Query 005717
Match_columns 681
No_of_seqs 458 out of 3141
Neff 8.8
Searched_HMMs 46136
Date Thu Mar 28 12:41:39 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/005717.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/005717hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1054 Glutamate-gated AMPA-t 100.0 1.6E-86 3.4E-91 681.1 33.3 565 3-588 233-845 (897)
2 KOG4440 NMDA selective glutama 100.0 9.7E-72 2.1E-76 574.5 23.0 532 1-588 249-857 (993)
3 KOG1052 Glutamate-gated kainat 100.0 1.2E-68 2.7E-73 616.3 50.9 549 1-588 38-624 (656)
4 KOG1053 Glutamate-gated NMDA-t 100.0 2.1E-66 4.5E-71 553.5 40.7 530 1-585 256-853 (1258)
5 cd06390 PBP1_iGluR_AMPA_GluR1 99.9 1.3E-26 2.9E-31 247.1 16.7 163 1-166 196-363 (364)
6 cd06387 PBP1_iGluR_AMPA_GluR3 99.9 1.6E-26 3.4E-31 246.1 16.6 163 1-166 204-371 (372)
7 cd06391 PBP1_iGluR_delta_2 N-t 99.9 6.7E-25 1.5E-29 236.6 15.4 162 1-167 224-399 (400)
8 cd06392 PBP1_iGluR_delta_1 N-t 99.9 3.9E-24 8.4E-29 228.7 15.9 162 1-167 224-399 (400)
9 PRK10797 glutamate and asparta 99.9 2.4E-21 5.1E-26 201.8 22.1 223 195-537 40-272 (302)
10 PRK09495 glnH glutamine ABC tr 99.9 2.7E-21 5.9E-26 196.2 21.8 219 195-537 25-244 (247)
11 cd06388 PBP1_iGluR_AMPA_GluR4 99.9 2.1E-21 4.6E-26 208.0 16.0 163 1-167 203-370 (371)
12 PF00497 SBP_bac_3: Bacterial 99.9 3.8E-21 8.3E-26 191.3 15.4 222 197-537 1-225 (225)
13 PRK11260 cystine transporter s 99.9 2.7E-20 5.9E-25 191.1 22.1 221 195-537 41-262 (266)
14 cd06389 PBP1_iGluR_AMPA_GluR2 99.9 5.1E-21 1.1E-25 205.4 17.1 164 1-167 201-369 (370)
15 PRK15010 ABC transporter lysin 99.8 1.3E-19 2.8E-24 185.4 22.7 223 194-537 25-255 (260)
16 PRK11917 bifunctional adhesin/ 99.8 1.7E-19 3.6E-24 184.1 21.3 217 195-535 38-258 (259)
17 PRK15007 putative ABC transpor 99.8 1.9E-19 4.1E-24 182.2 21.3 216 195-536 21-242 (243)
18 TIGR02995 ectoine_ehuB ectoine 99.8 2.7E-19 5.9E-24 184.5 21.0 223 195-536 33-261 (275)
19 TIGR01096 3A0103s03R lysine-ar 99.8 3.3E-19 7E-24 181.3 21.2 218 195-535 24-250 (250)
20 cd06393 PBP1_iGluR_Kainate_Glu 99.8 6.5E-20 1.4E-24 198.5 15.5 158 1-167 217-382 (384)
21 PRK15437 histidine ABC transpo 99.8 2E-18 4.3E-23 176.5 21.2 223 194-537 25-255 (259)
22 PRK10859 membrane-bound lytic 99.8 2.9E-18 6.2E-23 190.0 20.3 220 195-537 43-267 (482)
23 cd06380 PBP1_iGluR_AMPA N-term 99.8 1.6E-18 3.4E-23 187.8 16.5 166 1-166 208-381 (382)
24 PRK09959 hybrid sensory histid 99.8 9.8E-18 2.1E-22 207.4 22.4 217 195-537 302-521 (1197)
25 PF00060 Lig_chan: Ligand-gate 99.8 1.4E-19 3E-24 168.5 1.4 107 316-422 1-115 (148)
26 TIGR03870 ABC_MoxJ methanol ox 99.7 1.8E-16 4E-21 160.5 18.2 208 196-534 1-241 (246)
27 COG0834 HisJ ABC-type amino ac 99.7 3.1E-16 6.8E-21 161.5 19.8 224 195-537 34-265 (275)
28 cd06379 PBP1_iGluR_NMDA_NR1 N- 99.7 6.3E-17 1.4E-21 174.8 14.2 138 1-188 238-377 (377)
29 cd06378 PBP1_iGluR_NMDA_NR2 N- 99.7 8.2E-17 1.8E-21 171.7 12.9 141 1-188 218-362 (362)
30 cd06367 PBP1_iGluR_NMDA N-term 99.7 1.9E-16 4E-21 170.3 14.3 129 1-162 219-351 (362)
31 PRK09959 hybrid sensory histid 99.7 3.3E-16 7.2E-21 193.9 18.5 219 195-537 56-278 (1197)
32 TIGR02285 conserved hypothetic 99.7 5.2E-16 1.1E-20 159.4 16.9 230 194-537 17-262 (268)
33 smart00062 PBPb Bacterial peri 99.7 1.8E-15 4E-20 148.3 19.7 215 196-535 1-219 (219)
34 cd00134 PBPb Bacterial peripla 99.7 4.5E-15 9.8E-20 145.7 20.8 214 197-535 1-218 (218)
35 cd06381 PBP1_iGluR_delta_like 99.7 4.2E-16 9E-21 166.5 12.9 127 1-166 224-362 (363)
36 TIGR03871 ABC_peri_MoxJ_2 quin 99.7 4E-15 8.6E-20 149.5 19.3 212 196-535 1-228 (232)
37 cd06374 PBP1_mGluR_groupI Liga 99.5 1.1E-13 2.5E-18 153.8 14.7 157 2-168 270-469 (472)
38 cd06377 PBP1_iGluR_NMDA_NR3 N- 99.5 1.6E-13 3.4E-18 144.8 14.1 95 68-167 269-375 (382)
39 cd06376 PBP1_mGluR_groupIII Li 99.5 5.7E-13 1.2E-17 147.9 16.3 149 5-162 259-452 (463)
40 PF01094 ANF_receptor: Recepto 99.5 4.7E-13 1E-17 142.6 13.8 139 1-150 204-348 (348)
41 smart00079 PBPe Eukaryotic hom 99.5 5.4E-13 1.2E-17 121.7 11.7 122 411-536 1-133 (134)
42 cd06386 PBP1_NPR_C_like Ligand 99.4 4.7E-13 1E-17 145.0 12.9 140 1-162 219-378 (387)
43 cd06365 PBP1_Pheromone_recepto 99.4 7.5E-13 1.6E-17 146.8 14.5 152 2-162 255-452 (469)
44 cd06385 PBP1_NPR_A Ligand-bind 99.4 7.3E-13 1.6E-17 144.6 14.0 145 1-164 227-392 (405)
45 cd06372 PBP1_GC_G_like Ligand- 99.4 1E-12 2.2E-17 142.8 13.9 145 1-164 221-387 (391)
46 cd06394 PBP1_iGluR_Kainate_KA1 99.4 1.4E-13 3E-18 144.7 6.3 119 1-167 211-332 (333)
47 cd06383 PBP1_iGluR_AMPA_Like N 99.4 7.1E-14 1.5E-18 149.6 4.0 140 1-144 210-355 (368)
48 cd06362 PBP1_mGluR Ligand bind 99.4 2E-12 4.4E-17 143.2 15.4 154 4-166 257-450 (452)
49 cd06384 PBP1_NPR_B Ligand-bind 99.4 3E-12 6.6E-17 139.4 12.6 144 1-163 227-392 (399)
50 COG4623 Predicted soluble lyti 99.4 1.4E-11 3E-16 123.9 15.3 220 195-537 23-248 (473)
51 cd06382 PBP1_iGluR_Kainate N-t 99.3 1.8E-12 3.8E-17 137.4 8.4 118 1-166 206-326 (327)
52 KOG1055 GABA-B ion channel rec 99.3 9.5E-13 2.1E-17 143.3 5.5 173 1-195 258-451 (865)
53 cd06361 PBP1_GPC6A_like Ligand 99.3 5.9E-11 1.3E-15 129.0 14.5 133 4-167 259-398 (403)
54 cd06373 PBP1_NPR_like Ligand b 99.2 4.8E-11 1E-15 129.9 11.7 144 1-163 226-389 (396)
55 cd06364 PBP1_CaSR Ligand-bindi 99.2 2.5E-10 5.4E-15 127.8 16.7 153 4-162 270-493 (510)
56 cd06371 PBP1_sensory_GC_DEF_li 99.2 1.2E-10 2.5E-15 126.0 13.2 140 1-161 218-370 (382)
57 cd06375 PBP1_mGluR_groupII Lig 99.2 2.5E-10 5.3E-15 126.3 15.4 148 6-162 259-454 (458)
58 cd06368 PBP1_iGluR_non_NMDA_li 99.1 1.3E-10 2.8E-15 122.9 9.4 116 1-166 205-323 (324)
59 cd06363 PBP1_Taste_receptor Li 99.1 6.5E-10 1.4E-14 121.6 15.1 129 5-163 261-396 (410)
60 cd06352 PBP1_NPR_GC_like Ligan 99.1 4E-10 8.7E-15 122.4 12.9 146 1-165 219-384 (389)
61 cd06370 PBP1_Speract_GC_like L 99.1 3.4E-10 7.3E-15 123.5 11.2 110 24-153 266-385 (404)
62 cd06366 PBP1_GABAb_receptor Li 99.1 3.2E-10 6.9E-15 121.3 9.5 122 1-167 217-347 (350)
63 cd06351 PBP1_iGluR_N_LIVBP_lik 99.0 6E-10 1.3E-14 117.7 8.8 110 1-162 211-322 (328)
64 TIGR01098 3A0109s03R phosphate 99.0 8.2E-09 1.8E-13 105.1 14.3 200 194-520 31-254 (254)
65 PF10613 Lig_chan-Glu_bd: Liga 98.9 3.4E-10 7.3E-15 87.1 1.2 46 218-263 13-65 (65)
66 PRK00489 hisG ATP phosphoribos 98.9 1.2E-08 2.7E-13 105.4 11.3 170 244-537 46-220 (287)
67 KOG1056 Glutamate-gated metabo 98.8 2.8E-08 6.1E-13 112.5 13.2 152 5-165 280-474 (878)
68 cd06342 PBP1_ABC_LIVBP_like Ty 98.5 7.2E-07 1.6E-11 94.6 10.4 95 25-149 236-334 (334)
69 cd06369 PBP1_GC_C_enterotoxin_ 98.3 4.6E-06 1E-10 86.6 11.8 130 3-163 231-365 (380)
70 TIGR03431 PhnD phosphonate ABC 98.3 2.2E-05 4.8E-10 81.4 16.3 119 411-532 126-260 (288)
71 PRK15404 leucine ABC transport 98.2 8.2E-06 1.8E-10 87.9 10.7 100 25-153 262-363 (369)
72 cd06345 PBP1_ABC_ligand_bindin 97.8 6.2E-05 1.3E-09 80.2 8.6 87 25-141 246-338 (344)
73 cd06338 PBP1_ABC_ligand_bindin 97.8 6.4E-05 1.4E-09 80.1 8.8 92 26-148 244-344 (345)
74 cd06348 PBP1_ABC_ligand_bindin 97.8 0.0001 2.3E-09 78.5 10.2 101 25-145 238-342 (344)
75 cd06332 PBP1_aromatic_compound 97.7 0.00014 3E-09 77.0 9.7 91 24-142 233-327 (333)
76 cd06360 PBP1_alkylbenzenes_lik 97.7 0.00013 2.8E-09 77.3 9.5 92 25-144 237-332 (336)
77 cd06357 PBP1_AmiC Periplasmic 97.6 0.00035 7.5E-09 75.1 10.4 97 25-149 237-337 (360)
78 cd06359 PBP1_Nba_like Type I p 97.5 0.00042 9E-09 73.5 10.0 88 25-140 234-325 (333)
79 PF13458 Peripla_BP_6: Peripla 97.5 0.00049 1.1E-08 73.0 10.3 99 25-151 238-340 (343)
80 TIGR03669 urea_ABC_arch urea A 97.4 0.00098 2.1E-08 71.9 11.8 108 26-161 236-349 (374)
81 cd06344 PBP1_ABC_ligand_bindin 97.4 0.00035 7.5E-09 74.1 7.5 88 25-142 237-327 (332)
82 PF12974 Phosphonate-bd: ABC t 97.3 0.0023 5.1E-08 64.5 12.5 122 410-534 95-230 (243)
83 cd06355 PBP1_FmdD_like Peripla 97.3 0.0013 2.8E-08 70.3 10.7 97 26-150 237-337 (348)
84 cd06347 PBP1_ABC_ligand_bindin 97.3 0.00092 2E-08 70.6 9.4 90 25-143 237-330 (334)
85 cd06331 PBP1_AmiC_like Type I 97.2 0.00084 1.8E-08 71.2 8.0 87 26-140 236-326 (333)
86 PRK11553 alkanesulfonate trans 97.2 0.0029 6.3E-08 66.5 12.0 71 411-483 120-194 (314)
87 cd06350 PBP1_GPCR_family_C_lik 97.1 0.0011 2.4E-08 70.7 7.8 93 3-163 243-340 (348)
88 TIGR03407 urea_ABC_UrtA urea A 97.1 0.0031 6.8E-08 67.6 11.0 97 26-150 238-338 (359)
89 cd06329 PBP1_SBP_like_3 Peripl 97.0 0.0025 5.3E-08 67.9 9.4 81 25-135 246-329 (342)
90 cd06358 PBP1_NHase Type I peri 96.9 0.0037 8.1E-08 66.2 9.5 87 26-138 235-324 (333)
91 cd06340 PBP1_ABC_ligand_bindin 96.9 0.0031 6.7E-08 67.3 8.4 89 25-142 247-342 (347)
92 TIGR01729 taurine_ABC_bnd taur 96.8 0.0079 1.7E-07 62.7 10.7 69 411-481 91-163 (300)
93 cd06327 PBP1_SBP_like_1 Peripl 96.8 0.0038 8.2E-08 66.2 8.4 88 25-142 237-330 (334)
94 cd06328 PBP1_SBP_like_2 Peripl 96.8 0.0044 9.6E-08 65.7 8.8 81 26-135 239-320 (333)
95 COG3221 PhnD ABC-type phosphat 96.7 0.031 6.7E-07 57.7 13.6 112 409-522 133-260 (299)
96 cd06336 PBP1_ABC_ligand_bindin 96.6 0.0061 1.3E-07 65.0 7.8 91 25-144 241-344 (347)
97 cd06349 PBP1_ABC_ligand_bindin 96.5 0.015 3.3E-07 61.6 10.4 95 26-152 237-338 (340)
98 cd06330 PBP1_Arsenic_SBP_like 96.5 0.0091 2E-07 63.5 8.5 105 5-136 223-332 (346)
99 cd06337 PBP1_ABC_ligand_bindin 96.4 0.0077 1.7E-07 64.5 7.4 95 27-152 252-355 (357)
100 cd06346 PBP1_ABC_ligand_bindin 96.4 0.0047 1E-07 64.8 5.5 69 25-145 239-309 (312)
101 cd06356 PBP1_Amide_Urea_BP_lik 96.3 0.014 3E-07 61.9 8.9 83 25-134 235-320 (334)
102 COG0683 LivK ABC-type branched 96.3 0.017 3.7E-07 62.1 9.1 86 41-153 268-356 (366)
103 TIGR03427 ABC_peri_uca ABC tra 96.2 0.013 2.8E-07 61.7 7.4 69 412-482 98-170 (328)
104 TIGR03863 PQQ_ABC_bind ABC tra 95.8 0.026 5.6E-07 60.1 7.8 71 41-141 232-308 (347)
105 cd06343 PBP1_ABC_ligand_bindin 95.7 0.062 1.4E-06 57.5 10.7 103 25-153 247-361 (362)
106 PF13379 NMT1_2: NMT1-like fam 95.6 0.044 9.6E-07 55.5 8.5 72 411-483 105-188 (252)
107 PF09084 NMT1: NMT1/THI5 like; 95.6 0.051 1.1E-06 53.4 8.6 58 411-470 84-145 (216)
108 PF07885 Ion_trans_2: Ion chan 95.5 0.071 1.5E-06 43.3 7.6 56 349-404 21-78 (79)
109 TIGR02122 TRAP_TAXI TRAP trans 95.4 0.12 2.6E-06 54.3 11.1 59 411-472 132-197 (320)
110 TIGR01728 SsuA_fam ABC transpo 95.3 0.12 2.6E-06 53.0 10.6 71 411-483 92-166 (288)
111 cd08468 PBP2_Pa0477 The C-term 95.3 0.71 1.5E-05 44.1 15.3 73 225-302 13-85 (202)
112 TIGR00363 lipoprotein, YaeC fa 94.8 1.1 2.4E-05 45.4 15.6 122 410-534 106-250 (258)
113 cd05466 PBP2_LTTR_substrate Th 94.8 1.4 2.9E-05 41.0 15.6 70 225-302 13-82 (197)
114 PF03466 LysR_substrate: LysR 94.5 0.85 1.8E-05 43.6 13.7 183 225-522 19-206 (209)
115 cd06339 PBP1_YraM_LppC_lipopro 94.4 0.078 1.7E-06 56.2 6.4 76 26-140 251-330 (336)
116 TIGR00787 dctP tripartite ATP- 94.1 0.15 3.3E-06 51.8 7.5 105 410-523 126-233 (257)
117 cd08459 PBP2_DntR_NahR_LinR_li 93.9 1.7 3.7E-05 41.1 14.4 70 225-302 13-82 (201)
118 cd08463 PBP2_DntR_like_4 The C 93.8 3.3 7.2E-05 39.6 16.2 71 225-302 13-83 (203)
119 cd06335 PBP1_ABC_ligand_bindin 93.6 0.27 5.9E-06 52.3 8.8 85 26-134 240-332 (347)
120 cd08418 PBP2_TdcA The C-termin 93.6 3.1 6.6E-05 39.2 15.5 71 225-301 13-83 (201)
121 PF13433 Peripla_BP_5: Peripla 93.5 0.45 9.8E-06 50.2 9.8 81 26-134 238-321 (363)
122 cd08417 PBP2_Nitroaromatics_li 93.4 2.6 5.7E-05 39.7 14.6 70 225-302 13-82 (200)
123 cd08462 PBP2_NodD The C-termin 93.1 2.8 6.1E-05 39.8 14.4 69 225-302 13-81 (200)
124 PRK11480 tauA taurine transpor 93.0 0.46 9.9E-06 50.0 9.1 64 411-477 113-181 (320)
125 PRK11151 DNA-binding transcrip 92.6 3.8 8.3E-05 42.5 15.6 83 195-302 91-173 (305)
126 cd08421 PBP2_LTTR_like_1 The C 92.3 6.3 0.00014 36.9 15.6 70 225-302 13-82 (198)
127 cd06341 PBP1_ABC_ligand_bindin 92.1 0.56 1.2E-05 49.6 8.5 81 25-130 234-318 (341)
128 PRK11063 metQ DL-methionine tr 91.9 4.8 0.0001 41.2 14.7 121 411-534 120-263 (271)
129 cd06334 PBP1_ABC_ligand_bindin 91.7 0.65 1.4E-05 49.6 8.5 100 25-135 241-343 (351)
130 cd08461 PBP2_DntR_like_3 The C 91.6 7.2 0.00016 36.6 15.1 69 225-301 13-81 (198)
131 cd08460 PBP2_DntR_like_1 The C 91.6 3.9 8.4E-05 38.7 13.2 69 225-302 13-81 (200)
132 cd06326 PBP1_STKc_like Type I 91.5 0.61 1.3E-05 49.1 8.0 88 26-140 238-330 (336)
133 PF03480 SBP_bac_7: Bacterial 91.4 2.5 5.4E-05 43.6 12.2 105 409-522 125-232 (286)
134 cd08433 PBP2_Nac The C-teminal 91.1 9.3 0.0002 35.8 15.3 70 225-302 13-82 (198)
135 PF13531 SBP_bac_11: Bacterial 91.1 2 4.4E-05 42.5 10.9 193 225-533 11-226 (230)
136 cd08426 PBP2_LTTR_like_5 The C 90.9 8.7 0.00019 36.0 14.9 70 225-302 13-82 (199)
137 PRK12679 cbl transcriptional r 90.9 6.5 0.00014 41.1 15.0 209 195-537 93-307 (316)
138 cd08440 PBP2_LTTR_like_4 TThe 90.7 11 0.00025 34.8 15.4 70 225-302 13-82 (197)
139 cd08466 PBP2_LeuO The C-termin 90.7 9.6 0.00021 35.8 15.0 70 225-302 13-82 (200)
140 cd08442 PBP2_YofA_SoxR_like Th 90.7 9.6 0.00021 35.4 14.8 69 225-301 13-81 (193)
141 cd08465 PBP2_ToxR The C-termin 90.6 5.1 0.00011 38.0 13.0 70 225-302 13-82 (200)
142 cd08419 PBP2_CbbR_RubisCO_like 90.6 14 0.00031 34.3 16.0 69 225-301 12-80 (197)
143 CHL00180 rbcR LysR transcripti 90.5 9 0.0002 39.7 15.6 86 195-302 95-180 (305)
144 cd08464 PBP2_DntR_like_2 The C 90.2 9.4 0.0002 35.8 14.4 69 225-301 13-81 (200)
145 PRK12684 transcriptional regul 90.1 11 0.00023 39.4 15.9 206 195-535 93-304 (313)
146 PF12727 PBP_like: PBP superfa 90.1 4.9 0.00011 38.8 12.1 103 411-520 82-192 (193)
147 cd08438 PBP2_CidR The C-termin 90.1 14 0.0003 34.3 15.4 70 225-302 13-82 (197)
148 cd08412 PBP2_PAO1_like The C-t 90.0 13 0.00027 34.7 15.1 71 224-302 12-82 (198)
149 PRK11242 DNA-binding transcrip 90.0 7.9 0.00017 39.8 14.6 70 225-302 104-173 (296)
150 PRK10341 DNA-binding transcrip 90.0 6.4 0.00014 41.1 14.0 72 225-302 110-181 (312)
151 TIGR01256 modA molybdenum ABC 89.6 6.6 0.00014 38.4 13.0 71 451-523 135-206 (216)
152 PRK11233 nitrogen assimilation 89.5 7.6 0.00017 40.3 14.1 69 225-301 105-173 (305)
153 cd08434 PBP2_GltC_like The sub 89.4 12 0.00026 34.7 14.4 70 225-302 13-82 (195)
154 PRK09791 putative DNA-binding 89.2 10 0.00022 39.2 14.7 85 195-302 95-179 (302)
155 cd08413 PBP2_CysB_like The C-t 89.1 7.3 0.00016 36.8 12.7 71 225-302 13-83 (198)
156 cd08441 PBP2_MetR The C-termin 88.7 14 0.00029 34.7 14.3 68 226-301 14-81 (198)
157 cd08414 PBP2_LTTR_aromatics_li 88.6 17 0.00037 33.7 14.8 70 225-302 13-82 (197)
158 cd08469 PBP2_PnbR The C-termin 88.4 12 0.00025 36.1 13.8 70 225-302 13-82 (221)
159 cd08467 PBP2_SyrM The C-termin 88.3 18 0.00038 34.2 14.8 70 225-302 13-82 (200)
160 cd08411 PBP2_OxyR The C-termin 88.2 17 0.00037 34.0 14.6 70 225-302 14-83 (200)
161 cd06269 PBP1_glutamate_recepto 88.1 0.3 6.5E-06 50.0 2.3 26 137-162 265-291 (298)
162 PRK12682 transcriptional regul 87.9 15 0.00033 38.1 15.1 71 225-302 106-176 (309)
163 cd08435 PBP2_GbpR The C-termin 87.4 25 0.00053 32.7 16.6 72 225-302 13-84 (201)
164 cd08444 PBP2_Cbl The C-termina 87.1 26 0.00057 32.9 15.3 71 225-302 13-83 (198)
165 cd08420 PBP2_CysL_like C-termi 86.9 23 0.00049 32.9 14.6 70 225-302 13-82 (201)
166 TIGR02424 TF_pcaQ pca operon t 86.9 17 0.00037 37.4 14.7 85 195-302 93-177 (300)
167 cd08423 PBP2_LTTR_like_6 The C 86.9 23 0.0005 32.9 14.7 73 225-302 13-87 (200)
168 cd08425 PBP2_CynR The C-termin 86.6 18 0.00039 33.7 13.7 70 225-302 14-83 (197)
169 cd08415 PBP2_LysR_opines_like 86.6 19 0.0004 33.5 13.8 69 225-301 13-81 (196)
170 PRK10837 putative DNA-binding 85.9 31 0.00066 35.2 15.9 83 195-302 89-171 (290)
171 cd08429 PBP2_NhaR The C-termin 85.7 33 0.00072 32.6 15.8 71 225-300 13-83 (204)
172 COG1910 Periplasmic molybdate- 85.6 21 0.00046 34.6 12.9 105 411-523 88-200 (223)
173 COG1638 DctP TRAP-type C4-dica 85.2 3.6 7.9E-05 43.3 8.5 210 228-523 47-264 (332)
174 cd08443 PBP2_CysB The C-termin 84.4 33 0.00071 32.2 14.4 72 224-302 12-83 (198)
175 cd08437 PBP2_MleR The substrat 84.0 37 0.00079 31.6 14.7 72 225-302 13-84 (198)
176 cd08458 PBP2_NocR The C-termin 83.9 33 0.00072 32.0 14.2 69 225-301 13-81 (196)
177 PRK12683 transcriptional regul 83.6 30 0.00065 35.9 14.7 183 225-523 106-294 (309)
178 cd08427 PBP2_LTTR_like_2 The C 83.2 38 0.00083 31.3 15.2 71 225-301 13-83 (195)
179 PRK11482 putative DNA-binding 82.6 35 0.00075 35.7 14.7 81 195-302 117-197 (317)
180 cd08416 PBP2_MdcR The C-termin 82.4 41 0.00088 31.3 14.1 72 225-302 13-84 (199)
181 PRK15421 DNA-binding transcrip 82.4 22 0.00047 37.2 13.1 69 226-302 103-171 (317)
182 cd08448 PBP2_LTTR_aromatics_li 82.4 41 0.00089 31.1 15.9 70 225-302 13-82 (197)
183 cd08436 PBP2_LTTR_like_3 The C 82.3 41 0.00089 30.9 16.4 71 225-302 13-83 (194)
184 COG0715 TauA ABC-type nitrate/ 82.1 4.4 9.6E-05 42.7 7.8 72 410-483 126-202 (335)
185 PRK09861 cytoplasmic membrane 81.9 34 0.00074 35.0 13.8 122 410-534 120-264 (272)
186 PRK09508 leuO leucine transcri 81.7 22 0.00048 37.0 12.9 70 225-302 125-194 (314)
187 cd08453 PBP2_IlvR The C-termin 81.5 46 0.00099 31.0 15.9 73 225-302 13-85 (200)
188 TIGR03339 phn_lysR aminoethylp 80.7 58 0.0013 32.8 15.4 69 226-302 98-166 (279)
189 PRK10537 voltage-gated potassi 80.7 6.5 0.00014 42.5 8.4 56 348-403 164-221 (393)
190 PLN03192 Voltage-dependent pot 80.3 3.3 7.1E-05 49.7 6.7 54 352-405 250-305 (823)
191 cd08449 PBP2_XapR The C-termin 80.3 49 0.0011 30.6 15.8 72 225-302 13-84 (197)
192 PRK12680 transcriptional regul 79.9 64 0.0014 33.9 15.7 196 195-523 93-294 (327)
193 PRK12681 cysB transcriptional 79.9 39 0.00084 35.4 14.0 83 195-301 93-175 (324)
194 cd08456 PBP2_LysR The C-termin 79.4 52 0.0011 30.4 14.3 69 225-301 13-81 (196)
195 COG0725 ModA ABC-type molybdat 77.7 45 0.00099 33.8 13.0 118 412-534 124-252 (258)
196 PRK11013 DNA-binding transcrip 77.6 60 0.0013 33.6 14.6 70 225-302 107-176 (309)
197 COG2358 Imp TRAP-type uncharac 77.1 20 0.00044 37.3 10.3 78 410-491 127-214 (321)
198 cd08457 PBP2_OccR The C-termin 76.9 63 0.0014 30.0 14.5 69 225-301 13-81 (196)
199 PRK10094 DNA-binding transcrip 76.2 92 0.002 32.3 15.4 71 226-302 107-177 (308)
200 KOG1419 Voltage-gated K+ chann 75.5 5.1 0.00011 43.9 5.6 87 318-404 235-323 (654)
201 cd08451 PBP2_BudR The C-termin 74.5 72 0.0016 29.4 15.8 70 226-302 15-84 (199)
202 cd08486 PBP2_CbnR The C-termin 74.5 44 0.00095 31.4 11.7 70 225-302 14-83 (198)
203 PF14503 YhfZ_C: YhfZ C-termin 74.3 2.7 5.8E-05 41.5 3.0 82 422-508 114-201 (232)
204 cd08430 PBP2_IlvY The C-termin 74.2 73 0.0016 29.4 14.8 70 225-301 13-82 (199)
205 PRK11074 putative DNA-binding 73.9 73 0.0016 32.8 13.9 85 195-302 92-176 (300)
206 PRK14498 putative molybdopteri 72.9 54 0.0012 38.1 13.7 103 413-523 514-624 (633)
207 cd08450 PBP2_HcaR The C-termin 72.2 81 0.0018 29.0 14.8 70 225-302 13-82 (196)
208 PLN02245 ATP phosphoribosyl tr 72.2 38 0.00082 36.4 11.0 103 411-521 178-295 (403)
209 PRK10677 modA molybdate transp 72.1 63 0.0014 32.7 12.5 70 228-302 42-117 (257)
210 PRK11716 DNA-binding transcrip 70.0 1E+02 0.0022 30.8 13.7 70 225-301 80-149 (269)
211 PRK09906 DNA-binding transcrip 68.3 1.4E+02 0.003 30.5 14.5 70 225-302 103-172 (296)
212 PF03401 TctC: Tripartite tric 66.8 78 0.0017 32.4 12.0 129 402-533 81-241 (274)
213 cd08446 PBP2_Chlorocatechol Th 65.0 1.2E+02 0.0025 28.1 15.9 70 225-302 14-83 (198)
214 cd08445 PBP2_BenM_CatM_CatR Th 63.4 1.3E+02 0.0028 28.0 15.2 70 225-302 14-83 (203)
215 PRK11062 nhaR transcriptional 63.1 1.2E+02 0.0027 31.0 12.9 72 225-301 106-177 (296)
216 cd08452 PBP2_AlsR The C-termin 61.5 1.4E+02 0.003 27.7 16.3 69 225-301 13-81 (197)
217 PRK07377 hypothetical protein; 61.3 22 0.00047 33.5 5.9 61 195-271 75-135 (184)
218 cd08432 PBP2_GcdR_TrpI_HvrB_Am 57.6 1.2E+02 0.0025 27.8 10.8 64 226-300 14-77 (194)
219 cd08485 PBP2_ClcR The C-termin 56.4 1.7E+02 0.0037 27.2 14.2 69 225-301 14-82 (198)
220 cd04509 PBP1_ABC_transporter_G 56.0 6 0.00013 40.1 1.5 68 4-77 218-290 (299)
221 cd08481 PBP2_GcdR_like The C-t 53.4 1.1E+02 0.0024 28.0 9.9 100 413-517 86-191 (194)
222 cd01324 cbb3_Oxidase_CcoQ Cyto 53.2 16 0.00034 26.4 2.8 28 317-344 11-38 (48)
223 PRK13583 hisG ATP phosphoribos 52.5 2E+02 0.0043 28.5 11.3 90 411-508 110-212 (228)
224 PRK13348 chromosome replicatio 52.4 2.7E+02 0.0058 28.3 15.3 65 228-301 106-170 (294)
225 cd08431 PBP2_HupR The C-termin 51.5 2E+02 0.0042 26.4 12.6 70 225-301 13-82 (195)
226 cd08428 PBP2_IciA_ArgP The C-t 51.4 2E+02 0.0043 26.4 14.5 65 227-300 15-79 (195)
227 PRK11139 DNA-binding transcrip 51.2 2.2E+02 0.0047 29.1 12.3 105 413-521 181-289 (297)
228 TIGR00070 hisG ATP phosphoribo 49.5 1E+02 0.0022 29.4 8.5 76 411-495 100-175 (182)
229 PRK01686 hisG ATP phosphoribos 49.1 2.5E+02 0.0055 27.5 11.4 92 422-521 115-208 (215)
230 PF06305 DUF1049: Protein of u 48.5 33 0.00071 26.5 4.3 25 563-587 26-50 (68)
231 PF14981 FAM165: FAM165 family 48.2 30 0.00065 24.4 3.4 33 555-587 3-35 (51)
232 PF01634 HisG: ATP phosphoribo 47.6 24 0.00052 33.0 3.9 101 412-521 58-160 (163)
233 PRK03635 chromosome replicatio 46.5 3.3E+02 0.0072 27.7 14.1 66 227-301 105-170 (294)
234 TIGR03414 ABC_choline_bnd chol 45.3 1.5E+02 0.0032 30.6 9.8 41 227-272 23-63 (290)
235 KOG3713 Voltage-gated K+ chann 43.7 27 0.00059 38.0 4.0 64 327-394 356-421 (477)
236 PRK00072 hemC porphobilinogen 42.3 3.3E+02 0.0072 28.1 11.5 60 413-476 113-173 (295)
237 KOG0498 K+-channel ERG and rel 40.8 36 0.00079 39.6 4.7 69 352-420 294-369 (727)
238 cd06333 PBP1_ABC-type_HAAT_lik 40.6 39 0.00085 34.9 4.8 33 41-79 260-293 (312)
239 TIGR00212 hemC porphobilinogen 39.8 3.2E+02 0.0069 28.2 10.9 61 413-477 109-170 (292)
240 cd00494 HMBS Hydroxymethylbila 39.6 3.6E+02 0.0077 27.9 11.2 61 413-477 109-170 (292)
241 PRK10216 DNA-binding transcrip 37.0 4.9E+02 0.011 26.8 16.9 72 225-302 110-188 (319)
242 TIGR02976 phageshock_pspB phag 36.6 1.1E+02 0.0024 24.4 5.5 19 596-614 53-71 (75)
243 PF05545 FixQ: Cbb3-type cytoc 35.8 37 0.00081 24.5 2.6 25 318-342 11-35 (49)
244 PRK09986 DNA-binding transcrip 35.2 4.8E+02 0.01 26.3 16.5 85 195-302 97-181 (294)
245 cd08447 PBP2_LTTR_aromatics_li 34.2 3.6E+02 0.0079 24.5 14.9 69 225-301 13-81 (198)
246 cd08487 PBP2_BlaA The C-termin 33.5 3.6E+02 0.0079 24.3 12.4 66 450-517 121-186 (189)
247 COG3114 CcmD Heme exporter pro 32.1 27 0.00058 26.7 1.3 42 561-602 16-59 (67)
248 PF07204 Orthoreo_P10: Orthore 32.1 83 0.0018 26.1 4.1 9 536-544 17-25 (98)
249 PF15179 Myc_target_1: Myc tar 31.5 61 0.0013 30.4 3.7 38 550-587 13-51 (197)
250 TIGR01276 thiB thiamine ABC tr 30.9 6E+02 0.013 26.0 14.9 74 450-523 175-251 (309)
251 PRK03601 transcriptional regul 30.8 93 0.002 31.5 5.6 83 195-302 89-171 (275)
252 PF01102 Glycophorin_A: Glycop 30.3 79 0.0017 27.9 4.1 28 560-587 66-93 (122)
253 cd08439 PBP2_LrhA_like The C-t 29.5 1.7E+02 0.0036 26.8 6.8 67 226-302 14-80 (185)
254 PF12273 RCR: Chitin synthesis 28.9 61 0.0013 29.0 3.3 28 560-587 3-30 (130)
255 PF14851 FAM176: FAM176 family 27.7 2.2E+02 0.0048 26.3 6.7 27 559-585 22-50 (153)
256 COG3181 Uncharacterized protei 27.7 4E+02 0.0088 27.9 9.4 124 407-532 129-283 (319)
257 PRK11119 proX glycine betaine 27.1 3E+02 0.0066 29.0 8.7 44 226-274 43-87 (331)
258 PF01007 IRK: Inward rectifier 26.7 2.5E+02 0.0055 29.6 8.0 58 351-408 83-144 (336)
259 PF06679 DUF1180: Protein of u 25.6 92 0.002 29.1 3.9 31 557-587 93-123 (163)
260 TIGR03298 argP transcriptional 25.1 7.1E+02 0.015 25.0 14.6 64 229-301 107-170 (292)
261 TIGR02136 ptsS_2 phosphate bin 24.6 77 0.0017 32.6 3.7 74 225-302 48-127 (287)
262 PF03180 Lipoprotein_9: NLPA l 24.2 1.3E+02 0.0028 30.0 5.0 81 446-528 28-123 (237)
263 COG0107 HisF Imidazoleglycerol 24.0 69 0.0015 31.5 2.9 51 218-272 178-229 (256)
264 PF06667 PspB: Phage shock pro 24.0 3.1E+02 0.0067 22.0 6.0 19 596-614 53-71 (75)
265 PF03908 Sec20: Sec20; InterP 23.2 83 0.0018 26.2 2.9 24 317-340 68-91 (92)
266 PF11675 DUF3271: Protein of u 22.9 43 0.00093 32.8 1.2 16 3-18 74-89 (249)
267 COG4905 Predicted membrane pro 22.3 2.4E+02 0.0052 26.8 5.8 64 311-394 56-126 (243)
268 cd06268 PBP1_ABC_transporter_L 21.7 1.2E+02 0.0025 30.4 4.4 48 25-79 236-287 (298)
269 PRK10918 phosphate ABC transpo 21.6 1.7E+02 0.0038 31.0 5.6 68 230-302 44-112 (346)
270 PF00558 Vpu: Vpu protein; In 20.3 2.1E+02 0.0045 23.3 4.4 16 563-578 10-25 (81)
No 1
>KOG1054 consensus Glutamate-gated AMPA-type ion channel receptor subunit GluR2 and related subunits [Inorganic ion transport and metabolism; Amino acid transport and metabolism; Signal transduction mechanisms]
Probab=100.00 E-value=1.6e-86 Score=681.12 Aligned_cols=565 Identities=19% Similarity=0.330 Sum_probs=480.5
Q ss_pred CCCeEEEecCCccccCCccccccCccceEEEEEecCCChhHHHHHHHHHhh--cCCCCCCCCCCchhHHHHHHHHHHHHH
Q 005717 3 SEGYAWIATQGLSTLLDPVKDMESMQGVLGLRPYIPSSKKLEHFKLRWIKS--ADKPDGSTGGSNLFGLWAYDTVWAIAM 80 (681)
Q Consensus 3 ~~~y~WI~t~~~~~~~~~~~~~~~~~Gvlg~~~~~~~~~~~~~f~~~~~~~--~~~~~~~~~~~~~~~~~aYDav~~lA~ 80 (681)
.+|||+|+.+..-...|...+.....++.||+...-+++-+++|.++|++. .++|+.....+..-++++|||+.++|+
T Consensus 233 ~~~YHYvlaNl~f~d~dl~~f~~g~aNitgFqivn~~~~~~~k~~~~~~~l~~~~~~g~~~~~~k~tsAlthDailV~~e 312 (897)
T KOG1054|consen 233 VKGYHYVLANLGFTDIDLERFQHGGANITGFQIVNKNNPMVKKFIQRWKELDEREYPGASNDPIKYTSALTHDAILVMAE 312 (897)
T ss_pred ccceEEEEeeCCCchhhHHHHhcCCcceeEEEEecCCChHHHHHHHHHhhhcccccCCCCCCCcchhhhhhhhHHHHHHH
Confidence 589999999965445555577888999999999999999999999999986 777877766788889999999999999
Q ss_pred HHHHHcccCCcccccCCCCCCCccc--ccCCCcchHHHHHHHhccceecceeeEEE-eCCcccCccEEEEEeeeCCeeEe
Q 005717 81 AVERAGIENSSFLKSNTSKSRVDIA--ALGTFEMGAKLLDTLINTTFEGLSGNFHL-VNGQLEPSAFEIFNVIGTSERVI 157 (681)
Q Consensus 81 Al~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~G~~l~~~l~~~~f~GltG~i~F-~~G~~~~~~~~I~n~~~~~~~~v 157 (681)
|+..+.+.+....+ ..+..||- ...+|..|..+-++++++.++|+||+|+| ..|.|.+.+.+|++++.++.++|
T Consensus 313 af~~~~~q~~~~~r---RG~~GD~~an~~~p~~qG~~I~ralk~v~~eGLTGniqFd~~G~R~Nyt~~i~elk~~~~rk~ 389 (897)
T KOG1054|consen 313 AFRSLRRQRIDISR---RGNAGDCLANPAVPWEQGIDIERALKQVQVEGLTGNIQFDKYGRRTNYTIDIVELKSNGSRKV 389 (897)
T ss_pred HHHHHHHhhhchhc---cCCCccccCCCCCchhcchhHHHHHHheeecccccceeecccCccccceEEEEEeccCCccee
Confidence 99999877654433 33456774 46789999999999999999999999999 88999999999999999999999
Q ss_pred eeeeCCCCccccccCCCCccCCCCCCccCCCCCcCCCceEEEEeeccCCccceEEEeecCCCCeeEEeehHHHHHHHHHH
Q 005717 158 GYWTKEKELLSELNDNNGRATNNLKNPIWPGNTIDQPRKLKIGVPVREGFTEFIKVVENKNKTTQVSGFCYDMFHAVLQV 237 (681)
Q Consensus 158 G~W~~~~gl~~~~~~~~~~~~~~l~~i~Wpg~~~~~p~~lrV~v~~~~p~~~~~~~~~~~~~~~~~~G~~idll~~l~~~ 237 (681)
|+|....|+........+ +.. ......++..|.+....||.++......-.++.+++|||+||+.+|+++
T Consensus 390 ~~W~e~~~fv~~~t~a~~------~~d----~~~~~n~tvvvttiL~spyvm~kkn~~~~egn~ryEGyCvdLa~~iAkh 459 (897)
T KOG1054|consen 390 GYWNEGEGFVPGSTVAQS------RND----QASKENRTVVVTTILESPYVMLKKNHEQLEGNERYEGYCVDLAAEIAKH 459 (897)
T ss_pred eeecccCceeeccccccc------ccc----ccccccceEEEEEecCCchhHHHhhHHHhcCCcccceeHHHHHHHHHHh
Confidence 999998888754321000 000 0112236777888887787665432111178899999999999999999
Q ss_pred cCCCcCeEEEeCCC-------CC-HHHHHHHHHhCccceEEEeEEEeeccccccccccceeecceEEEEEeccCCCcCce
Q 005717 238 LEFPLPYEFVPFHD-------GS-FDELLHKIEKQEFDTAVGDTTIVANRSTFVDFTLPYSESGVSMLVLVKDDERKNFW 309 (681)
Q Consensus 238 l~f~~~~~~v~~~~-------g~-~~gli~~l~~g~~Dia~~~~~it~~R~~~vdFT~P~~~~~~~~vv~~~~~~~~~~~ 309 (681)
.+++|.+.++.++. ++ |+||+++|..|++|++++++|||.+|++++|||.|||..|+++|++||+...+..|
T Consensus 460 i~~~Y~l~iv~dgkyGardaD~k~WnGMvGeLv~grAdiavApLTIt~~REeviDFSKPfMslGISIMIKKPqKsk~gVF 539 (897)
T KOG1054|consen 460 IGIKYKLFIVGDGKYGARDADTKIWNGMVGELVYGRADIAVAPLTITLVREEVIDFSKPFMSLGISIMIKKPQKSKPGVF 539 (897)
T ss_pred cCceEEEEEecCCcccccCCCcccccchhHHHhcCccceEEeeeeeehhhhhhhccccchhhcCeEEEEeCcccCCCCee
Confidence 99887777786654 55 99999999999999999999999999999999999999999999999999888999
Q ss_pred eeeccCcHhHHHHHHHHHHHHHHHhhhhhcccCCCCC------CC-------CCCchhhHHHHHHHHHhccCcc-ccccc
Q 005717 310 IFLKPLSWDLWLTTGAAFIFTGLVVWVLEHRINTEFR------GP-------PQHQIGTIFWFSFSTLVFAHRE-RVVNN 375 (681)
Q Consensus 310 ~fl~PF~~~vW~~i~~~~~~v~~v~~~~~~~~~~~~~------~~-------~~~~~~~~~~~~~~~l~~~~~~-~~~s~ 375 (681)
.||.|+..++|+||+.+++-|++++++..|++|+||+ |+ ..+++.|++||+++++|||+.. .|||.
