
+.. -++..++.
T Consensus 92 GGGS~iD~aK~ia 104 (383)
T cd08186 92 GGGSPIDSAKSAA 104 (383)
T ss_pred CCccHHHHHHHHH
Confidence 653 34444443
No 311
>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=60.66 E-value=42 Score=36.97 Aligned_cols=85 Identities=12% Similarity=0.121 Sum_probs=59.8
Q ss_pred HHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcCh-
Q 043276 10 GAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLP- 88 (829)
Q Consensus 10 ~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~~- 88 (829)
.-+.++++.+|-+++.||+....+ ..+.+.+.|++.|+.+.....+..+++.+.+.+.+..+++.++++||-.+..
T Consensus 12 ~~l~~~~~~~g~~~~livtd~~~~---~~~~~~~~l~~~~~~~~~~~~~~~~p~~~~v~~~~~~~~~~~~D~IIavGGGs 88 (367)
T cd08182 12 AKLPSLLKGLGGKRVLLVTGPRSA---IASGLTDILKPLGTLVVVFDDVQPNPDLEDLAAGIRLLREFGPDAVLAVGGGS 88 (367)
T ss_pred HHHHHHHHhcCCCeEEEEeCchHH---HHHHHHHHHHHcCCeEEEEcCcCCCcCHHHHHHHHHHHHhcCcCEEEEeCCcH
Confidence 346677888899999999855444 4566778888888766544445556666678888888888899999987754
Q ss_pred -hHHHHHHHH
Q 043276 89 -SLGSRIFEK 97 (829)
Q Consensus 89 -~~~~~i~~~ 97 (829)
-++..++..
T Consensus 89 ~~D~aK~ia~ 98 (367)
T cd08182 89 VLDTAKALAA 98 (367)
T ss_pred HHHHHHHHHH
Confidence 344444443
No 312
>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=60.52 E-value=1e+02 Score=31.87 Aligned_cols=96 Identities=10% Similarity=-0.001 Sum_probs=52.4
Q ss_pred HHHHHHHHHH-HHcCC--cEEEEEEEeCc--cccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhc--CCC
Q 043276 7 SQVGAITAII-KAFGW--REAVPIYVDNQ--YGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFT--MQT 79 (829)
Q Consensus 7 ~q~~ai~~ll-~~fgW--~~V~iI~~dd~--yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~--~~a 79 (829)
.-+..+++.+ +.+|. +++++|..... ....-.+.+.+++++.+..+.....+....+.+.....+.++.+ ...
T Consensus 108 ~~g~~~~~~l~~~~g~~~~~i~~i~~~~~~~~~~~R~~gf~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~ 187 (275)
T cd06307 108 AAGRTAAWLIGRFLGRRPGKVAVLAGSHRFRGHEEREMGFRSVLREEFPGLRVLETLEGLDDPARAYEATRKLLARHPDL 187 (275)
T ss_pred HHHHHHHHHHHHHhCCCCCeEEEEecCCCCcchHHHHHHHHHHHHhhCCCcEEEeeccCCCChHHHHHHHHHHHHhCCCc
Confidence 3344445555 44465 59998875432 22344677888888877544333222222222233344445432 234
Q ss_pred eEEEEEcChhHHHHHHHHHHHcCcc
Q 043276 80 RVFILHMLPSLGSRIFEKANEIGLM 104 (829)
Q Consensus 80 rViIv~~~~~~~~~i~~~a~~~gm~ 104 (829)
++|++..+ . +..++..+++.|+.
T Consensus 188 ~ai~~~~d-~-~~g~~~al~~~g~~ 210 (275)
T cd06307 188 VGIYNAGG-G-NRGVIRALREAGRA 210 (275)
T ss_pred eEEEECCC-C-hHHHHHHHHHcCCC
Confidence 55555543 3 46888899999963
No 313
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=60.09 E-value=77 Score=34.04 Aligned_cols=108 Identities=9% Similarity=-0.072 Sum_probs=62.5
Q ss_pred hHHHHHHHHHHHHHcCCcEEEEEEEeCc-cccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCe-EE
Q 043276 5 DSSQVGAITAIIKAFGWREAVPIYVDNQ-YGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTR-VF 82 (829)
Q Consensus 5 D~~q~~ai~~ll~~fgW~~V~iI~~dd~-yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~ar-Vi 82 (829)
+..-+..+++.|...|-+.+++|....+ ....-...+.+++++.|+... ...+....+.+.-...+.++.+...+ -.
T Consensus 164 n~~~~~~a~~~L~~~Gh~~I~~i~~~~~~~~~~R~~Gf~~al~~~g~~~~-~~~~~~~~~~~~~~~~~~~~l~~~~~~~a 242 (331)
T PRK14987 164 NFEAARQMTTAIIARGHRHIAYLGARLDERTIIKQKGYEQAMLDAGLVPY-SVMVEQSSSYSSGIELIRQARREYPQLDG 242 (331)
T ss_pred cHHHHHHHHHHHHHCCCceEEEEcCCCcccHHHHHHHHHHHHHHcCCCcc-ceeecCCCChhhHHHHHHHHHhcCCCCCE
Confidence 3334455667777789999999964322 122345778888999886321 11111111111222344444333222 24
Q ss_pred EEEcChhHHHHHHHHHHHcCccccCeEEEEc
Q 043276 83 ILHMLPSLGSRIFEKANEIGLMNKGCVWIMT 113 (829)
Q Consensus 83 Iv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t 113 (829)
|++++...|..++..+++.|+..++-+-|.+
T Consensus 243 i~~~nD~~A~g~~~al~~~g~~vP~disvig 273 (331)
T PRK14987 243 VFCTNDDLAVGAAFECQRLGLKVPDDMAIAG 273 (331)
T ss_pred EEECCcHHHHHHHHHHHHcCCCCCCccEEEe
Confidence 5566777888899999999987666665553
No 314
>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=60.05 E-value=1.1e+02 Score=31.49 Aligned_cols=108 Identities=13% Similarity=0.011 Sum_probs=62.9
Q ss_pred hHHH-HHHHHHHHHHcCCcEEEEEEEeCc--cccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcC---C
Q 043276 5 DSSQ-VGAITAIIKAFGWREAVPIYVDNQ--YGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTM---Q 78 (829)
Q Consensus 5 D~~q-~~ai~~ll~~fgW~~V~iI~~dd~--yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~---~ 78 (829)
|..+ +..+++.+..-|-++++++..+.. ......+.+.+.+++.|+.+..........+.+.....+.++.+. .
T Consensus 99 d~~~~g~~~~~~l~~~g~~~i~~i~~~~~~~~~~~R~~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~ 178 (264)
T cd06274 99 DNRDGAAELTRELLAAPPEEVLFLGGLPELSPSRERLAGFRQALADAGLPVQPDWIYAEGYSPESGYQLMAELLARLGRL 178 (264)
T ss_pred ccHHHHHHHHHHHHHCCCCcEEEEeCCCcccchHHHHHHHHHHHHHcCCCCCcceeecCCCChHHHHHHHHHHHccCCCC
Confidence 3344 355677666689999999975433 234456788888998885432221211122222333344444322 2
Q ss_pred CeEEEEEcChhHHHHHHHHHHHcCccccCeEEEEc
Q 043276 79 TRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMT 113 (829)
Q Consensus 79 arViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t 113 (829)
.+.|+ +++...|..++..+++.|+..++.+-|++
T Consensus 179 ~~ai~-~~~d~~A~g~~~al~~~g~~ip~dv~v~g 212 (264)
T cd06274 179 PRALF-TTSYTLLEGVLRFLRERPGLAPSDLRIAT 212 (264)
T ss_pred CcEEE-EcChHHHHHHHHHHHHcCCCCCcceEEEE
Confidence 44444 55667788899999999976556555553
No 315
>cd08470 PBP2_CrgA_like_1 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding domain. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 1. 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
Probab=59.95 E-value=32 Score=32.99 Aligned_cols=69 Identities=14% Similarity=0.020 Sum_probs=38.2
Q ss_pred eecCChHHHHHHHhcCCcCCceeEEEcchhHHHHHHhcCCCceEEe--CcccccCCceeeecCCCCchhhHHHHHHhh
Q 043276 568 VVYNSHEECDELFQKGSANGGIAAAFDEIPYAKLLIGQHCSKYTMV--EPTFKTAGFGFAFPLHSPLVHDVSKAILNV 643 (829)
Q Consensus 568 ~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~~c~~l~~v--~~~~~~~~~~~~~~k~spl~~~in~~il~l 643 (829)
...++.....+.+..|. ..+++.+.. +....... .+..+ ........++++.+++......+...+..+
T Consensus 123 ~~~~~~~~~~~~v~~g~----Gi~~lp~~~-~~~~~~~~--~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l 193 (197)
T cd08470 123 WRCNSGVALLDAALKGM----GLAQLPDYY-VDEHLAAG--RLVPVLEDYRPPDEGIWALYPHNRHLSPKVRLLVDYL 193 (197)
T ss_pred EEECCHHHHHHHHHcCC----cEEEechHH-hHHHHHcC--CcEEccccccCCCCcEEEEeCCchhccHHHHHHHHHH
Confidence 45677888889999987 455555433 33222222 13322 212234567788888766555555444433
No 316
>PF08374 Protocadherin: Protocadherin; InterPro: IPR013585 The structure of protocadherins is similar to that of classic cadherins (IPR002126 from INTERPRO), but they also have some unique features associated with the cytoplasmic domains. They are expressed in a variety of organisms and are found in high concentrations in the brain where they seem to be localised mainly at cell-cell contact sites. Their expression seems to be developmentally regulated [].
Probab=59.82 E-value=37 Score=33.53 Aligned_cols=36 Identities=19% Similarity=0.158 Sum_probs=22.8
Q ss_pred cccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q 043276 674 SLGLNSFWGLFLIAGIAAILALIIFLAVFVHEHWNV 709 (829)
Q Consensus 674 ~L~l~~~~g~f~il~vg~~lallvf~~E~~~~~~~~ 709 (829)
..+-+.+.-++-+++..+.+.|++|+.-++.+.|+.
T Consensus 31 ~~~~d~~~I~iaiVAG~~tVILVI~i~v~vR~CRq~ 66 (221)
T PF08374_consen 31 SRSKDYVKIMIAIVAGIMTVILVIFIVVLVRYCRQS 66 (221)
T ss_pred cccccceeeeeeeecchhhhHHHHHHHHHHHHHhhc
Confidence 344455566667777777777777777666444433
No 317
>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=59.17 E-value=84 Score=32.25 Aligned_cols=104 Identities=13% Similarity=0.132 Sum_probs=62.9
Q ss_pred hHHHHHHHHHHHHHcCCcEEEEEEEeCc-cccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcC--CCeE
Q 043276 5 DSSQVGAITAIIKAFGWREAVPIYVDNQ-YGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTM--QTRV 81 (829)
Q Consensus 5 D~~q~~ai~~ll~~fgW~~V~iI~~dd~-yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~--~arV 81 (829)
+..-+..+++.+...|-++++++..+.. ....-...+.+++++.|+.+... .+. .+.+...+.+.++.+. ...
T Consensus 99 ~~~~g~~a~~~L~~~g~~~i~~~~~~~~~~~~~R~~gf~~~~~~~~~~~~~~-~~~--~~~~~~~~~~~~~l~~~~~~~- 174 (263)
T cd06280 99 NRAAARTLVEHLVAQGYRRIGGLFGNASTTGAERRAGYEDAMRRHGLAPDAR-FVA--PTAEAAEAALAAWLAAPERPE- 174 (263)
T ss_pred cHHHHHHHHHHHHHCCCceEEEEeCCCCCCHHHHHHHHHHHHHHcCCCCChh-hcc--cCHHHHHHHHHHHhcCCCCCc-
Confidence 3344556667777789999999864321 22344677788888888754321 112 1222333444444333 334
Q ss_pred EEEEcChhHHHHHHHHHHHcCccccCeEEEE
Q 043276 82 FILHMLPSLGSRIFEKANEIGLMNKGCVWIM 112 (829)
Q Consensus 82 iIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~ 112 (829)
.|++.+...+..+++.+++.|+..++-+.|.
T Consensus 175 ai~~~~d~~a~g~~~~l~~~g~~~p~di~ii 205 (263)
T cd06280 175 ALVASNGLLLLGALRAVRAAGLRIPQDLALA 205 (263)
T ss_pred EEEECCcHHHHHHHHHHHHcCCCCCCcEEEE
Confidence 4556677778889999999997656555554
No 318
>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=58.80 E-value=1.1e+02 Score=31.43 Aligned_cols=108 Identities=6% Similarity=-0.032 Sum_probs=61.7
Q ss_pred ChHHHHHHHHHHHHHc--CCcEEEEEEEeCcc--ccchHHHHHHHHHhC-CceeeeEEecCCCCChhHHHHHHHHhhcC-
Q 043276 4 NDSSQVGAITAIIKAF--GWREAVPIYVDNQY--GEELIPSLTDALQAI-DTRVPYRSVISPLATDDQIEKELYKLFTM- 77 (829)
Q Consensus 4 sD~~q~~ai~~ll~~f--gW~~V~iI~~dd~y--G~~~~~~l~~~l~~~-gi~I~~~~~i~~~~~~~~~~~~l~~lk~~- 77 (829)
++...+..+++.+... |-++++++..+.+. ...-.+.+.+++++. ++++... .....+.++..+.+.++.+.
T Consensus 105 d~~~~g~~~~~~l~~~~~g~~~i~~i~~~~~~~~~~~R~~Gf~~~l~~~~~~~~~~~--~~~~~~~~~~~~~~~~~l~~~ 182 (273)
T cd06309 105 DFVEEGRRAADWLAKATGGKGNIVELQGTVGSSVAIDRKKGFAEVIKKYPNMKIVAS--QTGDFTRAKGKEVMEALLKAH 182 (273)
T ss_pred ChHHHHHHHHHHHHHHcCCCceEEEEeCCCCCchHHHHHHHHHHHHHHCCCCEEeec--cCCcccHHHHHHHHHHHHHhC
Confidence 4455566666777555 88999999754332 234467778888886 4544321 11111222333444444433
Q ss_pred --CCeEEEEEcChhHHHHHHHHHHHcCccccCeEEEEcC
Q 043276 78 --QTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTD 114 (829)
Q Consensus 78 --~arViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t~ 114 (829)
..+ .|++.+...+..+++.+++.|+..++.+-|++-
T Consensus 183 ~~~~~-aI~~~~d~~a~g~~~a~~~~g~~ip~di~iig~ 220 (273)
T cd06309 183 GDDID-AVYAHNDEMALGAIQAIKAAGKKPGKDIKIVSI 220 (273)
T ss_pred CCCcc-EEEECCcHHHHHHHHHHHHcCCCCCCCeEEEec
Confidence 233 344455666677888999999765555555543
No 319
>KOG1419 consensus Voltage-gated K+ channel KCNQ [Inorganic ion transport and metabolism]
Probab=58.52 E-value=18 Score=40.63 Aligned_cols=85 Identities=14% Similarity=0.240 Sum_probs=64.1
Q ss_pred hHHHHHHHHHHHHHHHHHhhhcccCCCCCCCccCccchhHHHHHHHhhhcC--ccccccchhHHHHHHHHHHHHHHHHHh
Q 043276 438 DLWVTSGCFFIFIGFVVWVLEHRVNEDFRGPARHQVGTSFWFSFSTMVFSQ--RERVISNLARFVVIVWCFVVLILIQSY 515 (829)
Q Consensus 438 ~vW~~i~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~--~~~~~s~~~R~v~~~w~~~~lil~~~Y 515 (829)
..|+.-++.+++.++++++.|.-...+-.+..-.+.-.++|+..-+++..| ...|..+.+|++...+.++++-.-+.=
T Consensus 235 Tt~YIGFL~LIfsSflVYLaEKd~~~e~~n~~F~TyADALWWG~ITltTIGYGDk~P~TWlGr~laa~fsligiSFFALP 314 (654)
T KOG1419|consen 235 TTWYIGFLVLIFSSFLVYLAEKDAQGEGTNDEFPTYADALWWGVITLTTIGYGDKTPQTWLGRLLAACFSLIGISFFALP 314 (654)
T ss_pred HHHHHHHHHHHHHHHHHHHhhcccccccccccchhHHHHHHhhheeEEeeccCCcCcccchhHHHHHHHHHHHHHHHhcc
Confidence 578888999999999999999874443333333467789999999998776 457899999999988877776655554
Q ss_pred HHHHHHH
Q 043276 516 TASLTSL 522 (829)
Q Consensus 516 tA~L~s~ 522 (829)
.+-|-|=
T Consensus 315 AGILGSG 321 (654)
T KOG1419|consen 315 AGILGSG 321 (654)
T ss_pred cccccch
Confidence 4445443
No 320
>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=58.47 E-value=43 Score=36.29 Aligned_cols=100 Identities=14% Similarity=0.101 Sum_probs=64.9
Q ss_pred HHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcCh--
Q 043276 11 AITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLP-- 88 (829)
Q Consensus 11 ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~~-- 88 (829)
-+.+.++.+|.+++.+|+....+ .+..+.+.+.|++. +.+.....+....+.+++.+.+..+++.+.++||-.+..
T Consensus 13 ~l~~~~~~~g~~~~liv~~~~~~-~~~~~~v~~~l~~~-~~~~~~~~~~~~p~~~~v~~~~~~~~~~~~d~IIaiGGGs~ 90 (332)
T cd07766 13 KIGEEIKRGGFDRALVVSDEGVV-KGVGEKVADSLKKL-IAVHIFDGVGPNPTFEEVKEAVERARAAEVDAVIAVGGGST 90 (332)
T ss_pred HHHHHHHhcCCCeEEEEeCCchh-hhHHHHHHHHHHhc-CcEEEeCCcCCCcCHHHHHHHHHHHHhcCcCEEEEeCCchH
Confidence 45667788899999999844443 37778888888876 655433333344566678888888888889999987754
Q ss_pred hHHHHHHHHHHHcCccccCeEEEEcCc
Q 043276 89 SLGSRIFEKANEIGLMNKGCVWIMTDG 115 (829)
Q Consensus 89 ~~~~~i~~~a~~~gm~~~~~vwI~t~~ 115 (829)
-++..+.......|+ .++-|-|..
T Consensus 91 ~D~aK~ia~~~~~~~---p~i~iPTt~ 114 (332)
T cd07766 91 LDTAKAVAALLNRGL---PIIIVPTTA 114 (332)
T ss_pred HHHHHHHHHHhcCCC---CEEEEeCCC
Confidence 344444444333242 355555543
No 321
>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=58.24 E-value=44 Score=36.43 Aligned_cols=77 Identities=10% Similarity=0.036 Sum_probs=54.7
Q ss_pred HHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcCh
Q 043276 10 GAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLP 88 (829)
Q Consensus 10 ~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~~ 88 (829)
.-+.+.++.+| +++.+|+....+ ....+.+.+.|++.|+.+.....+....+.+.+.+.....++.++++||-.+..
T Consensus 12 ~~l~~~~~~~~-~r~liv~d~~~~-~~~~~~v~~~l~~~~~~~~~~~~~~~~p~~~~v~~~~~~~~~~~~d~iiavGGG 88 (345)
T cd08171 12 KKIPEVCEKYG-KKVVVIGGKTAL-AAAKDKIKAALEQSGIEITDFIWYGGESTYENVERLKKNPAVQEADMIFAVGGG 88 (345)
T ss_pred HHHHHHHHhcC-CEEEEEeCHHHH-HHHHHHHHHHHHHCCCeEEEEEecCCCCCHHHHHHHHHHHhhcCCCEEEEeCCc
Confidence 34556677788 888888744333 445778888899889876544455555666677777777778899999987754
No 322
>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=58.17 E-value=1.1e+02 Score=31.76 Aligned_cols=100 Identities=10% Similarity=0.065 Sum_probs=55.5
Q ss_pred HHHHcCC--cEEEEEEE-eC--ccccchHHHHHHHHHhCCceeeeEEecCCC-CChhHHHHHHHHhhcC--CCeE-EEEE
Q 043276 15 IIKAFGW--REAVPIYV-DN--QYGEELIPSLTDALQAIDTRVPYRSVISPL-ATDDQIEKELYKLFTM--QTRV-FILH 85 (829)
Q Consensus 15 ll~~fgW--~~V~iI~~-dd--~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~-~~~~~~~~~l~~lk~~--~arV-iIv~ 85 (829)
.+..-|| +++++|.. .. .....-.+.+.+++++.|+........+.. .+.+...+.+..+... ..+. +|++
T Consensus 121 ~~~~~g~~~~~i~~i~~~~~~~~~~~~R~~G~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~i~~ 200 (289)
T cd01540 121 EMKKRGWDPKEVGALRITYDELDTAKPRTDGALEALKAPGFPEANIFQAPQKTTDTEGAFDAAASTLTKNPNVKNWIIYG 200 (289)
T ss_pred HHHhhcCCCcceEEEEecCCCCcchhhHHHHHHHHHhcCCCCcceEecccccCcchhhHHHHHHHHHHhCCCcCeeEEEe
Confidence 3334688 78888852 22 344566788888888877643211111111 1112222334444322 3343 5677
Q ss_pred cChhHHHHHHHHHHHcCccccCeEEEEcC
Q 043276 86 MLPSLGSRIFEKANEIGLMNKGCVWIMTD 114 (829)
Q Consensus 86 ~~~~~~~~i~~~a~~~gm~~~~~vwI~t~ 114 (829)
++...+..++..+.+.|....+...|.-|
T Consensus 201 ~~d~~a~g~~~al~~~g~~~~di~vig~d 229 (289)
T cd01540 201 LNDETVLGAVRATEQSGIAAADVIGVGIN 229 (289)
T ss_pred CCcHHHHHHHHHHHHcCCCCcceEEEecC
Confidence 77778888999999999753233344433
No 323
>PRK13583 hisG ATP phosphoribosyltransferase catalytic subunit; Provisional
Probab=58.02 E-value=87 Score=31.76 Aligned_cols=91 Identities=12% Similarity=0.074 Sum_probs=50.9
Q ss_pred CCCHHHHHh--------CC--CcEEEEeCchHHHHHHhcCCCccceeecCChHHHHHHHhcCCcCCceeEEEcchhHHHH
Q 043276 532 ITDVNLLIK--------RG--DNVGYQKGSFVLGILKQLGFDERKLVVYNSHEECDELFQKGSANGGIAAAFDEIPYAKL 601 (829)
Q Consensus 532 I~s~~dL~~--------~~--~~vg~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~ 601 (829)
+++++||.. .+ .+|+..--...+.||++.+.+...++.....-|. +-..|- .|++++-.....-
T Consensus 111 ~~~~~dl~~~~~~~~~~~g~~~RIATkYp~it~~yf~~~Gv~~~~Iv~l~GsvEl--aP~~Gl----AD~IvDivsTG~T 184 (228)
T PRK13583 111 VDTMADLDDVAADFRARHGRRLRIATKYWRLTQQFLSQKGVQDYRIVESLGATEG--APANGS----AEIIVDITSTGET 184 (228)
T ss_pred cCCHHHhhhhhhhhhhccCCceEEEeCCHHHHHHHHHHcCCceeEEEECCCceec--ccccCc----chhhhhhhchhHH
Confidence 567777741 12 4788877777889998877754344443332222 223344 5555555444333
Q ss_pred HHhcCCCceEEeC-cccccCCceeeecCCCC
Q 043276 602 LIGQHCSKYTMVE-PTFKTAGFGFAFPLHSP 631 (829)
Q Consensus 602 ~~~~~c~~l~~v~-~~~~~~~~~~~~~k~sp 631 (829)
+.++ .|.+++ +.+......+..++.|.
T Consensus 185 Lr~N---gL~~i~~~~Il~SsA~LI~n~~s~ 212 (228)
T PRK13583 185 LRAN---HLKILSDGVILRSQACLVRARKAD 212 (228)
T ss_pred HHHC---CCEEecCceEEEEEEEEEEecccc
Confidence 3333 366775 34555555666677764
No 324
>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=57.76 E-value=55 Score=31.10 Aligned_cols=65 Identities=9% Similarity=0.111 Sum_probs=39.0
Q ss_pred EEeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccEEEeccccccccceeccccccccccceEEE
Q 043276 338 VGYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMI 417 (829)
Q Consensus 338 ~G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~v 417 (829)
.++-.+++..+.++.+ .++++.... +.+. .+.+|++|+++..... ....+. +.++....++++
T Consensus 13 ~~~l~~~l~~~~~~~P-~v~i~i~~~-----------~~~~-~l~~~~~D~~i~~~~~---~~~~~~-~~~l~~~~~~~v 75 (197)
T cd08422 13 RLHLAPLLAEFLARYP-DVRLELVLS-----------DRLV-DLVEEGFDLAIRIGEL---PDSSLV-ARRLGPVRRVLV 75 (197)
T ss_pred HHHHHHHHHHHHHhCC-ceEEEEecC-----------cccc-chhhcCccEEEEeCCC---CCcchh-hhhhhccCcEEE
Confidence 3456678888888876 455555421 2233 4567889999853221 122233 356777777777
Q ss_pred EE
Q 043276 418 VP 419 (829)
Q Consensus 418 v~ 419 (829)
++
T Consensus 76 ~~ 77 (197)
T cd08422 76 AS 77 (197)
T ss_pred EC
Confidence 76
No 325
>PRK03601 transcriptional regulator HdfR; Provisional
Probab=57.67 E-value=21 Score=37.44 Aligned_cols=83 Identities=7% Similarity=0.069 Sum_probs=57.2
Q ss_pred CceEEEecccccCccceEEEeecCCCCCceEEEeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcc
Q 043276 307 EKKLRVGVPVKKGFSDFVKVTIDPKTQETSVVGYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEF 386 (829)
Q Consensus 307 ~~~lrv~v~~~~~~~p~~~~~~~~~~~~~~~~G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~ 386 (829)
.+.++||+. +. ....+-.+++..+.+..+ .+++++.. +...+++..|.+|++
T Consensus 88 ~~~l~Ig~~--~~----------------~~~~~l~~~l~~f~~~~P-~v~v~~~~---------~~~~~~~~~l~~g~~ 139 (275)
T PRK03601 88 HNELSIGAS--AS----------------LWECMLTPWLGRLYQNQE-ALQFEARI---------AQRQSLVKQLHERQL 139 (275)
T ss_pred CceEEEecc--HH----------------HHHHHHHHHHHHHHHhCC-CcEEEEEE---------CChHHHHHHHHcCCC
Confidence 467999987 22 123556778888888776 35666554 246789999999999
Q ss_pred cEEEeccccccccceeccccccccccceEEEEEcc
Q 043276 387 DAVVGDTTIVFNRSNYVDFTLPYTESGVSMIVPIK 421 (829)
Q Consensus 387 Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv~~~ 421 (829)
|+++....... ..+ ...|+....++++++..
T Consensus 140 Dl~i~~~~~~~---~~l-~~~~l~~~~~~~v~~~~ 170 (275)
T PRK03601 140 DLLITTEAPKM---DEF-SSQLLGHFTLALYTSAP 170 (275)
T ss_pred CEEEEcCCCcc---CCc-cEEEecceeEEEEecCc
Confidence 99996433221 233 35688888888888744
No 326
>cd08478 PBP2_CrgA The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains the type 2 periplasmic binding domain. This CD represents the substrate binding domain of LysR-type transcriptional regulator (LTTR) CrgA. 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 gene and activates the expression of the mdaB gene wh
Probab=57.60 E-value=49 Score=31.78 Aligned_cols=65 Identities=9% Similarity=0.187 Sum_probs=40.3
Q ss_pred EeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccEEEeccccccccceeccccccccccceEEEE
Q 043276 339 GYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMIV 418 (829)
Q Consensus 339 G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv 418 (829)
++-.+++..+.++.+ +++++... ...+ .++.+|++|+++..... ....+ .+.|+....+++++
T Consensus 16 ~~l~~~l~~f~~~~P-~v~i~~~~-----------~~~~-~~l~~~~~D~~i~~~~~---~~~~l-~~~~l~~~~~~~v~ 78 (199)
T cd08478 16 HLLAPLIAKFRERYP-DIELELVS-----------NEGI-IDLIERKTDVAIRIGEL---TDSTL-HARPLGKSRLRILA 78 (199)
T ss_pred HHHHHHHHHHHHHCC-CeEEEEEe-----------cccc-ccchhccccEEEEecCC---CCCCc-eEEEcccccEEEEE
Confidence 345678888888876 45665542 1223 34678999999853222 22233 24677788888887
Q ss_pred Ec
Q 043276 419 PI 420 (829)
Q Consensus 419 ~~ 420 (829)
+.
T Consensus 79 ~~ 80 (199)
T cd08478 79 SP 80 (199)
T ss_pred CH
Confidence 73
No 327
>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=57.05 E-value=1.6e+02 Score=27.67 Aligned_cols=64 Identities=5% Similarity=-0.039 Sum_probs=39.2
Q ss_pred eeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccEEEeccccccccceeccccccccccceEEEEE
Q 043276 340 YSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMIVP 419 (829)
Q Consensus 340 ~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv~ 419 (829)
+-..++..+.++.+ .++++.... + .+.+|.+|++|+++..... ....+ .+.++....++++++
T Consensus 14 ~l~~~l~~~~~~~P-~v~i~~~~~-----------~-~~~~l~~g~~D~~i~~~~~---~~~~~-~~~~l~~~~~~~v~~ 76 (194)
T cd08432 14 WLIPRLARFQARHP-DIDLRLSTS-----------D-RLVDFAREGIDLAIRYGDG---DWPGL-EAERLMDEELVPVCS 76 (194)
T ss_pred HHHHHhHHHHHHCC-CeEEEEEec-----------C-CccccccccccEEEEecCC---CCCCc-ceEEccCCcEEEecC
Confidence 34566777777776 456655431 1 4567899999999853221 11222 246677777777776
Q ss_pred c
Q 043276 420 I 420 (829)
Q Consensus 420 ~ 420 (829)
.
T Consensus 77 ~ 77 (194)
T cd08432 77 P 77 (194)
T ss_pred H
Confidence 3
No 328
>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=57.00 E-value=1.3e+02 Score=30.89 Aligned_cols=98 Identities=4% Similarity=-0.060 Sum_probs=55.5
Q ss_pred ChHHHHHHHHHHHHHc--CCcEEEEEEEeCcc--ccchHHHHHHHHHhCC-ceeeeEEecCCCCChhHHHHHHHHhhcC-
Q 043276 4 NDSSQVGAITAIIKAF--GWREAVPIYVDNQY--GEELIPSLTDALQAID-TRVPYRSVISPLATDDQIEKELYKLFTM- 77 (829)
Q Consensus 4 sD~~q~~ai~~ll~~f--gW~~V~iI~~dd~y--G~~~~~~l~~~l~~~g-i~I~~~~~i~~~~~~~~~~~~l~~lk~~- 77 (829)
++...+..+++.+... |=+++++|....+. ...-.+.+.+++++.| +.+.. ......+.+...+.+.++.+.
T Consensus 104 d~~~~g~~~~~~l~~~~~~~~~i~~i~~~~~~~~~~~R~~gf~~~l~~~~~~~~~~--~~~~~~~~~~~~~~~~~~l~~~ 181 (272)
T cd06301 104 DEVVAGRLQAEYVADKLGGKGNVAILMGPLGQSAQIDRTKGVEEVLAKYPDIKVVE--EQTANWSRAEAMDLMENWLSSG 181 (272)
T ss_pred ChHHHHHHHHHHHHHHhCCCccEEEEECCCCCccHHHHHHHHHHHHHHCCCcEEEe--cCCCCccHHHHHHHHHHHHHhC
Confidence 4445566666766443 45699999754332 3344677888888887 33321 111111222223444443322
Q ss_pred -CCeEEEEEcChhHHHHHHHHHHHcCcc
Q 043276 78 -QTRVFILHMLPSLGSRIFEKANEIGLM 104 (829)
Q Consensus 78 -~arViIv~~~~~~~~~i~~~a~~~gm~ 104 (829)
..++ |++++...+..++..+++.|..
T Consensus 182 ~~~~a-i~~~~d~~a~~~~~~l~~~g~~ 208 (272)
T cd06301 182 GKIDA-VVANNDEMALGAIMALKAAGKS 208 (272)
T ss_pred CCCCE-EEECCCchHHHHHHHHHHcCCC
Confidence 3343 4556666777899999999975
No 329
>PRK09423 gldA glycerol dehydrogenase; Provisional
Probab=56.84 E-value=48 Score=36.52 Aligned_cols=76 Identities=14% Similarity=0.098 Sum_probs=55.9
Q ss_pred HHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcCh
Q 043276 10 GAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLP 88 (829)
Q Consensus 10 ~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~~ 88 (829)
..+.+.++.+| +++.||+...-+ ....+.+.+.|++.|+.+.+. .++...+.+.+.+.+..+++.++++||-.+..
T Consensus 19 ~~l~~~l~~~g-~~~livtd~~~~-~~~~~~v~~~l~~~~~~~~~~-~~~~ep~~~~v~~~~~~~~~~~~d~IIavGGG 94 (366)
T PRK09423 19 ARLGEYLKPLG-KRALVIADEFVL-GIVGDRVEASLKEAGLTVVFE-VFNGECSDNEIDRLVAIAEENGCDVVIGIGGG 94 (366)
T ss_pred HHHHHHHHHcC-CEEEEEEChhHH-HHHHHHHHHHHHhCCCeEEEE-EeCCCCCHHHHHHHHHHHHhcCCCEEEEecCh
Confidence 44566788889 888888844433 346788888899999877554 45555666677788888888899999988765
No 330
>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=56.48 E-value=1.1e+02 Score=32.16 Aligned_cols=123 Identities=23% Similarity=0.275 Sum_probs=73.3
Q ss_pred CCCCCCCHHHHHhC----C--CcEEEE-eCchHH---HHH-HhcCCCccceeecCChHHHHHHHhcCCcCCceeEEEcch
Q 043276 528 LQPTITDVNLLIKR----G--DNVGYQ-KGSFVL---GIL-KQLGFDERKLVVYNSHEECDELFQKGSANGGIAAAFDEI 596 (829)
Q Consensus 528 ~~~~I~s~~dL~~~----~--~~vg~~-~~s~~~---~~l-~~~~~~~~~~~~~~~~~~~~~~l~~g~~~~g~~a~~~~~ 596 (829)
...+++|++||++. . ..+|.. .|+..+ ..| +..+.+ .+.++|+.-.+.+.+|..|. +|+.+...
T Consensus 86 ~dsp~~t~~eli~~ak~~p~~~~~g~~g~g~~~hl~~~~l~~~~G~~-~~~Vpy~G~~~~~~allgG~----vd~~~~~~ 160 (274)
T PF03401_consen 86 ADSPYKTLEELIEYAKANPGKLTFGSSGPGSSDHLAAALLAKAAGIK-FTHVPYDGGAEALTALLGGH----VDAAFGSP 160 (274)
T ss_dssp TTSS-SSHHHHHHHHHCSCCC-EEEESSTTSHHHHHHHHHHHHHT----EEEE-SSHHHHHHHHHTTS----SSEEEEEH
T ss_pred CCCccccHHHHHHHHHhCCCCeEEEecCCCchHHHHHHHHHHHhCCc-eEEEEeCCccHHHHHHhCCe----eeEEeecH
Confidence 46779999999742 2 256654 233222 222 445553 46789999999999999999 99988775
Q ss_pred hHHHHHHhc-CCCceEEeC----------ccccc---------CCceeeecCCCC--chhhHHHHHHhhhccChhHHHHH
Q 043276 597 PYAKLLIGQ-HCSKYTMVE----------PTFKT---------AGFGFAFPLHSP--LVHDVSKAILNVTEGDKMKEIED 654 (829)
Q Consensus 597 ~~~~~~~~~-~c~~l~~v~----------~~~~~---------~~~~~~~~k~sp--l~~~in~~il~l~e~G~~~~~~~ 654 (829)
....-+.+. .-+-+.+.+ +.+.. ...++++|||-| .++.+..++.+..++-.+++..+
T Consensus 161 ~~~~~~~~~G~~k~Lav~~~~r~~~~pdvPT~~E~G~~d~~~~~~~g~~~p~gtp~~~~~~l~~a~~~~~~~pe~~~~~~ 240 (274)
T PF03401_consen 161 GEALPYVEAGDLKPLAVFSDERSPALPDVPTFKEQGYPDIVFGSWRGLFAPKGTPDEIVDKLADAIKKALEDPEFQEFLE 240 (274)
T ss_dssp HHHHHHHHTTSEEEEEECSSS-BTTCTTS-BTTTTT-TTG--EEEEEEEEETTS-HHHHHHHHHHHHHHHT-HHHHHHHH
T ss_pred HHHHHHHhCCCceEEEEecCccccccCCCCCHHHhCccceeeeeeeeeecCCCCCHHHHHHHHHHHHHHhCCHHHHHHHH
Confidence 555444432 111011111 11122 233888999988 99999999999998877665555
Q ss_pred H
Q 043276 655 A 655 (829)
Q Consensus 655 ~ 655 (829)
+
T Consensus 241 ~ 241 (274)
T PF03401_consen 241 K 241 (274)
T ss_dssp H
T ss_pred H
Confidence 4
No 331
>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=56.36 E-value=1.1e+02 Score=32.46 Aligned_cols=106 Identities=16% Similarity=0.061 Sum_probs=59.4
Q ss_pred ChHHHHHHHHHHHHHcCCcE--------EEEEEEeC--ccccchHHHHHHHHHhCC-ceeeeEEecCCCCChhHHHHHHH
Q 043276 4 NDSSQVGAITAIIKAFGWRE--------AVPIYVDN--QYGEELIPSLTDALQAID-TRVPYRSVISPLATDDQIEKELY 72 (829)
Q Consensus 4 sD~~q~~ai~~ll~~fgW~~--------V~iI~~dd--~yG~~~~~~l~~~l~~~g-i~I~~~~~i~~~~~~~~~~~~l~ 72 (829)
++..-+..+++.+...|-++ ++++.... .....-.+.+.++++++| +.+.. .+....+.+...+.+.
T Consensus 117 d~~~~g~~~~~~l~~~g~~~~~~~g~~~i~~i~~~~~~~~~~~R~~Gf~~~~~~~g~~~~~~--~~~~~~~~~~~~~~~~ 194 (305)
T cd06324 117 NDEEAGYLMAEALISQARSVQAPGGRIDLLAISGDPTTPAAILREAGLRRALAEHPDVRLRQ--VVYAGWSEDEAYEQAE 194 (305)
T ss_pred CcHHHHHHHHHHHHHHhhcccCCCCceeEEEEeCCCCChHHHHHHHHHHHHHHHCCCceEee--eecCCCCHHHHHHHHH
Confidence 34445566677776667664 66665322 223445677888898887 33321 2222222223334444
Q ss_pred HhhcC--CCeEEEEEcChhHHHHHHHHHHHcCccccCeEEEE
Q 043276 73 KLFTM--QTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIM 112 (829)
Q Consensus 73 ~lk~~--~arViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~ 112 (829)
++.+. ..++ |++.+...+..+++.+++.|+..++.+=|+
T Consensus 195 ~~l~~~~~~~a-i~~~~d~~A~g~~~al~~~g~~vp~di~vi 235 (305)
T cd06324 195 NLLKRYPDVRL-IWAANDQMAFGALRAAKEAGRKPGRDVLFG 235 (305)
T ss_pred HHHHHCCCccE-EEECCchHHHHHHHHHHHcCCCcCCCEEEE
Confidence 44332 3444 445667778889999999997654444333
No 332
>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=56.23 E-value=13 Score=27.47 Aligned_cols=28 Identities=29% Similarity=0.595 Sum_probs=22.9
Q ss_pred hHHHHHHHHHHHHHHHHHhhhcccCCCC
Q 043276 438 DLWVTSGCFFIFIGFVVWVLEHRVNEDF 465 (829)
Q Consensus 438 ~vW~~i~~~~~~~~~v~~~~~~~~~~~~ 465 (829)
++|.+++.+++++++++|.+..+..+.+
T Consensus 12 ~~~~l~~~~~~Figiv~wa~~p~~k~~f 39 (48)
T cd01324 12 DSWGLLYLALFFLGVVVWAFRPGRKKAF 39 (48)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCCcchhH
Confidence 6788888899999999999987655443
No 333
>PRK01686 hisG ATP phosphoribosyltransferase catalytic subunit; Reviewed
Probab=55.84 E-value=85 Score=31.55 Aligned_cols=92 Identities=12% Similarity=0.017 Sum_probs=54.7
Q ss_pred CCCcEEEEeCchHHHHHHhcCCCccceeecCChHHHHHHHhcCCcCCceeEEEcchhHHHHHHhcCCCceEEeCcccccC
Q 043276 541 RGDNVGYQKGSFVLGILKQLGFDERKLVVYNSHEECDELFQKGSANGGIAAAFDEIPYAKLLIGQHCSKYTMVEPTFKTA 620 (829)
Q Consensus 541 ~~~~vg~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~~c~~l~~v~~~~~~~ 620 (829)
.+.+|+...-...+.||++.+.+ .+++...-.-|. +-..|- .|++++-.....-+.++. |.++...+. .
T Consensus 114 ~~~rIATkYp~it~~yf~~~gv~-~~iv~l~GsvE~--aP~~Gl----AD~IvDivsTG~TLr~Ng---L~~ie~Il~-s 182 (215)
T PRK01686 114 PRLRVATKYPNIARRYFAEKGEQ-VEIIKLYGSVEL--APLVGL----ADAIVDIVETGNTLRANG---LVEVEEIMD-I 182 (215)
T ss_pred CCCEEEeCCHHHHHHHHHHcCCe-EEEEECcCceee--ccccCC----ccEEEEeecChHHHHHCc---CEEeeEEEe-e
Confidence 46688887778888999887775 444444433333 233355 677777665555554443 556655444 4
Q ss_pred CceeeecCCCC--chhhHHHHHHhh
Q 043276 621 GFGFAFPLHSP--LVHDVSKAILNV 643 (829)
Q Consensus 621 ~~~~~~~k~sp--l~~~in~~il~l 643 (829)
.-.+..++.|. -.+.++..+.++
T Consensus 183 ~A~LI~n~~s~~~k~~~i~~l~~~l 207 (215)
T PRK01686 183 SARLIVNRASLKLKREEIRPLIEKL 207 (215)
T ss_pred EEEEEEecccchhhHHHHHHHHHHH
Confidence 44566677765 224556555555
No 334
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=55.40 E-value=93 Score=33.32 Aligned_cols=103 Identities=8% Similarity=-0.037 Sum_probs=58.0
Q ss_pred HHHHHHHHHHHcCCcEEEEEEEeCc--cccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcC--CCeEEE
Q 043276 8 QVGAITAIIKAFGWREAVPIYVDNQ--YGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTM--QTRVFI 83 (829)
Q Consensus 8 q~~ai~~ll~~fgW~~V~iI~~dd~--yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~--~arViI 83 (829)
-+..+++.+...|.+++++|..... ....-...+.+++++.|+ +.....+....+.+.-.+.+.++.+. ... .|
T Consensus 161 ~~~~a~~~l~~~G~~~i~~i~~~~~~~~~~~R~~gf~~~~~~~g~-~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-ai 238 (327)
T PRK10339 161 ISKEIIDFYINQGVNRIGFIGGEDEPGKADIREVAFAEYGRLKQV-VREEDIWRGGFSSSSGYELAKQMLAREDYPK-AL 238 (327)
T ss_pred HHHHHHHHHHHCCCCeEEEeCCccccchhhHHHHHHHHHHHHcCC-CChhheeecCcChhHHHHHHHHHHhCCCCCC-EE
Confidence 3456667777779999999964332 223335567777887776 11111111111122223344444332 233 46
Q ss_pred EEcChhHHHHHHHHHHHcCccccCeEEEE
Q 043276 84 LHMLPSLGSRIFEKANEIGLMNKGCVWIM 112 (829)
Q Consensus 84 v~~~~~~~~~i~~~a~~~gm~~~~~vwI~ 112 (829)
+|++...|..+++.+++.|...++-+=|+
T Consensus 239 ~~~~D~~A~g~~~al~~~g~~vP~di~vi 267 (327)
T PRK10339 239 FVASDSIAIGVLRAIHERGLNIPQDISLI 267 (327)
T ss_pred EECCcHHHHHHHHHHHHcCCCCCCceEEE
Confidence 66677788899999999997555444333
No 335
>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=55.39 E-value=1.1e+02 Score=31.63 Aligned_cols=105 Identities=11% Similarity=0.078 Sum_probs=63.9
Q ss_pred CChHHHHHHHHHHHHH-cCCcEEEEEEEeCc--cccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCC
Q 043276 3 LNDSSQVGAITAIIKA-FGWREAVPIYVDNQ--YGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQT 79 (829)
Q Consensus 3 psD~~q~~ai~~ll~~-fgW~~V~iI~~dd~--yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~a 79 (829)
.++...+..+++.+.. -|-++++++..+.+ .+....+.+.+++++.++.+.. +....+.+...+.+.++.+...
T Consensus 106 ~d~~~~g~~~~~~l~~~~g~~~i~~i~g~~~~~~~~~r~~g~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~l~~~~ 182 (271)
T cd06312 106 QDEYAAGEAAGERLAELKGGKNVLCVIHEPGNVTLEDRCAGFADGLGGAGITEEV---IETGADPTEVASRIAAYLRANP 182 (271)
T ss_pred cChHHHHHHHHHHHHHhcCCCeEEEEecCCCCccHHHHHHHHHHHHHhcCceeeE---eecCCCHHHHHHHHHHHHHhCC
Confidence 3556677888888877 89999999975333 3455677888888888765321 1112222233344444432222
Q ss_pred e-EEEEEcChhHHHHHHHHHHHcCccccCeEEEE
Q 043276 80 R-VFILHMLPSLGSRIFEKANEIGLMNKGCVWIM 112 (829)
Q Consensus 80 r-ViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~ 112 (829)
+ -.|++.+...+..+++.+++.|+. +.+-|.
T Consensus 183 ~~~aI~~~~d~~a~g~~~al~~~g~~--~di~vv 214 (271)
T cd06312 183 DVDAVLTLGAPSAAPAAKALKQAGLK--GKVKLG 214 (271)
T ss_pred CccEEEEeCCccchHHHHHHHhcCCC--CCeEEE
Confidence 2 234455566677888889999864 445554
No 336
>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=54.93 E-value=1.6e+02 Score=30.22 Aligned_cols=100 Identities=9% Similarity=0.008 Sum_probs=56.9
Q ss_pred HHHHHHHHHHHHc--CCcEEEEEEEeCc-cccchHHHHHHHHHhC-CceeeeEEecCCCCChhHHHHHHHHhhcC--CCe
Q 043276 7 SQVGAITAIIKAF--GWREAVPIYVDNQ-YGEELIPSLTDALQAI-DTRVPYRSVISPLATDDQIEKELYKLFTM--QTR 80 (829)
Q Consensus 7 ~q~~ai~~ll~~f--gW~~V~iI~~dd~-yG~~~~~~l~~~l~~~-gi~I~~~~~i~~~~~~~~~~~~l~~lk~~--~ar 80 (829)
.-+..+++.+... |-+++++++..+. ....-.+.+.+++++. |+.+... ....+.+.....+.++.+. ..+
T Consensus 105 ~~g~~~~~~l~~~~~g~~~i~~i~~~~~~~~~~R~~gf~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~l~~~~~~~ 181 (267)
T cd06322 105 AGGVLAGELAAKVLNGKGQVAIIDYPTVQSVVDRVRGFKEALADYPNIKIVAV---QPGITRAEALTAAQNILQANPDLD 181 (267)
T ss_pred HHHHHHHHHHHHHhCCCceEEEEecCCCccHHHHHHHHHHHHHhCCCcEEEEe---cCCCChHHHHHHHHHHHHhCCCCC
Confidence 3445566666554 8889999974322 2233467778888888 8765321 1111222333334444322 234
Q ss_pred EEEEEcChhHHHHHHHHHHHcCccccCeEEEEc
Q 043276 81 VFILHMLPSLGSRIFEKANEIGLMNKGCVWIMT 113 (829)
Q Consensus 81 ViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t 113 (829)
.|++++...+..++..+++.|+ +.+.|.+
T Consensus 182 -ai~~~~d~~a~~~~~al~~~g~---~di~vvg 210 (267)
T cd06322 182 -GIFAFGDDAALGAVSAIKAAGR---DNVKVIG 210 (267)
T ss_pred -EEEEcCCcHHHHHHHHHHHCCC---CCeEEEE
Confidence 4555566677788888899885 4455554
No 337
>PF12273 RCR: Chitin synthesis regulation, resistance to Congo red; InterPro: IPR020999 RCR proteins are ER membrane proteins that regulate chitin deposition in fungal cell walls. Although chitin, a linear polymer of beta-1,4-linked N-acetylglucosamine, constitutes only 2% of the cell wall it plays a vital role in the overall protection of the cell wall against stress, noxious chemicals and osmotic pressure changes. Congo red is a cell wall-disrupting benzidine-type dye extensively used in many cell wall mutant studies that specifically targets chitin in yeast cells and inhibits growth. RCR proteins render the yeasts resistant to Congo red by diminishing the content of chitin in the cell wall []. RCR proteins are probably regulating chitin synthase III interact directly with ubiquitin ligase Rsp5, and the VPEY motif is necessary for this, via interaction with the WW domains of Rsp5 [].
Probab=53.47 E-value=10 Score=34.75 Aligned_cols=10 Identities=30% Similarity=0.411 Sum_probs=5.1
Q ss_pred cccCCCchhh
Q 043276 809 VELTNPDQEI 818 (829)
Q Consensus 809 ~~~~~~~~~~ 818 (829)
+|+..|.+.+
T Consensus 97 ~~~~~P~~~~ 106 (130)
T PF12273_consen 97 PELQPPPHAY 106 (130)
T ss_pred cccCCCCccc
Confidence 4555555544
No 338
>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=53.44 E-value=57 Score=33.65 Aligned_cols=77 Identities=6% Similarity=0.129 Sum_probs=52.3
Q ss_pred EEEEEE--eCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcC-hhHHHHHHHHHHH
Q 043276 24 AVPIYV--DNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHML-PSLGSRIFEKANE 100 (829)
Q Consensus 24 V~iI~~--dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~-~~~~~~i~~~a~~ 100 (829)
|++|.. ++.|.......+.+++++.|.++.... ...+.+...+.+..+...+.+.+|+... ......++.++.+
T Consensus 2 Ig~i~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~---~~~~~~~~~~~l~~~~~~~vdgii~~~~~~~~~~~~i~~~~~ 78 (273)
T cd06305 2 IAVVRYGGSGDFDQAYLAGTKAEAEALGGDLRVYD---AGGDDAKQADQIDQAIAQKVDAIIIQHGRAEVLKPWVKRALD 78 (273)
T ss_pred eEEEeecCCCcHHHHHHHHHHHHHHHcCCEEEEEC---CCCCHHHHHHHHHHHHHcCCCEEEEecCChhhhHHHHHHHHH
Confidence 566654 577778889999999999999876532 2222333445666666678999988753 3334566777888
Q ss_pred cCc
Q 043276 101 IGL 103 (829)
Q Consensus 101 ~gm 103 (829)
.|+
T Consensus 79 ~~i 81 (273)
T cd06305 79 AGI 81 (273)
T ss_pred cCC
Confidence 774
No 339
>COG2358 Imp TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]
Probab=53.06 E-value=1e+02 Score=33.08 Aligned_cols=59 Identities=27% Similarity=0.358 Sum_probs=37.9
Q ss_pred CCCHHHHHhCCCcEEE-EeCc----hHHHHHHhcCCCccceeecC--ChHHHHHHHhcCCcCCceeEEEcch
Q 043276 532 ITDVNLLIKRGDNVGY-QKGS----FVLGILKQLGFDERKLVVYN--SHEECDELFQKGSANGGIAAAFDEI 596 (829)
Q Consensus 532 I~s~~dL~~~~~~vg~-~~~s----~~~~~l~~~~~~~~~~~~~~--~~~~~~~~l~~g~~~~g~~a~~~~~ 596 (829)
|++++|| .|+||.+ ..|| ..+..|+..++......... ...+..+++..|. +||++.-.
T Consensus 129 Ikti~DL--~GKrV~iG~~gSgt~~~a~~il~a~Gi~~~~~~~~~~~~~a~~~~~l~~g~----iDA~~~~~ 194 (321)
T COG2358 129 IKTIADL--KGKRVAIGPPGSGTEATARQILEALGITYDDYELDLGLGDAESADALKNGT----IDAAFYVA 194 (321)
T ss_pred cceehhc--CCCEEeecCCCCccHHHHHHHHHHcCCCCcchhhhhhcCchhhHHHhhCCc----ccEEEEec
Confidence 8999999 5999887 3344 34455666666544332211 2234578899999 89887553
No 340
>cd08479 PBP2_CrgA_like_9 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 9. 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=53.02 E-value=1.1e+02 Score=29.16 Aligned_cols=64 Identities=5% Similarity=-0.077 Sum_probs=38.4
Q ss_pred EeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccEEEeccccccccceeccccccccccceEEEE
Q 043276 339 GYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMIV 418 (829)
Q Consensus 339 G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv 418 (829)
.+-..++..+.++.+ .+++++.... ....+.+|++|+++..- ......+. +.++.....++++
T Consensus 14 ~~l~~~l~~f~~~~P-~i~i~~~~~~------------~~~~l~~g~~Dl~i~~~---~~~~~~l~-~~~l~~~~~~~~~ 76 (198)
T cd08479 14 RHIAPALSDFAKRYP-ELEVQLELTD------------RPVDLVEEGFDLDIRVG---DLPDSSLI-ARKLAPNRRILCA 76 (198)
T ss_pred HHHHHHHHHHHHHCC-CeEEEEEecC------------ccccccccCccEEEEcC---CCCCccce-eeeccCCceEEEE
Confidence 456788888888887 4566655311 23578899999998421 11122233 3456666666665
Q ss_pred E
Q 043276 419 P 419 (829)
Q Consensus 419 ~ 419 (829)
+
T Consensus 77 ~ 77 (198)
T cd08479 77 S 77 (198)
T ss_pred C
Confidence 4
No 341
>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=53.02 E-value=1.7e+02 Score=30.13 Aligned_cols=108 Identities=9% Similarity=-0.034 Sum_probs=59.9
Q ss_pred ChHHHHHHHHHHHHHc--CCcEEEEEEEeCc-cccchHHHHHHHHHhC-CceeeeEEecCCCCChhHHHHHHHHhhc--C
Q 043276 4 NDSSQVGAITAIIKAF--GWREAVPIYVDNQ-YGEELIPSLTDALQAI-DTRVPYRSVISPLATDDQIEKELYKLFT--M 77 (829)
Q Consensus 4 sD~~q~~ai~~ll~~f--gW~~V~iI~~dd~-yG~~~~~~l~~~l~~~-gi~I~~~~~i~~~~~~~~~~~~l~~lk~--~ 77 (829)
++..-++.+++.+... |.+++++|..... ....-.+.+.+++++. ++++... ......+.+.-.+.+.++.+ .
T Consensus 102 d~~~~g~~~~~~l~~~~~g~~~i~~i~g~~~~~~~~R~~g~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~l~~~~ 180 (271)
T cd06321 102 DNVQAGEISCQYLADRLGGKGNVAILNGPPVSAVLDRVAGCKAALAKYPGIKLLSD-DQNGKGSRDGGLRVMQGLLTRFP 180 (271)
T ss_pred chHHHHHHHHHHHHHHhCCCceEEEEeCCCCchHHHHHHHHHHHHHhCCCcEEEee-ecCCCCChhhHHHHHHHHHHhCC
Confidence 4444556666777666 9999999975432 2234457777888887 5653211 11111111122233344322 2
Q ss_pred CCeEEEEEcChhHHHHHHHHHHHcCccccCeEEEEcCc
Q 043276 78 QTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDG 115 (829)
Q Consensus 78 ~arViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t~~ 115 (829)
..+. |++.+...+..++...++.|+ .+..++..|.
T Consensus 181 ~~~a-i~~~~d~~a~g~~~al~~~g~--~di~v~g~d~ 215 (271)
T cd06321 181 KLDG-VFAINDPTAIGADLAAKQAGR--NDIKITSVDG 215 (271)
T ss_pred CCCE-EEECCchhHHHHHHHHHHcCC--CCcEEEEecC
Confidence 3444 444566677788899999886 3445554443
No 342
>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=52.72 E-value=67 Score=31.35 Aligned_cols=74 Identities=18% Similarity=0.225 Sum_probs=46.4
Q ss_pred CCCHHHHHhCCCcEEEEeCchHHHHHHhcCCCccceeecCChHHHHHHHhcCCcCCceeEEEcchhHHHHHHhcCCCceE
Q 043276 532 ITDVNLLIKRGDNVGYQKGSFVLGILKQLGFDERKLVVYNSHEECDELFQKGSANGGIAAAFDEIPYAKLLIGQHCSKYT 611 (829)
Q Consensus 532 I~s~~dL~~~~~~vg~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~~c~~l~ 611 (829)
+++.+|| .+++|+.......+.||++.+.+ ..++.....-|. +-..|- .|++++-.....-+.++. |.
T Consensus 101 ~~~~~~l--~~~rIATkyp~i~~~~f~~~Gi~-v~ii~l~GsvE~--aP~~Gl----aD~IvDiv~TG~TL~~Ng---L~ 168 (182)
T TIGR00070 101 ISSVEDL--KGKRIATKYPNLARRYFEKKGID-VEIIKLNGSVEL--APLLGL----ADAIVDIVSTGTTLRENG---LR 168 (182)
T ss_pred CCChHHh--CCCEEEECCHHHHHHHHHHcCCe-EEEEECcceeec--ccCCCc----eeEEEEEeCCHHHHHHCC---CE
Confidence 5778898 48899998778889999988774 344444333222 223555 788877665555555543 44
Q ss_pred EeCccc
Q 043276 612 MVEPTF 617 (829)
Q Consensus 612 ~v~~~~ 617 (829)
++.+.+
T Consensus 169 ~ie~i~ 174 (182)
T TIGR00070 169 IIEVIL 174 (182)
T ss_pred EeeEEE
Confidence 554433
No 343
>PRK07377 hypothetical protein; Provisional
Probab=52.36 E-value=27 Score=33.55 Aligned_cols=62 Identities=19% Similarity=0.263 Sum_probs=45.1
Q ss_pred CceEEEecccccCccceEEEeecCCCCCceEEEeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcc
Q 043276 307 EKKLRVGVPVKKGFSDFVKVTIDPKTQETSVVGYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEF 386 (829)
Q Consensus 307 ~~~lrv~v~~~~~~~p~~~~~~~~~~~~~~~~G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~ 386 (829)
..++|+|+....+ ..+..-+-.++.++.+.++++. +.++++++ +-..+.+.+.+|++
T Consensus 74 s~~~Rlgv~~~~~-------------~~~~~~~~l~~~l~~~~~~y~~--rlElv~y~--------~~~~l~~aL~~~eV 130 (184)
T PRK07377 74 SLVMRLGVLEIET-------------ETSSVFDQLIDQLRTILDKYHL--RLELVVYP--------DLQALEQALRDKEV 130 (184)
T ss_pred ccEEEEEEEeccc-------------cccccHHHHHHHHHHHHHHhCc--eeeEEecC--------CHHHHHHHHhcCCc
Confidence 4568999873210 1222344467888889998875 67788886 67999999999999
Q ss_pred cEEEe
Q 043276 387 DAVVG 391 (829)
Q Consensus 387 Di~~~ 391 (829)
|++.+
T Consensus 131 h~~c~ 135 (184)
T PRK07377 131 HAICL 135 (184)
T ss_pred cEEec
Confidence 98875
No 344
>COG3107 LppC Putative lipoprotein [General function prediction only]
Probab=52.30 E-value=1.7e+02 Score=33.31 Aligned_cols=48 Identities=10% Similarity=0.163 Sum_probs=40.6
Q ss_pred HHHHHHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceee
Q 043276 6 SSQVGAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVP 53 (829)
Q Consensus 6 ~~q~~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~ 53 (829)
+-.++..|+-+-.-|-|...++...+++|+...+.|.++.++.|...+
T Consensus 368 EDEa~~AA~~l~~qG~R~plvlvPr~~lG~Rv~~AF~~~Wq~~gg~~v 415 (604)
T COG3107 368 EDEARDAANHLWDQGKRNPLVLVPRNDLGDRVANAFNQEWQKLGGGTV 415 (604)
T ss_pred hHHHHHHHHHHHHccccCceEEecchHHHHHHHHHHHHHHHHhcCCch
Confidence 345667777777789999999999999999999999999999877433
No 345
>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=52.08 E-value=2.2e+02 Score=29.20 Aligned_cols=108 Identities=13% Similarity=0.110 Sum_probs=62.2
Q ss_pred ChHHHHHHHHHHHHHc--CCcEEEEEEEeCccc--cchHHHHHHHHHhC-CceeeeEEecCCCCChhHHHHHHHHhhc--
Q 043276 4 NDSSQVGAITAIIKAF--GWREAVPIYVDNQYG--EELIPSLTDALQAI-DTRVPYRSVISPLATDDQIEKELYKLFT-- 76 (829)
Q Consensus 4 sD~~q~~ai~~ll~~f--gW~~V~iI~~dd~yG--~~~~~~l~~~l~~~-gi~I~~~~~i~~~~~~~~~~~~l~~lk~-- 76 (829)
++...+..+++.+... |-+++++|....... ..-.+.+.+++++. |+.+... .....+.+.....+.++.+
T Consensus 103 d~~~~g~~~~~~l~~~~~g~~~i~~l~~~~~~~~~~~R~~g~~~~l~~~~~~~~~~~--~~~~~~~~~~~~~~~~~l~~~ 180 (270)
T cd06308 103 DNYEIGRQAGEYIANLLPGKGNILEIWGLEGSSPAIERHDGFKEALSKYPKIKIVAQ--QDGDWLKEKAEEKMEELLQAN 180 (270)
T ss_pred CcHHHHHHHHHHHHHHcCCCceEEEEECCCCCchHHHHHHHHHHHHHHCCCCEEEEe--cCCCccHHHHHHHHHHHHHhC
Confidence 3444555666666554 899999997443332 33467778888888 8765422 1111122222233444332
Q ss_pred CCCeEEEEEcChhHHHHHHHHHHHcCccccCeEEEEcCc
Q 043276 77 MQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTDG 115 (829)
Q Consensus 77 ~~arViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t~~ 115 (829)
...+ .|++.+...+..++..+++.|+. .+..-+.-|.
T Consensus 181 ~~~~-aI~~~~d~~a~g~~~al~~~g~~-~dv~vvg~d~ 217 (270)
T cd06308 181 PDID-LVYAHNDPMALGAYLAAKRAGRE-KEIKFIGIDG 217 (270)
T ss_pred CCCc-EEEeCCcHHHHHHHHHHHHcCCC-CCcEEEEecC
Confidence 2344 45556777788899999999975 4444444433
No 346
>PRK09492 treR trehalose repressor; Provisional
Probab=51.79 E-value=1.5e+02 Score=31.38 Aligned_cols=95 Identities=14% Similarity=0.063 Sum_probs=58.4
Q ss_pred hHHHHHHHHHHHHHcCCcEEEEEEEe-C--ccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeE
Q 043276 5 DSSQVGAITAIIKAFGWREAVPIYVD-N--QYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRV 81 (829)
Q Consensus 5 D~~q~~ai~~ll~~fgW~~V~iI~~d-d--~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arV 81 (829)
+..-+..+++.+...|-+++++|... . ..+..-.+.+.+++++.|+.+... .... +.+.-...+.++.+.....
T Consensus 159 ~~~~~~~a~~~L~~~G~~~I~~i~~~~~~~~~~~~R~~Gf~~al~~~g~~~~~~--~~~~-~~~~~~~~~~~~l~~~~~a 235 (315)
T PRK09492 159 DEGAIKLLMQRLYDQGHRHISYLGVDHSDVTTGKRRHQAYLAFCKQHKLTPVAA--LGGL-SMQSGYELVAKVLTPETTA 235 (315)
T ss_pred cHHHHHHHHHHHHHcCCCeEEEEcCCcccchhHHHHHHHHHHHHHHcCCCceee--cCCC-CchHHHHHHHHHhhcCCCE
Confidence 33444556676767799999999632 2 234556788899999999864321 1111 1122223344443344554
Q ss_pred EEEEcChhHHHHHHHHHHHcCc
Q 043276 82 FILHMLPSLGSRIFEKANEIGL 103 (829)
Q Consensus 82 iIv~~~~~~~~~i~~~a~~~gm 103 (829)
| +|++...+..+++.+++.|+
T Consensus 236 i-~~~~D~~A~g~~~al~~~g~ 256 (315)
T PRK09492 236 L-VCATDTLALGASKYLQEQGR 256 (315)
T ss_pred E-EEcCcHHHHHHHHHHHHcCC
Confidence 4 45566788889999999985
No 347
>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=51.67 E-value=2.8e+02 Score=29.39 Aligned_cols=42 Identities=17% Similarity=0.177 Sum_probs=30.4
Q ss_pred eHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccEEEecc
Q 043276 341 SIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDAVVGDT 393 (829)
Q Consensus 341 ~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di~~~~~ 393 (829)
...|+..+.+.+||++++. .. +-.-+...|.+|++|+.+...
T Consensus 23 ~~~i~~~iLE~~Gy~Ve~~--~~---------~~~~~~~al~~GdiD~~~e~W 64 (290)
T TIGR03414 23 TTALASVLLEGLGYQPKVT--LL---------SVPVTYAGLKDGDLDVFLGNW 64 (290)
T ss_pred HHHHHHHHHHHcCCcceeE--Ec---------cHHHHHHHHHcCCceEecccc
Confidence 3467778888889977653 32 346678888999999988553
No 348
>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=51.47 E-value=1.5e+02 Score=30.60 Aligned_cols=108 Identities=11% Similarity=0.193 Sum_probs=62.2
Q ss_pred ChHHHHHHHHHHHHHcCCcEEEEEEEeCc-cccchHHHHHHHHHhCCceeeeEE--ecCCCCChhHHHHHHHHhhcC--C
Q 043276 4 NDSSQVGAITAIIKAFGWREAVPIYVDNQ-YGEELIPSLTDALQAIDTRVPYRS--VISPLATDDQIEKELYKLFTM--Q 78 (829)
Q Consensus 4 sD~~q~~ai~~ll~~fgW~~V~iI~~dd~-yG~~~~~~l~~~l~~~gi~I~~~~--~i~~~~~~~~~~~~l~~lk~~--~ 78 (829)
++..-+..+++.+...|.++++++...++ .+..-.+.+.+.+++.|..+.... ........+...+.+.++.+. .
T Consensus 104 D~~~~g~~~~~~l~~~G~~~i~~l~~~~~~~~~~r~~g~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~ 183 (273)
T cd01541 104 DDEKGGYKATEYLIELGHRKIAGIFKADDLQGVKRMKGFIKAYREHGIPFNPSNVITYTTEEKEEKLFEKIKEILKRPER 183 (273)
T ss_pred CcHHHHHHHHHHHHHcCCcCEEEecCCCcccHHHHHHHHHHHHHHcCCCCChHHEEeccccchhhHHHHHHHHHHcCCCC
Confidence 34445566777777779999998864322 233445667888888886432111 111111112233445444332 2
Q ss_pred CeEEEEEcChhHHHHHHHHHHHcCccccCeEEEE
Q 043276 79 TRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIM 112 (829)
Q Consensus 79 arViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~ 112 (829)
.++ |++.+...+..+++.+++.|+..++.+-|.
T Consensus 184 ~~a-v~~~~d~~a~g~~~al~~~g~~~p~dv~vv 216 (273)
T cd01541 184 PTA-IVCYNDEIALRVIDLLKELGLKIPEDISVV 216 (273)
T ss_pred CCE-EEEcCcHHHHHHHHHHHHcCCCCCCcEEEE
Confidence 343 455666777789999999997655555544
No 349
>PF14981 FAM165: FAM165 family
Probab=51.33 E-value=24 Score=25.26 Aligned_cols=33 Identities=15% Similarity=0.185 Sum_probs=28.5
Q ss_pred ccchhHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q 043276 677 LNSFWGLFLIAGIAAILALIIFLAVFVHEHWNV 709 (829)
Q Consensus 677 l~~~~g~f~il~vg~~lallvf~~E~~~~~~~~ 709 (829)
++++--++||++.-..+.++.|..--+|++++.
T Consensus 3 L~~vPlLlYILaaKtlilClaFAgvK~yQ~krl 35 (51)
T PF14981_consen 3 LDNVPLLLYILAAKTLILCLAFAGVKMYQRKRL 35 (51)
T ss_pred hhhchHHHHHHHHHHHHHHHHHhhHHHHHHHHH
Confidence 467778999999999999999999988887765
No 350
>cd08483 PBP2_HvrB The C-terminal substrate-binding domain of LysR-type transcriptional regulator HvrB, an activator of S-adenosyl-L-homocysteine hydrolase expression, contains the type 2 periplasmic binding fold. The transcriptional regulator HvrB of the LysR family is required for the light-dependent activation of both ahcY, which encoding the enzyme S-adenosyl-L-homocysteine hydrolase (AdoHcyase) that responsible for the reversible hydrolysis of AdoHcy to adenosine and homocysteine, and orf5, a gene of unknown. The topology of this C-terminal domain of HvrB 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 transp
Probab=51.00 E-value=2.2e+02 Score=26.77 Aligned_cols=63 Identities=8% Similarity=0.147 Sum_probs=37.7
Q ss_pred eeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccEEEeccccccccceeccccccccccceEEEEE
Q 043276 340 YSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMIVP 419 (829)
Q Consensus 340 ~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv~ 419 (829)
+-..++..+.++.+ .+++++.. .+.+.++.+|++|+++..... ....+. ..++....++++++
T Consensus 14 ~l~~~l~~~~~~~P-~i~l~~~~------------~~~~~~l~~g~~Dl~i~~~~~---~~~~~~-~~~l~~~~~~~v~~ 76 (190)
T cd08483 14 WLMPRLGSFWAKHP-EIELSLLP------------SADLVDLRPDGIDVAIRYGNG---DWPGLE-SEPLTAAPFVVVAA 76 (190)
T ss_pred hHHhhHHHHHHHCC-CceEEEEe------------cCCcCCCCCCCcCEEEEecCC---CCCCcE-EEeecccceEeeeC
Confidence 34466777777776 35555532 112467899999999853221 112233 35677777777776
No 351
>PF06305 DUF1049: Protein of unknown function (DUF1049); InterPro: IPR010445 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=50.70 E-value=47 Score=26.26 Aligned_cols=27 Identities=11% Similarity=0.215 Sum_probs=14.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhcc
Q 043276 683 LFLIAGIAAILALIIFLAVFVHEHWNV 709 (829)
Q Consensus 683 ~f~il~vg~~lallvf~~E~~~~~~~~ 709 (829)
++..+++|.+++.++.+...+..+++.
T Consensus 24 il~~f~~G~llg~l~~~~~~~~~r~~~ 50 (68)
T PF06305_consen 24 ILIAFLLGALLGWLLSLPSRLRLRRRI 50 (68)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344456666666666666554444433
No 352
>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=50.53 E-value=68 Score=35.04 Aligned_cols=76 Identities=17% Similarity=0.103 Sum_probs=52.5
Q ss_pred HHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcCh
Q 043276 10 GAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLP 88 (829)
Q Consensus 10 ~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~~ 88 (829)
..+.++++.+| +++.+|+....+ ....+.+.+.|++.|+.+.... +....+.+.+.+.+..+++.++++||-.+..
T Consensus 12 ~~l~~~~~~~g-~~~liv~~~~~~-~~~~~~v~~~l~~~~i~~~~~~-~~~~p~~~~v~~~~~~~~~~~~d~IIavGGG 87 (349)
T cd08550 12 KEIAAILSTFG-SKVAVVGGKTVL-KKSRPRFEAALAKSIIVVDVIV-FGGECSTEEVVKALCGAEEQEADVIIGVGGG 87 (349)
T ss_pred HHHHHHHHHcC-CeEEEEEChHHH-HHHHHHHHHHHHhcCCeeEEEE-cCCCCCHHHHHHHHHHHHhcCCCEEEEecCc
Confidence 34567788899 888777643333 3556788888988887654332 4444455667777788888889999987764
No 353
>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=50.51 E-value=74 Score=35.14 Aligned_cols=82 Identities=13% Similarity=0.091 Sum_probs=57.1
Q ss_pred HHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcChh
Q 043276 10 GAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPS 89 (829)
Q Consensus 10 ~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~~~ 89 (829)
..+.++++.++ +++.||+..... ..+.+.+.|++.|+.+.... +...++.+.+.+.+..+++.++++||-.+...
T Consensus 12 ~~l~~~l~~~~-~r~livtd~~~~---~~~~v~~~L~~~g~~~~~~~-~~~~p~~~~v~~~~~~~~~~~~D~IIaiGGGS 86 (374)
T cd08183 12 KELPALAAELG-RRVLLVTGASSL---RAAWLIEALRAAGIEVTHVV-VAGEPSVELVDAAVAEARNAGCDVVIAIGGGS 86 (374)
T ss_pred HHHHHHHHHcC-CcEEEEECCchH---HHHHHHHHHHHcCCeEEEec-CCCCcCHHHHHHHHHHHHhcCCCEEEEecCch
Confidence 34566777776 888888744333 67778888999998765433 34455666788888888889999999987653
Q ss_pred --HHHHHHH
Q 043276 90 --LGSRIFE 96 (829)
Q Consensus 90 --~~~~i~~ 96 (829)
++..+..
T Consensus 87 ~~D~aK~ia 95 (374)
T cd08183 87 VIDAGKAIA 95 (374)
T ss_pred HHHHHHHHH
Confidence 4444433
No 354
>cd08471 PBP2_CrgA_like_2 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 2. 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=50.17 E-value=1e+02 Score=29.44 Aligned_cols=64 Identities=6% Similarity=0.091 Sum_probs=36.5
Q ss_pred EeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccEEEeccccccccceeccccccccccceEEEE
Q 043276 339 GYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMIV 418 (829)
Q Consensus 339 G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv 418 (829)
++-..++..+.++.+ .+++++... +.+. .+.+|++|+++...... ...+. +.++....+++++
T Consensus 14 ~~l~~~l~~~~~~~P-~v~i~i~~~-----------~~~~-~~~~~~~Dl~i~~~~~~---~~~~~-~~~l~~~~~~~v~ 76 (201)
T cd08471 14 LHVLPIITDFLDAYP-EVSVRLLLL-----------DRVV-NLLEEGVDVAVRIGHLP---DSSLV-ATRVGSVRRVVCA 76 (201)
T ss_pred HHHHHHHHHHHHHCC-CcEEEEEEc-----------Cccc-hhhcccccEEEEecCCC---CCCeE-EEEccccceEEEE
Confidence 345678888888877 456655431 1222 35678999988432211 12232 3466666666666
Q ss_pred E
Q 043276 419 P 419 (829)
Q Consensus 419 ~ 419 (829)
+
T Consensus 77 ~ 77 (201)
T cd08471 77 S 77 (201)
T ss_pred C
Confidence 5
No 355
>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=49.94 E-value=1.3e+02 Score=30.76 Aligned_cols=110 Identities=8% Similarity=0.052 Sum_probs=62.0
Q ss_pred ChHHHHHHHHHHHHHcCCcEEEEEEEeCcc-ccchHHHHHHHHHhCCceeeeEEe--cCCCCChhHHHHHHHHhhcC--C
Q 043276 4 NDSSQVGAITAIIKAFGWREAVPIYVDNQY-GEELIPSLTDALQAIDTRVPYRSV--ISPLATDDQIEKELYKLFTM--Q 78 (829)
Q Consensus 4 sD~~q~~ai~~ll~~fgW~~V~iI~~dd~y-G~~~~~~l~~~l~~~gi~I~~~~~--i~~~~~~~~~~~~l~~lk~~--~ 78 (829)
++..-+..+++.+...|-+.++++...... ...-.+.+.+++++.|+.+..... .....+.+.-...+.++.+. .
T Consensus 92 d~~~~g~~~~~~l~~~g~~~i~~i~~~~~~~~~~R~~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~ 171 (265)
T cd01543 92 DNAAIGRMAAEHFLERGFRHFAFYGLPGARWSDEREEAFRQLVAEAGYECSFFYRGLSTDAQSWEEEQEELAQWLQSLPK 171 (265)
T ss_pred CHHHHHHHHHHHHHHCCCcEEEEEcCCCCHHHHHHHHHHHHHHHHcCCccccccCccccccccHHHHHHHHHHHHhcCCC
Confidence 444455566677777799999998643331 123356788889998876521111 11011111223344443322 2
Q ss_pred CeEEEEEcChhHHHHHHHHHHHcCcccc-CeEEEEcC
Q 043276 79 TRVFILHMLPSLGSRIFEKANEIGLMNK-GCVWIMTD 114 (829)
Q Consensus 79 arViIv~~~~~~~~~i~~~a~~~gm~~~-~~vwI~t~ 114 (829)
.+ .|++++...+..+++.+++.|+..+ +...|.-|
T Consensus 172 ~~-ai~~~~d~~a~g~~~~l~~~g~~vp~di~vigfd 207 (265)
T cd01543 172 PV-GIFACTDARARQLLEACRRAGIAVPEEVAVLGVD 207 (265)
T ss_pred Cc-EEEecChHHHHHHHHHHHHhCCCCCCceEEEeeC
Confidence 33 4666677788889999999997444 34444433
No 356
>cd08472 PBP2_CrgA_like_3 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 3. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene a
Probab=49.68 E-value=1.8e+02 Score=27.56 Aligned_cols=64 Identities=9% Similarity=0.045 Sum_probs=36.9
Q ss_pred EeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccEEEeccccccccceeccccccccccceEEEE
Q 043276 339 GYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMIV 418 (829)
Q Consensus 339 G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv 418 (829)
++..+++..+.++.+ .+++++.. .+.+.. +.++++|+++.... .....+. +.++....+++++
T Consensus 14 ~~l~~~l~~~~~~~P-~i~v~~~~-----------~~~~~~-~l~~~~D~~i~~~~---~~~~~l~-~~~l~~~~~~~v~ 76 (202)
T cd08472 14 LLLIPALPDFLARYP-DIELDLGV-----------SDRPVD-LIREGVDCVIRVGE---LADSSLV-ARRLGELRMVTCA 76 (202)
T ss_pred HHHHHHHHHHHHHCC-CcEEEEEE-----------CCCcch-hhcccccEEEEcCC---CCCccEE-EEEccceeEEEEE
Confidence 455678888888876 35555532 123344 34567999985321 1112232 4566677777776
Q ss_pred E
Q 043276 419 P 419 (829)
Q Consensus 419 ~ 419 (829)
+
T Consensus 77 ~ 77 (202)
T cd08472 77 S 77 (202)
T ss_pred C
Confidence 6
No 357
>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=49.66 E-value=2.4e+02 Score=29.04 Aligned_cols=95 Identities=11% Similarity=0.021 Sum_probs=53.6
Q ss_pred HHHHHHHHHHHHHc--CCcEEEEEEEeCc-cccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhc--CCCe
Q 043276 6 SSQVGAITAIIKAF--GWREAVPIYVDNQ-YGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFT--MQTR 80 (829)
Q Consensus 6 ~~q~~ai~~ll~~f--gW~~V~iI~~dd~-yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~--~~ar 80 (829)
...+..+++.+... |-++|+++..... ....-.+.+.+.+++.++++... .....+.+.....+..+.+ ...+
T Consensus 110 ~~~g~~aa~~l~~~~~g~~~i~~~~g~~~~~~~~R~~gf~~~l~~~~~~~~~~--~~~~~~~~~~~~~~~~~l~~~~~~~ 187 (274)
T cd06311 110 YGMGRVAGEYIATKLGGNGNIVVLRGIPTPIDNERVDAFDAAIAKYPIKILDR--QYANWNRDDAFSVMQDLLTKFPKID 187 (274)
T ss_pred HHHHHHHHHHHHHHhCCCCeEEEEECCCCcchhHHHHHHHHHHhhCCcEEEec--cCCCCcHHHHHHHHHHHHHhCCCcC
Confidence 34455666766544 8899999974332 22334577888888888665432 2212122222333444322 2344
Q ss_pred EEEEEcChhHHHHHHHHHHHcCc
Q 043276 81 VFILHMLPSLGSRIFEKANEIGL 103 (829)
Q Consensus 81 ViIv~~~~~~~~~i~~~a~~~gm 103 (829)
+| ++.+...+..++..+++.|.
T Consensus 188 ai-~~~~d~~a~g~~~al~~~g~ 209 (274)
T cd06311 188 AV-WAHDDDMAVGVLAAIKQAGR 209 (274)
T ss_pred EE-EECCCcHHHHHHHHHHHcCC
Confidence 43 44455567788888888885
No 358
>cd08474 PBP2_CrgA_like_5 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 5. 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=49.26 E-value=1.3e+02 Score=28.78 Aligned_cols=64 Identities=14% Similarity=-0.003 Sum_probs=35.3
Q ss_pred eecCChHHHHHHHhcCCcCCceeEEEcchhHHHHHHhcCCCceEEe-Ccc-cccCCceeeecCCCCchhhHHH
Q 043276 568 VVYNSHEECDELFQKGSANGGIAAAFDEIPYAKLLIGQHCSKYTMV-EPT-FKTAGFGFAFPLHSPLVHDVSK 638 (829)
Q Consensus 568 ~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~~c~~l~~v-~~~-~~~~~~~~~~~k~spl~~~in~ 638 (829)
...++.+...+.+..|. ..+++.+.....+ ..... +... .+. .....++++.+++.+....+..
T Consensus 132 ~~~~~~~~~~~~v~~g~----gi~~lp~~~~~~~-~~~~~--l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~ 197 (202)
T cd08474 132 LILNDSDLMLDAALDGL----GIAYLFEDLVAEH-LASGR--LVRVLEDWSPPFPGGYLYYPSRRRVPPALRA 197 (202)
T ss_pred EEECCHHHHHHHHHcCC----CEEEeeHHHHHHH-HHCCC--cEEeCCcccCCCCCEEEEEeCCCCCCHHHHH
Confidence 45678888899999987 4556555433222 22221 2222 221 2345678888777654444443
No 359
>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=48.67 E-value=67 Score=35.85 Aligned_cols=80 Identities=13% Similarity=0.025 Sum_probs=56.6
Q ss_pred HHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcCh--hHHHHH
Q 043276 17 KAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLP--SLGSRI 94 (829)
Q Consensus 17 ~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~~--~~~~~i 94 (829)
...+.+++.||+...-...+..+.+.+.|++.|+.+.....+..+++.+.+.+.+..+++.++++||-.+.. -++..+
T Consensus 17 ~~~~~~k~liVtd~~~~~~g~~~~v~~~L~~~gi~~~~f~~v~~~p~~~~v~~~~~~~~~~~~D~IIaiGGGS~iD~AK~ 96 (398)
T cd08178 17 DLKGKKRAFIVTDRFMVKLGYVDKVIDVLKRRGVETEVFSDVEPDPSLETVRKGLELMNSFKPDTIIALGGGSPMDAAKI 96 (398)
T ss_pred HhcCCCeEEEEcChhHHhCccHHHHHHHHHHCCCeEEEecCCCCCcCHHHHHHHHHHHHhcCCCEEEEeCCccHHHHHHH
Confidence 344668888887444344557888999999999877654455566666778888888888899999987653 344444
Q ss_pred HH
Q 043276 95 FE 96 (829)
Q Consensus 95 ~~ 96 (829)
+.