T Consensus 540 SFldPLa~eIWm~ivfaYiGVSvvlFLVSrFSPYEwh~Ee~~rg~~t~~~~~NeFgifNsLWFsLgAFMQQG~DI~PRsl 619 (897)
T KOG1054|consen 540 SFLDPLAYEIWMCIVFAYIGVSVVLFLVSRFSPYEWHTEEFERGRFTPSDPPNEFGIFNSLWFSLGAFMQQGCDISPRSL 619 (897)
T ss_pred eecchhHHHHHHHHHHHHhcceEEEEEEeccCchheeccccccCCCCCCCCCccchhhHHHHHHHHHHHhcCCCCCcccc
Confidence 9999999999999999999999999999999998764 22 1247899999999999988865 49999
Q ss_pred chhHHHHHHHHHHHHHHhHhhhhhhheeeecccCCCCCCHHHHHhCCC-eEEEecChhHHHHHhhhcCCccccccccC--
Q 005717 376 LSRFVLIIWVFVVLILTQSYTASLTSMLTVQRLQPSFTDVKDIQKNGY-FVGYQTNSFVKDLLTKKLNFNETRLKNYT-- 452 (681)
Q Consensus 376 ~~R~l~~~w~~~~lil~s~YtA~L~s~LT~~~~~~~i~s~~dL~~~~~-~vg~~~~s~~~~~l~~~~~~~~~~~~~~~-- 452 (681)
++||+..+||||+|||+++|||||+||||++++.+||+++|||++|.+ .+|+..+....+++ + .+++..|+
T Consensus 620 SGRIvggvWWFFTlIIiSSYTANLAAFLTvErMvsPIESaEDLAkQteIaYGt~~~GSTkeFF-r-----~Skiavy~kM 693 (897)
T KOG1054|consen 620 SGRIVGGVWWFFTLIIISSYTANLAAFLTVERMVSPIESAEDLAKQTEIAYGTLDSGSTKEFF-R-----RSKIAVYEKM 693 (897)
T ss_pred ccceeccchhhhhhhhhhhhhhHHHHHHhHHhhcCcchhHHHHhhcceeeeeecCCCchHHHH-h-----hhhHHHHHHH
Confidence 999999999999999999999999999999999999999999999987 67888777777777 2 22333333
Q ss_pred --------------ChhHHHHHH-ccCcceEEecchhhHHHHHhhc-CCceEEECcccccCCcEEEecCCCCChHHHHHH
Q 005717 453 --------------TSEDYHDAL-SNGEVAAIFDEIPYIKIFLASY-CSRYMMVGPTYRTDGFGFAFPLGSPLVPYISRA 516 (681)
Q Consensus 453 --------------~~~~~~~~l-~~g~~~a~i~e~~~~~~~~~~~-c~~l~~v~~~~~~~~~~~~~~k~spl~~~in~~ 516 (681)
+..|..+.+ +..+.+|++.|...-+|..++. | +-+.||..+.+.+||+|.||||.|+..+|.|
T Consensus 694 W~yM~SaepsVFv~t~aeGv~rVRksKGkyAfLLEsTmNey~eqRkPC-DTMKVGgNLds~GYGiATp~Gsslr~~vNLA 772 (897)
T KOG1054|consen 694 WTYMKSAEPSVFVRTTAEGVARVRKSKGKYAFLLESTMNEYIEQRKPC-DTMKVGGNLDSKGYGIATPKGSSLRNAVNLA 772 (897)
T ss_pred HHHHhcCCcceeeehhhhHHHHHHhcCCceEeehHhhhhhhhhccCCc-cceecccccCCcceeecCCCCcccccchhhh
Confidence 445555566 4445689999999889988776 9 7788999999999999999999999999999
Q ss_pred HHhhccCccHHHHHHHHHcCC-CCCCCCCCC-cccccccccccchhHHHHHHHHHHHHHHHHHHHHHHhhcCCC
Q 005717 517 ILKVTEDKEKMENIEKALGNQ-ATCEGQGPT-TLSSDSLSVYSFGGLFIIAGIASMSSLLIYVFNFVCFHRPEL 588 (681)
Q Consensus 517 Il~l~e~~G~l~~i~~kw~~~-~~c~~~~~~-~~~~~~L~l~~~~g~F~il~~g~~lallvfi~E~l~~~~~~~ 588 (681)
+++|.|. |+++++++|||.+ ++|...... .++...|+|.+++|+||||..|+++|.++.++||+|+.|...
T Consensus 773 vLkL~E~-G~LdKLkNKWWYDkGeC~sg~~ds~~ktsaLsLSnVAGvFYIL~gGl~laMlvALiEF~yksr~Ea 845 (897)
T KOG1054|consen 773 VLKLNEQ-GLLDKLKNKWWYDKGECGSGGGDSKDKTSALSLSNVAGVFYILVGGLGLAMLVALIEFCYKSRAEA 845 (897)
T ss_pred hhhhccc-chHHHhhhhhcccccccCCCCCCCCcchhhcchhhccceeeeehhhHHHHHHHHHHHHHHHhhHHH
Confidence 9999999 9999999999988 999886644 245689999999999999999999999999999999987763
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=9.7e-72 Score=574.53 Aligned_cols=532 Identities=19% Similarity=0.357 Sum_probs=442.4
Q ss_pred CCCCCeEEEecCCccccCCccccccCccceEEEEEecCCChhHHHHHHHHHhhcCCCCCCCCCCchhHHHHHHHHHHHHH
Q 005717 1 MMSEGYAWIATQGLSTLLDPVKDMESMQGVLGLRPYIPSSKKLEHFKLRWIKSADKPDGSTGGSNLFGLWAYDTVWAIAM 80 (681)
Q Consensus 1 mm~~~y~WI~t~~~~~~~~~~~~~~~~~Gvlg~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~aYDav~~lA~ 80 (681)
|.|+|||||++.--... .....|++|++.....+. ....-|+|.++|.
T Consensus 249 mTG~G~VWiV~E~a~~~------nn~PdG~LGlqL~~~~~~--------------------------~~hirDsv~vlas 296 (993)
T KOG4440|consen 249 MTGSGYVWIVGERAISG------NNLPDGILGLQLINGKNE--------------------------SAHIRDSVGVLAS 296 (993)
T ss_pred ccCceEEEEEecccccc------CCCCCceeeeEeecCccc--------------------------cceehhhHHHHHH
Confidence 78999999999842211 234789999999543221 1224699999999
Q ss_pred HHHHHcccCCcccccCCCCC-CCcccccCCCcchHHHHHHHhccc-eecceeeEEE-eCCcccCccEEEEEee-eCCeeE
Q 005717 81 AVERAGIENSSFLKSNTSKS-RVDIAALGTFEMGAKLLDTLINTT-FEGLSGNFHL-VNGQLEPSAFEIFNVI-GTSERV 156 (681)
Q Consensus 81 Al~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~G~~l~~~l~~~~-f~GltG~i~F-~~G~~~~~~~~I~n~~-~~~~~~ 156 (681)
|++.+..... .... ..+|++...|..|+.|.+.++..+ -.|.||++.| ++|+|....|+|+|+. ....+.
T Consensus 297 Av~e~~~~e~------I~~~P~~c~d~~~~w~~g~~l~~~l~s~~~~~g~TgrV~Fnd~gdRi~a~YdiiN~hq~rk~Vg 370 (993)
T KOG4440|consen 297 AVHELLEKEN------ITDPPRGCVDNTNIWKTGPLLKRVLMSSKYADGVTGRVEFNDDGDRIFANYDIINLHQNRKLVG 370 (993)
T ss_pred HHHHHHhhcc------CCCCCCcccCccchhcccHHHHHHHhhhcccCCcceeEEEcCCCceeeccceeEehhhhhhhhh
Confidence 9999865421 1111 345677888999999999988755 5799999999 9999999999999995 555667
Q ss_pred eeeeeCCCCccccccCCCCccCCCCCCccCCCCCcCCC------ceEEEEeeccCCccceEEEe-e------------c-
Q 005717 157 IGYWTKEKELLSELNDNNGRATNNLKNPIWPGNTIDQP------RKLKIGVPVREGFTEFIKVV-E------------N- 216 (681)
Q Consensus 157 vG~W~~~~gl~~~~~~~~~~~~~~l~~i~Wpg~~~~~p------~~lrV~v~~~~p~~~~~~~~-~------------~- 216 (681)
+|.++. +.... +-+.|+|||+.+.+| ++|||.+.+++||. |+... . |
T Consensus 371 ~~~yd~---~r~~~---------nd~~IiWpGg~~~KP~gi~~pthLrivTi~~~PFV-Yv~p~~sd~~c~eef~~~~d~ 437 (993)
T KOG4440|consen 371 VGIYDG---TRVIP---------NDRKIIWPGGETEKPRGIQMPTHLRIVTIHQEPFV-YVKPTLSDGTCKEEFTVNGDP 437 (993)
T ss_pred hccccc---eeecc---------CCceeecCCCCcCCCccccccceeEEEEeccCCeE-EEecCCCCcchhhhccccCCc
Confidence 777763 22211 235799999976655 89999999999875 44310 0 1
Q ss_pred -------------C-----CCCeeEEeehHHHHHHHHHHcCCCcCeEEEeCCC---------------CCHHHHHHHHHh
Q 005717 217 -------------K-----NKTTQVSGFCYDMFHAVLQVLEFPLPYEFVPFHD---------------GSFDELLHKIEK 263 (681)
Q Consensus 217 -------------~-----~~~~~~~G~~idll~~l~~~l~f~~~~~~v~~~~---------------g~~~gli~~l~~ 263 (681)
| +..-|+.||||||+-++++.+||+++..+++++. ..|+|++++|.+
T Consensus 438 ~~k~~c~gpn~s~p~s~~~t~~fCC~G~cIDLLi~Ls~~~Nftyd~~l~~dg~fg~~~~vnnsseT~~kew~G~iGEL~~ 517 (993)
T KOG4440|consen 438 VKKVICTGPNDSSPGSPRHTVPFCCYGFCIDLLIKLSRTMNFTYDVHLVADGKFGTQERVNNSSETNKKEWNGMIGELLS 517 (993)
T ss_pred ccceeecCCCCCCCCCcccCcchhhhHHHHHHHHHHHHhhcceEEEEEeecccccceeeeecccccccceehhhhhhhhC
Confidence 1 1134789999999999999999999888888754 579999999999
Q ss_pred CccceEEEeEEEeeccccccccccceeecceEEEEEeccCCCcCceeeeccCcHhHHHHHHHHHHHHHHHhhhhhcccCC
Q 005717 264 QEFDTAVGDTTIVANRSTFVDFTLPYSESGVSMLVLVKDDERKNFWIFLKPLSWDLWLTTGAAFIFTGLVVWVLEHRINT 343 (681)
Q Consensus 264 g~~Dia~~~~~it~~R~~~vdFT~P~~~~~~~~vv~~~~~~~~~~~~fl~PF~~~vW~~i~~~~~~v~~v~~~~~~~~~~ 343 (681)
+++||+++++||++||.++++||.||...|+.++.+++...+ ....||+||+..+|+++.++..+|++++++++|++|.
T Consensus 518 ~~ADMivaplTINpERa~yieFskPfkYqGitILeKk~~r~S-tl~SFlQPfqstLW~lv~~SVhvVal~lYlLDrfSPF 596 (993)
T KOG4440|consen 518 GQADMIVAPLTINPERAQYIEFSKPFKYQGITILEKKEIRRS-TLDSFLQPFQSTLWLLVGLSVHVVALMLYLLDRFSPF 596 (993)
T ss_pred CccceEeeceeeChhhhhheeccCcccccceEEEeeCCCCCc-hHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHhcCcc
Confidence 999999999999999999999999999999999999887655 8999999999999999999999999999999999986
Q ss_pred C-CCCC-------CCCchhhHHHHHHHHHhccC-ccc-ccccchhHHHHHHHHHHHHHHhHhhhhhhheeeecccCCCCC
Q 005717 344 E-FRGP-------PQHQIGTIFWFSFSTLVFAH-RER-VVNNLSRFVLIIWVFVVLILTQSYTASLTSMLTVQRLQPSFT 413 (681)
Q Consensus 344 ~-~~~~-------~~~~~~~~~~~~~~~l~~~~-~~~-~~s~~~R~l~~~w~~~~lil~s~YtA~L~s~LT~~~~~~~i~ 413 (681)
+ |... ..-+++.++||+||.|+..+ ++. |+|.++|++.++|+-|++|++++|||||+|||...+.+..++
T Consensus 597 gRFk~~ds~~~ee~alnlssAmWF~WGVLLNSGigEgtPRSfSARvLGmVWaGFaMIiVASYTANLAAFLVLdrPe~~lt 676 (993)
T KOG4440|consen 597 GRFKVNDSEEEEEDALNLSSAMWFSWGVLLNSGIGEGTPRSFSARVLGMVWAGFAMIIVASYTANLAAFLVLDRPEERLT 676 (993)
T ss_pred cceeeccCccchhhhcchhhhHHHHhHhhhccccCCCCCcchhHHHHHHHHhhhheeeehhhhhhhhhheeecCcccccc
Confidence 5 3222 23478999999999999988 554 999999999999999999999999999999999999999999
Q ss_pred CHHHHHhCC----CeEEEecChhHHHHHhhhcC----CccccccccCChhHHHHHHccCcceEEecchhhHHHHHhhcCC
Q 005717 414 DVKDIQKNG----YFVGYQTNSFVKDLLTKKLN----FNETRLKNYTTSEDYHDALSNGEVAAIFDEIPYIKIFLASYCS 485 (681)
Q Consensus 414 s~~dL~~~~----~~vg~~~~s~~~~~l~~~~~----~~~~~~~~~~~~~~~~~~l~~g~~~a~i~e~~~~~~~~~~~c~ 485 (681)
.+.|-+-.+ ...|++++|.+..|++++-. +..-.-..|.+.+++.+++++|+.+||+.++.-++|..+++|
T Consensus 677 GinDpRLRNps~nf~~aTVk~SsVd~YFrRqVELS~MyR~ME~hNy~~A~eAiq~v~~gkL~AFIWDS~rLEfEAs~~C- 755 (993)
T KOG4440|consen 677 GINDPRLRNPSDNFIYATVKQSSVDIYFRRQVELSTMYRHMEKHNYESAAEAIQAVRDGKLHAFIWDSARLEFEASQKC- 755 (993)
T ss_pred CCCCccccCcccceeEEEecCccHHHHHHHHhHHHHHHHhhhhcchhhHHHHHHHHHcCceeEEEeecceeeehhhccc-
Confidence 999976543 36888999999999944311 111122357788899999999999999999999999999999
Q ss_pred ceEEECcccccCCcEEEecCCCCChHHHHHHHHhhccCccHHHHHHHHHcCC--CCCCCCCCCcccccccccccchhHHH
Q 005717 486 RYMMVGPTYRTDGFGFAFPLGSPLVPYISRAILKVTEDKEKMENIEKALGNQ--ATCEGQGPTTLSSDSLSVYSFGGLFI 563 (681)
Q Consensus 486 ~l~~v~~~~~~~~~~~~~~k~spl~~~in~~Il~l~e~~G~l~~i~~kw~~~--~~c~~~~~~~~~~~~L~l~~~~g~F~ 563 (681)
.|...|+.|...+||+.++||||+.+.+..+|++.+|+ |.|+++.++|... ++|..... ..+..|+|.+++|+|+
T Consensus 756 eLvT~GeLFgRSgyGIGlqK~SPWt~~vtlaIL~~hEs-GfMEkLDk~Wi~~Ggpq~c~~~~--k~PatLgl~NMagvFi 832 (993)
T KOG4440|consen 756 ELVTTGELFGRSGYGIGLQKDSPWTQNVTLAILKSHES-GFMEKLDKTWIRYGGPQECDSRS--KAPATLGLENMAGVFI 832 (993)
T ss_pred ceEeccccccccccccccccCCCCcchhhHHHHHhhhc-chHHHHHHHHHhcCCcchhhhhc--cCcccccccccccEEE
Confidence 89999999999999999999999999999999999999 9999999999977 34443333 3688999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHhhcCCC
Q 005717 564 IAGIASMSSLLIYVFNFVCFHRPEL 588 (681)
Q Consensus 564 il~~g~~lallvfi~E~l~~~~~~~ 588 (681)
+.+.|+++++.+.++|..|+|++..
T Consensus 833 LV~~Gia~GifLifiEv~Ykrh~~~ 857 (993)
T KOG4440|consen 833 LVAGGIAAGIFLIFIEVAYKRHKDA 857 (993)
T ss_pred EEecchhheeeEEEEeehhhhhhhh
Confidence 9999999999999999999998873
No 3
>KOG1052 consensus Glutamate-gated kainate-type ion channel receptor subunit GluR5 and related subunits [Inorganic ion transport and metabolism; Amino acid transport and metabolism; Signal transduction mechanisms]
Probab=100.00 E-value=1.2e-68 Score=616.27 Aligned_cols=549 Identities=32% Similarity=0.533 Sum_probs=464.4
Q ss_pred CCCCCeEEEecCCccccCCcc---ccccCccceEEEEEecCCChhHHHHHHHHHhhcCCCCCCCCCCchhHHHHHHHHHH
Q 005717 1 MMSEGYAWIATQGLSTLLDPV---KDMESMQGVLGLRPYIPSSKKLEHFKLRWIKSADKPDGSTGGSNLFGLWAYDTVWA 77 (681)
Q Consensus 1 mm~~~y~WI~t~~~~~~~~~~---~~~~~~~Gvlg~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~aYDav~~ 77 (681)
||+.+|+||+|+++.+..+.. ...+.++|+++.+.+.+.++..++|..+|++. ...++.+++++||++++
T Consensus 38 ~~~~~~~~i~t~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~s~~~~~~~~~~~~~-------~~~~~~~~~~~~D~~~~ 110 (656)
T KOG1052|consen 38 MMQFGYVWILTNLLTDALDLDELYSLIDVMNGVLGLRGHIPRSELLQNFVTRWQTS-------NVELLVYALWAYDAIQA 110 (656)
T ss_pred ccccCeEEEEEecchhhhcccccccchhheeeEEeeccCCCccHHHHHHHHHHhhc-------cccccchhhHHHHHHHH
Confidence 799999999999988766644 45678999999999999999999999999753 22467789999999999
Q ss_pred HHHHHHHHcccCCcccccCCCCCCCcccccCCCcchHHHHHHHhcccee---cceeeEEE-eCCcccCccEEEEEeeeCC
Q 005717 78 IAMAVERAGIENSSFLKSNTSKSRVDIAALGTFEMGAKLLDTLINTTFE---GLSGNFHL-VNGQLEPSAFEIFNVIGTS 153 (681)
Q Consensus 78 lA~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~l~~~l~~~~f~---GltG~i~F-~~G~~~~~~~~I~n~~~~~ 153 (681)
+|.|++++... ..-...|.....|..|..+.+.+.+.... |++|.+++ .++.+....|+|+|+.+.+
T Consensus 111 ~a~~~~~~~~~---------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~n~~~~~ 181 (656)
T KOG1052|consen 111 LARAVESLLNI---------GNLSLSCGRNNSWLDALGVFNFGKKLLVVNLSGVTGQFQFFRGGLLEYFKYEILNLNGSG 181 (656)
T ss_pred HHHHHHHhhcC---------CCCceecCCCCcccchhHHHHHHHhhhhhccccceeEEEecCCCccccceEEEEEecCcC
Confidence 99999997631 11235566566788889999988887554 45678888 5889999999999999999
Q ss_pred eeEeeeeeCCCCccccccCCCCccCCCCCCccCCCCCcCC---------CceEEEEeeccCCccceEEEeecC-CCCeeE
Q 005717 154 ERVIGYWTKEKELLSELNDNNGRATNNLKNPIWPGNTIDQ---------PRKLKIGVPVREGFTEFIKVVENK-NKTTQV 223 (681)
Q Consensus 154 ~~~vG~W~~~~gl~~~~~~~~~~~~~~l~~i~Wpg~~~~~---------p~~lrV~v~~~~p~~~~~~~~~~~-~~~~~~ 223 (681)
.+.||.|++..|. .+.||+..... .++|||+++..+||..++... .. .++.++
T Consensus 182 ~~~ig~W~~~~~~----------------~i~~~~~~~~~~~~~~~~~~~~~l~v~~~~~~P~~~~~~~~-~~~~~~~~~ 244 (656)
T KOG1052|consen 182 ERRIGYWYPRGGE----------------NISWPGKDYFVPKGWFFPTNGKPLRVGVVTEPPFVDLVEDL-AILNGNDRI 244 (656)
T ss_pred ceeEEEecCCCCc----------------eeeccCCcccCcCCccccCCCceEEEEEeccCCceeeeecc-cccCCCCcc
Confidence 9999999987762 34555543322 378999999999987666532 12 467799
Q ss_pred EeehHHHHHHHHHHcCCCcCeEEEeCCC------CCHHHHHHHHHhCccceEEEeEEEeeccccccccccceeecceEEE
Q 005717 224 SGFCYDMFHAVLQVLEFPLPYEFVPFHD------GSFDELLHKIEKQEFDTAVGDTTIVANRSTFVDFTLPYSESGVSML 297 (681)
Q Consensus 224 ~G~~idll~~l~~~l~f~~~~~~v~~~~------g~~~gli~~l~~g~~Dia~~~~~it~~R~~~vdFT~P~~~~~~~~v 297 (681)
.|||+||++++++.|||+++++.++++. |+|+|++++|.+|++|++ ++++++++|+++||||.||++.+++++
T Consensus 245 ~G~~idll~~l~~~l~f~~~~~~~~~~~g~~~~~g~~~g~v~~l~~~~advg-~~~tit~~R~~~vdfT~p~~~~~~~i~ 323 (656)
T KOG1052|consen 245 EGFEIDLLQALAKRLNFSYEIIFVPDGSGSRDPNGNWDGLVGQLVDGEADVG-ADITITPERSKYVDFTIPYLQFGIVII 323 (656)
T ss_pred ceEEehHHHHHHHhCCCceEEEEcCCCCCCCCCCCChhHHHHHHhcCccccc-cceEEeecccccEEeccceEeccEEEE
Confidence 9999999999999999998888888754 689999999999999999 899999999999999999999999999
Q ss_pred EEeccCCCcCceeeeccCcHhHHHHHHHHHHHHHHHhhhhhcccCCCCCCCC-----CCchhhHHHHHHHHHhccC-ccc
Q 005717 298 VLVKDDERKNFWIFLKPLSWDLWLTTGAAFIFTGLVVWVLEHRINTEFRGPP-----QHQIGTIFWFSFSTLVFAH-RER 371 (681)
Q Consensus 298 v~~~~~~~~~~~~fl~PF~~~vW~~i~~~~~~v~~v~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~l~~~~-~~~ 371 (681)
+++++.... .|.|++||++++|++++++++++++++|+++|+.+.++ .++ .....+++|+++++++.|+ .+.
T Consensus 324 ~~~~~~~~~-~~~fl~Pf~~~vW~~i~~~~l~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~q~~~~~ 401 (656)
T KOG1052|consen 324 VRKPDSRSK-LWNFLAPFSPEVWLLILASLLLVGLLLWILERLSPYEL-PPRQIVTSLFSLLNCLWLTVGSLLQQGSDEI 401 (656)
T ss_pred EEecCCccc-ceEEecCCcHHHHHHHHHHHHHHHHHHHHHhccccccC-CccccceeEeecccchhhhhHHHhccCCCcc
Confidence 999998876 99999999999999999999999999999999999888 222 1234668899999999877 467
Q ss_pred ccccchhHHHHHHHHHHHHHHhHhhhhhhheeeecccCCCCCCHHHHHh-CCCeEEEecChhHHHHHhhh---cCCccc-
Q 005717 372 VVNNLSRFVLIIWVFVVLILTQSYTASLTSMLTVQRLQPSFTDVKDIQK-NGYFVGYQTNSFVKDLLTKK---LNFNET- 446 (681)
Q Consensus 372 ~~s~~~R~l~~~w~~~~lil~s~YtA~L~s~LT~~~~~~~i~s~~dL~~-~~~~vg~~~~s~~~~~l~~~---~~~~~~- 446 (681)
|++.++|+++++|||+++|++++|||+|+|+||++++.++|++++||.+ .+..+|+..+++...++... ..+..+
T Consensus 402 p~~~~~Rll~~~w~~~~lil~ssYTa~L~a~Lt~~~~~~~i~~~~dL~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~ 481 (656)
T KOG1052|consen 402 PRSLSTRLLLGAWWLFVLILISSYTANLTAFLTVPRLRSPIDSLDDLADQSNIPYGTQRGSFTRIYLEESEDMWAFKVSQ 481 (656)
T ss_pred ccchhhhHHHHHHHHHHHHHHHHHHHHHHHHhcccccCCcccCHHHHHHhcCCeEEEEecchHHHHHHHHHHHHhhhccC
Confidence 9999999999999999999999999999999999999999999999995 67799999999999999443 234444
Q ss_pred cccccCChhHHHHHHccC---cceEEecchhhHHHHHhhc-CCceEEECcccccCCcEEEecCCCCChHHHHHHHHhhcc
Q 005717 447 RLKNYTTSEDYHDALSNG---EVAAIFDEIPYIKIFLASY-CSRYMMVGPTYRTDGFGFAFPLGSPLVPYISRAILKVTE 522 (681)
Q Consensus 447 ~~~~~~~~~~~~~~l~~g---~~~a~i~e~~~~~~~~~~~-c~~l~~v~~~~~~~~~~~~~~k~spl~~~in~~Il~l~e 522 (681)
..+.+.+.+++.+++++| +++++..+.++..++.+++ | +++++++.+...+++ ++||||||++.+|++|+++.|
T Consensus 482 ~~~~~~~~~e~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~c-~~~~v~~~~~~~~~~-~~~~~Spl~~~is~~Il~l~e 559 (656)
T KOG1052|consen 482 RSVPLASPEEGVERVRKGPSGGYAFASDELYLAYLFLRDEIC-DLTEVGEPFLYKGYG-AFPKGSPLRSLISRAILKLQE 559 (656)
T ss_pred CCccCCCHHHHHHHHHcCCCCceEEEeccHHHHHHHhhcCCC-ceEEeCCcccCCCcc-eecCCCccHHHHHHHHHhhcc
Confidence 678899999999999888 4655555555555555544 8 999999999999999 999999999999999999999
Q ss_pred CccHHHHHHHHHcCCCCCCCCCCCcccccccccccchhHHHHHHHHHHHHHHHHHHHHHHhhcCCC
Q 005717 523 DKEKMENIEKALGNQATCEGQGPTTLSSDSLSVYSFGGLFIIAGIASMSSLLIYVFNFVCFHRPEL 588 (681)
Q Consensus 523 ~~G~l~~i~~kw~~~~~c~~~~~~~~~~~~L~l~~~~g~F~il~~g~~lallvfi~E~l~~~~~~~ 588 (681)
. |.++++++||+....|............|++++++|+|+++++|+++|+++|++|++|++++.+
T Consensus 560 ~-g~l~~~~~kw~~~~~~~~~~~~~~~~~~l~~~~~~g~F~i~~~g~~lal~vfi~E~~~~~~~~~ 624 (656)
T KOG1052|consen 560 T-GILQKLKRKWFSKKPCLPKCSQTEKTKALDLESFWGLFLILLVGYLLALLVFILELLYSRRRTL 624 (656)
T ss_pred c-cHHHHHHHHhccCCCCCCCCCCcccccccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 9 9999999999987433222122023678999999999999999999999999999999998874
No 4
>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=2.1e-66 Score=553.53 Aligned_cols=530 Identities=22% Similarity=0.415 Sum_probs=431.8
Q ss_pred CCCCCeEEEecCCccccCCccccccCccceEEEEEecCCChhHHHHHHHHHhhcCCCCCCCCCCchhHHHHHHHHHHHHH
Q 005717 1 MMSEGYAWIATQGLSTLLDPVKDMESMQGVLGLRPYIPSSKKLEHFKLRWIKSADKPDGSTGGSNLFGLWAYDTVWAIAM 80 (681)
Q Consensus 1 mm~~~y~WI~t~~~~~~~~~~~~~~~~~Gvlg~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~aYDav~~lA~ 80 (681)
|||.||+||++...... +. .-.+...|.+.+..-. |+. .+....-|+|-++|.
T Consensus 256 l~g~~y~Wi~pqlv~g~-~~-~pa~~P~GLisv~~~~------------w~~-------------~l~~rVrdgvaiva~ 308 (1258)
T KOG1053|consen 256 LTGPGYVWIVPQLVEGL-EP-RPAEFPLGLISVSYDT------------WRY-------------SLEARVRDGVAIVAR 308 (1258)
T ss_pred CcCCceEEEeehhccCC-CC-CCccCccceeeeeccc------------hhh-------------hHHHHHhhhHHHHHH
Confidence 79999999998865442 11 1123456666665422 221 145567899999999
Q ss_pred HHHHHcccCCcccccCCCCCCCccccc--CCCcchHHHHHHHhccceecceeeEEE-eCCcccCccEEEEEeee-CCeeE
Q 005717 81 AVERAGIENSSFLKSNTSKSRVDIAAL--GTFEMGAKLLDTLINTTFEGLSGNFHL-VNGQLEPSAFEIFNVIG-TSERV 156 (681)
Q Consensus 81 Al~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~G~~l~~~l~~~~f~GltG~i~F-~~G~~~~~~~~I~n~~~-~~~~~ 156 (681)
|...+......+. ....+|-.. .....|..|..+|.|+.|+| ++++| ++|-..++..-|+-+.+ ..|.+
T Consensus 309 aa~s~~~~~~~lp-----~~~~~C~~~~~~~~~~~~~l~r~l~NvT~~g--~~lsf~~~g~~v~p~lvvI~l~~~r~We~ 381 (1258)
T KOG1053|consen 309 AASSMLRIHGFLP-----EPKMDCREQEETRLTSGETLHRFLANVTWDG--RDLSFNEDGYLVHPNLVVIDLNRDRTWER 381 (1258)
T ss_pred HHHHHHhhcccCC-----CcccccccccCccccchhhhhhhhheeeecc--cceeecCCceeeccceEEEecCCCcchhe
Confidence 9999876544332 224455322 23457889999999999999 89999 89988888877777654 45999
Q ss_pred eeeeeCCCCccccccCCCCccCCCCCCccCCCCCcC---CC--ceEEEEeeccCCccceEEEee----------------
Q 005717 157 IGYWTKEKELLSELNDNNGRATNNLKNPIWPGNTID---QP--RKLKIGVPVREGFTEFIKVVE---------------- 215 (681)
Q Consensus 157 vG~W~~~~gl~~~~~~~~~~~~~~l~~i~Wpg~~~~---~p--~~lrV~v~~~~p~~~~~~~~~---------------- 215 (681)
||.|... .|. ++..+||..... .| .||+|++.+++||..-..++-
T Consensus 382 VG~We~~-~L~-------------M~y~vWPr~~~~~q~~~d~~HL~VvTLeE~PFVive~vDP~t~~C~~ntvpc~s~~ 447 (1258)
T KOG1053|consen 382 VGSWENG-TLV-------------MKYPVWPRYHKFLQPVPDKLHLTVVTLEERPFVIVEDVDPLTQTCVRNTVPCRSQL 447 (1258)
T ss_pred eceecCC-eEE-------------EeccccccccCccCCCCCcceeEEEEeccCCeEEEecCCCCcCcCCCCCCcchhhh
Confidence 9999853 233 246789964432 22 599999999988753222210
Q ss_pred ----c-----C-CCCeeEEeehHHHHHHHHHHcCCCcCeEEEeCCC------CCHHHHHHHHHhCccceEEEeEEEeecc
Q 005717 216 ----N-----K-NKTTQVSGFCYDMFHAVLQVLEFPLPYEFVPFHD------GSFDELLHKIEKQEFDTAVGDTTIVANR 279 (681)
Q Consensus 216 ----~-----~-~~~~~~~G~~idll~~l~~~l~f~~~~~~v~~~~------g~~~gli~~l~~g~~Dia~~~~~it~~R 279 (681)
. + +-..|++||||||+++|++.+||+|+.++|.++. |.|+|||++|..+++|||+++++|+.+|
T Consensus 448 ~~t~ss~~~~~~tvKkCCkGfCIDiLkKlA~~v~FtYDLYlVtnGKhGkk~ng~WnGmIGev~~~rA~MAVgSltINeeR 527 (1258)
T KOG1053|consen 448 NSTFSSGDEANRTVKKCCKGFCIDILKKLARDVKFTYDLYLVTNGKHGKKINGVWNGMIGEVVYQRADMAVGSLTINEER 527 (1258)
T ss_pred hhccCCCccCCchHHhhhhhhhHHHHHHHHhhcCcceEEEEecCCcccceecCcchhhHHHHHhhhhheeeeeeEechhh
Confidence 0 0 1135899999999999999999998888888765 8999999999999999999999999999
Q ss_pred ccccccccceeecceEEEEEeccCCCcCceeeeccCcHhHHHHHHHHHHHH-HHHhhhhhcccCCCCC---------CCC
Q 005717 280 STFVDFTLPYSESGVSMLVLVKDDERKNFWIFLKPLSWDLWLTTGAAFIFT-GLVVWVLEHRINTEFR---------GPP 349 (681)
Q Consensus 280 ~~~vdFT~P~~~~~~~~vv~~~~~~~~~~~~fl~PF~~~vW~~i~~~~~~v-~~v~~~~~~~~~~~~~---------~~~ 349 (681)
+++||||.||.++|+.++|......- ..-+||.||++.+|+.++++++++ ++.++++|++++..+. |.+
T Consensus 528 SevVDFSvPFveTgIsVmV~rsngtv-spsAFLePfs~svWVmmFVm~livaai~vFlFEy~SPvgyn~~l~~gkkpggp 606 (1258)
T KOG1053|consen 528 SEVVDFSVPFVETGISVMVARSNGTV-SPSAFLEPFSPSVWVMMFVMCLIVAAITVFLFEYFSPVGYNRNLANGKKPGGP 606 (1258)
T ss_pred hccccccccccccceEEEEEecCCcc-CchhhcCCcchHHHHHHHHHHHHHHHHHHHHHhhcCcccccccccCCCCCCCc
Confidence 99999999999999999999887654 778999999999999999998765 6667899998876542 334
Q ss_pred CCchhhHHHHHHHHHhccC--cccccccchhHHHHHHHHHHHHHHhHhhhhhhheeeecccCCCCCCHHHHHhC------
Q 005717 350 QHQIGTIFWFSFSTLVFAH--RERVVNNLSRFVLIIWVFVVLILTQSYTASLTSMLTVQRLQPSFTDVKDIQKN------ 421 (681)
Q Consensus 350 ~~~~~~~~~~~~~~l~~~~--~~~~~s~~~R~l~~~w~~~~lil~s~YtA~L~s~LT~~~~~~~i~s~~dL~~~------ 421 (681)
.++++.++|+.++.++... .+.|++..+||++.+|.||++|+.++|||||+|||....+..++..+.|-+-|
T Consensus 607 ~FtigkaiwllwaLvFnnsVpv~nPKgtTskiMv~VWAfFavifLAsYTANLAAfMIqE~~~d~vSGlsD~KfqrP~dq~ 686 (1258)
T KOG1053|consen 607 SFTIGKAIWLLWALVFNNSVPVENPKGTTSKIMVLVWAFFAVIFLASYTANLAAFMIQEEYYDTVSGLSDPKFQRPHDQY 686 (1258)
T ss_pred ceehhhHHHHHHHHHhCCCcCCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhccccCcccccCccccC
Confidence 6799999999999888765 56799999999999999999999999999999999999999999999887644
Q ss_pred -CCeEEEecChhHHHHHhhhcCCcc--ccccccC--ChhHHHHHHccCcceEEecchhhHHHHHhhc--CCceEEEC--c
Q 005717 422 -GYFVGYQTNSFVKDLLTKKLNFNE--TRLKNYT--TSEDYHDALSNGEVAAIFDEIPYIKIFLASY--CSRYMMVG--P 492 (681)
Q Consensus 422 -~~~vg~~~~s~~~~~l~~~~~~~~--~~~~~~~--~~~~~~~~l~~g~~~a~i~e~~~~~~~~~~~--c~~l~~v~--~ 492 (681)
..++|++.++..++++++ ++++ ..++.|+ ..+++++.|++|+.||||++...++|...++ | +|..+| .