T Consensus 97 iA 98 (398)
T cd08178 97 MW 98 (398)
T ss_pred HH
Confidence 43
No 360
>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=48.51 E-value=1.2e+02 Score=31.47 Aligned_cols=85 Identities=15% Similarity=0.169 Sum_probs=54.5
Q ss_pred EEEEEEE----eCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcChhHHHHHHHHH
Q 043276 23 EAVPIYV----DNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKA 98 (829)
Q Consensus 23 ~V~iI~~----dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~~~~~~~i~~~a 98 (829)
+|+++++ |..|.....+.+.+..++.|+++.+.+..+ +.+++.+.+..+.+.+.++||..+. .....+.+.|
T Consensus 1 kva~l~~g~~~D~~~n~~~~~G~~~~~~~~gv~~~~~e~~~---~~~~~~~~i~~~~~~g~dlIi~~g~-~~~~~~~~vA 76 (258)
T cd06353 1 KVAFVYVGPIGDQGWNYAHDEGRKAAEKALGVEVTYVENVP---EGADAERVLRELAAQGYDLIFGTSF-GFMDAALKVA 76 (258)
T ss_pred CEEEEEeCCCCccchhHHHHHHHHHHHHhcCCeEEEEecCC---chHhHHHHHHHHHHcCCCEEEECch-hhhHHHHHHH
Confidence 4778875 333444556777777777899888776543 2457788888888888999988443 3333444555
Q ss_pred HHcCccccCeEEEEcCc
Q 043276 99 NEIGLMNKGCVWIMTDG 115 (829)
Q Consensus 99 ~~~gm~~~~~vwI~t~~ 115 (829)
.+- ++..|+..++
T Consensus 77 ~~~----p~~~F~~~d~ 89 (258)
T cd06353 77 KEY----PDVKFEHCSG 89 (258)
T ss_pred HHC----CCCEEEECCC
Confidence 553 4566776554
No 361
>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=48.50 E-value=1.7e+02 Score=28.18 Aligned_cols=96 Identities=8% Similarity=-0.018 Sum_probs=52.7
Q ss_pred HHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhC--CceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcC
Q 043276 10 GAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAI--DTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHML 87 (829)
Q Consensus 10 ~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~--gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~ 87 (829)
..+.+.+..-+ .+|.++....+. ++.+.+.+++. |+.|+....-+.. .++-.+.+..|+++++++|++.+.
T Consensus 36 ~~ll~~~~~~~-~~v~llG~~~~~----~~~~~~~l~~~yp~l~i~g~~~g~~~--~~~~~~i~~~I~~~~pdiv~vglG 108 (171)
T cd06533 36 PALLELAAQKG-LRVFLLGAKPEV----LEKAAERLRARYPGLKIVGYHHGYFG--PEEEEEIIERINASGADILFVGLG 108 (171)
T ss_pred HHHHHHHHHcC-CeEEEECCCHHH----HHHHHHHHHHHCCCcEEEEecCCCCC--hhhHHHHHHHHHHcCCCEEEEECC
Confidence 33444444334 355566544443 34444444443 6666653322222 233334677888888999988887
Q ss_pred hhHHHHHHHHHHHcCccccCeEEEEcCc
Q 043276 88 PSLGSRIFEKANEIGLMNKGCVWIMTDG 115 (829)
Q Consensus 88 ~~~~~~i~~~a~~~gm~~~~~vwI~t~~ 115 (829)
.+.-..++.+..+.. ..-+|+...+
T Consensus 109 ~PkQE~~~~~~~~~l---~~~v~~~vG~ 133 (171)
T cd06533 109 APKQELWIARHKDRL---PVPVAIGVGG 133 (171)
T ss_pred CCHHHHHHHHHHHHC---CCCEEEEece
Confidence 776666666655543 3456665444
No 362
>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=47.76 E-value=73 Score=32.86 Aligned_cols=78 Identities=8% Similarity=0.096 Sum_probs=53.8
Q ss_pred EEEEEEEe--CccccchHHHHHHHHHh-CCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcCh-hHHHHHHHHH
Q 043276 23 EAVPIYVD--NQYGEELIPSLTDALQA-IDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLP-SLGSRIFEKA 98 (829)
Q Consensus 23 ~V~iI~~d--d~yG~~~~~~l~~~l~~-~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~~-~~~~~i~~~a 98 (829)
+|++|..+ +.|.......+.+++++ .|..+.+... ..+.+...+.+..+.+.+.+.+|+.... +....++.++
T Consensus 1 ~igvi~~~~~~~~~~~~~~gi~~~~~~~~~~~~~~~~~---~~~~~~~~~~i~~l~~~~vdgiii~~~~~~~~~~~~~~l 77 (272)
T cd06301 1 KIGVSMANFDDNFLTLLRNAMKEHAKVLGGVELQFEDA---KNDVATQLSQVENFIAQGVDAIIVVPVDTAATAPIVKAA 77 (272)
T ss_pred CeeEeecccCCHHHHHHHHHHHHHHHHcCCcEEEEeCC---CCCHHHHHHHHHHHHHcCCCEEEEecCchhhhHHHHHHH
Confidence 36777754 77888889999999999 8988765421 1223345566777777889988887644 3345667777
Q ss_pred HHcCc
Q 043276 99 NEIGL 103 (829)
Q Consensus 99 ~~~gm 103 (829)
.+.|+
T Consensus 78 ~~~~i 82 (272)
T cd06301 78 NAAGI 82 (272)
T ss_pred HHCCC
Confidence 77663
No 363
>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=47.71 E-value=1.5e+02 Score=30.35 Aligned_cols=100 Identities=15% Similarity=-0.001 Sum_probs=56.4
Q ss_pred HHHHHHHHHHHcCCcEEEEEEEeCccc--cchHHHHHHHHHhCCceeeeEEecCCC-CChhHHHHHHHHhhcCCCeEEEE
Q 043276 8 QVGAITAIIKAFGWREAVPIYVDNQYG--EELIPSLTDALQAIDTRVPYRSVISPL-ATDDQIEKELYKLFTMQTRVFIL 84 (829)
Q Consensus 8 q~~ai~~ll~~fgW~~V~iI~~dd~yG--~~~~~~l~~~l~~~gi~I~~~~~i~~~-~~~~~~~~~l~~lk~~~arViIv 84 (829)
-+..+++.+...|.+++++|..+.+.. ..-.+.|.+++++.|+.+......... .....+...+..+. ...+ .|+
T Consensus 105 ~~~~a~~~l~~~g~~~i~~i~~~~~~~~~~~R~~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~-~~~~-ai~ 182 (268)
T cd06277 105 GAYAATEYLIEKGHRKIGFVGDPLYSPSFEERYEGYKKALLDHGIPFNEDYDITEKEEDEEDIGKFIDELK-PLPT-AFF 182 (268)
T ss_pred HHHHHHHHHHHCCCCcEEEECCCCCCcchHHHHHHHHHHHHHcCCCCCcceEEEcchhHHHHHHHHHhcCC-CCCC-EEE
Confidence 344455667667999999997554422 334567888898888765322111111 11122333333321 1233 455
Q ss_pred EcChhHHHHHHHHHHHcCccccCeE
Q 043276 85 HMLPSLGSRIFEKANEIGLMNKGCV 109 (829)
Q Consensus 85 ~~~~~~~~~i~~~a~~~gm~~~~~v 109 (829)
+++...+..+++.+++.|+..++-+
T Consensus 183 ~~~d~~a~g~~~a~~~~g~~~p~di 207 (268)
T cd06277 183 CSNDGVAFLLIKVLKEMGIRVPEDV 207 (268)
T ss_pred ECCcHHHHHHHHHHHHcCCCCCCcc
Confidence 5566677788888888887544433
No 364
>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=47.63 E-value=1.7e+02 Score=25.86 Aligned_cols=81 Identities=15% Similarity=0.143 Sum_probs=43.2
Q ss_pred HHHcCCcEEEEEEEeCcc-ccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcChhHHHHH
Q 043276 16 IKAFGWREAVPIYVDNQY-GEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRI 94 (829)
Q Consensus 16 l~~fgW~~V~iI~~dd~y-G~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~~~~~~~i 94 (829)
++..|.+.|.-+-.|++- +....+.+.+++++.|+...+.-......+.+++......|.+....|.+-|.+..-+..+
T Consensus 23 la~~GfktVInlRpd~E~~~qp~~~~~~~~a~~~Gl~y~~iPv~~~~~~~~~v~~f~~~l~~~~~Pvl~hC~sG~Ra~~l 102 (110)
T PF04273_consen 23 LAAQGFKTVINLRPDGEEPGQPSSAEEAAAAEALGLQYVHIPVDGGAITEEDVEAFADALESLPKPVLAHCRSGTRASAL 102 (110)
T ss_dssp HHHCT--EEEE-S-TTSTTT-T-HHCHHHHHHHCT-EEEE----TTT--HHHHHHHHHHHHTTTTSEEEE-SCSHHHHHH
T ss_pred HHHCCCcEEEECCCCCCCCCCCCHHHHHHHHHHcCCeEEEeecCCCCCCHHHHHHHHHHHHhCCCCEEEECCCChhHHHH
Confidence 455899999998877543 4556677888999999886654333333445566665555655555666666565555444
Q ss_pred HH
Q 043276 95 FE 96 (829)
Q Consensus 95 ~~ 96 (829)
..
T Consensus 103 ~~ 104 (110)
T PF04273_consen 103 WA 104 (110)
T ss_dssp HH
T ss_pred HH
Confidence 43
No 365
>cd03770 SR_TndX_transposase Serine Recombinase (SR) family, TndX-like transposase subfamily, catalytic domain; composed of large serine recombinases similar to Clostridium TndX and TnpX transposases. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining mechanism which involves a transient phosphoserine linkage between DNA and the enzyme. They are functionally versatile and include resolvases, invertases, integrases, and transposases. TndX mediates the excision and circularization of the conjugative transposon Tn5397 from Clostridium difficile. TnpX is responsible for the movement of the nonconjugative chloramphenicol resistance elements of the Tn4451/3 family. Mobile genetic elements such as transposons are important vehicles for the transmission of virulence and antibiotic resistance in many microorganisms.
Probab=47.38 E-value=1.8e+02 Score=26.94 Aligned_cols=20 Identities=15% Similarity=0.127 Sum_probs=11.1
Q ss_pred HHHHHHHHHHHHHcCCcEEE
Q 043276 6 SSQVGAITAIIKAFGWREAV 25 (829)
Q Consensus 6 ~~q~~ai~~ll~~fgW~~V~ 25 (829)
..|-+++-++.+..||.-+.
T Consensus 21 e~Q~~~l~~~a~~~g~~i~~ 40 (140)
T cd03770 21 ENQKAILEEYAKENGLENIR 40 (140)
T ss_pred HHHHHHHHHHHHHCCCEEEE
Confidence 44555555556666665444
No 366
>PRK10653 D-ribose transporter subunit RbsB; Provisional
Probab=47.03 E-value=2.7e+02 Score=29.15 Aligned_cols=98 Identities=12% Similarity=0.024 Sum_probs=55.3
Q ss_pred ChHHH-HHHHHHHH-HHcCCc-EEEEEEEeCc--cccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCC
Q 043276 4 NDSSQ-VGAITAII-KAFGWR-EAVPIYVDNQ--YGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQ 78 (829)
Q Consensus 4 sD~~q-~~ai~~ll-~~fgW~-~V~iI~~dd~--yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~ 78 (829)
.|..+ +..+++.+ +..|.+ .++++..+.+ ......+.+.+++++.|+.+... .....+..+....+.++.+..
T Consensus 128 ~D~~~~g~~~~~~l~~~~~~~~~i~~~~~~~~~~~~~~R~~gf~~al~~~g~~~~~~--~~~~~~~~~~~~~~~~~l~~~ 205 (295)
T PRK10653 128 SDNVAGGKMAGDFIAKKLGEGAKVIQLEGIAGTSAARERGEGFKQAVAAHKFNVLAS--QPADFDRTKGLNVMQNLLTAH 205 (295)
T ss_pred cChHHHHHHHHHHHHHHhCCCceEEEEEccCCCccHHHHHHHHHHHHhhCCCEEEEe--cCCCCCHHHHHHHHHHHHHhC
Confidence 45555 46666655 445653 5555543222 23455688889999999765321 111222223334455554433
Q ss_pred CeE-EEEEcChhHHHHHHHHHHHcCc
Q 043276 79 TRV-FILHMLPSLGSRIFEKANEIGL 103 (829)
Q Consensus 79 arV-iIv~~~~~~~~~i~~~a~~~gm 103 (829)
.++ .|++.+...+..++.++++.|+
T Consensus 206 ~~~~ai~~~~d~~A~g~l~al~~~G~ 231 (295)
T PRK10653 206 PDVQAVFAQNDEMALGALRALQTAGK 231 (295)
T ss_pred CCcCEEEECCChhHHHHHHHHHHcCC
Confidence 333 3445556666678999999985
No 367
>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=46.79 E-value=1.2e+02 Score=28.95 Aligned_cols=67 Identities=12% Similarity=0.039 Sum_probs=46.7
Q ss_pred CCcEEEEEEEeCccc---cchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhh-cCCCeEEEEEcCh
Q 043276 20 GWREAVPIYVDNQYG---EELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLF-TMQTRVFILHMLP 88 (829)
Q Consensus 20 gW~~V~iI~~dd~yG---~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk-~~~arViIv~~~~ 88 (829)
..-+|++|...|+-+ ......+...+++.|..+.....++++ .+.+.+.+.+.. ..++++||..+..
T Consensus 3 ~~~rv~vit~~d~~~~~~d~n~~~l~~~L~~~G~~v~~~~iv~Dd--~~~i~~~l~~~~~~~~~DlVIttGGt 73 (163)
T TIGR02667 3 IPLRIAILTVSDTRTEEDDTSGQYLVERLTEAGHRLADRAIVKDD--IYQIRAQVSAWIADPDVQVILITGGT 73 (163)
T ss_pred CccEEEEEEEeCcCCccCCCcHHHHHHHHHHCCCeEEEEEEcCCC--HHHHHHHHHHHHhcCCCCEEEECCCc
Confidence 345788887665433 233567788899999998887777755 556777777764 3568888887653
No 368
>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=46.45 E-value=1.9e+02 Score=29.78 Aligned_cols=102 Identities=7% Similarity=-0.105 Sum_probs=59.4
Q ss_pred hHHHHHHHHHHHHHcCC-----cEEEEEEEeCc--cccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhc-
Q 043276 5 DSSQVGAITAIIKAFGW-----REAVPIYVDNQ--YGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFT- 76 (829)
Q Consensus 5 D~~q~~ai~~ll~~fgW-----~~V~iI~~dd~--yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~- 76 (829)
+..-+..+++.+...|- ++++++....+ ....-.+.+.+++++.++++... .....+.+.-.+.+.++.+
T Consensus 104 ~~~~g~~~~~~l~~~g~~~~~~~~i~~l~g~~~~~~~~~R~~g~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~l~~ 181 (268)
T cd06306 104 WYEMGYQAGEYLAQRHPKGSKPAKVAWFPGPKGAGWVKAVEKGFRDALAGSAIEISAI--KYGDTGKEVQRKLVEEALEA 181 (268)
T ss_pred hHHHHHHHHHHHHHHhhcCCCCceEEEEeCCCCCchHHHHHHHHHHHHhhcCcEEeee--ccCCccHHHHHHHHHHHHHh
Confidence 33445667777766665 89999975433 23445677888898888876431 1112222233344444432
Q ss_pred -CCCeEEEEEcChhHHHHHHHHHHHcCccccCeEEEE
Q 043276 77 -MQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIM 112 (829)
Q Consensus 77 -~~arViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~ 112 (829)
...++|+. ....+..+++.+++.|+ ++-+=|.
T Consensus 182 ~~~~~~i~~--~d~~a~~~~~~l~~~g~--p~di~vi 214 (268)
T cd06306 182 HPDIDYIVG--SAVAAEAAVGILRQRGL--TDQIKIV 214 (268)
T ss_pred CCCcCEEee--cchhhhHHHHHHHhcCC--CCCeEEE
Confidence 34566553 36677788888888885 3334444
No 369
>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=46.40 E-value=76 Score=32.23 Aligned_cols=76 Identities=17% Similarity=0.144 Sum_probs=53.2
Q ss_pred EEEEEEe--CccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcChhHHHHHHHHHHHc
Q 043276 24 AVPIYVD--NQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEI 101 (829)
Q Consensus 24 V~iI~~d--d~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~~~~~~~i~~~a~~~ 101 (829)
|+++..+ +.|.......+++++++.|+.+... ....+.+.....++.+.+.+.+.+|+......... +..+.+.
T Consensus 2 i~~v~~~~~~~~~~~~~~g~~~~~~~~g~~~~~~---~~~~~~~~~~~~~~~~~~~~~d~iii~~~~~~~~~-~~~~~~~ 77 (264)
T cd06267 2 IGVIVPDISNPFFAELLRGIEEAAREAGYSVLLC---NSDEDPEKEREALELLLSRRVDGIILAPSRLDDEL-LEELAAL 77 (264)
T ss_pred EEEEECCCCCHHHHHHHHHHHHHHHHcCCEEEEE---cCCCCHHHHHHHHHHHHHcCcCEEEEecCCcchHH-HHHHHHc
Confidence 4566644 7888899999999999999877643 22222334556677777778999988776655555 7777777
Q ss_pred Cc
Q 043276 102 GL 103 (829)
Q Consensus 102 gm 103 (829)
|+
T Consensus 78 ~i 79 (264)
T cd06267 78 GI 79 (264)
T ss_pred CC
Confidence 74
No 370
>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=46.13 E-value=1.4e+02 Score=30.60 Aligned_cols=106 Identities=12% Similarity=0.031 Sum_probs=59.2
Q ss_pred hHHHH-HHHHHHHHHcCCcEEEEEEEeCcc--ccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhc--CCC
Q 043276 5 DSSQV-GAITAIIKAFGWREAVPIYVDNQY--GEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFT--MQT 79 (829)
Q Consensus 5 D~~q~-~ai~~ll~~fgW~~V~iI~~dd~y--G~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~--~~a 79 (829)
|..++ ..+++.+...|-++++++.....+ +..-.+.+.+++++.|+.+.......... .+...+.+.++.+ ...
T Consensus 99 d~~~~g~~a~~~l~~~G~~~i~~l~~~~~~~~~~~R~~Gf~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~l~~~~~~ 177 (269)
T cd06281 99 DHAAGMRQAVEYLISLGHRRIALVGGGSNTRPGRERLEGYKAAFAAAGLPPDPALVRLSTP-AASGFDATRALLALPDRP 177 (269)
T ss_pred CcHHHHHHHHHHHHHCCCcEEEEecCccccccHHHHHHHHHHHHHHcCCCCCHHHeecCcH-HHHHHHHHHHHHcCCCCC
Confidence 34444 445566655699999999654332 23345777888888886542111111111 2222334444432 234
Q ss_pred eEEEEEcChhHHHHHHHHHHHcCccccCeEEEE
Q 043276 80 RVFILHMLPSLGSRIFEKANEIGLMNKGCVWIM 112 (829)
Q Consensus 80 rViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~ 112 (829)
++++ +.+...+..+++.+.+.|+..++.+=|+
T Consensus 178 ~ai~-~~~d~~a~g~~~~l~~~g~~ip~dv~ii 209 (269)
T cd06281 178 TAII-AGGTQVLVGVLRALREAGLRIPRDLSVI 209 (269)
T ss_pred cEEE-EcCcHHHHHHHHHHHHcCCCCCcceeEE
Confidence 6554 4566677788999999997555444333
No 371
>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=46.02 E-value=67 Score=33.51 Aligned_cols=80 Identities=15% Similarity=0.182 Sum_probs=50.2
Q ss_pred EEEEEEEe---CccccchHHHHHHHHHhCCceeeeEEecCCC-CChhHHHHHHHHhhcCCCeEEEEEcChhHHHHHHHHH
Q 043276 23 EAVPIYVD---NQYGEELIPSLTDALQAIDTRVPYRSVISPL-ATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKA 98 (829)
Q Consensus 23 ~V~iI~~d---d~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~-~~~~~~~~~l~~lk~~~arViIv~~~~~~~~~i~~~a 98 (829)
++++|..+ ++|....+..+.+++++.|..+.....-+.. .+.+.-...+..+.+.+.+.+|+..........+..+
T Consensus 1 ~Igvi~~~~~~~~~~~~~~~~i~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~i~~l~~~~vDgiIv~~~~~~~~~~~~~l 80 (280)
T cd06303 1 KIAVIYPGQQISDYWVRNIASFTARLEELNIPYELTQFSSRPGIDHRLQSQQLNEALQSKPDYLIFTLDSLRHRKLIERV 80 (280)
T ss_pred CeeEEecCccHHHHHHHHHHHHHHHHHHcCCcEEEEEeccCcccCHHHHHHHHHHHHHcCCCEEEEcCCchhhHHHHHHH
Confidence 36777754 4677888899999999999776543221111 1222334566677778899998875433233455666
Q ss_pred HHcC
Q 043276 99 NEIG 102 (829)
Q Consensus 99 ~~~g 102 (829)
.+.+
T Consensus 81 ~~~~ 84 (280)
T cd06303 81 LASG 84 (280)
T ss_pred HhCC
Confidence 6655
No 372
>cd00338 Ser_Recombinase Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or C-terminal to the catalytic domain. These enzymes perform site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining mechanism which involves a transient phosphoserine linkage between DNA and serine recombinase. Serine recombinases demonstrate functional versatility and include resolvases, invertases, integrases, and transposases. Resolvases and invertases (i.e. Tn3, gamma-delta, Tn5044 resolvases, Gin and Hin invertases) in this family contain a C-terminal DNA binding domain and comprise a major phylogenic group. Also included are phage- and bacterial-encoded recombinases such as phiC31 integrase, SpoIVCA excisionase, and Tn4451 TnpX transposase. These integrases and transposases have larger C-terminal domains compared to resolvases/invertases and are referred to as large serine recombinases. Also belonging to this family are protei
Probab=45.75 E-value=2.1e+02 Score=25.83 Aligned_cols=27 Identities=19% Similarity=0.091 Sum_probs=17.4
Q ss_pred ChHHHHHHHHHHHHHcCCcEEEEEEEeC
Q 043276 4 NDSSQVGAITAIIKAFGWREAVPIYVDN 31 (829)
Q Consensus 4 sD~~q~~ai~~ll~~fgW~~V~iI~~dd 31 (829)
+-..|.+.+-++....||.-+.+ |.|.
T Consensus 15 s~~~Q~~~~~~~a~~~g~~i~~~-~~d~ 41 (137)
T cd00338 15 SLERQREALREYAARNGLEVVGE-YEDA 41 (137)
T ss_pred CHHHHHHHHHHHHHHCCCEEEEE-EEeC
Confidence 33467777778887778876554 4443
No 373
>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=45.68 E-value=1.1e+02 Score=28.88 Aligned_cols=64 Identities=14% Similarity=0.148 Sum_probs=44.1
Q ss_pred EEEEEEEeCccc-----cchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhc-CCCeEEEEEcCh
Q 043276 23 EAVPIYVDNQYG-----EELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFT-MQTRVFILHMLP 88 (829)
Q Consensus 23 ~V~iI~~dd~yG-----~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~-~~arViIv~~~~ 88 (829)
++++|...|+-. ......|.+.+++.|..+.....++++ .+.+.+.+.+..+ +.+++||..+..
T Consensus 2 ~~~ii~~~~e~~~g~i~d~n~~~l~~~l~~~G~~v~~~~~v~Dd--~~~i~~~l~~~~~~~~~DlVittGG~ 71 (152)
T cd00886 2 RAAVLTVSDTRSAGEAEDRSGPALVELLEEAGHEVVAYEIVPDD--KDEIREALIEWADEDGVDLILTTGGT 71 (152)
T ss_pred EEEEEEEcCcccCCCCccchHHHHHHHHHHcCCeeeeEEEcCCC--HHHHHHHHHHHHhcCCCCEEEECCCc
Confidence 577776665332 233567888899999988877777655 4567777776543 378888887654
No 374
>PRK09801 transcriptional activator TtdR; Provisional
Probab=44.43 E-value=1.2e+02 Score=32.25 Aligned_cols=70 Identities=10% Similarity=-0.054 Sum_probs=43.2
Q ss_pred eecCChHHHHHHHhcCCcCCceeEEEcchhHHHHHHhcCCCceE-EeCcccccCCceeeecCCCCchhhHHHHHHhhh
Q 043276 568 VVYNSHEECDELFQKGSANGGIAAAFDEIPYAKLLIGQHCSKYT-MVEPTFKTAGFGFAFPLHSPLVHDVSKAILNVT 644 (829)
Q Consensus 568 ~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~~c~~l~-~v~~~~~~~~~~~~~~k~spl~~~in~~il~l~ 644 (829)
...++.+...+++..|. .-+++-+.. +....... .+. +..+......++++.+++.++.......+..+.
T Consensus 223 ~~~~~~~~i~~~v~~g~----Gia~lp~~~-~~~~~~~~--~l~~~~~~~~~~~~~~lv~~~~~~~~~~~~~~i~~l~ 293 (310)
T PRK09801 223 LSSNSGEIVLQWALEGK----GIMLRSEWD-VLPFLESG--KLVQVLPEYAQSANIWAVYREPLYRSMKLRVCVEFLA 293 (310)
T ss_pred EEECCHHHHHHHHHcCC----CEEecchhh-HHHHHhCC--CeEEeCCCCCCCCcEEEEEcCCCcCCHHHHHHHHHHH
Confidence 45567888899999987 455554433 33222221 132 233333456788999999888777777776653
No 375
>TIGR00249 sixA phosphohistidine phosphatase SixA.
Probab=44.20 E-value=1.2e+02 Score=28.64 Aligned_cols=93 Identities=11% Similarity=0.022 Sum_probs=55.3
Q ss_pred HHHHHHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEE
Q 043276 6 SSQVGAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILH 85 (829)
Q Consensus 6 ~~q~~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~ 85 (829)
..|++.+++.++..+...-.|+.|.-.-....++.+.+.+.. ...+.....+.++.+..++.+.+..+.....+.++++
T Consensus 28 ~~qa~~~~~~l~~~~~~~d~i~sSp~~Ra~qTa~~l~~~~~~-~~~~~~~~~l~p~~~~~~~~~~l~~~~~~~~~~vliV 106 (152)
T TIGR00249 28 CDESRLVAQWLKGQGVEIERILVSPFVRAEQTAEIVGDCLNL-PSSAEVLEGLTPCGDIGLVSDYLEALTNEGVASVLLV 106 (152)
T ss_pred HHHHHHHHHHHHhCCCCCCEEEECCcHHHHHHHHHHHHHcCC-CcceEEccCcCCCCCHHHHHHHHHHHHhcCCCEEEEE
Confidence 468889999998776655556666655555555555444321 1233333334333344456666766655455667777
Q ss_pred cChhHHHHHHHHHH
Q 043276 86 MLPSLGSRIFEKAN 99 (829)
Q Consensus 86 ~~~~~~~~i~~~a~ 99 (829)
+.......++....
T Consensus 107 gH~P~i~~l~~~l~ 120 (152)
T TIGR00249 107 SHLPLVGYLVAELC 120 (152)
T ss_pred eCCCCHHHHHHHHh
Confidence 87777777777664
No 376
>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=43.67 E-value=2.6e+02 Score=29.52 Aligned_cols=95 Identities=13% Similarity=0.030 Sum_probs=58.7
Q ss_pred hHHHHHHHHHHHHHcCCcEEEEEEEe-C--ccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeE
Q 043276 5 DSSQVGAITAIIKAFGWREAVPIYVD-N--QYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRV 81 (829)
Q Consensus 5 D~~q~~ai~~ll~~fgW~~V~iI~~d-d--~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arV 81 (829)
+..-+..+++.+...|-+++++|..+ . .++..-.+.+.+++++.|+.... .....+.+.....+.++.+.+..
T Consensus 156 ~~~~~~~a~~~L~~~Ghr~I~~i~~~~~~~~~~~~R~~gf~~a~~~~gi~~~~---~~~~~~~~~~~~~~~~~l~~~~t- 231 (311)
T TIGR02405 156 DYGAIELLMANLYQQGHRHISFLGVDPSDKTTGLMRHNAYLAYCESANLEPIY---QTGQLSHESGYVLTDKVLKPETT- 231 (311)
T ss_pred cHHHHHHHHHHHHHcCCCcEEEEccCcccchhHHHHHHHHHHHHHHcCCCcee---eeCCCCHHHHHHHHHHHHhcCCC-
Confidence 33344456666766799999999632 2 23455677889999999985221 11111222223334443333444
Q ss_pred EEEEcChhHHHHHHHHHHHcCc
Q 043276 82 FILHMLPSLGSRIFEKANEIGL 103 (829)
Q Consensus 82 iIv~~~~~~~~~i~~~a~~~gm 103 (829)
.|+|++...|..++..+.+.|.
T Consensus 232 Ai~~~~D~~A~g~~~~l~~~g~ 253 (311)
T TIGR02405 232 ALVCATDTLALGAAKYLQELDR 253 (311)
T ss_pred EEEECCcHHHHHHHHHHHHcCC
Confidence 4567788888899999999884
No 377
>PRK10632 transcriptional regulator; Provisional
Probab=43.57 E-value=2.5e+02 Score=29.74 Aligned_cols=78 Identities=10% Similarity=0.159 Sum_probs=44.8
Q ss_pred CceEEEecccccCccceEEEeecCCCCCceEEEeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcc
Q 043276 307 EKKLRVGVPVKKGFSDFVKVTIDPKTQETSVVGYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEF 386 (829)
Q Consensus 307 ~~~lrv~v~~~~~~~p~~~~~~~~~~~~~~~~G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~ 386 (829)
.+.++||++ +.+. .-+-.+++..+.++.+ ++.+++.... . ...+.+|++
T Consensus 91 ~g~l~I~~~--~~~~----------------~~~l~~~l~~~~~~~P-~i~i~l~~~~--------~----~~~l~~~~~ 139 (309)
T PRK10632 91 IGTLRIGCS--STMA----------------QNVLAGLTAKMLKEYP-GLSVNLVTGI--------P----APDLIADGL 139 (309)
T ss_pred ceEEEEecc--HHHH----------------HHHHHHHHHHHHHHCC-CeEEEEEecC--------c----ccCcccCCe
Confidence 467999987 2211 1233567778888776 4556654421 1 135678999
Q ss_pred cEEEeccccccccceeccccccccccceEEEEE
Q 043276 387 DAVVGDTTIVFNRSNYVDFTLPYTESGVSMIVP 419 (829)
Q Consensus 387 Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv~ 419 (829)
|++++.-.. ....+. ..++....++++++
T Consensus 140 Dl~i~~~~~---~~~~l~-~~~l~~~~~~~v~~ 168 (309)
T PRK10632 140 DVVIRVGAL---QDSSLF-SRRLGAMPMVVCAA 168 (309)
T ss_pred eEEEEecCC---CCCCeE-EEEEeccceEEEEC
Confidence 999853222 122232 34666777776654
No 378
>cd06278 PBP1_LacI_like_2 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=43.44 E-value=2.1e+02 Score=29.07 Aligned_cols=96 Identities=15% Similarity=0.072 Sum_probs=55.0
Q ss_pred ChHHHHHHHHHHHHHcCCcEEEEEEEeCc--cccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcC--CC
Q 043276 4 NDSSQVGAITAIIKAFGWREAVPIYVDNQ--YGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTM--QT 79 (829)
Q Consensus 4 sD~~q~~ai~~ll~~fgW~~V~iI~~dd~--yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~--~a 79 (829)
++...+..+++.+...|-++|+++..+.. +.....+.+.+.+++.|..+... .... .+.+...+.+.++.+. ..
T Consensus 98 d~~~~g~~~~~~l~~~g~~~i~~i~~~~~~~~~~~R~~gf~~~~~~~~~~~~~~-~~~~-~~~~~~~~~~~~~l~~~~~~ 175 (266)
T cd06278 98 DNYEAGRLAAELLLAKGCRRIAFIGGPADTSTSRERERGFRDALAAAGVPVVVE-EAGD-YSYEGGYEAARRLLASRPRP 175 (266)
T ss_pred ChHHHHHHHHHHHHHCCCceEEEEcCCCcccchHHHHHHHHHHHHHcCCChhhh-ccCC-CCHHHHHHHHHHHHhcCCCC
Confidence 45556667778777779999999975433 33445677888888888764221 1111 1222333444444333 34
Q ss_pred eEEEEEcChhHHHHHHHHHHHcC
Q 043276 80 RVFILHMLPSLGSRIFEKANEIG 102 (829)
Q Consensus 80 rViIv~~~~~~~~~i~~~a~~~g 102 (829)
++|++ .+...+..+++..++.+
T Consensus 176 ~~i~~-~~~~~a~~~~~~l~~~~ 197 (266)
T cd06278 176 DAIFC-ANDLLAIGVMDAARQEG 197 (266)
T ss_pred CEEEE-cCcHHHHHHHHHHHHhc
Confidence 44443 44555666777777653
No 379
>PF15179 Myc_target_1: Myc target protein 1
Probab=42.54 E-value=35 Score=32.59 Aligned_cols=38 Identities=8% Similarity=0.152 Sum_probs=28.8
Q ss_pred cccccccchhHHHHH-HHHHHHHHHHHHHHHHHHHhhcc
Q 043276 672 ARSLGLNSFWGLFLI-AGIAAILALIIFLAVFVHEHWNV 709 (829)
Q Consensus 672 ~~~L~l~~~~g~f~i-l~vg~~lallvf~~E~~~~~~~~ 709 (829)
.+.++++++.-.|.+ ++||++++.+|+++-.+..|||.
T Consensus 13 ~~~f~~~~lIlaF~vSm~iGLviG~li~~LltwlSRRRA 51 (197)
T PF15179_consen 13 LENFDWEDLILAFCVSMAIGLVIGALIWALLTWLSRRRA 51 (197)
T ss_pred hhhcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence 345678888888887 78899999999888666555554
No 380
>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=42.19 E-value=74 Score=32.25 Aligned_cols=76 Identities=14% Similarity=0.135 Sum_probs=51.2
Q ss_pred EEEEEEe--CccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcChhHHHHHHHHHHHc
Q 043276 24 AVPIYVD--NQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEI 101 (829)
Q Consensus 24 V~iI~~d--d~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~~~~~~~i~~~a~~~ 101 (829)
++++... +.++......+++++++.|+.+.+.. ...+.+...+.++++.+.+++.+|+..........+..+.+.
T Consensus 2 ig~v~~~~~~~~~~~~~~g~~~~~~~~g~~l~~~~---~~~~~~~~~~~~~~~~~~~~d~ii~~~~~~~~~~~~~~l~~~ 78 (264)
T cd01537 2 IGVLVPDLDNPFFAQVLKGIEEAAKAAGYQVLLAN---SQNDAEKQLSALENLIARGVDGIIIAPSDLTAPTIVKLARKA 78 (264)
T ss_pred eEEEEcCCCChHHHHHHHHHHHHHHHcCCeEEEEe---CCCCHHHHHHHHHHHHHcCCCEEEEecCCCcchhHHHHhhhc
Confidence 6777754 67788889999999999998765442 222334456677777777888888876544443356666665
Q ss_pred C
Q 043276 102 G 102 (829)
Q Consensus 102 g 102 (829)
|
T Consensus 79 ~ 79 (264)
T cd01537 79 G 79 (264)
T ss_pred C
Confidence 5
No 381
>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=41.84 E-value=1.5e+02 Score=30.50 Aligned_cols=89 Identities=9% Similarity=0.056 Sum_probs=51.4
Q ss_pred HHHHHHc-CCcEEEEEEEeC-ccccchHHHHHHHHHhCCceeeeEEecCCCCC-hhHHHHHHHHhhcCCCeEEEEEcChh
Q 043276 13 TAIIKAF-GWREAVPIYVDN-QYGEELIPSLTDALQAIDTRVPYRSVISPLAT-DDQIEKELYKLFTMQTRVFILHMLPS 89 (829)
Q Consensus 13 ~~ll~~f-gW~~V~iI~~dd-~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~-~~~~~~~l~~lk~~~arViIv~~~~~ 89 (829)
+.++..+ |-+++++|..+. .....-...|.+++++.|..+..........+ .+.-...+.++.+...++ |++.+..
T Consensus 111 ~~l~~~~~g~~~I~~i~~~~~~~~~~R~~Gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~a-i~~~~d~ 189 (260)
T cd06304 111 GVLAALMTKTGKVGFVGGMPIPEVNRFINGFAAGAKSVNPDITVLVIYTGSFFDPAKGKEAALALIDQGADV-IFAAAGG 189 (260)
T ss_pred HHHHHHhccCCceEEEeccccHHHHHHHHHHHHHHHHhCCCcEEEEEEecCccCcHHHHHHHHHHHhCCCCE-EEEcCCC
Confidence 3555554 899999997432 22333466778888888764332212111111 122333445544444555 4667777
Q ss_pred HHHHHHHHHHHcC
Q 043276 90 LGSRIFEKANEIG 102 (829)
Q Consensus 90 ~~~~i~~~a~~~g 102 (829)
.+..++..+++.|
T Consensus 190 ~A~gv~~al~~~g 202 (260)
T cd06304 190 TGPGVIQAAKEAG 202 (260)
T ss_pred CchHHHHHHHHcC
Confidence 7878888888877
No 382
>cd08487 PBP2_BlaA The C-terminal substrate-binding domain of LysR-type trnascriptional regulator BlaA which involved in control of the beta-lactamase gene expression; contains the type 2 periplasmic binding fold. This CD represents the C-terminal substrate binding domain of LysR-type transcriptional regulator, BlaA, that involved in control of the expression of beta-lactamase genes, blaA and blaB. Beta-lactamases are responsible for bacterial resistance to beta-lactam antibiotics such as penicillins. The blaA gene is located just upstream of blaB in the opposite direction and regulates the expression of the blaB. BlaA also negatively auto-regulates the expression of its own gene, blaA. BlaA (a constitutive class A penicllinase) belongs to the LysR family of transcriptional regulators, whereas BlaB (an inducible class C cephalosporinase or AmpC) can be referred to as a penicillin binding protein but it does not act as a beta-lactamase. The topology of this substrate-binding domain is
Probab=41.80 E-value=3e+02 Score=25.76 Aligned_cols=99 Identities=12% Similarity=0.004 Sum_probs=47.3
Q ss_pred CHHHHHhCCCcEEE-EeCchHHHHHHhcCCCccce--eecCChHHHHHHHhcCCcCCceeEEEcchhHHHHHHhcCCCce
Q 043276 534 DVNLLIKRGDNVGY-QKGSFVLGILKQLGFDERKL--VVYNSHEECDELFQKGSANGGIAAAFDEIPYAKLLIGQHCSKY 610 (829)
Q Consensus 534 s~~dL~~~~~~vg~-~~~s~~~~~l~~~~~~~~~~--~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~~c~~l 610 (829)
+++||.+. ++.. ........++.+.+...... ...++.....+.+..|. ..+++.+.. ......... ..
T Consensus 85 ~~~~l~~~--~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~----Gi~~~p~~~-~~~~~~~~~-l~ 156 (189)
T cd08487 85 HPADLINE--TLLRSYRTDEWLQWFEAANMPPIKIRGPVFDSSRLMVEAAMQGA----GVALAPAKM-FSREIENGQ-LV 156 (189)
T ss_pred CHHHHhcC--ceeecCCchHHHHHHHHcCCCCccccCCccccHHHHHHHHHhCC----CeEeehHHH-HHHHHhCCC-EE
Confidence 46777533 3322 11122344555544432211 24566777788888877 455554432 222222221 11
Q ss_pred EEeCcccccCCceeeecCCCCchhhHHHHH
Q 043276 611 TMVEPTFKTAGFGFAFPLHSPLVHDVSKAI 640 (829)
Q Consensus 611 ~~v~~~~~~~~~~~~~~k~spl~~~in~~i 640 (829)
..+........++++.+|+.+....+...+
T Consensus 157 ~~l~~~~~~~~~~~~~~~~~~~~~~~~~f~ 186 (189)
T cd08487 157 QPFKIEVETGSYWLTWLKSKPMTPAMELFR 186 (189)
T ss_pred cccCcccCCCcEEEEecccccCCHHHHHHH
Confidence 122222234466778888877655555444
No 383
>COG2984 ABC-type uncharacterized transport system, periplasmic component [General function prediction only]
Probab=41.32 E-value=2.3e+02 Score=30.27 Aligned_cols=94 Identities=15% Similarity=0.151 Sum_probs=62.6
Q ss_pred ChHHHHHHHHHHHHH--cCCcEEEEEEEeCc-cccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCe
Q 043276 4 NDSSQVGAITAIIKA--FGWREAVPIYVDNQ-YGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTR 80 (829)
Q Consensus 4 sD~~q~~ai~~ll~~--fgW~~V~iI~~dd~-yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~ar 80 (829)
||..-...-+++++. =+-++++++|..++ ......+.|.+++++.|+.|.-. .++.. .++....+.|. .+++
T Consensus 140 sD~~~v~q~i~lik~~~Pnak~Igv~Y~p~E~ns~~l~eelk~~A~~~Gl~vve~-~v~~~---ndi~~a~~~l~-g~~d 214 (322)
T COG2984 140 SDLLPVAQQIELIKALLPNAKSIGVLYNPGEANSVSLVEELKKEARKAGLEVVEA-AVTSV---NDIPRAVQALL-GKVD 214 (322)
T ss_pred CCcchHHHHHHHHHHhCCCCeeEEEEeCCCCcccHHHHHHHHHHHHHCCCEEEEE-ecCcc---cccHHHHHHhc-CCCc
Confidence 455544445555544 38999999996544 66788999999999999998643 33322 24555565554 5678
Q ss_pred EEEEEcChh---HHHHHHHHHHHcC
Q 043276 81 VFILHMLPS---LGSRIFEKANEIG 102 (829)
Q Consensus 81 ViIv~~~~~---~~~~i~~~a~~~g 102 (829)
+|+.-++.. ....++..|.+.+
T Consensus 215 ~i~~p~dn~i~s~~~~l~~~a~~~k 239 (322)
T COG2984 215 VIYIPTDNLIVSAIESLLQVANKAK 239 (322)
T ss_pred EEEEecchHHHHHHHHHHHHHHHhC
Confidence 888877653 4445667777755
No 384
>cd08473 PBP2_CrgA_like_4 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 4. 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=40.99 E-value=2e+02 Score=27.21 Aligned_cols=66 Identities=6% Similarity=0.026 Sum_probs=37.9
Q ss_pred eeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccEEEeccccccccceeccccccccccceEEEEE
Q 043276 340 YSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMIVP 419 (829)
Q Consensus 340 ~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv~ 419 (829)
+-.+++..+.++.+ .+++++.... ... ++.+|++|+++.... .......+ .+.|+....++++++
T Consensus 17 ~l~~~l~~~~~~~P-~i~i~~~~~~-----------~~~-~~~~~~~D~~i~~~~-~~~~~~~~-~~~~l~~~~~~~v~~ 81 (202)
T cd08473 17 LLAPLLPRFMAAYP-QVRLQLEATN-----------RRV-DLIEEGIDVALRVRF-PPLEDSSL-VMRVLGQSRQRLVAS 81 (202)
T ss_pred HHHHHHHHHHHHCC-CeEEEEEEcC-----------Ccc-cccccCccEEEEeCC-CCCCCcce-eEEeccCcceEEEEC
Confidence 44577888888877 4566554311 112 455889999985211 11111222 246777778888876
Q ss_pred c
Q 043276 420 I 420 (829)
Q Consensus 420 ~ 420 (829)
.
T Consensus 82 ~ 82 (202)
T cd08473 82 P 82 (202)
T ss_pred H
Confidence 3
No 385
>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=40.60 E-value=2.7e+02 Score=29.86 Aligned_cols=68 Identities=15% Similarity=0.178 Sum_probs=48.9
Q ss_pred cCCcEEEEEEEeCcc--c---cchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcCh
Q 043276 19 FGWREAVPIYVDNQY--G---EELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLP 88 (829)
Q Consensus 19 fgW~~V~iI~~dd~y--G---~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~~ 88 (829)
|.=.+|++|.+.++- | ......+...+++.|..+.....++++ .+.+.+.+.++.+.++++||+.+..
T Consensus 157 ~r~~rv~II~TG~Ev~~G~i~D~~~~~l~~~L~~~G~~v~~~~iv~Dd--~~~I~~ai~~~~~~g~DlIItTGGt 229 (312)
T cd03522 157 FRPLRVGLIVTGSEVYGGRIEDKFGPVLRARLAALGVELVEQVIVPHD--EAAIAAAIAEALEAGAELLILTGGA 229 (312)
T ss_pred cCCCEEEEEEcCCcCCCCcEEEhHHHHHHHHHHHCCCEEEEEEEcCCC--HHHHHHHHHHHhcCCCCEEEEeCCc
Confidence 344467888766533 2 234667888899999998887777755 5578888887766668999988764
No 386
>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=40.41 E-value=1.2e+02 Score=27.65 Aligned_cols=62 Identities=18% Similarity=0.221 Sum_probs=42.0
Q ss_pred EEEEEEeCcc--c---cchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcCh
Q 043276 24 AVPIYVDNQY--G---EELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLP 88 (829)
Q Consensus 24 V~iI~~dd~y--G---~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~~ 88 (829)
|++|...|+- | ......+.+.+++.|..+.+...++++ .+.+.+.+.++.+. +++||..+..
T Consensus 2 v~ii~~G~El~~g~i~d~n~~~l~~~l~~~G~~v~~~~~v~Dd--~~~i~~~i~~~~~~-~DlvittGG~ 68 (133)
T cd00758 2 VAIVTVSDELSQGQIEDTNGPALEALLEDLGCEVIYAGVVPDD--ADSIRAALIEASRE-ADLVLTTGGT 68 (133)
T ss_pred EEEEEeCccccCCceEEchHHHHHHHHHHCCCEEEEeeecCCC--HHHHHHHHHHHHhc-CCEEEECCCC
Confidence 5566555432 2 344667888899999988877666644 55777888776544 8899887653
No 387
>PRK10086 DNA-binding transcriptional regulator DsdC; Provisional
Probab=40.37 E-value=4e+02 Score=28.24 Aligned_cols=79 Identities=8% Similarity=-0.002 Sum_probs=48.5
Q ss_pred CceEEEecccccCccceEEEeecCCCCCceEEEeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcc
Q 043276 307 EKKLRVGVPVKKGFSDFVKVTIDPKTQETSVVGYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEF 386 (829)
Q Consensus 307 ~~~lrv~v~~~~~~~p~~~~~~~~~~~~~~~~G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~ 386 (829)
.+.+|||++... ..++...++..+.++.+ ++++++.... .. ..+.+|++
T Consensus 101 ~g~lrIg~~~~~------------------~~~~l~~~l~~f~~~~P-~i~i~~~~~~---------~~---~~l~~~~~ 149 (311)
T PRK10086 101 SGTLTVYSRPSI------------------AQCWLVPRLADFTRRYP-SISLTILTGN---------EN---VNFQRAGI 149 (311)
T ss_pred CceEEEEecchH------------------HHHHHHHHHHHHHHHCC-CeEEEEEeCC---------cc---cCCccCCc
Confidence 457999987211 12455677888888887 4566555421 11 15788999
Q ss_pred cEEEeccccccccceeccccccccccceEEEEEc
Q 043276 387 DAVVGDTTIVFNRSNYVDFTLPYTESGVSMIVPI 420 (829)
Q Consensus 387 Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv~~ 420 (829)
|+++..-.. ....+. ..|+....++++++.
T Consensus 150 Di~i~~~~~---~~~~l~-~~~l~~~~~~lv~~~ 179 (311)
T PRK10086 150 DLAIYFDDA---PSAQLT-HHFLMDEEILPVCSP 179 (311)
T ss_pred cEEEEeCCC---CCCCce-EEEeecccEEEecCH
Confidence 999953222 122232 467777788888763
No 388
>KOG0498 consensus K+-channel ERG and related proteins, contain PAS/PAC sensor domain [Inorganic ion transport and metabolism; Signal transduction mechanisms]
Probab=40.30 E-value=41 Score=40.15 Aligned_cols=69 Identities=14% Similarity=0.221 Sum_probs=53.9
Q ss_pred cchhHHHHHHHhhhcC--ccccccchhHHHHHHHHHHHHHHHHHhHHHHHHHhhc-----ccCCCCCCCHHHHHhC
Q 043276 473 VGTSFWFSFSTMVFSQ--RERVISNLARFVVIVWCFVVLILIQSYTASLTSLLTV-----DQLQPTITDVNLLIKR 541 (829)
Q Consensus 473 ~~~~~~~~~~~l~~~~--~~~~~s~~~R~v~~~w~~~~lil~~~YtA~L~s~Lt~-----~~~~~~I~s~~dL~~~ 541 (829)
...++|+.+++|.--| ...+.+....++.++.+++++++.+..-+|++++|.. ..+...+.++++-.+.
T Consensus 295 Y~~aLyw~l~tLstvG~g~~~s~~~~E~iFsi~~mi~GllL~A~lIGNmt~~iqs~tsR~~~~r~k~rd~e~~m~~ 370 (727)
T KOG0498|consen 295 YVYALYWGLSTLSTVGYGLVHANNMGEKIFSIFIMLFGLLLFAYLIGNMTALLQSLTSRTEEMRDKMRDAEQWMSR 370 (727)
T ss_pred HHHHHHHHhhHhhhccCCccCCCCcHHHHHHHHHHHHhHHHHHHHHhhHHHhHHHHhHHHHHHHHHHHHHHHHHHh
Confidence 4468999999998544 4567888889999999999999999999999999754 4455555666665533
No 389
>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=40.29 E-value=1.7e+02 Score=30.15 Aligned_cols=89 Identities=9% Similarity=0.029 Sum_probs=50.5
Q ss_pred HHHHHH-cCCcEEEEEEEeCc-cccchHHHHHHHHHhCC---ceeeeEEecCCCCC-hhHHHHHHHHhhcCCCeEEEEEc
Q 043276 13 TAIIKA-FGWREAVPIYVDNQ-YGEELIPSLTDALQAID---TRVPYRSVISPLAT-DDQIEKELYKLFTMQTRVFILHM 86 (829)
Q Consensus 13 ~~ll~~-fgW~~V~iI~~dd~-yG~~~~~~l~~~l~~~g---i~I~~~~~i~~~~~-~~~~~~~l~~lk~~~arViIv~~ 86 (829)
+.++.. .|-+++++|..+.. ......+.+.+.+++.| ..+..........+ .++-.+.+.++.+..+++ |++.
T Consensus 112 ~~ll~~~~G~~~I~~i~~~~~~~~~~r~~gf~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~pda-I~~~ 190 (265)
T cd06354 112 GYLAALMTKTGKVGFIGGMDIPLIRRFEAGFEAGVKYVNPGVPDIEVLVQYAGSFNDPAKGKEIAQAMYDQGADV-IFAA 190 (265)
T ss_pred HHHHHhhcCCCeEEEEecccChHHHHHHHHHHHHHHHHhccCCCceEEEEEcCcccCHHHHHHHHHHHHHCCCcE-EEEC
Confidence 355554 39999999974322 11222367788888877 54432222211111 123334455554444554 5555
Q ss_pred ChhHHHHHHHHHHHcC
Q 043276 87 LPSLGSRIFEKANEIG 102 (829)
Q Consensus 87 ~~~~~~~i~~~a~~~g 102 (829)
+...+..+++.+++.|
T Consensus 191 nd~~A~gv~~al~~~g 206 (265)
T cd06354 191 AGGTGNGVFQAAKEAG 206 (265)
T ss_pred CCCCchHHHHHHHhcC
Confidence 7777888889999877
No 390
>PF05545 FixQ: Cbb3-type cytochrome oxidase component FixQ; InterPro: IPR008621 This family consists of several Cbb3-type cytochrome oxidase components (FixQ/CcoQ). FixQ is found in nitrogen fixing bacteria. Since nitrogen fixation is an energy-consuming process, effective symbioses depend on operation of a respiratory chain with a high affinity for O2, closely coupled to ATP production. This requirement is fulfilled by a special three-subunit terminal oxidase (cytochrome terminal oxidase cbb3), which was first identified in Bradyrhizobium japonicum as the product of the fixNOQP operon [].
Probab=40.23 E-value=30 Score=25.57 Aligned_cols=26 Identities=31% Similarity=0.515 Sum_probs=20.2
Q ss_pred hHHHHHHHHHHHHHHHHHhhhcccCC
Q 043276 438 DLWVTSGCFFIFIGFVVWVLEHRVNE 463 (829)
Q Consensus 438 ~vW~~i~~~~~~~~~v~~~~~~~~~~ 463 (829)
..|.+++.+++++++++|.+.++..+
T Consensus 11 ~~~~~v~~~~~F~gi~~w~~~~~~k~ 36 (49)
T PF05545_consen 11 RSIGTVLFFVFFIGIVIWAYRPRNKK 36 (49)
T ss_pred HHHHHHHHHHHHHHHHHHHHcccchh
Confidence 45777888888999999999766433
No 391
>PF01102 Glycophorin_A: Glycophorin A; InterPro: IPR001195 Proteins in this group are responsible for the molecular basis of the blood group antigens, surface markers on the outside of the red blood cell membrane. Most of these markers are proteins, but some are carbohydrates attached to lipids or proteins [Reid M.E., Lomas-Francis C. The Blood Group Antigen FactsBook Academic Press, London / San Diego, (1997)]. Glycophorin A (PAS-2) and glycophorin B (PAS-3) belong to the MNS blood group system and are associated with antigens that include M/N, S/s, U, He, Mi(a), M(c), Vw, Mur, M(g), Vr, M(e), Mt(a), St(a), Ri(a), Cl(a), Ny(a), Hut, Hil, M(v), Far, Mit, Dantu, Hop, Nob, En(a), ENKT, amongst others. Glycophorin A is the major sialoglycoprotein of the erythrocyte membrane []. Structurally, glycophorin A consists of an N-terminal extracellular domain, heavily glycosylated on serine and threonine residues, followed by a transmembrane region and a C-terminal cytoplasmic domain. Other glycophorins in this entry such as Glycophorin B and Glycophorin E represent minor sialoglycoproteins in the erythrocyte membrane.; GO: 0016021 integral to membrane; PDB: 2KPF_B 1AFO_B 2KPE_A.
Probab=39.07 E-value=46 Score=30.07 Aligned_cols=27 Identities=22% Similarity=0.244 Sum_probs=13.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhcc
Q 043276 683 LFLIAGIAAILALIIFLAVFVHEHWNV 709 (829)
Q Consensus 683 ~f~il~vg~~lallvf~~E~~~~~~~~ 709 (829)
..+++|+.+++.++++++-++.+|+++
T Consensus 67 ~~Ii~gv~aGvIg~Illi~y~irR~~K 93 (122)
T PF01102_consen 67 IGIIFGVMAGVIGIILLISYCIRRLRK 93 (122)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHS-
T ss_pred eehhHHHHHHHHHHHHHHHHHHHHHhc
Confidence 445555555555555555544444433
No 392
>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=38.93 E-value=3.1e+02 Score=30.05 Aligned_cols=99 Identities=10% Similarity=-0.001 Sum_probs=62.7
Q ss_pred HHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCC---CCChhHHHHHHHHhhcCCCe---EEEE
Q 043276 11 AITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISP---LATDDQIEKELYKLFTMQTR---VFIL 84 (829)
Q Consensus 11 ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~---~~~~~~~~~~l~~lk~~~ar---ViIv 84 (829)
-+.++++.+|-+++.+|++.+-+ ....+.+.+.|++.|+.+... .++. ..+.+.+.+.+..+++.+++ +||.
T Consensus 13 ~l~~~l~~~g~~rvlvVtd~~v~-~~~~~~l~~~L~~~g~~~~~~-~~~~~e~~k~~~~v~~~~~~~~~~~~dr~~~IIA 90 (355)
T cd08197 13 SVLGYLPELNADKYLLVTDSNVE-DLYGHRLLEYLREAGAPVELL-SVPSGEEHKTLSTLSDLVERALALGATRRSVIVA 90 (355)
T ss_pred HHHHHHHhcCCCeEEEEECccHH-HHHHHHHHHHHHhcCCceEEE-EeCCCCCCCCHHHHHHHHHHHHHcCCCCCcEEEE
Confidence 35566777777888888855444 336678888899888765332 2332 33445677778888887777 7877
Q ss_pred EcCh--hHHHHHHHHHHHcCccccCeEEEEcC
Q 043276 85 HMLP--SLGSRIFEKANEIGLMNKGCVWIMTD 114 (829)
Q Consensus 85 ~~~~--~~~~~i~~~a~~~gm~~~~~vwI~t~ 114 (829)
.+.. -++..+.......| ..++-|-|.
T Consensus 91 vGGGsv~D~ak~~A~~~~rg---ip~I~IPTT 119 (355)
T cd08197 91 LGGGVVGNIAGLLAALLFRG---IRLVHIPTT 119 (355)
T ss_pred ECCcHHHHHHHHHHHHhccC---CCEEEecCc
Confidence 7654 34445544433334 356776664
No 393
>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=38.88 E-value=1.1e+02 Score=31.62 Aligned_cols=79 Identities=9% Similarity=0.115 Sum_probs=52.8
Q ss_pred EEEEEEE---eCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcCh-hHHHHHHHHH
Q 043276 23 EAVPIYV---DNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLP-SLGSRIFEKA 98 (829)
Q Consensus 23 ~V~iI~~---dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~~-~~~~~i~~~a 98 (829)
+|++|.. ++.|.....+.+.+++++.|..+.... +...+.+.....+.++...+++.+|+.... +.....+..+
T Consensus 1 ~i~~i~~~~~~~~~~~~~~~g~~~~~~~~g~~v~~~~--~~~~~~~~~~~~i~~l~~~~vdgiii~~~~~~~~~~~l~~~ 78 (271)
T cd06312 1 KIAFVTHGPAGDPFWTVVKNGAEDAAKDLGVDVEYRG--PETFDVADMARLIEAAIAAKPDGIVVTIPDPDALDPAIKRA 78 (271)
T ss_pred CEEEecCCCCCCcHHHHHHHHHHHHHHHhCCEEEEEC--CCCCCHHHHHHHHHHHHHhCCCEEEEeCCChHHhHHHHHHH
Confidence 3666764 357888899999999999998875432 222123345566777777889988887643 3334566777
Q ss_pred HHcCc
Q 043276 99 NEIGL 103 (829)
Q Consensus 99 ~~~gm 103 (829)
.+.|+
T Consensus 79 ~~~~i 83 (271)
T cd06312 79 VAAGI 83 (271)
T ss_pred HHCCC
Confidence 77663
No 394
>PF03180 Lipoprotein_9: NLPA lipoprotein; InterPro: IPR004872 This family of bacterial lipoproteins contains several antigenic members, that may be involved in bacterial virulence. Their precise function is unknown. However they are probably distantly related to IPR001638 from INTERPRO which are solute binding proteins.; PDB: 4EF2_A 4EF1_B 3GXA_C 3IR1_D 3TQW_A 3K2D_B 3UP9_A 1XS5_A 1P99_A.
Probab=38.86 E-value=1.3e+02 Score=30.93 Aligned_cols=101 Identities=22% Similarity=0.330 Sum_probs=65.9
Q ss_pred cEEEEeCch------HHHHHHhcCCCccceeecCChHHHHHHHhcCCcCCceeEE-EcchhHHHHHHhcCCCceEEeCcc
Q 043276 544 NVGYQKGSF------VLGILKQLGFDERKLVVYNSHEECDELFQKGSANGGIAAA-FDEIPYAKLLIGQHCSKYTMVEPT 616 (829)
Q Consensus 544 ~vg~~~~s~------~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~g~~~~g~~a~-~~~~~~~~~~~~~~c~~l~~v~~~ 616 (829)
+||+..+.. +...+++.++ ...++.+++..+.-++|..|+ +|+- +--.+|+..+.+.+..++..+++.
T Consensus 2 kIG~~~~~~~~i~~~v~~~~~~~Gi-~vevv~f~D~~~~N~AL~~G~----iDaN~fQh~~yl~~~n~~~~~~L~~v~~~ 76 (237)
T PF03180_consen 2 KIGVTPGPDAEILEAVKEKLKKKGI-DVEVVEFSDYVQPNEALADGE----IDANFFQHIPYLEQFNKENGYNLVPVGPT 76 (237)
T ss_dssp EEEEETTCHHHHHHHHHHHHHHTTE-EEEEEEESSTTHHHHHHHTTS----SSEEEEEEHHHHHHHHHHHT--EEEEEEE
T ss_pred EEEEeCCCHHHHHHHHHHHHHhcCC-eEEEEEecchhhcChHHHCCC----cceeccCCHHHHHHHHHHCCCcEEEecce
Confidence 567765542 2233445554 446778889999999999999 8874 444678888887765567777764
Q ss_pred cccCCceeeecCCCCch--------------hhHHHHHHhhhccChhH
Q 043276 617 FKTAGFGFAFPLHSPLV--------------HDVSKAILNVTEGDKMK 650 (829)
Q Consensus 617 ~~~~~~~~~~~k~spl~--------------~~in~~il~l~e~G~~~ 650 (829)
+ ..++|++-.|-..+. .-..++|.-|.+.|++.
T Consensus 77 ~-~~p~glYS~k~~sl~~lp~Ga~VaIpnD~sN~~RaL~lLq~aGLI~ 123 (237)
T PF03180_consen 77 Y-IEPMGLYSKKYKSLDDLPDGATVAIPNDPSNQARALKLLQEAGLIT 123 (237)
T ss_dssp E-E---EEEESSSSSGGGS-TTEEEEEESSHHHHHHHHHHHHHTTSEE
T ss_pred e-EEeEEEeecccCchhhcCCCCEEEEeCCccchhHHHHHHHhCCeEE
Confidence 3 446777755543332 23678999999999865
No 395
>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=38.49 E-value=1.3e+02 Score=32.90 Aligned_cols=84 Identities=17% Similarity=0.173 Sum_probs=54.3
Q ss_pred HHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCC--CChhHHHHHHHHhhcCCCeEEEEEcC
Q 043276 10 GAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPL--ATDDQIEKELYKLFTMQTRVFILHML 87 (829)
Q Consensus 10 ~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~--~~~~~~~~~l~~lk~~~arViIv~~~ 87 (829)
.-+.++++.+|-+++.+|+...-+.. ..+.+.+.|++.|+.+......... .+.+.+.+.+..+++ +.++||-.+.
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 34667788889899888874333322 2578888899999865433333222 455667777777776 8899988775
Q ss_pred h--hHHHHHH
Q 043276 88 P--SLGSRIF 95 (829)
Q Consensus 88 ~--~~~~~i~ 95 (829)
. -++..++
T Consensus 90 Gs~~D~aK~v 99 (348)
T cd08175 90 GTINDITKYV 99 (348)
T ss_pred cHHHHHHHHH
Confidence 4 2444444
No 396
>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=38.36 E-value=96 Score=33.68 Aligned_cols=98 Identities=12% Similarity=-0.015 Sum_probs=63.1
Q ss_pred HHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcChh
Q 043276 10 GAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPS 89 (829)
Q Consensus 10 ~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~~~ 89 (829)
+-+.+.++.+|.+++.+|+...-+-. ..+.+.+.|++.+..+ + ..+....+.+.+.+....+++.+.+.||-.+...
T Consensus 12 ~~l~~~l~~~g~~~~livt~~~~~~~-~~~~v~~~l~~~~~~~-~-~~~~~~p~~~~v~~~~~~~~~~~~d~IIaiGGGs 88 (337)
T cd08177 12 AALAAELERLGASRALVLTTPSLATK-LAERVASALGDRVAGT-F-DGAVMHTPVEVTEAAVAAAREAGADGIVAIGGGS 88 (337)
T ss_pred HHHHHHHHHcCCCeEEEEcChHHHHH-HHHHHHHHhccCCcEE-e-CCCCCCCCHHHHHHHHHHHHhcCCCEEEEeCCcH
Confidence 45677889999999998885444443 6677788887775432 2 2344455566777788888888999999887642
Q ss_pred --HHHHHHHHHHHcCccccCeEEEEcCc
Q 043276 90 --LGSRIFEKANEIGLMNKGCVWIMTDG 115 (829)
Q Consensus 90 --~~~~i~~~a~~~gm~~~~~vwI~t~~ 115 (829)
++..++.... + ..++-|-|..
T Consensus 89 ~iD~aK~ia~~~--~---~p~i~IPTta 111 (337)
T cd08177 89 TIDLAKAIALRT--G---LPIIAIPTTL 111 (337)
T ss_pred HHHHHHHHHHHh--c---CCEEEEcCCc
Confidence 3444433222 3 3466666654
No 397
>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=38.31 E-value=1.2e+02 Score=31.11 Aligned_cols=77 Identities=16% Similarity=0.154 Sum_probs=49.9
Q ss_pred EEEEEE--eCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcChhHHHHHHHHHHHc
Q 043276 24 AVPIYV--DNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEI 101 (829)
Q Consensus 24 V~iI~~--dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~~~~~~~i~~~a~~~ 101 (829)
+++|.. .+.|.......+.+++++.|.++... ....+.+...+.+..+.+.+++.+|+..........+.++.+.
T Consensus 2 I~vi~~~~~~~~~~~~~~g~~~~a~~~g~~~~~~---~~~~~~~~~~~~i~~~~~~~vdgiii~~~~~~~~~~~~~~~~~ 78 (268)
T cd06289 2 IGLVINDLTNPFFAELAAGLEEVLEEAGYTVFLA---NSGEDVERQEQLLSTMLEHGVAGIILCPAAGTSPDLLKRLAES 78 (268)
T ss_pred EEEEecCCCcchHHHHHHHHHHHHHHcCCeEEEe---cCCCChHHHHHHHHHHHHcCCCEEEEeCCCCccHHHHHHHHhc
Confidence 455553 46777788888999999999876432 2222233345667777777888888876544333466777776
Q ss_pred Cc
Q 043276 102 GL 103 (829)
Q Consensus 102 gm 103 (829)
|.
T Consensus 79 ~i 80 (268)
T cd06289 79 GI 80 (268)
T ss_pred CC
Confidence 64
No 398
>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=38.13 E-value=1.6e+02 Score=30.85 Aligned_cols=77 Identities=12% Similarity=0.103 Sum_probs=53.4
Q ss_pred EEEEEE--eCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcC-hhHHHHHHHHHHH
Q 043276 24 AVPIYV--DNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHML-PSLGSRIFEKANE 100 (829)
Q Consensus 24 V~iI~~--dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~-~~~~~~i~~~a~~ 100 (829)
|++|.. ++.|.....+.+.+++++.|..+..... ..+.+...+.++.+.+.+++.||+... .+.....+.++.+
T Consensus 2 I~vi~~~~~~~~~~~~~~gi~~~a~~~g~~~~~~~~---~~~~~~~~~~i~~~~~~~vdgiii~~~~~~~~~~~l~~l~~ 78 (288)
T cd01538 2 IGLSLPTKTEERWIRDRPNFEAALKELGAEVIVQNA---NGDPAKQISQIENMIAKGVDVLVIAPVDGEALASAVEKAAD 78 (288)
T ss_pred eEEEEeCCCcHHHHHHHHHHHHHHHHcCCEEEEECC---CCCHHHHHHHHHHHHHcCCCEEEEecCChhhHHHHHHHHHH
Confidence 566764 4677788889999999999988765422 222334456677777788998888754 3444667778887
Q ss_pred cCc
Q 043276 101 IGL 103 (829)
Q Consensus 101 ~gm 103 (829)
.|.
T Consensus 79 ~~i 81 (288)
T cd01538 79 AGI 81 (288)
T ss_pred CCC
Confidence 763
No 399
>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=37.93 E-value=1.9e+02 Score=29.46 Aligned_cols=76 Identities=16% Similarity=0.090 Sum_probs=51.6
Q ss_pred EEEEEE--eCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcChhHHHHHHHHHHHc
Q 043276 24 AVPIYV--DNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEI 101 (829)
Q Consensus 24 V~iI~~--dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~~~~~~~i~~~a~~~ 101 (829)
|++|.. +++|-....+.+.+++++.|..+..... ..+.+...+.+..+.+.+.+.||+....... ..+.++.+.
T Consensus 2 igvv~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~---~~~~~~~~~~~~~l~~~~vdgiIi~~~~~~~-~~~~~l~~~ 77 (265)
T cd06299 2 IGVIVPDIRNPYFASLATAIQDAASAAGYSTIIGNS---DENPETENRYLDNLLSQRVDGIIVVPHEQSA-EQLEDLLKR 77 (265)
T ss_pred EEEEecCCCCccHHHHHHHHHHHHHHcCCEEEEEeC---CCCHHHHHHHHHHHHhcCCCEEEEcCCCCCh-HHHHHHHhC
Confidence 566664 4677788889999999999987765422 2223344466777778889988887644333 346777777
Q ss_pred Cc
Q 043276 102 GL 103 (829)
Q Consensus 102 gm 103 (829)
|.
T Consensus 78 ~i 79 (265)
T cd06299 78 GI 79 (265)
T ss_pred CC
Confidence 63
No 400
>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=37.72 E-value=1.2e+02 Score=31.30 Aligned_cols=79 Identities=6% Similarity=0.042 Sum_probs=51.4
Q ss_pred EEEEEEe--CccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcChhHHHHHHHHHHHc
Q 043276 24 AVPIYVD--NQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEI 101 (829)
Q Consensus 24 V~iI~~d--d~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~~~~~~~i~~~a~~~ 101 (829)
|++|..+ +.|.......+.+++++.|..+..... ....+.+.....+..+.+.+++.+|+..........+.++.+.
T Consensus 2 Igvi~~~~~~~f~~~~~~gi~~~a~~~g~~~~~~~~-~~~~~~~~~~~~i~~~~~~~vdgiI~~~~~~~~~~~~~~~~~~ 80 (268)
T cd06306 2 LCVLYPHLKDAYWLSVNYGMVEEAKRLGVSLKLLEA-GGYPNLAKQIAQLEDCAAWGADAILLGAVSPDGLNEILQQVAA 80 (268)
T ss_pred eEEEcCCCCCHHHHHHHHHHHHHHHHcCCEEEEecC-CCCCCHHHHHHHHHHHHHcCCCEEEEcCCChhhHHHHHHHHHC
Confidence 6677643 677788888999999999988765421 1111223344567777778899998876543332256677777
Q ss_pred Cc
Q 043276 102 GL 103 (829)
Q Consensus 102 gm 103 (829)
|+
T Consensus 81 gi 82 (268)
T cd06306 81 SI 82 (268)
T ss_pred CC
Confidence 74
No 401
>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=37.50 E-value=80 Score=34.22 Aligned_cols=72 Identities=14% Similarity=0.124 Sum_probs=49.7
Q ss_pred HHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcCh
Q 043276 16 IKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLP 88 (829)
Q Consensus 16 l~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~~ 88 (829)
++.++.+++.+|+...-+..+..+.+.+.|++. +.+.....+..+.+.+.+.+.+..+++.++++||-.+..
T Consensus 17 l~~~~~~~~lvv~~~~~~~~g~~~~v~~~l~~~-~~~~~~~~v~~~p~~~~v~~~~~~~~~~~~d~IiaiGGG 88 (332)
T cd08180 17 LKELKNKRVLIVTDPFMVKSGMLDKVTDHLDSS-IEVEIFSDVVPDPPIEVVAKGIKKFLDFKPDIVIALGGG 88 (332)
T ss_pred HHHhCCCeEEEEeCchhhhCccHHHHHHHHHhc-CcEEEeCCCCCCcCHHHHHHHHHHHHhcCCCEEEEECCc
Confidence 455666899888854444445778888888876 544333334445556677788888888899999987654
No 402
>PRK10936 TMAO reductase system periplasmic protein TorT; Provisional
Probab=37.02 E-value=3.2e+02 Score=29.50 Aligned_cols=103 Identities=6% Similarity=-0.078 Sum_probs=58.2
Q ss_pred hHHHHHHHHHHH-HHc----CCcEEEEEEEeCc--cccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhc-
Q 043276 5 DSSQVGAITAII-KAF----GWREAVPIYVDNQ--YGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFT- 76 (829)
Q Consensus 5 D~~q~~ai~~ll-~~f----gW~~V~iI~~dd~--yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~- 76 (829)
+...+..+++.+ +.. |-+++++|..+.. ....-.+.+.+.+++.|+++... .... .+.+.-.+.+.++.+
T Consensus 151 ~~~~g~~aa~~L~~~~~~~~g~~~i~~i~g~~~~~~~~~R~~Gf~~~l~~~~i~~~~~-~~~~-~~~~~~~~~~~~~l~~ 228 (343)
T PRK10936 151 WYQMGYQAGRYLAQWHPKGSKPLNVALLPGPEGAGGSKAVEQGFRAAIAGSDVRIVDI-AYGD-NDKELQRNLLQELLER 228 (343)
T ss_pred hHHHHHHHHHHHHHHHHhcCCCceEEEEECCCCCchHHHHHHHHHHHHhcCCCEEEEe-ecCC-CcHHHHHHHHHHHHHh
Confidence 344455555655 433 5789999974332 22334677888888888876542 1111 122222234444432
Q ss_pred -CCCeEEEEEcChhHHHHHHHHHHHcCccccCeEEEEc
Q 043276 77 -MQTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMT 113 (829)
Q Consensus 77 -~~arViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t 113 (829)
...+.|+ +....+..++..+++.|+ ++.+.|.+
T Consensus 229 ~~~~~ai~--~~d~~A~ga~~al~~~g~--~~di~Vvg 262 (343)
T PRK10936 229 HPDIDYIA--GSAVAAEAAIGELRGRNL--TDKIKLVS 262 (343)
T ss_pred CCCccEEE--eCCHHHHHHHHHHHhcCC--CCCeEEEE
Confidence 2356665 445667778888888886 45566554
No 403
>cd08549 G1PDH_related Glycerol-1-phosphate_dehydrogenase and related proteins. Bacterial and archeal glycerol-1-phosphate dehydrogenase-like oxidoreductases. The proteins have similarity with glycerol-1-phosphate dehydrogenase (G1PDH). G1PDH plays a role in the synthesis of phosphoglycerolipids in gram-positive bacterial species. It catalyzes the reversibly reduction of dihydroxyacetone phosphate (DHAP) to glycerol-1-phosphate (G1P) in a NADH-dependent manner. Its activity requires Ni++ ion. It also contains archaeal Sn-glycerol-1-phosphate dehydrogenase (Gro1PDH) that plays an important role in the formation of the enantiomeric configuration of the glycerophosphate backbone (sn-glycerol-1-phosphate) of archaeal ether lipids.
Probab=37.02 E-value=1.3e+02 Score=32.56 Aligned_cols=98 Identities=13% Similarity=0.072 Sum_probs=59.5
Q ss_pred HHHHHHHHHcCC-cEEEEEEEeCccccchHHHHHHHHHhCCceeeeEE-ecCCCCChhHHHHHHHHhhcCCCeEEEEEcC
Q 043276 10 GAITAIIKAFGW-REAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRS-VISPLATDDQIEKELYKLFTMQTRVFILHML 87 (829)
Q Consensus 10 ~ai~~ll~~fgW-~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~-~i~~~~~~~~~~~~l~~lk~~~arViIv~~~ 87 (829)
..+.++++.++. +++.+|+....+... .+.+.+.|++.|+.+.... ....+.+.+.+.+....+++ +.++||-.+.
T Consensus 12 ~~l~~~~~~~~~~~kvlivtd~~~~~~~-~~~i~~~L~~~~~~~~i~~~~~~~~p~~~~v~~~~~~~~~-~~d~IIaiGG 89 (332)
T cd08549 12 NDIGPIINKIGVNSKIMIVCGNNTYKVA-GKEIIERLESNNFTKEVLERDSLLIPDEYELGEVLIKLDK-DTEFLLGIGS 89 (332)
T ss_pred HHHHHHHHHcCCCCcEEEEECCcHHHHH-HHHHHHHHHHcCCeEEEEecCCCCCCCHHHHHHHHHHhhc-CCCEEEEECC
Confidence 345667777887 688888754443333 3778888988887554321 22233345667777777777 8888888775
Q ss_pred h--hHHHHHHHHHHHcCccccCeEEEEcC
Q 043276 88 P--SLGSRIFEKANEIGLMNKGCVWIMTD 114 (829)
Q Consensus 88 ~--~~~~~i~~~a~~~gm~~~~~vwI~t~ 114 (829)
. -++..++. ...|+ .++-|-|.
T Consensus 90 Gsv~D~aK~iA--~~~gi---p~I~VPTT 113 (332)
T cd08549 90 GTIIDLVKFVS--FKVGK---PFISVPTA 113 (332)
T ss_pred cHHHHHHHHHH--HHcCC---CEEEeCCC
Confidence 4 34444443 33342 45555554
No 404
>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=36.92 E-value=49 Score=29.62 Aligned_cols=87 Identities=15% Similarity=0.124 Sum_probs=46.3
Q ss_pred cEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhh--cCCCeEEEEEcChhHHHHHHHHHH
Q 043276 22 REAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLF--TMQTRVFILHMLPSLGSRIFEKAN 99 (829)
Q Consensus 22 ~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk--~~~arViIv~~~~~~~~~i~~~a~ 99 (829)
|.+++|-..++-+.-+ ..+.+.|.+.|..|... .+...+-.=......+. ....+.++++..++....++.++.
T Consensus 1 ksiAVvGaS~~~~~~g-~~v~~~l~~~G~~v~~V---np~~~~i~G~~~y~sl~e~p~~iDlavv~~~~~~~~~~v~~~~ 76 (116)
T PF13380_consen 1 KSIAVVGASDNPGKFG-YRVLRNLKAAGYEVYPV---NPKGGEILGIKCYPSLAEIPEPIDLAVVCVPPDKVPEIVDEAA 76 (116)
T ss_dssp -EEEEET--SSTTSHH-HHHHHHHHHTT-EEEEE---STTCSEETTEE-BSSGGGCSST-SEEEE-S-HHHHHHHHHHHH
T ss_pred CEEEEEcccCCCCChH-HHHHHHHHhCCCEEEEE---CCCceEECcEEeeccccCCCCCCCEEEEEcCHHHHHHHHHHHH
Confidence 4678886444434333 33444455577665422 22211100001222333 357899999999999999999999
Q ss_pred HcCccccCeEEEEcCc
Q 043276 100 EIGLMNKGCVWIMTDG 115 (829)
Q Consensus 100 ~~gm~~~~~vwI~t~~ 115 (829)
++| .+.+|+.++.
T Consensus 77 ~~g---~~~v~~~~g~ 89 (116)
T PF13380_consen 77 ALG---VKAVWLQPGA 89 (116)
T ss_dssp HHT----SEEEE-TTS
T ss_pred HcC---CCEEEEEcch
Confidence 998 5799999873
No 405
>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=36.86 E-value=1.4e+02 Score=28.73 Aligned_cols=47 Identities=17% Similarity=0.165 Sum_probs=29.2
Q ss_pred hHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEc
Q 043276 37 LIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHM 86 (829)
Q Consensus 37 ~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~ 86 (829)
....|.+.|++.|+.+.....++++ .+.+.+.+..+.+ .+++||+.+
T Consensus 20 n~~~l~~~L~~~G~~v~~~~~v~Dd--~~~I~~~l~~~~~-~~dlVIttG 66 (170)
T cd00885 20 NAAFLAKELAELGIEVYRVTVVGDD--EDRIAEALRRASE-RADLVITTG 66 (170)
T ss_pred HHHHHHHHHHHCCCEEEEEEEeCCC--HHHHHHHHHHHHh-CCCEEEECC
Confidence 3567777788888887776666544 4456666665542 455665544
No 406
>PRK00002 aroB 3-dehydroquinate synthase; Reviewed
Probab=36.81 E-value=3.1e+02 Score=30.06 Aligned_cols=101 Identities=10% Similarity=0.016 Sum_probs=61.9
Q ss_pred HHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeE--EecCCCCChhHHHHHHHHhhcCCC---eEEEE
Q 043276 10 GAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYR--SVISPLATDDQIEKELYKLFTMQT---RVFIL 84 (829)
Q Consensus 10 ~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~--~~i~~~~~~~~~~~~l~~lk~~~a---rViIv 84 (829)
+.+.++++.++++++.+|++. .......+.+.+.|++.|+.+... .......+.+.+.+.+..+++.+. ++||.
T Consensus 20 ~~l~~~l~~~~~~~~livtd~-~~~~~~~~~v~~~L~~~gi~~~~~~~~~~e~~~~~~~v~~~~~~~~~~~~~r~d~IIa 98 (358)
T PRK00002 20 SELGELLAPLKGKKVAIVTDE-TVAPLYLEKLRASLEAAGFEVDVVVLPDGEQYKSLETLEKIYDALLEAGLDRSDTLIA 98 (358)
T ss_pred HHHHHHHHhcCCCeEEEEECC-chHHHHHHHHHHHHHhcCCceEEEEeCCCCCCCCHHHHHHHHHHHHHcCCCCCCEEEE
Confidence 345667777888999998844 334467788888898888765421 122223445567777777776554 88887
Q ss_pred EcCh--hHHHHHHHHHHHcCccccCeEEEEcC
Q 043276 85 HMLP--SLGSRIFEKANEIGLMNKGCVWIMTD 114 (829)
Q Consensus 85 ~~~~--~~~~~i~~~a~~~gm~~~~~vwI~t~ 114 (829)
.+.. -++..+.......|+ .++-|-|.
T Consensus 99 vGGGsv~D~aK~iA~~~~~gi---p~i~IPTT 127 (358)
T PRK00002 99 LGGGVIGDLAGFAAATYMRGI---RFIQVPTT 127 (358)
T ss_pred EcCcHHHHHHHHHHHHhcCCC---CEEEcCch
Confidence 7654 344444443344442 35555554
No 407
>cd08480 PBP2_CrgA_like_10 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 10. 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
Probab=36.74 E-value=2.9e+02 Score=26.28 Aligned_cols=64 Identities=9% Similarity=0.156 Sum_probs=37.8
Q ss_pred eeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccEEEeccccccccceeccccccccccceEEEEE
Q 043276 340 YSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMIVP 419 (829)
Q Consensus 340 ~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv~ 419 (829)
+-.+++..+.++.+ .+++++.. .+.+.. +.+|++|+++..- ......+ -+.|+....++++++
T Consensus 15 ~l~~~l~~~~~~~P-~i~i~i~~-----------~~~~~~-~~~~~~D~~i~~~---~~~~~~~-~~~~l~~~~~~~~~~ 77 (198)
T cd08480 15 FLLPLLPAFLARYP-EILVDLSL-----------TDEVVD-LLAERTDVAIRVG---PLPDSSL-VARKLGESRRVIVAS 77 (198)
T ss_pred hhHHHHHHHHHHCC-CeEEEEEe-----------cCCccc-cccccccEEEEeC---CCCCCCe-EEEEcccceEEEEEC
Confidence 44677888888876 45555542 123333 4589999998532 1111222 246677777777776
Q ss_pred c
Q 043276 420 I 420 (829)
Q Consensus 420 ~ 420 (829)
.