T Consensus 687 PpFRFGTVpngSTE~niR~--Nyp~MHeYM~kyNq~~v~dal~sLK~gKLDAFIyDaAVLnY~agkDegC-KLvTIGsgK 763 (1258)
T KOG1053|consen 687 PPFRFGTVPNGSTERNIRS--NYPEMHEYMVKYNQPGVEDALESLKNGKLDAFIYDAAVLNYMAGKDEGC-KLVTIGSGK 763 (1258)
T ss_pred CCcccccCCCCchhhhHHh--ccHHHHHHHHHhccCchHHHHHHHhcccchhHHHHHHHHHHhhccCCCc-eEEEecCCc
Confidence 337898887777888733 3443 3444454 6799999999999999999999999999988 9 899998 8
Q ss_pred ccccCCcEEEecCCCCChHHHHHHHHhhccCccHHHHHHHHHcCCCCCCCCCCCcccccccccccchhHHHHHHHHHHHH
Q 005717 493 TYRTDGFGFAFPLGSPLVPYISRAILKVTEDKEKMENIEKALGNQATCEGQGPTTLSSDSLSVYSFGGLFIIAGIASMSS 572 (681)
Q Consensus 493 ~~~~~~~~~~~~k~spl~~~in~~Il~l~e~~G~l~~i~~kw~~~~~c~~~~~~~~~~~~L~l~~~~g~F~il~~g~~la 572 (681)
.|.+.+||+++|||||++..||.+|++.... |+|+++++.|+. +.|.+...+ +.+.+|++++|+|+||+|++|+++|
T Consensus 764 vFAttGYGIal~k~Spwkr~IdlallQy~gd-Geme~Le~~Wlt-gic~n~k~e-vmSsqLdIdnmaGvFymL~~amgLS 840 (1258)
T KOG1053|consen 764 VFATTGYGIALPKNSPWKRQIDLALLQYLGD-GEMEMLETLWLT-GICHNSKNE-VMSSQLDIDNMAGVFYMLAVAMGLS 840 (1258)
T ss_pred eeeecceeeecCCCCcchhhHHHHHHHHhcc-chHHHHHHHHhh-cccccchhh-hhhcccChhhhhhHHHHHHHHHHHH
Confidence 9999999999999999999999999999999 999999999997 778777777 7899999999999999999999999
Q ss_pred HHHHHHHHHHhhc
Q 005717 573 LLIYVFNFVCFHR 585 (681)
Q Consensus 573 llvfi~E~l~~~~ 585 (681)
+++|++|.+++.+
T Consensus 841 llvfi~EHlvYw~ 853 (1258)
T KOG1053|consen 841 LLVFIWEHLVYWK 853 (1258)
T ss_pred HHHHHHHHHHHHH
Confidence 9999999876553
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=99.94 E-value=1.3e-26 Score=247.07 Aligned_cols=163 Identities=21% Similarity=0.280 Sum_probs=137.3
Q ss_pred CCCCCeEEEecCCccccCCccccccCccceEEEEEecCCChhHHHHHHHHHhh--cCCCCCCCCCCchhHHHHHHHHHHH
Q 005717 1 MMSEGYAWIATQGLSTLLDPVKDMESMQGVLGLRPYIPSSKKLEHFKLRWIKS--ADKPDGSTGGSNLFGLWAYDTVWAI 78 (681)
Q Consensus 1 mm~~~y~WI~t~~~~~~~~~~~~~~~~~Gvlg~~~~~~~~~~~~~f~~~~~~~--~~~~~~~~~~~~~~~~~aYDav~~l 78 (681)
||++|||||+|+......+..++.+.++|++|+|++.+.++.+++|..+|++. .++|+....+++.+++|+|||||++
T Consensus 196 ~~~~gy~wI~t~l~~~~~~~~~~~~~~~nitg~r~~~~~~~~~~~~~~~w~~~~~~~~~~~~~~~~~~~~~l~yDaV~~~ 275 (364)
T cd06390 196 KNGIGYHYILANLGFMDIDLTKFRESGANVTGFQLVNYTDTTVSRIMQQWKNFDARDLPRVDWKRPKYTSALTYDGVRVM 275 (364)
T ss_pred ccCCceEEEecCCCcccccHHHHhcCCcCceEEEEecCCCHHHHHHHHHHHhhccccCCCCCcCCcchHHHHHHHHHHHH
Confidence 78999999999966555555477889999999999999999999999999875 5566665557889999999999999
Q ss_pred HHHHHHHcccCCcccccCCCCCCCcccc--cCCCcchHHHHHHHhccceecceeeEEE-eCCcccCccEEEEEeeeCCee
Q 005717 79 AMAVERAGIENSSFLKSNTSKSRVDIAA--LGTFEMGAKLLDTLINTTFEGLSGNFHL-VNGQLEPSAFEIFNVIGTSER 155 (681)
Q Consensus 79 A~Al~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~G~~l~~~l~~~~f~GltG~i~F-~~G~~~~~~~~I~n~~~~~~~ 155 (681)
|+|++++......... ..+..+|.. ..+|..|+.|+++|++++|+|+||+|+| ++|+|.++.|+|+|+.++|++
T Consensus 276 A~A~~~l~~~~~~~~~---~~~~~~C~~~~~~~w~~G~~l~~~i~~~~f~GlTG~i~F~~~G~r~~~~~~I~~~~~~g~~ 352 (364)
T cd06390 276 AEAFQNLRKQRIDISR---RGNAGDCLANPAVPWGQGIDIQRALQQVRFEGLTGNVQFNEKGRRTNYTLHVIEMKHDGIR 352 (364)
T ss_pred HHHHHHHHHcCCCccc---CCCCCCCCCCCCCCCccHHHHHHHHHhhcccccccceeeCCCCCcccceEEEEEecCCcce
Confidence 9999998643322211 122346754 3479999999999999999999999999 889999999999999999999
Q ss_pred EeeeeeCCCCc
Q 005717 156 VIGYWTKEKEL 166 (681)
Q Consensus 156 ~vG~W~~~~gl 166 (681)
+||+|++..|+
T Consensus 353 ~vG~W~~~~g~ 363 (364)
T cd06390 353 KIGYWNEDEKL 363 (364)
T ss_pred EEEEECCCCCc
Confidence 99999998887
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=99.94 E-value=1.6e-26 Score=246.09 Aligned_cols=163 Identities=17% Similarity=0.283 Sum_probs=137.8
Q ss_pred CCCCCeEEEecCCccccCCccccccCccceEEEEEecCCChhHHHHHHHHHhh--cCCCCCCCCCCchhHHHHHHHHHHH
Q 005717 1 MMSEGYAWIATQGLSTLLDPVKDMESMQGVLGLRPYIPSSKKLEHFKLRWIKS--ADKPDGSTGGSNLFGLWAYDTVWAI 78 (681)
Q Consensus 1 mm~~~y~WI~t~~~~~~~~~~~~~~~~~Gvlg~~~~~~~~~~~~~f~~~~~~~--~~~~~~~~~~~~~~~~~aYDav~~l 78 (681)
||+++||||+|+...+..+..++.....+++|+|++.+.++.+++|..+|++. .++|+.....++.+++|+|||||++
T Consensus 204 M~~~~y~~ilt~ld~~~~dl~~~~~g~~NItg~rl~~~~~~~~~~f~~~w~~~~~~~~~~~~~~~l~~~~al~yDaV~~~ 283 (372)
T cd06387 204 KHSRGYHYMLANLGFTDISLERVMHGGANITGFQIVNNENPMVQQFLQRWVRLDEREFPEAKNSPLKYTSALTHDAILVI 283 (372)
T ss_pred ccccceEEEEecCCcccccHHHhccCCcceeEEEEecCCCchHHHHHHHHHhCCcccCCCCCCCCcchHHHHHHHHHHHH
Confidence 89999999999977666665555666666999999999999999999999876 5666666556789999999999999
Q ss_pred HHHHHHHcccCCcccccCCCCCCCcccc--cCCCcchHHHHHHHhccceecceeeEEE-eCCcccCccEEEEEeeeCCee
Q 005717 79 AMAVERAGIENSSFLKSNTSKSRVDIAA--LGTFEMGAKLLDTLINTTFEGLSGNFHL-VNGQLEPSAFEIFNVIGTSER 155 (681)
Q Consensus 79 A~Al~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~G~~l~~~l~~~~f~GltG~i~F-~~G~~~~~~~~I~n~~~~~~~ 155 (681)
|+|++++......+... .++.+|.. ..+|..|+.|+++|++++|+|+||+|+| ++|+|.+++|+|+|+.++|++
T Consensus 284 A~A~~~l~~~~~~~~~~---~~~~~C~~~~~~~W~~G~~l~~~ik~v~~~GLTG~i~F~~~G~R~~~~ldIinl~~~g~~ 360 (372)
T cd06387 284 AEAFRYLRRQRVDVSRR---GSAGDCLANPAVPWSQGIDIERALKMVQVQGMTGNIQFDTYGRRTNYTIDVYEMKPSGSR 360 (372)
T ss_pred HHHHHHHHhcCCCcccC---CCCCCcCCCCCCCccchHHHHHHHHhcccCCCccceeeCCCCCcccceEEEEEecCCCce
Confidence 99999986544333321 13446743 4579999999999999999999999999 789999999999999999999
Q ss_pred EeeeeeCCCCc
Q 005717 156 VIGYWTKEKEL 166 (681)
Q Consensus 156 ~vG~W~~~~gl 166 (681)
+||+|++..|+
T Consensus 361 kIG~W~~~~g~ 371 (372)
T cd06387 361 KAGYWNEYERF 371 (372)
T ss_pred eEEEECCCCCc
Confidence 99999999887
No 7
>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=99.92 E-value=6.7e-25 Score=236.60 Aligned_cols=162 Identities=20% Similarity=0.284 Sum_probs=132.7
Q ss_pred CCCCCeEEEecCCccccCCcc-ccccCccceEEEEEecCCChhHHHHHHHHHhh--cC--CCCCC-CCCCchhHHHHHHH
Q 005717 1 MMSEGYAWIATQGLSTLLDPV-KDMESMQGVLGLRPYIPSSKKLEHFKLRWIKS--AD--KPDGS-TGGSNLFGLWAYDT 74 (681)
Q Consensus 1 mm~~~y~WI~t~~~~~~~~~~-~~~~~~~Gvlg~~~~~~~~~~~~~f~~~~~~~--~~--~~~~~-~~~~~~~~~~aYDa 74 (681)
||+++||||+|+++++.++.. ...+.|+|+.|+|++.|.++.+.+|..||+.+ .. +|... ...++.+++|||||
T Consensus 224 m~~~~y~wi~t~~~~~~~dl~~~~~~~~~~v~~~r~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~alayDa 303 (400)
T cd06391 224 LVAFDCHWIIINEEISDMDVQELVRRSIGRLTIIRQTFPLPQNISQRCFRGNHRISSSLCDPKDPFAQMMEISNLYIYDT 303 (400)
T ss_pred CCCCCeEEEEeCccccccccchHHhcccceEEEeccCCchHHHHHHHHHHHhhhccccccCccccccccccchhhHHHHH
Confidence 899999999999999988865 33567899999999999989999999999865 21 23322 12467899999999
Q ss_pred HHHHHHHHHHHcccCCcccccCCCCCCCccc--ccCCCcchHHHHHHHhccceecceeeEEE-eCCcccCccEEEEEee-
Q 005717 75 VWAIAMAVERAGIENSSFLKSNTSKSRVDIA--ALGTFEMGAKLLDTLINTTFEGLSGNFHL-VNGQLEPSAFEIFNVI- 150 (681)
Q Consensus 75 v~~lA~Al~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~G~~l~~~l~~~~f~GltG~i~F-~~G~~~~~~~~I~n~~- 150 (681)
||++|+|++++....... .....+|. ...+|..|+.|+++|++++|+|+||+|+| ++|+|.+++|+|+|++
T Consensus 304 V~~~A~A~~~l~~~~~~~-----~~~~~~c~~~~~~~w~~G~~ll~~i~~~~f~GlTG~i~f~~~g~r~~~~~dIin~~~ 378 (400)
T cd06391 304 VLLLANAFHKKLEDRKWH-----SMASLSCIRKNSKPWQGGRSMLETIKKGGVSGLTGELEFNENGGNPNVHFEILGTNY 378 (400)
T ss_pred HHHHHHHHHHHHhhcccc-----CCCCcccccCCCCCCCChHHHHHHHHhcCcccceeceEECCCCCccCCceEEEEeec
Confidence 999999999975322111 12234564 35689999999999999999999999999 7799999999999996
Q ss_pred ----eCCeeEeeeeeCCCCcc
Q 005717 151 ----GTSERVIGYWTKEKELL 167 (681)
Q Consensus 151 ----~~~~~~vG~W~~~~gl~ 167 (681)
++|+++||+|++..|+.
T Consensus 379 ~~~~~~g~rkiG~Ws~~~gl~ 399 (400)
T cd06391 379 GEDLGRGVRKLGCWNPITGLN 399 (400)
T ss_pred cccCCCcceEEEEEcCCcCCC
Confidence 89999999999998874
No 8
>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=99.91 E-value=3.9e-24 Score=228.67 Aligned_cols=162 Identities=21% Similarity=0.287 Sum_probs=126.3
Q ss_pred CCCCCeEEEecCCccccCCccccccCcc-ceEEEEEecCCChhHHHHH----HHHHhh-cCCCCCCCCCCchhHHHHHHH
Q 005717 1 MMSEGYAWIATQGLSTLLDPVKDMESMQ-GVLGLRPYIPSSKKLEHFK----LRWIKS-ADKPDGSTGGSNLFGLWAYDT 74 (681)
Q Consensus 1 mm~~~y~WI~t~~~~~~~~~~~~~~~~~-Gvlg~~~~~~~~~~~~~f~----~~~~~~-~~~~~~~~~~~~~~~~~aYDa 74 (681)
||++|||||+|+|+.+..+..++..... +++|+|.+.+.++...+|. .+|++. .+..+.....++.++++||||
T Consensus 224 M~~~~y~wI~t~~~~~~~dl~~~~~g~~~niT~~r~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~l~~~aalayDa 303 (400)
T cd06392 224 LASKDSHWVFVNEEISDTEILELVHSALGRMTVIRQIFPLSKDNNQRCIRNNHRISSLLCDPQEGYLQMLQVSNLYLYDS 303 (400)
T ss_pred cccCCeEEEEecCCcccccHHHHhcccccceeeEEEecCCcHHHHHHHHHHHHHHHhhhcccccccccccchhHHHHHHH
Confidence 8999999999999888776656655554 5677999988877555553 677644 221111112578899999999
Q ss_pred HHHHHHHHHHHcccCCcccccCCCCCCCcc--cccCCCcchHHHHHHHhccceecceeeEEE-eCCcccCccEEEEEe--
Q 005717 75 VWAIAMAVERAGIENSSFLKSNTSKSRVDI--AALGTFEMGAKLLDTLINTTFEGLSGNFHL-VNGQLEPSAFEIFNV-- 149 (681)
Q Consensus 75 v~~lA~Al~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~G~~l~~~l~~~~f~GltG~i~F-~~G~~~~~~~~I~n~-- 149 (681)
||++|+|++++....... .....+| +...+|..|..|+++|++++|+|+||+|+| ++|+|.+++|+|+|+
T Consensus 304 V~~~A~Al~~ll~~~~~~-----~~~~l~C~~~~~~~w~~G~~ll~~ik~v~f~GLTG~I~F~~~G~r~~~~ldIi~l~~ 378 (400)
T cd06392 304 VLMLANAFHRKLEDRKWH-----SMASLNCIRKSTKPWNGGRSMLETIKKGHITGLTGVMEFKEDGANPHVQFEILGTSY 378 (400)
T ss_pred HHHHHHHHHHHhhccccC-----CCCCCccCCCCCCCCCChHHHHHHHHhCCCccCccceeECCCCCCcCCceEEEeccc
Confidence 999999999864221111 2224678 557899999999999999999999999999 899999999999995
Q ss_pred ---eeCCeeEeeeeeCCCCcc
Q 005717 150 ---IGTSERVIGYWTKEKELL 167 (681)
Q Consensus 150 ---~~~~~~~vG~W~~~~gl~ 167 (681)
.|.|+++||+|++.+|+.
T Consensus 379 ~~~~g~g~~~iG~W~~~~gl~ 399 (400)
T cd06392 379 SETFGKDVRRLATWDSEKGLN 399 (400)
T ss_pred cccCCCCceEeEEecCCCCCC
Confidence 477899999999998874
No 9
>PRK10797 glutamate and aspartate transporter subunit; Provisional
Probab=99.88 E-value=2.4e-21 Score=201.84 Aligned_cols=223 Identities=17% Similarity=0.206 Sum_probs=184.8
Q ss_pred ceEEEEeeccCCccceEEEeecCCCCeeEEeehHHHHHHHHH----HcCC-CcCeEEEeCCCCCHHHHHHHHHhCccceE
Q 005717 195 RKLKIGVPVREGFTEFIKVVENKNKTTQVSGFCYDMFHAVLQ----VLEF-PLPYEFVPFHDGSFDELLHKIEKQEFDTA 269 (681)
Q Consensus 195 ~~lrV~v~~~~p~~~~~~~~~~~~~~~~~~G~~idll~~l~~----~l~f-~~~~~~v~~~~g~~~gli~~l~~g~~Dia 269 (681)
+.|+||+.. .|+||.+. +++++++||++|++++|++ ++|. .+++++++. +|..++..|..|++|++
T Consensus 40 g~L~Vg~~~--~~pP~~f~----~~~g~~~G~didl~~~ia~~l~~~lg~~~~~~~~v~~---~~~~~i~~L~~G~~Di~ 110 (302)
T PRK10797 40 GVIVVGHRE--SSVPFSYY----DNQQKVVGYSQDYSNAIVEAVKKKLNKPDLQVKLIPI---TSQNRIPLLQNGTFDFE 110 (302)
T ss_pred CeEEEEEcC--CCCCcceE----CCCCCEeeecHHHHHHHHHHHHHhhCCCCceEEEEEc---ChHhHHHHHHCCCccEE
Confidence 679999876 34455543 4456899999998777665 6664 367899997 78899999999999999
Q ss_pred EEeEEEeeccccccccccceeecceEEEEEeccCCCcCceeeeccCcHhHHHHHHHHHHHHHHHhhhhhcccCCCCCCCC
Q 005717 270 VGDTTIVANRSTFVDFTLPYSESGVSMLVLVKDDERKNFWIFLKPLSWDLWLTTGAAFIFTGLVVWVLEHRINTEFRGPP 349 (681)
Q Consensus 270 ~~~~~it~~R~~~vdFT~P~~~~~~~~vv~~~~~~~~~~~~fl~PF~~~vW~~i~~~~~~v~~v~~~~~~~~~~~~~~~~ 349 (681)
++++++|++|.+.++||.||+.++..+++++..
T Consensus 111 ~~~~~~t~eR~~~~~fS~Py~~~~~~lv~r~~~----------------------------------------------- 143 (302)
T PRK10797 111 CGSTTNNLERQKQAAFSDTIFVVGTRLLTKKGG----------------------------------------------- 143 (302)
T ss_pred ecCCccCcchhhcceecccEeeccEEEEEECCC-----------------------------------------------
Confidence 989999999999999999999999999998652
Q ss_pred CCchhhHHHHHHHHHhccCcccccccchhHHHHHHHHHHHHHHhHhhhhhhheeeecccCCCCCCHHHHHhCCCeEEEec
Q 005717 350 QHQIGTIFWFSFSTLVFAHRERVVNNLSRFVLIIWVFVVLILTQSYTASLTSMLTVQRLQPSFTDVKDIQKNGYFVGYQT 429 (681)
Q Consensus 350 ~~~~~~~~~~~~~~l~~~~~~~~~s~~~R~l~~~w~~~~lil~s~YtA~L~s~LT~~~~~~~i~s~~dL~~~~~~vg~~~ 429 (681)
.|++++||. |++||+..
T Consensus 144 -------------------------------------------------------------~i~sl~dL~--Gk~V~v~~ 160 (302)
T PRK10797 144 -------------------------------------------------------------DIKDFADLK--GKAVVVTS 160 (302)
T ss_pred -------------------------------------------------------------CCCChHHcC--CCEEEEeC
Confidence 378899997 88999999
Q ss_pred ChhHHHHHhhhc--CCccccccccCChhHHHHHHccCcceEEecchhhHHHHHhh--cCCceEEECcccccCCcEEEecC
Q 005717 430 NSFVKDLLTKKL--NFNETRLKNYTTSEDYHDALSNGEVAAIFDEIPYIKIFLAS--YCSRYMMVGPTYRTDGFGFAFPL 505 (681)
Q Consensus 430 ~s~~~~~l~~~~--~~~~~~~~~~~~~~~~~~~l~~g~~~a~i~e~~~~~~~~~~--~c~~l~~v~~~~~~~~~~~~~~k 505 (681)
|+....++.+.. ..+..+++.+.+.++.+++|.+|++|+++.+...+.+...+ ..+.+.++++.+...+++++++|
T Consensus 161 gs~~~~~l~~~~~~~~~~~~i~~~~~~~~~l~~L~~GrvDa~i~d~~~~~~~~~~~~~~~~l~i~~~~~~~~~~~~a~~k 240 (302)
T PRK10797 161 GTTSEVLLNKLNEEQKMNMRIISAKDHGDSFRTLESGRAVAFMMDDALLAGERAKAKKPDNWEIVGKPQSQEAYGCMLRK 240 (302)
T ss_pred CCcHHHHHHHHhhhcCCceEEEEeCCHHHHHHHHHcCCceEEEccHHHHHHHHHcCCCCcceEECCccCCcCceeEEEeC
Confidence 999888873211 12235678889999999999999999999998776654433 23457888887777889999999
Q ss_pred CCC-ChHHHHHHHHhhccCccHHHHHHHHHcCC
Q 005717 506 GSP-LVPYISRAILKVTEDKEKMENIEKALGNQ 537 (681)
Q Consensus 506 ~sp-l~~~in~~Il~l~e~~G~l~~i~~kw~~~ 537 (681)
+++ ++..+|++|.+++++ |.+++|.+||+..
T Consensus 241 ~~~~L~~~in~~L~~l~~~-G~l~~i~~kw~~~ 272 (302)
T PRK10797 241 DDPQFKKLMDDTIAQAQTS-GEAEKWFDKWFKN 272 (302)
T ss_pred CCHHHHHHHHHHHHHHHhC-chHHHHHHHHcCC
Confidence 988 999999999999999 9999999999975
No 10
>PRK09495 glnH glutamine ABC transporter periplasmic protein; Reviewed
Probab=99.88 E-value=2.7e-21 Score=196.23 Aligned_cols=219 Identities=23% Similarity=0.425 Sum_probs=186.2
Q ss_pred ceEEEEeeccCCccceEEEeecCCCCeeEEeehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEE
Q 005717 195 RKLKIGVPVREGFTEFIKVVENKNKTTQVSGFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTT 274 (681)
Q Consensus 195 ~~lrV~v~~~~p~~~~~~~~~~~~~~~~~~G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~ 274 (681)
++|+||+.. .++||.. .+++.+.|+++|+++++++++|. ++++++. +|.+++..+.+|++|+++++++
T Consensus 25 ~~l~v~~~~--~~~P~~~-----~~~g~~~G~~vdl~~~ia~~lg~--~~~~~~~---~~~~~~~~l~~G~vDi~~~~~~ 92 (247)
T PRK09495 25 KKLVVATDT--AFVPFEF-----KQGDKYVGFDIDLWAAIAKELKL--DYTLKPM---DFSGIIPALQTKNVDLALAGIT 92 (247)
T ss_pred CeEEEEeCC--CCCCeee-----cCCCceEEEeHHHHHHHHHHhCC--ceEEEeC---CHHHHHHHHhCCCcCEEEecCc
Confidence 689999764 3445654 23567999999999999999994 5777776 7999999999999999988889
Q ss_pred EeeccccccccccceeecceEEEEEeccCCCcCceeeeccCcHhHHHHHHHHHHHHHHHhhhhhcccCCCCCCCCCCchh
Q 005717 275 IVANRSTFVDFTLPYSESGVSMLVLVKDDERKNFWIFLKPLSWDLWLTTGAAFIFTGLVVWVLEHRINTEFRGPPQHQIG 354 (681)
Q Consensus 275 it~~R~~~vdFT~P~~~~~~~~vv~~~~~~~~~~~~fl~PF~~~vW~~i~~~~~~v~~v~~~~~~~~~~~~~~~~~~~~~ 354 (681)
.+++|.+.++||.||+.+++.+++++...
T Consensus 93 ~t~~R~~~~~fs~p~~~~~~~~~~~~~~~--------------------------------------------------- 121 (247)
T PRK09495 93 ITDERKKAIDFSDGYYKSGLLVMVKANNN--------------------------------------------------- 121 (247)
T ss_pred cCHHHHhhccccchheecceEEEEECCCC---------------------------------------------------
Confidence 99999999999999999999999875431
Q ss_pred hHHHHHHHHHhccCcccccccchhHHHHHHHHHHHHHHhHhhhhhhheeeecccCCCCCCHHHHHhCCCeEEEecChhHH
Q 005717 355 TIFWFSFSTLVFAHRERVVNNLSRFVLIIWVFVVLILTQSYTASLTSMLTVQRLQPSFTDVKDIQKNGYFVGYQTNSFVK 434 (681)
Q Consensus 355 ~~~~~~~~~l~~~~~~~~~s~~~R~l~~~w~~~~lil~s~YtA~L~s~LT~~~~~~~i~s~~dL~~~~~~vg~~~~s~~~ 434 (681)
++++++||. +.+||+..|+...
T Consensus 122 --------------------------------------------------------~~~~~~dL~--g~~I~v~~g~~~~ 143 (247)
T PRK09495 122 --------------------------------------------------------DIKSVKDLD--GKVVAVKSGTGSV 143 (247)
T ss_pred --------------------------------------------------------CCCChHHhC--CCEEEEecCchHH
Confidence 478999998 8899999998888
Q ss_pred HHHhhhcCCccccccccCChhHHHHHHccCcceEEecchhhHHHHHhhc-CCceEEECcccccCCcEEEecCCCCChHHH
Q 005717 435 DLLTKKLNFNETRLKNYTTSEDYHDALSNGEVAAIFDEIPYIKIFLASY-CSRYMMVGPTYRTDGFGFAFPLGSPLVPYI 513 (681)
Q Consensus 435 ~~l~~~~~~~~~~~~~~~~~~~~~~~l~~g~~~a~i~e~~~~~~~~~~~-c~~l~~v~~~~~~~~~~~~~~k~spl~~~i 513 (681)
.++.+ ..+..+++.+++.+++.+++.+|++|+++.+...+.+++++. ...+..++.......++++++|++.+++.+
T Consensus 144 ~~l~~--~~~~~~i~~~~~~~~~~~~L~~grvDa~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~l~~~~ 221 (247)
T PRK09495 144 DYAKA--NIKTKDLRQFPNIDNAYLELGTGRADAVLHDTPNILYFIKTAGNGQFKAVGDSLEAQQYGIAFPKGSELREKV 221 (247)
T ss_pred HHHHh--cCCCCceEEcCCHHHHHHHHHcCceeEEEeChHHHHHHHHhCCCCceEEecCcccccceEEEEcCcHHHHHHH
Confidence 88833 345567778889999999999999999999988888877765 446777777677778999999999999999
Q ss_pred HHHHHhhccCccHHHHHHHHHcCC
Q 005717 514 SRAILKVTEDKEKMENIEKALGNQ 537 (681)
Q Consensus 514 n~~Il~l~e~~G~l~~i~~kw~~~ 537 (681)
|++|.++.++ |.++++.+||+..
T Consensus 222 n~al~~~~~~-g~~~~i~~k~~~~ 244 (247)
T PRK09495 222 NGALKTLKEN-GTYAEIYKKWFGT 244 (247)
T ss_pred HHHHHHHHHC-CcHHHHHHHHcCC
Confidence 9999999999 9999999999964
No 11
>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=99.86 E-value=2.1e-21 Score=208.01 Aligned_cols=163 Identities=20% Similarity=0.303 Sum_probs=129.9
Q ss_pred CCCCCeEEEecCCccccCCccccccCccceEEEEEecCCChhHHHHHHHHHhh--cCCCCCCCCCCchhHHHHHHHHHHH
Q 005717 1 MMSEGYAWIATQGLSTLLDPVKDMESMQGVLGLRPYIPSSKKLEHFKLRWIKS--ADKPDGSTGGSNLFGLWAYDTVWAI 78 (681)
Q Consensus 1 mm~~~y~WI~t~~~~~~~~~~~~~~~~~Gvlg~~~~~~~~~~~~~f~~~~~~~--~~~~~~~~~~~~~~~~~aYDav~~l 78 (681)
|++++||||+++...+..+..++.....+++|++.+.+.++.+++|..+|++. .++|+... .++.+++++||||+++
T Consensus 203 m~~~~y~~il~~~~~~~~~l~~~~~g~~nitg~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~-~~~~~aAl~YDaV~l~ 281 (371)
T cd06388 203 KHVKGYHYIIANLGFKDISLERFMHGGANVTGFQLVDFNTPMVTKLMQRWKKLDQREYPGSES-PPKYTSALTYDGVLVM 281 (371)
T ss_pred ccccceEEEEccCccccccHHHHhccCCceEEEEeecCCChhHHHHHHHHHhcCccccCCCCC-CccchHHHHHHHHHHH
Confidence 78999999999964444443344445555999999998889999999999775 44444322 5778999999999999
Q ss_pred HHHHHHHcccCCcccccCCCCCCCcccc--cCCCcchHHHHHHHhccceecceeeEEE-eCCcccCccEEEEEeeeCCee
Q 005717 79 AMAVERAGIENSSFLKSNTSKSRVDIAA--LGTFEMGAKLLDTLINTTFEGLSGNFHL-VNGQLEPSAFEIFNVIGTSER 155 (681)
Q Consensus 79 A~Al~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~G~~l~~~l~~~~f~GltG~i~F-~~G~~~~~~~~I~n~~~~~~~ 155 (681)
|.|++++......... ..++.+|.. ..+|..|+.|+++|++++|+|+||+|+| ++|+|.++.++|++++++|++
T Consensus 282 a~A~~~l~~~~~~~~~---~~~~~~C~~~~~~~w~~G~~i~~~lk~~~~~GlTG~i~Fd~~G~r~~~~l~Ii~l~~~g~~ 358 (371)
T cd06388 282 AEAFRNLRRQKIDISR---RGNAGDCLANPAAPWGQGIDMERTLKQVRIQGLTGNIQFDHYGRRVNYTMDVFELKSNGPR 358 (371)
T ss_pred HHHHHHHHhcCCCccc---CCCCCCcCCCCCCCCcccHHHHHHHHhcCcCCCccceeECCCCCcccceEEEEEccCCCce
Confidence 9999998533221111 112346743 5689999999999999999999999999 889999899999999999999
Q ss_pred EeeeeeCCCCcc
Q 005717 156 VIGYWTKEKELL 167 (681)
Q Consensus 156 ~vG~W~~~~gl~ 167 (681)
+||+|++..|+.
T Consensus 359 kvG~W~~~~g~~ 370 (371)
T cd06388 359 KIGYWNDMDKLV 370 (371)
T ss_pred EEEEEcCCCCcc
Confidence 999999998874
No 12
>PF00497 SBP_bac_3: Bacterial extracellular solute-binding proteins, family 3; InterPro: IPR001638 Bacterial high affinity transport systems are involved in active transport of solutes across the cytoplasmic membrane. The protein components of these traffic systems include one or two transmembrane protein components, one or two membrane-associated ATP-binding proteins (ABC transporters; see IPR003439 from INTERPRO) and a high affinity periplasmic solute-binding protein. The latter are thought to bind the substrate in the vicinity of the inner membrane, and to transfer it to a complex of inner membrane proteins for concentration into the cytoplasm. In Gram-positive bacteria which are surrounded by a single membrane and have therefore no periplasmic region, the equivalent proteins are bound to the membrane via an N-terminal lipid anchor. These homologue proteins do not play an integral role in the transport process per se, but probably serve as receptors to trigger or initiate translocation of the solute throught the membrane by binding to external sites of the integral membrane proteins of the efflux system. In addition, at least some solute-binding proteins function in the initiation of sensory transduction pathways. On the basis of sequence similarities, the vast majority of these solute-binding proteins can be grouped [] into eight families or clusters, which generally correlate with the nature of the solute bound. Family 3 groups together specific amino acids and opine-binding periplasmic proteins and a periplasmic homologue with catalytic activity.; GO: 0005215 transporter activity, 0006810 transport, 0030288 outer membrane-bounded periplasmic space; PDB: 3N26_A 3QAX_A 3I6V_A 2VHA_B 2IA4_B 2Q89_A 2Q88_A 2YJP_C 1II5_A 1IIW_A ....
Probab=99.86 E-value=3.8e-21 Score=191.34 Aligned_cols=222 Identities=22% Similarity=0.341 Sum_probs=179.7
Q ss_pred EEEEee-ccCCccceEEEeecCCCCeeEEeehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEEE
Q 005717 197 LKIGVP-VREGFTEFIKVVENKNKTTQVSGFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTTI 275 (681)
Q Consensus 197 lrV~v~-~~~p~~~~~~~~~~~~~~~~~~G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~i 275 (681)
||||+. ..+|| .+. +.++...|+++||++++++++|++ ++++.. +|.+++.+|.+|++|+++++++.
T Consensus 1 l~V~~~~~~~P~---~~~----~~~~~~~G~~~dl~~~i~~~~g~~--~~~~~~---~~~~~~~~l~~g~~D~~~~~~~~ 68 (225)
T PF00497_consen 1 LRVGVDEDYPPF---SYI----DEDGEPSGIDVDLLRAIAKRLGIK--IEFVPM---PWSRLLEMLENGKADIIIGGLSI 68 (225)
T ss_dssp EEEEEESEBTTT---BEE----ETTSEEESHHHHHHHHHHHHHTCE--EEEEEE---EGGGHHHHHHTTSSSEEESSEB-
T ss_pred CEEEEcCCCCCe---EEE----CCCCCEEEEhHHHHHHHHhhcccc--cceeec---ccccccccccccccccccccccc
Confidence 689994 44444 443 457899999999999999999965 666665 79999999999999999988999
Q ss_pred eeccccccccccceeecceEEEEEeccCCCcCceeeeccCcHhHHHHHHHHHHHHHHHhhhhhcccCCCCCCCCCCchhh
Q 005717 276 VANRSTFVDFTLPYSESGVSMLVLVKDDERKNFWIFLKPLSWDLWLTTGAAFIFTGLVVWVLEHRINTEFRGPPQHQIGT 355 (681)
Q Consensus 276 t~~R~~~vdFT~P~~~~~~~~vv~~~~~~~~~~~~fl~PF~~~vW~~i~~~~~~v~~v~~~~~~~~~~~~~~~~~~~~~~ 355 (681)
+++|.+.++||.||+..+.++++++.+...
T Consensus 69 ~~~r~~~~~~s~p~~~~~~~~~~~~~~~~~-------------------------------------------------- 98 (225)
T PF00497_consen 69 TPERAKKFDFSDPYYSSPYVLVVRKGDAPP-------------------------------------------------- 98 (225)
T ss_dssp BHHHHTTEEEESESEEEEEEEEEETTSTCS--------------------------------------------------
T ss_pred cccccccccccccccchhheeeeccccccc--------------------------------------------------
Confidence 999999999999999999999999743111
Q ss_pred HHHHHHHHHhccCcccccccchhHHHHHHHHHHHHHHhHhhhhhhheeeecccCCCCCCHHHHHhCCCeEEEecChhHHH
Q 005717 356 IFWFSFSTLVFAHRERVVNNLSRFVLIIWVFVVLILTQSYTASLTSMLTVQRLQPSFTDVKDIQKNGYFVGYQTNSFVKD 435 (681)
Q Consensus 356 ~~~~~~~~l~~~~~~~~~s~~~R~l~~~w~~~~lil~s~YtA~L~s~LT~~~~~~~i~s~~dL~~~~~~vg~~~~s~~~~ 435 (681)
...+++++||. +.+||+..|+...+
T Consensus 99 -----------------------------------------------------~~~~~~~~dl~--~~~i~~~~g~~~~~ 123 (225)
T PF00497_consen 99 -----------------------------------------------------IKTIKSLDDLK--GKRIGVVRGSSYAD 123 (225)
T ss_dssp -----------------------------------------------------TSSHSSGGGGT--TSEEEEETTSHHHH
T ss_pred -----------------------------------------------------cccccchhhhc--CcccccccchhHHH
Confidence 01467788995 78999999998888
Q ss_pred HHhhhcCCccccccccCChhHHHHHHccCcceEEecchhhHHHHHhhcC-CceEEECcccccCCcEEEecCCCC-ChHHH
Q 005717 436 LLTKKLNFNETRLKNYTTSEDYHDALSNGEVAAIFDEIPYIKIFLASYC-SRYMMVGPTYRTDGFGFAFPLGSP-LVPYI 513 (681)
Q Consensus 436 ~l~~~~~~~~~~~~~~~~~~~~~~~l~~g~~~a~i~e~~~~~~~~~~~c-~~l~~v~~~~~~~~~~~~~~k~sp-l~~~i 513 (681)
++ +.......+++.+.+.+++++++.+|++|+++.+...+.+++++.. .............+++++++++.+ |++.|
T Consensus 124 ~l-~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~ 202 (225)
T PF00497_consen 124 YL-KQQYPSNINIVEVDSPEEALEALLSGRIDAFIVDESTAEYLLKRHPLENIVVIPPPISPSPVYFAVRKKNPELLEIF 202 (225)
T ss_dssp HH-HHHTHHTSEEEEESSHHHHHHHHHTTSSSEEEEEHHHHHHHHHHTTTCEEEEEEEEEEEEEEEEEEETTTHHHHHHH
T ss_pred Hh-hhhccchhhhcccccHHHHHHHHhcCCeeeeeccchhhhhhhhhcccccccccccccccceeEEeecccccHHHHHH
Confidence 88 3321114567789999999999999999999999999999999873 233333455566677777777555 99999
Q ss_pred HHHHHhhccCccHHHHHHHHHcCC
Q 005717 514 SRAILKVTEDKEKMENIEKALGNQ 537 (681)
Q Consensus 514 n~~Il~l~e~~G~l~~i~~kw~~~ 537 (681)
|++|.++.++ |.+++|.+||+++
T Consensus 203 n~~i~~l~~~-G~~~~i~~ky~g~ 225 (225)
T PF00497_consen 203 NKAIRELKQS-GEIQKILKKYLGD 225 (225)
T ss_dssp HHHHHHHHHT-THHHHHHHHHHSS
T ss_pred HHHHHHHHhC-cHHHHHHHHHcCC
Confidence 9999999999 9999999999863
No 13
>PRK11260 cystine transporter subunit; Provisional
Probab=99.86 E-value=2.7e-20 Score=191.07 Aligned_cols=221 Identities=19% Similarity=0.338 Sum_probs=187.7
Q ss_pred ceEEEEeeccCCccceEEEeecCCCCeeEEeehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEE
Q 005717 195 RKLKIGVPVREGFTEFIKVVENKNKTTQVSGFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTT 274 (681)
Q Consensus 195 ~~lrV~v~~~~p~~~~~~~~~~~~~~~~~~G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~ 274 (681)
++|+||+.. .++||... +.++.+.|+.+|+++++++++|. ++++++. .|.+++.+|.+|++|+++++++
T Consensus 41 ~~l~v~~~~--~~~P~~~~----~~~g~~~G~~~dl~~~i~~~lg~--~~e~~~~---~~~~~~~~l~~G~~D~~~~~~~ 109 (266)
T PRK11260 41 GTLLVGLEG--TYPPFSFQ----GEDGKLTGFEVEFAEALAKHLGV--KASLKPT---KWDGMLASLDSKRIDVVINQVT 109 (266)
T ss_pred CeEEEEeCC--CcCCceEE----CCCCCEEEehHHHHHHHHHHHCC--eEEEEeC---CHHHHHHHHhcCCCCEEEeccc
Confidence 789999864 34456543 45678999999999999999995 4777776 7999999999999999998889
Q ss_pred EeeccccccccccceeecceEEEEEeccCCCcCceeeeccCcHhHHHHHHHHHHHHHHHhhhhhcccCCCCCCCCCCchh
Q 005717 275 IVANRSTFVDFTLPYSESGVSMLVLVKDDERKNFWIFLKPLSWDLWLTTGAAFIFTGLVVWVLEHRINTEFRGPPQHQIG 354 (681)
Q Consensus 275 it~~R~~~vdFT~P~~~~~~~~vv~~~~~~~~~~~~fl~PF~~~vW~~i~~~~~~v~~v~~~~~~~~~~~~~~~~~~~~~ 354 (681)
.+++|.+.+.||.||+..+..+++++....
T Consensus 110 ~~~~r~~~~~fs~p~~~~~~~~~~~~~~~~-------------------------------------------------- 139 (266)
T PRK11260 110 ISDERKKKYDFSTPYTVSGIQALVKKGNEG-------------------------------------------------- 139 (266)
T ss_pred cCHHHHhccccCCceeecceEEEEEcCCcC--------------------------------------------------
Confidence 999999999999999999999988765321
Q ss_pred hHHHHHHHHHhccCcccccccchhHHHHHHHHHHHHHHhHhhhhhhheeeecccCCCCCCHHHHHhCCCeEEEecChhHH
Q 005717 355 TIFWFSFSTLVFAHRERVVNNLSRFVLIIWVFVVLILTQSYTASLTSMLTVQRLQPSFTDVKDIQKNGYFVGYQTNSFVK 434 (681)
Q Consensus 355 ~~~~~~~~~l~~~~~~~~~s~~~R~l~~~w~~~~lil~s~YtA~L~s~LT~~~~~~~i~s~~dL~~~~~~vg~~~~s~~~ 434 (681)
.+++++||. +.+||+..|+...
T Consensus 140 --------------------------------------------------------~~~~~~dL~--g~~Igv~~G~~~~ 161 (266)
T PRK11260 140 --------------------------------------------------------TIKTAADLK--GKKVGVGLGTNYE 161 (266)
T ss_pred --------------------------------------------------------CCCCHHHcC--CCEEEEecCCcHH
Confidence 478899986 8899999999888
Q ss_pred HHHhhhcCCccccccccCChhHHHHHHccCcceEEecchhhHHHHHhhcCCceEEECcccccCCcEEEecCCCC-ChHHH
Q 005717 435 DLLTKKLNFNETRLKNYTTSEDYHDALSNGEVAAIFDEIPYIKIFLASYCSRYMMVGPTYRTDGFGFAFPLGSP-LVPYI 513 (681)
Q Consensus 435 ~~l~~~~~~~~~~~~~~~~~~~~~~~l~~g~~~a~i~e~~~~~~~~~~~c~~l~~v~~~~~~~~~~~~~~k~sp-l~~~i 513 (681)
.++ ++ .++..++..+++..++++++.+|++|+++.+.....+++++....+.+....+...++++++++++| +++.+
T Consensus 162 ~~l-~~-~~~~~~i~~~~~~~~~l~~L~~GrvD~~i~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~l~~~l 239 (266)
T PRK11260 162 QWL-RQ-NVQGVDVRTYDDDPTKYQDLRVGRIDAILVDRLAALDLVKKTNDTLAVAGEAFSRQESGVALRKGNPDLLKAV 239 (266)
T ss_pred HHH-HH-hCCCCceEecCCHHHHHHHHHcCCCCEEEechHHHHHHHHhCCCcceecCCccccCceEEEEeCCCHHHHHHH
Confidence 887 33 4555677889999999999999999999999888888887765345555666777889999999988 99999
Q ss_pred HHHHHhhccCccHHHHHHHHHcCC
Q 005717 514 SRAILKVTEDKEKMENIEKALGNQ 537 (681)
Q Consensus 514 n~~Il~l~e~~G~l~~i~~kw~~~ 537 (681)
|++|.++.++ |.++++.+||+..
T Consensus 240 n~~l~~~~~~-g~~~~i~~k~~~~ 262 (266)
T PRK11260 240 NQAIAEMQKD-GTLKALSEKWFGA 262 (266)
T ss_pred HHHHHHHHhC-CcHHHHHHHhcCC
Confidence 9999999999 9999999999965
No 14
>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=99.86 E-value=5.1e-21 Score=205.44 Aligned_cols=164 Identities=20% Similarity=0.262 Sum_probs=131.9
Q ss_pred CCCCCeEEEecCCccccCCccccccCccceEEEEEecCCChhHHHHHHHHHhh--cCCCCCCCCCCchhHHHHHHHHHHH
Q 005717 1 MMSEGYAWIATQGLSTLLDPVKDMESMQGVLGLRPYIPSSKKLEHFKLRWIKS--ADKPDGSTGGSNLFGLWAYDTVWAI 78 (681)
Q Consensus 1 mm~~~y~WI~t~~~~~~~~~~~~~~~~~Gvlg~~~~~~~~~~~~~f~~~~~~~--~~~~~~~~~~~~~~~~~aYDav~~l 78 (681)
|++++||||+++...+..+..++.....++.|++...+.++.+++|.++|++. .++|+.....++.+++++||||+++
T Consensus 201 m~~~~y~~il~~~~~~~~~l~~~~~~~~nitg~~~~~~~~~~v~~f~~~~~~~~~~~~~~~~~~~~~~~aAl~yDAV~v~ 280 (370)
T cd06389 201 KHVKGYHYIIANLGFTDGDLSKIQFGGANVSGFQIVDYDDPLVSKFIQRWSTLEEKEYPGAHTKTIKYTSALTYDAVQVM 280 (370)
T ss_pred ccccceEEEEccCCccccchhhhccCCcceEEEEEecCCCchHHHHHHHHHhcCccccCCCCCcCcchHHHHHHHHHHHH
Confidence 78899999999964444333233345667999999999899999999999864 4455544346788999999999999
Q ss_pred HHHHHHHcccCCcccccCCCCCCCcccc--cCCCcchHHHHHHHhccceecceeeEEE-eCCcccCccEEEEEeeeCCee
Q 005717 79 AMAVERAGIENSSFLKSNTSKSRVDIAA--LGTFEMGAKLLDTLINTTFEGLSGNFHL-VNGQLEPSAFEIFNVIGTSER 155 (681)
Q Consensus 79 A~Al~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~G~~l~~~l~~~~f~GltG~i~F-~~G~~~~~~~~I~n~~~~~~~ 155 (681)
|.|++++......+.. ..+..+|.+ ..+|..|..|.++|++++|+|+||+|+| ++|+|.++.++|++++++|++
T Consensus 281 a~A~~~l~~~~~~~~~---~~~~~~C~~~~~~~w~~G~~i~~~l~~~~~~GlTG~i~Fd~~G~r~~~~~~ii~l~~~g~~ 357 (370)
T cd06389 281 TEAFRNLRKQRIEISR---RGNAGDCLANPAVPWGQGVEIERALKQVQVEGLTGNIKFDQNGKRINYTINVMELKSNGPR 357 (370)
T ss_pred HHHHHHHHHcCCCccc---CCCCCCcCCCCCCCCCCcHHHHHHHHhcccCccccceEeCCCCccccceEEEEEecCCcce
Confidence 9999998544332221 122446753 5689999999999999999999999999 899999889999999999999
Q ss_pred EeeeeeCCCCcc
Q 005717 156 VIGYWTKEKELL 167 (681)
Q Consensus 156 ~vG~W~~~~gl~ 167 (681)
+||+|++..|+.