T Consensus 78 ~ 78 (198)
T cd08480 78 P 78 (198)
T ss_pred H
Confidence 3
No 408
>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=36.37 E-value=1.5e+02 Score=30.46 Aligned_cols=75 Identities=15% Similarity=0.053 Sum_probs=48.0
Q ss_pred EEEEEEe-----CccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcChhHHHHHHHHH
Q 043276 24 AVPIYVD-----NQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKA 98 (829)
Q Consensus 24 V~iI~~d-----d~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~~~~~~~i~~~a 98 (829)
|+++..+ +.|.....+.+++++++.|..+..... . ..++.....+..+.+.+++.||+....... .+..+
T Consensus 2 vgv~~~~~~~~~~~~~~~~~~~i~~~~~~~g~~~~~~~~-~--~~~~~~~~~~~~l~~~~vdgiii~~~~~~~--~~~~l 76 (268)
T cd06277 2 IGLIASKRILNSPAFYSEIYRAIEEEAKKYGYNLILKFV-S--DEDEEEFELPSFLEDGKVDGIILLGGISTE--YIKEI 76 (268)
T ss_pred eEEEEeccccccCCcHHHHHHHHHHHHHHcCCEEEEEeC-C--CChHHHHHHHHHHHHCCCCEEEEeCCCChH--HHHHH
Confidence 5666655 778888889999999999987654421 1 122233344555666788888887654332 36666
Q ss_pred HHcCc
Q 043276 99 NEIGL 103 (829)
Q Consensus 99 ~~~gm 103 (829)
.+.|.
T Consensus 77 ~~~~i 81 (268)
T cd06277 77 KELGI 81 (268)
T ss_pred hhcCC
Confidence 66663
No 409
>PF10777 YlaC: Inner membrane protein YlaC; InterPro: IPR019713 The extracytoplasmic function (ECF) sigma factors are small regulatory proteins that are quite divergent in sequence relative to most other sigma factors. YlaC, regulated by YlaA, is important in oxidative stress resistance. It contributes to hydrogen peroxide resistance in Bacillus subtilis [].
Probab=36.15 E-value=90 Score=28.96 Aligned_cols=23 Identities=4% Similarity=-0.014 Sum_probs=19.1
Q ss_pred HhHHHHHHHHHHHHHHHHHhhhc
Q 043276 437 WDLWVTSGCFFIFIGFVVWVLEH 459 (829)
Q Consensus 437 ~~vW~~i~~~~~~~~~v~~~~~~ 459 (829)
+.+|++++++++.+++++|.-+.
T Consensus 36 P~L~~~M~~~y~~~~~lm~~spy 58 (155)
T PF10777_consen 36 PYLCLAMYAAYLAVAALMYYSPY 58 (155)
T ss_pred cHHHHHHHHHHHHHHHHHHhcch
Confidence 46889999999999999887664
No 410
>TIGR00854 pts-sorbose PTS system, mannose/fructose/sorbose family, IIB component. Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains.The Man family is unique in several respects among PTS permease families.It is the only PTS family in which members possess a IID protein. It is the only PTS family in which the IIB constituent is phosphorylated on a histidyl rather than a cysteyl residue. Its permease members exhibit broad specificity for a range of sugars, rather than being specific for just one or a few sugars. The mannose permease of E. coli, for example, can transport and phosphorylate glucose, mannose, fructose, glucosamine, N-acetylglucosamine, and other sugars. Other members of this can transport sorbose, fructose and N-acetylglucosamine. This family is specific for the IIB components of this family of PTS transporters.
Probab=36.09 E-value=2.4e+02 Score=26.60 Aligned_cols=81 Identities=16% Similarity=0.135 Sum_probs=53.5
Q ss_pred HHHHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcC
Q 043276 8 QVGAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHML 87 (829)
Q Consensus 8 q~~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~ 87 (829)
.++++...+++++-+.+.++- |.--.....+.+.+.+.-.|+.+.+.. .++..+.+.+-+..+.|++|++-+
T Consensus 13 HGQV~~~W~~~~~~~~IiVvd-D~~A~D~~~k~~lkma~P~gvk~~i~s-------ve~a~~~l~~~~~~~~~v~vl~k~ 84 (151)
T TIGR00854 13 HGQVGTTWTKVAGANRIIVVN-DDVANDEVRQTLMGIVAPTGFKVRFVS-------LEKTINVIHKPAYHDQTIFLLFRN 84 (151)
T ss_pred hhHhhhhhhcccCCCEEEEEc-ccccCCHHHHHHHHhhCCCCCEEEEEE-------HHHHHHHHhCcCCCCceEEEEECC
Confidence 466777788888888888874 323233455555555555787765542 223444454444566799999999
Q ss_pred hhHHHHHHH
Q 043276 88 PSLGSRIFE 96 (829)
Q Consensus 88 ~~~~~~i~~ 96 (829)
+..+..++.
T Consensus 85 ~~da~~l~~ 93 (151)
T TIGR00854 85 PQDVLTLVE 93 (151)
T ss_pred HHHHHHHHH
Confidence 999988864
No 411
>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=35.84 E-value=1.7e+02 Score=27.25 Aligned_cols=50 Identities=16% Similarity=0.111 Sum_probs=37.3
Q ss_pred chHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcCh
Q 043276 36 ELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLP 88 (829)
Q Consensus 36 ~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~~ 88 (829)
.....+.+.|++.|.++.....++++ .+++.+.+.++.+ ++++||+.+..
T Consensus 27 ~n~~~l~~~l~~~G~~v~~~~~v~Dd--~~~i~~~l~~~~~-~~DliIttGG~ 76 (144)
T TIGR00177 27 SNGPLLAALLEEAGFNVSRLGIVPDD--PEEIREILRKAVD-EADVVLTTGGT 76 (144)
T ss_pred CcHHHHHHHHHHCCCeEEEEeecCCC--HHHHHHHHHHHHh-CCCEEEECCCC
Confidence 34668888899999998887777655 5567777776643 68999987754
No 412
>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=35.79 E-value=3.5e+02 Score=28.32 Aligned_cols=99 Identities=5% Similarity=-0.050 Sum_probs=54.8
Q ss_pred HHHHHHHHHH-cC----CcEEEEEEEeCc--cccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhc--CCC
Q 043276 9 VGAITAIIKA-FG----WREAVPIYVDNQ--YGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFT--MQT 79 (829)
Q Consensus 9 ~~ai~~ll~~-fg----W~~V~iI~~dd~--yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~--~~a 79 (829)
+..+++.|.. +. =.++++|....+ ....-.+.+.+++++.|+.+... .....+.+.-.+.+.++.+ ...
T Consensus 108 g~~~~~~L~~~~~~~~g~~~I~~i~g~~~~~~~~~R~~Gf~~al~~~g~~~~~~--~~~~~~~~~~~~~~~~~L~~~~~~ 185 (295)
T TIGR02955 108 GYQAGEYLAQRHPKGSGPTTLAWLPGPKNRGGTKPVTQGFRAALEGSDVEISAI--LWADNDKELQRNLLQDLLKKHPDI 185 (295)
T ss_pred HHHHHHHHHHhcccCCCCeeEEEEeCCCcCCchhHHHHHHHHHHhcCCcEEEEE--ecCCCcHHHHHHHHHHHHHhCCCc
Confidence 3445555543 22 236999874433 23445778888998888876532 2212222222333444332 234
Q ss_pred eEEEEEcChhHHHHHHHHHHHcCccccCeEEEEc
Q 043276 80 RVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMT 113 (829)
Q Consensus 80 rViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t 113 (829)
++| +++...+..++..+++.|+ ++-+.+.+
T Consensus 186 d~i--~~~d~~a~g~l~al~~~g~--~~dv~vvg 215 (295)
T TIGR02955 186 DYL--VGSAVAAEAAISELRSLHM--TQQIKLVS 215 (295)
T ss_pred CEE--EeccHHHHHHHHHHHhhCc--cCCeEEEE
Confidence 543 5566667788888888775 45555554
No 413
>cd00001 PTS_IIB_man PTS_IIB, PTS system, Mannose/sorbose specific IIB subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family is one of four structurally and functionally distinct group IIB PTS system cytoplasmic enzymes, necessary for the uptake of carbohydrates across the cytoplasmic membrane and their phosphorylation. The active site histidine receives a phosphate group from the IIA subunit and transfers it to the substrate.
Probab=35.57 E-value=2.4e+02 Score=26.55 Aligned_cols=81 Identities=16% Similarity=0.130 Sum_probs=53.7
Q ss_pred HHHHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcC
Q 043276 8 QVGAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHML 87 (829)
Q Consensus 8 q~~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~ 87 (829)
.++++...+++++-+.+.++- |..-.....+.+.+.+.-.|+.+.... .++..+.+.+-+..+.|++|++-+
T Consensus 12 HGQV~~~W~~~~~~~~IvVvd-D~~A~D~~~k~~l~ma~P~gvk~~i~s-------ve~a~~~l~~~~~~~~~v~il~k~ 83 (151)
T cd00001 12 HGQVATTWTKELNANRIIVVN-DEVANDELRKTLLKLAAPPGVKLRIFT-------VEKAIEAINSPKYDKQRVFLLFKN 83 (151)
T ss_pred hhHhhhhhhcccCCCEEEEEc-ccccCCHHHHHHHHhhCCCCCeEEEEE-------HHHHHHHHhCcCCCCceEEEEECC
Confidence 567778888899999888874 322233455555555555787765442 223444455444567799999999
Q ss_pred hhHHHHHHH
Q 043276 88 PSLGSRIFE 96 (829)
Q Consensus 88 ~~~~~~i~~ 96 (829)
++.+..+..
T Consensus 84 ~~~~~~l~~ 92 (151)
T cd00001 84 PQDVLRLVE 92 (151)
T ss_pred HHHHHHHHH
Confidence 999988865
No 414
>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=35.49 E-value=5.1e+02 Score=26.57 Aligned_cols=107 Identities=10% Similarity=0.035 Sum_probs=58.2
Q ss_pred ChHHHHHHHHHHH-HHcCCc--EEEEEEEeC--ccccchHHHHHHHHHhCCcee----eeEEe--cCCCCChhHHHHHHH
Q 043276 4 NDSSQVGAITAII-KAFGWR--EAVPIYVDN--QYGEELIPSLTDALQAIDTRV----PYRSV--ISPLATDDQIEKELY 72 (829)
Q Consensus 4 sD~~q~~ai~~ll-~~fgW~--~V~iI~~dd--~yG~~~~~~l~~~l~~~gi~I----~~~~~--i~~~~~~~~~~~~l~ 72 (829)
++...+..+++.| +..|=+ .++++..+. ..+..-.+.|.+++++.|+.. ..... .....+..+....+.
T Consensus 103 d~~~~g~~~~~~l~~~~g~~~~~i~~i~~~~~~~~~~~R~~gf~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 182 (282)
T cd06318 103 SNAKNGNLVGEWVVGELGDKPMKIILLSGDAGNLVGQARRDGFLLGVSEAQLRKYGKTNFTIVAQGYGDWTREGGLKAME 182 (282)
T ss_pred CcHHHHHHHHHHHHHHhCCCCceEEEEECCCCCchHhHHHHhHHHHHhhCcccccccCCeEEEecCCCCCCHHHHHHHHH
Confidence 3444566777766 447865 888886432 335556677888888876421 11111 111112222233444
Q ss_pred HhhcCCCe-EEEEEcChhHHHHHHHHHHHcCccccCeEEEE
Q 043276 73 KLFTMQTR-VFILHMLPSLGSRIFEKANEIGLMNKGCVWIM 112 (829)
Q Consensus 73 ~lk~~~ar-ViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~ 112 (829)
.+.....+ -.|++.+...+..++..+++.|+. +-+-|.
T Consensus 183 ~~l~~~~~~~ai~~~~d~~a~g~~~al~~~g~~--~dv~vv 221 (282)
T cd06318 183 DLLVAHPDINVVYSENDDMALGAMRVLAEAGKT--DDVKVA 221 (282)
T ss_pred HHHHhCCCcCEEEECCcchHHHHHHHHHHcCCC--CCeEEE
Confidence 43322222 245556666778899999999963 444444
No 415
>KOG0025 consensus Zn2+-binding dehydrogenase (nuclear receptor binding factor-1) [Transcription; Energy production and conversion]
Probab=35.38 E-value=2.2e+02 Score=29.89 Aligned_cols=85 Identities=14% Similarity=0.144 Sum_probs=62.4
Q ss_pred hHHHHHHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHH-HHHHHh--hcCCCeE
Q 043276 5 DSSQVGAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIE-KELYKL--FTMQTRV 81 (829)
Q Consensus 5 D~~q~~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~-~~l~~l--k~~~arV 81 (829)
.+.-++++.++.+++|.+.+.+|-+.++ ++.|.+.|+..|...++.+. ++. +...+. ...+.|.
T Consensus 170 nS~VG~~ViQlaka~GiktinvVRdR~~-----ieel~~~Lk~lGA~~ViTee--------el~~~~~~k~~~~~~~prL 236 (354)
T KOG0025|consen 170 NSGVGQAVIQLAKALGIKTINVVRDRPN-----IEELKKQLKSLGATEVITEE--------ELRDRKMKKFKGDNPRPRL 236 (354)
T ss_pred ccHHHHHHHHHHHHhCcceEEEeecCcc-----HHHHHHHHHHcCCceEecHH--------HhcchhhhhhhccCCCceE
Confidence 3566789999999999999999986555 78999999999987654432 211 222222 2356777
Q ss_pred EEEEcChhHHHHHHHHHHHcC
Q 043276 82 FILHMLPSLGSRIFEKANEIG 102 (829)
Q Consensus 82 iIv~~~~~~~~~i~~~a~~~g 102 (829)
-+-|.....+..+.+...+-|
T Consensus 237 alNcVGGksa~~iar~L~~Gg 257 (354)
T KOG0025|consen 237 ALNCVGGKSATEIARYLERGG 257 (354)
T ss_pred EEeccCchhHHHHHHHHhcCc
Confidence 888888888888888887755
No 416
>PF07302 AroM: AroM protein; InterPro: IPR010843 This family consists of several bacterial and archaeal AroM proteins. In Escherichia coli the aroM gene is cotranscribed with aroL []. The function of this family is unknown.
Probab=35.18 E-value=3.4e+02 Score=27.39 Aligned_cols=74 Identities=11% Similarity=0.078 Sum_probs=47.8
Q ss_pred cEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEc--ChhHHHHHHHHHH
Q 043276 22 REAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHM--LPSLGSRIFEKAN 99 (829)
Q Consensus 22 ~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~--~~~~~~~i~~~a~ 99 (829)
..+++|....+- .+...+..+..+..+.+...-|...+.+++.+.-..|++.++++||++| +....+.+++++.
T Consensus 126 ~~vGVivP~~eQ----~~~~~~kW~~l~~~~~~a~asPy~~~~~~l~~Aa~~L~~~gadlIvLDCmGYt~~~r~~~~~~~ 201 (221)
T PF07302_consen 126 HQVGVIVPLPEQ----IAQQAEKWQPLGNPVVVAAASPYEGDEEELAAAARELAEQGADLIVLDCMGYTQEMRDIVQRAL 201 (221)
T ss_pred CeEEEEecCHHH----HHHHHHHHHhcCCCeEEEEeCCCCCCHHHHHHHHHHHHhcCCCEEEEECCCCCHHHHHHHHHHh
Confidence 788888866542 2223344555555555554444434566788888889889999999976 4556666666553
No 417
>cd08477 PBP2_CrgA_like_8 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 8. 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=34.98 E-value=2.5e+02 Score=26.48 Aligned_cols=64 Identities=14% Similarity=0.169 Sum_probs=37.5
Q ss_pred EeeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccEEEeccccccccceeccccccccccceEEEE
Q 043276 339 GYSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMIV 418 (829)
Q Consensus 339 G~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv 418 (829)
++-.+++..+.++.+ .+++++... +.+.. +.+|++|+++...... ...+. +.|+.+..+++++
T Consensus 14 ~~l~~~l~~~~~~~P-~i~l~i~~~-----------~~~~~-~~~~~~D~~i~~~~~~---~~~~~-~~~l~~~~~~~v~ 76 (197)
T cd08477 14 HVLTPALAEYLARYP-DVRVDLVLS-----------DRLVD-LVEEGFDAAFRIGELA---DSSLV-ARPLAPYRMVLCA 76 (197)
T ss_pred HHHHHHHHHHHHHCC-CcEEEEEec-----------CCcch-hhhcCccEEEECCCCC---CCCee-EEEeeeeEEEEEE
Confidence 344678888888876 456665431 12444 3457899998432221 12222 4567777878777
Q ss_pred E
Q 043276 419 P 419 (829)
Q Consensus 419 ~ 419 (829)
+
T Consensus 77 ~ 77 (197)
T cd08477 77 S 77 (197)
T ss_pred C
Confidence 6
No 418
>KOG3713 consensus Voltage-gated K+ channel KCNB/KCNC [Inorganic ion transport and metabolism]
Probab=34.97 E-value=45 Score=37.25 Aligned_cols=60 Identities=13% Similarity=0.288 Sum_probs=43.8
Q ss_pred HHHHHHhhhcccCCCCCCCccCccchhHHHHHHHhhhcC-c-cccccchhHHHHHHHHHHHHHHHH
Q 043276 450 IGFVVWVLEHRVNEDFRGPARHQVGTSFWFSFSTMVFSQ-R-ERVISNLARFVVIVWCFVVLILIQ 513 (829)
Q Consensus 450 ~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~-~-~~~~s~~~R~v~~~w~~~~lil~~ 513 (829)
.+.+++++|+-.+. +.-.++--++|++.-+|..-| + -.|++.++|++...-.+.++++.+
T Consensus 359 FStlvY~~Ek~~~~----~~FtSIPa~~WWaiVTMTTVGYGDm~P~T~~Gklvas~cil~GVLvlA 420 (477)
T KOG3713|consen 359 FSTLVYFAEKDEPD----TKFTSIPAGFWWAVVTMTTVGYGDMVPVTVLGKLVASLCILCGVLVLA 420 (477)
T ss_pred HHHHHHHhhhcCCC----CCCccccchhheeeEEEeeecccCccccccchHHHHHHHHHHhHHHhh
Confidence 34455677765432 224467789999999998777 3 468999999999888888877654
No 419
>COG0521 MoaB Molybdopterin biosynthesis enzymes [Coenzyme metabolism]
Probab=34.87 E-value=1.9e+02 Score=27.86 Aligned_cols=63 Identities=19% Similarity=0.202 Sum_probs=44.1
Q ss_pred EEEEEEEeCc--cccc---hHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcC
Q 043276 23 EAVPIYVDNQ--YGEE---LIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHML 87 (829)
Q Consensus 23 ~V~iI~~dd~--yG~~---~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~ 87 (829)
.++||..+|. -|.. .-+.+.+.|++.|-.+.....+|++ .+.+.+.+.++-....++|+..+.
T Consensus 9 ~~~VvTVSd~r~~~~~~D~sG~~l~~~L~~ag~~~~~~~iV~D~--~~~I~~~l~~~~~~~~DvvlttGG 76 (169)
T COG0521 9 RIAVVTVSDRRSTGEYEDKSGPLLVELLEEAGHNVAAYTIVPDD--KEQIRATLIALIDEDVDVVLTTGG 76 (169)
T ss_pred eEEEEEEecccccCCccccchhHHHHHHHHcCCccceEEEeCCC--HHHHHHHHHHHhcCCCCEEEEcCC
Confidence 4666664433 2333 5678899999999999778788765 456777777765444888888764
No 420
>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=34.74 E-value=4.9e+02 Score=27.24 Aligned_cols=101 Identities=9% Similarity=-0.090 Sum_probs=54.5
Q ss_pred ChHHHHHHHHHHHHHc-CC-cEEEEEEEeCcc--ccchHHHHHHHHHhCCce-eeeEEecCCCCChhHHHHHHHHhhcCC
Q 043276 4 NDSSQVGAITAIIKAF-GW-REAVPIYVDNQY--GEELIPSLTDALQAIDTR-VPYRSVISPLATDDQIEKELYKLFTMQ 78 (829)
Q Consensus 4 sD~~q~~ai~~ll~~f-gW-~~V~iI~~dd~y--G~~~~~~l~~~l~~~gi~-I~~~~~i~~~~~~~~~~~~l~~lk~~~ 78 (829)
++...+..+++.+... += ++++++..+... ...-.+.+.++++++|.. +.....+....+.+.-.+.+.++.+..
T Consensus 104 D~~~~g~~a~~~l~~~~~~~~~I~~l~g~~~~~~~~~R~~Gf~~~l~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~ 183 (298)
T cd06302 104 DNKAIGETLMDSLAEQMGGKGEYAIFVGSLTATNQNAWIDAAKAYQKEKYYPMLELVDRQYGDDDADKSYQTAQELLKAY 183 (298)
T ss_pred CHHHHHHHHHHHHHHHcCCCCEEEEEeCCCCCcchHHHHHHHHHHHhhcCCCCeEEeCcccCCCCHHHHHHHHHHHHHhC
Confidence 4455556667766444 43 699998744332 234457788889888721 211112221222222223344432222
Q ss_pred Ce-EEEEEcChhHHHHHHHHHHHcCcc
Q 043276 79 TR-VFILHMLPSLGSRIFEKANEIGLM 104 (829)
Q Consensus 79 ar-ViIv~~~~~~~~~i~~~a~~~gm~ 104 (829)
.+ -.|++++...+..+++.+++.|+.
T Consensus 184 ~~~~ai~~~~D~~A~g~~~al~~~g~~ 210 (298)
T cd06302 184 PDLKGIIGPTSVGIPGAARAVEEAGLK 210 (298)
T ss_pred CCceEEEECCCcchhHHHHHHHhcCCC
Confidence 22 244455667888899999999963
No 421
>PF01007 IRK: Inward rectifier potassium channel; InterPro: IPR013521 Potassium channels are the most diverse group of the ion channel family [, ]. They are important in shaping the action potential, and in neuronal excitability and plasticity []. The potassium channel family is composed of several functionally distinct isoforms, which can be broadly separated into 2 groups []: the practically non-inactivating 'delayed' group and the rapidly inactivating 'transient' group. These are all highly similar proteins, with only small amino acid changes causing the diversity of the voltage-dependent gating mechanism, channel conductance and toxin binding properties. Each type of K+ channel is activated by different signals and conditions depending on their type of regulation: some open in response to depolarisation of the plasma membrane; others in response to hyperpolarisation or an increase in intracellular calcium concentration; some can be regulated by binding of a transmitter, together with intracellular kinases; while others are regulated by GTP-binding proteins or other second messengers []. In eukaryotic cells, K+ channels are involved in neural signalling and generation of the cardiac rhythm, act as effectors in signal transduction pathways involving G protein-coupled receptors (GPCRs) and may have a role in target cell lysis by cytotoxic T-lymphocytes []. In prokaryotic cells, they play a role in the maintenance of ionic homeostasis []. All K+ channels discovered so far possess a core of alpha subunits, each comprising either one or two copies of a highly conserved pore loop domain (P-domain). The P-domain contains the sequence (T/SxxTxGxG), which has been termed the K+ selectivity sequence. In families that contain one P-domain, four subunits assemble to form a selective pathway for K+ across the membrane. However, it remains unclear how the 2 P-domain subunits assemble to form a selective pore. The functional diversity of these families can arise through homo- or hetero-associations of alpha subunits or association with auxiliary cytoplasmic beta subunits. K+ channel subunits containing one pore domain can be assigned into one of two superfamilies: those that possess six transmembrane (TM) domains and those that possess only two TM domains. The six TM domain superfamily can be further subdivided into conserved gene families: the voltage-gated (Kv) channels; the KCNQ channels (originally known as KvLQT channels); the EAG-like K+ channels; and three types of calcium (Ca)-activated K+ channels (BK, IK and SK) []. The 2TM domain family comprises inward-rectifying K+ channels. In addition, there are K+ channel alpha-subunits that possess two P-domains. These are usually highly regulated K+ selective leak channels. Inwardly-rectifying potassium channels (Kir) are the principal class of two-TM domain potassium channels. They are characterised by the property of inward-rectification, which is described as the ability to allow large inward currents and smaller outward currents. Inwardly rectifying potassium channels (Kir) are responsible for regulating diverse processes including: cellular excitability, vascular tone, heart rate, renal salt flow, and insulin release []. To date, around twenty members of this superfamily have been cloned, which can be grouped into six families by sequence similarity, and these are designated Kir1.x-6.x [, ]. Cloned Kir channel cDNAs encode proteins of between ~370-500 residues, both N- and C-termini are thought to be cytoplasmic, and the N terminus lacks a signal sequence. Kir channel alpha subunits possess only 2TM domains linked with a P-domain. Thus, Kir channels share similarity with the fifth and sixth domains, and P-domain of the other families. It is thought that four Kir subunits assemble to form a tetrameric channel complex, which may be hetero- or homomeric [].; PDB: 3AT9_A 3AUW_D 3SYA_A 3ATE_A 3SYQ_A 3SYO_A 3ATB_A 3SYC_A 3AT8_A 3ATA_A ....
Probab=34.60 E-value=2.2e+02 Score=30.90 Aligned_cols=59 Identities=19% Similarity=0.161 Sum_probs=48.3
Q ss_pred CccchhHHHHHHHhhhcC-cc---ccccchhHHHHHHHHHHHHHHHHHhHHHHHHHhhcccCC
Q 043276 471 HQVGTSFWFSFSTMVFSQ-RE---RVISNLARFVVIVWCFVVLILIQSYTASLTSLLTVDQLQ 529 (829)
Q Consensus 471 ~~~~~~~~~~~~~l~~~~-~~---~~~s~~~R~v~~~w~~~~lil~~~YtA~L~s~Lt~~~~~ 529 (829)
.++..+|+|++.++...| +. .+.+..+-+++.+=.++++++.+.-++-+.+-++.|+..
T Consensus 83 ~~f~~aF~FSveT~tTIGYG~~~~~~~c~~a~~l~~~q~~~g~l~~a~~~Glvfar~srP~~R 145 (336)
T PF01007_consen 83 NSFTSAFLFSVETQTTIGYGSRYPTPECPYAIFLVTIQSLVGLLLDAFMTGLVFARFSRPKKR 145 (336)
T ss_dssp TTHHHHHHHHHHHHTT---SSSEB-CSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTSCCCG
T ss_pred cchhhheeEEEEEEEEeccCCcccCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccc
Confidence 478899999999999776 32 457788889999999999999999999999999988764
No 422
>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=34.52 E-value=1.4e+02 Score=30.37 Aligned_cols=77 Identities=9% Similarity=0.056 Sum_probs=50.1
Q ss_pred EEEEEE--eCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcChhHHHHHHHHHHHc
Q 043276 24 AVPIYV--DNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEI 101 (829)
Q Consensus 24 V~iI~~--dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~~~~~~~i~~~a~~~ 101 (829)
|+++.. ++.|.....+.+.+++++.|..+..... ..+.+...+.++++...+.+.+|+..........+..+.+.
T Consensus 2 igvv~~~~~~~~~~~~~~~i~~~~~~~g~~~~~~~~---~~~~~~~~~~~~~l~~~~vdgiii~~~~~~~~~~~~~~~~~ 78 (266)
T cd06282 2 VGVVLPSLANPVFAECVQGIQEEARAAGYSLLLATT---DYDAEREADAVETLLRQRVDGLILTVADAATSPALDLLDAE 78 (266)
T ss_pred eEEEeCCCCcchHHHHHHHHHHHHHHCCCEEEEeeC---CCCHHHHHHHHHHHHhcCCCEEEEecCCCCchHHHHHHhhC
Confidence 455553 4667788889999999999988765422 22233445666777777888888764322223466777777
Q ss_pred Cc
Q 043276 102 GL 103 (829)
Q Consensus 102 gm 103 (829)
|+
T Consensus 79 ~i 80 (266)
T cd06282 79 RV 80 (266)
T ss_pred CC
Confidence 74
No 423
>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=34.28 E-value=1.6e+02 Score=30.26 Aligned_cols=80 Identities=11% Similarity=0.124 Sum_probs=50.7
Q ss_pred EEEEEEE--eCccccchHHHHHHHHHhC---CceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcChhH-HHHHHH
Q 043276 23 EAVPIYV--DNQYGEELIPSLTDALQAI---DTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSL-GSRIFE 96 (829)
Q Consensus 23 ~V~iI~~--dd~yG~~~~~~l~~~l~~~---gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~~~~-~~~i~~ 96 (829)
+|+++.. ++.|-......+.+++++. |..+..... ....+.+...+.+.++...+.+.||+...... ....+.
T Consensus 1 ~Ig~i~~~~~~~~~~~~~~~i~~~~~~~~~~g~~~~l~i~-~~~~~~~~~~~~~~~~~~~~vdgiIi~~~~~~~~~~~l~ 79 (272)
T cd06300 1 KIGLSNSYAGNTWRAQMLDEFKAQAKELKKAGLISEFIVT-SADGDVAQQIADIRNLIAQGVDAIIINPASPTALNPVIE 79 (272)
T ss_pred CeEEeccccCChHHHHHHHHHHHHHHhhhccCCeeEEEEe-cCCCCHHHHHHHHHHHHHcCCCEEEEeCCChhhhHHHHH
Confidence 3566653 4556677888888999888 874433322 22223344567777777788999999765433 344667
Q ss_pred HHHHcCc
Q 043276 97 KANEIGL 103 (829)
Q Consensus 97 ~a~~~gm 103 (829)
.+.+.|.
T Consensus 80 ~~~~~~i 86 (272)
T cd06300 80 EACEAGI 86 (272)
T ss_pred HHHHCCC
Confidence 7777663
No 424
>PRK09756 PTS system N-acetylgalactosamine-specific transporter subunit IIB; Provisional
Probab=33.91 E-value=3e+02 Score=26.17 Aligned_cols=80 Identities=10% Similarity=0.102 Sum_probs=52.8
Q ss_pred HHHHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHH-hCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEc
Q 043276 8 QVGAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQ-AIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHM 86 (829)
Q Consensus 8 q~~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~-~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~ 86 (829)
.++++...+++++-+.+.++- |.--.....+.+.+.+. -.|+.+.+.. .++..+.+.+ +..+.|++|++-
T Consensus 17 HGQV~~~W~~~~~~~~IiVvd-D~vA~D~~~k~~lkma~~P~gvk~~i~s-------v~~a~~~l~~-~~~~~~vlvl~~ 87 (158)
T PRK09756 17 HGQVGVTWTSTIGANLLVVVD-DVVANDDIQQKLMGITAETYGFGIRFFT-------IEKTINVIGK-AAPHQKIFLICR 87 (158)
T ss_pred hHHHHHhhhcccCCCEEEEEc-chhcCCHHHHHHHHhcCCCCCCEEEEEE-------HHHHHHHHHh-ccCCceEEEEEC
Confidence 567778888899999888873 32223344555555444 4677765432 2244455555 556679999999
Q ss_pred ChhHHHHHHH
Q 043276 87 LPSLGSRIFE 96 (829)
Q Consensus 87 ~~~~~~~i~~ 96 (829)
+++.+..++.
T Consensus 88 ~~~da~~l~~ 97 (158)
T PRK09756 88 TPQTVRKLVE 97 (158)
T ss_pred CHHHHHHHHH
Confidence 9999988865
No 425
>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=33.87 E-value=1.7e+02 Score=29.94 Aligned_cols=77 Identities=10% Similarity=0.092 Sum_probs=50.4
Q ss_pred EEEEEEe--CccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcChhH-HHHHHHHHHH
Q 043276 24 AVPIYVD--NQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSL-GSRIFEKANE 100 (829)
Q Consensus 24 V~iI~~d--d~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~~~~-~~~i~~~a~~ 100 (829)
|+++..+ +.|.....+.+.+++++.|..+.... ...+.+.....+..+.+.+++.+|+...... ....+.++.+
T Consensus 2 i~~~~~~~~~~~~~~~~~~i~~~~~~~g~~~~i~~---~~~~~~~~~~~~~~~~~~~vdgiii~~~~~~~~~~~~~~~~~ 78 (267)
T cd06322 2 IGASLLTQQHPFYIELANAMKEEAKKQKVNLIVSI---ANQDLNKQLSDVEDFITKKVDAIVLSPVDSKGIRAAIAKAKK 78 (267)
T ss_pred eeEeecCcccHHHHHHHHHHHHHHHhcCCEEEEec---CCCCHHHHHHHHHHHHHcCCCEEEEcCCChhhhHHHHHHHHH
Confidence 4555544 67778889999999999998775431 1222333455666777778999988654332 3456677777
Q ss_pred cCc
Q 043276 101 IGL 103 (829)
Q Consensus 101 ~gm 103 (829)
.|+
T Consensus 79 ~~i 81 (267)
T cd06322 79 AGI 81 (267)
T ss_pred CCC
Confidence 664
No 426
>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=33.62 E-value=95 Score=34.31 Aligned_cols=72 Identities=10% Similarity=0.002 Sum_probs=51.6
Q ss_pred HHcCCcEEEEEEEeCccc-cchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcCh
Q 043276 17 KAFGWREAVPIYVDNQYG-EELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLP 88 (829)
Q Consensus 17 ~~fgW~~V~iI~~dd~yG-~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~~ 88 (829)
..++-+++.+|+....+- .+..+.+.+.|++.|+.+.....+..+++.+.+.+.+..+++.++++||-.+..
T Consensus 19 ~~~~~~r~livt~~~~~~~~g~~~~v~~~L~~~g~~~~~~~~v~~~p~~~~v~~~~~~~~~~~~D~IIavGGG 91 (375)
T cd08179 19 KTLKGKKAFIVTGGGSMKKFGFLDKVEAYLKEAGIEVEVFEGVEPDPSVETVLKGAEAMREFEPDWIIALGGG 91 (375)
T ss_pred HHhcCCeEEEEeCchHHHhCChHHHHHHHHHHcCCeEEEeCCCCCCcCHHHHHHHHHHHHhcCCCEEEEeCCc
Confidence 334457888887443332 356788889999999876544445556667778888888988999999988764
No 427
>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=33.22 E-value=4.8e+02 Score=27.11 Aligned_cols=106 Identities=9% Similarity=0.052 Sum_probs=56.7
Q ss_pred hHHH-HHHHHHHHHHc--CCcEEEEEEEeCccc--cchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcC--
Q 043276 5 DSSQ-VGAITAIIKAF--GWREAVPIYVDNQYG--EELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTM-- 77 (829)
Q Consensus 5 D~~q-~~ai~~ll~~f--gW~~V~iI~~dd~yG--~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~-- 77 (829)
|..+ +..+++.+... |-+++++|..+.+.. ..-.+.+.+.+++.+..+....... ..+.....+.+..+.+.
T Consensus 107 d~~~~g~~~~~~l~~~~~g~~~i~~l~~~~~~~~~~~R~~gf~~~l~~~~~~~~~~~~~~-~~~~~~~~~~~~~~l~~~~ 185 (294)
T cd06316 107 DNYGNGQIAADALAKALPGKGKVGLIYHGADYFVTNQRDQGFKETIKKNYPDITIVAEKG-IDGPSKAEDIANAMLTQNP 185 (294)
T ss_pred CcHHHHHHHHHHHHHHhCCCceEEEEeCCCCcccHHHHHHHHHHHHHHhCCCcEEEeecC-CcchhHHHHHHHHHHHhCC
Confidence 3344 46667777555 889999997544432 3335667777776553222111111 11112223344443322
Q ss_pred CCeEEEEEcChhHHHHHHHHHHHcCccccCeEEEEcC
Q 043276 78 QTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIMTD 114 (829)
Q Consensus 78 ~arViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t~ 114 (829)
..++ |++.+...+..+++.+++.|+ .+-..++-|
T Consensus 186 ~~~a-i~~~~d~~a~g~~~~l~~~g~--~di~vvg~d 219 (294)
T cd06316 186 DLKG-IYAVWDVPAEGVIAALRAAGR--DDIKVTTVD 219 (294)
T ss_pred CeeE-EEeCCCchhHHHHHHHHHcCC--CCceEEEeC
Confidence 3344 344556678889999999985 344444433
No 428
>KOG1420 consensus Ca2+-activated K+ channel Slowpoke, alpha subunit [Inorganic ion transport and metabolism; Signal transduction mechanisms]
Probab=33.19 E-value=26 Score=39.28 Aligned_cols=60 Identities=18% Similarity=0.285 Sum_probs=44.9
Q ss_pred CCCCccCccchhHHHHHHHhhhcCcc--ccccchhHHHHHHHHHHHHHHHHHhHHHHHHHhh
Q 043276 465 FRGPARHQVGTSFWFSFSTMVFSQRE--RVISNLARFVVIVWCFVVLILIQSYTASLTSLLT 524 (829)
Q Consensus 465 ~~~~~~~~~~~~~~~~~~~l~~~~~~--~~~s~~~R~v~~~w~~~~lil~~~YtA~L~s~Lt 524 (829)
|.+..+.....+.+|.+.++-..|-. -.....+|++++++++++|-+-++|.-.++-+.-
T Consensus 281 f~n~hrltyw~cvyfl~vtmstvgygdvyc~t~lgrlfmvffil~glamfasyvpeiielig 342 (1103)
T KOG1420|consen 281 FQNNHRLTYWECVYFLMVTMSTVGYGDVYCKTTLGRLFMVFFILGGLAMFASYVPEIIELIG 342 (1103)
T ss_pred ccCcccchhhheeeeeEEEeeeccccceeehhhhhHHHHHHHHHHHHHHHHhhhHHHHHHHc
Confidence 56666666777777777666655533 3478889999999999999999999777665543
No 429
>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=33.01 E-value=2e+02 Score=31.31 Aligned_cols=75 Identities=12% Similarity=-0.026 Sum_probs=50.2
Q ss_pred HHHHHHHHHcCC--cEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcC---CCeEEEE
Q 043276 10 GAITAIIKAFGW--REAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTM---QTRVFIL 84 (829)
Q Consensus 10 ~ai~~ll~~fgW--~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~---~arViIv 84 (829)
..+.++++.+|. +.+.+|+...-.. +.+.+.|++.|+.+.....+..+++.+++.+.....++. ++++||-
T Consensus 12 ~~l~~~~~~~g~~~~~~lvvtd~~~~~----~~v~~~L~~~g~~~~~f~~v~~nPt~~~v~~~~~~~~~~~~~~~D~IIa 87 (347)
T cd08184 12 DQLNDLLAPKRKNKDPAVFFVDDVFQG----KDLISRLPVESEDMIIWVDATEEPKTDQIDALTAQVKSFDGKLPCAIVG 87 (347)
T ss_pred HHHHHHHHHcCCCCCeEEEEECcchhh----hHHHHHHHhcCCcEEEEcCCCCCcCHHHHHHHHHHHHhhCCCCCCEEEE
Confidence 456677777764 5566666222221 567777888887654444566667777788877778766 8999998
Q ss_pred EcCh
Q 043276 85 HMLP 88 (829)
Q Consensus 85 ~~~~ 88 (829)
.+..
T Consensus 88 iGGG 91 (347)
T cd08184 88 IGGG 91 (347)
T ss_pred eCCc
Confidence 7754
No 430
>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=32.93 E-value=1.7e+02 Score=29.69 Aligned_cols=77 Identities=10% Similarity=0.084 Sum_probs=50.0
Q ss_pred EEEEEEEe--CccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcCh-hHHHHHHHHHH
Q 043276 23 EAVPIYVD--NQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLP-SLGSRIFEKAN 99 (829)
Q Consensus 23 ~V~iI~~d--d~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~~-~~~~~i~~~a~ 99 (829)
+|++|..+ +.|.......+.+++++.|+.+..... ..+.+...+.++++...+.+.+|+.... +.....+..+.
T Consensus 1 ~ig~i~p~~~~~~~~~~~~~~~~~a~~~g~~~~~~~~---~~~~~~~~~~~~~l~~~~vdgvi~~~~~~~~~~~~~~~l~ 77 (267)
T cd01536 1 KIGLVVPSLNNPFWQAMNKGAEAAAKELGVELIVLDA---QNDVSKQIQQIEDLIAQGVDGIIISPVDSAALTPALKKAN 77 (267)
T ss_pred CEEEEeccccCHHHHHHHHHHHHHHHhcCceEEEECC---CCCHHHHHHHHHHHHHcCCCEEEEeCCCchhHHHHHHHHH
Confidence 36777754 678888999999999999987654322 1123344466777776788888876543 33333556666
Q ss_pred HcC
Q 043276 100 EIG 102 (829)
Q Consensus 100 ~~g 102 (829)
+.+
T Consensus 78 ~~~ 80 (267)
T cd01536 78 AAG 80 (267)
T ss_pred HCC
Confidence 655
No 431
>smart00857 Resolvase Resolvase, N terminal domain. The N-terminal domain of the resolvase family contains the active site and the dimer interface. The extended arm at the C-terminus of this domain connects to the C-terminal helix-turn-helix domain of resolvase.
Probab=32.81 E-value=3.4e+02 Score=24.90 Aligned_cols=37 Identities=16% Similarity=0.128 Sum_probs=19.0
Q ss_pred HHHHHHHHhhcCCCeEEEEEcCh------hHHHHHHHHHHHcC
Q 043276 66 QIEKELYKLFTMQTRVFILHMLP------SLGSRIFEKANEIG 102 (829)
Q Consensus 66 ~~~~~l~~lk~~~arViIv~~~~------~~~~~i~~~a~~~g 102 (829)
.+.+.+..+++...++||+.-.. .+...++....+.|
T Consensus 53 ~l~~ll~~~~~g~~~~ivv~~~~Rl~R~~~~~~~~~~~l~~~g 95 (148)
T smart00857 53 GLQRLLADLRAGDIDVLVVYKLDRLGRSLRDLLALLELLEKKG 95 (148)
T ss_pred HHHHHHHHHHcCCCCEEEEeccchhhCcHHHHHHHHHHHHHCC
Confidence 45556666655555566654433 23344445555554
No 432
>PRK09701 D-allose transporter subunit; Provisional
Probab=32.77 E-value=6e+02 Score=26.82 Aligned_cols=97 Identities=10% Similarity=0.029 Sum_probs=57.0
Q ss_pred ChHHHHHHHHHHH-HHcCC--cEEEEEEEeCc--cccchHHHHHHHHHhCC-ceeeeEEecCCCCChhHHHHHHHHhhcC
Q 043276 4 NDSSQVGAITAII-KAFGW--REAVPIYVDNQ--YGEELIPSLTDALQAID-TRVPYRSVISPLATDDQIEKELYKLFTM 77 (829)
Q Consensus 4 sD~~q~~ai~~ll-~~fgW--~~V~iI~~dd~--yG~~~~~~l~~~l~~~g-i~I~~~~~i~~~~~~~~~~~~l~~lk~~ 77 (829)
++...+..+++.+ +..|- ++++++..+.. ....-.+.+.++++++| +.+... .....+.+.-.+.+.++.+.
T Consensus 136 d~~~~g~~aa~~L~~~~g~~~~~i~~l~g~~~~~~~~~R~~Gf~~al~~~~~~~~~~~--~~~~~~~~~~~~~~~~ll~~ 213 (311)
T PRK09701 136 DNVAVGAKGASFIIDKLGAEGGEVAIIEGKAGNASGEARRNGATEAFKKASQIKLVAS--QPADWDRIKALDVATNVLQR 213 (311)
T ss_pred chHHHHHHHHHHHHHHhCCCCCEEEEEECCCCCccHHHHHHHHHHHHHhCCCcEEEEe--cCCCCCHHHHHHHHHHHHHh
Confidence 3445566677766 44564 79998864433 23455677888888887 665332 11111222223444444322
Q ss_pred --CCeEEEEEcChhHHHHHHHHHHHcCc
Q 043276 78 --QTRVFILHMLPSLGSRIFEKANEIGL 103 (829)
Q Consensus 78 --~arViIv~~~~~~~~~i~~~a~~~gm 103 (829)
..+ .|++.+...+..++..+++.|.
T Consensus 214 ~~~~~-~I~~~~d~~A~g~~~al~~~G~ 240 (311)
T PRK09701 214 NPNIK-AIYCANDTMAMGVAQAVANAGK 240 (311)
T ss_pred CCCCC-EEEECCcchHHHHHHHHHHcCC
Confidence 234 4556667788889999999886
No 433
>PRK15408 autoinducer 2-binding protein lsrB; Provisional
Probab=32.26 E-value=2.3e+02 Score=30.66 Aligned_cols=82 Identities=9% Similarity=-0.020 Sum_probs=56.7
Q ss_pred CCcEEEEEEE--eCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcCh-hHHHHHHH
Q 043276 20 GWREAVPIYV--DNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLP-SLGSRIFE 96 (829)
Q Consensus 20 gW~~V~iI~~--dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~~-~~~~~i~~ 96 (829)
.=.++++|.. +++|.......+.+++++.|+++.+. .+...+...-...+..+.+.+.+.|++.... +.....++
T Consensus 22 ~~~~i~~v~k~~~~pf~~~~~~Gi~~aa~~~G~~v~~~--~~~~~d~~~q~~~i~~li~~~vdgIiv~~~d~~al~~~l~ 99 (336)
T PRK15408 22 AAERIAFIPKLVGVGFFTSGGNGAKEAGKELGVDVTYD--GPTEPSVSGQVQLINNFVNQGYNAIIVSAVSPDGLCPALK 99 (336)
T ss_pred CCcEEEEEECCCCCHHHHHHHHHHHHHHHHhCCEEEEE--CCCCCCHHHHHHHHHHHHHcCCCEEEEecCCHHHHHHHHH
Confidence 3447777774 57888888889999999999888653 2322222223356677777889988886543 34467888
Q ss_pred HHHHcCc
Q 043276 97 KANEIGL 103 (829)
Q Consensus 97 ~a~~~gm 103 (829)
+|.+.|+
T Consensus 100 ~a~~~gI 106 (336)
T PRK15408 100 RAMQRGV 106 (336)
T ss_pred HHHHCCC
Confidence 8998874
No 434
>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=32.23 E-value=1.6e+02 Score=30.17 Aligned_cols=79 Identities=9% Similarity=0.064 Sum_probs=50.4
Q ss_pred EEEEEEEe--CccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcChhH-HHHHHHHHH
Q 043276 23 EAVPIYVD--NQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSL-GSRIFEKAN 99 (829)
Q Consensus 23 ~V~iI~~d--d~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~~~~-~~~i~~~a~ 99 (829)
+|++|..+ +.|.......+.+++++.|..+.....-. ..+.....+.+.++...+.+.+|+...... ....+..+.
T Consensus 1 ~Igvi~~~~~~~~~~~~~~g~~~~~~~~g~~~~~~~~~~-~~~~~~~~~~i~~l~~~~vdgvii~~~~~~~~~~~l~~~~ 79 (273)
T cd06310 1 KIALVPKGTTSDFWQAVKAGAEAAAKELGVKVTFQGPAS-ETDVAGQVNLLENAIARGPDAILLAPTDAKALVPPLKEAK 79 (273)
T ss_pred CeEEEecCCCcHHHHHHHHHHHHHHHHcCCEEEEecCcc-CCCHHHHHHHHHHHHHhCCCEEEEcCCChhhhHHHHHHHH
Confidence 46777644 67778888999999999998875442110 112334455666777778888888654333 244666666
Q ss_pred HcC
Q 043276 100 EIG 102 (829)
Q Consensus 100 ~~g 102 (829)
+.|
T Consensus 80 ~~~ 82 (273)
T cd06310 80 DAG 82 (273)
T ss_pred HCC
Confidence 655
No 435
>cd00757 ThiF_MoeB_HesA_family ThiF_MoeB_HesA. Family of E1-like enzymes involved in molybdopterin and thiamine biosynthesis family. The common reaction mechanism catalyzed by MoeB and ThiF, like other E1 enzymes, begins with a nucleophilic attack of the C-terminal carboxylate of MoaD and ThiS, respectively, 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 MoaD and ThiS. MoeB, as the MPT synthase (MoaE/MoaD complex) sulfurase, is involved in the biosynthesis of the molybdenum cofactor, a derivative of the tricyclic pterin, molybdopterin (MPT). ThiF catalyzes the adenylation of ThiS, as part of the biosynthesis pathway of thiamin pyrophosphate (vitamin B1).
Probab=32.00 E-value=4.8e+02 Score=26.36 Aligned_cols=88 Identities=10% Similarity=0.086 Sum_probs=55.1
Q ss_pred HHHHHHHHHHcCCcEEEEEE---------------EeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHH
Q 043276 9 VGAITAIIKAFGWREAVPIY---------------VDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYK 73 (829)
Q Consensus 9 ~~ai~~ll~~fgW~~V~iI~---------------~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~ 73 (829)
+..+++.|...|-.++.++- ..++-|..-.+.+.+.+++.+-.+... .++...+.+++.+.+
T Consensus 33 Gs~va~~La~~Gvg~i~lvD~D~ve~sNL~Rq~l~~~~diG~~Ka~~~~~~l~~~np~~~i~-~~~~~i~~~~~~~~~-- 109 (228)
T cd00757 33 GSPAAEYLAAAGVGKLGLVDDDVVELSNLQRQILHTEADVGQPKAEAAAERLRAINPDVEIE-AYNERLDAENAEELI-- 109 (228)
T ss_pred HHHHHHHHHHcCCCEEEEEcCCEEcCcccccccccChhhCCChHHHHHHHHHHHhCCCCEEE-EecceeCHHHHHHHH--
Confidence 45677778888999999883 234678888889999998876433222 222222233333333
Q ss_pred hhcCCCeEEEEEcChhHHHHHHH-HHHHcC
Q 043276 74 LFTMQTRVFILHMLPSLGSRIFE-KANEIG 102 (829)
Q Consensus 74 lk~~~arViIv~~~~~~~~~i~~-~a~~~g 102 (829)
.+.++||.+.+...+...+. .+++.+
T Consensus 110 ---~~~DvVi~~~d~~~~r~~l~~~~~~~~ 136 (228)
T cd00757 110 ---AGYDLVLDCTDNFATRYLINDACVKLG 136 (228)
T ss_pred ---hCCCEEEEcCCCHHHHHHHHHHHHHcC
Confidence 24789988887766665554 455555
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=32.00 E-value=1.7e+02 Score=29.21 Aligned_cols=77 Identities=14% Similarity=0.099 Sum_probs=51.6
Q ss_pred EEEEEEe---CccccchHHHHHHHHHh--CCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcChhHHHHHHHHH
Q 043276 24 AVPIYVD---NQYGEELIPSLTDALQA--IDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKA 98 (829)
Q Consensus 24 V~iI~~d---d~yG~~~~~~l~~~l~~--~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~~~~~~~i~~~a 98 (829)
|++|..+ +.|+......+.+++++ .++++.+.. ...+..+....+.++...+...+|..........+...+
T Consensus 2 Ig~i~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~d~ii~~~~~~~~~~~~~~~ 78 (269)
T cd01391 2 IGVLLPLSGSAPFGAQLLAGIELAAEEIGRGLEVILAD---SQSDPERALEALRDLIQQGVDGIIGPPSSSSALAVVELA 78 (269)
T ss_pred ceEEeecCCCcHHHHHHHHHHHHHHHHhCCceEEEEec---CCCCHHHHHHHHHHHHHcCCCEEEecCCCHHHHHHHHHH
Confidence 6777653 57778888889999999 777665432 222233555666777777888888877665555466777
Q ss_pred HHcCc
Q 043276 99 NEIGL 103 (829)
Q Consensus 99 ~~~gm 103 (829)
.+.+.
T Consensus 79 ~~~~i 83 (269)
T cd01391 79 AAAGI 83 (269)
T ss_pred HHcCC
Confidence 77663
No 437
>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=31.67 E-value=1.8e+02 Score=31.51 Aligned_cols=95 Identities=12% Similarity=-0.006 Sum_probs=60.0
Q ss_pred HHHHHH-HcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcCh--
Q 043276 12 ITAIIK-AFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLP-- 88 (829)
Q Consensus 12 i~~ll~-~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~~-- 88 (829)
+.++++ ..+.+++.+|+...- .....+.+.+.|++.| .+... +....+.+.+.+.+..+++.+.++||..+..
T Consensus 15 l~~~l~~~~~~~~~liv~d~~~-~~~~~~~v~~~l~~~~-~~~~~--~~~~~~~~~v~~~~~~~~~~~~d~iIaiGGGs~ 90 (339)
T cd08173 15 IPNVLRDLLLGGRVLVVTGPTT-KSIAGKKVEALLEDEG-EVDVV--IVEDATYEEVEKVESSARDIGADFVIGVGGGRV 90 (339)
T ss_pred HHHHHHHhCCCCeEEEEECCch-HHHHHHHHHHHHHhcC-CeEEE--EeCCCCHHHHHHHHHHhhhcCCCEEEEeCCchH
Confidence 456676 467899988884433 3466778888888888 44322 2334456678888888888889999988764
Q ss_pred hHHHHHHHHHHHcCccccCeEEEEcCc
Q 043276 89 SLGSRIFEKANEIGLMNKGCVWIMTDG 115 (829)
Q Consensus 89 ~~~~~i~~~a~~~gm~~~~~vwI~t~~ 115 (829)
-++..++. ...|+ .++-|-|..
T Consensus 91 ~D~aK~~a--~~~~~---p~i~iPTT~ 112 (339)
T cd08173 91 IDVAKVAA--YKLGI---PFISVPTAA 112 (339)
T ss_pred HHHHHHHH--HhcCC---CEEEecCcc
Confidence 34444443 33342 455555543
No 438
>PF10566 Glyco_hydro_97: Glycoside hydrolase 97 ; InterPro: IPR019563 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. This is the 97th family of glycosidases, in this case bacterial. The central part of the GH97 family protein sequences represents a typical and complete (beta/alpha)8-barrel or catalytic TIM-barrel type domain. The N- and C-terminal parts of the sequences, mainly consisting of beta-strands, most probably form two additional non-catalytic domains with as yet unknown functions. The non-catalytic domains of glycosidases from the alpha-galactosidase and alpha-glucosidase superfamilies are also predominantly composed of beta-strands, and at least some of these domains are involved in oligomerisation and carbohydrate binding. In all known glycosidases with the (beta-alpha)8-barrel fold, the amino acid residues at the active site are located on the C-termini of the beta-strands []. ; PDB: 2JKP_A 2JKE_A 2D73_B 2ZQ0_B 2JKA_A 3A24_A.
Probab=31.64 E-value=3.9e+02 Score=28.04 Aligned_cols=99 Identities=13% Similarity=0.079 Sum_probs=62.5
Q ss_pred ChHHHHHHHHHHHHHcCCcEEEEEEEeCcc---------------ccchHHHHHHHHHhCCceeeeEEecCCCC----Ch
Q 043276 4 NDSSQVGAITAIIKAFGWREAVPIYVDNQY---------------GEELIPSLTDALQAIDTRVPYRSVISPLA----TD 64 (829)
Q Consensus 4 sD~~q~~ai~~ll~~fgW~~V~iI~~dd~y---------------G~~~~~~l~~~l~~~gi~I~~~~~i~~~~----~~ 64 (829)
.+..-.+..+++...+||..|-| |..+ ...-++.|.+..++.|+.|-.-..-.... -+
T Consensus 29 ~~t~~~k~yIDfAa~~G~eYvlv---D~GW~~~~~~~~~d~~~~~~~~dl~elv~Ya~~KgVgi~lw~~~~~~~~~~~~~ 105 (273)
T PF10566_consen 29 ATTETQKRYIDFAAEMGIEYVLV---DAGWYGWEKDDDFDFTKPIPDFDLPELVDYAKEKGVGIWLWYHSETGGNVANLE 105 (273)
T ss_dssp SSHHHHHHHHHHHHHTT-SEEEE---BTTCCGS--TTT--TT-B-TT--HHHHHHHHHHTT-EEEEEEECCHTTBHHHHH
T ss_pred CCHHHHHHHHHHHHHcCCCEEEe---ccccccccccccccccccCCccCHHHHHHHHHHcCCCEEEEEeCCcchhhHhHH
Confidence 35566788999999999999988 6555 35668999999999997775433322110 12
Q ss_pred hHHHHHHHHhhcCCCeEEEE-EcCh--h----HHHHHHHHHHHcCccc
Q 043276 65 DQIEKELYKLFTMQTRVFIL-HMLP--S----LGSRIFEKANEIGLMN 105 (829)
Q Consensus 65 ~~~~~~l~~lk~~~arViIv-~~~~--~----~~~~i~~~a~~~gm~~ 105 (829)
.+..+.+..+++.+.+-|=+ ++.. + .-..+++.|.+.+||.
T Consensus 106 ~~~~~~f~~~~~~Gv~GvKidF~~~d~Q~~v~~y~~i~~~AA~~~Lmv 153 (273)
T PF10566_consen 106 KQLDEAFKLYAKWGVKGVKIDFMDRDDQEMVNWYEDILEDAAEYKLMV 153 (273)
T ss_dssp CCHHHHHHHHHHCTEEEEEEE--SSTSHHHHHHHHHHHHHHHHTT-EE
T ss_pred HHHHHHHHHHHHcCCCEEeeCcCCCCCHHHHHHHHHHHHHHHHcCcEE
Confidence 23567788888888877744 3333 2 3345777787777643
No 439
>PRK00072 hemC porphobilinogen deaminase; Reviewed
Probab=31.53 E-value=6.5e+02 Score=26.68 Aligned_cols=60 Identities=15% Similarity=0.038 Sum_probs=38.2
Q ss_pred CCHHHHHhCCCcEEEEeCchHHH-HHHhcCCCccceeecC-ChHHHHHHHhcCCcCCceeEEEcchhHHH
Q 043276 533 TDVNLLIKRGDNVGYQKGSFVLG-ILKQLGFDERKLVVYN-SHEECDELFQKGSANGGIAAAFDEIPYAK 600 (829)
Q Consensus 533 ~s~~dL~~~~~~vg~~~~s~~~~-~l~~~~~~~~~~~~~~-~~~~~~~~l~~g~~~~g~~a~~~~~~~~~ 600 (829)
.+++||- .|.+||+ +|.=+. .+++ .+|..+++... +.+..+..|..|. .||++.-..-+.
T Consensus 113 ~~l~~Lp-~ga~IGT--sS~RR~aql~~-~~Pdl~~~~iRGNV~TRL~KL~~g~----~DaivLA~AGL~ 174 (295)
T PRK00072 113 KSLDDLP-EGAVVGT--SSLRRQAQLLA-LRPDLEIKPLRGNVDTRLRKLDEGE----YDAIILAAAGLK 174 (295)
T ss_pred CChhHCC-CCCEEec--CcHHHHHHHHH-HCcCCEEEECccCHHHHHHHhhCCC----CCEeehHhhHHH
Confidence 5688885 4556665 232222 2333 35666666554 7888999999998 888887654443
No 440
>cd08484 PBP2_LTTR_beta_lactamase The C-terminal substrate-domain of LysR-type transcriptional regulators for beta-lactamase genes, contains the type 2 periplasmic binding fold. This CD includes the C-terminal substrate binding domain of LysR-type transcriptional regulators, BlaA and AmpR, that are involved in control of the expression of beta-lactamase genes. Beta-lactamases are responsible for bacterial resistance to beta-lactam antibiotics such as penicillins. BlaA (a constitutive class A penicillinase) belongs to the LysR family of transcriptional regulators, while BlaB (an inducible class C cephalosporinase or AmpC) can be referred to as a penicillin-binding protein, but it does not act as a beta-lactamase. AmpR regulates the expression of beta-lactamases in many enterobacterial strains and many other gram-negative bacilli. In contrast to BlaA, AmpR acts an activator only in the presence of the beta-lactam inducer. In the absence of the inducer, AmpR acts as a repressor. The topol
Probab=31.46 E-value=4.4e+02 Score=24.62 Aligned_cols=99 Identities=11% Similarity=-0.064 Sum_probs=48.6
Q ss_pred CHHHHHhCCCcEEEEeC-chHHHHHHhcCCCccc--eeecCChHHHHHHHhcCCcCCceeEEEcchhHHHHHHhcCCCce
Q 043276 534 DVNLLIKRGDNVGYQKG-SFVLGILKQLGFDERK--LVVYNSHEECDELFQKGSANGGIAAAFDEIPYAKLLIGQHCSKY 610 (829)
Q Consensus 534 s~~dL~~~~~~vg~~~~-s~~~~~l~~~~~~~~~--~~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~~c~~l 610 (829)
+++||. +.++..... .....++++.+..... ...+++.+...+.+..|. .-+++.+. .......+.. ..
T Consensus 85 ~~~~L~--~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~----Gi~~lp~~-~~~~~~~~~~-l~ 156 (189)
T cd08484 85 EPADLA--NETLLRSYRADEWPQWFEAAGVPPPPINGPVFDSSLLMVEAALQGA----GVALAPPS-MFSRELASGA-LV 156 (189)
T ss_pred ChhHhh--cCceEecCCCchHHHHHHHcCCCCCcccCcccccHHHHHHHHHhCC----CeEEecHH-hHHHHHHCCC-EE
Confidence 577885 333332222 2234556554443211 234567778888898887 45555443 2222222221 11
Q ss_pred EEeCcccccCCceeeecCCCCchhhHHHHH
Q 043276 611 TMVEPTFKTAGFGFAFPLHSPLVHDVSKAI 640 (829)
Q Consensus 611 ~~v~~~~~~~~~~~~~~k~spl~~~in~~i 640 (829)
..+........++++.+|+.+....+...+
T Consensus 157 ~~~~~~~~~~~~~l~~~~~~~~~~~~~~f~ 186 (189)
T cd08484 157 QPFKITVSTGSYWLTRLKSKPETPAMSAFS 186 (189)
T ss_pred eecccccCCCCEEEEeccccccchhhHHHH
Confidence 122222233467778888766544444433
No 441
>PRK11425 PTS system N-acetylgalactosamine-specific transporter subunit IIB; Provisional
Probab=31.42 E-value=3.2e+02 Score=25.93 Aligned_cols=80 Identities=8% Similarity=0.052 Sum_probs=52.7
Q ss_pred HHHHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcC
Q 043276 8 QVGAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHML 87 (829)
Q Consensus 8 q~~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~ 87 (829)
.++++....++++-+.+.++- |..-.....+.+.+.+.-.|+.+.... .++..+.+.+ +..+.|++|++-+
T Consensus 15 HGQV~~~W~~~~~~~~IvVvd-D~~A~D~~~k~~l~ma~P~gvk~~i~s-------v~~a~~~l~~-~~~~~~v~il~k~ 85 (157)
T PRK11425 15 HGQVGVQWVGFAGANLVLVAN-DEVAEDPVQQNLMEMVLAEGIAVRFWT-------LQKVIDNIHR-AADRQKILLVCKT 85 (157)
T ss_pred hHHhhhhhhcccCCCEEEEEc-chhcCCHHHHHHHHhhCCCCCeEEEEE-------HHHHHHHHhc-cCCCceEEEEECC
Confidence 567777888899998877763 322233445555555555787765432 2344455555 5566799999999
Q ss_pred hhHHHHHHH
Q 043276 88 PSLGSRIFE 96 (829)
Q Consensus 88 ~~~~~~i~~ 96 (829)
++.+..+..
T Consensus 86 ~~d~~~l~~ 94 (157)
T PRK11425 86 PADFLTLVK 94 (157)
T ss_pred HHHHHHHHH
Confidence 999988764
No 442
>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=31.16 E-value=5e+02 Score=25.20 Aligned_cols=80 Identities=5% Similarity=-0.099 Sum_probs=44.6
Q ss_pred HHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhC--CceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcCh
Q 043276 11 AITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAI--DTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLP 88 (829)
Q Consensus 11 ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~--gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~~ 88 (829)
.+.+....-+| .|.++....+ .++.+.+.+++. |+.|+.. ....++++-...+..|.++++++++|.+..
T Consensus 39 ~l~~~~~~~~~-~vfllG~~~~----v~~~~~~~l~~~yP~l~i~g~---~g~f~~~~~~~i~~~I~~s~~dil~VglG~ 110 (177)
T TIGR00696 39 ELCQRAGKEKL-PIFLYGGKPD----VLQQLKVKLIKEYPKLKIVGA---FGPLEPEERKAALAKIARSGAGIVFVGLGC 110 (177)
T ss_pred HHHHHHHHcCC-eEEEECCCHH----HHHHHHHHHHHHCCCCEEEEE---CCCCChHHHHHHHHHHHHcCCCEEEEEcCC
Confidence 33343444554 5556554433 344445555443 6666654 122223344556778888888888888776
Q ss_pred hHHHHHHHHH
Q 043276 89 SLGSRIFEKA 98 (829)
Q Consensus 89 ~~~~~i~~~a 98 (829)
+.-..++.+.
T Consensus 111 PkQE~~~~~~ 120 (177)
T TIGR00696 111 PKQEIWMRNH 120 (177)
T ss_pred cHhHHHHHHh
Confidence 6555555544
No 443
>cd01545 PBP1_SalR Ligand-binding domain of DNA transcription repressor SalR, a member of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressor SalR, a member of the LacI-GalR family of bacterial transcription regulators. The SalR binds to glucose based compound Salicin which is chemically related to aspirin. The ligand-binding of SalR is structurally homologous to the periplasmic sugar-binding domain of ABC-transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand bind
Probab=30.63 E-value=1.8e+02 Score=29.70 Aligned_cols=77 Identities=17% Similarity=0.107 Sum_probs=48.1
Q ss_pred EEEEEE--eCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcChhHHHHHHHHHHHc
Q 043276 24 AVPIYV--DNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEI 101 (829)
Q Consensus 24 V~iI~~--dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~~~~~~~i~~~a~~~ 101 (829)
|++|.. ++.|.....+.+.+++++.|..+..... . ...+......+..+...+.+.+|+..........+..+.+.
T Consensus 2 I~vi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~-~-~~~~~~~~~~~~~l~~~~vdgiii~~~~~~~~~~~~~~~~~ 79 (270)
T cd01545 2 IGLLYDNPSPGYVSEIQLGALDACRDTGYQLVIEPC-D-SGSPDLAERVRALLQRSRVDGVILTPPLSDNPELLDLLDEA 79 (270)
T ss_pred EEEEEcCCCcccHHHHHHHHHHHHHhCCCeEEEEeC-C-CCchHHHHHHHHHHHHCCCCEEEEeCCCCCccHHHHHHHhc
Confidence 466663 4678888899999999999988765422 1 11122344555566667888887764332234556666666
Q ss_pred C
Q 043276 102 G 102 (829)
Q Consensus 102 g 102 (829)
|
T Consensus 80 ~ 80 (270)
T cd01545 80 G 80 (270)
T ss_pred C
Confidence 5
No 444
>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=30.63 E-value=1.7e+02 Score=30.21 Aligned_cols=77 Identities=10% Similarity=0.025 Sum_probs=51.0
Q ss_pred EEEEEE--eCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcCh-hHHHHHHHHHHH
Q 043276 24 AVPIYV--DNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLP-SLGSRIFEKANE 100 (829)
Q Consensus 24 V~iI~~--dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~~-~~~~~i~~~a~~ 100 (829)
|+++.. .+.|.......+.+++++.|..+.... ...+.+...+.+..+.+.+++.||+.... +.....+..+.+
T Consensus 2 igv~~~~~~~~~~~~~~~~i~~~~~~~g~~v~~~~---~~~~~~~~~~~i~~~~~~~~Dgiii~~~~~~~~~~~i~~~~~ 78 (282)
T cd06318 2 IGFSQYTLNSPFFAALTEAAKAHAKALGYELISTD---AQGDLTKQIADVEDLLTRGVNVLIINPVDPEGLVPAVAAAKA 78 (282)
T ss_pred eeEEeccccCHHHHHHHHHHHHHHHHcCCEEEEEc---CCCCHHHHHHHHHHHHHcCCCEEEEecCCccchHHHHHHHHH
Confidence 555553 477788889999999999998875432 22223334456777778889998887543 333456677777
Q ss_pred cCc
Q 043276 101 IGL 103 (829)
Q Consensus 101 ~gm 103 (829)
.|.
T Consensus 79 ~~i 81 (282)
T cd06318 79 AGV 81 (282)
T ss_pred CCC
Confidence 663
No 445
>PRK01215 competence damage-inducible protein A; Provisional
Probab=30.42 E-value=2.4e+02 Score=29.45 Aligned_cols=62 Identities=15% Similarity=0.061 Sum_probs=42.6
Q ss_pred EEEEEEEeCc--ccc---chHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcC
Q 043276 23 EAVPIYVDNQ--YGE---ELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHML 87 (829)
Q Consensus 23 ~V~iI~~dd~--yG~---~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~ 87 (829)
+++||...|+ .|. .....|.+.|++.|+.+.....++++ .+++.+.+....+ .+++||+.+.
T Consensus 5 ~v~Ii~~GdEll~G~i~dtn~~~l~~~L~~~G~~v~~~~~v~Dd--~~~I~~~l~~a~~-~~DlVIttGG 71 (264)
T PRK01215 5 FAWIITIGNELLIGRTVNTNASWIARRLTYLGYTVRRITVVMDD--IEEIVSAFREAID-RADVVVSTGG 71 (264)
T ss_pred EEEEEEEChhccCCeEEEhhHHHHHHHHHHCCCeEEEEEEeCCC--HHHHHHHHHHHhc-CCCEEEEeCC
Confidence 5777776665 332 33667888899999998877776654 5567777776654 4577777654
No 446
>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=29.98 E-value=4.7e+02 Score=24.49 Aligned_cols=67 Identities=12% Similarity=0.033 Sum_probs=37.6
Q ss_pred eeecCChHHHHHHHhcCCcCCceeEEEcchhHHHHHHhcCCCceEEeC--cccccCCceeeecCCCCchhhHHHHH
Q 043276 567 LVVYNSHEECDELFQKGSANGGIAAAFDEIPYAKLLIGQHCSKYTMVE--PTFKTAGFGFAFPLHSPLVHDVSKAI 640 (829)
Q Consensus 567 ~~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~~c~~l~~v~--~~~~~~~~~~~~~k~spl~~~in~~i 640 (829)
....++.....+++..|. .-+++.+. .+...... . .+..+. .......+.++.+|+......+...+
T Consensus 128 ~~~~~~~~~~~~~v~~g~----gi~~~p~~-~~~~~~~~-~-~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 196 (199)
T cd08475 128 RLQFDDGEAIADAALAGL----GIAQLPTW-LVADHLQR-G-ELVEVLPELAPEGLPIHAVWPRTRHLPPKVRAAV 196 (199)
T ss_pred cEEECCHHHHHHHHHhCC----CEEeeeHH-HHHhHhhc-C-cEEEecCCCcCCCccEEEEeCCcccCCHHHHHHH
Confidence 455678888899999987 44454443 33332222 1 233322 22334567888888766555544443
No 447
>PRK03692 putative UDP-N-acetyl-D-mannosaminuronic acid transferase; Provisional
Probab=29.91 E-value=5.3e+02 Score=26.49 Aligned_cols=82 Identities=7% Similarity=0.020 Sum_probs=40.3
Q ss_pred HHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHh-CCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcChhH
Q 043276 12 ITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQA-IDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSL 90 (829)
Q Consensus 12 i~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~-~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~~~~ 90 (829)
+.+.....| .+|.++..+.+. ++.+.+.+++ .|+.|+.... ...+.++....+..|.++++++++|.+..+.
T Consensus 97 ll~~~~~~~-~~v~llG~~~~v----~~~a~~~l~~~y~l~i~g~~~--Gyf~~~e~~~i~~~I~~s~~dil~VglG~Pk 169 (243)
T PRK03692 97 LMARAGKEG-TPVFLVGGKPEV----LAQTEAKLRTQWNVNIVGSQD--GYFTPEQRQALFERIHASGAKIVTVAMGSPK 169 (243)
T ss_pred HHHHHHhcC-CeEEEECCCHHH----HHHHHHHHHHHhCCEEEEEeC--CCCCHHHHHHHHHHHHhcCCCEEEEECCCcH
Confidence 344444455 455555544433 3333333322 3566543321 1112334445677777778888777776655
Q ss_pred HHHHHHHHHH
Q 043276 91 GSRIFEKANE 100 (829)
Q Consensus 91 ~~~i~~~a~~ 100 (829)
-..++.+..+
T Consensus 170 QE~~~~~~~~ 179 (243)
T PRK03692 170 QEIFMRDCRL 179 (243)
T ss_pred HHHHHHHHHH
Confidence 4445444333
No 448
>PF03830 PTSIIB_sorb: PTS system sorbose subfamily IIB component; InterPro: IPR004720 Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains.The Man family is unique in several respects among PTS permease families: It is the only PTS family in which members possess a IID protein. It is the only PTS family in which the IIB constituent is phosphorylated on a histidyl rather than a cysteyl residue. Its permease members exhibit broad specificity for a range of sugars, rather than being specific for just one or a few sugars. The mannose permease of Escherichia coli, for example, can transport and phosphorylate glucose, mannose, fructose, glucosamine, N-acetylglucosamine, and other sugars. Other members of this can transport sorbose, fructose and N-acetylglucosamine. This entry is specific for the IIB components of this family of PTS transporters [].; GO: 0008982 protein-N(PI)-phosphohistidine-sugar phosphotransferase activity, 0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system, 0005737 cytoplasm; PDB: 3LFJ_B 1BLE_A 3P3V_B 1NRZ_C 3EYE_A 1VSQ_C 2JZH_A 2JZN_C 2JZO_D.
Probab=29.62 E-value=1.7e+02 Score=27.66 Aligned_cols=83 Identities=16% Similarity=0.122 Sum_probs=57.4
Q ss_pred HHHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcCh
Q 043276 9 VGAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLP 88 (829)
Q Consensus 9 ~~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~~ 88 (829)
++.+...+++++-+.+.++- |..-.....+.+.+.+.-.|+.+.+.. .++..+.+.+-...+.|++|++-++
T Consensus 14 GQV~~~W~~~~~~~~IiVvd-D~~A~D~~~k~~l~ma~P~gvk~~i~s-------v~~a~~~l~~~~~~~~~v~ii~k~~ 85 (151)
T PF03830_consen 14 GQVATAWVKKLNANRIIVVD-DEVANDPFQKMILKMAAPAGVKLSIFS-------VEEAIEKLKKPEYSKKRVLIIVKSP 85 (151)
T ss_dssp TTHHHHHHHHHTTSEEEEE--HHHHHSHHHHHHHHHTSHTTSEEEEE--------HHHHHHHHCGGGGTTEEEEEEESSH
T ss_pred eeeeEEEhhhcccCEEEEEC-HHHhcCHHHHHHHHHhhcCCCceEEEE-------HHHHHHHHHhcccCCceEEEEECCH
Confidence 45677888999999998874 444445566666666666788876542 2344455555555778999999999
Q ss_pred hHHHHHHHHHH
Q 043276 89 SLGSRIFEKAN 99 (829)
Q Consensus 89 ~~~~~i~~~a~ 99 (829)
..+..+...-.
T Consensus 86 ~d~~~l~~~g~ 96 (151)
T PF03830_consen 86 EDALRLVEAGV 96 (151)
T ss_dssp HHHHHHHHTT-
T ss_pred HHHHHHHhcCC
Confidence 99988876443
No 449
>PF13314 DUF4083: Domain of unknown function (DUF4083)
Probab=29.09 E-value=2.7e+02 Score=21.42 Aligned_cols=15 Identities=7% Similarity=0.277 Sum_probs=11.2
Q ss_pred hhHHHHHHHHHhhhc
Q 043276 716 SLLSRIRIFLRIFVS 730 (829)
Q Consensus 716 ~~~~~~~~~~~~~~~ 730 (829)
...++|.+..+..++
T Consensus 43 ~~eqKLDrIIeLLEK 57 (58)
T PF13314_consen 43 SMEQKLDRIIELLEK 57 (58)
T ss_pred HHHHHHHHHHHHHcc
Confidence 678888888877543
No 450
>COG3473 Maleate cis-trans isomerase [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=28.91 E-value=6e+02 Score=25.40 Aligned_cols=76 Identities=12% Similarity=0.075 Sum_probs=51.2
Q ss_pred HHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecC--CCC-----ChhHHHHHHHHhhcCCCeEE
Q 043276 10 GAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVIS--PLA-----TDDQIEKELYKLFTMQTRVF 82 (829)
Q Consensus 10 ~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~--~~~-----~~~~~~~~l~~lk~~~arVi 82 (829)
-|.++=++.+|-++++++. .|-....+...+.++++|..|+....+- .+. +....-+.-+.+...+++.+
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 4666778999999999997 6777788888899999999988665432 111 11123334445556677776
Q ss_pred EEEcCh
Q 043276 83 ILHMLP 88 (829)
Q Consensus 83 Iv~~~~ 88 (829)
++-|..
T Consensus 184 FiSCTn 189 (238)
T COG3473 184 FISCTN 189 (238)
T ss_pred EEEeec
Confidence 665543
No 451
>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=28.88 E-value=3.7e+02 Score=27.87 Aligned_cols=89 Identities=15% Similarity=0.161 Sum_probs=59.7
Q ss_pred HHHHHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEc
Q 043276 7 SQVGAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHM 86 (829)
Q Consensus 7 ~q~~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~ 86 (829)
.....++.-....|-.-++|++ |..|..+..+.|...-+..++.|-....|- +. .++..-+..+++.|++..
T Consensus 68 ~d~~~~a~~y~~~GA~aiSVlT-e~~~F~Gs~~dL~~v~~~~~~PvL~KDFIi---d~----~QI~eA~~~GADaVLLI~ 139 (254)
T PF00218_consen 68 FDPAEIAKAYEEAGAAAISVLT-EPKFFGGSLEDLRAVRKAVDLPVLRKDFII---DP----YQIYEARAAGADAVLLIA 139 (254)
T ss_dssp -SHHHHHHHHHHTT-SEEEEE---SCCCHHHHHHHHHHHHHSSS-EEEES------SH----HHHHHHHHTT-SEEEEEG
T ss_pred CCHHHHHHHHHhcCCCEEEEEC-CCCCCCCCHHHHHHHHHHhCCCcccccCCC---CH----HHHHHHHHcCCCEeehhH
Confidence 3456677777888999999997 777777889999888777787765433221 11 256666678999998876
Q ss_pred C---hhHHHHHHHHHHHcCc
Q 043276 87 L---PSLGSRIFEKANEIGL 103 (829)
Q Consensus 87 ~---~~~~~~i~~~a~~~gm 103 (829)
. .+....++..|.++||
T Consensus 140 ~~L~~~~l~~l~~~a~~lGl 159 (254)
T PF00218_consen 140 AILSDDQLEELLELAHSLGL 159 (254)
T ss_dssp GGSGHHHHHHHHHHHHHTT-
T ss_pred HhCCHHHHHHHHHHHHHcCC
Confidence 4 3556789999999998
No 452
>cd08439 PBP2_LrhA_like The C-terminal substrate domain of LysR-like regulator LrhA (LysR homologue A) and that of closely related homologs, contains the type 2 periplasmic binding fold. This CD represents the LrhA subfamily of LysR-like bacterial transcriptional regulators, including LrhA, HexA, PecT, and DgdR. LrhA is involved in control of the transcription of flagellar, motility, and chemotaxis genes by regulating the synthesis and concentration of FlhD(2)C(2), the master regulator for the expression of flagellar and chemotaxis genes. The LrhA protein has strong homology to HexA and PecT from plant pathogenic bacteria, in which HexA and PecT act as repressors of motility and of virulence factors, such as exoenzymes required for lytic reactions. DgdR also shares similar characteristics to those of LrhA, HexA and PecT. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a vari
Probab=28.40 E-value=1.7e+02 Score=27.55 Aligned_cols=66 Identities=12% Similarity=-0.022 Sum_probs=44.4
Q ss_pred eeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccEEEeccccccccceeccccccccccceEEEEE
Q 043276 340 YSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDAVVGDTTIVFNRSNYVDFTLPYTESGVSMIVP 419 (829)
Q Consensus 340 ~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di~~~~~~it~~R~~~vdft~p~~~~~~~~vv~ 419 (829)
+-.+++..+.++.+ ++++++.. +....+..+|.+|++|+++.... . ..+ .+.++....++++++
T Consensus 14 ~l~~~l~~~~~~~P-~v~i~~~~---------~~~~~~~~~l~~~~~Dl~i~~~~----~-~~~-~~~~l~~~~~~~v~~ 77 (185)
T cd08439 14 ILPFLLNRFASVYP-RLAIEVVC---------KRTPRLMEMLERGEVDLALITHP----P-PGA-SATILRRSPTVWYCA 77 (185)
T ss_pred HHHHHHHHHHHHCC-CeEEEEEE---------CChHHHHHHHHCCCCcEEEEecc----C-CCC-CceEEEEecCEEEEC
Confidence 44577788888776 35666654 24578999999999999985321 1 112 246777788888877
Q ss_pred cc
Q 043276 420 IK 421 (829)
Q Consensus 420 ~~ 421 (829)
..
T Consensus 78 ~~ 79 (185)
T cd08439 78 AG 79 (185)
T ss_pred CC
Confidence 44
No 453
>COG1058 CinA Predicted nucleotide-utilizing enzyme related to molybdopterin-biosynthesis enzyme MoeA [General function prediction only]
Probab=28.23 E-value=1.4e+02 Score=30.78 Aligned_cols=62 Identities=19% Similarity=0.169 Sum_probs=44.8
Q ss_pred EEEEEEEeCcc--c---cchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcC
Q 043276 23 EAVPIYVDNQY--G---EELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHML 87 (829)
Q Consensus 23 ~V~iI~~dd~y--G---~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~ 87 (829)
++++|...|+- | ..-++.|.+.|.+.|+.+.....+++. .+++.+.+..+.+. +++||+.+.
T Consensus 3 ~a~iI~vG~ElL~G~ivdtNa~~la~~L~~~G~~v~~~~~VgD~--~~~I~~~l~~a~~r-~D~vI~tGG 69 (255)
T COG1058 3 KAEIIAVGDELLSGRIVDTNAAFLADELTELGVDLARITTVGDN--PDRIVEALREASER-ADVVITTGG 69 (255)
T ss_pred eEEEEEEccceecCceecchHHHHHHHHHhcCceEEEEEecCCC--HHHHHHHHHHHHhC-CCEEEECCC
Confidence 34555544432 2 345789999999999999988887765 56788888877655 888888653
No 454
>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=28.01 E-value=2.6e+02 Score=24.65 Aligned_cols=70 Identities=17% Similarity=0.093 Sum_probs=0.0
Q ss_pred HHHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEe-cCCCCChhHHHHHHHHhhcCCCeEEEEEc
Q 043276 9 VGAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSV-ISPLATDDQIEKELYKLFTMQTRVFILHM 86 (829)
Q Consensus 9 ~~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~-i~~~~~~~~~~~~l~~lk~~~arViIv~~ 86 (829)
...++.+++..|| .|.++-.+... +.+.+.+.+.+..+..... .... .....+.++.+|+...++.|+.+
T Consensus 17 l~~la~~l~~~G~-~v~~~d~~~~~-----~~l~~~~~~~~pd~V~iS~~~~~~--~~~~~~l~~~~k~~~p~~~iv~G 87 (121)
T PF02310_consen 17 LLYLAAYLRKAGH-EVDILDANVPP-----EELVEALRAERPDVVGISVSMTPN--LPEAKRLARAIKERNPNIPIVVG 87 (121)
T ss_dssp HHHHHHHHHHTTB-EEEEEESSB-H-----HHHHHHHHHTTCSEEEEEESSSTH--HHHHHHHHHHHHTTCTTSEEEEE
T ss_pred HHHHHHHHHHCCC-eEEEECCCCCH-----HHHHHHHhcCCCcEEEEEccCcCc--HHHHHHHHHHHHhcCCCCEEEEE
No 455
>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=28.00 E-value=1.9e+02 Score=30.78 Aligned_cols=88 Identities=18% Similarity=0.251 Sum_probs=55.8
Q ss_pred EEEEEE----EeCccccchHHHHHHHHHhC-CceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcChhHHHHHHHH
Q 043276 23 EAVPIY----VDNQYGEELIPSLTDALQAI-DTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEK 97 (829)
Q Consensus 23 ~V~iI~----~dd~yG~~~~~~l~~~l~~~-gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~~~~~~~i~~~ 97 (829)
+++++. .|..|.....+.+.+..++. |+.+.+.+..+. +..++...+..+.+.+.++||+++.. ....+...