T Consensus 358 kvG~W~~~~~~~ 369 (370)
T cd06389 358 KIGYWSEVDKMV 369 (370)
T ss_pred EEEEEcCCCCcc
Confidence 999999998874
No 15
>PRK15010 ABC transporter lysine/arginine/ornithine binding periplasmic protein; Provisional
Probab=99.85 E-value=1.3e-19 Score=185.43 Aligned_cols=223 Identities=15% Similarity=0.272 Sum_probs=176.3
Q ss_pred CceEEEEeeccCCccceEEEeecCCCCeeEEeehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeE
Q 005717 194 PRKLKIGVPVREGFTEFIKVVENKNKTTQVSGFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDT 273 (681)
Q Consensus 194 p~~lrV~v~~~~p~~~~~~~~~~~~~~~~~~G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~ 273 (681)
+++|+|++.. .|+||... ++++.+.|+++||++++++++|. ++++++. +|..++.++..|++|++++++
T Consensus 25 ~~~l~v~~~~--~~pPf~~~----~~~g~~~G~~vdl~~~ia~~lg~--~~~~~~~---~~~~~~~~l~~g~~Di~~~~~ 93 (260)
T PRK15010 25 PETVRIGTDT--TYAPFSSK----DAKGDFVGFDIDLGNEMCKRMQV--KCTWVAS---DFDALIPSLKAKKIDAIISSL 93 (260)
T ss_pred CCeEEEEecC--CcCCceeE----CCCCCEEeeeHHHHHHHHHHhCC--ceEEEeC---CHHHHHHHHHCCCCCEEEecC
Confidence 3789999863 24456554 45678999999999999999995 5777776 799999999999999999889
Q ss_pred EEeeccccccccccceeecceEEEEEeccCCCcCceeeeccCcHhHHHHHHHHHHHHHHHhhhhhcccCCCCCCCCCCch
Q 005717 274 TIVANRSTFVDFTLPYSESGVSMLVLVKDDERKNFWIFLKPLSWDLWLTTGAAFIFTGLVVWVLEHRINTEFRGPPQHQI 353 (681)
Q Consensus 274 ~it~~R~~~vdFT~P~~~~~~~~vv~~~~~~~~~~~~fl~PF~~~vW~~i~~~~~~v~~v~~~~~~~~~~~~~~~~~~~~ 353 (681)
..+++|.+.++||.||+.++.++++++...
T Consensus 94 ~~t~eR~~~~~fs~p~~~~~~~~~~~~~~~-------------------------------------------------- 123 (260)
T PRK15010 94 SITDKRQQEIAFSDKLYAADSRLIAAKGSP-------------------------------------------------- 123 (260)
T ss_pred cCCHHHHhhcccccceEeccEEEEEECCCC--------------------------------------------------
Confidence 999999999999999999999999886642
Q ss_pred hhHHHHHHHHHhccCcccccccchhHHHHHHHHHHHHHHhHhhhhhhheeeecccCCCCCCHHHHHhCCCeEEEecChhH
Q 005717 354 GTIFWFSFSTLVFAHRERVVNNLSRFVLIIWVFVVLILTQSYTASLTSMLTVQRLQPSFTDVKDIQKNGYFVGYQTNSFV 433 (681)
Q Consensus 354 ~~~~~~~~~~l~~~~~~~~~s~~~R~l~~~w~~~~lil~s~YtA~L~s~LT~~~~~~~i~s~~dL~~~~~~vg~~~~s~~ 433 (681)
...+++||. |.+||+..|+..
T Consensus 124 ---------------------------------------------------------~~~~~~dl~--g~~Igv~~gs~~ 144 (260)
T PRK15010 124 ---------------------------------------------------------IQPTLDSLK--GKHVGVLQGSTQ 144 (260)
T ss_pred ---------------------------------------------------------CCCChhHcC--CCEEEEecCchH
Confidence 123678886 889999999987
Q ss_pred HHHHhhhcCCccccccccCChhHHHHHHccCcceEEecchhhHHH-HHhhc-CCceEEECccc-----ccCCcEEEecCC
Q 005717 434 KDLLTKKLNFNETRLKNYTTSEDYHDALSNGEVAAIFDEIPYIKI-FLASY-CSRYMMVGPTY-----RTDGFGFAFPLG 506 (681)
Q Consensus 434 ~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~g~~~a~i~e~~~~~~-~~~~~-c~~l~~v~~~~-----~~~~~~~~~~k~ 506 (681)
..++.+.......++..+++.++++++|.+|++|+++.+.....+ +.++. ..++...++.+ ...+++++++++
T Consensus 145 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~griDa~i~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~ 224 (260)
T PRK15010 145 EAYANETWRSKGVDVVAYANQDLVYSDLAAGRLDAALQDEVAASEGFLKQPAGKDFAFAGPSVKDKKYFGDGTGVGLRKD 224 (260)
T ss_pred HHHHHHhcccCCceEEecCCHHHHHHHHHcCCccEEEeCcHHHHHHHHhCCCCCceEEecCccccccccCCceEEEEeCC
Confidence 777633221122355667888999999999999999998776654 33332 44555554332 223467999998
Q ss_pred CC-ChHHHHHHHHhhccCccHHHHHHHHHcCC
Q 005717 507 SP-LVPYISRAILKVTEDKEKMENIEKALGNQ 537 (681)
Q Consensus 507 sp-l~~~in~~Il~l~e~~G~l~~i~~kw~~~ 537 (681)
.+ |+..+|++|.++.++ |.+++|.+||+..
T Consensus 225 ~~~L~~~ln~~l~~l~~~-G~~~~i~~ky~~~ 255 (260)
T PRK15010 225 DAELTAAFNKALGELRQD-GTYDKMAKKYFDF 255 (260)
T ss_pred CHHHHHHHHHHHHHHHhC-CcHHHHHHHhcCC
Confidence 77 999999999999999 9999999999964
No 16
>PRK11917 bifunctional adhesin/ABC transporter aspartate/glutamate-binding protein; Reviewed
Probab=99.84 E-value=1.7e-19 Score=184.11 Aligned_cols=217 Identities=14% Similarity=0.292 Sum_probs=176.8
Q ss_pred ceEEEEeeccCCccceEEEeecCCCCeeEEeehHHHHHHHHHHc-CCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeE
Q 005717 195 RKLKIGVPVREGFTEFIKVVENKNKTTQVSGFCYDMFHAVLQVL-EFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDT 273 (681)
Q Consensus 195 ~~lrV~v~~~~p~~~~~~~~~~~~~~~~~~G~~idll~~l~~~l-~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~ 273 (681)
++||||+.. +|+||...+ ..++++.||++||++++++++ |..+++++++. +|...+.+|.+|++|++++.+
T Consensus 38 g~l~vg~~~--~~pP~~~~~---~~~g~~~G~~vdl~~~ia~~llg~~~~~~~~~~---~~~~~~~~l~~g~~D~~~~~~ 109 (259)
T PRK11917 38 GQLIVGVKN--DVPHYALLD---QATGEIKGFEIDVAKLLAKSILGDDKKIKLVAV---NAKTRGPLLDNGSVDAVIATF 109 (259)
T ss_pred CEEEEEECC--CCCCceeee---CCCCceeEeeHHHHHHHHHHhcCCCccEEEEEc---ChhhHHHHHHCCCccEEEecc
Confidence 789999985 455666531 235789999999999999995 86667888876 678888999999999999999
Q ss_pred EEeeccccccccccceeecceEEEEEeccCCCcCceeeeccCcHhHHHHHHHHHHHHHHHhhhhhcccCCCCCCCCCCch
Q 005717 274 TIVANRSTFVDFTLPYSESGVSMLVLVKDDERKNFWIFLKPLSWDLWLTTGAAFIFTGLVVWVLEHRINTEFRGPPQHQI 353 (681)
Q Consensus 274 ~it~~R~~~vdFT~P~~~~~~~~vv~~~~~~~~~~~~fl~PF~~~vW~~i~~~~~~v~~v~~~~~~~~~~~~~~~~~~~~ 353 (681)
++|++|.+.++||.||+.++..+++++..
T Consensus 110 ~~t~eR~~~~~fs~py~~~~~~lvv~~~~--------------------------------------------------- 138 (259)
T PRK11917 110 TITPERKRIYNFSEPYYQDAIGLLVLKEK--------------------------------------------------- 138 (259)
T ss_pred cCChhhhheeeeccCceeeceEEEEECCC---------------------------------------------------
Confidence 99999999999999999999999998653
Q ss_pred hhHHHHHHHHHhccCcccccccchhHHHHHHHHHHHHHHhHhhhhhhheeeecccCCCCCCHHHHHhCCCeEEEecChhH
Q 005717 354 GTIFWFSFSTLVFAHRERVVNNLSRFVLIIWVFVVLILTQSYTASLTSMLTVQRLQPSFTDVKDIQKNGYFVGYQTNSFV 433 (681)
Q Consensus 354 ~~~~~~~~~~l~~~~~~~~~s~~~R~l~~~w~~~~lil~s~YtA~L~s~LT~~~~~~~i~s~~dL~~~~~~vg~~~~s~~ 433 (681)
++++++||. |.+||+..|+..
T Consensus 139 ---------------------------------------------------------~~~s~~dL~--g~~V~v~~gs~~ 159 (259)
T PRK11917 139 ---------------------------------------------------------NYKSLADMK--GANIGVAQAATT 159 (259)
T ss_pred ---------------------------------------------------------CCCCHHHhC--CCeEEEecCCcH
Confidence 378899998 889999999887
Q ss_pred HHHHhhhcC--CccccccccCChhHHHHHHccCcceEEecchhhHHHHHhhcCCceEEECcccccCCcEEEecCCCC-Ch
Q 005717 434 KDLLTKKLN--FNETRLKNYTTSEDYHDALSNGEVAAIFDEIPYIKIFLASYCSRYMMVGPTYRTDGFGFAFPLGSP-LV 510 (681)
Q Consensus 434 ~~~l~~~~~--~~~~~~~~~~~~~~~~~~l~~g~~~a~i~e~~~~~~~~~~~c~~l~~v~~~~~~~~~~~~~~k~sp-l~ 510 (681)
.+.+.+... ....++..+++..+..+++.+|++|+++.+...+.++.++ +..++++.+...+++++++|+++ ++
T Consensus 160 ~~~l~~~~~~~~~~~~~~~~~~~~~~~~~l~~GrvDa~~~d~~~~~~~~~~---~~~~~~~~~~~~~~~~a~~k~~~~l~ 236 (259)
T PRK11917 160 KKAIGEAAKKIGIDVKFSEFPDYPSIKAALDAKRVDAFSVDKSILLGYVDD---KSEILPDSFEPQSYGIVTKKDDPAFA 236 (259)
T ss_pred HHHHHHhhHhcCCceeEEecCCHHHHHHHHHcCCCcEEEecHHHHHHhhhc---CCeecCCcCCCCceEEEEeCCCHHHH
Confidence 766522111 1123556788899999999999999999988766655543 33566677778889999999988 99
Q ss_pred HHHHHHHHhhccCccHHHHHHHHHc
Q 005717 511 PYISRAILKVTEDKEKMENIEKALG 535 (681)
Q Consensus 511 ~~in~~Il~l~e~~G~l~~i~~kw~ 535 (681)
+.+|++|.++. +.+++|.+||-
T Consensus 237 ~~ln~~l~~~~---~~~~~i~~kw~ 258 (259)
T PRK11917 237 KYVDDFVKEHK---NEIDALAKKWG 258 (259)
T ss_pred HHHHHHHHHHH---HHHHHHHHHhC
Confidence 99999999984 47999999994
No 17
>PRK15007 putative ABC transporter arginine-biding protein; Provisional
Probab=99.84 E-value=1.9e-19 Score=182.23 Aligned_cols=216 Identities=21% Similarity=0.363 Sum_probs=176.4
Q ss_pred ceEEEEeeccCCccceEEEeecCCCCeeEEeehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEE
Q 005717 195 RKLKIGVPVREGFTEFIKVVENKNKTTQVSGFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTT 274 (681)
Q Consensus 195 ~~lrV~v~~~~p~~~~~~~~~~~~~~~~~~G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~ 274 (681)
++|+||+.. .++||... +.++++.|+++|+++++++++|.+ ++++.. +|..++..+.+|++|+++++++
T Consensus 21 ~~l~v~~~~--~~~P~~~~----~~~g~~~G~~~dl~~~i~~~lg~~--~~~~~~---~~~~~~~~l~~g~~D~~~~~~~ 89 (243)
T PRK15007 21 ETIRFATEA--SYPPFESI----DANNQIVGFDVDLAQALCKEIDAT--CTFSNQ---AFDSLIPSLKFRRVEAVMAGMD 89 (243)
T ss_pred CcEEEEeCC--CCCCceee----CCCCCEEeeeHHHHHHHHHHhCCc--EEEEeC---CHHHHhHHHhCCCcCEEEEcCc
Confidence 679999973 23445543 456789999999999999999955 677665 7999999999999999988888
Q ss_pred EeeccccccccccceeecceEEEEEeccCCCcCceeeeccCcHhHHHHHHHHHHHHHHHhhhhhcccCCCCCCCCCCchh
Q 005717 275 IVANRSTFVDFTLPYSESGVSMLVLVKDDERKNFWIFLKPLSWDLWLTTGAAFIFTGLVVWVLEHRINTEFRGPPQHQIG 354 (681)
Q Consensus 275 it~~R~~~vdFT~P~~~~~~~~vv~~~~~~~~~~~~fl~PF~~~vW~~i~~~~~~v~~v~~~~~~~~~~~~~~~~~~~~~ 354 (681)
.+++|.+.++||.||+..+..++.+..
T Consensus 90 ~~~~r~~~~~fs~p~~~~~~~~v~~~~----------------------------------------------------- 116 (243)
T PRK15007 90 ITPEREKQVLFTTPYYDNSALFVGQQG----------------------------------------------------- 116 (243)
T ss_pred cCHHHhcccceecCccccceEEEEeCC-----------------------------------------------------
Confidence 999999999999999988877765532
Q ss_pred hHHHHHHHHHhccCcccccccchhHHHHHHHHHHHHHHhHhhhhhhheeeecccCCCCCCHHHHHhCCCeEEEecChhHH
Q 005717 355 TIFWFSFSTLVFAHRERVVNNLSRFVLIIWVFVVLILTQSYTASLTSMLTVQRLQPSFTDVKDIQKNGYFVGYQTNSFVK 434 (681)
Q Consensus 355 ~~~~~~~~~l~~~~~~~~~s~~~R~l~~~w~~~~lil~s~YtA~L~s~LT~~~~~~~i~s~~dL~~~~~~vg~~~~s~~~ 434 (681)
.+++++||. +.+||+..|+...
T Consensus 117 --------------------------------------------------------~~~~~~dL~--g~~Igv~~g~~~~ 138 (243)
T PRK15007 117 --------------------------------------------------------KYTSVDQLK--GKKVGVQNGTTHQ 138 (243)
T ss_pred --------------------------------------------------------CCCCHHHhC--CCeEEEecCcHHH
Confidence 256789997 8899999999888
Q ss_pred HHHhhhcCCccccccccCChhHHHHHHccCcceEEecchhhHHHHHhhcCCceEEECcc-----cccCCcEEEecCCCC-
Q 005717 435 DLLTKKLNFNETRLKNYTTSEDYHDALSNGEVAAIFDEIPYIKIFLASYCSRYMMVGPT-----YRTDGFGFAFPLGSP- 508 (681)
Q Consensus 435 ~~l~~~~~~~~~~~~~~~~~~~~~~~l~~g~~~a~i~e~~~~~~~~~~~c~~l~~v~~~-----~~~~~~~~~~~k~sp- 508 (681)
+++.+ ..+..+++.+++.++..++|.+|++|+++.+...+.+++++.. .+..++.. +...+++|+++++.+
T Consensus 139 ~~l~~--~~~~~~~~~~~~~~~~~~~L~~grvDa~i~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 215 (243)
T PRK15007 139 KFIMD--KHPEITTVPYDSYQNAKLDLQNGRIDAVFGDTAVVTEWLKDNP-KLAAVGDKVTDKDYFGTGLGIAVRQGNTE 215 (243)
T ss_pred HHHHH--hCCCCeEEEcCCHHHHHHHHHcCCCCEEEeCHHHHHHHHhcCC-CceeecCcccccccCCcceEEEEeCCCHH
Confidence 88833 2445566778899999999999999999999888888777664 45444332 223457899998876
Q ss_pred ChHHHHHHHHhhccCccHHHHHHHHHcC
Q 005717 509 LVPYISRAILKVTEDKEKMENIEKALGN 536 (681)
Q Consensus 509 l~~~in~~Il~l~e~~G~l~~i~~kw~~ 536 (681)
|+..||++|.++.++ |.++++.+||+.
T Consensus 216 l~~~ln~~l~~l~~~-g~~~~i~~~w~~ 242 (243)
T PRK15007 216 LQQKLNTALEKVKKD-GTYETIYNKWFQ 242 (243)
T ss_pred HHHHHHHHHHHHHhC-CcHHHHHHHhcC
Confidence 999999999999999 999999999985
No 18
>TIGR02995 ectoine_ehuB ectoine/hydroxyectoine ABC transporter solute-binding protein. Members of this family are the extracellular solute-binding proteins of ABC transporters that closely resemble amino acid transporters. The member from Sinorhizobium meliloti is involved in ectoine uptake, both for osmoprotection and for catabolism. All other members of the seed alignment are found associated with ectoine catabolic genes.
Probab=99.83 E-value=2.7e-19 Score=184.49 Aligned_cols=223 Identities=17% Similarity=0.160 Sum_probs=179.5
Q ss_pred ceEEEEeeccCCccceEEEeecCCCCeeEEeehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEE
Q 005717 195 RKLKIGVPVREGFTEFIKVVENKNKTTQVSGFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTT 274 (681)
Q Consensus 195 ~~lrV~v~~~~p~~~~~~~~~~~~~~~~~~G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~ 274 (681)
++|+|++...+| |... +.++++.|+++||++++++++|.+. +++... +|+.++..+.+|++|+++++++
T Consensus 33 ~~l~v~~~~~pP---~~~~----~~~g~~~G~~~dl~~~i~~~lg~~~-~~~~~~---~w~~~~~~l~~G~~Di~~~~~~ 101 (275)
T TIGR02995 33 GFARIAIANEPP---FTYV----GADGKVSGAAPDVARAIFKRLGIAD-VNASIT---EYGALIPGLQAGRFDAIAAGLF 101 (275)
T ss_pred CcEEEEccCCCC---ceeE----CCCCceecchHHHHHHHHHHhCCCc-eeeccC---CHHHHHHHHHCCCcCEEeeccc
Confidence 789999876544 5443 4567889999999999999999541 445544 8999999999999999988889
Q ss_pred EeeccccccccccceeecceEEEEEeccCCCcCceeeeccCcHhHHHHHHHHHHHHHHHhhhhhcccCCCCCCCCCCchh
Q 005717 275 IVANRSTFVDFTLPYSESGVSMLVLVKDDERKNFWIFLKPLSWDLWLTTGAAFIFTGLVVWVLEHRINTEFRGPPQHQIG 354 (681)
Q Consensus 275 it~~R~~~vdFT~P~~~~~~~~vv~~~~~~~~~~~~fl~PF~~~vW~~i~~~~~~v~~v~~~~~~~~~~~~~~~~~~~~~ 354 (681)
++++|.+.++||.||+.++.++++++....
T Consensus 102 ~t~eR~~~~~fs~py~~~~~~~~~~~~~~~-------------------------------------------------- 131 (275)
T TIGR02995 102 IKPERCKQVAFTQPILCDAEALLVKKGNPK-------------------------------------------------- 131 (275)
T ss_pred CCHHHHhccccccceeecceeEEEECCCCC--------------------------------------------------
Confidence 999999999999999999999998875421
Q ss_pred hHHHHHHHHHhccCcccccccchhHHHHHHHHHHHHHHhHhhhhhhheeeecccCCCCCCHHHHHhC-CCeEEEecChhH
Q 005717 355 TIFWFSFSTLVFAHRERVVNNLSRFVLIIWVFVVLILTQSYTASLTSMLTVQRLQPSFTDVKDIQKN-GYFVGYQTNSFV 433 (681)
Q Consensus 355 ~~~~~~~~~l~~~~~~~~~s~~~R~l~~~w~~~~lil~s~YtA~L~s~LT~~~~~~~i~s~~dL~~~-~~~vg~~~~s~~ 433 (681)
.+++++||... +.+||+..|+..
T Consensus 132 --------------------------------------------------------~i~~~~dl~~~~g~~Igv~~g~~~ 155 (275)
T TIGR02995 132 --------------------------------------------------------GLKSYKDIAKNPDAKIAAPGGGTE 155 (275)
T ss_pred --------------------------------------------------------CCCCHHHhccCCCceEEEeCCcHH
Confidence 36788888642 679999999998
Q ss_pred HHHHhhhcCCccccccccCChhHHHHHHccCcceEEecchhhHHHHHhhc-CCceEEECccc---ccCCcEEEecCCCC-
Q 005717 434 KDLLTKKLNFNETRLKNYTTSEDYHDALSNGEVAAIFDEIPYIKIFLASY-CSRYMMVGPTY---RTDGFGFAFPLGSP- 508 (681)
Q Consensus 434 ~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~g~~~a~i~e~~~~~~~~~~~-c~~l~~v~~~~---~~~~~~~~~~k~sp- 508 (681)
.+++ ++.+++..++..+++.++++++|.+|++|+++.+...+.+++++. -.++..+.+.- ....++|+++++++
T Consensus 156 ~~~l-~~~~~~~~~i~~~~~~~~~i~~L~~grvDa~i~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 234 (275)
T TIGR02995 156 EKLA-REAGVKREQIIVVPDGQSGLKMVQDGRADAYSLTVLTINDLASKAGDPNVEVLAPFKDAPVRYYGGAAFRPEDKE 234 (275)
T ss_pred HHHH-HHcCCChhhEEEeCCHHHHHHHHHcCCCCEEecChHHHHHHHHhCCCCCceeecCccCCccccceeEEECCCCHH
Confidence 8888 544555557778899999999999999999999998888887764 22444443321 11233788888776
Q ss_pred ChHHHHHHHHhhccCccHHHHHHHHHcC
Q 005717 509 LVPYISRAILKVTEDKEKMENIEKALGN 536 (681)
Q Consensus 509 l~~~in~~Il~l~e~~G~l~~i~~kw~~ 536 (681)
|++.||++|.++.++ |.+++|.+||--
T Consensus 235 l~~~~n~~l~~~~~s-G~~~~i~~ky~~ 261 (275)
T TIGR02995 235 LRDAFNVELAKLKES-GEFAKIIAPYGF 261 (275)
T ss_pred HHHHHHHHHHHHHhC-hHHHHHHHHhCC
Confidence 999999999999999 999999999943
No 19
>TIGR01096 3A0103s03R lysine-arginine-ornithine-binding periplasmic protein.
Probab=99.83 E-value=3.3e-19 Score=181.26 Aligned_cols=218 Identities=22% Similarity=0.409 Sum_probs=180.7
Q ss_pred ceEEEEeeccCCccceEEEeecCCCCeeEEeehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEE
Q 005717 195 RKLKIGVPVREGFTEFIKVVENKNKTTQVSGFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTT 274 (681)
Q Consensus 195 ~~lrV~v~~~~p~~~~~~~~~~~~~~~~~~G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~ 274 (681)
++|||++.. .++||... +++++++|+++|+++++++.+|. ++++++. +|..++.++.+|++|+++++++
T Consensus 24 ~~l~v~~~~--~~~P~~~~----~~~g~~~G~~~dl~~~i~~~lg~--~~~~~~~---~~~~~~~~l~~G~~D~~~~~~~ 92 (250)
T TIGR01096 24 GSVRIGTET--GYPPFESK----DANGKLVGFDVDLAKALCKRMKA--KCKFVEQ---NFDGLIPSLKAKKVDAIMATMS 92 (250)
T ss_pred CeEEEEECC--CCCCceEE----CCCCCEEeehHHHHHHHHHHhCC--eEEEEeC---CHHHHHHHHhCCCcCEEEecCc
Confidence 579999853 34456554 45678999999999999999994 5777776 8999999999999999988888
Q ss_pred EeeccccccccccceeecceEEEEEeccCCCcCceeeeccCcHhHHHHHHHHHHHHHHHhhhhhcccCCCCCCCCCCchh
Q 005717 275 IVANRSTFVDFTLPYSESGVSMLVLVKDDERKNFWIFLKPLSWDLWLTTGAAFIFTGLVVWVLEHRINTEFRGPPQHQIG 354 (681)
Q Consensus 275 it~~R~~~vdFT~P~~~~~~~~vv~~~~~~~~~~~~fl~PF~~~vW~~i~~~~~~v~~v~~~~~~~~~~~~~~~~~~~~~ 354 (681)
.+.+|.+.+.||.|++..+..+++++...
T Consensus 93 ~~~~r~~~~~~s~p~~~~~~~~~~~~~~~--------------------------------------------------- 121 (250)
T TIGR01096 93 ITPKRQKQIDFSDPYYATGQGFVVKKGSD--------------------------------------------------- 121 (250)
T ss_pred cCHHHhhccccccchhcCCeEEEEECCCC---------------------------------------------------
Confidence 99999999999999999999999876532
Q ss_pred hHHHHHHHHHhccCcccccccchhHHHHHHHHHHHHHHhHhhhhhhheeeecccCCCCCCHHHHHhCCCeEEEecChhHH
Q 005717 355 TIFWFSFSTLVFAHRERVVNNLSRFVLIIWVFVVLILTQSYTASLTSMLTVQRLQPSFTDVKDIQKNGYFVGYQTNSFVK 434 (681)
Q Consensus 355 ~~~~~~~~~l~~~~~~~~~s~~~R~l~~~w~~~~lil~s~YtA~L~s~LT~~~~~~~i~s~~dL~~~~~~vg~~~~s~~~ 434 (681)
.+.+++||. +.++|+..|+...
T Consensus 122 --------------------------------------------------------~~~~~~dl~--g~~i~~~~g~~~~ 143 (250)
T TIGR01096 122 --------------------------------------------------------LAKTLEDLD--GKTVGVQSGTTHE 143 (250)
T ss_pred --------------------------------------------------------cCCChHHcC--CCEEEEecCchHH
Confidence 245788887 8899999999888
Q ss_pred HHHhhhcCCc-cccccccCChhHHHHHHccCcceEEecchhhHHHHHhhcC--CceEEECccccc-----CCcEEEecCC
Q 005717 435 DLLTKKLNFN-ETRLKNYTTSEDYHDALSNGEVAAIFDEIPYIKIFLASYC--SRYMMVGPTYRT-----DGFGFAFPLG 506 (681)
Q Consensus 435 ~~l~~~~~~~-~~~~~~~~~~~~~~~~l~~g~~~a~i~e~~~~~~~~~~~c--~~l~~v~~~~~~-----~~~~~~~~k~ 506 (681)
.++.+. ++ ..++..+.+.+++.++|.+|++|+++.+...+.+.+++.. +++.+++..+.. ..++++++++
T Consensus 144 ~~l~~~--~~~~~~~~~~~s~~~~~~~L~~g~vD~~v~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~ 221 (250)
T TIGR01096 144 QYLKDY--FKPGVDIVEYDSYDNANMDLKAGRIDAVFTDASVLAEGFLKPPNGKDFKFVGPSVTDEKYFGDGYGIGLRKG 221 (250)
T ss_pred HHHHHh--ccCCcEEEEcCCHHHHHHHHHcCCCCEEEeCHHHHHHHHHhCCCCCceEEeccccccccccCCceEEEEeCC
Confidence 887332 22 4456778899999999999999999999999998887753 247777654432 2478999999
Q ss_pred CC-ChHHHHHHHHhhccCccHHHHHHHHHc
Q 005717 507 SP-LVPYISRAILKVTEDKEKMENIEKALG 535 (681)
Q Consensus 507 sp-l~~~in~~Il~l~e~~G~l~~i~~kw~ 535 (681)
++ |+..+|++|.++.++ |.+++|.+||+
T Consensus 222 ~~~l~~~ln~~l~~l~~~-g~~~~i~~kw~ 250 (250)
T TIGR01096 222 DTELKAAFNKALAAIRAD-GTYQKISKKWF 250 (250)
T ss_pred CHHHHHHHHHHHHHHHHC-CcHHHHHHhhC
Confidence 87 999999999999999 99999999996
No 20
>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=99.82 E-value=6.5e-20 Score=198.46 Aligned_cols=158 Identities=18% Similarity=0.257 Sum_probs=127.8
Q ss_pred CCCCCeEEEecCCccccCCccccccCccceEEEEEecCCChhHHHHHHHHHhh--cCCCC--CCC--CCCchhHHHHHHH
Q 005717 1 MMSEGYAWIATQGLSTLLDPVKDMESMQGVLGLRPYIPSSKKLEHFKLRWIKS--ADKPD--GST--GGSNLFGLWAYDT 74 (681)
Q Consensus 1 mm~~~y~WI~t~~~~~~~~~~~~~~~~~Gvlg~~~~~~~~~~~~~f~~~~~~~--~~~~~--~~~--~~~~~~~~~aYDa 74 (681)
|++++|+||+|+.....++...+......++|++...+.++.+++|.++|+.+ ...|. ... ..++.+++++|||
T Consensus 217 m~~~~~~~~~~~~~~~~~~~~~~~~~~~~it~~~~~~~~~~~~~~f~~~~~~~~~~~~p~~~~~~~~~~~~~~aal~yDa 296 (384)
T cd06393 217 MMTEYYHFIFTTLDLYALDLEPYRYSGVNLTGFRILNVDNPHVSSIVEKWSMERLQAAPKPETGLLDGVMMTDAALLYDA 296 (384)
T ss_pred cccCceEEEEccCccccccchhhhcCcceEEEEEecCCCcHHHHHHHHHHHhhhhccccccccccccccccchhHHhhhh
Confidence 78899999999986655554333334455799999999999999999999753 22221 111 1246789999999
Q ss_pred HHHHHHHHHHHcccCCcccccCCCCCCCcccccCCCcchHHHHHHHhccceecceeeEEE-e-CCcccCccEEEEEeeeC
Q 005717 75 VWAIAMAVERAGIENSSFLKSNTSKSRVDIAALGTFEMGAKLLDTLINTTFEGLSGNFHL-V-NGQLEPSAFEIFNVIGT 152 (681)
Q Consensus 75 v~~lA~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~l~~~l~~~~f~GltG~i~F-~-~G~~~~~~~~I~n~~~~ 152 (681)
||++|+|++++... +...++|+...+|..|..|+++|++++|+|+||+|+| + +|+|.++.|+|+|+.++
T Consensus 297 v~~~a~A~~~~~~~---------~~~~~~c~~~~~w~~G~~i~~~l~~~~~~GltG~i~Fd~~~g~r~~~~~~i~~~~~~ 367 (384)
T cd06393 297 VHMVSVCYQRAPQM---------TVNSLQCHRHKAWRFGGRFMNFIKEAQWEGLTGRIVFNKTSGLRTDFDLDIISLKED 367 (384)
T ss_pred HHHHHHHHhhhhhc---------CCCCCCCCCCCCCcccHHHHHHHhheeecccccceEecCCCCeeeeeEEEEEEecCC
Confidence 99999999976421 1234678888899999999999999999999999999 4 57999999999999999
Q ss_pred CeeEeeeeeCCCCcc
Q 005717 153 SERVIGYWTKEKELL 167 (681)
Q Consensus 153 ~~~~vG~W~~~~gl~ 167 (681)
++++||+|++..|+.
T Consensus 368 g~~~vg~W~~~~g~~ 382 (384)
T cd06393 368 GLEKVGVWNPNTGLN 382 (384)
T ss_pred cceeeEEEcCCCCcC
Confidence 999999999999985
No 21
>PRK15437 histidine ABC transporter substrate-binding protein HisJ; Provisional
Probab=99.81 E-value=2e-18 Score=176.48 Aligned_cols=223 Identities=18% Similarity=0.288 Sum_probs=173.9
Q ss_pred CceEEEEeeccCCccceEEEeecCCCCeeEEeehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeE
Q 005717 194 PRKLKIGVPVREGFTEFIKVVENKNKTTQVSGFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDT 273 (681)
Q Consensus 194 p~~lrV~v~~~~p~~~~~~~~~~~~~~~~~~G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~ 273 (681)
+++|+|++.. .++||... +.++++.|+++|+++++++++|. ++++++. .|+.++.++.+|++|++++++
T Consensus 25 ~~~l~v~~~~--~~~P~~~~----~~~g~~~G~~vdi~~~ia~~lg~--~i~~~~~---pw~~~~~~l~~g~~D~~~~~~ 93 (259)
T PRK15437 25 PQNIRIGTDP--TYAPFESK----NSQGELVGFDIDLAKELCKRINT--QCTFVEN---PLDALIPSLKAKKIDAIMSSL 93 (259)
T ss_pred CCeEEEEeCC--CCCCccee----CCCCCEEeeeHHHHHHHHHHcCC--ceEEEeC---CHHHHHHHHHCCCCCEEEecC
Confidence 4789999864 23445543 45678999999999999999995 5777776 799999999999999999889
Q ss_pred EEeeccccccccccceeecceEEEEEeccCCCcCceeeeccCcHhHHHHHHHHHHHHHHHhhhhhcccCCCCCCCCCCch
Q 005717 274 TIVANRSTFVDFTLPYSESGVSMLVLVKDDERKNFWIFLKPLSWDLWLTTGAAFIFTGLVVWVLEHRINTEFRGPPQHQI 353 (681)
Q Consensus 274 ~it~~R~~~vdFT~P~~~~~~~~vv~~~~~~~~~~~~fl~PF~~~vW~~i~~~~~~v~~v~~~~~~~~~~~~~~~~~~~~ 353 (681)
+.|++|.+.++||.||...+.++++++...
T Consensus 94 ~~t~eR~~~~~fs~p~~~~~~~~~~~~~~~-------------------------------------------------- 123 (259)
T PRK15437 94 SITEKRQQEIAFTDKLYAADSRLVVAKNSD-------------------------------------------------- 123 (259)
T ss_pred CCCHHHhhhccccchhhcCceEEEEECCCC--------------------------------------------------
Confidence 999999999999999999999999886532
Q ss_pred hhHHHHHHHHHhccCcccccccchhHHHHHHHHHHHHHHhHhhhhhhheeeecccCCCCCCHHHHHhCCCeEEEecChhH
Q 005717 354 GTIFWFSFSTLVFAHRERVVNNLSRFVLIIWVFVVLILTQSYTASLTSMLTVQRLQPSFTDVKDIQKNGYFVGYQTNSFV 433 (681)
Q Consensus 354 ~~~~~~~~~~l~~~~~~~~~s~~~R~l~~~w~~~~lil~s~YtA~L~s~LT~~~~~~~i~s~~dL~~~~~~vg~~~~s~~ 433 (681)
...+++||. +.+||+..|+..
T Consensus 124 ---------------------------------------------------------~~~~~~dl~--g~~Igv~~g~~~ 144 (259)
T PRK15437 124 ---------------------------------------------------------IQPTVESLK--GKRVGVLQGTTQ 144 (259)
T ss_pred ---------------------------------------------------------CCCChHHhC--CCEEEEecCcHH
Confidence 123688886 889999999988
Q ss_pred HHHHhhhcCCccccccccCChhHHHHHHccCcceEEecchhhHHH-HHhhc-CCceEEECc-----ccccCCcEEEecCC
Q 005717 434 KDLLTKKLNFNETRLKNYTTSEDYHDALSNGEVAAIFDEIPYIKI-FLASY-CSRYMMVGP-----TYRTDGFGFAFPLG 506 (681)
Q Consensus 434 ~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~g~~~a~i~e~~~~~~-~~~~~-c~~l~~v~~-----~~~~~~~~~~~~k~ 506 (681)
..++.........++..+.+.++.+++|.+|++|+++.+.....+ +.++. -..+...+. .+...+++++++++
T Consensus 145 ~~~~~~~~~~~~~~~~~~~~~~~~i~~L~~grvD~~v~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~ia~~~~ 224 (259)
T PRK15437 145 ETFGNEHWAPKGIEIVSYQGQDNIYSDLTAGRIDAAFQDEVAASEGFLKQPVGKDYKFGGPSVKDEKLFGVGTGMGLRKE 224 (259)
T ss_pred HHHHHhhccccCceEEecCCHHHHHHHHHcCCccEEEechHHHHHHHHhCCCCCceEEecCccccccccCcceEEEEeCC
Confidence 777732211123456778888999999999999999988766543 33332 223443322 22234567888887
Q ss_pred CC-ChHHHHHHHHhhccCccHHHHHHHHHcCC
Q 005717 507 SP-LVPYISRAILKVTEDKEKMENIEKALGNQ 537 (681)
Q Consensus 507 sp-l~~~in~~Il~l~e~~G~l~~i~~kw~~~ 537 (681)
.+ |++.+|++|.++..+ |.+++|.+||+..
T Consensus 225 ~~~l~~~~n~~l~~~~~~-G~~~~i~~k~~~~ 255 (259)
T PRK15437 225 DNELREALNKAFAEMRAD-GTYEKLAKKYFDF 255 (259)
T ss_pred CHHHHHHHHHHHHHHHHC-CcHHHHHHHhcCC
Confidence 66 999999999999999 9999999999964
No 22
>PRK10859 membrane-bound lytic transglycosylase F; Provisional
Probab=99.79 E-value=2.9e-18 Score=190.01 Aligned_cols=220 Identities=15% Similarity=0.192 Sum_probs=176.0
Q ss_pred ceEEEEeeccCCccceEEEeecCCCCeeEEeehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEE
Q 005717 195 RKLKIGVPVREGFTEFIKVVENKNKTTQVSGFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTT 274 (681)
Q Consensus 195 ~~lrV~v~~~~p~~~~~~~~~~~~~~~~~~G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~ 274 (681)
++||||+.. +|+..+. .+ +...||++||++++++++|.+ ++++.. .+|++++.+|.+|++|+++++++
T Consensus 43 g~LrVg~~~-~P~~~~~------~~-~~~~G~~~DLl~~ia~~LGv~--~e~v~~--~~~~~ll~aL~~G~iDi~~~~lt 110 (482)
T PRK10859 43 GELRVGTIN-SPLTYYI------GN-DGPTGFEYELAKRFADYLGVK--LEIKVR--DNISQLFDALDKGKADLAAAGLT 110 (482)
T ss_pred CEEEEEEec-CCCeeEe------cC-CCcccHHHHHHHHHHHHhCCc--EEEEec--CCHHHHHHHHhCCCCCEEeccCc
Confidence 689999985 4443332 22 334999999999999999955 666644 48999999999999999988899
Q ss_pred EeeccccccccccceeecceEEEEEeccCCCcCceeeeccCcHhHHHHHHHHHHHHHHHhhhhhcccCCCCCCCCCCchh
Q 005717 275 IVANRSTFVDFTLPYSESGVSMLVLVKDDERKNFWIFLKPLSWDLWLTTGAAFIFTGLVVWVLEHRINTEFRGPPQHQIG 354 (681)
Q Consensus 275 it~~R~~~vdFT~P~~~~~~~~vv~~~~~~~~~~~~fl~PF~~~vW~~i~~~~~~v~~v~~~~~~~~~~~~~~~~~~~~~ 354 (681)
+|++|.+.++||.||+..+.++++++...
T Consensus 111 ~T~eR~~~~~FS~Py~~~~~~lv~r~~~~--------------------------------------------------- 139 (482)
T PRK10859 111 YTPERLKQFRFGPPYYSVSQQLVYRKGQP--------------------------------------------------- 139 (482)
T ss_pred CChhhhccCcccCCceeeeEEEEEeCCCC---------------------------------------------------
Confidence 99999999999999999999999876531
Q ss_pred hHHHHHHHHHhccCcccccccchhHHHHHHHHHHHHHHhHhhhhhhheeeecccCCCCCCHHHHHhCCCeEEEecChhHH
Q 005717 355 TIFWFSFSTLVFAHRERVVNNLSRFVLIIWVFVVLILTQSYTASLTSMLTVQRLQPSFTDVKDIQKNGYFVGYQTNSFVK 434 (681)
Q Consensus 355 ~~~~~~~~~l~~~~~~~~~s~~~R~l~~~w~~~~lil~s~YtA~L~s~LT~~~~~~~i~s~~dL~~~~~~vg~~~~s~~~ 434 (681)
.+++++||. |.+||+..|+...
T Consensus 140 --------------------------------------------------------~i~~l~dL~--Gk~I~V~~gS~~~ 161 (482)
T PRK10859 140 --------------------------------------------------------RPRSLGDLK--GGTLTVAAGSSHV 161 (482)
T ss_pred --------------------------------------------------------CCCCHHHhC--CCeEEEECCCcHH
Confidence 478899998 8899999999888
Q ss_pred HHHhhhc-CCccccc--cccCChhHHHHHHccCcceEEecchhhHHHHHhhcCCceEEECcccccCCcEEEecCC-CC-C
Q 005717 435 DLLTKKL-NFNETRL--KNYTTSEDYHDALSNGEVAAIFDEIPYIKIFLASYCSRYMMVGPTYRTDGFGFAFPLG-SP-L 509 (681)
Q Consensus 435 ~~l~~~~-~~~~~~~--~~~~~~~~~~~~l~~g~~~a~i~e~~~~~~~~~~~c~~l~~v~~~~~~~~~~~~~~k~-sp-l 509 (681)
+.+.+.. .++..++ ..+.+.++++++|.+|++|+++.+...+.+....+. ++.+........+++++++|+ .+ |
T Consensus 162 ~~L~~l~~~~p~i~~~~~~~~s~~e~l~aL~~G~iDa~v~d~~~~~~~~~~~p-~l~v~~~l~~~~~~~~av~k~~~~~L 240 (482)
T PRK10859 162 ETLQELKKKYPELSWEESDDKDSEELLEQVAEGKIDYTIADSVEISLNQRYHP-ELAVAFDLTDEQPVAWALPPSGDDSL 240 (482)
T ss_pred HHHHHHHHhCCCceEEecCCCCHHHHHHHHHCCCCCEEEECcHHHHHHHHhCC-CceeeeecCCCceeEEEEeCCCCHHH
Confidence 7773211 1233332 346789999999999999999998877665544444 666655555567789999994 55 9
Q ss_pred hHHHHHHHHhhccCccHHHHHHHHHcCC
Q 005717 510 VPYISRAILKVTEDKEKMENIEKALGNQ 537 (681)
Q Consensus 510 ~~~in~~Il~l~e~~G~l~~i~~kw~~~ 537 (681)
+..+|++|.++.++ |.+++|.+||+..
T Consensus 241 ~~~ln~~L~~i~~~-G~l~~L~~kyfg~ 267 (482)
T PRK10859 241 YAALLDFFNQIKED-GTLARLEEKYFGH 267 (482)
T ss_pred HHHHHHHHHHhhcC-CHHHHHHHHHhhh
Confidence 99999999999999 9999999999975
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=99.79 E-value=1.6e-18 Score=187.79 Aligned_cols=166 Identities=21% Similarity=0.282 Sum_probs=130.0
Q ss_pred CCCCCeEEEecCCccccCCccccccCccceEEEEEecCCChhHHHHHHHHHhh--cCCCCCCCCCCchhHHHHHHHHHHH
Q 005717 1 MMSEGYAWIATQGLSTLLDPVKDMESMQGVLGLRPYIPSSKKLEHFKLRWIKS--ADKPDGSTGGSNLFGLWAYDTVWAI 78 (681)
Q Consensus 1 mm~~~y~WI~t~~~~~~~~~~~~~~~~~Gvlg~~~~~~~~~~~~~f~~~~~~~--~~~~~~~~~~~~~~~~~aYDav~~l 78 (681)
|++++||||++++..+.++...+.....+++|++...+..+..++|.++|++. .++|......++.+++++|||||++
T Consensus 208 m~~~~y~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~aa~aYDav~~~ 287 (382)
T cd06380 208 KNRKGYHYILANLGFDDIDLSKFLFGGVNITGFQLVDNTNPTVQKFLQRWKKLDPREWPGAGTSPIKYTAALAHDAVLVM 287 (382)
T ss_pred hcccceEEEEccCCcccccHHHhccCceeeEEEeccCCCCHHHHHHHHHHHhcCccccCcCCcCCcchHHHHHHHHHHHH
Confidence 67899999999987766654334445567899998888788999999999876 2334333335677999999999999
Q ss_pred HHHHHHHcccCCcc---cccCCCCCCCccc--ccCCCcchHHHHHHHhccceecceeeEEE-eCCcccCccEEEEEeeeC
Q 005717 79 AMAVERAGIENSSF---LKSNTSKSRVDIA--ALGTFEMGAKLLDTLINTTFEGLSGNFHL-VNGQLEPSAFEIFNVIGT 152 (681)
Q Consensus 79 A~Al~~~~~~~~~~---~~~~~~~~~~~~~--~~~~~~~G~~l~~~l~~~~f~GltG~i~F-~~G~~~~~~~~I~n~~~~ 152 (681)
|+|++++....... ...+....+..|. ...+|.+|..|+++|++++|+|+||+++| ++|++.+..++|+|++++
T Consensus 288 a~Al~~~~~~~~~~~~~~~~~~~~~~~~C~~~~~~~~~~g~~i~~~l~~~~~~G~tG~i~Fd~~G~~~~~~~~i~~~~~~ 367 (382)
T cd06380 288 AEAFRSLRRQRGSGRHRIDISRRGNGGDCLANPAVPWEHGIDIERALKKVQFEGLTGNVQFDEFGQRTNYTLDVVELKTR 367 (382)
T ss_pred HHHHHHHHHhccccccccccccCCCCCcCCCCCCCCccchHHHHHHHHhcccCCcccceEECCCCCcccccEEEEEecCC
Confidence 99999986432110 0001112244564 35679999999999999999999999999 899999889999999999
Q ss_pred CeeEeeeeeCCCCc
Q 005717 153 SERVIGYWTKEKEL 166 (681)
Q Consensus 153 ~~~~vG~W~~~~gl 166 (681)
++++||+|++..|+
T Consensus 368 ~~~~vg~w~~~~g~ 381 (382)
T cd06380 368 GLRKVGYWNEDDGL 381 (382)
T ss_pred CceEEEEECCCcCc
Confidence 99999999998886
No 24
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=99.77 E-value=9.8e-18 Score=207.43 Aligned_cols=217 Identities=14% Similarity=0.186 Sum_probs=177.8
Q ss_pred ceEEEEeeccCCccceEEEeecCCCCeeEEeehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEE
Q 005717 195 RKLKIGVPVREGFTEFIKVVENKNKTTQVSGFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTT 274 (681)
Q Consensus 195 ~~lrV~v~~~~p~~~~~~~~~~~~~~~~~~G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~ 274 (681)
++++||+.. .|+||.+. +.++++.||++|+++++++++| +++++++. ..|..+...|.+|++|++.+ ++
T Consensus 302 ~~l~v~~~~--~~pP~~~~----d~~g~~~G~~~Dll~~i~~~~g--~~~~~v~~--~~~~~~~~~l~~g~~D~i~~-~~ 370 (1197)
T PRK09959 302 PDLKVLENP--YSPPYSMT----DENGSVRGVMGDILNIITLQTG--LNFSPITV--SHNIHAGTQLNPGGWDIIPG-AI 370 (1197)
T ss_pred CceEEEcCC--CCCCeeEE----CCCCcEeeehHHHHHHHHHHHC--CeEEEEec--CCHHHHHHHHHCCCceEeec-cc
Confidence 578998765 45677776 5668999999999999999999 55788887 57888999999999998765 56
Q ss_pred EeeccccccccccceeecceEEEEEeccCCCcCceeeeccCcHhHHHHHHHHHHHHHHHhhhhhcccCCCCCCCCCCchh
Q 005717 275 IVANRSTFVDFTLPYSESGVSMLVLVKDDERKNFWIFLKPLSWDLWLTTGAAFIFTGLVVWVLEHRINTEFRGPPQHQIG 354 (681)
Q Consensus 275 it~~R~~~vdFT~P~~~~~~~~vv~~~~~~~~~~~~fl~PF~~~vW~~i~~~~~~v~~v~~~~~~~~~~~~~~~~~~~~~ 354 (681)
.+++|.+.++||.||+.++.++++++...
T Consensus 371 ~t~~r~~~~~fs~py~~~~~~~v~~~~~~--------------------------------------------------- 399 (1197)
T PRK09959 371 YSEDRENNVLFAEAFITTPYVFVMQKAPD--------------------------------------------------- 399 (1197)
T ss_pred CCccccccceeccccccCCEEEEEecCCC---------------------------------------------------
Confidence 89999999999999999999999875421
Q ss_pred hHHHHHHHHHhccCcccccccchhHHHHHHHHHHHHHHhHhhhhhhheeeecccCCCCCCHHHHHhCCCeEEEecChhHH
Q 005717 355 TIFWFSFSTLVFAHRERVVNNLSRFVLIIWVFVVLILTQSYTASLTSMLTVQRLQPSFTDVKDIQKNGYFVGYQTNSFVK 434 (681)
Q Consensus 355 ~~~~~~~~~l~~~~~~~~~s~~~R~l~~~w~~~~lil~s~YtA~L~s~LT~~~~~~~i~s~~dL~~~~~~vg~~~~s~~~ 434 (681)
.+.+ +. .|.+||+..|+...
T Consensus 400 --------------------------------------------------------~~~~---~~-~g~~vav~~g~~~~ 419 (1197)
T PRK09959 400 --------------------------------------------------------SEQT---LK-KGMKVAIPYYYELH 419 (1197)
T ss_pred --------------------------------------------------------Cccc---cc-cCCEEEEeCCcchH
Confidence 1222 22 48899999999888
Q ss_pred HHHhhhcCCccccccccCChhHHHHHHccCcceEEecchhhHHHHHhhc-CCce-EEECcccccCCcEEEecCCCC-ChH
Q 005717 435 DLLTKKLNFNETRLKNYTTSEDYHDALSNGEVAAIFDEIPYIKIFLASY-CSRY-MMVGPTYRTDGFGFAFPLGSP-LVP 511 (681)
Q Consensus 435 ~~l~~~~~~~~~~~~~~~~~~~~~~~l~~g~~~a~i~e~~~~~~~~~~~-c~~l-~~v~~~~~~~~~~~~~~k~sp-l~~ 511 (681)
+++.+ .++..+++.|++.++++++|.+|++||++.+...+.|+++++ -.++ ....+.+....++|+++|+.| |++
T Consensus 420 ~~~~~--~~p~~~~~~~~~~~~~l~av~~G~~Da~i~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~av~k~~~~L~~ 497 (1197)
T PRK09959 420 SQLKE--MYPEVEWIKVDNASAAFHKVKEGELDALVATQLNSRYMIDHYYPNELYHFLIPGVPNASLSFAFPRGEPELKD 497 (1197)
T ss_pred HHHHH--HCCCcEEEEcCCHHHHHHHHHcCCCCEEehhhHHHHHHHHhcccccceeeecCCCCchheEEeeCCCCHHHHH
Confidence 88733 356678899999999999999999999999999999998875 2233 333444556778999999998 999
Q ss_pred HHHHHHHhhccCccHHHHHHHHHcCC
Q 005717 512 YISRAILKVTEDKEKMENIEKALGNQ 537 (681)
Q Consensus 512 ~in~~Il~l~e~~G~l~~i~~kw~~~ 537 (681)
.+|++|..+.++ .++++.+||+..
T Consensus 498 ~lnk~l~~i~~~--~~~~i~~kW~~~ 521 (1197)
T PRK09959 498 IINKALNAIPPS--EVLRLTEKWIKM 521 (1197)
T ss_pred HHHHHHHhCCHH--HHHHHHhhcccC
Confidence 999999999998 788999999963
No 25
>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=99.75 E-value=1.4e-19 Score=168.51 Aligned_cols=107 Identities=33% Similarity=0.641 Sum_probs=81.9
Q ss_pred cHhHHHHHHHHHHHHHHHhhhhhcccCCCCCC-------CCCCchhhHHHHHHHHHhccC-cccccccchhHHHHHHHHH
Q 005717 316 SWDLWLTTGAAFIFTGLVVWVLEHRINTEFRG-------PPQHQIGTIFWFSFSTLVFAH-RERVVNNLSRFVLIIWVFV 387 (681)
Q Consensus 316 ~~~vW~~i~~~~~~v~~v~~~~~~~~~~~~~~-------~~~~~~~~~~~~~~~~l~~~~-~~~~~s~~~R~l~~~w~~~ 387 (681)
++++|++++++++++++++|+++|..+.+++. ....++.+++|++++++++|+ ...|++.++|++.++|+++
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 57899999999999999999999988777665 223468899999999998755 4568999999999999999
Q ss_pred HHHHHhHhhhhhhheeeecccCCCCCCHHHHHhCC
Q 005717 388 VLILTQSYTASLTSMLTVQRLQPSFTDVKDIQKNG 422 (681)
Q Consensus 388 ~lil~s~YtA~L~s~LT~~~~~~~i~s~~dL~~~~ 422 (681)
++++.++|||+|+|+||.++.+++|+|++||.+++
T Consensus 81 ~lil~~~Yta~L~s~Lt~~~~~~~i~sl~dL~~~~ 115 (148)
T PF00060_consen 81 SLILIASYTANLTSFLTVPKYEPPIDSLEDLANSG 115 (148)
T ss_dssp HHHHHHHHHHHHHHHHHCHHHTSS-SSHHHHHTHS
T ss_pred HHHHHHHHHHHHHHHhcccCcCCCCCCHHHHHHCC
Confidence 99999999999999999999999999999999765
No 26
>TIGR03870 ABC_MoxJ methanol oxidation system protein MoxJ. This predicted periplasmic protein, called MoxJ or MxaJ, is required for methanol oxidation in Methylobacterium extorquens. Two differing lines of evidence suggest two different roles. Forming one view, homology suggests it is the substrate-binding protein of an ABC transporter associated with methanol oxidation. The gene, furthermore, is found regular in genomes with, and only two or three genes away from, a corresponding permease and ATP-binding cassette gene pair. The other view is that this protein is an accessory factor or additional subunit of methanol dehydrogenase itself. Mutational studies show a dependence on this protein for expression of the PQQ-dependent, two-subunit methanol dehydrogenase (MxaF and MxaI) in Methylobacterium extorquens, as if it is a chaperone for enzyme assembly or a third subunit. A homologous N-terminal sequence was found in Paracoccus denitrificans as a 32Kd third subunit. This protein may, in
Probab=99.72 E-value=1.8e-16 Score=160.54 Aligned_cols=208 Identities=15% Similarity=0.172 Sum_probs=154.3
Q ss_pred eEEEEeeccCCccceEEEeecCCCCeeEEeehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHH---HHHHhCccceEEEe
Q 005717 196 KLKIGVPVREGFTEFIKVVENKNKTTQVSGFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELL---HKIEKQEFDTAVGD 272 (681)
Q Consensus 196 ~lrV~v~~~~p~~~~~~~~~~~~~~~~~~G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli---~~l~~g~~Dia~~~ 272 (681)
+||||+.. .|+||.+. ++ .||++||+++|++++|+ ++++++. +|++++ ..|.+|++|++++
T Consensus 1 ~l~vg~~~--~~pPf~~~----~~----~Gfdvdl~~~ia~~lg~--~~~~~~~---~~~~~~~~~~~L~~g~~Dii~~- 64 (246)
T TIGR03870 1 TLRVCAAT--KEAPYSTK----DG----SGFENKIAAALAAAMGR--KVVFVWL---AKPAIYLVRDGLDKKLCDVVLG- 64 (246)
T ss_pred CeEEEeCC--CCCCCccC----CC----CcchHHHHHHHHHHhCC--CeEEEEe---ccchhhHHHHHHhcCCccEEEe-
Confidence 47898865 45566653 22 69999999999999995 5777776 788876 6999999999884
Q ss_pred EEEeeccccccccccceeecceEEEEEeccCCCcCceeeeccCcHhHHHHHHHHHHHHHHHhhhhhcccCCCCCCCCCCc
Q 005717 273 TTIVANRSTFVDFTLPYSESGVSMLVLVKDDERKNFWIFLKPLSWDLWLTTGAAFIFTGLVVWVLEHRINTEFRGPPQHQ 352 (681)
Q Consensus 273 ~~it~~R~~~vdFT~P~~~~~~~~vv~~~~~~~~~~~~fl~PF~~~vW~~i~~~~~~v~~v~~~~~~~~~~~~~~~~~~~ 352 (681)
++++++| ++||.||+.++.++++++....
T Consensus 65 ~~~t~~r---~~fS~PY~~~~~~~v~~k~~~~------------------------------------------------ 93 (246)
T TIGR03870 65 LDTGDPR---VLTTKPYYRSSYVFLTRKDRNL------------------------------------------------ 93 (246)
T ss_pred CCCChHH---HhcccCcEEeeeEEEEeCCCCC------------------------------------------------
Confidence 8888777 6899999999999999876431
Q ss_pred hhhHHHHHHHHHhccCcccccccchhHHHHHHHHHHHHHHhHhhhhhhheeeecccCCCCCCHHH--HHhCCC-eEEEec
Q 005717 353 IGTIFWFSFSTLVFAHRERVVNNLSRFVLIIWVFVVLILTQSYTASLTSMLTVQRLQPSFTDVKD--IQKNGY-FVGYQT 429 (681)
Q Consensus 353 ~~~~~~~~~~~l~~~~~~~~~s~~~R~l~~~w~~~~lil~s~YtA~L~s~LT~~~~~~~i~s~~d--L~~~~~-~vg~~~ 429 (681)
.+++++| |. |+ +||+..
T Consensus 94 ----------------------------------------------------------~~~~~~d~~L~--g~~~vgv~~ 113 (246)
T TIGR03870 94 ----------------------------------------------------------DIKSWNDPRLK--KVSKIGVIF 113 (246)
T ss_pred ----------------------------------------------------------CCCCccchhhc--cCceEEEec
Confidence 3677765 55 87 999999
Q ss_pred ChhHHHHHhhhcCC-c-----cccccccC---------ChhHHHHHHccCcceEEecchhhHHHHHhhcCCceE--EECc
Q 005717 430 NSFVKDLLTKKLNF-N-----ETRLKNYT---------TSEDYHDALSNGEVAAIFDEIPYIKIFLASYCSRYM--MVGP 492 (681)
Q Consensus 430 ~s~~~~~l~~~~~~-~-----~~~~~~~~---------~~~~~~~~l~~g~~~a~i~e~~~~~~~~~~~c~~l~--~v~~ 492 (681)
|+..+.++ ++... . ...+..++ +.++++++|.+|++||++.+.+.+.+++.+.-..+. .+++
T Consensus 114 gs~~~~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~aL~~GrvDa~i~~~~~~~~~~~~~~~~~~~~~~~~ 192 (246)
T TIGR03870 114 GSPAETML-KQIGRYEDNFAYLYSLVNFKSPRNQYTQIDPRKLVSEVATGKADLAVAFAPEVARYVKASPEPLRMTVIPD 192 (246)
T ss_pred CChHHHHH-HhcCccccccccccccccccCcccccccCCHHHHHHHHHcCCCCEEEeeHHhHHHHHHhCCCCceEEeccc
Confidence 99999988 43211 0 01122222 357889999999999999987777777665322233 2332
Q ss_pred cc-------c--cCCcEEEecCCCC-ChHHHHHHHHhhccCccHHHHHHHHH
Q 005717 493 TY-------R--TDGFGFAFPLGSP-LVPYISRAILKVTEDKEKMENIEKAL 534 (681)
Q Consensus 493 ~~-------~--~~~~~~~~~k~sp-l~~~in~~Il~l~e~~G~l~~i~~kw 534 (681)
.. . ..+++++++|+.+ |++.||++|.++. |.+++|..+|
T Consensus 193 ~~~~~~~~~~~~~~~~~iav~k~~~~L~~~in~aL~~l~---~~~~~i~~~y 241 (246)
T TIGR03870 193 DATRSDGAKIPMQYDQSMGVRKDDTALLAEIDAALAKAK---PRIDAILKEE 241 (246)
T ss_pred cccccCCCCcceeeEEEEEEccCCHHHHHHHHHHHHHhH---HHHHHHHHHc
Confidence 21 0 1135899999998 9999999999998 4799999988
No 27
>COG0834 HisJ ABC-type amino acid transport/signal transduction systems, periplasmic component/domain [Amino acid transport and metabolism / Signal transduction mechanisms]
Probab=99.72 E-value=3.1e-16 Score=161.51 Aligned_cols=224 Identities=22% Similarity=0.326 Sum_probs=180.1
Q ss_pred ceEEEEeeccCCccceEEEeecCCCC-eeEEeehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeE
Q 005717 195 RKLKIGVPVREGFTEFIKVVENKNKT-TQVSGFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDT 273 (681)
Q Consensus 195 ~~lrV~v~~~~p~~~~~~~~~~~~~~-~~~~G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~ 273 (681)
+.++|++.... +.||... +.. +++.||++|+++++++.++.....++++. .|++++..|..|++|++++.+
T Consensus 34 ~~~~v~~~~~~-~~p~~~~----~~~~~~~~G~dvdl~~~ia~~l~~~~~~~~~~~---~~~~~~~~l~~g~~D~~~~~~ 105 (275)
T COG0834 34 GKLRVGTEATY-APPFEFL----DAKGGKLVGFDVDLAKAIAKRLGGDKKVEFVPV---AWDGLIPALKAGKVDIIIAGM 105 (275)
T ss_pred CeEEEEecCCC-CCCcccc----cCCCCeEEeeeHHHHHHHHHHhCCcceeEEecc---chhhhhHHHhcCCcCEEEecc
Confidence 56888887532 2345443 344 59999999999999999986434667775 899999999999999999999
Q ss_pred EEeeccccccccccceeecceEEEEEeccCCCcCceeeeccCcHhHHHHHHHHHHHHHHHhhhhhcccCCCCCCCCCCch
Q 005717 274 TIVANRSTFVDFTLPYSESGVSMLVLVKDDERKNFWIFLKPLSWDLWLTTGAAFIFTGLVVWVLEHRINTEFRGPPQHQI 353 (681)
Q Consensus 274 ~it~~R~~~vdFT~P~~~~~~~~vv~~~~~~~~~~~~fl~PF~~~vW~~i~~~~~~v~~v~~~~~~~~~~~~~~~~~~~~ 353 (681)
++|++|.+.++||.||+..+..+++++....
T Consensus 106 ~~t~er~~~~~fs~py~~~~~~~~~~~~~~~------------------------------------------------- 136 (275)
T COG0834 106 TITPERKKKVDFSDPYYYSGQVLLVKKDSDI------------------------------------------------- 136 (275)
T ss_pred ccCHHHhccccccccccccCeEEEEECCCCc-------------------------------------------------
Confidence 9999999999999999999999999877542
Q ss_pred hhHHHHHHHHHhccCcccccccchhHHHHHHHHHHHHHHhHhhhhhhheeeecccCCCCCCHHHHHhCCCeEEEecChh-
Q 005717 354 GTIFWFSFSTLVFAHRERVVNNLSRFVLIIWVFVVLILTQSYTASLTSMLTVQRLQPSFTDVKDIQKNGYFVGYQTNSF- 432 (681)
Q Consensus 354 ~~~~~~~~~~l~~~~~~~~~s~~~R~l~~~w~~~~lil~s~YtA~L~s~LT~~~~~~~i~s~~dL~~~~~~vg~~~~s~- 432 (681)
.+.+++||. ++++|+..|+.
T Consensus 137 ---------------------------------------------------------~~~~~~DL~--gk~v~v~~gt~~ 157 (275)
T COG0834 137 ---------------------------------------------------------GIKSLEDLK--GKKVGVQLGTTD 157 (275)
T ss_pred ---------------------------------------------------------CcCCHHHhC--CCEEEEEcCcch
Confidence 267899999 89999999998
Q ss_pred -HHHHHhhhcCCccccccccCChhHHHHHHccCcceEEecchhhHHHH--HhhcCCceEEECccccc-CCcEEEecCC--
Q 005717 433 -VKDLLTKKLNFNETRLKNYTTSEDYHDALSNGEVAAIFDEIPYIKIF--LASYCSRYMMVGPTYRT-DGFGFAFPLG-- 506 (681)
Q Consensus 433 -~~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~g~~~a~i~e~~~~~~~--~~~~c~~l~~v~~~~~~-~~~~~~~~k~-- 506 (681)
..... . ...+...+..|++..+.+.++.+|++|+++.+.+.+.+. ..+.-............ .+++++++|+
T Consensus 158 ~~~~~~-~-~~~~~~~~~~~~~~~~~~~al~~Gr~Da~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 235 (275)
T COG0834 158 EAEEKA-K-KPGPNAKIVAYDSNAEALLALKNGRADAVVSDSAVLAGLKLLKKNPGLYVLLVFPGLSVEYLGIALRKGDD 235 (275)
T ss_pred hHHHHH-h-hccCCceEEeeCCHHHHHHHHHcCCccEEEcchHhhhhhhhhhcCCCCceeeeccCCCcceeEEEeccCCc
Confidence 44443 2 123345778899999999999999999999999988884 33333122333333334 6899999999
Q ss_pred CCChHHHHHHHHhhccCccHHHHHHHHHcCC
Q 005717 507 SPLVPYISRAILKVTEDKEKMENIEKALGNQ 537 (681)
Q Consensus 507 spl~~~in~~Il~l~e~~G~l~~i~~kw~~~ 537 (681)
..+++.+|++|.++.++ |.++++.++|+..
T Consensus 236 ~~l~~~in~~l~~l~~~-G~~~~i~~kw~~~ 265 (275)
T COG0834 236 PELLEAVNKALKELKAD-GTLQKISDKWFGP 265 (275)
T ss_pred HHHHHHHHHHHHHHHhC-ccHHHHHHHhcCc
Confidence 46999999999999999 9999999999974
No 28
>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=99.71 E-value=6.3e-17 Score=174.84 Aligned_cols=138 Identities=21% Similarity=0.370 Sum_probs=107.4
Q ss_pred CCCCCeEEEecCCccccCCccccccCccceEEEEEecCCChhHHHHHHHHHhhcCCCCCCCCCCchhHHHHHHHHHHHHH
Q 005717 1 MMSEGYAWIATQGLSTLLDPVKDMESMQGVLGLRPYIPSSKKLEHFKLRWIKSADKPDGSTGGSNLFGLWAYDTVWAIAM 80 (681)
Q Consensus 1 mm~~~y~WI~t~~~~~~~~~~~~~~~~~Gvlg~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~aYDav~~lA~ 80 (681)
|++++|+||+|+++... .+.++|++|+++..+. .++.++|||||++|+
T Consensus 238 ~~~~~~~wi~t~~~~~~------~~~~~g~~g~~~~~~~--------------------------~~~~~~yDAV~~~A~ 285 (377)
T cd06379 238 MTGEGYVWIVSEQAGAA------RNAPDGVLGLQLINGK--------------------------NESSHIRDAVAVLAS 285 (377)
T ss_pred CCCCCEEEEEecccccc------ccCCCceEEEEECCCC--------------------------CHHHHHHHHHHHHHH
Confidence 67899999999975322 3457899999986521 256789999999999
Q ss_pred HHHHHcccCCcccccCCCCCCCcccccC-CCcchHHHHHHHhccceecceeeEEE-eCCcccCccEEEEEeeeCCeeEee
Q 005717 81 AVERAGIENSSFLKSNTSKSRVDIAALG-TFEMGAKLLDTLINTTFEGLSGNFHL-VNGQLEPSAFEIFNVIGTSERVIG 158 (681)
Q Consensus 81 Al~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~G~~l~~~l~~~~f~GltG~i~F-~~G~~~~~~~~I~n~~~~~~~~vG 158 (681)
|++++..... .+.....|.+.. +|..|..|+++|++++|+|+||+|+| ++|+|.+..|+|+|+++.++++||
T Consensus 286 Al~~~~~~~~------~~~~~~~c~~~~~~~~~g~~l~~~l~~v~f~G~tg~i~Fd~~Gd~~~~~~~I~~~~~~~~~~VG 359 (377)
T cd06379 286 AIQELFEKEN------ITEPPRECVGNTVIWETGPLFKRALMSSKYPGETGRVEFNDDGDRKFANYDIMNIQNRKLVQVG 359 (377)
T ss_pred HHHHHHcCCC------CCCCCccccCCCCCCcchHHHHHHHHhCCcCCccCceEECCCCCccCccEEEEEecCCCceEee
Confidence 9999864211 111234565433 68899999999999999999999999 899998889999999999999999
Q ss_pred eeeCCCCccccccCCCCccCCCCCCccCCC
Q 005717 159 YWTKEKELLSELNDNNGRATNNLKNPIWPG 188 (681)
Q Consensus 159 ~W~~~~gl~~~~~~~~~~~~~~l~~i~Wpg 188 (681)
+|++. .+... -+.|.||+
T Consensus 360 ~w~~~-~l~~~-----------~~~i~W~~ 377 (377)
T cd06379 360 LYNGD-ILRLN-----------DRSIIWPG 377 (377)
T ss_pred EEcCc-EEEec-----------CceeeCCC
Confidence 99864 33321 14688985
No 29
>cd06378 PBP1_iGluR_NMDA_NR2 N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the NR2 subunit of NMDA receptor family. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the NR2 subunit of NMDA receptor family. The ionotropic N-methyl-d-asparate (NMDA) subtype of glutamate receptor serves critical functions in neuronal development, functioning, and degeneration in the mammalian central nervous system. The functional NMDA receptor is a heterotetramer composed of two NR1 and two NR2 (A, B, C, and D) or of NR3 (A and B) subunits. The receptor controls a cation channel that is highly permeable to monovalent ions and calcium and exhibits voltage-dependent inhibition by magnesium. Dual agonists, glutamate and glycine, are required for efficient activation of the NMDA receptor. Among NMDA receptor subtypes, the NR2B subunit containing receptors appear particularly important for pain perception; thus NR2B-selective antagonists may be useful in
Probab=99.70 E-value=8.2e-17 Score=171.68 Aligned_cols=141 Identities=19% Similarity=0.261 Sum_probs=106.6
Q ss_pred CCCCCeEEEecCCccccCCccccccCccceEEEEEecCCChhHHHHHHHHHhhcCCCCCCCCCCchhHHHHHHHHHHHHH
Q 005717 1 MMSEGYAWIATQGLSTLLDPVKDMESMQGVLGLRPYIPSSKKLEHFKLRWIKSADKPDGSTGGSNLFGLWAYDTVWAIAM 80 (681)
Q Consensus 1 mm~~~y~WI~t~~~~~~~~~~~~~~~~~Gvlg~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~aYDav~~lA~ 80 (681)
||++||+||+|+++.+..+. ...+..+|++|++. .+|+.. +.+.+||||+++|+
T Consensus 218 m~g~~yvWI~t~~~~~~~~~-~~~~~~~G~i~v~~------------~~w~~~-------------~~a~~~DaV~vva~ 271 (362)
T cd06378 218 LTGPGYVWIVPSLVLGNTDL-GPSEFPVGLISVSY------------DGWRYS-------------LRARVRDGVAIIAT 271 (362)
T ss_pred CcCCCeEEEecccccCCCcc-ccccCCcceEeecc------------cccccc-------------HHHHHHHHHHHHHH
Confidence 89999999999998776321 11234588888774 234311 35678999999999
Q ss_pred HHHHHcccCCcccccCCCCCCCcccc-cC-CCcchHHHHHHHhccceecceeeEEE-eCCcccCccEEEEEeee-CCeeE
Q 005717 81 AVERAGIENSSFLKSNTSKSRVDIAA-LG-TFEMGAKLLDTLINTTFEGLSGNFHL-VNGQLEPSAFEIFNVIG-TSERV 156 (681)
Q Consensus 81 Al~~~~~~~~~~~~~~~~~~~~~~~~-~~-~~~~G~~l~~~l~~~~f~GltG~i~F-~~G~~~~~~~~I~n~~~-~~~~~ 156 (681)
|++.+......+ +....+|.. .. +|..|+.|+++|++++|+|+ +|+| ++|+|.++.|+|+|+++ .+|++
T Consensus 272 Al~~l~~~~~~~-----~~~~~~C~~~~~~~~~~G~~l~~~l~~v~~~G~--~i~F~~~G~r~~~~ldIinl~~~~g~~k 344 (362)
T cd06378 272 GASAMLRQHGFI-----PEAKGSCYGQAEKRDLPPNTLHRYMMNVTWEGR--DLSFTEDGYLVNPKLVVISLNKERVWEE 344 (362)
T ss_pred HHHHHHhccCCC-----CCCCCCcCCCCCCCCCchHHHHHHhhcceECCC--ceeECCCCeEccceEEEEEecCCCCceE
Confidence 999886432222 223456753 33 48899999999999999997 9999 89999999999999997 59999
Q ss_pred eeeeeCCCCccccccCCCCccCCCCCCccCCC
Q 005717 157 IGYWTKEKELLSELNDNNGRATNNLKNPIWPG 188 (681)
Q Consensus 157 vG~W~~~~gl~~~~~~~~~~~~~~l~~i~Wpg 188 (681)
||+|+ +.+|.+ +.++|||
T Consensus 345 VG~W~-~~~L~~-------------~~~~wp~ 362 (362)
T cd06378 345 VGKWE-NGSLRL-------------KYPVWPR 362 (362)
T ss_pred EEEEc-CCeEEE-------------ecCCCCC
Confidence 99999 455653 4678986
No 30
>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=99.69 E-value=1.9e-16 Score=170.26 Aligned_cols=129 Identities=21% Similarity=0.264 Sum_probs=102.8
Q ss_pred CCCCCeEEEecCCccccCCccccccCccceEEEEEecCCChhHHHHHHHHHhhcCCCCCCCCCCchhHHHHHHHHHHHHH
Q 005717 1 MMSEGYAWIATQGLSTLLDPVKDMESMQGVLGLRPYIPSSKKLEHFKLRWIKSADKPDGSTGGSNLFGLWAYDTVWAIAM 80 (681)
Q Consensus 1 mm~~~y~WI~t~~~~~~~~~~~~~~~~~Gvlg~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~aYDav~~lA~ 80 (681)
|++++|+||+++++.+.. ....+.++|++|+++..+ ..+.+++||||+++|+
T Consensus 219 ~~~~~~~wI~~~~~~~~~--~~~~~~~~G~~g~~~~~~--------------------------~~~~~~~~Dav~~~a~ 270 (362)
T cd06367 219 LTGPGYVWIVGELALGSG--LAPEGLPVGLLGVGLDTW--------------------------YSLEARVRDAVAIVAR 270 (362)
T ss_pred CCCCCcEEEECccccccc--CCccCCCCeeEEEEeccc--------------------------ccHHHHHHHHHHHHHH
Confidence 678899999999765421 123456789999998642 1257889999999999
Q ss_pred HHHHHcccCCcccccCCCCCCCcccccC--CCcchHHHHHHHhccceecceeeEEE-eCCcccCccEEEEEee-eCCeeE
Q 005717 81 AVERAGIENSSFLKSNTSKSRVDIAALG--TFEMGAKLLDTLINTTFEGLSGNFHL-VNGQLEPSAFEIFNVI-GTSERV 156 (681)
Q Consensus 81 Al~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~G~~l~~~l~~~~f~GltG~i~F-~~G~~~~~~~~I~n~~-~~~~~~ 156 (681)
|++++..+.... ..+..+|.... .|..|..|+++|++++|.|+||+|+| ++|++.+..|+|+|++ +.+|++
T Consensus 271 Al~~~~~~~~~~-----~~~~~~C~~~~~~~~~~g~~l~~~l~~~~f~G~tg~v~F~~~G~~~~~~~~I~~l~~~~~~~~ 345 (362)
T cd06367 271 AAESLLRDKGAL-----PEPPVNCYDTANKRESSGQYLARFLMNVTFDGETGDVSFNEDGYLSNPKLVIINLRRNRKWER 345 (362)
T ss_pred HHHHHHHhcCCC-----CCCCCCcCCCCCCCCCchHHHHHHHhcccccCCCCceeECCCcccccceEEEEEecCCCcceE
Confidence 999987543211 11235676653 28899999999999999999999999 8999988899999999 889999
Q ss_pred eeeeeC
Q 005717 157 IGYWTK 162 (681)
Q Consensus 157 vG~W~~ 162 (681)
||.|++
T Consensus 346 VG~W~~ 351 (362)
T cd06367 346 VGSWEN 351 (362)
T ss_pred EEEEcC
Confidence 999984
No 31
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=99.69 E-value=3.3e-16 Score=193.88 Aligned_cols=219 Identities=12% Similarity=0.146 Sum_probs=182.5
Q ss_pred ceEEEEeecc-CCccceEEEeecCCCCeeEEeehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeE
Q 005717 195 RKLKIGVPVR-EGFTEFIKVVENKNKTTQVSGFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDT 273 (681)
Q Consensus 195 ~~lrV~v~~~-~p~~~~~~~~~~~~~~~~~~G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~ 273 (681)
++|+||+... +|| +... +.++++.||.+|+++.+++++| +++++++. .+|++++.+|.+|++|++.+.+
T Consensus 56 ~~l~vgv~~~~~p~--~~~~----~~~g~~~G~~~D~l~~ia~~lG--~~~e~v~~--~~~~~~l~~l~~g~iDl~~~~~ 125 (1197)
T PRK09959 56 KNLVIAVHKSQTAT--LLHT----DSQQRVRGINADYLNLLKRALN--IKLTLREY--ADHQKAMDALEEGEVDIVLSHL 125 (1197)
T ss_pred CeEEEEecCCCCCC--ceee----cCCCccceecHHHHHHHHHhcC--CceEEEeC--CCHHHHHHHHHcCCCcEecCcc
Confidence 6799998763 332 2221 4578899999999999999999 66899886 5899999999999999998888
Q ss_pred EEeeccccccccccceeecceEEEEEeccCCCcCceeeeccCcHhHHHHHHHHHHHHHHHhhhhhcccCCCCCCCCCCch
Q 005717 274 TIVANRSTFVDFTLPYSESGVSMLVLVKDDERKNFWIFLKPLSWDLWLTTGAAFIFTGLVVWVLEHRINTEFRGPPQHQI 353 (681)
Q Consensus 274 ~it~~R~~~vdFT~P~~~~~~~~vv~~~~~~~~~~~~fl~PF~~~vW~~i~~~~~~v~~v~~~~~~~~~~~~~~~~~~~~ 353 (681)
+.+++|.+.++||.||+.+..++++++..
T Consensus 126 ~~~~~r~~~~~fs~py~~~~~~~v~~~~~--------------------------------------------------- 154 (1197)
T PRK09959 126 VASPPLNDDIAATKPLIITFPALVTTLHD--------------------------------------------------- 154 (1197)
T ss_pred ccccccccchhcCCCccCCCceEEEeCCC---------------------------------------------------
Confidence 99999999999999999999999998753
Q ss_pred hhHHHHHHHHHhccCcccccccchhHHHHHHHHHHHHHHhHhhhhhhheeeecccCCCCCCHHHHHhCCCeEEEecChhH
Q 005717 354 GTIFWFSFSTLVFAHRERVVNNLSRFVLIIWVFVVLILTQSYTASLTSMLTVQRLQPSFTDVKDIQKNGYFVGYQTNSFV 433 (681)
Q Consensus 354 ~~~~~~~~~~l~~~~~~~~~s~~~R~l~~~w~~~~lil~s~YtA~L~s~LT~~~~~~~i~s~~dL~~~~~~vg~~~~s~~ 433 (681)
.+++++|+. +.++++..|+..
T Consensus 155 ---------------------------------------------------------~~~~~~~l~--~~~i~~~~g~~~ 175 (1197)
T PRK09959 155 ---------------------------------------------------------SMRPLTSSK--PVNIARVANYPP 175 (1197)
T ss_pred ---------------------------------------------------------CCCCccccc--CeEEEEeCCCCC
Confidence 255666775 788999999988
Q ss_pred HHHHhhhcCCccccccccCChhHHHHHHccCcceEEecchhhHHHHHhhc-CCceEEECcc-cccCCcEEEecCCCC-Ch
Q 005717 434 KDLLTKKLNFNETRLKNYTTSEDYHDALSNGEVAAIFDEIPYIKIFLASY-CSRYMMVGPT-YRTDGFGFAFPLGSP-LV 510 (681)
Q Consensus 434 ~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~g~~~a~i~e~~~~~~~~~~~-c~~l~~v~~~-~~~~~~~~~~~k~sp-l~ 510 (681)
.+++.+ .+|..+++.|++.+++++++.+|++||++.+...+.|+++++ -.++.+++.. .....+.++++|+.| |.
T Consensus 176 ~~~~~~--~~p~~~i~~~~s~~~al~av~~G~~Da~i~~~~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~L~ 253 (1197)
T PRK09959 176 DEVIHQ--SFPKATIISFTNLYQALASVSAGQNDYFIGSNIITSSMISRYFTHSLNVVKYYNSPRQYNFFLTRKESVILN 253 (1197)
T ss_pred HHHHHH--hCCCCEEEeCCCHHHHHHHHHcCCCCEEEccHHHHHHHHhcccccceEEEeeccCCCCceeEEEcCCcHHHH
Confidence 888833 577788999999999999999999999999999999998875 2355555332 233446788999999 88
Q ss_pred HHHHHHHHhhccCccHHHHHHHHHcCC
Q 005717 511 PYISRAILKVTEDKEKMENIEKALGNQ 537 (681)
Q Consensus 511 ~~in~~Il~l~e~~G~l~~i~~kw~~~ 537 (681)
..+|++|..+.++ |.. ++.+||+..
T Consensus 254 ~~lnkal~~i~~~-~~~-~i~~kW~~~ 278 (1197)
T PRK09959 254 EVLNRFVDALTNE-VRY-EVSQNWLDT 278 (1197)
T ss_pred HHHHHHHHhCCHH-HHH-HHHHhccCC
Confidence 9999999999999 777 899999975
No 32
>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=5.2e-16 Score=159.45 Aligned_cols=230 Identities=14% Similarity=0.126 Sum_probs=164.0
Q ss_pred CceEEEEeeccCCccceEEEeecCCCCeeEEeehHHHHHHHHHHc-CCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEe
Q 005717 194 PRKLKIGVPVREGFTEFIKVVENKNKTTQVSGFCYDMFHAVLQVL-EFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGD 272 (681)
Q Consensus 194 p~~lrV~v~~~~p~~~~~~~~~~~~~~~~~~G~~idll~~l~~~l-~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~ 272 (681)
+++|++++...|| |.+. ++++...|+..++++++++++ ++ ++++... .|++++..+ .|+.|+++.+
T Consensus 17 ~~~l~~~~~~~pP---f~~~----~~~~~~~G~~~~i~~~i~~~~~~~--~~~~~~~---pw~r~l~~l-~~~~d~~~~~ 83 (268)
T TIGR02285 17 KEAITWIVNDFPP---FFIF----SGPSKGRGVFDVILQEIRRALPQY--EHRFVRV---SFARSLKEL-QGKGGVCTVN 83 (268)
T ss_pred cceeEEEecccCC---eeEe----CCCCCCCChHHHHHHHHHHHcCCC--ceeEEEC---CHHHHHHHH-hcCCCeEEee
Confidence 3789998876544 5543 345677999999999999998 74 4666665 799999999 7888888777
Q ss_pred EEEeeccccccccccceee-cceEEEEEeccCCCcCceeeeccCcHhHHHHHHHHHHHHHHHhhhhhcccCCCCCCCCCC
Q 005717 273 TTIVANRSTFVDFTLPYSE-SGVSMLVLVKDDERKNFWIFLKPLSWDLWLTTGAAFIFTGLVVWVLEHRINTEFRGPPQH 351 (681)
Q Consensus 273 ~~it~~R~~~vdFT~P~~~-~~~~~vv~~~~~~~~~~~~fl~PF~~~vW~~i~~~~~~v~~v~~~~~~~~~~~~~~~~~~ 351 (681)
+++|++|.+.++||.||+. ...++++++......