T Consensus 3 ~v~~~~~g~~~D~g~n~~~~~G~~~~~~~~~~i~~~~~e~~~~--~~~~~~~~~~~~~~~g~dlIi~~g~~-~~~~~~~v 79 (306)
T PF02608_consen 3 KVALLDPGGINDKGFNQSAYEGLKRAEKELDGIEIIYVENVPE--TDADYEEAIRQLADQGYDLIIGHGFE-YSDALQEV 79 (306)
T ss_dssp EEEEESSS-CCCSSHHHHHHHHHHHHHHHCTTEEEEEEES-S---TCHHHHHHHHHHHHTT-SEEEEESGG-GHHHHHHH
T ss_pred EEEEEECCCCCCccHHHHHHHHHHHHHHHcCCceEEEEecCCc--cHHHHHHHHHHHHHcCCCEEEEccHH-HHHHHHHH
Confidence 455554 34455566777777777788 999888776553 24578888888888999999997754 33344444
Q ss_pred HHHcCccccCeEEEEcCccc
Q 043276 98 ANEIGLMNKGCVWIMTDGMT 117 (829)
Q Consensus 98 a~~~gm~~~~~vwI~t~~~~ 117 (829)
|.+- ++..|+..++..
T Consensus 80 A~~y----Pd~~F~~~d~~~ 95 (306)
T PF02608_consen 80 AKEY----PDTKFIIIDGYI 95 (306)
T ss_dssp HTC-----TTSEEEEESS--
T ss_pred HHHC----CCCEEEEEecCc
Confidence 5442 566777776544
No 456
>PF00731 AIRC: AIR carboxylase; InterPro: IPR000031 Phosphoribosylaminoimidazole carboxylase is a fusion protein in plants and fungi, but consists of two non-interacting proteins in bacteria, PurK and PurE. PurK, N5-carboxyaminoimidazole ribonucleotide (N5_CAIR) synthetase, catalyzes the conversion of 5-aminoimidazole ribonucleotide (AIR), ATP, and bicarbonate to N5-CAIR, ADP, and Pi. PurE converts N5-CAIR to CAIR, the sixth step of de novo purine biosynthesis. In the presence of high concentrations of bicarbonate, PurE is reported able to convert AIR to CAIR directly and without ATP. Some members of this family contain two copies of this domain []. The crystal structure of PurE indicates a unique quaternary structure that confirms the octameric nature of the enzyme [].; GO: 0004638 phosphoribosylaminoimidazole carboxylase activity, 0006189 'de novo' IMP biosynthetic process; PDB: 3TRH_O 2YWX_A 2NSL_A 1D7A_A 2NSJ_A 1QCZ_A 2ATE_A 2NSH_A 3RG8_C 3RGG_D ....
Probab=27.87 E-value=3.8e+02 Score=25.26 Aligned_cols=65 Identities=14% Similarity=0.049 Sum_probs=39.8
Q ss_pred EEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcChh
Q 043276 23 EAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPS 89 (829)
Q Consensus 23 ~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~~~ 89 (829)
+|+||. .+......++...+.|++.|+....+ ..+..-+.+.+.+.++++.+.+.+|||.....+
T Consensus 2 ~V~Ii~-gs~SD~~~~~~a~~~L~~~gi~~~~~-V~saHR~p~~l~~~~~~~~~~~~~viIa~AG~~ 66 (150)
T PF00731_consen 2 KVAIIM-GSTSDLPIAEEAAKTLEEFGIPYEVR-VASAHRTPERLLEFVKEYEARGADVIIAVAGMS 66 (150)
T ss_dssp EEEEEE-SSGGGHHHHHHHHHHHHHTT-EEEEE-E--TTTSHHHHHHHHHHTTTTTESEEEEEEESS
T ss_pred eEEEEe-CCHHHHHHHHHHHHHHHHcCCCEEEE-EEeccCCHHHHHHHHHHhccCCCEEEEEECCCc
Confidence 466665 33333456777778888888665543 233333455677777777767778888875543
No 457
>PF09651 Cas_APE2256: CRISPR-associated protein (Cas_APE2256); InterPro: IPR013442 Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) are a family of DNA direct repeats separated by regularly sized non-repetitive spacer sequences that are found in most bacterial and archaeal genomes []. CRISPRs appear to provide acquired resistance against bacteriophages, possibly acting with an RNA interference-like mechanism to inhibit gene functions of invasive DNA elements [, ]. Differences in the number and type of spacers between CRISPR repeats correlate with phage sensitivity. It is thought that following phage infection, bacteria integrate new spacers derived from phage genomic sequences, and that the removal or addition of particular spacers modifies the phage-resistance phenotype of the cell. Therefore, the specificity of CRISPRs may be determined by spacer-phage sequence similarity. In addition, there are many protein families known as CRISPR-associated sequences (Cas), which are encoded in the vicinity of CRISPR loci []. CRISPR/cas gene regions can be quite large, with up to 20 different, tandem-arranged cas genes next to a CRISPR cluster or filling the region between two repeat clusters. Cas genes and CRISPRs are found on mobile genetic elements such as plasmids, and have undergone extensive horizontal transfer. Cas proteins are thought to be involved in the propagation and functioning of CRISPRs. Some Cas proteins show similarity to helicases and repair proteins, although the functions of most are unknown. Cas families can be divided into subtypes according to operon organisation and phylogeny. This entry represents a conserved region of about 150 amino acids found in a family of Cas proteins in at least five archaeal and three bacterial species. In six of eight species, the protein is encoded the vicinity of a CRISPR/Cas locus.; PDB: 3QYF_A.
Probab=27.57 E-value=2.1e+02 Score=26.41 Aligned_cols=50 Identities=16% Similarity=0.129 Sum_probs=37.9
Q ss_pred HHHHHHHHHHHHHcCCc---EEEEEEEeCccccchHHHHHHHHHhCCceeeeE
Q 043276 6 SSQVGAITAIIKAFGWR---EAVPIYVDNQYGEELIPSLTDALQAIDTRVPYR 55 (829)
Q Consensus 6 ~~q~~ai~~ll~~fgW~---~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~ 55 (829)
++...++..+++..... .+.++++|+.-|+-....+++.+.+.|+.+...
T Consensus 4 sAElnsl~~~~~~~~~~~~~~~~Ll~SDT~~G~~~a~il~~~l~~~g~~v~~~ 56 (136)
T PF09651_consen 4 SAELNSLVRLLEKGKDDDKDEVVLLHSDTPDGRLCAEILKEYLEEKGINVEVV 56 (136)
T ss_dssp -HHHHHHHHHHHHHT--GGGEEEEEEESSHHHHHHHHHHHHHHHHTT-EEEEE
T ss_pred cHhHHHHHHHHHhCccccCcEEEEEeCCCHHHHHHHHHHHHHHHHcCCeEEEE
Confidence 45566777777655443 899999999999999999999999998875543
No 458
>PRK09061 D-glutamate deacylase; Validated
Probab=27.56 E-value=4.2e+02 Score=30.68 Aligned_cols=97 Identities=13% Similarity=0.063 Sum_probs=64.0
Q ss_pred HHHHHHHHHHHH---HcCCcEEEEE--EEeCccccchHHHHHHHHHhCCceeeeEEecCCC--C--ChhHHHHHHHHhhc
Q 043276 6 SSQVGAITAIIK---AFGWREAVPI--YVDNQYGEELIPSLTDALQAIDTRVPYRSVISPL--A--TDDQIEKELYKLFT 76 (829)
Q Consensus 6 ~~q~~ai~~ll~---~fgW~~V~iI--~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~--~--~~~~~~~~l~~lk~ 76 (829)
..|...|.++++ .-|..-++.. |... -....+..+.+.+++.|.-|..-..-... . ....+.+.+...+.
T Consensus 165 ~~el~~m~~ll~~al~~Ga~gis~~~~y~p~-~~~~eL~~l~~~A~~~g~~v~~H~e~~~~~~~~~e~~av~~~i~lA~~ 243 (509)
T PRK09061 165 PAELAEILELLEQGLDEGALGIGIGAGYAPG-TGHKEYLELARLAARAGVPTYTHVRYLSNVDPRSSVDAYQELIAAAAE 243 (509)
T ss_pred HHHHHHHHHHHHHHHHCCCCEEecCCccCCC-CCHHHHHHHHHHHHHcCCEEEEEecCcccCCchhHHHHHHHHHHHHHH
Confidence 467778888886 6787777642 4221 23445677777788888766553332110 0 11234555566667
Q ss_pred CCCeEEEEEcCh------hHHHHHHHHHHHcCc
Q 043276 77 MQTRVFILHMLP------SLGSRIFEKANEIGL 103 (829)
Q Consensus 77 ~~arViIv~~~~------~~~~~i~~~a~~~gm 103 (829)
.+.++.|.|++. ..+..++.+|++.|+
T Consensus 244 ~G~rv~IsHlss~g~~~~~~~le~I~~Ar~~Gi 276 (509)
T PRK09061 244 TGAHMHICHVNSTSLRDIDRCLALVEKAQAQGL 276 (509)
T ss_pred hCCCEEEEeeccCCcccHHHHHHHHHHHHHcCC
Confidence 889999999988 788899999999885
No 459
>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=27.55 E-value=2.3e+02 Score=29.00 Aligned_cols=76 Identities=11% Similarity=0.036 Sum_probs=48.7
Q ss_pred EEEEEE--eCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcChhHHHHHHHHHHHc
Q 043276 24 AVPIYV--DNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEI 101 (829)
Q Consensus 24 V~iI~~--dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~~~~~~~i~~~a~~~ 101 (829)
|++|.. ++.|-......+.+++++.|..+..... ..+.+...+.+..+.+.+.+.+|+.........++..+++.
T Consensus 2 Igvv~~~~~~~~~~~~~~~i~~~a~~~g~~~~~~~~---~~~~~~~~~~i~~l~~~~vdgii~~~~~~~~~~~~~~~~~~ 78 (269)
T cd06281 2 IGCLVSDITNPLLAQLFSGAEDRLRAAGYSLLIANS---LNDPERELEILRSFEQRRMDGIIIAPGDERDPELVDALASL 78 (269)
T ss_pred EEEEecCCccccHHHHHHHHHHHHHHcCCEEEEEeC---CCChHHHHHHHHHHHHcCCCEEEEecCCCCcHHHHHHHHhC
Confidence 566664 4677778888889999999987654321 12233345566677777888888865433334456666665
Q ss_pred C
Q 043276 102 G 102 (829)
Q Consensus 102 g 102 (829)
+
T Consensus 79 ~ 79 (269)
T cd06281 79 D 79 (269)
T ss_pred C
Confidence 5
No 460
>cd01540 PBP1_arabinose_binding Periplasmic L-arabinose-binding protein (ABP), a member of a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily. Periplasmic L-arabinose-binding protein (ABP), a member of a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily. ABP is only involved in transport contrary to other related sugar-binding proteins such as the glucose/galactose-binding protein (GGBP) and the ribose-binding protein (RBP), both of which are involved in chemotaxis as well as transport. The periplasmic ABP consists of two alpha/beta globular domains connected by a three-stranded hinge, a Venus flytrap-like domain, which undergoes a transition from an open to a closed conformational state upon ligand binding. Moreover, ABP is homologous to the ligand-binding domain of eukaryotic receptors such as metabotropic glutamate receptor (mGluR) and DNA-binding transcriptional repressors such a
Probab=27.50 E-value=2e+02 Score=29.79 Aligned_cols=76 Identities=13% Similarity=0.077 Sum_probs=51.5
Q ss_pred EEEEEE--eCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcCh-hHHHHHHHHHHH
Q 043276 24 AVPIYV--DNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLP-SLGSRIFEKANE 100 (829)
Q Consensus 24 V~iI~~--dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~~-~~~~~i~~~a~~ 100 (829)
|++|.. ++.|.......+.+++++.|..+... ... +.+...+.+..+...+++.+|+.... +....++.++.+
T Consensus 2 Ig~v~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~---~~~-~~~~~~~~i~~~~~~~~dgiii~~~~~~~~~~~~~~~~~ 77 (289)
T cd01540 2 IGFIVKQPEEPWFQTEWKFAKKAAKEKGFTVVKI---DVP-DGEKVLSAIDNLGAQGAKGFVICVPDVKLGPAIVAKAKA 77 (289)
T ss_pred eeeecCCCCCcHHHHHHHHHHHHHHHcCCEEEEc---cCC-CHHHHHHHHHHHHHcCCCEEEEccCchhhhHHHHHHHHh
Confidence 566664 35677788888999999999876543 222 23344456777777889988887543 345567788888
Q ss_pred cCc
Q 043276 101 IGL 103 (829)
Q Consensus 101 ~gm 103 (829)
.|+
T Consensus 78 ~~i 80 (289)
T cd01540 78 YNM 80 (289)
T ss_pred CCC
Confidence 773
No 461
>cd03364 TOPRIM_DnaG_primases TOPRIM_DnaG_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of proteins similar to Escherichia coli DnaG. Primases synthesize RNA primers for the initiation of DNA replication. DnaG type primases are often closely associated with DNA helicases in primosome assemblies. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function. E. coli DnaG is a single subunit enzyme.
Probab=27.49 E-value=1.1e+02 Score=25.01 Aligned_cols=41 Identities=12% Similarity=0.214 Sum_probs=29.3
Q ss_pred HHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceee
Q 043276 12 ITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVP 53 (829)
Q Consensus 12 i~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~ 53 (829)
..++++.+ -+.|.+.+++|.-|......+.+.+.+.|..+.
T Consensus 35 ~~~~L~~~-~~~vii~~D~D~aG~~a~~~~~~~l~~~g~~~~ 75 (79)
T cd03364 35 QAELLKRL-AKEVILAFDGDEAGQKAALRALELLLKLGLNVR 75 (79)
T ss_pred HHHHHHhc-CCeEEEEECCCHHHHHHHHHHHHHHHHCCCeEE
Confidence 34555544 477888787788888888888888888876643
No 462
>PLN02428 lipoic acid synthase
Probab=27.41 E-value=5.3e+02 Score=28.12 Aligned_cols=75 Identities=16% Similarity=0.208 Sum_probs=41.7
Q ss_pred hHHHHHHHHHHHHHcCCcEEEEEEEe----CccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCe
Q 043276 5 DSSQVGAITAIIKAFGWREAVPIYVD----NQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTR 80 (829)
Q Consensus 5 D~~q~~ai~~ll~~fgW~~V~iI~~d----d~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~ar 80 (829)
|......+++.+...|.+.|+++..+ .|.|......+.+++.+....+......|....+ .+.|..|++++.+
T Consensus 131 d~~Ep~~vA~~v~~~Glk~vvltSg~rddl~D~ga~~~~elir~Ir~~~P~i~Ie~L~pdf~~d---~elL~~L~eAG~d 207 (349)
T PLN02428 131 DPDEPENVAEAIASWGVDYVVLTSVDRDDLPDGGSGHFAETVRRLKQLKPEILVEALVPDFRGD---LGAVETVATSGLD 207 (349)
T ss_pred ChhhHHHHHHHHHHcCCCEEEEEEcCCCCCCcccHHHHHHHHHHHHHhCCCcEEEEeCccccCC---HHHHHHHHHcCCC
Confidence 34444566777888999998777653 2444444555555566544222222233322111 3467777777776
Q ss_pred EE
Q 043276 81 VF 82 (829)
Q Consensus 81 Vi 82 (829)
++
T Consensus 208 ~i 209 (349)
T PLN02428 208 VF 209 (349)
T ss_pred EE
Confidence 63
No 463
>PRK13957 indole-3-glycerol-phosphate synthase; Provisional
Probab=27.32 E-value=4.8e+02 Score=26.89 Aligned_cols=87 Identities=14% Similarity=0.189 Sum_probs=61.1
Q ss_pred HHHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcC-
Q 043276 9 VGAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHML- 87 (829)
Q Consensus 9 ~~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~- 87 (829)
...++......|-.-++|++ |..|..+..+.|...-+...+.|-....+- +. .++...+..+++.|++...
T Consensus 63 ~~~~A~~y~~~GA~aISVlT-e~~~F~Gs~~~l~~v~~~v~~PvL~KDFIi---d~----~QI~ea~~~GADavLLI~~~ 134 (247)
T PRK13957 63 PVQIAKTYETLGASAISVLT-DQSYFGGSLEDLKSVSSELKIPVLRKDFIL---DE----IQIREARAFGASAILLIVRI 134 (247)
T ss_pred HHHHHHHHHHCCCcEEEEEc-CCCcCCCCHHHHHHHHHhcCCCEEeccccC---CH----HHHHHHHHcCCCEEEeEHhh
Confidence 34567777888998888887 666667778888877666666654332221 11 2455555689999888764
Q ss_pred --hhHHHHHHHHHHHcCc
Q 043276 88 --PSLGSRIFEKANEIGL 103 (829)
Q Consensus 88 --~~~~~~i~~~a~~~gm 103 (829)
.+....+...|.++||
T Consensus 135 L~~~~l~~l~~~a~~lGl 152 (247)
T PRK13957 135 LTPSQIKSFLKHASSLGM 152 (247)
T ss_pred CCHHHHHHHHHHHHHcCC
Confidence 3568889999999998
No 464
>PF02602 HEM4: Uroporphyrinogen-III synthase HemD; InterPro: IPR003754 Tetrapyrroles are large macrocyclic compounds derived from a common biosynthetic pathway []. The end-product, uroporphyrinogen III, is used to synthesise a number of important molecules, including vitamin B12, haem, sirohaem, chlorophyll, coenzyme F430 and phytochromobilin []. The first stage in tetrapyrrole synthesis is the synthesis of 5-aminoaevulinic acid ALA via two possible routes: (1) condensation of succinyl CoA and glycine (C4 pathway) using ALA synthase (2.3.1.37 from EC), or (2) decarboxylation of glutamate (C5 pathway) via three different enzymes, glutamyl-tRNA synthetase (6.1.1.17 from EC) to charge a tRNA with glutamate, glutamyl-tRNA reductase (1.2.1.70 from EC) to reduce glutamyl-tRNA to glutamate-1-semialdehyde (GSA), and GSA aminotransferase (5.4.3.8 from EC) to catalyse a transamination reaction to produce ALA. The second stage is to convert ALA to uroporphyrinogen III, the first macrocyclic tetrapyrrolic structure in the pathway. This is achieved by the action of three enzymes in one common pathway: porphobilinogen (PBG) synthase (or ALA dehydratase, 4.2.1.24 from EC) to condense two ALA molecules to generate porphobilinogen; hydroxymethylbilane synthase (or PBG deaminase, 2.5.1.61 from EC) to polymerise four PBG molecules into preuroporphyrinogen (tetrapyrrole structure); and uroporphyrinogen III synthase (4.2.1.75 from EC) to link two pyrrole units together (rings A and D) to yield uroporphyrinogen III. Uroporphyrinogen III is the first branch point of the pathway. To synthesise cobalamin (vitamin B12), sirohaem, and coenzyme F430, uroporphyrinogen III needs to be converted into precorrin-2 by the action of uroporphyrinogen III methyltransferase (2.1.1.107 from EC). To synthesise haem and chlorophyll, uroporphyrinogen III needs to be decarboxylated into coproporphyrinogen III by the action of uroporphyrinogen III decarboxylase (4.1.1.37 from EC) []. This entry represents uroporphyrinogen III synthase (4.2.1.75 from EC) which functions during the second stage of tetrapyrrole biosynthesis. This enzyme catalyses the inversion of the final pyrrole unit (ring D) of the linear tetrapyrrole molecule, linking it to the first pyrrole unit (ring A), thereby generating a large macrocyclic structure called uroporphyrinogen III []. The enzyme folds into two alpha/beta domains connected by a beta-ladder, the active site being located between the two domains []. Congenital erythropoietic porphyria (CEP) is an autosomal recessive inborn error of metabolism that results from the markedly deficient activity of uroporphyrinogen III synthase []. ; GO: 0004852 uroporphyrinogen-III synthase activity, 0033014 tetrapyrrole biosynthetic process; PDB: 1WD7_B 1WCX_A 1WCW_A 3D8R_A 3D8T_B 3D8S_A 3D8N_A 3RE1_A 3MW8_A 3P9Z_A ....
Probab=27.31 E-value=62 Score=32.73 Aligned_cols=90 Identities=13% Similarity=0.128 Sum_probs=48.4
Q ss_pred ChHHHHHHHHHHHHH-cCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEE
Q 043276 4 NDSSQVGAITAIIKA-FGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVF 82 (829)
Q Consensus 4 sD~~q~~ai~~ll~~-fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arVi 82 (829)
++...++.+++.+.. ..=++|.++. |....+.|.+.|++.|..|.....+.. ............+..... -+
T Consensus 99 ~~~~~s~~L~~~l~~~~~~~~vl~~~-----g~~~~~~l~~~L~~~g~~v~~~~vY~~-~~~~~~~~~~~~l~~~~~-~~ 171 (231)
T PF02602_consen 99 SSEGSSEGLAELLKEQLRGKRVLILR-----GEGGRPDLPEKLREAGIEVTEVIVYET-PPEELSPELKEALDRGEI-DA 171 (231)
T ss_dssp TTSSSHHHHHGGHHHCCTTEEEEEEE-----SSSSCHHHHHHHHHTTEEEEEEECEEE-EEHHHHHHHHHHHHHTTT-SE
T ss_pred CCCCCHHHHHHHHHhhCCCCeEEEEc-----CCCccHHHHHHHHHCCCeEEEEEEeec-ccccchHHHHHHHHcCCC-CE
Confidence 334445667776653 3225655554 334466777888888877665555443 212222233334444344 34
Q ss_pred EEEcChhHHHHHHHHHHH
Q 043276 83 ILHMLPSLGSRIFEKANE 100 (829)
Q Consensus 83 Iv~~~~~~~~~i~~~a~~ 100 (829)
|++.++..+..++....+
T Consensus 172 v~ftS~~~~~~~~~~~~~ 189 (231)
T PF02602_consen 172 VVFTSPSAVRAFLELLKK 189 (231)
T ss_dssp EEESSHHHHHHHHHHSSG
T ss_pred EEECCHHHHHHHHHHhHh
Confidence 555666667666666554
No 465
>cd03767 SR_Res_par Serine recombinase (SR) family, Partitioning (par)-Resolvase subfamily, catalytic domain; Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining mechanism which involves a transient phosphoserine linkage between DNA and the enzyme. They are functionally versatile and include resolvases, invertases, integrases, and transposases. This subgroup is composed of proteins similar to the E. coli resolvase found in the par region of the RP4 plasmid, which encodes a highly efficient partitioning system. This protein is part of a complex stabilization system involved in the resolution of plasmid dimers during cell division. Similar to Tn3 and other resolvases, members of this family may contain a C-terminal DNA binding domain.
Probab=27.21 E-value=5.1e+02 Score=24.05 Aligned_cols=28 Identities=25% Similarity=0.357 Sum_probs=15.9
Q ss_pred HHHHHHHHHHHHHcCCcEEEEEEEeCccc
Q 043276 6 SSQVGAITAIIKAFGWREAVPIYVDNQYG 34 (829)
Q Consensus 6 ~~q~~ai~~ll~~fgW~~V~iI~~dd~yG 34 (829)
..|-+.+-++.+..||.-+. +|.|...|
T Consensus 15 ~~Q~~~l~~~a~~~g~~~~~-i~~d~~SG 42 (146)
T cd03767 15 TRAKESLEAFATERGFYIAG-FYVENASG 42 (146)
T ss_pred HHHHHHHHHHHHHCCCEEEE-EEEECCcC
Confidence 44555566666667886443 45555444
No 466
>COG0134 TrpC Indole-3-glycerol phosphate synthase [Amino acid transport and metabolism]
Probab=27.20 E-value=1.6e+02 Score=30.27 Aligned_cols=88 Identities=16% Similarity=0.175 Sum_probs=66.1
Q ss_pred HHHHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEc-
Q 043276 8 QVGAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHM- 86 (829)
Q Consensus 8 q~~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~- 86 (829)
....+++..+++|-.-+++++ |..|..+..+.|...-+...+.|--...|. +. .++..-+..+++.|.+..
T Consensus 67 dp~~ia~~Ye~~GAa~iSVLT-d~~~F~Gs~e~L~~v~~~v~~PvL~KDFii---D~----yQI~~Ar~~GADavLLI~~ 138 (254)
T COG0134 67 DPVEIAKAYEEGGAAAISVLT-DPKYFQGSFEDLRAVRAAVDLPVLRKDFII---DP----YQIYEARAAGADAVLLIVA 138 (254)
T ss_pred CHHHHHHHHHHhCCeEEEEec-CccccCCCHHHHHHHHHhcCCCeeeccCCC---CH----HHHHHHHHcCcccHHHHHH
Confidence 345688888999999999997 888999999999888787777654332221 11 255666668888886654
Q ss_pred --ChhHHHHHHHHHHHcCc
Q 043276 87 --LPSLGSRIFEKANEIGL 103 (829)
Q Consensus 87 --~~~~~~~i~~~a~~~gm 103 (829)
+.+....+...|.++||
T Consensus 139 ~L~~~~l~el~~~A~~LGm 157 (254)
T COG0134 139 ALDDEQLEELVDRAHELGM 157 (254)
T ss_pred hcCHHHHHHHHHHHHHcCC
Confidence 45668999999999998
No 467
>TIGR02976 phageshock_pspB phage shock protein B. This model describes the PspB protein of the psp (phage shock protein) operon, as found in Escherichia coli and many related species. Expression of a phage protein called secretin protein IV, and a number of other stresses including ethanol, heat shock, and defects in protein secretion trigger sigma-54-dependent expression of the phage shock regulon. PspB is both a regulator and an effector protein of the phage shock response.
Probab=27.17 E-value=2.6e+02 Score=22.88 Aligned_cols=17 Identities=24% Similarity=0.251 Sum_probs=8.7
Q ss_pred HHHHHHHHHhhhcccCc
Q 043276 718 LSRIRIFLRIFVSRDLS 734 (829)
Q Consensus 718 ~~~~~~~~~~~~~~~~~ 734 (829)
.+++..+.+..|..++.
T Consensus 55 ~eRI~tLE~ILd~e~P~ 71 (75)
T TIGR02976 55 EERIDTLERILDAEHPN 71 (75)
T ss_pred HHHHHHHHHHHcCCCcC
Confidence 33455555555555443
No 468
>PRK00843 egsA NAD(P)-dependent glycerol-1-phosphate dehydrogenase; Reviewed
Probab=27.05 E-value=2.6e+02 Score=30.49 Aligned_cols=97 Identities=14% Similarity=0.022 Sum_probs=60.7
Q ss_pred HHHHHHHHHcCC-cEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcCh
Q 043276 10 GAITAIIKAFGW-REAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLP 88 (829)
Q Consensus 10 ~ai~~ll~~fgW-~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~~ 88 (829)
..+.++++.++- +++.+|++...+. ...+.+.+.|++.| .+.. .+....+.+.+.+.+..+++.+.++||..+..
T Consensus 22 ~~l~~~l~~~~~~~~~livtd~~~~~-~~~~~l~~~l~~~~-~~~~--~~~~~~t~~~v~~~~~~~~~~~~d~IIaiGGG 97 (350)
T PRK00843 22 DDIGDVCSDLKLTGRALIVTGPTTKK-IAGDRVEENLEDAG-DVEV--VIVDEATMEEVEKVEEKAKDVNAGFLIGVGGG 97 (350)
T ss_pred HHHHHHHHHhCCCCeEEEEECCcHHH-HHHHHHHHHHHhcC-CeeE--EeCCCCCHHHHHHHHHHhhccCCCEEEEeCCc
Confidence 345567777776 7888887554443 24567788888777 4432 23345566678888888888888999887764
Q ss_pred --hHHHHHHHHHHHcCccccCeEEEEcCc
Q 043276 89 --SLGSRIFEKANEIGLMNKGCVWIMTDG 115 (829)
Q Consensus 89 --~~~~~i~~~a~~~gm~~~~~vwI~t~~ 115 (829)
-+...+.. ...| -.++-|-|..
T Consensus 98 sv~D~ak~vA--~~rg---ip~I~IPTT~ 121 (350)
T PRK00843 98 KVIDVAKLAA--YRLG---IPFISVPTAA 121 (350)
T ss_pred hHHHHHHHHH--HhcC---CCEEEeCCCc
Confidence 24444443 3334 2455555543
No 469
>PRK03670 competence damage-inducible protein A; Provisional
Probab=26.73 E-value=3.1e+02 Score=28.34 Aligned_cols=61 Identities=13% Similarity=0.181 Sum_probs=35.9
Q ss_pred EEEEEEeCcc--c---cchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEc
Q 043276 24 AVPIYVDNQY--G---EELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHM 86 (829)
Q Consensus 24 V~iI~~dd~y--G---~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~ 86 (829)
++||...|+- | ......|.+.|.+.|+.+.....++++ .+.+.+.+..+.+...++||+.+
T Consensus 3 a~Ii~iGdEll~G~i~dtN~~~la~~L~~~G~~v~~~~iV~Dd--~~~I~~~l~~a~~~~~DlVIttG 68 (252)
T PRK03670 3 AEIITVGDELLTGNTVDSNSAFIAQKLTEKGYWVRRITTVGDD--VEEIKSVVLEILSRKPEVLVISG 68 (252)
T ss_pred EEEEEeCCcCcCCeEEehhHHHHHHHHHHCCCEEEEEEEcCCC--HHHHHHHHHHHhhCCCCEEEECC
Confidence 4555555432 2 233567778888888888776666644 44566666654433345555543
No 470
>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=26.54 E-value=7.2e+02 Score=25.71 Aligned_cols=96 Identities=9% Similarity=-0.035 Sum_probs=51.3
Q ss_pred HHHHHHHHHHc------CCcEEEEEEEeCcc--ccchHHHHHHHHHhCC----ceeeeEEecCCCCChhHHHHHHHHhhc
Q 043276 9 VGAITAIIKAF------GWREAVPIYVDNQY--GEELIPSLTDALQAID----TRVPYRSVISPLATDDQIEKELYKLFT 76 (829)
Q Consensus 9 ~~ai~~ll~~f------gW~~V~iI~~dd~y--G~~~~~~l~~~l~~~g----i~I~~~~~i~~~~~~~~~~~~l~~lk~ 76 (829)
+..+++.+... |-++++++..+.+. .....+.|.+++++.+ +.+... ......+...-.+.+..+.+
T Consensus 107 g~~~~~~l~~~~~~~~~g~~~i~~l~g~~~~~~~~~R~~gf~~~l~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~l~ 185 (288)
T cd01538 107 GELQGQALVDGLGAKGKPPGNIELIAGSPTDNNAKLFFNGAMSVLKPLIDSGKITIVGE-VATPDWDPETAQKRMENALT 185 (288)
T ss_pred HHHHHHHHHHHHhhcCCCCceEEEEECCCCCchHHHHHHHHHHHHHhccccCCeeEEec-cccCCCCHHHHHHHHHHHHH
Confidence 44445554333 88899998644332 2334677788888887 333221 11111122222233444433
Q ss_pred CCC-e-EEEEEcChhHHHHHHHHHHHcCccc
Q 043276 77 MQT-R-VFILHMLPSLGSRIFEKANEIGLMN 105 (829)
Q Consensus 77 ~~a-r-ViIv~~~~~~~~~i~~~a~~~gm~~ 105 (829)
... + -.|++.+...+..++..+++.|+..
T Consensus 186 ~~~~~~~~I~~~~d~~a~g~~~al~~~g~~~ 216 (288)
T cd01538 186 ANYNKVDGVLAANDGTAGGAIAALKAAGLAG 216 (288)
T ss_pred hCCCCccEEEeCCcHHHHHHHHHHHHcCCCC
Confidence 222 2 3344455667778888899988643
No 471
>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=26.38 E-value=2.6e+02 Score=28.56 Aligned_cols=75 Identities=17% Similarity=0.078 Sum_probs=47.4
Q ss_pred EEEEEE--eCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcChhHHHHHHHHHHHc
Q 043276 24 AVPIYV--DNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEI 101 (829)
Q Consensus 24 V~iI~~--dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~~~~~~~i~~~a~~~ 101 (829)
|+++.. ++.|.......+.+++++.|..+... ....+.+...+.++++.+.+.+.+|+..... ....+..+.+.
T Consensus 2 i~vv~p~~~~~~~~~~~~~i~~~~~~~g~~~~~~---~~~~~~~~~~~~~~~l~~~~vdgiii~~~~~-~~~~~~~l~~~ 77 (268)
T cd06273 2 IGAIVPTLDNAIFARVIQAFQETLAAHGYTLLVA---SSGYDLDREYAQARKLLERGVDGLALIGLDH-SPALLDLLARR 77 (268)
T ss_pred eEEEeCCCCCchHHHHHHHHHHHHHHCCCEEEEe---cCCCCHHHHHHHHHHHHhcCCCEEEEeCCCC-CHHHHHHHHhC
Confidence 566664 46777888888999999999887652 2222233344566777777788887765432 22445566665
Q ss_pred C
Q 043276 102 G 102 (829)
Q Consensus 102 g 102 (829)
|
T Consensus 78 ~ 78 (268)
T cd06273 78 G 78 (268)
T ss_pred C
Confidence 5
No 472
>PRK10936 TMAO reductase system periplasmic protein TorT; Provisional
Probab=26.27 E-value=2.8e+02 Score=30.05 Aligned_cols=80 Identities=5% Similarity=0.040 Sum_probs=51.8
Q ss_pred cEEEEEEEe--CccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcChh-HHHHHHHHH
Q 043276 22 REAVPIYVD--NQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPS-LGSRIFEKA 98 (829)
Q Consensus 22 ~~V~iI~~d--d~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~~~-~~~~i~~~a 98 (829)
+.|++|..+ +.|.....+.+++++++.|..+.+...-. ..+.+...+.+..+.+.+++.||+..... .....+ ++
T Consensus 47 ~~Igvv~p~~~~~f~~~~~~gi~~aa~~~G~~l~i~~~~~-~~~~~~q~~~i~~l~~~~vdgIIl~~~~~~~~~~~l-~~ 124 (343)
T PRK10936 47 WKLCALYPHLKDSYWLSVNYGMVEEAKRLGVDLKVLEAGG-YYNLAKQQQQLEQCVAWGADAILLGAVTPDGLNPDL-EL 124 (343)
T ss_pred eEEEEEecCCCchHHHHHHHHHHHHHHHhCCEEEEEcCCC-CCCHHHHHHHHHHHHHhCCCEEEEeCCChHHhHHHH-HH
Confidence 477877744 67778888899999999998876543211 11223344567777778899888876443 323444 67
Q ss_pred HHcCc
Q 043276 99 NEIGL 103 (829)
Q Consensus 99 ~~~gm 103 (829)
.+.|.
T Consensus 125 ~~~gi 129 (343)
T PRK10936 125 QAANI 129 (343)
T ss_pred HHCCC
Confidence 77663
No 473
>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=25.85 E-value=2.3e+02 Score=29.91 Aligned_cols=77 Identities=9% Similarity=0.101 Sum_probs=49.8
Q ss_pred EEEEEE---eCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcC--CCeEEEEEcChhHHHHHHHHH
Q 043276 24 AVPIYV---DNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTM--QTRVFILHMLPSLGSRIFEKA 98 (829)
Q Consensus 24 V~iI~~---dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~--~arViIv~~~~~~~~~i~~~a 98 (829)
|++|.. ++.|.......+++++++.|..+.... ...+.+.-...+..+.+. +++.||+.........++..+
T Consensus 2 Igvi~~~~~~~~~~~~~~~gi~~~~~~~g~~v~~~~---~~~~~~~~~~~i~~~~~~~~~vdgiIi~~~~~~~~~~~~~~ 78 (305)
T cd06324 2 VVFLNPGKSDEPFWNSVARFMQAAADDLGIELEVLY---AERDRFLMLQQARTILQRPDKPDALIFTNEKSVAPELLRLA 78 (305)
T ss_pred eEEecCCCCCCcHHHHHHHHHHHHHHhcCCeEEEEe---CCCCHHHHHHHHHHHHHhccCCCEEEEcCCccchHHHHHHH
Confidence 556652 456777888889999999998765532 122233344566667777 899988865433344566777
Q ss_pred HHcCc
Q 043276 99 NEIGL 103 (829)
Q Consensus 99 ~~~gm 103 (829)
.+.|+
T Consensus 79 ~~~gi 83 (305)
T cd06324 79 EGAGV 83 (305)
T ss_pred HhCCC
Confidence 77663
No 474
>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=25.74 E-value=2.7e+02 Score=28.26 Aligned_cols=76 Identities=13% Similarity=0.054 Sum_probs=49.0
Q ss_pred EEEEEE--eCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcChhH-HHHHHHHHHH
Q 043276 24 AVPIYV--DNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSL-GSRIFEKANE 100 (829)
Q Consensus 24 V~iI~~--dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~~~~-~~~i~~~a~~ 100 (829)
+++|.. ++.|.......+.+++++.|..+... +...+.+...+.+.++...+++.+|+...... ....+.++.+
T Consensus 2 I~vv~~~~~~~~~~~~~~~i~~~~~~~g~~v~~~---~~~~~~~~~~~~~~~~~~~~~dgii~~~~~~~~~~~~l~~l~~ 78 (268)
T cd06323 2 IGLSVSTLNNPFFVTLKDGAQKEAKELGYELTVL---DAQNDAAKQLNDIEDLITRGVDAIIINPTDSDAVVPAVKAANE 78 (268)
T ss_pred eeEecccccCHHHHHHHHHHHHHHHHcCceEEec---CCCCCHHHHHHHHHHHHHcCCCEEEEcCCChHHHHHHHHHHHH
Confidence 455553 46778888999999999999877532 22223334556677777778888877643322 2345666666
Q ss_pred cC
Q 043276 101 IG 102 (829)
Q Consensus 101 ~g 102 (829)
.|
T Consensus 79 ~~ 80 (268)
T cd06323 79 AG 80 (268)
T ss_pred CC
Confidence 55
No 475
>PF06679 DUF1180: Protein of unknown function (DUF1180); InterPro: IPR009565 This entry consists of several hypothetical eukaryotic proteins thought to be membrane proteins. Their function is unknown.
Probab=25.70 E-value=79 Score=30.16 Aligned_cols=30 Identities=10% Similarity=0.029 Sum_probs=22.1
Q ss_pred chhHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 043276 679 SFWGLFLIAGIAAILALIIFLAVFVHEHWN 708 (829)
Q Consensus 679 ~~~g~f~il~vg~~lallvf~~E~~~~~~~ 708 (829)
-+.-.||++++.++++++.|++..+..+|+
T Consensus 93 ~l~R~~~Vl~g~s~l~i~yfvir~~R~r~~ 122 (163)
T PF06679_consen 93 MLKRALYVLVGLSALAILYFVIRTFRLRRR 122 (163)
T ss_pred chhhhHHHHHHHHHHHHHHHHHHHHhhccc
Confidence 355677888888888888888887655543
No 476
>COG3181 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.63 E-value=7e+02 Score=26.77 Aligned_cols=124 Identities=13% Similarity=0.094 Sum_probs=78.0
Q ss_pred cCCCCCCCHHHHHhCCC----cEEEE-eC--chH----HHHHHhcCCCccceeecCChHHHHHHHhcCCcCCceeEEEcc
Q 043276 527 QLQPTITDVNLLIKRGD----NVGYQ-KG--SFV----LGILKQLGFDERKLVVYNSHEECDELFQKGSANGGIAAAFDE 595 (829)
Q Consensus 527 ~~~~~I~s~~dL~~~~~----~vg~~-~~--s~~----~~~l~~~~~~~~~~~~~~~~~~~~~~l~~g~~~~g~~a~~~~ 595 (829)
+...+.+|++||++.-+ .+-+- .| +.. ..+.+..+. +.+.++|+...+.+.+|..|. +++....