T Consensus 84 ~~~t~eR~~~~~Fs~P~~~~~~~~~~~~~~~~~~~--------------------------------------------- 118 (268)
T TIGR02285 84 LLRTPEREKFLIFSDPTLRALPVGLVLRKELTAGV--------------------------------------------- 118 (268)
T ss_pred ccCCcchhhceeecCCccccCCceEEEccchhhhc---------------------------------------------
Confidence 9999999999999999975 578888886532110
Q ss_pred chhhHHHHHHHHHhccCcccccccchhHHHHHHHHHHHHHHhHhhhhhhheeeecccCCCCCCHHHHHh-CCCeEEEecC
Q 005717 352 QIGTIFWFSFSTLVFAHRERVVNNLSRFVLIIWVFVVLILTQSYTASLTSMLTVQRLQPSFTDVKDIQK-NGYFVGYQTN 430 (681)
Q Consensus 352 ~~~~~~~~~~~~l~~~~~~~~~s~~~R~l~~~w~~~~lil~s~YtA~L~s~LT~~~~~~~i~s~~dL~~-~~~~vg~~~~ 430 (681)
......-.++.+|.+ .+.++|+..|
T Consensus 119 ------------------------------------------------------~~~~d~~~~~~~l~~l~g~~vgv~~g 144 (268)
T TIGR02285 119 ------------------------------------------------------RDEQDGDVDLKKLLASKKKRLGVIAS 144 (268)
T ss_pred ------------------------------------------------------cccCCCCccHHHHhcCCCeEEEEecc
Confidence 000000012333321 2678999887
Q ss_pred hhH----HHHHhhhcCCc-cccccccCChhHHHHHHccCcceEEecchhhHHHHHhhc---CCceEEECccc--ccCCcE
Q 005717 431 SFV----KDLLTKKLNFN-ETRLKNYTTSEDYHDALSNGEVAAIFDEIPYIKIFLASY---CSRYMMVGPTY--RTDGFG 500 (681)
Q Consensus 431 s~~----~~~l~~~~~~~-~~~~~~~~~~~~~~~~l~~g~~~a~i~e~~~~~~~~~~~---c~~l~~v~~~~--~~~~~~ 500 (681)
+.. ..++ +..... ..++..+.+.++.+++|.+|++|+++.+...+.+++++. ...+..+.... ...+++
T Consensus 145 ~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~L~~GrvD~~v~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 223 (268)
T TIGR02285 145 RSYGQQIDDIL-SDSGYQHNTRIIGNAAMGNLFKMLEKGRVNYTLAYPPEKTYYEELNNGALPPLKFLPVAGMPAHISVW 223 (268)
T ss_pred eeccHHHHHHH-HhCCcccceeeeccchHHHHHHHHHcCCccEEEeCcHHHHHHHHhccCCcCCeeEeecCCCccceEEE
Confidence 654 3444 322221 124555677888999999999999999998888887743 22454443221 223578
Q ss_pred EEecCCC---CChHHHHHHHHhhccCccHHHHHHHHHcCC
Q 005717 501 FAFPLGS---PLVPYISRAILKVTEDKEKMENIEKALGNQ 537 (681)
Q Consensus 501 ~~~~k~s---pl~~~in~~Il~l~e~~G~l~~i~~kw~~~ 537 (681)
++++|+. .++..||++|.+|.++ |.++++.+||+..
T Consensus 224 i~~~k~~~~~~l~~~in~~L~~l~~d-G~~~~i~~k~~~~ 262 (268)
T TIGR02285 224 VACPKTEWGRKVIADIDQALSELNVD-PKYYKYFDRWLSP 262 (268)
T ss_pred EEeCCCHHHHHHHHHHHHHHHHHhhC-HHHHHHHHHhCCH
Confidence 9999974 3999999999999999 9999999999964
No 33
>smart00062 PBPb Bacterial periplasmic substrate-binding proteins. bacterial proteins, eukaryotic ones are in PBPe
Probab=99.68 E-value=1.8e-15 Score=148.26 Aligned_cols=215 Identities=27% Similarity=0.462 Sum_probs=178.4
Q ss_pred eEEEEeeccCCccceEEEeecCCCCeeEEeehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEEE
Q 005717 196 KLKIGVPVREGFTEFIKVVENKNKTTQVSGFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTTI 275 (681)
Q Consensus 196 ~lrV~v~~~~p~~~~~~~~~~~~~~~~~~G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~i 275 (681)
+|+||+.. .+.||... +.++...|+.+|+++.+.+++| +++++++. .|..++..+.+|++|++++....
T Consensus 1 ~l~v~~~~--~~~p~~~~----~~~g~~~G~~~~~~~~~~~~~g--~~~~~~~~---~~~~~~~~l~~g~~D~~~~~~~~ 69 (219)
T smart00062 1 TLRVGTNG--DYPPFSFA----DEDGELTGFDVDLAKAIAKELG--LKVEFVEV---SFDNLLTALKSGKIDVVAAGMTI 69 (219)
T ss_pred CEEEEecC--CCCCcEEE----CCCCCcccchHHHHHHHHHHhC--CeEEEEec---cHHHHHHHHHCCcccEEeccccC
Confidence 47899852 45556554 4567799999999999999999 55777775 79999999999999999987777
Q ss_pred eeccccccccccceeecceEEEEEeccCCCcCceeeeccCcHhHHHHHHHHHHHHHHHhhhhhcccCCCCCCCCCCchhh
Q 005717 276 VANRSTFVDFTLPYSESGVSMLVLVKDDERKNFWIFLKPLSWDLWLTTGAAFIFTGLVVWVLEHRINTEFRGPPQHQIGT 355 (681)
Q Consensus 276 t~~R~~~vdFT~P~~~~~~~~vv~~~~~~~~~~~~fl~PF~~~vW~~i~~~~~~v~~v~~~~~~~~~~~~~~~~~~~~~~ 355 (681)
+.+|...+.|+.|+...+.++++++..
T Consensus 70 ~~~~~~~~~~~~~~~~~~~~~~~~~~~----------------------------------------------------- 96 (219)
T smart00062 70 TPERAKQVDFSDPYYKSGQVILVRKDS----------------------------------------------------- 96 (219)
T ss_pred CHHHHhheeeccceeeceeEEEEecCC-----------------------------------------------------
Confidence 888888899999999999988887543
Q ss_pred HHHHHHHHHhccCcccccccchhHHHHHHHHHHHHHHhHhhhhhhheeeecccCCCCCCHHHHHhCCCeEEEecChhHHH
Q 005717 356 IFWFSFSTLVFAHRERVVNNLSRFVLIIWVFVVLILTQSYTASLTSMLTVQRLQPSFTDVKDIQKNGYFVGYQTNSFVKD 435 (681)
Q Consensus 356 ~~~~~~~~l~~~~~~~~~s~~~R~l~~~w~~~~lil~s~YtA~L~s~LT~~~~~~~i~s~~dL~~~~~~vg~~~~s~~~~ 435 (681)
++.+++||. |.++++..|+....
T Consensus 97 -------------------------------------------------------~~~~~~dL~--g~~i~~~~g~~~~~ 119 (219)
T smart00062 97 -------------------------------------------------------PIKSLEDLK--GKKVAVVAGTTGEE 119 (219)
T ss_pred -------------------------------------------------------CCCChHHhC--CCEEEEecCccHHH
Confidence 478899996 88999998888887
Q ss_pred HHhhhcCCccccccccCChhHHHHHHccCcceEEecchhhHHHHHhhc--CCceEEECccccc-CCcEEEecCCCC-ChH
Q 005717 436 LLTKKLNFNETRLKNYTTSEDYHDALSNGEVAAIFDEIPYIKIFLASY--CSRYMMVGPTYRT-DGFGFAFPLGSP-LVP 511 (681)
Q Consensus 436 ~l~~~~~~~~~~~~~~~~~~~~~~~l~~g~~~a~i~e~~~~~~~~~~~--c~~l~~v~~~~~~-~~~~~~~~k~sp-l~~ 511 (681)
++ ... .+..++..+.+..+...++.+|++|+++...+...+...+. + ++.++.+.... ..++++++++++ +.+
T Consensus 120 ~~-~~~-~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 196 (219)
T smart00062 120 LL-KKL-YPEAKIVSYDSQAEALAALKAGRADAAVADAPALAALVKQHGLP-ELKIVGDPLDTPEGYAFAVRKGDPELLD 196 (219)
T ss_pred HH-HHh-CCCceEEEcCCHHHHHHHhhcCcccEEEeccHHHHHHHHhcCCC-ceeeccCCCCCCcceEEEEECCCHHHHH
Confidence 77 433 23446667788899999999999999999988888877765 4 67777665555 788999999997 999
Q ss_pred HHHHHHHhhccCccHHHHHHHHHc
Q 005717 512 YISRAILKVTEDKEKMENIEKALG 535 (681)
Q Consensus 512 ~in~~Il~l~e~~G~l~~i~~kw~ 535 (681)
.++++|.++.++ |.++++.++|+
T Consensus 197 ~~~~~l~~~~~~-~~~~~i~~~~~ 219 (219)
T smart00062 197 KINKALKELKAD-GTLKKIYEKWF 219 (219)
T ss_pred HHHHHHHHHHhC-chHHHHHhccC
Confidence 999999999999 99999999986
No 34
>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=99.67 E-value=4.5e-15 Score=145.66 Aligned_cols=214 Identities=25% Similarity=0.401 Sum_probs=176.0
Q ss_pred EEEEeeccCCccceEEEeecCCCCeeEEeehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEEEe
Q 005717 197 LKIGVPVREGFTEFIKVVENKNKTTQVSGFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTTIV 276 (681)
Q Consensus 197 lrV~v~~~~p~~~~~~~~~~~~~~~~~~G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~it 276 (681)
|+|++... ++||... ++++.+.|++.|+++.+.+++| +++++++. .|.+++.+|.+|++|+++.....+
T Consensus 1 l~i~~~~~--~~p~~~~----~~~g~~~G~~~~~~~~~~~~~g--~~~~~~~~---~~~~~~~~l~~g~~D~~~~~~~~~ 69 (218)
T cd00134 1 LTVGTAGT--YPPFSFR----DANGELTGFDVDLAKAIAKELG--VKVKFVEV---DWDGLITALKSGKVDLIAAGMTIT 69 (218)
T ss_pred CEEecCCC--CCCeeEE----CCCCCEEeeeHHHHHHHHHHhC--CeEEEEeC---CHHHHHHHHhcCCcCEEeecCcCC
Confidence 56777663 4456654 5778899999999999999999 56888887 599999999999999999877788
Q ss_pred eccccccccccceeecceEEEEEeccCCCcCceeeeccCcHhHHHHHHHHHHHHHHHhhhhhcccCCCCCCCCCCchhhH
Q 005717 277 ANRSTFVDFTLPYSESGVSMLVLVKDDERKNFWIFLKPLSWDLWLTTGAAFIFTGLVVWVLEHRINTEFRGPPQHQIGTI 356 (681)
Q Consensus 277 ~~R~~~vdFT~P~~~~~~~~vv~~~~~~~~~~~~fl~PF~~~vW~~i~~~~~~v~~v~~~~~~~~~~~~~~~~~~~~~~~ 356 (681)
.+|...+.|+.|+...+.++++++..
T Consensus 70 ~~~~~~~~~~~~~~~~~~~~~~~~~~------------------------------------------------------ 95 (218)
T cd00134 70 PERAKQVDFSDPYYKSGQVILVKKGS------------------------------------------------------ 95 (218)
T ss_pred HHHHhhccCcccceeccEEEEEECCC------------------------------------------------------
Confidence 89999999999999999999998664
Q ss_pred HHHHHHHHhccCcccccccchhHHHHHHHHHHHHHHhHhhhhhhheeeecccCCCCCCHHHHHhCCCeEEEecChhHHHH
Q 005717 357 FWFSFSTLVFAHRERVVNNLSRFVLIIWVFVVLILTQSYTASLTSMLTVQRLQPSFTDVKDIQKNGYFVGYQTNSFVKDL 436 (681)
Q Consensus 357 ~~~~~~~l~~~~~~~~~s~~~R~l~~~w~~~~lil~s~YtA~L~s~LT~~~~~~~i~s~~dL~~~~~~vg~~~~s~~~~~ 436 (681)
++.+++||. |.++++..|+....+
T Consensus 96 ------------------------------------------------------~~~~~~dl~--g~~i~~~~~~~~~~~ 119 (218)
T cd00134 96 ------------------------------------------------------PIKSVKDLK--GKKVAVQKGSTAEKY 119 (218)
T ss_pred ------------------------------------------------------CCCChHHhC--CCEEEEEcCchHHHH
Confidence 355889997 888999888877777
Q ss_pred HhhhcCCccccccccCChhHHHHHHccCcceEEecchhhHHHHHhhc-CCceEEECcc--cccCCcEEEecCCCC-ChHH
Q 005717 437 LTKKLNFNETRLKNYTTSEDYHDALSNGEVAAIFDEIPYIKIFLASY-CSRYMMVGPT--YRTDGFGFAFPLGSP-LVPY 512 (681)
Q Consensus 437 l~~~~~~~~~~~~~~~~~~~~~~~l~~g~~~a~i~e~~~~~~~~~~~-c~~l~~v~~~--~~~~~~~~~~~k~sp-l~~~ 512 (681)
+.+. .....+..+.+.++..+++.+|++|+++.+.....+..++. + ++.++... .....++++..++++ +...
T Consensus 120 ~~~~--~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~~~~~~~~~~~~-~l~~~~~~~~~~~~~~~~~~~~~~~~l~~~ 196 (218)
T cd00134 120 LKKA--LPEAKVVSYDDNAEALAALENGRADAVIVDEIALAALLKKHPP-ELKIVGPSIDLEPLGFGVAVGKDNKELLDA 196 (218)
T ss_pred HHHh--CCcccEEEeCCHHHHHHHHHcCCccEEEeccHHHHHHHHhcCC-CcEEeccccCCCccceEEEEcCCCHHHHHH
Confidence 7332 22345667888999999999999999999988888877765 5 67777653 345556777777775 9999
Q ss_pred HHHHHHhhccCccHHHHHHHHHc
Q 005717 513 ISRAILKVTEDKEKMENIEKALG 535 (681)
Q Consensus 513 in~~Il~l~e~~G~l~~i~~kw~ 535 (681)
++++|..++++ |.++.+.+||+
T Consensus 197 ~~~~l~~~~~~-g~~~~i~~~~~ 218 (218)
T cd00134 197 VNKALKELRAD-GELKKISKKWF 218 (218)
T ss_pred HHHHHHHHHhC-ccHHHHHHhhC
Confidence 99999999999 99999999996
No 35
>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=99.66 E-value=4.2e-16 Score=166.45 Aligned_cols=127 Identities=17% Similarity=0.196 Sum_probs=102.5
Q ss_pred CCCCCeEEEecC-CccccCCccccccCccceEEEEEecCCChhHH----HHHHHHHhh-cCCCCCCCCCCchhHHHHHHH
Q 005717 1 MMSEGYAWIATQ-GLSTLLDPVKDMESMQGVLGLRPYIPSSKKLE----HFKLRWIKS-ADKPDGSTGGSNLFGLWAYDT 74 (681)
Q Consensus 1 mm~~~y~WI~t~-~~~~~~~~~~~~~~~~Gvlg~~~~~~~~~~~~----~f~~~~~~~-~~~~~~~~~~~~~~~~~aYDa 74 (681)
||++|||||+++ |..+..+...+.+.+.|++|||++++.++..+ +|.+.|+.. ...++ ....++..++++|||
T Consensus 224 m~~~~~~wi~~~~l~~~~~~l~~~~~~~~nitgfrl~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~al~yDa 302 (363)
T cd06381 224 LAIKDSHWFLINEEISDTEIDELVRYAHGRMTVIRQTFSKEKTNQRCLRNNHRISSLLCDPKDG-YLQMLEISNLYIYDS 302 (363)
T ss_pred CCcCceEEEEeccccccchhhHHHhhcCccEEEEEEecCCcCchHHHHHHHHHHHHhhcCCCCC-CCCChhHHHHHHHHH
Confidence 789999998766 66655555577889999999999998877766 455566542 11132 223567889999999
Q ss_pred HHHHHHHHHHHcccCCcccccCCCCCCCcccccCCCcchHHHHHHHhccceecceeeEEE-eCCcccCccEEEEEeeeCC
Q 005717 75 VWAIAMAVERAGIENSSFLKSNTSKSRVDIAALGTFEMGAKLLDTLINTTFEGLSGNFHL-VNGQLEPSAFEIFNVIGTS 153 (681)
Q Consensus 75 v~~lA~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~l~~~l~~~~f~GltG~i~F-~~G~~~~~~~~I~n~~~~~ 153 (681)
||++ +++|++++|+||||+|+| ++|+|.+++++|+++.-++
T Consensus 303 V~~~--------------------------------------~~~~~~~~~~GLTG~i~F~~~g~r~~~~l~i~~~~~~~ 344 (363)
T cd06381 303 VLLL--------------------------------------LETIKKGPITGLTGKLEFNEGGDNSNVQFEILGTGYSE 344 (363)
T ss_pred HHHH--------------------------------------HHHHHhcCccCcceeEEeCCCCCccccEEEEEEeccCC
Confidence 9998 588999999999999999 8999999999999998555
Q ss_pred -----eeEeeeeeCCCCc
Q 005717 154 -----ERVIGYWTKEKEL 166 (681)
Q Consensus 154 -----~~~vG~W~~~~gl 166 (681)
.+.||+|++.+|+
T Consensus 345 ~~~~~~~~~~~w~~~~~~ 362 (363)
T cd06381 345 TLGKDGRWLATWNPSKGL 362 (363)
T ss_pred ccccceEEeeeccCCCCC
Confidence 8899999998886
No 36
>TIGR03871 ABC_peri_MoxJ_2 quinoprotein dehydrogenase-associated probable ABC transporter substrate-binding protein. This protein family, a sister family to TIGR03870, is found more broadly. It occurs a range of PQQ-biosynthesizing species, not just in known methanotrophs. Interpretation of evidence by homology and by direct experimental work suggest two different roles. By homology, this family appears to be the periplasmic substrate-binding protein of an ABC transport family. However, mutational studies and direct characterization for some sequences related to this family suggests this family may act as a maturation chaperone or additional subunit of a methanol dehydrogenase-like enzyme.
Probab=99.66 E-value=4e-15 Score=149.45 Aligned_cols=212 Identities=14% Similarity=0.151 Sum_probs=156.1
Q ss_pred eEEEEeeccCCccceEEEeecCCCCeeEEeehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEEE
Q 005717 196 KLKIGVPVREGFTEFIKVVENKNKTTQVSGFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTTI 275 (681)
Q Consensus 196 ~lrV~v~~~~p~~~~~~~~~~~~~~~~~~G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~i 275 (681)
.|||++.. .|+||.. + ...||++||++++++++|.++++.+.+. .+..++..+.+|++|++++
T Consensus 1 ~l~v~~~~--~~~P~~~------~--~~~G~~~el~~~i~~~~g~~i~~~~~~~---~~~~~~~~l~~g~~Di~~~---- 63 (232)
T TIGR03871 1 ALRVCADP--NNLPFSN------E--KGEGFENKIAQLLADDLGLPLEYTWFPQ---RRGFVRNTLNAGRCDVVIG---- 63 (232)
T ss_pred CeEEEeCC--CCCCccC------C--CCCchHHHHHHHHHHHcCCceEEEecCc---chhhHHHHHhcCCccEEEe----
Confidence 37888765 3455543 1 2369999999999999997655554443 3444677899999999876
Q ss_pred eeccccccccccceeecceEEEEEeccCCCcCceeeeccCcHhHHHHHHHHHHHHHHHhhhhhcccCCCCCCCCCCchhh
Q 005717 276 VANRSTFVDFTLPYSESGVSMLVLVKDDERKNFWIFLKPLSWDLWLTTGAAFIFTGLVVWVLEHRINTEFRGPPQHQIGT 355 (681)
Q Consensus 276 t~~R~~~vdFT~P~~~~~~~~vv~~~~~~~~~~~~fl~PF~~~vW~~i~~~~~~v~~v~~~~~~~~~~~~~~~~~~~~~~ 355 (681)
+++|.+.++||.||+..+.++++++....
T Consensus 64 ~~~r~~~~~fs~py~~~~~~lv~~~~~~~--------------------------------------------------- 92 (232)
T TIGR03871 64 VPAGYEMVLTTRPYYRSTYVFVTRKDSLL--------------------------------------------------- 92 (232)
T ss_pred ccCccccccccCCcEeeeEEEEEeCCCcc---------------------------------------------------
Confidence 47788999999999999999999876421
Q ss_pred HHHHHHHHHhccCcccccccchhHHHHHHHHHHHHHHhHhhhhhhheeeecccCCCCCCHHHHHhCCCeEEEecChhHHH
Q 005717 356 IFWFSFSTLVFAHRERVVNNLSRFVLIIWVFVVLILTQSYTASLTSMLTVQRLQPSFTDVKDIQKNGYFVGYQTNSFVKD 435 (681)
Q Consensus 356 ~~~~~~~~l~~~~~~~~~s~~~R~l~~~w~~~~lil~s~YtA~L~s~LT~~~~~~~i~s~~dL~~~~~~vg~~~~s~~~~ 435 (681)
.+++++|+...+.+||+..|+...+
T Consensus 93 -------------------------------------------------------~~~~~~d~~l~g~~V~v~~g~~~~~ 117 (232)
T TIGR03871 93 -------------------------------------------------------DVKSLDDPRLKKLRIGVFAGTPPAH 117 (232)
T ss_pred -------------------------------------------------------cccchhhhhhcCCeEEEEcCChHHH
Confidence 4778888322378999999999988
Q ss_pred HHhhhcCCccccccc---------cCChhHHHHHHccCcceEEecchhhHHHHHhhcCCceEEECccc------ccCCcE
Q 005717 436 LLTKKLNFNETRLKN---------YTTSEDYHDALSNGEVAAIFDEIPYIKIFLASYCSRYMMVGPTY------RTDGFG 500 (681)
Q Consensus 436 ~l~~~~~~~~~~~~~---------~~~~~~~~~~l~~g~~~a~i~e~~~~~~~~~~~c~~l~~v~~~~------~~~~~~ 500 (681)
++ ++.+.. .+++. ..+.++.+.+|.+|++|+++.+...+.++.++.-..+.+..... ...+++
T Consensus 118 ~l-~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~l~~G~~Da~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 195 (232)
T TIGR03871 118 WL-ARHGLV-ENVVGYSLFGDYRPESPPGRMVEDLAAGEIDVAIVWGPIAGYFAKQAGPPLVVVPLLPEDGGIPFDYRIA 195 (232)
T ss_pred HH-HhcCcc-cccccccccccccccCCHHHHHHHHHcCCcCEEEeccHHHHHHHHhCCCCceeeccccCCCCCCccceEE
Confidence 88 433322 12221 34678999999999999999988888887775422344433211 233568
Q ss_pred EEecCCCC-ChHHHHHHHHhhccCccHHHHHHHHHc
Q 005717 501 FAFPLGSP-LVPYISRAILKVTEDKEKMENIEKALG 535 (681)
Q Consensus 501 ~~~~k~sp-l~~~in~~Il~l~e~~G~l~~i~~kw~ 535 (681)
++++++.+ ++..+|++|.++. |.+++|.+||.
T Consensus 196 ~~~~~~~~~l~~~~n~~l~~~~---~~~~~i~~kyg 228 (232)
T TIGR03871 196 MGVRKGDKAWKDELNAVLDRRQ---AEIDAILREYG 228 (232)
T ss_pred EEEecCCHHHHHHHHHHHHHHH---HHHHHHHHHcC
Confidence 88999877 9999999999974 57999999995
No 37
>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=99.51 E-value=1.1e-13 Score=153.76 Aligned_cols=157 Identities=20% Similarity=0.281 Sum_probs=107.4
Q ss_pred CCCCeEEEecCCccccCCcc-ccccCccceEEEEEecCCChhHHHHHH---------------HHHhh--cCC---CCC-
Q 005717 2 MSEGYAWIATQGLSTLLDPV-KDMESMQGVLGLRPYIPSSKKLEHFKL---------------RWIKS--ADK---PDG- 59 (681)
Q Consensus 2 m~~~y~WI~t~~~~~~~~~~-~~~~~~~Gvlg~~~~~~~~~~~~~f~~---------------~~~~~--~~~---~~~- 59 (681)
|..+|+||.++++...-... ...+.++|++|+.++.+..+.+++|.+ .|+.. ... +..
T Consensus 270 ~~~~~~wi~s~~~~~~~~~~~~~~~~~~G~l~~~~~~~~~~~F~~~l~~l~~~~~~~~~~~~~~w~~~f~c~~~~~~~~~ 349 (472)
T cd06374 270 VGGEFQLIGSDGWADRDDVVEGYEEEAEGGITIKLQSPEVPSFDDYYLKLRPETNTRNPWFREFWQHRFQCRLPGHPQEN 349 (472)
T ss_pred CCCceEEEEecccccchHhhhcchhhhheeEEEEecCCCCccHHHHHHhCCcccCCCChHHHHHHHHhcCCCcCCccCcC
Confidence 44558999999644321111 234578999999999888877777544 34432 111 100
Q ss_pred --------CC--C----CCchhHHHHHHHHHHHHHHHHHHcccCCcccccCCCCCCCcccccCCCcchHHHHHHHhccce
Q 005717 60 --------ST--G----GSNLFGLWAYDTVWAIAMAVERAGIENSSFLKSNTSKSRVDIAALGTFEMGAKLLDTLINTTF 125 (681)
Q Consensus 60 --------~~--~----~~~~~~~~aYDav~~lA~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~l~~~l~~~~f 125 (681)
.. . ....+..++|||||++|+|||++....- ..+...|.... +..|.+|+++|++++|
T Consensus 350 ~~~~~~c~~~~~~~~~~~~~~~~~~vyDAVyaiA~ALh~~~~~~~-------~~~~~~c~~~~-~~~~~~l~~~l~~v~F 421 (472)
T cd06374 350 PNYIKICTGNESLDEQYVQDSKMGFVINAIYAMAHGLHNMHQDLC-------PGHVGLCDAMK-PIDGRKLLEYLLKTSF 421 (472)
T ss_pred CccCCCCCCcccccccccccceeHHHHHHHHHHHHHHHHHHHhhC-------CCCCCCCcCCC-CCCHHHHHHHHHhCcc
Confidence 00 0 0124566999999999999999864321 11123465543 4579999999999999
Q ss_pred eccee-eEEE-eCCcccCccEEEEEeeeC-----CeeEeeeeeCCCCccc
Q 005717 126 EGLSG-NFHL-VNGQLEPSAFEIFNVIGT-----SERVIGYWTKEKELLS 168 (681)
Q Consensus 126 ~GltG-~i~F-~~G~~~~~~~~I~n~~~~-----~~~~vG~W~~~~gl~~ 168 (681)
+|+|| +|.| .+|++. ..|+|+|++.. ++++||.|++ .+|.+
T Consensus 422 ~g~tG~~v~Fd~~G~~~-~~ydI~n~~~~~~~~~~~~~VG~w~~-~~l~~ 469 (472)
T cd06374 422 SGVSGEEVYFDENGDSP-GRYDIMNLQYTEDLRFDYINVGSWHE-GDLGI 469 (472)
T ss_pred cCCCCCeEEEcCCCCCC-CceEEEEEEECCCCCEEEEEEEEEeC-Ccccc
Confidence 99999 6999 899987 48999999952 4899999984 46643
No 38
>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=99.51 E-value=1.6e-13 Score=144.78 Aligned_cols=95 Identities=19% Similarity=0.323 Sum_probs=76.3
Q ss_pred HHHHHHHHHHHHHHHHHHcc--cCCcccccCCCCCCCccccc--C-CCcchHHHHHHHhccceecceeeEEEeCCcc--c
Q 005717 68 GLWAYDTVWAIAMAVERAGI--ENSSFLKSNTSKSRVDIAAL--G-TFEMGAKLLDTLINTTFEGLSGNFHLVNGQL--E 140 (681)
Q Consensus 68 ~~~aYDav~~lA~Al~~~~~--~~~~~~~~~~~~~~~~~~~~--~-~~~~G~~l~~~l~~~~f~GltG~i~F~~G~~--~ 140 (681)
.+++||||+++|+|++.+.. ....+ ..+..+|... . +|..|..|.++|++++|+|+||+|.|+.|.| .
T Consensus 269 ~ali~DAV~lvA~a~~~l~~~~~~~~l-----~~~~~~C~~~~~~~~W~~G~~l~~~Lknv~~eGlTG~I~F~~g~R~~~ 343 (382)
T cd06377 269 EAYVQDALELVARAVGSATLVQPELAL-----IPATVNCMDLPTKGNESSGQYLARFLANTSFDGRTGPVWVTGSSQVHS 343 (382)
T ss_pred HHHHHHHHHHHHHHHHHhhhccccccc-----CCCCCCcccCCCCCCCCchHHHHHHHHhCcccccceeEEEccCeeecc
Confidence 78999999999999998731 11111 2234678644 5 8999999999999999999999999977888 7
Q ss_pred CccEEEEEee--eCC---eeEeeeeeCCCCcc
Q 005717 141 PSAFEIFNVI--GTS---ERVIGYWTKEKELL 167 (681)
Q Consensus 141 ~~~~~I~n~~--~~~---~~~vG~W~~~~gl~ 167 (681)
+..++|++++ ..| |++||+|++...+.
T Consensus 344 ~~~l~I~~L~~~~~G~~~W~kVG~W~~~~~~~ 375 (382)
T cd06377 344 SRHFKVWSLRRDPVGQPTWTTVGSWQGGRKIV 375 (382)
T ss_pred cceEEEEEeccccCCCccceEEEEecCCCcee
Confidence 8999999998 455 59999999864443
No 39
>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=99.47 E-value=5.7e-13 Score=147.85 Aligned_cols=149 Identities=19% Similarity=0.326 Sum_probs=104.9
Q ss_pred CeEEEecCCccccCCcc-ccccCccceEEEEEecCCChhHHHHHH---------------HHHhh-cCC-C--C------
Q 005717 5 GYAWIATQGLSTLLDPV-KDMESMQGVLGLRPYIPSSKKLEHFKL---------------RWIKS-ADK-P--D------ 58 (681)
Q Consensus 5 ~y~WI~t~~~~~~~~~~-~~~~~~~Gvlg~~~~~~~~~~~~~f~~---------------~~~~~-~~~-~--~------ 58 (681)
.|+||.+|++....... ...+.+.|++|+.+.....+.+++|.. -|+.. ... + .
T Consensus 259 ~~~wig~d~~~~~~~~~~~~~~~~~G~~~~~~~~~~~~~F~~~~~~l~~~~~~~~~~~~~~w~~~f~c~~~~~~~~~~~~ 338 (463)
T cd06376 259 HFLWVGSDSWGAKISPILQQEDVAEGAITILPKRASIEGFDAYFTSRTLENNRRNVWFAEFWEENFNCKLTISGSKKEDT 338 (463)
T ss_pred ceEEEEeccccccccccccCcceeeeEEEEEeccccchhHHHHHHhCCcccCCCCcHHHHHHHHhCCCcccCCCCccccc
Confidence 49999999654433222 234578999999998888887877665 34332 100 0 0
Q ss_pred ----CCCCC--------CchhHHHHHHHHHHHHHHHHHHcccCCcccccCCCCCCCcccccCCCcchHHHHHHHhcccee
Q 005717 59 ----GSTGG--------SNLFGLWAYDTVWAIAMAVERAGIENSSFLKSNTSKSRVDIAALGTFEMGAKLLDTLINTTFE 126 (681)
Q Consensus 59 ----~~~~~--------~~~~~~~aYDav~~lA~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~l~~~l~~~~f~ 126 (681)
..... ...++.++||||||+|+|||++...+ +......|.... |.+|.+|+++|++++|+
T Consensus 339 ~~~C~~~~~~~~~~~~~~~~~~~~v~dAVyaiA~ALh~l~~~~-------c~~~~~~C~~~~-~~~~~~l~~~L~~v~F~ 410 (463)
T cd06376 339 DRKCTGQERIGRDSTYEQEGKVQFVIDAVYAMAHALHSMHKDL-------CPGYTGVCPEME-PADGKKLLKYIRAVNFN 410 (463)
T ss_pred cCcCcchhhccccCcccccchhHHHHHHHHHHHHHHHHHHHhh-------CCCCCCCCccCC-CCCHHHHHHHHHhCCcc
Confidence 00000 12267899999999999999986432 111123576543 66899999999999999
Q ss_pred ccee-eEEE-eCCcccCccEEEEEeee-----CCeeEeeeeeC
Q 005717 127 GLSG-NFHL-VNGQLEPSAFEIFNVIG-----TSERVIGYWTK 162 (681)
Q Consensus 127 GltG-~i~F-~~G~~~~~~~~I~n~~~-----~~~~~vG~W~~ 162 (681)
|+|| +|.| ++|++. ..|+|+|++. .++++||.|++
T Consensus 411 g~tg~~v~Fd~~G~~~-~~Ydi~n~q~~~~~~~~~~~VG~w~~ 452 (463)
T cd06376 411 GSAGTPVMFNENGDAP-GRYDIFQYQITNTSSPGYRLIGQWTD 452 (463)
T ss_pred CCCCCeEEeCCCCCCC-CceEEEEEEecCCCceeEEEEEEECC
Confidence 9999 6999 899987 4799999983 34899999985
No 40
>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=99.46 E-value=4.7e-13 Score=142.62 Aligned_cols=139 Identities=31% Similarity=0.530 Sum_probs=111.7
Q ss_pred CCCCCeEEEecCCccccC--CccccccCccceEEEEEecCCChhHHHHHHHHHhh--cCCCCCCCCCCchhHHHHHHHHH
Q 005717 1 MMSEGYAWIATQGLSTLL--DPVKDMESMQGVLGLRPYIPSSKKLEHFKLRWIKS--ADKPDGSTGGSNLFGLWAYDTVW 76 (681)
Q Consensus 1 mm~~~y~WI~t~~~~~~~--~~~~~~~~~~Gvlg~~~~~~~~~~~~~f~~~~~~~--~~~~~~~~~~~~~~~~~aYDav~ 76 (681)
|++++|+||++++..... ........+.|++++++..+..+.+++|.++|+.. ..........+..+++++||||+
T Consensus 204 ~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~yDAv~ 283 (348)
T PF01094_consen 204 MTSGDYVWILTDLDNSSFWQNNEDFREAFQGVLGFTPPPPSSPEFEDFMKKWKESNNQSSTSGSDQEPSPYAAYAYDAVY 283 (348)
T ss_dssp TSSTTSEEEEETTTTTTHTSTHCHHHCCHTTEEEEEESTTTSHHHHHHHHHHHTTTHTTTTTTTTSSGCHHHHHHHHHHH
T ss_pred ccccceeEEeecccccccccccccccccccceeeeeeecccccchhhhhcccChhhccCcccccccccceeeeeehhhhH
Confidence 568999999999876653 33367889999999999999999999999999875 11122333456789999999999
Q ss_pred HHHHHHHHHcccCCcccccCCCCCCCcccccCCCcchHHHHHHHhccceecceeeEEE-e-CCcccCccEEEEEee
Q 005717 77 AIAMAVERAGIENSSFLKSNTSKSRVDIAALGTFEMGAKLLDTLINTTFEGLSGNFHL-V-NGQLEPSAFEIFNVI 150 (681)
Q Consensus 77 ~lA~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~l~~~l~~~~f~GltG~i~F-~-~G~~~~~~~~I~n~~ 150 (681)
++|+|++++.+.+.... .....|..|..|.++|++++|+|+||++.| + +|++.+..|+|+|++
T Consensus 284 ~~a~al~~~~~~~~~~~-----------~~~~~~~~g~~l~~~l~~~~f~G~tG~v~f~~~~G~~~~~~~~i~~~~ 348 (348)
T PF01094_consen 284 LLAHALNRALQDGGPVT-----------NGRNPWQNGSQLLKYLRNVSFEGLTGRVSFDSNDGDRTNYDYDILNMQ 348 (348)
T ss_dssp HHHHHHHHHHHHHSTTT-----------SSSGTSTTHHHHHHHHHTEEEEETTEEEEEETTTSBEESEEEEEEEE-
T ss_pred HHHHHHHHHHHhccCCC-----------CCccccccHHHHHHHHhheeeeCCCCCEEEeCCCCCcCCCEEEEEECC
Confidence 99999999975532111 111568899999999999999999999999 6 799989999999975
No 41
>smart00079 PBPe Eukaryotic homologues of bacterial periplasmic substrate binding proteins. Prokaryotic homologues are represented by a separate alignment: PBPb
Probab=99.45 E-value=5.4e-13 Score=121.72 Aligned_cols=122 Identities=27% Similarity=0.388 Sum_probs=107.0
Q ss_pred CCCCHHHHHhC-CCeEEEecChhHHHHHhhhcCCcc----------ccccccCChhHHHHHHccCcceEEecchhhHHHH
Q 005717 411 SFTDVKDIQKN-GYFVGYQTNSFVKDLLTKKLNFNE----------TRLKNYTTSEDYHDALSNGEVAAIFDEIPYIKIF 479 (681)
Q Consensus 411 ~i~s~~dL~~~-~~~vg~~~~s~~~~~l~~~~~~~~----------~~~~~~~~~~~~~~~l~~g~~~a~i~e~~~~~~~ 479 (681)
+|++++||..+ +.+||++.|++.+.++ +....+. .++..|++..++..+|.+|+ ||++.+.+.+.++
T Consensus 1 ~i~~~~dl~~~~~~~vgv~~gs~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~-da~v~d~~~~~~~ 78 (134)
T smart00079 1 PITSVEDLAKQTKIEYGTIRGSSTLAFF-KRSGNPEYSRMWNYMSASPSVFVKSYAEGVQRVRVSN-YAFLMESTYLDYE 78 (134)
T ss_pred CCCChHHHhhCCCccceEecCchHHHHH-HhCCChHHHHHHHHHHhCCCCCCCCHHHHHHHHHcCC-CEEEeehHhHHHH
Confidence 47899999854 2689999999999999 4332221 25678899999999999999 9999999999998
Q ss_pred HhhcCCceEEECcccccCCcEEEecCCCCChHHHHHHHHhhccCccHHHHHHHHHcC
Q 005717 480 LASYCSRYMMVGPTYRTDGFGFAFPLGSPLVPYISRAILKVTEDKEKMENIEKALGN 536 (681)
Q Consensus 480 ~~~~c~~l~~v~~~~~~~~~~~~~~k~spl~~~in~~Il~l~e~~G~l~~i~~kw~~ 536 (681)
.++.| ++.+++..+...++|++++||++|++.+|.+|.++.++ |.++++.++|+.
T Consensus 79 ~~~~~-~~~~~~~~~~~~~~~ia~~k~~~l~~~vn~~l~~l~~~-G~~~~l~~kw~~ 133 (134)
T smart00079 79 LSQNC-DLMTVGENFGRKGYGIAFPKGSPLRDDLSRAILKLSES-GELQKLENKWWK 133 (134)
T ss_pred HhCCC-CeEEcCcccCCCceEEEecCCCHHHHHHHHHHHHHHhc-CcHHHHHHhhcc
Confidence 88788 79999888888899999999999999999999999999 999999999985
No 42
>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=99.45 E-value=4.7e-13 Score=144.98 Aligned_cols=140 Identities=20% Similarity=0.273 Sum_probs=105.2
Q ss_pred CCCCCeEEEecCCccc------cCC---cc-----ccccCccceEEEEEecCCChhHHHHHHHHHhh-cCCCCCC-CCCC
Q 005717 1 MMSEGYAWIATQGLST------LLD---PV-----KDMESMQGVLGLRPYIPSSKKLEHFKLRWIKS-ADKPDGS-TGGS 64 (681)
Q Consensus 1 mm~~~y~WI~t~~~~~------~~~---~~-----~~~~~~~Gvlg~~~~~~~~~~~~~f~~~~~~~-~~~~~~~-~~~~ 64 (681)
|++++|+||.+|+.++ .|. .. .....++|+++++++. +++++|..+++++ ..++... ..+.
T Consensus 219 m~~~~yv~i~~d~~~~~~~~~~~w~~~~~~~~~~~~a~~~~~~v~~~~~~~---~~~~~f~~~~~~~~~~~~~~~~~~~~ 295 (387)
T cd06386 219 LTSGDYIFFNIELFNSSSYGDGSWKRGDKHDFEAKQAYSSLNTVTLLRTVK---PEFEKFSMEVKSSVEKAGDLNDCDYV 295 (387)
T ss_pred CCCCCEEEEEEecccccccCCCCCccCCCcCHHHHHHHHhheEEeccCCCC---hHHHHHHHHHHHHHHhCCCCcccccc
Confidence 7889999999997641 111 01 2345678888887765 5677888888754 2222111 1246
Q ss_pred chhHHHHHHHHHHHHHHHHHHcccCCcccccCCCCCCCcccccCCCcchHHHHHHHhccceecceeeEEE-eCCcccCcc
Q 005717 65 NLFGLWAYDTVWAIAMAVERAGIENSSFLKSNTSKSRVDIAALGTFEMGAKLLDTLINTTFEGLSGNFHL-VNGQLEPSA 143 (681)
Q Consensus 65 ~~~~~~aYDav~~lA~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~l~~~l~~~~f~GltG~i~F-~~G~~~~~~ 143 (681)
+.|++++|||||++|+|++++...+. .|.+|+.|.++|++++|+|+||++.| ++|+|. ..
T Consensus 296 ~~~aa~~yDav~l~A~Al~~~~~~g~------------------~~~~g~~l~~~l~~~~f~G~tG~v~~d~~g~r~-~~ 356 (387)
T cd06386 296 NMFVEGFHDAILLYALALHEVLKNGY------------------SKKDGTKITQRMWNRTFEGIAGQVSIDANGDRY-GD 356 (387)
T ss_pred hHHHHHHHHHHHHHHHHHHHHhhCCC------------------CCCCHHHHHHHHhCCceeeccccEEECCCCCcc-cc
Confidence 68999999999999999999853221 25689999999999999999999999 889997 59
Q ss_pred EEEEEeee---CCeeEeeeeeC
Q 005717 144 FEIFNVIG---TSERVIGYWTK 162 (681)
Q Consensus 144 ~~I~n~~~---~~~~~vG~W~~ 162 (681)
|.|+.+++ .+++.||.|..
T Consensus 357 ~~v~~~~~~~~~~~~~~~~~~~ 378 (387)
T cd06386 357 FSVIAMTDVEAGTYEVVGNYFG 378 (387)
T ss_pred EEEEEccCCCCccEEEEeEEcc
Confidence 99999964 35899999984
No 43
>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=99.45 E-value=7.5e-13 Score=146.79 Aligned_cols=152 Identities=18% Similarity=0.176 Sum_probs=106.1
Q ss_pred CCCCeEEEecCCc-cccCCccccccCccceEEEEEecCCChhHHHHHHHHHhh-c---------------CC--------
Q 005717 2 MSEGYAWIATQGL-STLLDPVKDMESMQGVLGLRPYIPSSKKLEHFKLRWIKS-A---------------DK-------- 56 (681)
Q Consensus 2 m~~~y~WI~t~~~-~~~~~~~~~~~~~~Gvlg~~~~~~~~~~~~~f~~~~~~~-~---------------~~-------- 56 (681)
++.+++||.++++ +..-......+.++|++|+.++.+..+.+++|.++.... . ..
T Consensus 255 ~~~~~~wi~s~~w~~~~~~~~~~~~~~~G~lg~~~~~~~~~~f~~fl~~l~~~~~~~npw~~efwe~~f~c~~~~~~~~~ 334 (469)
T cd06365 255 LLIGKVWITTSQWDVTTSPKDFTLNSFHGTLIFSHHHSEIPGFKDFLQTVNPSKYPEDIFLEKLWWIYFNCSLSKSSCKT 334 (469)
T ss_pred ccCceEEEeeccccccccccccccceeeEEEEEEeccCcCcchHHHhhccCcccCCCccHHHhhHhHhcCcccCcCCccc
Confidence 4678999999843 332111245668999999999999999998887774221 0 00
Q ss_pred --CCCCC------------CCCchhHHHHHHHHHHHHHHHHHHcccCCcccccCCCCCCCcccccCCCcchHHHHHHHhc
Q 005717 57 --PDGST------------GGSNLFGLWAYDTVWAIAMAVERAGIENSSFLKSNTSKSRVDIAALGTFEMGAKLLDTLIN 122 (681)
Q Consensus 57 --~~~~~------------~~~~~~~~~aYDav~~lA~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~l~~~l~~ 122 (681)
.+... .....++.++||||+|+|||||++..++... ++..+|.. ....+.+|+++|++
T Consensus 335 ~~~c~~~~~~~~~~~~~~~~~~~~~~~~v~dAVya~AhALh~~l~c~~~~------~~~~~~~~--~~~~~~~l~~~l~~ 406 (469)
T cd06365 335 LKNCLSNASLEWLPLHYFDMAMSEESYNVYNAVYAVAHALHEMLLQQVET------QSENNGKR--LIFLPWQLHSFLKN 406 (469)
T ss_pred cCCCCCCccccccccccccchhhhhHHHHHHHHHHHHHHHHHHHHhhccC------CCcCCCCC--CCccHHHHHHHHHh
Confidence 01000 0012356789999999999999998654211 11233332 12356789999999
Q ss_pred cceecceee-EEE-eCCcccCccEEEEEeee--CC---eeEeeeeeC
Q 005717 123 TTFEGLSGN-FHL-VNGQLEPSAFEIFNVIG--TS---ERVIGYWTK 162 (681)
Q Consensus 123 ~~f~GltG~-i~F-~~G~~~~~~~~I~n~~~--~~---~~~vG~W~~ 162 (681)
++|+|.+|. |.| ++|++. ..|+|+|++. ++ +++||.|++
T Consensus 407 v~F~~~~g~~v~Fd~nGd~~-~~YdI~n~q~~~~~~~~~~~VG~~~~ 452 (469)
T cd06365 407 IQFKNPAGDEVNLNQKRKLD-TEYDILNYWNFPQGLGLKVKVGEFSP 452 (469)
T ss_pred ccccCCCCCEEEecCCCCcC-ceeeEEEEEECCCCCEEEEEEEEEeC
Confidence 999999995 999 899985 6899999983 22 689999985
No 44
>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=99.44 E-value=7.3e-13 Score=144.61 Aligned_cols=145 Identities=20% Similarity=0.237 Sum_probs=108.7
Q ss_pred CCCCCeEEEecCCccccCCc--------c------ccccCccceEEEEEecCCChhHHHHHHHHHhh-cCCCCC--CCCC
Q 005717 1 MMSEGYAWIATQGLSTLLDP--------V------KDMESMQGVLGLRPYIPSSKKLEHFKLRWIKS-ADKPDG--STGG 63 (681)
Q Consensus 1 mm~~~y~WI~t~~~~~~~~~--------~------~~~~~~~Gvlg~~~~~~~~~~~~~f~~~~~~~-~~~~~~--~~~~ 63 (681)
|++++|+||++++....++. . .....++|++++....+.++..++|.++|+++ ....+. ....
T Consensus 227 ~~~~~y~~i~~~~~~~~~~~~~~~~~w~~~~~~~~~~~~a~~~v~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~ 306 (405)
T cd06385 227 LPSEDYVFFYIDLFGASLQGPDPKRPWYRGDADDAAAREAFQSVKILTYKEPQNPEYKEFLSDLKTDAKEMFNFTVEDSL 306 (405)
T ss_pred CCCCcEEEEEeecchhhccCCCCCCCCCCCCcccHHHHHhhheeEEEeCCCCCChhHHHHHHHHHHHhhccCCCccchhh
Confidence 67889999999875433221 0 22446799999887777778899999999875 211111 1112
Q ss_pred CchhHHHHHHHHHHHHHHHHHHcccCCcccccCCCCCCCcccccCCCcchHHHHHHHhccceecceeeEEE-eCCcccCc
Q 005717 64 SNLFGLWAYDTVWAIAMAVERAGIENSSFLKSNTSKSRVDIAALGTFEMGAKLLDTLINTTFEGLSGNFHL-VNGQLEPS 142 (681)
Q Consensus 64 ~~~~~~~aYDav~~lA~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~l~~~l~~~~f~GltG~i~F-~~G~~~~~ 142 (681)
++.+++++|||||++|.||+++.... +.+.+|..|.++|++++|+|+||+|.| ++|+|. .
T Consensus 307 ~~~~aa~~YDav~l~a~Al~~~~~~~------------------~~~~~g~~i~~~l~~~~f~G~tG~v~fd~~G~r~-~ 367 (405)
T cd06385 307 MNIIAGGFYDGVMLYAHALNETMAKG------------------GTRPPGTAITQRMWNRTFYGVTGFVKIDDNGDRE-T 367 (405)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcC------------------CCCCCHHHHHHHhhCceEeeceeEEEEcCCCCEe-c
Confidence 56899999999999999999974321 124578999999999999999999999 889996 5
Q ss_pred cEEEEEe---eeCCeeEeeeeeCCC
Q 005717 143 AFEIFNV---IGTSERVIGYWTKEK 164 (681)
Q Consensus 143 ~~~I~n~---~~~~~~~vG~W~~~~ 164 (681)
.|.|+.+ ++++++.||+|+..+
T Consensus 368 ~~~~~~~~~~~~g~~~~v~~~~~~~ 392 (405)
T cd06385 368 DFALWDMTDTESGDFQVVSVYNGTQ 392 (405)
T ss_pred eeEEEEccCCCCCcEEEEEEEcccC
Confidence 7877754 667799999998543
No 45
>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=99.43 E-value=1e-12 Score=142.79 Aligned_cols=145 Identities=14% Similarity=0.177 Sum_probs=105.0
Q ss_pred CCCCCeEEEecCCccccCCcc--------ccccCccceEEEEEecCCC-hhHHHHHHHHHhh-cCCCC----CCCCCCch
Q 005717 1 MMSEGYAWIATQGLSTLLDPV--------KDMESMQGVLGLRPYIPSS-KKLEHFKLRWIKS-ADKPD----GSTGGSNL 66 (681)
Q Consensus 1 mm~~~y~WI~t~~~~~~~~~~--------~~~~~~~Gvlg~~~~~~~~-~~~~~f~~~~~~~-~~~~~----~~~~~~~~ 66 (681)
|++++|+||++++..+.+|.. ...+.++|++++.+..+.. +..++|.++|+.+ ...|- ......+.
T Consensus 221 ~~~~~y~~i~~~~~~~~~w~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~f~~~~~~~~~~~p~~~~~~~~~~~~~ 300 (391)
T cd06372 221 LMKGKFVFFLLQQFEDNFWKEVLTDDQVQHLPKVYESVFLIAPSSYGGYSGGYEFRKQVYQKLKRPPFQSSLSSEEQVSP 300 (391)
T ss_pred CCCCCEEEEEehhhcCccccccCCCcchHHHHHHHhhEEEEecCCCCCCcchhHHHHHHHHHHhcCCccccccccccchH
Confidence 566789999987654443321 1234678999988865432 4456777777655 32231 11123467
Q ss_pred hHHHHHHHHHHHHHHHHHHcccCCcccccCCCCCCCcccccCCCcchHHHHHHHh---ccceecceeeEEE-eCCcccCc
Q 005717 67 FGLWAYDTVWAIAMAVERAGIENSSFLKSNTSKSRVDIAALGTFEMGAKLLDTLI---NTTFEGLSGNFHL-VNGQLEPS 142 (681)
Q Consensus 67 ~~~~aYDav~~lA~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~l~~~l~---~~~f~GltG~i~F-~~G~~~~~ 142 (681)
|++++|||||++|+|++++...+ ..|.+|..|.++|+ +++|+|+||+|.| ++|+|. .
T Consensus 301 ~a~~~yDav~~~A~Al~~~~~~g------------------~~~~~g~~l~~~l~~~~~~~f~G~tG~v~fd~~G~r~-~ 361 (391)
T cd06372 301 YSAYLHDAVLLYALAVKEMLKAG------------------KDFRNGRQLVSTLRGANQVELQGITGLVLLDEQGKRQ-M 361 (391)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcC------------------CCCCCHHHHHHHHhhccCceEeccceeEEECCCCCcc-e
Confidence 89999999999999999976321 12567899999999 6999999999999 889985 7
Q ss_pred cEEEEEeee--C--CeeEeeeeeCCC
Q 005717 143 AFEIFNVIG--T--SERVIGYWTKEK 164 (681)
Q Consensus 143 ~~~I~n~~~--~--~~~~vG~W~~~~ 164 (681)
.|.|+++++ . .+..||+|+..+
T Consensus 362 ~y~i~~~~~~~~~~~~~~vg~~~~~~ 387 (391)
T cd06372 362 DYSVYALQKSGNSSLFLPFLHYDSHQ 387 (391)
T ss_pred eEEEEeccccCCccceeeEEEecchh
Confidence 999999986 2 378999999643
No 46
>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=99.42 E-value=1.4e-13 Score=144.75 Aligned_cols=119 Identities=24% Similarity=0.325 Sum_probs=95.8
Q ss_pred CCCCCeEEEecCCccccCCccccccCccceEEEEEecCCChhHHHHHHHHHhh-cC-CCCCCCCCCchhHHHHHHHHHHH
Q 005717 1 MMSEGYAWIATQGLSTLLDPVKDMESMQGVLGLRPYIPSSKKLEHFKLRWIKS-AD-KPDGSTGGSNLFGLWAYDTVWAI 78 (681)
Q Consensus 1 mm~~~y~WI~t~~~~~~~~~~~~~~~~~Gvlg~~~~~~~~~~~~~f~~~~~~~-~~-~~~~~~~~~~~~~~~aYDav~~l 78 (681)
||+++|+||+|++..+.++..++......++|+++..+..+.+++|.+.|+++ .+ ............++++||||+++
T Consensus 211 m~~~~y~~i~T~l~~~~~~L~~~~~~~~niTgF~l~d~~~~~v~~f~~~~~~~~~~~~~~~~~~~~~~~~al~~D~v~~~ 290 (333)
T cd06394 211 MTSAFYKYILTTMDFPLLRLDSIVDDRSNILGFSMFNQSHAFYQEFIRSLNQSWRENCDHSPYTGPALSSALLFDAVYAV 290 (333)
T ss_pred CCCCceEEEEecCCcccccHHHhhcCCcceEEEEeecCCcHHHHHHHHHHHHhhhhhcccccCCCcccceeeecceEEEE
Confidence 89999999999998876665555556777999999999999999999987753 11 00000011223578899998766
Q ss_pred HHHHHHHcccCCcccccCCCCCCCcccccCCCcchHHHHHHHhccceecceeeEEE-eCCcccCccEEEEEeeeCCeeEe
Q 005717 79 AMAVERAGIENSSFLKSNTSKSRVDIAALGTFEMGAKLLDTLINTTFEGLSGNFHL-VNGQLEPSAFEIFNVIGTSERVI 157 (681)
Q Consensus 79 A~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~l~~~l~~~~f~GltG~i~F-~~G~~~~~~~~I~n~~~~~~~~v 157 (681)
|+||+|+| ++|+|.+.+++|++++.+|.++|
T Consensus 291 ------------------------------------------------glTg~i~f~~~g~R~~~~l~v~~l~~~g~~ki 322 (333)
T cd06394 291 ------------------------------------------------GLTGRIEFNSKGQRSNYTLKILQKTRSGFRQI 322 (333)
T ss_pred ------------------------------------------------eeecceecCCCCcCcccEEEEEEecCCcceEE
Confidence 99999999 88999999999999999999999
Q ss_pred eeeeCCCCcc
Q 005717 158 GYWTKEKELL 167 (681)
Q Consensus 158 G~W~~~~gl~ 167 (681)
|+|++..|+.
T Consensus 323 g~W~~~~gl~ 332 (333)
T cd06394 323 GQWHSNETLS 332 (333)
T ss_pred EEEeCCCCcC
Confidence 9999999875
No 47
>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=99.42 E-value=7.1e-14 Score=149.60 Aligned_cols=140 Identities=14% Similarity=0.105 Sum_probs=101.8
Q ss_pred CCCCCeEEEecCCccccCCccccccCccceEEEEEecCCChhHHHHHHHHHhhcCCCCCCCCCCchhHHHHHHHHHHHHH
Q 005717 1 MMSEGYAWIATQGLSTLLDPVKDMESMQGVLGLRPYIPSSKKLEHFKLRWIKSADKPDGSTGGSNLFGLWAYDTVWAIAM 80 (681)
Q Consensus 1 mm~~~y~WI~t~~~~~~~~~~~~~~~~~Gvlg~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~aYDav~~lA~ 80 (681)
||+++||||+|+|+.+.+|..++...-.+++|+|+..+.+...+++..+|... +.+......+...++++||||+++|.
T Consensus 210 m~~~~y~wilt~ld~~~~dl~~~~~~~~Nitgfrl~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~aL~~Dav~~~~~ 288 (368)
T cd06383 210 FMGRKYAWFLGNPDLGIYDDLSCQLRNASIFVTRPMMDYQSSVRGALLRTDEP-TLRPVFYFEWAFRLFLAYDAVLAVGE 288 (368)
T ss_pred CcCCceEEEEcCCCchhhhhhhhccccCcEEEeeccccchhhhccceeeccCC-ccCchhHHHHHHHHHHHHHHHHHhcc
Confidence 89999999999998887776666777889999999877777778888777322 21222222345568999999999999
Q ss_pred HHHHHcccCCcccccCCCC-CCCcccccC---CC-cchHHHHHHHhccceecceeeEEE-eCCcccCccE
Q 005717 81 AVERAGIENSSFLKSNTSK-SRVDIAALG---TF-EMGAKLLDTLINTTFEGLSGNFHL-VNGQLEPSAF 144 (681)
Q Consensus 81 Al~~~~~~~~~~~~~~~~~-~~~~~~~~~---~~-~~G~~l~~~l~~~~f~GltG~i~F-~~G~~~~~~~ 144 (681)
|++.+........ +.. ....|.... +| ..|..+.++|++++|+|+||+|+| ++|+|.+.++
T Consensus 289 a~~~l~~~~~~~~---~~~~~~~~~~g~~~~~~w~~~g~~~~~~~k~~~~~gltG~i~f~~~g~R~~~~l 355 (368)
T cd06383 289 WPRRMRKKRVEDG---STGTSVLPGFGISPESPLMTLQSSPFNGSSEIKFEMLAGRVAIDEGSSVSTKTI 355 (368)
T ss_pred ccchhheeeccCC---CcCccccCCCCCCcccchhhcccccccCccceeEeeecCeEEEecCceeeeeee
Confidence 9998742211111 111 123454432 57 778899999999999999999999 8899975443
No 48
>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=99.42 E-value=2e-12 Score=143.23 Aligned_cols=154 Identities=21% Similarity=0.291 Sum_probs=105.1
Q ss_pred CCeEEEecCCccccCCc-cccccCccceEEEEEecCCChhHHHHHHH---------------HHhh-c-C---CCCCC--
Q 005717 4 EGYAWIATQGLSTLLDP-VKDMESMQGVLGLRPYIPSSKKLEHFKLR---------------WIKS-A-D---KPDGS-- 60 (681)
Q Consensus 4 ~~y~WI~t~~~~~~~~~-~~~~~~~~Gvlg~~~~~~~~~~~~~f~~~---------------~~~~-~-~---~~~~~-- 60 (681)
..|+||.++.+...... .......+|++++.+.....+.+++|.+. |+.. . . .....
T Consensus 257 ~~~~~i~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~i~~f~~~l~~l~~~~~~~~~~~~~~w~~~~~c~~~~~~~~~~~ 336 (452)
T cd06362 257 GHFQWIASDGWGARNSVVEGLEDVAEGAITIELQSAEVPGFDEYFLSLTPENNSRNPWFREFWEQKFNCKLTGNGSTKDN 336 (452)
T ss_pred CceEEEEeccccccchhhcccccccceEEEEEecccccccHHHHhhhCCcCcCCCChHHHHHHHHhcCCCcCCCCccccC
Confidence 35899999954332111 13345789999998887666555554322 2221 1 0 00000
Q ss_pred -----C------CCCchhHHHHHHHHHHHHHHHHHHcccCCcccccCCCCCCCcccccCCCcchHHHHHHHhccceecce
Q 005717 61 -----T------GGSNLFGLWAYDTVWAIAMAVERAGIENSSFLKSNTSKSRVDIAALGTFEMGAKLLDTLINTTFEGLS 129 (681)
Q Consensus 61 -----~------~~~~~~~~~aYDav~~lA~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~l~~~l~~~~f~Glt 129 (681)
. .....++.++|||||++|+||+++....- ......|.... |.+|.+|+++|++++|+|+|
T Consensus 337 ~~c~~~~~~~~~~~~~~~~~~vyDAV~a~A~AL~~~l~~~~-------~~~~~~c~~~~-~~~~~~l~~~l~~v~f~g~t 408 (452)
T cd06362 337 TCCTERILLLSNYEQESKVQFVIDAVYAMAHALHNMHRDLC-------PGTTGLCDAMK-PIDGRKLLFYLRNVSFSGLA 408 (452)
T ss_pred CCCccccccccccccccchhHHHHHHHHHHHHHHHHHHhhC-------CCCCCCCcCcc-CCCHHHHHHHHHhCCcCCCC
Confidence 0 12244789999999999999999864321 11123465443 66899999999999999999
Q ss_pred e-eEEE-eCCcccCccEEEEEeeeC----CeeEeeeeeCCCCc
Q 005717 130 G-NFHL-VNGQLEPSAFEIFNVIGT----SERVIGYWTKEKEL 166 (681)
Q Consensus 130 G-~i~F-~~G~~~~~~~~I~n~~~~----~~~~vG~W~~~~gl 166 (681)
| .|+| ++|++. ..|+|+|++.. ++++||+|++..|+
T Consensus 409 g~~v~Fd~~G~~~-~~y~I~~~~~~~~~~~~~~VG~w~~~~~~ 450 (452)
T cd06362 409 GGPVRFDANGDGP-GRYDIFNYQRTNGKYDYVKVGSWKGELSL 450 (452)
T ss_pred CceEEECCCCCCC-CceEEEEEEEcCCceEEEEEEEEeccccc
Confidence 8 7999 899987 49999999842 48999999987665
No 49
>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=99.37 E-value=3e-12 Score=139.39 Aligned_cols=144 Identities=15% Similarity=0.183 Sum_probs=109.1
Q ss_pred CCCCCeEEEecCCccccCCc---------------cccccCccceEEEEEecCCChhHHHHHHHHHhh-cC-CCCC-CCC
Q 005717 1 MMSEGYAWIATQGLSTLLDP---------------VKDMESMQGVLGLRPYIPSSKKLEHFKLRWIKS-AD-KPDG-STG 62 (681)
Q Consensus 1 mm~~~y~WI~t~~~~~~~~~---------------~~~~~~~~Gvlg~~~~~~~~~~~~~f~~~~~~~-~~-~~~~-~~~ 62 (681)
|++++|+||..|+....+.. ....+.+++++++.++.+.++.+++|.++|+++ .+ +... ...
T Consensus 227 ~~~~~y~~i~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~v~~~~~~~~~~~~~~~F~~~~~~~~~~~~~~~~~p~ 306 (399)
T cd06384 227 LTPGDYVFFYLDVFGESLRVKSPRESYKQMNHSSWTVLKEAFKSVFVITYREPENPEYKEFQRELHARAKEDFGVELEPS 306 (399)
T ss_pred CCCCcEEEEEehhcccccccCCCCccccCCCCcccHHHHHHHhheEEeecCCCCCchHHHHHHHHHHHHhhhcCCCcCcc
Confidence 67889999999976543321 022347899999998888888899999999874 21 2111 011
Q ss_pred CCchhHHHHHHHHHHHHHHHHHHcccCCcccccCCCCCCCcccccCCCcchHHHHHHHhccceecceeeEEE-eCCcccC
Q 005717 63 GSNLFGLWAYDTVWAIAMAVERAGIENSSFLKSNTSKSRVDIAALGTFEMGAKLLDTLINTTFEGLSGNFHL-VNGQLEP 141 (681)
Q Consensus 63 ~~~~~~~~aYDav~~lA~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~l~~~l~~~~f~GltG~i~F-~~G~~~~ 141 (681)
..+.+++++||||+++|.|++++.... +.|.+|..|.++|++++|+|+||++.| ++|+|.
T Consensus 307 ~~~~~aa~~YDav~l~a~Al~~~~~~~------------------~~~~~g~~i~~~l~~~~f~GvtG~v~fd~~G~r~- 367 (399)
T cd06384 307 LMNFIAGCFYDGVMLYAMALNETLAEG------------------GSQKDGLNITRKMQDRRFWGVTGLVSIDKNNDRD- 367 (399)
T ss_pred hHhhhhhhhHHHHHHHHHHHHHHHhcC------------------CCCCCcHhHHHHHhCceeecceeEEEECCCCCcc-
Confidence 136689999999999999999975321 235678999999999999999999999 899996
Q ss_pred ccEEE---EEeeeCCeeEeeeeeCC
Q 005717 142 SAFEI---FNVIGTSERVIGYWTKE 163 (681)
Q Consensus 142 ~~~~I---~n~~~~~~~~vG~W~~~ 163 (681)
..|.+ .+++++++..||+|+..
T Consensus 368 ~~~~~~~~~~~~~g~~~~v~~~~~~ 392 (399)
T cd06384 368 IDFDLWAMTDHETGKYEVVAHYNGI 392 (399)
T ss_pred cceEEEEeecCCCCeEEEEEEEcCC
Confidence 45666 46678889999999864
No 50
>COG4623 Predicted soluble lytic transglycosylase fused to an ABC-type amino acid-binding protein [Cell envelope biogenesis, outer membrane]
Probab=99.36 E-value=1.4e-11 Score=123.89 Aligned_cols=220 Identities=13% Similarity=0.160 Sum_probs=178.6
Q ss_pred ceEEEEeeccCCccceEEEeecCCCCeeEEeehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEE
Q 005717 195 RKLKIGVPVREGFTEFIKVVENKNKTTQVSGFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTT 274 (681)
Q Consensus 195 ~~lrV~v~~~~p~~~~~~~~~~~~~~~~~~G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~ 274 (681)
+.|||+|... |-..| ..++..+|+++++.+++++.|| ++.++.+. .+-+.+..+|.+|++|++.+++.
T Consensus 23 GvLrV~tins-p~sy~-------~~~~~p~G~eYelak~Fa~yLg--V~Lki~~~--~n~dqLf~aL~ng~~DL~Aagl~ 90 (473)
T COG4623 23 GVLRVSTINS-PLSYF-------EDKGGPTGLEYELAKAFADYLG--VKLKIIPA--DNIDQLFDALDNGNADLAAAGLL 90 (473)
T ss_pred CeEEEEeecC-cccee-------ccCCCccchhHHHHHHHHHHhC--CeEEEEec--CCHHHHHHHHhCCCcceeccccc
Confidence 7899999875 43333 3556677999999999999999 66888887 57899999999999999999999
Q ss_pred EeeccccccccccceeecceEEEEEeccCCCcCceeeeccCcHhHHHHHHHHHHHHHHHhhhhhcccCCCCCCCCCCchh
Q 005717 275 IVANRSTFVDFTLPYSESGVSMLVLVKDDERKNFWIFLKPLSWDLWLTTGAAFIFTGLVVWVLEHRINTEFRGPPQHQIG 354 (681)
Q Consensus 275 it~~R~~~vdFT~P~~~~~~~~vv~~~~~~~~~~~~fl~PF~~~vW~~i~~~~~~v~~v~~~~~~~~~~~~~~~~~~~~~ 354 (681)
..++|.+.+.....|+...+.+|.++....
T Consensus 91 ~~~~~l~~~~~gP~y~svs~qlVyRkG~~R-------------------------------------------------- 120 (473)
T COG4623 91 YNSERLKNFQPGPTYYSVSQQLVYRKGQYR-------------------------------------------------- 120 (473)
T ss_pred CChhHhcccCCCCceecccHHHHhhcCCCC--------------------------------------------------
Confidence 999999988888889988888888877643
Q ss_pred hHHHHHHHHHhccCcccccccchhHHHHHHHHHHHHHHhHhhhhhhheeeecccCCCCCCHHHHHhCCCeEEEecChhHH
Q 005717 355 TIFWFSFSTLVFAHRERVVNNLSRFVLIIWVFVVLILTQSYTASLTSMLTVQRLQPSFTDVKDIQKNGYFVGYQTNSFVK 434 (681)
Q Consensus 355 ~~~~~~~~~l~~~~~~~~~s~~~R~l~~~w~~~~lil~s~YtA~L~s~LT~~~~~~~i~s~~dL~~~~~~vg~~~~s~~~ 434 (681)
.+++++|. |..+.+.+|+...
T Consensus 121 ---------------------------------------------------------p~~l~~L~--g~~i~v~~gs~~~ 141 (473)
T COG4623 121 ---------------------------------------------------------PRSLGQLK--GRQITVAKGSAHV 141 (473)
T ss_pred ---------------------------------------------------------CCCHHHcc--CceeeccCCcHHH
Confidence 47789998 7778888888766
Q ss_pred HHHh--hhcCCcccccc--ccCChhHHHHHHccCcceEEecchhhHHHHHhhcCCceEEECcccccCCcEEEecCCCC--
Q 005717 435 DLLT--KKLNFNETRLK--NYTTSEDYHDALSNGEVAAIFDEIPYIKIFLASYCSRYMMVGPTYRTDGFGFAFPLGSP-- 508 (681)
Q Consensus 435 ~~l~--~~~~~~~~~~~--~~~~~~~~~~~l~~g~~~a~i~e~~~~~~~~~~~c~~l~~v~~~~~~~~~~~~~~k~sp-- 508 (681)
+-+. ++..+|+-..+ .-...++.++.+..|+++..+.++..+..+.+-+. ++.+.-+.-...+.++.+|.+..
T Consensus 142 ~~l~~lk~~kyP~l~~k~d~~~~~~dLle~v~~Gkldytiads~~is~~q~i~P-~laVafd~tde~~v~Wy~~~~dd~t 220 (473)
T COG4623 142 EDLKLLKETKYPELIWKVDDKLGVEDLLEMVAEGKLDYTIADSVEISLFQRVHP-ELAVAFDLTDEQPVAWYLPRDDDST 220 (473)
T ss_pred HHHHHHHHhhcchhhhhhcccccHHHHHHHHhcCCcceeeeccHHHHHHHHhCc-cceeeeecccccCceeeccCCchHH
Confidence 5541 22344443222 22367899999999999999999998888777776 77777666666889999999644
Q ss_pred ChHHHHHHHHhhccCccHHHHHHHHHcCC
Q 005717 509 LVPYISRAILKVTEDKEKMENIEKALGNQ 537 (681)
Q Consensus 509 l~~~in~~Il~l~e~~G~l~~i~~kw~~~ 537 (681)
|...++..+..+.|. |.++.+++||++.
T Consensus 221 L~a~ll~F~~~~~e~-g~larleeky~gH 248 (473)
T COG4623 221 LSAALLDFLNEAKED-GLLARLEEKYLGH 248 (473)
T ss_pred HHHHHHHHHHHhhcc-hHHHHHHHHHhcc
Confidence 999999999999999 9999999999976
No 51
>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=99.34 E-value=1.8e-12 Score=137.37 Aligned_cols=118 Identities=24% Similarity=0.283 Sum_probs=98.7
Q ss_pred CCCCCeEEEecCCccccCCccccccCccceEEEEEecCCChhHHHHHHHHHhh--cCCCCCCCCCCchhHHHHHHHHHHH
Q 005717 1 MMSEGYAWIATQGLSTLLDPVKDMESMQGVLGLRPYIPSSKKLEHFKLRWIKS--ADKPDGSTGGSNLFGLWAYDTVWAI 78 (681)
Q Consensus 1 mm~~~y~WI~t~~~~~~~~~~~~~~~~~Gvlg~~~~~~~~~~~~~f~~~~~~~--~~~~~~~~~~~~~~~~~aYDav~~l 78 (681)
|+++.|+||++++.....+.........++++++++.+.++..++|.++|+++ .++++.....++.+++++|||++++
T Consensus 206 ~~~~~~~~i~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~p~~~~a~~yDav~~~ 285 (327)
T cd06382 206 MMSEYYHYIITNLDLHTLDLEDYRYSGVNITGFRLVDPDSPEVKEVIRSLELSWDEGCRILPSTGVTTESALMYDAVYLF 285 (327)
T ss_pred ccccceEEEEecCCccccchhhhccCceeEEEEEEecCCchhHHHHHHHHHhhcccccccCCCCCcchhhhhhhceEEEe
Confidence 56788999999987666554444556678999999998888999999999987 2233333445788999999999876
Q ss_pred HHHHHHHcccCCcccccCCCCCCCcccccCCCcchHHHHHHHhccceecceeeEEE-eCCcccCccEEEEEeeeCCeeEe
Q 005717 79 AMAVERAGIENSSFLKSNTSKSRVDIAALGTFEMGAKLLDTLINTTFEGLSGNFHL-VNGQLEPSAFEIFNVIGTSERVI 157 (681)
Q Consensus 79 A~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~l~~~l~~~~f~GltG~i~F-~~G~~~~~~~~I~n~~~~~~~~v 157 (681)
|+||.|+| ++|+|.+..++|+|++++++++|
T Consensus 286 ------------------------------------------------g~tG~v~f~~~g~r~~~~~~~~~~~~~~~~~v 317 (327)
T cd06382 286 ------------------------------------------------GLTGRIEFDSSGQRSNFTLDVIELTESGLRKV 317 (327)
T ss_pred ------------------------------------------------ecccceeeCCCCCEeeeEEEEEeccccCceEE
Confidence 99999999 89999999999999999999999
Q ss_pred eeeeCCCCc
Q 005717 158 GYWTKEKEL 166 (681)
Q Consensus 158 G~W~~~~gl 166 (681)
|+|++..|+
T Consensus 318 g~w~~~~~~ 326 (327)
T cd06382 318 GTWNSSEGL 326 (327)
T ss_pred EEECCCCCc
Confidence 999988775
No 52
>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=99.33 E-value=9.5e-13 Score=143.35 Aligned_cols=173 Identities=20% Similarity=0.314 Sum_probs=120.5
Q ss_pred CCCCCeEEEecCCccccCCcc----------ccccCccceEEEEEecCCCh--------hHHHHHHHHHhh-cCCCCCCC
Q 005717 1 MMSEGYAWIATQGLSTLLDPV----------KDMESMQGVLGLRPYIPSSK--------KLEHFKLRWIKS-ADKPDGST 61 (681)
Q Consensus 1 mm~~~y~WI~t~~~~~~~~~~----------~~~~~~~Gvlg~~~~~~~~~--------~~~~f~~~~~~~-~~~~~~~~ 61 (681)
|+|..|+|++..|+.+.|+.. +..++++|.+++....-+.. ..+.|+..+.+. ...+ ..
T Consensus 258 myg~ky~w~~~g~y~d~w~ev~~~~~~ctveem~~A~eg~~s~e~~pl~~~~~~tisg~T~~~~l~~~~~~r~~~~--~~ 335 (865)
T KOG1055|consen 258 LYGRKYVWFLIGWYADNWWEITHPSENCTVEEMTEAAEGHITTEFVMLSPANITTISGMTAQEFLEELTKYRKRHP--EE 335 (865)
T ss_pred cccceeEEEEEEeeccchhhccCchhhhhHHHHHHHHhhheeeeeeccccccceeeccchhHHHHHHHHhhhcccc--cc
Confidence 789999999999999998743 44567899888877543322 235676666544 2111 11
Q ss_pred CCCchhHHHHHHHHHHHHHHHHHHcccCCcccccCCCCCCCccccc--CCCcchHHHHHHHhccceecceeeEEEeCCcc
Q 005717 62 GGSNLFGLWAYDTVWAIAMAVERAGIENSSFLKSNTSKSRVDIAAL--GTFEMGAKLLDTLINTTFEGLSGNFHLVNGQL 139 (681)
Q Consensus 62 ~~~~~~~~~aYDav~~lA~Al~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~G~~l~~~l~~~~f~GltG~i~F~~G~~ 139 (681)
.+...++.+||||||++|+|++++.....+ ....+.++ ..-..+..|+++|.+++|+|+||.+.|.+|+|
T Consensus 336 ~~~~~~~~~ayd~Iwa~ala~n~t~e~l~~--------~~~~l~~f~y~~k~i~d~i~eamn~tsF~GvsG~V~F~~geR 407 (865)
T KOG1055|consen 336 TGGFQEAPLAYDAIWALALALNKTMEGLGR--------SHVRLEDFNYNNKTIADQIYEAMNSTSFEGVSGHVVFSNGER 407 (865)
T ss_pred ccCcccCchHHHHHHHHHHHHHHHHhcCCc--------cceeccccchhhhHHHHHHHHHhhcccccccccceEecchhh
Confidence 234567899999999999999998654320 01111111 11235689999999999999999999977999
Q ss_pred cCccEEEEEeeeCCeeEeeeeeCCCCccccccCCCCccCCCCCCccCCCCCcCCCc
Q 005717 140 EPSAFEIFNVIGTSERVIGYWTKEKELLSELNDNNGRATNNLKNPIWPGNTIDQPR 195 (681)
Q Consensus 140 ~~~~~~I~n~~~~~~~~vG~W~~~~gl~~~~~~~~~~~~~~l~~i~Wpg~~~~~p~ 195 (681)
. ...+|.+++++.++++|+|+...+-. + ..+...|-|+..+.+.
T Consensus 408 ~-a~t~ieQ~qdg~y~k~g~Yds~~D~l---s--------~~n~~~w~~g~ppkd~ 451 (865)
T KOG1055|consen 408 M-ALTLIEQFQDGKYKKIGYYDSTKDDL---S--------WINTEKWIGGSPPKDS 451 (865)
T ss_pred H-HHHHHHHHhCCceEeecccccccchh---h--------ccccceEeccCCCccc
Confidence 8 67889999999999999999765421 1 2345678777433333
No 53
>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=99.26 E-value=5.9e-11 Score=129.01 Aligned_cols=133 Identities=17% Similarity=0.188 Sum_probs=97.7
Q ss_pred CCeEEEecCCccccCCcc--ccccCccceEEEEEecCCChhHHHHHHHHHhhcCCCCCCCCCCchhHHHHHHHHHHHHHH
Q 005717 4 EGYAWIATQGLSTLLDPV--KDMESMQGVLGLRPYIPSSKKLEHFKLRWIKSADKPDGSTGGSNLFGLWAYDTVWAIAMA 81 (681)
Q Consensus 4 ~~y~WI~t~~~~~~~~~~--~~~~~~~Gvlg~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~aYDav~~lA~A 81 (681)
-+++||.++++....... .....+.|++|+.+..+..+.+ .+.+++. +...+||||+++|+|
T Consensus 259 ~~~~wigs~~w~~~~~~~~~~~~~~~~g~ig~~~~~~~~~~F---~~~~~~~-------------~~~~v~~AVyaiA~A 322 (403)
T cd06361 259 INKVWIASDNWSTAKKILTDPNVKKIGKVVGFTFKSGNISSF---HQFLKNL-------------LIHSIQLAVFALAHA 322 (403)
T ss_pred CCeEEEEECcccCccccccCCcccccceEEEEEecCCccchH---HHHHHHh-------------hHHHHHHHHHHHHHH
Confidence 379999999654322222 2346789999999977555554 4444432 244689999999999
Q ss_pred HHHHcccCCcccccCCCCCCCcccccCCCcchHHHHHHHhccceecceeeEEE-eCCcccCccEEEEEeeeCC----eeE
Q 005717 82 VERAGIENSSFLKSNTSKSRVDIAALGTFEMGAKLLDTLINTTFEGLSGNFHL-VNGQLEPSAFEIFNVIGTS----ERV 156 (681)
Q Consensus 82 l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~l~~~l~~~~f~GltG~i~F-~~G~~~~~~~~I~n~~~~~----~~~ 156 (681)
||++... ..|.... ..++.+|+++|++++|+|++|++.| .+|+. ...|+|+|++.++ +++
T Consensus 323 l~~~~~~-------------~~c~~~~-~~~~~~l~~~L~~~~f~g~~~~v~Fd~~gd~-~~~y~I~~~~~~~~~~~~~~ 387 (403)
T cd06361 323 IRDLCQE-------------RQCQNPN-AFQPWELLGQLKNVTFEDGGNMYHFDANGDL-NLGYDVVLWKEDNGHMTVTI 387 (403)
T ss_pred HHHhccC-------------CCCCCCC-CcCHHHHHHHHheeEEecCCceEEECCCCCC-CcceEEEEeEecCCcEEEEE
Confidence 9997532 2354322 2367899999999999999889999 88987 4689999999643 699
Q ss_pred eeeeeCCCCcc
Q 005717 157 IGYWTKEKELL 167 (681)
Q Consensus 157 vG~W~~~~gl~ 167 (681)
||.|++.+...
T Consensus 388 vg~~~~~~~~~ 398 (403)
T cd06361 388 MAEYDPQNDVF 398 (403)
T ss_pred EEEEeCCCCEE
Confidence 99999876543
No 54
>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=99.22 E-value=4.8e-11 Score=129.90 Aligned_cols=144 Identities=21% Similarity=0.293 Sum_probs=106.0
Q ss_pred CCCCCeEEEecCCcccc------CC---cc----ccccCccceEEEEEecCCChhHHHHHHHHHhh--cCCC-CCCCCCC
Q 005717 1 MMSEGYAWIATQGLSTL------LD---PV----KDMESMQGVLGLRPYIPSSKKLEHFKLRWIKS--ADKP-DGSTGGS 64 (681)
Q Consensus 1 mm~~~y~WI~t~~~~~~------~~---~~----~~~~~~~Gvlg~~~~~~~~~~~~~f~~~~~~~--~~~~-~~~~~~~ 64 (681)
|++++||||.+++++.. |. .. ...+.++|++++....+.++..++|.++|+++ ..+. ......+
T Consensus 226 ~~~~~yv~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~F~~~~~~~~~~~~~~~~~~~~~ 305 (396)
T cd06373 226 LTSGEYVFFNIDLFGSSLYGGGPWWWERGDEDDEKAKEAYQALMTITLREPDNPEYKEFSLEVKERAKKKFNTTSDDSLV 305 (396)
T ss_pred CCCCcEEEEEEccchhhhccCCCCcCCCCCcccHHHHHHHHHheEEecCCCCChHHHHHHHHHHHHhhhcCCCCcchhHH
Confidence 45689999998865321 11 11 12235678999998888888899999999874 1121 1111235
Q ss_pred chhHHHHHHHHHHHHHHHHHHcccCCcccccCCCCCCCcccccCCCcchHHHHHHHhccceecceeeEEE-eCCcccCcc
Q 005717 65 NLFGLWAYDTVWAIAMAVERAGIENSSFLKSNTSKSRVDIAALGTFEMGAKLLDTLINTTFEGLSGNFHL-VNGQLEPSA 143 (681)
Q Consensus 65 ~~~~~~aYDav~~lA~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~l~~~l~~~~f~GltG~i~F-~~G~~~~~~ 143 (681)
+.+++++||||+++|+|++++..... .+.+|..|.++|++++|+|++|++.| ++|++. ..
T Consensus 306 ~~~a~~~YDav~~~a~Al~~~~~~~~------------------~~~~~~~i~~~l~~~~f~G~tG~v~fd~~G~~~-~~ 366 (396)
T cd06373 306 NFFAGAFYDAVLLYALALNETLAEGG------------------DPRDGTNITRRMWNRTFEGITGNVSIDENGDRE-SD 366 (396)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhccC------------------CCCChHHHHHHhcCCceecccCceEeecCCccc-ce
Confidence 67999999999999999999853211 12467899999999999999999999 889986 57
Q ss_pred EEEEEe---eeCCeeEeeeeeCC
Q 005717 144 FEIFNV---IGTSERVIGYWTKE 163 (681)
Q Consensus 144 ~~I~n~---~~~~~~~vG~W~~~ 163 (681)
|.|+++ +++.++.||++++.
T Consensus 367 ~~v~~~~~~~~g~~~~~~~~~~~ 389 (396)
T cd06373 367 FSLWDMTDTETGTFEVVANYNGS 389 (396)
T ss_pred eeeeeccCCCCceEEEEeecccc
Confidence 888765 45668999998863
No 55
>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=99.21 E-value=2.5e-10 Score=127.77 Aligned_cols=153 Identities=17% Similarity=0.212 Sum_probs=102.5
Q ss_pred CCeEEEecC-Ccccc-CCccccccCccceEEEEEecCCChhHHHHHHH---------------HHhh-c-CCCC---C--
Q 005717 4 EGYAWIATQ-GLSTL-LDPVKDMESMQGVLGLRPYIPSSKKLEHFKLR---------------WIKS-A-DKPD---G-- 59 (681)
Q Consensus 4 ~~y~WI~t~-~~~~~-~~~~~~~~~~~Gvlg~~~~~~~~~~~~~f~~~---------------~~~~-~-~~~~---~-- 59 (681)
.+++||.++ |.+.. .......+.+.|++|+.+.....+.+++|.+. |+.. + ..+. .