T Consensus 129 ~~~s~~~t~~dlv~~~k~~p~~v~~~~~g~Gs~dhl~~~~~~k~~Gi-~~~~Vpy~g~gea~taLlgg~----v~a~~~~ 203 (319)
T COG3181 129 RADSPYKTLKDLVAYAKADPGSVIGGGSGLGSADHLAGALFAKAAGI-KITYVPYKGGGEALTALLGGH----VDAGSTN 203 (319)
T ss_pred eCCCCcccHHHHHHHHHhCCCeEEecCCCCCcHHHHHHHHHHHHhCC-ceeEEeecCccHHHHHHhcCc----eeeeecC
Confidence 45567899999884321 12221 11 111 122344555 567889999999999999999 9999888
Q ss_pred hhHHHHHHhcC-CC--------ceEEeCc----------ccccCCceeeecCCCC--chhhHHHHHHhhhccChhHHHHH
Q 043276 596 IPYAKLLIGQH-CS--------KYTMVEP----------TFKTAGFGFAFPLHSP--LVHDVSKAILNVTEGDKMKEIED 654 (829)
Q Consensus 596 ~~~~~~~~~~~-c~--------~l~~v~~----------~~~~~~~~~~~~k~sp--l~~~in~~il~l~e~G~~~~~~~ 654 (829)
...+.-+.+.- .+ ++..... .+.....+++.|+|-| ....++.++.++.++..+++..+
T Consensus 204 ~se~~~~vksG~lr~Lav~s~eRl~~~pdvPT~~E~G~~~~~~~wrgvfap~g~~~e~~~~~~~a~kk~l~s~e~~~~~~ 283 (319)
T COG3181 204 LSELLSQVKSGTLRLLAVFSEERLPGLPDVPTLKEQGYDVVMSIWRGVFAPAGTPDEIIAKLSAALKKALASPEWQKRLK 283 (319)
T ss_pred hhhhhhhhccCceEEEEeechhhcCCCCCCCChHhcCCceeeeeeeEEEeCCCCCHHHHHHHHHHHHHHhcCHHHHHHHH
Confidence 76655544431 11 1111110 1223344788899976 99999999999999987665444
Q ss_pred H
Q 043276 655 A 655 (829)
Q Consensus 655 ~ 655 (829)
+
T Consensus 284 ~ 284 (319)
T COG3181 284 E 284 (319)
T ss_pred h
Confidence 3
No 477
>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=25.56 E-value=5.5e+02 Score=25.93 Aligned_cols=107 Identities=9% Similarity=0.060 Sum_probs=60.4
Q ss_pred CChHHHHHHHHHHHH-HcCC-cEEEEEEEeCccc--cchHHHHHHHHHhC-CceeeeEEecCCCCChhHHHHHHHHhhcC
Q 043276 3 LNDSSQVGAITAIIK-AFGW-REAVPIYVDNQYG--EELIPSLTDALQAI-DTRVPYRSVISPLATDDQIEKELYKLFTM 77 (829)
Q Consensus 3 psD~~q~~ai~~ll~-~fgW-~~V~iI~~dd~yG--~~~~~~l~~~l~~~-gi~I~~~~~i~~~~~~~~~~~~l~~lk~~ 77 (829)
+++...+..+++.+. ..+= .+|+++....++. ......+.+.+++. ++++... ......+.+...+.+.++.+.
T Consensus 102 ~d~~~~G~~~a~~l~~~~~~~~~v~~~~~~~~~~~~~~r~~g~~~~l~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~l~~ 180 (257)
T PF13407_consen 102 TDNYEAGKLAAEYLAEKLGAKGKVLILSGSPGNPNTQERLEGFRDALKEYPGVEIVDE-YEYTDWDPEDARQAIENLLQA 180 (257)
T ss_dssp E-HHHHHHHHHHHHHHHHTTTEEEEEEESSTTSHHHHHHHHHHHHHHHHCTTEEEEEE-EEECTTSHHHHHHHHHHHHHH
T ss_pred ccHHHHHHHHHHHHHHHhccCceEEeccCCCCchHHHHHHHHHHHHHhhcceeeeeee-eeccCCCHHHHHHHHHHhhhc
Confidence 345566677777774 3332 5777775443332 34577788888884 5555442 222233344444445544433
Q ss_pred CCeEEEEEcChhHHHHHHHHHHHcCccccCeEEEE
Q 043276 78 QTRVFILHMLPSLGSRIFEKANEIGLMNKGCVWIM 112 (829)
Q Consensus 78 ~arViIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~ 112 (829)
..-..|++++...+..+.....+.|+ .+.++|.
T Consensus 181 ~~~~~i~~~~~~~~~g~~~al~~~g~--~~~~~v~ 213 (257)
T PF13407_consen 181 NPVDAIIACNDGMALGAAQALQQAGR--AGKVIVV 213 (257)
T ss_dssp TTEEEEEESSHHHHHHHHHHHHHTTC--TTTSEEE
T ss_pred CCceEEEeCCChHHHHHHHHHHHcCC--cccceee
Confidence 33334456677777778889999986 3344444
No 478
>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=25.55 E-value=3e+02 Score=28.97 Aligned_cols=78 Identities=6% Similarity=0.137 Sum_probs=0.0
Q ss_pred EEEEEEEe--CccccchHHHHHHHHHh--CCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEc-ChhHHHHHHHH
Q 043276 23 EAVPIYVD--NQYGEELIPSLTDALQA--IDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHM-LPSLGSRIFEK 97 (829)
Q Consensus 23 ~V~iI~~d--d~yG~~~~~~l~~~l~~--~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~-~~~~~~~i~~~ 97 (829)
+|++|..+ +.|.......+.+++++ .|..+... +...+.+.....+..+...+++.||+.. .++.....+.+
T Consensus 1 ~Igviv~~~~~~~~~~~~~gi~~~a~~~~~g~~~~~~---~~~~~~~~q~~~i~~l~~~~vdgiii~~~~~~~~~~~~~~ 77 (303)
T cd01539 1 KIGVFLYKFDDTFISLVRKNLEDIQKENGGKVEFTFY---DAKNNQSTQNEQIDTALAKGVDLLAVNLVDPTAAQTVINK 77 (303)
T ss_pred CeEEEeeCCCChHHHHHHHHHHHHHHhhCCCeeEEEe---cCCCCHHHHHHHHHHHHHcCCCEEEEecCchhhHHHHHHH
Q ss_pred HHHcCc
Q 043276 98 ANEIGL 103 (829)
Q Consensus 98 a~~~gm 103 (829)
+.+.|+
T Consensus 78 ~~~~gi 83 (303)
T cd01539 78 AKQKNI 83 (303)
T ss_pred HHHCCC
No 479
>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=25.41 E-value=2.8e+02 Score=28.44 Aligned_cols=79 Identities=8% Similarity=0.069 Sum_probs=49.0
Q ss_pred EEEEEE--eCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcCh-hHHHHHHHHHHH
Q 043276 24 AVPIYV--DNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLP-SLGSRIFEKANE 100 (829)
Q Consensus 24 V~iI~~--dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~~-~~~~~i~~~a~~ 100 (829)
+++|.. ++.|.....+.+.+++++.|..+..... +...+...-.+.+.++.+.+.+.+|+.... +.....+..+.+
T Consensus 2 igvi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~-~~~~~~~~~~~~i~~l~~~~vdgiIi~~~~~~~~~~~~~~~~~ 80 (275)
T cd06320 2 YGVVLKTLSNEFWRSLKEGYENEAKKLGVSVDIQAA-PSEGDQQGQLSIAENMINKGYKGLLFSPISDVNLVPAVERAKK 80 (275)
T ss_pred eeEEEecCCCHHHHHHHHHHHHHHHHhCCeEEEEcc-CCCCCHHHHHHHHHHHHHhCCCEEEECCCChHHhHHHHHHHHH
Confidence 566653 4667788888999999999987654321 111122233455666767788888776543 323345667766
Q ss_pred cCc
Q 043276 101 IGL 103 (829)
Q Consensus 101 ~gm 103 (829)
.|.
T Consensus 81 ~~i 83 (275)
T cd06320 81 KGI 83 (275)
T ss_pred CCC
Confidence 663
No 480
>COG0807 RibA GTP cyclohydrolase II [Coenzyme metabolism]
Probab=24.61 E-value=2.6e+02 Score=27.54 Aligned_cols=54 Identities=17% Similarity=0.127 Sum_probs=40.8
Q ss_pred CChHHHHHHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCCh
Q 043276 3 LNDSSQVGAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATD 64 (829)
Q Consensus 3 psD~~q~~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~ 64 (829)
+.|.-..-.-|+|++++|-+++=++.++.. =...++..|++|+-+..+....+.
T Consensus 123 ~~D~R~ygigAqIL~dLGI~~irLLtnnp~--------K~~~l~~~Gi~vverv~~~~~~~~ 176 (193)
T COG0807 123 PADERDYGIGAQILKDLGIKKIRLLTNNPR--------KIYGLEGFGINVVERVPLIVGANP 176 (193)
T ss_pred CchHHHHHHHHHHHHHcCCcEEEEecCChH--------HHHHHHhCCceEEEEeecCCCCCc
Confidence 456667778889999999999999985322 134578899999988877666543
No 481
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=24.38 E-value=2.6e+02 Score=29.94 Aligned_cols=78 Identities=21% Similarity=0.156 Sum_probs=51.7
Q ss_pred cEEEEEEEe--CccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcChhHHHHHHHHHH
Q 043276 22 REAVPIYVD--NQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKAN 99 (829)
Q Consensus 22 ~~V~iI~~d--d~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~~~~~~~i~~~a~ 99 (829)
+.++++..+ +.|.......+.+++++.|..+... ....+.+.....+..+.+.+++.||+..........+..+.
T Consensus 65 ~~Igvv~~~~~~~~~~~i~~gi~~~a~~~g~~~~~~---~~~~~~~~~~~~~~~l~~~~vdgiIi~~~~~~~~~~~~~l~ 141 (342)
T PRK10014 65 GVIGLIVRDLSAPFYAELTAGLTEALEAQGRMVFLL---QGGKDGEQLAQRFSTLLNQGVDGVVIAGAAGSSDDLREMAE 141 (342)
T ss_pred CEEEEEeCCCccchHHHHHHHHHHHHHHcCCEEEEE---eCCCCHHHHHHHHHHHHhCCCCEEEEeCCCCCcHHHHHHHh
Confidence 367888753 6777888889999999999776432 12222334456677777788999988754433345566666
Q ss_pred HcC
Q 043276 100 EIG 102 (829)
Q Consensus 100 ~~g 102 (829)
+.|
T Consensus 142 ~~~ 144 (342)
T PRK10014 142 EKG 144 (342)
T ss_pred hcC
Confidence 665
No 482
>cd00494 HMBS Hydroxymethylbilane synthase (HMBS), also known as porphobilinogen deaminase (PBGD), is an intermediate enzyme in the biosynthetic pathway of tetrapyrrolic ring systems, such as heme, chlorophylls, and vitamin B12. HMBS catalyzes the conversion of porphobilinogen (PBG) into hydroxymethylbilane (HMB). HMBS consists of three domains, and is believed to bind substrate through a hinge-bending motion of domains I and II. HMBS is found in all organisms except viruses.
Probab=24.34 E-value=8.7e+02 Score=25.74 Aligned_cols=60 Identities=18% Similarity=0.094 Sum_probs=37.8
Q ss_pred CCHHHHHhCCCcEEEEeCchHHH-HHHhcCCCccceeecC-ChHHHHHHHhcCCcCCceeEEEcchhHHH
Q 043276 533 TDVNLLIKRGDNVGYQKGSFVLG-ILKQLGFDERKLVVYN-SHEECDELFQKGSANGGIAAAFDEIPYAK 600 (829)
Q Consensus 533 ~s~~dL~~~~~~vg~~~~s~~~~-~l~~~~~~~~~~~~~~-~~~~~~~~l~~g~~~~g~~a~~~~~~~~~ 600 (829)
.+++||- .|.+||+ +|.=+. .+++. +|..+++... +.+..++.|..|. .||++.-..-+.
T Consensus 109 ~~l~~Lp-~ga~IGT--sS~RR~aql~~~-rpdl~~~~iRGNV~TRL~KL~~ge----~DaiiLA~AGL~ 170 (292)
T cd00494 109 SSLEDLP-AGSVVGT--SSLRRQAQLKRK-RPDLKFEPLRGNVDTRLRKLDEGE----YDAIILAAAGLK 170 (292)
T ss_pred CChhHCC-CCCEEec--CCHHHHHHHHHH-CCCCEEEEcCCCHHHHHHHhcCCC----CCEeehHhhHHH
Confidence 4678885 4556665 222222 33333 5666666554 7888999999998 888887654443
No 483
>COG0040 HisG ATP phosphoribosyltransferase [Amino acid transport and metabolism]
Probab=24.20 E-value=3.8e+02 Score=28.26 Aligned_cols=102 Identities=12% Similarity=0.076 Sum_probs=56.8
Q ss_pred CCCHHHHHhCCCcEEEEeCchHHHHHHhcCCCccceeecCChHHHHHHHhcCCcCCceeEEEcchhHHHHHHhcCCCceE
Q 043276 532 ITDVNLLIKRGDNVGYQKGSFVLGILKQLGFDERKLVVYNSHEECDELFQKGSANGGIAAAFDEIPYAKLLIGQHCSKYT 611 (829)
Q Consensus 532 I~s~~dL~~~~~~vg~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~g~~~~g~~a~~~~~~~~~~~~~~~c~~l~ 611 (829)
+++.+||... .+|+...-...++||++.+.+- ++....-.-|. +-..|- .|++++-.....-+..+.+ .
T Consensus 107 ~~~~~~l~~~-~rIATkYp~l~~~yf~~~g~~~-~Ii~l~GsvE~--aP~~Gl----ADaIvDivsTG~TLkaNgL---~ 175 (290)
T COG0040 107 YTSPEDLKGR-LRIATKYPNLARKYFAEKGIDV-EIIKLSGSVEL--APALGL----ADAIVDIVSTGTTLKANGL---K 175 (290)
T ss_pred ccChhHhcCC-ceEEEccHHHHHHHHHHcCceE-EEEEccCcEee--ccccCc----cceEEEeecCCHhHHHCCC---E
Confidence 4678888522 4888877777889998766543 33333322222 234455 7888777666666555544 4
Q ss_pred EeCcccccCCceeeecCCCCch---hhHHHHHHhhhc
Q 043276 612 MVEPTFKTAGFGFAFPLHSPLV---HDVSKAILNVTE 645 (829)
Q Consensus 612 ~v~~~~~~~~~~~~~~k~spl~---~~in~~il~l~e 645 (829)
.+... ....-.+...+...+. +.+++.+.+++.
T Consensus 176 ~id~i-~~ssa~LI~n~~~~~~~k~~~i~~l~~rl~g 211 (290)
T COG0040 176 EIEVI-YDSSARLIVNAKASLKDKQELIDQLVTRLKG 211 (290)
T ss_pred EEEEE-EeeEEEEEeccccccchhHHHHHHHHHHHHH
Confidence 55333 3344445555332222 346666666643
No 484
>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=24.14 E-value=2.9e+02 Score=28.24 Aligned_cols=77 Identities=12% Similarity=0.012 Sum_probs=50.0
Q ss_pred EEEEEE---eCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcChh-HHHHHHHHHH
Q 043276 24 AVPIYV---DNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPS-LGSRIFEKAN 99 (829)
Q Consensus 24 V~iI~~---dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~~~-~~~~i~~~a~ 99 (829)
|++|.. ++.|+....+.+.+++++.|..+.... ...+.+.-.+.+..+...+++.+|+..... .....+.++.
T Consensus 2 i~vi~p~~~~~~~~~~~~~g~~~~~~~~g~~~~~~~---~~~~~~~~~~~~~~l~~~~vdgiii~~~~~~~~~~~l~~~~ 78 (275)
T cd06317 2 IGYTQNNVGSHSYQTTYNKAFQAAAEEDGVEVIVLD---ANGDVARQAAQVEDLIAQKVDGIILWPTDGQAYIPGLRKAK 78 (275)
T ss_pred eEEEecccCCCHHHHHHHHHHHHHHHhcCCEEEEEc---CCcCHHHHHHHHHHHHHcCCCEEEEecCCccccHHHHHHHH
Confidence 455653 467888889999999999998765432 222233344556666677899888876432 2345567777
Q ss_pred HcCc
Q 043276 100 EIGL 103 (829)
Q Consensus 100 ~~gm 103 (829)
+.|+
T Consensus 79 ~~~i 82 (275)
T cd06317 79 QAGI 82 (275)
T ss_pred HCCC
Confidence 7663
No 485
>KOG3603 consensus Predicted phospholipase D [General function prediction only]
Probab=24.13 E-value=1.9e+02 Score=31.99 Aligned_cols=91 Identities=14% Similarity=0.091 Sum_probs=50.3
Q ss_pred EEEEeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHH---HHHhhc------CCCeEEEEEcChhHHHHHHH
Q 043276 26 PIYVDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKE---LYKLFT------MQTRVFILHMLPSLGSRIFE 96 (829)
Q Consensus 26 iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~---l~~lk~------~~arViIv~~~~~~~~~i~~ 96 (829)
.||..+..--.+-+++++++- .|++|-+-..--.. ++..+... |+.|.. .+.|+|+|-.....-..+-+
T Consensus 303 ~~y~k~~~fw~iDdaiR~aa~-RgV~vR~lvs~~~~-~~~~m~~~L~SLq~l~~~~~~~~iqvk~f~VP~~~~~~ip~~R 380 (456)
T KOG3603|consen 303 TIYSKNHRFWEIDDAIRRAAV-RGVKVRLLVSCWKH-SEPSMFRFLRSLQDLSDPLENGSIQVKFFIVPQTNIEKIPFAR 380 (456)
T ss_pred heeecCcchhhhhHHHHHHhh-cceEEEEEEeccCC-CCchHHHHHHHHHHhcCccccCceEEEEEEeCCCccccCchhh
Confidence 356555444466667777666 89887665432111 22333344 444432 35677777654432223333
Q ss_pred HHHHcCccccCeEEEEcCcccc
Q 043276 97 KANEIGLMNKGCVWIMTDGMTN 118 (829)
Q Consensus 97 ~a~~~gm~~~~~vwI~t~~~~~ 118 (829)
..+..=|..+.-.+|+|..|.+
T Consensus 381 v~HnKymVTe~aayIGTSNws~ 402 (456)
T KOG3603|consen 381 VNHNKYMVTESAAYIGTSNWSG 402 (456)
T ss_pred hccceeEEeecceeeeccCCCc
Confidence 3333336667788999999975
No 486
>PRK10653 D-ribose transporter subunit RbsB; Provisional
Probab=23.92 E-value=3.4e+02 Score=28.39 Aligned_cols=80 Identities=9% Similarity=0.050 Sum_probs=52.1
Q ss_pred CcEEEEEEE--eCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcChh-HHHHHHHH
Q 043276 21 WREAVPIYV--DNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPS-LGSRIFEK 97 (829)
Q Consensus 21 W~~V~iI~~--dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~~~-~~~~i~~~ 97 (829)
=+.+++|.. ++.|.......+.+++++.|..+.... ...+.+.....++++.+.+++.+|+..... .....+..
T Consensus 26 ~~~I~vi~~~~~~~f~~~~~~~i~~~~~~~G~~~~~~~---~~~d~~~~~~~~~~l~~~~~dgiii~~~~~~~~~~~l~~ 102 (295)
T PRK10653 26 KDTIALVVSTLNNPFFVSLKDGAQKEADKLGYNLVVLD---SQNNPAKELANVQDLTVRGTKILLINPTDSDAVGNAVKM 102 (295)
T ss_pred CCeEEEEecCCCChHHHHHHHHHHHHHHHcCCeEEEec---CCCCHHHHHHHHHHHHHcCCCEEEEcCCChHHHHHHHHH
Confidence 567888875 466778889999999999998875431 121223344556666667888777765433 33355667
Q ss_pred HHHcCc
Q 043276 98 ANEIGL 103 (829)
Q Consensus 98 a~~~gm 103 (829)
+.+.|+
T Consensus 103 ~~~~~i 108 (295)
T PRK10653 103 ANQANI 108 (295)
T ss_pred HHHCCC
Confidence 777663
No 487
>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=23.90 E-value=3.4e+02 Score=27.75 Aligned_cols=76 Identities=12% Similarity=0.055 Sum_probs=48.6
Q ss_pred EEEEEE--eCccccchHHHHHHHHHh--CCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcChhH-HHHHHHHH
Q 043276 24 AVPIYV--DNQYGEELIPSLTDALQA--IDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSL-GSRIFEKA 98 (829)
Q Consensus 24 V~iI~~--dd~yG~~~~~~l~~~l~~--~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~~~~-~~~i~~~a 98 (829)
|++|.. ++.|-......+.+++++ .|.++... ....+.+...+.+..+...+++.+|++..... ....++.+
T Consensus 2 Ig~v~~~~~~~~~~~~~~gi~~~~~~~~~~~~~~~~---~~~~~~~~~~~~i~~~~~~~~dgiIi~~~~~~~~~~~i~~~ 78 (271)
T cd06321 2 IGVSVGDLGNPFFVALAKGAEAAAKKLNPGVKVTVV---SADYDLNKQVSQIDNFIAAKVDLILLNAVDSKGIAPAVKRA 78 (271)
T ss_pred eEEEecccCCHHHHHHHHHHHHHHHHhCCCeEEEEc---cCCCCHHHHHHHHHHHHHhCCCEEEEeCCChhHhHHHHHHH
Confidence 566664 467888889999999999 66665432 11222333445666666778888888754332 34566777
Q ss_pred HHcC
Q 043276 99 NEIG 102 (829)
Q Consensus 99 ~~~g 102 (829)
.+.|
T Consensus 79 ~~~~ 82 (271)
T cd06321 79 QAAG 82 (271)
T ss_pred HHCC
Confidence 7766
No 488
>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=23.86 E-value=4e+02 Score=27.09 Aligned_cols=75 Identities=13% Similarity=0.068 Sum_probs=48.3
Q ss_pred EEEEEE--eCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcChhHHHHHHHHHHHc
Q 043276 24 AVPIYV--DNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEI 101 (829)
Q Consensus 24 V~iI~~--dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~~~~~~~i~~~a~~~ 101 (829)
++++.. ++.|.......+.+++++.|.++..... ..+.+...+.+..+.+.+.+.+|+....... ..+.++.+.
T Consensus 2 i~vi~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~~---~~~~~~~~~~i~~l~~~~~dgiii~~~~~~~-~~~~~~~~~ 77 (270)
T cd06296 2 IGLVFPDLDSPWASEVLRGVEEAAAAAGYDVVLSES---GRRTSPERQWVERLSARRTDGVILVTPELTS-AQRAALRRT 77 (270)
T ss_pred eEEEECCCCCccHHHHHHHHHHHHHHcCCeEEEecC---CCchHHHHHHHHHHHHcCCCEEEEecCCCCh-HHHHHHhcC
Confidence 455553 4788888999999999999988754322 2122334456677777788888776543222 346666666
Q ss_pred C
Q 043276 102 G 102 (829)
Q Consensus 102 g 102 (829)
+
T Consensus 78 ~ 78 (270)
T cd06296 78 G 78 (270)
T ss_pred C
Confidence 5
No 489
>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=23.83 E-value=4.3e+02 Score=26.92 Aligned_cols=75 Identities=8% Similarity=0.049 Sum_probs=48.9
Q ss_pred EEEEE--EeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcChhHHHHHHHHHHHc
Q 043276 24 AVPIY--VDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEI 101 (829)
Q Consensus 24 V~iI~--~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~~~~~~~i~~~a~~~ 101 (829)
+++|. .++.|.......+.+++++.|..+..... . .+.+.-.+.+..+.+.+++.||+....... ..+.++.+.
T Consensus 2 igvi~p~~~~~~~~~~~~g~~~~a~~~g~~~~~~~~--~-~~~~~~~~~i~~~~~~~vdgii~~~~~~~~-~~~~~~~~~ 77 (268)
T cd06270 2 IGLVVSDLDGPFFGPLLSGVESVARKAGKHLIITAG--H-HSAEKEREAIEFLLERRCDALILHSKALSD-DELIELAAQ 77 (268)
T ss_pred EEEEEccccCcchHHHHHHHHHHHHHCCCEEEEEeC--C-CchHHHHHHHHHHHHcCCCEEEEecCCCCH-HHHHHHhhC
Confidence 45554 35777788889999999999988764322 1 122334456677777889999887653222 226677776
Q ss_pred C
Q 043276 102 G 102 (829)
Q Consensus 102 g 102 (829)
|
T Consensus 78 ~ 78 (268)
T cd06270 78 V 78 (268)
T ss_pred C
Confidence 6
No 490
>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=23.56 E-value=5.1e+02 Score=23.13 Aligned_cols=68 Identities=19% Similarity=0.143 Sum_probs=42.9
Q ss_pred eCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcCh----hHHHHHHHHHHHcCc
Q 043276 30 DNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLP----SLGSRIFEKANEIGL 103 (829)
Q Consensus 30 dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~~----~~~~~i~~~a~~~gm 103 (829)
.+|.-.-+...+...|+..|..+.+-.. ..+ ..+.+..+.+.++++|++++.. +.+..++.+.++.|.
T Consensus 8 ~gd~H~lG~~~~~~~l~~~G~~vi~lG~---~vp---~e~~~~~a~~~~~d~V~iS~~~~~~~~~~~~~~~~L~~~~~ 79 (122)
T cd02071 8 GLDGHDRGAKVIARALRDAGFEVIYTGL---RQT---PEEIVEAAIQEDVDVIGLSSLSGGHMTLFPEVIELLRELGA 79 (122)
T ss_pred CCChhHHHHHHHHHHHHHCCCEEEECCC---CCC---HHHHHHHHHHcCCCEEEEcccchhhHHHHHHHHHHHHhcCC
Confidence 3343344566777788999988776432 112 2345556667889999998754 345566666777663
No 491
>smart00852 MoCF_biosynth Probable molybdopterin binding domain. This domain is found a variety of proteins involved in biosynthesis of molybdopterin cofactor. The domain is presumed to bind molybdopterin. The structure of this domain is known, and it forms an alpha/beta structure. In the known structure of Gephyrin this domain mediates trimerisation.
Probab=23.55 E-value=3.2e+02 Score=24.85 Aligned_cols=50 Identities=14% Similarity=0.198 Sum_probs=37.1
Q ss_pred cchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcC
Q 043276 35 EELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHML 87 (829)
Q Consensus 35 ~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~ 87 (829)
......+.+.+++.|..+.....++++ .+.+.+.+.++.+ .+++||..+.
T Consensus 17 d~~~~~l~~~l~~~G~~~~~~~~v~Dd--~~~I~~~l~~~~~-~~dliittGG 66 (135)
T smart00852 17 DSNGPALAELLTELGIEVTRYVIVPDD--KEAIKEALREALE-RADLVITTGG 66 (135)
T ss_pred cCcHHHHHHHHHHCCCeEEEEEEeCCC--HHHHHHHHHHHHh-CCCEEEEcCC
Confidence 344678888899999988877777643 5578888877764 5788888764
No 492
>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=23.52 E-value=2.7e+02 Score=28.17 Aligned_cols=75 Identities=11% Similarity=-0.046 Sum_probs=48.2
Q ss_pred EEEEEEe--CccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcChhHHHHHHHHHHHc
Q 043276 24 AVPIYVD--NQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEI 101 (829)
Q Consensus 24 V~iI~~d--d~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~~~~~~~i~~~a~~~ 101 (829)
|++|..+ +.|.....+.+.+++++.|.++.... ...+.+...+.++++.+.+++.+|+...... ..++..+.+.
T Consensus 2 igvv~~~~~~~~~~~~~~gi~~~~~~~g~~~~~~~---~~~~~~~~~~~i~~l~~~~~dgii~~~~~~~-~~~~~~~~~~ 77 (259)
T cd01542 2 IGVIVPRLDSFSTSRTVKGILAALYENGYQMLLMN---TNFSIEKEIEALELLARQKVDGIILLATTIT-DEHREAIKKL 77 (259)
T ss_pred eEEEecCCccchHHHHHHHHHHHHHHCCCEEEEEe---CCCCHHHHHHHHHHHHhcCCCEEEEeCCCCC-HHHHHHHhcC
Confidence 5566543 56667888899999999998875432 2222334456677777788999988765322 2445555555
Q ss_pred C
Q 043276 102 G 102 (829)
Q Consensus 102 g 102 (829)
|
T Consensus 78 ~ 78 (259)
T cd01542 78 N 78 (259)
T ss_pred C
Confidence 5
No 493
>TIGR02136 ptsS_2 phosphate binding protein. Members of this family are phosphate-binding proteins. Most are found in phosphate ABC-transporter operons, but some are found in phosphate regulatory operons. This model separates members of the current family from the phosphate ABC transporter phosphate binding protein described by TIGRFAMs model TIGR00975.
Probab=23.27 E-value=94 Score=32.83 Aligned_cols=72 Identities=13% Similarity=0.069 Sum_probs=46.9
Q ss_pred eeHHHHHHHHHHCCCcccEEEEecCCCCCCCCCChhHHHHhHhcCcccEEEeccccccccc-----eecc-ccccccccc
Q 043276 340 YSIDVFKAVIEELPYAVAYDFVPYAQPDGTSSGSYNDLIYQVFLGEFDAVVGDTTIVFNRS-----NYVD-FTLPYTESG 413 (829)
Q Consensus 340 ~~idll~~ia~~l~f~~~~~~~~~~~~~g~~ng~~~~li~~l~~g~~Di~~~~~~it~~R~-----~~vd-ft~p~~~~~ 413 (829)
+-..++..+.++.+ .+++++.. ++..+++..|.+|++|+++..-....+.. +..+ -..|+....
T Consensus 49 ~lp~~l~~f~~~~P-~i~v~i~~---------~~s~~l~~~L~~G~iDlai~~~~~~~~~~~~~~~~~~~l~~~~l~~~~ 118 (287)
T TIGR02136 49 LAEAAAEEFQKIHP-GVSVTVQG---------AGSGTGIKALINGTVDIGNSSRPIKDEELQKDKQKGIKLIEHKVAVDG 118 (287)
T ss_pred HHHHHHHHHHhhCC-CceEEEcc---------CCchHHHHHHHcCCCchhhccCCCCHHHHHHHhhcCCCceEEEEEEee
Confidence 45677888888876 34555543 36799999999999999885432222210 0111 245888889
Q ss_pred eEEEEEcc
Q 043276 414 VSMIVPIK 421 (829)
Q Consensus 414 ~~~vv~~~ 421 (829)
++++++..
T Consensus 119 l~lvv~~~ 126 (287)
T TIGR02136 119 LAVVVNKK 126 (287)
T ss_pred EEEEECCC
Confidence 99998854
No 494
>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=23.09 E-value=3e+02 Score=28.01 Aligned_cols=75 Identities=9% Similarity=0.013 Sum_probs=48.5
Q ss_pred EEEEEE--eCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcChhHHHHHHHHHHHc
Q 043276 24 AVPIYV--DNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEI 101 (829)
Q Consensus 24 V~iI~~--dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~~~~~~~i~~~a~~~ 101 (829)
|++|.. ++.|.......+.+++++.|..+..... ..+.+...+.+..+...+++.+|+......... +.++.+.
T Consensus 2 igvi~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~---~~~~~~~~~~i~~l~~~~vdgiii~~~~~~~~~-~~~~~~~ 77 (264)
T cd06274 2 IGLIIPDLENRSFARIAKRLEALARERGYQLLIACS---DDDPETERETVETLIARQVDALIVAGSLPPDDP-YYLCQKA 77 (264)
T ss_pred EEEEeccccCchHHHHHHHHHHHHHHCCCEEEEEeC---CCCHHHHHHHHHHHHHcCCCEEEEcCCCCchHH-HHHHHhc
Confidence 455553 4677788888999999999988765422 212333446677777889998888764332222 5566666
Q ss_pred C
Q 043276 102 G 102 (829)
Q Consensus 102 g 102 (829)
|
T Consensus 78 ~ 78 (264)
T cd06274 78 G 78 (264)
T ss_pred C
Confidence 6
No 495
>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=22.99 E-value=3.1e+02 Score=27.89 Aligned_cols=75 Identities=9% Similarity=0.029 Sum_probs=49.1
Q ss_pred EEEEEE--eCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcChhHHHHHHHHHHHc
Q 043276 24 AVPIYV--DNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSLGSRIFEKANEI 101 (829)
Q Consensus 24 V~iI~~--dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~~~~~~~i~~~a~~~ 101 (829)
|++|.. ++.|.......+.+++++.|..+... ....+.....+.+..+.+.+++.+|+....... ..+.++.+.
T Consensus 2 igvi~p~~~~~~~~~~~~gi~~~~~~~~~~~~~~---~~~~~~~~~~~~i~~l~~~~~dgiii~~~~~~~-~~~~~~~~~ 77 (265)
T cd06285 2 IGVLVPRLTDTVMATMYEGIEEAAAERGYSTFVA---NTGDNPDAQRRAIEMLLDRRVDGLILGDARSDD-HFLDELTRR 77 (265)
T ss_pred EEEEeCCCCCccHHHHHHHHHHHHHHCCCEEEEE---eCCCCHHHHHHHHHHHHHcCCCEEEEecCCCCh-HHHHHHHHc
Confidence 566664 46777888899999999999886432 222222344456677777889988887543332 346677766
Q ss_pred C
Q 043276 102 G 102 (829)
Q Consensus 102 g 102 (829)
|
T Consensus 78 ~ 78 (265)
T cd06285 78 G 78 (265)
T ss_pred C
Confidence 6
No 496
>PF01936 NYN: NYN domain; InterPro: IPR021139 This highly conserved domain has no known function. However it contains many conserved aspartates, suggesting an enzymatic function such as an endonuclease or glycosyl hydrolase.; PDB: 2QIP_A.
Probab=22.97 E-value=4.4e+02 Score=23.97 Aligned_cols=100 Identities=15% Similarity=0.145 Sum_probs=46.6
Q ss_pred HHHHHHHHHHHcCCcEEEEEEEeCccccchHHHHHHHHHhCCceeeeEEec-----CCCCChhHHHHHHH-HhhcCCCeE
Q 043276 8 QVGAITAIIKAFGWREAVPIYVDNQYGEELIPSLTDALQAIDTRVPYRSVI-----SPLATDDQIEKELY-KLFTMQTRV 81 (829)
Q Consensus 8 q~~ai~~ll~~fgW~~V~iI~~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i-----~~~~~~~~~~~~l~-~lk~~~arV 81 (829)
....+.+.+...|--....+|.+ ........+.+.|+..|+.+...... .....+..+...+. ...+.....
T Consensus 21 ~~~~l~~~i~~~~~~~~~~~y~~--~~~~~~~~~~~~L~~~g~~v~~~~~~~~~~~~k~~~D~~l~~d~~~~~~~~~~d~ 98 (146)
T PF01936_consen 21 DFERLLEEIRKYGPLVRIRAYGN--WDDPNQKSFQEALQRAGIKVRHFPLRKRGGGGKKGVDVALAVDILELAYENPPDT 98 (146)
T ss_dssp -HHHHHHHHTTTEEEEEEEEEE------HHHHHHHHHHHHHT-EEEE------S---S---HHHHHHHHHHHG--GG-SE
T ss_pred CHHHHHHHHHhcCCeEEEEEEee--ccccchhhHHHHHHhCeeeEEeeecccccccccCCcHHHHHHHHHHHhhccCCCE
Confidence 34455555555433222333433 22233577788899999876544331 11222223333333 332233477
Q ss_pred EEEEcChhHHHHHHHHHHHcCccccCeEEEEc
Q 043276 82 FILHMLPSLGSRIFEKANEIGLMNKGCVWIMT 113 (829)
Q Consensus 82 iIv~~~~~~~~~i~~~a~~~gm~~~~~vwI~t 113 (829)
+|+.+...+...+++.+++.| ..|++++
T Consensus 99 ivLvSgD~Df~~~v~~l~~~g----~~V~v~~ 126 (146)
T PF01936_consen 99 IVLVSGDSDFAPLVRKLRERG----KRVIVVG 126 (146)
T ss_dssp EEEE---GGGHHHHHHHHHH------EEEEEE
T ss_pred EEEEECcHHHHHHHHHHHHcC----CEEEEEE
Confidence 777777778888999999887 3577776
No 497
>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=22.92 E-value=8.1e+02 Score=24.89 Aligned_cols=96 Identities=11% Similarity=0.071 Sum_probs=51.2
Q ss_pred HHHHHHHHHHHHc--CCcEEEEEEEeCc--cccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeE-
Q 043276 7 SQVGAITAIIKAF--GWREAVPIYVDNQ--YGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRV- 81 (829)
Q Consensus 7 ~q~~ai~~ll~~f--gW~~V~iI~~dd~--yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arV- 81 (829)
.-+..+++.+... +=.+++++..... ....-.+.+.+++++.|+++... .. ...+.++....+.++.+...++
T Consensus 104 ~~g~~a~~~l~~~~~~g~~~~~~~~~~~~~~~~~R~~gf~~~~~~~~~~~~~~-~~-~~~~~~~~~~~~~~~l~~~~~~~ 181 (271)
T cd06314 104 AAGRTAGEIMKKALPGGGKVAIFVGSLGADNAKERIQGIKDAIKDSKIEIVDT-RG-DEEDFAKAKSNAEDALNAHPDLK 181 (271)
T ss_pred HHHHHHHHHHHHHcCCCCEEEEEecCCCCCCHHHHHHHHHHHHhcCCcEEEEE-ec-CccCHHHHHHHHHHHHHhCCCcc
Confidence 3445666666443 2345666664322 23455677888898888876432 11 1112223344555544333322
Q ss_pred EEEEcChhHHHHHHHHHHHcCcc
Q 043276 82 FILHMLPSLGSRIFEKANEIGLM 104 (829)
Q Consensus 82 iIv~~~~~~~~~i~~~a~~~gm~ 104 (829)
.|++++...+..++..+++.|+.
T Consensus 182 ~i~~~~d~~a~~~~~al~~~g~~ 204 (271)
T cd06314 182 CMFGLYAYNGPAIAEAVKAAGKL 204 (271)
T ss_pred EEEecCCccHHHHHHHHHHcCCC
Confidence 33444555666677888888863
No 498
>PRK10355 xylF D-xylose transporter subunit XylF; Provisional
Probab=22.86 E-value=3.8e+02 Score=28.83 Aligned_cols=78 Identities=8% Similarity=0.060 Sum_probs=53.2
Q ss_pred cEEEEEE--EeCccccchHHHHHHHHHhCCceeeeEEecCCCCChhHHHHHHHHhhcCCCeEEEEEcChhH-HHHHHHHH
Q 043276 22 REAVPIY--VDNQYGEELIPSLTDALQAIDTRVPYRSVISPLATDDQIEKELYKLFTMQTRVFILHMLPSL-GSRIFEKA 98 (829)
Q Consensus 22 ~~V~iI~--~dd~yG~~~~~~l~~~l~~~gi~I~~~~~i~~~~~~~~~~~~l~~lk~~~arViIv~~~~~~-~~~i~~~a 98 (829)
..|+++. .++.|.....+.+.+++++.|..+... ....+.+...+.+..+.+.+++.+|+...... ....+..+
T Consensus 26 ~~Ig~i~~~~~~~f~~~~~~gi~~~a~~~g~~l~i~---~~~~~~~~~~~~i~~l~~~~vDGiIi~~~~~~~~~~~l~~~ 102 (330)
T PRK10355 26 VKIGMAIDDLRLERWQKDRDIFVKKAESLGAKVFVQ---SANGNEETQMSQIENMINRGVDVLVIIPYNGQVLSNVIKEA 102 (330)
T ss_pred ceEEEEecCCCchHHHHHHHHHHHHHHHcCCEEEEE---CCCCCHHHHHHHHHHHHHcCCCEEEEeCCChhhHHHHHHHH
Confidence 4566665 457888999999999999999887643 22222334556677787889999998764322 23455666
Q ss_pred HHcC
Q 043276 99 NEIG 102 (829)
Q Consensus 99 ~~~g 102 (829)
.+.|
T Consensus 103 ~~~~ 106 (330)
T PRK10355 103 KQEG 106 (330)
T ss_pred HHCC
Confidence 6655
No 499
>PF03908 Sec20: Sec20; InterPro: IPR005606 Sec20 is a membrane glycoprotein associated with secretory pathway.
Probab=22.85 E-value=89 Score=26.62 Aligned_cols=23 Identities=26% Similarity=0.397 Sum_probs=17.6
Q ss_pred hHHHHHHHHHHHHHHHHHhhhcc
Q 043276 438 DLWVTSGCFFIFIGFVVWVLEHR 460 (829)
Q Consensus 438 ~vW~~i~~~~~~~~~v~~~~~~~ 460 (829)
+-|+..+++++++++++|++.+|
T Consensus 69 D~~li~~~~~~f~~~v~yI~~rR 91 (92)
T PF03908_consen 69 DRILIFFAFLFFLLVVLYILWRR 91 (92)
T ss_pred hHHHHHHHHHHHHHHHHHHhhhc
Confidence 45677778888888888888765
No 500
>PRK13209 L-xylulose 5-phosphate 3-epimerase; Reviewed
Probab=22.84 E-value=6.3e+02 Score=26.23 Aligned_cols=94 Identities=19% Similarity=0.080 Sum_probs=0.0
Q ss_pred HHHHHHHHHcCCcEEEEEEEe-------CccccchHHHHHHHHHhCCceeeeEEe-----cCCCCChhH--------HHH
Q 043276 10 GAITAIIKAFGWREAVPIYVD-------NQYGEELIPSLTDALQAIDTRVPYRSV-----ISPLATDDQ--------IEK 69 (829)
Q Consensus 10 ~ai~~ll~~fgW~~V~iI~~d-------d~yG~~~~~~l~~~l~~~gi~I~~~~~-----i~~~~~~~~--------~~~ 69 (829)
.-..+.++..|++.|-+-..+ .++.....+.+.+.+++.|+.|..... ++....++. +.+
T Consensus 24 ~e~~~~~~~~G~~~iEl~~~~~~~~~~~~~~~~~~~~~l~~~l~~~gl~i~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~ 103 (283)
T PRK13209 24 LEKLAIAKTAGFDFVEMSVDESDERLARLDWSREQRLALVNALVETGFRVNSMCLSAHRRFPLGSEDDAVRAQALEIMRK 103 (283)
T ss_pred HHHHHHHHHcCCCeEEEecCccccchhccCCCHHHHHHHHHHHHHcCCceeEEecccccccCCCCCCHHHHHHHHHHHHH
Q ss_pred HHHHhhcCCCeEEEEEcC---------------hhHHHHHHHHHHHcCc
Q 043276 70 ELYKLFTMQTRVFILHML---------------PSLGSRIFEKANEIGL 103 (829)
Q Consensus 70 ~l~~lk~~~arViIv~~~---------------~~~~~~i~~~a~~~gm 103 (829)
.+...+..+++++++.+. .+....+...|.+.|+
T Consensus 104 ~i~~a~~lG~~~i~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~A~~~GV 152 (283)
T PRK13209 104 AIQLAQDLGIRVIQLAGYDVYYEQANNETRRRFIDGLKESVELASRASV 152 (283)
T ss_pred HHHHHHHcCCCEEEECCccccccccHHHHHHHHHHHHHHHHHHHHHhCC
Done!