T Consensus 270 ~~~iwI~s~~w~~~~~~~~~~~~~~~gg~lg~~~~~~~i~~f~~~l~~l~p~~~~~~~~~~~~we~~f~c~~~~~~~~~~ 349 (510)
T cd06364 270 TGKIWLASEAWASSSLIAMPEYFDVMGGTIGFALKAGQIPGFREFLQKVHPKKSSHNGFAKEFWEETFNCYLEDSPKNAL 349 (510)
T ss_pred CCcEEEEEchhhcccccccCCccceeeEEEEEEECCCcCccHHHHHHhCCcccCCCChHHHHHHHHhcCCCCCCCccccc
Confidence 468999998 43322 22224667899999999988777777666654 2222 1 0000 0
Q ss_pred ----------------------C-CC----C------------CchhHHHHHHHHHHHHHHHHHHcccCCcccccCCCCC
Q 005717 60 ----------------------S-TG----G------------SNLFGLWAYDTVWAIAMAVERAGIENSSFLKSNTSKS 100 (681)
Q Consensus 60 ----------------------~-~~----~------------~~~~~~~aYDav~~lA~Al~~~~~~~~~~~~~~~~~~ 100 (681)
. .. . ...+...+||||+|+|||||++..+..... ...
T Consensus 350 ~~~~~~~~~~~~~~~~~~~~~~~~~C~~~~~~~~~~~~~~~~~~~~~~~~v~~AVyAvAhaLh~~~~c~~~~~----~~~ 425 (510)
T cd06364 350 PVDTFLGHEESGDDSENGSTAFRPLCTGDENIASVETPYLDYTHLRISYNVYLAVYSIAHALQDIYTCTPGKG----LFT 425 (510)
T ss_pred ccccccccccccccccccccccCCCCCChhhhcccCCccccccchhhHHHHHHHHHHHHHHHHHHhcCCCCCC----Ccc
Confidence 0 00 0 123467899999999999999986532111 001
Q ss_pred CCcccccCCCcchHHHHHHHhccceecceee-EEE-eCCcccCccEEEEEeee---CC---eeEeeeeeC
Q 005717 101 RVDIAALGTFEMGAKLLDTLINTTFEGLSGN-FHL-VNGQLEPSAFEIFNVIG---TS---ERVIGYWTK 162 (681)
Q Consensus 101 ~~~~~~~~~~~~G~~l~~~l~~~~f~GltG~-i~F-~~G~~~~~~~~I~n~~~---~~---~~~vG~W~~ 162 (681)
...|..... ..+.+|+++|++++|+|.+|+ |.| .+|+.. ..|+|+|++. .+ +++||.|++
T Consensus 426 ~~~c~~~~~-~~~~~l~~~L~~v~F~~~~g~~v~Fd~~Gd~~-~~YdI~n~q~~~~~~~~~~v~VG~~~~ 493 (510)
T cd06364 426 NGSCADIKK-VEAWQVLKHLRHLNFTDNMGEQVRFDEGGDLV-GNYSIINWHLSPEDGSVVFKEVGYYNV 493 (510)
T ss_pred CCCCCCCCC-CCHHHHHHHHHhcEEecCCCCEEEEecCCCCc-cceeEEEeeecCCCCcEEEEEEEEEcC
Confidence 235755322 256799999999999999984 999 899985 6899999994 22 689999985
No 56
>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=99.20 E-value=1.2e-10 Score=126.03 Aligned_cols=140 Identities=19% Similarity=0.226 Sum_probs=100.3
Q ss_pred CCCCCeEEEecCCccccC----Ccc-------ccccCccceEEEEEecCCChhHHHHHHHHHhhcCCCCC-CCCCCchhH
Q 005717 1 MMSEGYAWIATQGLSTLL----DPV-------KDMESMQGVLGLRPYIPSSKKLEHFKLRWIKSADKPDG-STGGSNLFG 68 (681)
Q Consensus 1 mm~~~y~WI~t~~~~~~~----~~~-------~~~~~~~Gvlg~~~~~~~~~~~~~f~~~~~~~~~~~~~-~~~~~~~~~ 68 (681)
|++.+|+||.+|+..... ... +....++|++++.++.+..+..+.|.++|+.. ..|-. .....+.|+
T Consensus 218 m~~~~y~~i~~d~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~f~~~~~~~-~~~~~~~~~~~~~~~ 296 (382)
T cd06371 218 MTDGRYVFIPYDTLLYSLPYRNVSYPALRNNSKLRRAYDAVLTITMDSGEQSFYEAFRAAQERG-EIPSDLEPEQVSPLF 296 (382)
T ss_pred CcCCcEEEEEeccccccCCCCCccccCCCCCHHHHHHhHhhEEEEecCCCCcHHHHHHHHHhcC-CCCCCCCccccchhH
Confidence 678899999999643111 111 23357899999988765555566677765432 11111 111345677
Q ss_pred HHHHHHHHHHHHHHHHHcccCCcccccCCCCCCCcccccCCCcchHHHHHHHhccceecceeeEEE-eCCcccCccEEEE
Q 005717 69 LWAYDTVWAIAMAVERAGIENSSFLKSNTSKSRVDIAALGTFEMGAKLLDTLINTTFEGLSGNFHL-VNGQLEPSAFEIF 147 (681)
Q Consensus 69 ~~aYDav~~lA~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~l~~~l~~~~f~GltG~i~F-~~G~~~~~~~~I~ 147 (681)
+++|||+|++|+|++++...+. ..+|..+.++|.+++|+|++|+|+| ++|++. +.|.|+
T Consensus 297 ~~~YDav~~~a~Al~~a~~~g~-------------------~~d~~~l~~~l~~~~f~GvtG~v~fd~~g~~~-~~~~v~ 356 (382)
T cd06371 297 GTIYNSIYLLAHAVENARAAGG-------------------GVSGANLAQHTRNLEFQGFNQRLRTDSGGGGQ-APYVVL 356 (382)
T ss_pred HHHHHHHHHHHHHHHHHHHhCC-------------------CccHHHHHHHHhCccccccceEEEecCCCCcc-cceEEE
Confidence 7999999999999999864321 1367899999999999999999999 888874 899999
Q ss_pred EeeeCCeeEeeeee
Q 005717 148 NVIGTSERVIGYWT 161 (681)
Q Consensus 148 n~~~~~~~~vG~W~ 161 (681)
++.++|++-+=+++
T Consensus 357 ~~~~~~~~~~~~~~ 370 (382)
T cd06371 357 DTDGKGDQLYPTYT 370 (382)
T ss_pred ecCCCCCeeeeeEE
Confidence 99999887665443
No 57
>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=99.19 E-value=2.5e-10 Score=126.30 Aligned_cols=148 Identities=16% Similarity=0.253 Sum_probs=101.2
Q ss_pred eEEEecCCccccCCcc-ccccCccceEEEEEecCCChhHHHHHHHH---------------Hhh-c-CC--------CCC
Q 005717 6 YAWIATQGLSTLLDPV-KDMESMQGVLGLRPYIPSSKKLEHFKLRW---------------IKS-A-DK--------PDG 59 (681)
Q Consensus 6 y~WI~t~~~~~~~~~~-~~~~~~~Gvlg~~~~~~~~~~~~~f~~~~---------------~~~-~-~~--------~~~ 59 (681)
++||.++++...-... .....++|++|+.+.....+.+++|.+.+ +.. + .. .+.
T Consensus 259 ~~wigs~~~~~~~~~~~~~~~~~~G~i~~~~~~~~i~~f~~yl~~l~p~~~~~n~w~~e~w~~~f~c~~~~~~~~~~~C~ 338 (458)
T cd06375 259 FTWVASDGWGAQESIVKGSEDVAEGAITIELASHPIPDFDRYFQSLTPETNTRNPWFKDFWEQKFQCSLQNRDCANTTTN 338 (458)
T ss_pred EEEEEeccccccchhhhccchhhceEEEEEeccccchhHHHHHHhCCcCcCCCCcHHHHHHHHHcCCCCCCCCccCCCCC
Confidence 7999999643221111 23457899999999998888888877653 221 0 00 000
Q ss_pred CC--------CCCchhHHHHHHHHHHHHHHHHHHcccCCcccccCCCCCCCcccccCCCcchHHHH-HHHhcccee----
Q 005717 60 ST--------GGSNLFGLWAYDTVWAIAMAVERAGIENSSFLKSNTSKSRVDIAALGTFEMGAKLL-DTLINTTFE---- 126 (681)
Q Consensus 60 ~~--------~~~~~~~~~aYDav~~lA~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~l~-~~l~~~~f~---- 126 (681)
.. .....+..++||||+|+|||||++..+. +......|.... ..++.+|+ ++|++++|.
T Consensus 339 ~~~~~~~~~~~~~~~~~~~v~~AVyA~AhaLh~~l~~~-------c~~~~~~c~~~~-~~~~~~l~~~~L~~v~F~~~~~ 410 (458)
T cd06375 339 DKERLLDKVNYEQESKIMFVVNAVYAMAHALHNMQRDL-------CPNTTKLCDAMK-PLDGKKLYKEYLLNVSFTAPFR 410 (458)
T ss_pred chhcccccCcccccchHHHHHHHHHHHHHHHHHHHHhc-------CCCCCCCCCCCC-CCCHHHHHHHHHHhcccccccc
Confidence 00 0113467899999999999999997432 111124576543 23677899 599999999
Q ss_pred -cceee-EEE-eCCcccCccEEEEEeee--CC----eeEeeeeeC
Q 005717 127 -GLSGN-FHL-VNGQLEPSAFEIFNVIG--TS----ERVIGYWTK 162 (681)
Q Consensus 127 -GltG~-i~F-~~G~~~~~~~~I~n~~~--~~----~~~vG~W~~ 162 (681)
|.+|+ |.| .+|+.. ..|+|+|++. ++ +++||.|+.
T Consensus 411 ~~~~g~~v~Fd~nGd~~-~~YdI~n~q~~~~~~~~~~~~VG~w~~ 454 (458)
T cd06375 411 PDLADSEVKFDSQGDGL-GRYNIFNYQRTGNSYGYRYVGVGAWAN 454 (458)
T ss_pred CCCCCCeeEECCCCCCC-cceEEEEEEEcCCCCcEEEEEEEEEec
Confidence 99985 999 899975 6899999993 32 679999963
No 58
>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=99.13 E-value=1.3e-10 Score=122.87 Aligned_cols=116 Identities=26% Similarity=0.328 Sum_probs=94.1
Q ss_pred CCCCCeEEEecCCccccCCccccccCccceEEEEEecCCChhHHHHHHHHHhh--cCCCCCCCCCCchhHHHHHHHHHHH
Q 005717 1 MMSEGYAWIATQGLSTLLDPVKDMESMQGVLGLRPYIPSSKKLEHFKLRWIKS--ADKPDGSTGGSNLFGLWAYDTVWAI 78 (681)
Q Consensus 1 mm~~~y~WI~t~~~~~~~~~~~~~~~~~Gvlg~~~~~~~~~~~~~f~~~~~~~--~~~~~~~~~~~~~~~~~aYDav~~l 78 (681)
|++++|+||++++.....+.........++.|++...+.++..++|.++|+++ ..+|......+..+++++||||+++
T Consensus 205 ~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~p~~~aa~~yDav~~~ 284 (324)
T cd06368 205 MMSEYYHYILTNLDFHTLDLELFRYGGVNITGFRLVDPDNPEVQKFIQRWERSDHRICPGSGLKPIKTESALTYDAVLLF 284 (324)
T ss_pred cccCCcEEEEccCCccccchhhhhcCCceEEEEEEecCCChHHHHHHHHHHhccccccCCCCCCCcchhhHhhhcEEEEe
Confidence 45789999999975544333334456778999999998889999999999986 3233233335788999999999876
Q ss_pred HHHHHHHcccCCcccccCCCCCCCcccccCCCcchHHHHHHHhccceecceeeEEE-eCCcccCccEEEEEeeeCCeeEe
Q 005717 79 AMAVERAGIENSSFLKSNTSKSRVDIAALGTFEMGAKLLDTLINTTFEGLSGNFHL-VNGQLEPSAFEIFNVIGTSERVI 157 (681)
Q Consensus 79 A~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~l~~~l~~~~f~GltG~i~F-~~G~~~~~~~~I~n~~~~~~~~v 157 (681)
||+++| ++|+|.++.++|+|+.++++++|
T Consensus 285 --------------------------------------------------tg~~~f~~~g~~~~~~~~i~~~~~~~~~~~ 314 (324)
T cd06368 285 --------------------------------------------------TGRIQFDENGQRSNFTLDILELKEGGLRKV 314 (324)
T ss_pred --------------------------------------------------eeeeEeCCCCcCcceEEEEEEEcCCCceEE
Confidence 999999 88999999999999999999999
Q ss_pred eeeeCCCCc
Q 005717 158 GYWTKEKEL 166 (681)
Q Consensus 158 G~W~~~~gl 166 (681)
|+|++..|+
T Consensus 315 g~W~~~~~~ 323 (324)
T cd06368 315 GTWNPEDGL 323 (324)
T ss_pred EEECCCCCC
Confidence 999987775
No 59
>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=99.13 E-value=6.5e-10 Score=121.55 Aligned_cols=129 Identities=19% Similarity=0.242 Sum_probs=94.6
Q ss_pred CeEEEecCCcccc--CCccccccCccceEEEEEecCCChhHHHHHHHHHhhcCCCCCCCCCCchhHHHHHHHHHHHHHHH
Q 005717 5 GYAWIATQGLSTL--LDPVKDMESMQGVLGLRPYIPSSKKLEHFKLRWIKSADKPDGSTGGSNLFGLWAYDTVWAIAMAV 82 (681)
Q Consensus 5 ~y~WI~t~~~~~~--~~~~~~~~~~~Gvlg~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~aYDav~~lA~Al 82 (681)
+..||.++.+... .....-...+.+++|+....+..+..++|.++ +++.+|||||++|+|+
T Consensus 261 ~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~-----------------~~~~~YDaV~~~a~Al 323 (410)
T cd06363 261 GKVWIASEAWSLNDELPSLPGIRNIGTVLGVAQQTVTIPGFSDFIYS-----------------FAFSVYAAVYAVAHAL 323 (410)
T ss_pred CCEEEEeCcccccccccCCccceeeccEEEEEeCCCCCccHHHHHHH-----------------HHHHHHHHHHHHHHHH
Confidence 4589998853321 11112234567899998888777777777666 4567999999999999
Q ss_pred HHHcccCCcccccCCCCCCCcccccCCCcchHHHHHHHhccceecceeeEEE-eCCcccCccEEEEEeeeC----CeeEe
Q 005717 83 ERAGIENSSFLKSNTSKSRVDIAALGTFEMGAKLLDTLINTTFEGLSGNFHL-VNGQLEPSAFEIFNVIGT----SERVI 157 (681)
Q Consensus 83 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~l~~~l~~~~f~GltG~i~F-~~G~~~~~~~~I~n~~~~----~~~~v 157 (681)
+++...+ ...|... .+.++..|.++|++++|+|++|++.| ++|++. ..++|++++.. ++++|
T Consensus 324 ~~a~~~~-----------~~~~~~~-~~~~~~~l~~~L~~~~~~g~~g~i~fd~~G~~~-~~~~i~~~~~~~~~~~~~~v 390 (410)
T cd06363 324 HNVLQCG-----------SGGCPKR-VPVYPWQLLEELKKVNFTLLGQTVRFDENGDPN-FGYDIVVWWWDNSSGTFEEV 390 (410)
T ss_pred HHHhCCC-----------CCCCCCC-CCCCHHHHHHHHhccEEecCCcEEEeCCCCCCc-cceEEEEEEEcCCceeEEEE
Confidence 9985432 1234321 24467889999999999999999999 889964 57999999644 48999
Q ss_pred eeeeCC
Q 005717 158 GYWTKE 163 (681)
Q Consensus 158 G~W~~~ 163 (681)
|+|.+.
T Consensus 391 G~~~~~ 396 (410)
T cd06363 391 GSYSFY 396 (410)
T ss_pred EEEECC
Confidence 999984
No 60
>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=99.12 E-value=4e-10 Score=122.35 Aligned_cols=146 Identities=20% Similarity=0.291 Sum_probs=110.6
Q ss_pred CCCCCeEEEecCCccccCCc------------c-ccccCccceEEEEEecCCChhHHHHHHHHHhh-cCCCCC---CCCC
Q 005717 1 MMSEGYAWIATQGLSTLLDP------------V-KDMESMQGVLGLRPYIPSSKKLEHFKLRWIKS-ADKPDG---STGG 63 (681)
Q Consensus 1 mm~~~y~WI~t~~~~~~~~~------------~-~~~~~~~Gvlg~~~~~~~~~~~~~f~~~~~~~-~~~~~~---~~~~ 63 (681)
|.+++|+||.+++....++. . .....++|++++.+..+.++..++|.++|+++ .+.|.. ....
T Consensus 219 ~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~ 298 (389)
T cd06352 219 LTSGDYVFILIDLFNYSLPYQNSYPWERGDGDDEKAKEAYDAVLTITLRPPDNPEYEEFSEEVKEAAKRPPFNTDAEPEQ 298 (389)
T ss_pred CCCCcEEEEEEehhccccccCCCCCcccCCcccHHHHHHHHhheEEEecCCCCchHHHHHHHHHHHHhcccCccCCCccc
Confidence 34568999999876544310 0 23356789999999888778899999999876 332211 1224
Q ss_pred CchhHHHHHHHHHHHHHHHHHHcccCCcccccCCCCCCCcccccCCCcchHHHHHHHhccceecceeeEEE-eCCcccCc
Q 005717 64 SNLFGLWAYDTVWAIAMAVERAGIENSSFLKSNTSKSRVDIAALGTFEMGAKLLDTLINTTFEGLSGNFHL-VNGQLEPS 142 (681)
Q Consensus 64 ~~~~~~~aYDav~~lA~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~l~~~l~~~~f~GltG~i~F-~~G~~~~~ 142 (681)
++.++..+|||||++|+|++++..... .+.++..+.++|++++|.|++|++.| ++|++. .
T Consensus 299 ~~~~a~~~YDav~~~a~Al~~~~~~~~------------------~~~~~~~v~~~l~~~~f~g~~G~v~fd~~G~~~-~ 359 (389)
T cd06352 299 VSPYAGYLYDAVLLYAHALNETLAEGG------------------DYNGGLIITRRMWNRTFSGITGPVTIDENGDRE-G 359 (389)
T ss_pred cchhhhhHHHHHHHHHHHHHHHHHhCC------------------CCCchHHHHHHhcCcEEEeeeeeEEEcCCCCee-e
Confidence 577999999999999999999864321 13467889999999999999999999 899997 6
Q ss_pred cEEEEEeeeC--CeeEeeeeeCCCC
Q 005717 143 AFEIFNVIGT--SERVIGYWTKEKE 165 (681)
Q Consensus 143 ~~~I~n~~~~--~~~~vG~W~~~~g 165 (681)
.|+|++++++ .+..++.....++
T Consensus 360 ~~~v~~~~~~~~~~~~~~~~~~~~~ 384 (389)
T cd06352 360 DYSLLDLDSTGGQLEVVYLYDTSSG 384 (389)
T ss_pred eEEEEEecCCCceEEEEEeccccce
Confidence 8999999864 4788887765544
No 61
>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=99.10 E-value=3.4e-10 Score=123.52 Aligned_cols=110 Identities=20% Similarity=0.348 Sum_probs=85.2
Q ss_pred ccCccceEEEEEecCCChhHHHHHHHHHhh-cCCC--C-----CCCCCCchhHHHHHHHHHHHHHHHHHHcccCCccccc
Q 005717 24 MESMQGVLGLRPYIPSSKKLEHFKLRWIKS-ADKP--D-----GSTGGSNLFGLWAYDTVWAIAMAVERAGIENSSFLKS 95 (681)
Q Consensus 24 ~~~~~Gvlg~~~~~~~~~~~~~f~~~~~~~-~~~~--~-----~~~~~~~~~~~~aYDav~~lA~Al~~~~~~~~~~~~~ 95 (681)
..+++|++++.+..+ ++..++|.++|+++ ...| . ....+++.+++++|||||++|+|++++.....
T Consensus 266 ~~a~~~~~~~~~~~~-~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~aa~~yDAv~~~a~Al~~~~~~~~----- 339 (404)
T cd06370 266 LEAMKSVLIIVPTPV-SPDYDSFSIFVRKYNLEPPFNGDLGESELVLEIDIEAAYLYDAVMLYAKALDETLLEGG----- 339 (404)
T ss_pred HHHhHheEEEecCCC-CchHHHHHHHHHHhccCCCCcccccccccccccceeeehhHHHHHHHHHHHHHHHHhcC-----
Confidence 346899999887665 66788999999875 2211 1 12234677899999999999999999853211
Q ss_pred CCCCCCCcccccCCCcchHHHHHHHhccceeccee-eEEE-eCCcccCccEEEEEeeeCC
Q 005717 96 NTSKSRVDIAALGTFEMGAKLLDTLINTTFEGLSG-NFHL-VNGQLEPSAFEIFNVIGTS 153 (681)
Q Consensus 96 ~~~~~~~~~~~~~~~~~G~~l~~~l~~~~f~GltG-~i~F-~~G~~~~~~~~I~n~~~~~ 153 (681)
...+|..|.++|++++|+|+|| +|.| ++|++. ..|.|+++++..
T Consensus 340 -------------~~~~g~~i~~~l~~~~f~GvtG~~v~fd~~G~~~-~~y~v~~~~~~~ 385 (404)
T cd06370 340 -------------DIYNGTAIVSHILNRTYRSITGFDMYIDENGDAE-GNYSVLALQPIP 385 (404)
T ss_pred -------------CCCCHHHHHHHHhCcccccccCceEEEcCCCCcc-cceEEEEecccc
Confidence 0146789999999999999999 8999 899985 789999998753
No 62
>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=99.08 E-value=3.2e-10 Score=121.31 Aligned_cols=122 Identities=42% Similarity=0.784 Sum_probs=97.6
Q ss_pred CCCCCeEEEecCCccccCC----cc--ccccCccceEEEEEecCC-ChhHHHHHHHHHhh-cCCCCCCCCCCchhHHHHH
Q 005717 1 MMSEGYAWIATQGLSTLLD----PV--KDMESMQGVLGLRPYIPS-SKKLEHFKLRWIKS-ADKPDGSTGGSNLFGLWAY 72 (681)
Q Consensus 1 mm~~~y~WI~t~~~~~~~~----~~--~~~~~~~Gvlg~~~~~~~-~~~~~~f~~~~~~~-~~~~~~~~~~~~~~~~~aY 72 (681)
|.+++|+||++++..+.++ .. .....++|++++.++.+. ++..++|.++|+++ .+.+.. ...+..+++.+|
T Consensus 217 ~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~gv~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~-~~~p~~~a~~~Y 295 (350)
T cd06366 217 MMGKGYVWILTDWLSSNWWSSSDCTDEEMLEAMQGVIGVRSYVPNSSMTLQEFTSRWRKRFGNENPE-LTEPSIYALYAY 295 (350)
T ss_pred CcCCCEEEEECcchhhhhccCCCCChHHHHHhhceEEEEeecccccCccHHHHHHHHHHHhcccCcC-cCCCCcccchhh
Confidence 3457899999998776553 11 334678999999999887 77789999999876 321111 224667899999
Q ss_pred HHHHHHHHHHHHHcccCCcccccCCCCCCCcccccCCCcchHHHHHHHhccceecceeeEEE-eCCcccCccEEEEEeee
Q 005717 73 DTVWAIAMAVERAGIENSSFLKSNTSKSRVDIAALGTFEMGAKLLDTLINTTFEGLSGNFHL-VNGQLEPSAFEIFNVIG 151 (681)
Q Consensus 73 Dav~~lA~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~l~~~l~~~~f~GltG~i~F-~~G~~~~~~~~I~n~~~ 151 (681)
||+++ +++|+|++|+|+| .+|++.+..|+++++.+
T Consensus 296 Dav~~--------------------------------------------~~~~~G~~G~v~fd~~~~~~~~~~~~~~~~~ 331 (350)
T cd06366 296 DAVWA--------------------------------------------STNFNGLSGPVQFDGGRRLASPAFEIINIIG 331 (350)
T ss_pred hheee--------------------------------------------eceEEeeeeeEEEcCCCccCCcceEEEEecC
Confidence 99987 4589999999999 88999888999999999
Q ss_pred CCeeEeeeeeCCCCcc
Q 005717 152 TSERVIGYWTKEKELL 167 (681)
Q Consensus 152 ~~~~~vG~W~~~~gl~ 167 (681)
+++++||+|++++|+.
T Consensus 332 ~~~~~vg~~~~~~~~~ 347 (350)
T cd06366 332 KGYRKIGFWSSESGLS 347 (350)
T ss_pred CceEEEEEEeCCCCcc
Confidence 9999999999988876
No 63
>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=99.02 E-value=6e-10 Score=117.71 Aligned_cols=110 Identities=23% Similarity=0.373 Sum_probs=92.7
Q ss_pred CCCCCeEEEecCCccccCCccccccCccceEEEEEecCCChhHHHHHHHHHhhcCCCCCCCCCCchhHHHHHHHHHHHHH
Q 005717 1 MMSEGYAWIATQGLSTLLDPVKDMESMQGVLGLRPYIPSSKKLEHFKLRWIKSADKPDGSTGGSNLFGLWAYDTVWAIAM 80 (681)
Q Consensus 1 mm~~~y~WI~t~~~~~~~~~~~~~~~~~Gvlg~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~aYDav~~lA~ 80 (681)
||+++|+||++++..+.++...+....+|++|++...+..+..++|..+|.. .++......+...++++||+++++
T Consensus 211 m~~~~~~~i~~~~~~~~~d~~~~~~~~~~i~g~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~d~~~~~-- 286 (328)
T cd06351 211 MMGYGYHWILTNLDLSDIDLEPFQYGPANITGFRLVDPDSPDVSQFLQRWLE--ESPGVNLRAPIYDAALLYDAVLLL-- 286 (328)
T ss_pred cccCCcEEEEecCCccccchhhhccCCcceEEEEEeCCCchHHHHHHHhhhh--ccCCCCcCccchhhHhhhcEEEEE--
Confidence 7889999999999887766556778899999999999999999999999943 233344445666788888887644
Q ss_pred HHHHHcccCCcccccCCCCCCCcccccCCCcchHHHHHHHhccceecceeeEEE-eCCcccCccEEEEEee-eCCeeEee
Q 005717 81 AVERAGIENSSFLKSNTSKSRVDIAALGTFEMGAKLLDTLINTTFEGLSGNFHL-VNGQLEPSAFEIFNVI-GTSERVIG 158 (681)
Q Consensus 81 Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~l~~~l~~~~f~GltG~i~F-~~G~~~~~~~~I~n~~-~~~~~~vG 158 (681)
||+++| ++|+|.++.++|+++. ..++++||
T Consensus 287 ------------------------------------------------tg~i~f~~~g~r~~~~l~i~~l~~~~~~~~vg 318 (328)
T cd06351 287 ------------------------------------------------TGTVSFDEDGVRSNFTLDIIELNRSRGWRKVG 318 (328)
T ss_pred ------------------------------------------------EeeEEECCCCcccceEEEEEEecCCCCceEEE
Confidence 999999 8899999999999999 88999999
Q ss_pred eeeC
Q 005717 159 YWTK 162 (681)
Q Consensus 159 ~W~~ 162 (681)
.|+.
T Consensus 319 ~W~~ 322 (328)
T cd06351 319 TWNG 322 (328)
T ss_pred EecC
Confidence 9994
No 64
>TIGR01098 3A0109s03R phosphate/phosphite/phosphonate ABC transporters, periplasmic binding protein. A subset of this model in which nearly all members exhibit genomic context with elements of phosphonate metabolism, particularly the C-P lyase system has been built (TIGR03431) as an equivalog. Nevertheless, there are members of this subfamily (TIGR01098) which show up sporadically on a phylogenetic tree that also show phosphonate context and are most likely competent to transport phosphonates.
Probab=98.97 E-value=8.2e-09 Score=105.08 Aligned_cols=200 Identities=14% Similarity=0.123 Sum_probs=141.4
Q ss_pred CceEEEEeeccCCccceEEEeecCCCCeeEEeehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeE
Q 005717 194 PRKLKIGVPVREGFTEFIKVVENKNKTTQVSGFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDT 273 (681)
Q Consensus 194 p~~lrV~v~~~~p~~~~~~~~~~~~~~~~~~G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~ 273 (681)
+++|+||+... +.++ .+.+...++.+.+++++|. +++++.. ++|+.++..+.+|++|+++.+.
T Consensus 31 ~~~l~vg~~~~--~~~~-----------~~~~~~~~l~~~l~~~~g~--~v~~~~~--~~~~~~~~~l~~g~~Di~~~~~ 93 (254)
T TIGR01098 31 PKELNFGILPG--ENAS-----------NLTRRWEPLADYLEKKLGI--KVQLFVA--TDYSAVIEAMRFGRVDIAWFGP 93 (254)
T ss_pred CCceEEEECCC--CCHH-----------HHHHHHHHHHHHHHHHhCC--cEEEEeC--CCHHHHHHHHHcCCccEEEECc
Confidence 46899998652 2222 2234567999999999995 4677665 5899999999999999998655
Q ss_pred EEee---ccccccccccceeec------ceEEEEEeccCCCcCceeeeccCcHhHHHHHHHHHHHHHHHhhhhhcccCCC
Q 005717 274 TIVA---NRSTFVDFTLPYSES------GVSMLVLVKDDERKNFWIFLKPLSWDLWLTTGAAFIFTGLVVWVLEHRINTE 344 (681)
Q Consensus 274 ~it~---~R~~~vdFT~P~~~~------~~~~vv~~~~~~~~~~~~fl~PF~~~vW~~i~~~~~~v~~v~~~~~~~~~~~ 344 (681)
.... +|....+|+.||... ...+++++..
T Consensus 94 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lvv~~d~------------------------------------------ 131 (254)
T TIGR01098 94 SSYVLAHYRANAEVFALTAVSTDGSPGYYSVIIVKADS------------------------------------------ 131 (254)
T ss_pred HHHHHHHHhcCCceEEeeccccCCCCceEEEEEEECCC------------------------------------------
Confidence 4332 566667888876543 2456665432
Q ss_pred CCCCCCCchhhHHHHHHHHHhccCcccccccchhHHHHHHHHHHHHHHhHhhhhhhheeeecccCCCCCCHHHHHhCCCe
Q 005717 345 FRGPPQHQIGTIFWFSFSTLVFAHRERVVNNLSRFVLIIWVFVVLILTQSYTASLTSMLTVQRLQPSFTDVKDIQKNGYF 424 (681)
Q Consensus 345 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~s~~~R~l~~~w~~~~lil~s~YtA~L~s~LT~~~~~~~i~s~~dL~~~~~~ 424 (681)
+|++++||. |.+
T Consensus 132 ------------------------------------------------------------------~i~~~~dL~--gk~ 143 (254)
T TIGR01098 132 ------------------------------------------------------------------PIKSLKDLK--GKT 143 (254)
T ss_pred ------------------------------------------------------------------CCCChHHhc--CCE
Confidence 488999997 888
Q ss_pred EEEec-ChhH-----HHHHhhhcCCcc----ccccccCChhHHHHHHccCcceEEecchhhHHHHHhhc---CCceEEEC
Q 005717 425 VGYQT-NSFV-----KDLLTKKLNFNE----TRLKNYTTSEDYHDALSNGEVAAIFDEIPYIKIFLASY---CSRYMMVG 491 (681)
Q Consensus 425 vg~~~-~s~~-----~~~l~~~~~~~~----~~~~~~~~~~~~~~~l~~g~~~a~i~e~~~~~~~~~~~---c~~l~~v~ 491 (681)
|++.. ++.. ..++.+..+.+. .++....+..+..+++.+|++|+.+...+....+.++. -.++.+++
T Consensus 144 I~~~~~~s~~~~~~~~~~l~~~~~~~~~~~~~~i~~~~~~~~~~~al~~G~~Da~~~~~~~~~~~~~~~~~~~~~~~~~~ 223 (254)
T TIGR01098 144 FAFGDPASTSGYLVPRYQLKKEGGLDADGFFSEVVFSGSHDASALAVANGKVDAATNNSSAIGRLKKRGPSDMKKVRVIW 223 (254)
T ss_pred EEeeCCCCccchHhHHHHHHHhcCCChHHhhhheeecCchHHHHHHHHcCCCCeEEecHHHHHHHHHhCccchhheEEEE
Confidence 99864 3221 233423323221 24445556788999999999999999888887766654 23678887
Q ss_pred cccccCCcEEEecCC-CC-ChHHHHHHHHhh
Q 005717 492 PTYRTDGFGFAFPLG-SP-LVPYISRAILKV 520 (681)
Q Consensus 492 ~~~~~~~~~~~~~k~-sp-l~~~in~~Il~l 520 (681)
......+++++++|+ .+ +++.+|++|+.+
T Consensus 224 ~~~~~~~~~~~~~~~~~~~l~~~i~~~l~~~ 254 (254)
T TIGR01098 224 KSPLIPNDPIAVRKDLPPELKEKIRDAFLTL 254 (254)
T ss_pred ecCCCCCCCEEEECCCCHHHHHHHHHHHhhC
Confidence 766666789999999 55 999999999864
No 65
>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=98.91 E-value=3.4e-10 Score=87.06 Aligned_cols=46 Identities=20% Similarity=0.515 Sum_probs=38.5
Q ss_pred CCCeeEEeehHHHHHHHHHHcCCCcCeEEEeCCC-------CCHHHHHHHHHh
Q 005717 218 NKTTQVSGFCYDMFHAVLQVLEFPLPYEFVPFHD-------GSFDELLHKIEK 263 (681)
Q Consensus 218 ~~~~~~~G~~idll~~l~~~l~f~~~~~~v~~~~-------g~~~gli~~l~~ 263 (681)
+++.+++|||+||+++|++.|||++++..++++. |+|+|||++|.+
T Consensus 13 ~g~~~~eGyciDll~~la~~l~F~y~i~~~~Dg~yG~~~~~g~W~GmiGeli~ 65 (65)
T PF10613_consen 13 TGNDRYEGYCIDLLEELAEELNFTYEIYLVPDGKYGSKNPNGSWNGMIGELIR 65 (65)
T ss_dssp BGGGGEESHHHHHHHHHHHHHT-EEEEEE-TTS--EEBETTSEBEHHHHHHHT
T ss_pred CCCccEEEEHHHHHHHHHHHcCCeEEEEECCCCCCcCcCCCCcCcCHHHHhcC
Confidence 6788999999999999999999997777776644 899999999974
No 66
>PRK00489 hisG ATP phosphoribosyltransferase; Reviewed
Probab=98.87 E-value=1.2e-08 Score=105.36 Aligned_cols=170 Identities=12% Similarity=0.117 Sum_probs=134.9
Q ss_pred eEEEeCCCCCHHHHHHHHHhCccceEEEeEEEeeccccccccccc--eeecceEEEEEeccCCCcCceeeeccCcHhHHH
Q 005717 244 YEFVPFHDGSFDELLHKIEKQEFDTAVGDTTIVANRSTFVDFTLP--YSESGVSMLVLVKDDERKNFWIFLKPLSWDLWL 321 (681)
Q Consensus 244 ~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~it~~R~~~vdFT~P--~~~~~~~~vv~~~~~~~~~~~~fl~PF~~~vW~ 321 (681)
++++.. +|.+++..|.+|++|+++++..++.+|.+.++|+.| |....+++++|+..
T Consensus 46 ie~~~~---~~~~i~~~L~sG~vDlgi~g~~~~~er~~~v~~~~~l~~~~~~lvvvvp~~~------------------- 103 (287)
T PRK00489 46 IEVLFL---RPDDIPGYVADGVVDLGITGEDLLEESGADVEELLDLGFGKCRLVLAVPEDS------------------- 103 (287)
T ss_pred EEEEEE---CcHHHHHHHHcCCCCEEEcchHHHHHCCCCceEeeeccCCceEEEEEEECCC-------------------
Confidence 455554 789999999999999999999999999999999988 77777888887553
Q ss_pred HHHHHHHHHHHHhhhhhcccCCCCCCCCCCchhhHHHHHHHHHhccCcccccccchhHHHHHHHHHHHHHHhHhhhhhhh
Q 005717 322 TTGAAFIFTGLVVWVLEHRINTEFRGPPQHQIGTIFWFSFSTLVFAHRERVVNNLSRFVLIIWVFVVLILTQSYTASLTS 401 (681)
Q Consensus 322 ~i~~~~~~v~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~s~~~R~l~~~w~~~~lil~s~YtA~L~s 401 (681)
T Consensus 104 -------------------------------------------------------------------------------- 103 (287)
T PRK00489 104 -------------------------------------------------------------------------------- 103 (287)
T ss_pred --------------------------------------------------------------------------------
Confidence
Q ss_pred eeeecccCCCCCCHHHHHhCCCeEEEecChhHHHHHhhhcCCccccccccCChhHHHHHHccCcceEEecchhhHHHHHh
Q 005717 402 MLTVQRLQPSFTDVKDIQKNGYFVGYQTNSFVKDLLTKKLNFNETRLKNYTTSEDYHDALSNGEVAAIFDEIPYIKIFLA 481 (681)
Q Consensus 402 ~LT~~~~~~~i~s~~dL~~~~~~vg~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~g~~~a~i~e~~~~~~~~~ 481 (681)
+|++++||. |+++++..+.....++ ++.+. ..+++.+.+..+. ++..|..|++++.......+.+
T Consensus 104 ---------~i~sl~DL~--Gk~ia~~~~~~~~~~l-~~~gi-~~~iv~~~gs~ea--a~~~G~aDaivd~~~~~~~l~~ 168 (287)
T PRK00489 104 ---------DWQGVEDLA--GKRIATSYPNLTRRYL-AEKGI-DAEVVELSGAVEV--APRLGLADAIVDVVSTGTTLRA 168 (287)
T ss_pred ---------CCCChHHhC--CCEEEEcCcHHHHHHH-HHcCC-ceEEEECCCchhh--hhcCCcccEEEeeHHHHHHHHH
Confidence 478899998 8899998888888998 54454 2355566655554 5677999999987776666555
Q ss_pred hcCCceEEECcccccCCcEEEecC--CCC-ChHHHHHHHHhhccCccHHHHHHHHHcCC
Q 005717 482 SYCSRYMMVGPTYRTDGFGFAFPL--GSP-LVPYISRAILKVTEDKEKMENIEKALGNQ 537 (681)
Q Consensus 482 ~~c~~l~~v~~~~~~~~~~~~~~k--~sp-l~~~in~~Il~l~e~~G~l~~i~~kw~~~ 537 (681)
. ++.++ +.......+++.+| ++| ....++..+.++ . |.+.++.+||+..
T Consensus 169 ~---~L~~v-~~~~~~~~~li~~k~~~~~~~~~~i~~~l~~l--~-g~l~a~~~k~~~~ 220 (287)
T PRK00489 169 N---GLKIV-EVILRSEAVLIARKGWLDPEKQEKIDQLLTRL--Q-GVLRARESKYLMM 220 (287)
T ss_pred C---CCEEE-EeeeeeeEEEEEcccccChhHHHHHHHHHHHH--H-HHHHhhceEEEEE
Confidence 3 56777 45556678999999 667 788899999999 5 8999999999964
No 67
>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=98.83 E-value=2.8e-08 Score=112.51 Aligned_cols=152 Identities=20% Similarity=0.348 Sum_probs=109.5
Q ss_pred CeEEEecCCccccCCccc-cccCccceEEEEEecCCChhHHHHHHHHHh---------------h--cCCCCCC----C-
Q 005717 5 GYAWIATQGLSTLLDPVK-DMESMQGVLGLRPYIPSSKKLEHFKLRWIK---------------S--ADKPDGS----T- 61 (681)
Q Consensus 5 ~y~WI~t~~~~~~~~~~~-~~~~~~Gvlg~~~~~~~~~~~~~f~~~~~~---------------~--~~~~~~~----~- 61 (681)
.++||.+|++...-+... .....+|++++.+..+..+.+++|.+.... . ...++.. +
T Consensus 280 ~~~wiaSd~W~~~~~~~~~~e~~a~g~i~i~l~~~~v~~F~~y~~s~~p~nn~~n~w~~e~w~~~f~C~l~~~~~~~~~~ 359 (878)
T KOG1056|consen 280 EFLWIASDGWASQNSPTEAPEREAEGAITIKLASPQVPGFDRYFQSLHPENNRRNPWFAEFWEDKFNCSLPNSAFKNENL 359 (878)
T ss_pred ceEEEecchhhccCChhhhhhhhhceeEEEEecCCcchhHHHHHHhcCccccccCcccchhhhhcccCCCCcccccchhh
Confidence 389999997554433322 223789999999999888888777665322 1 1111100 0
Q ss_pred ----------CCC-----chhHHHHHHHHHHHHHHHHHHcccCCcccccCCCCCCCcccccCCCcchHHHHHHHhcccee
Q 005717 62 ----------GGS-----NLFGLWAYDTVWAIAMAVERAGIENSSFLKSNTSKSRVDIAALGTFEMGAKLLDTLINTTFE 126 (681)
Q Consensus 62 ----------~~~-----~~~~~~aYDav~~lA~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~l~~~l~~~~f~ 126 (681)
... ......++|||+++|+||+++.+.- .......|..... .+|.+|++++++++|.
T Consensus 360 ~~~Ct~~e~~~~~~~~~q~~k~~~Vi~aVya~A~aLh~m~~~l-------c~~~~~~C~~m~~-~dg~~L~~~l~~vnF~ 431 (878)
T KOG1056|consen 360 IRLCTAVERITLDSAYEQDSKVQFVIDAVYAMAHALHNMHQDL-------CPGTSGLCSAMKA-IDGSLLLKYLLNVNFT 431 (878)
T ss_pred hhhcccchhhccccchhhhcccccHHHHHHHHHHHHHHHHHhh-------cCCccccCcCccc-cCHHHHHhhhheeEEe
Confidence 000 1134679999999999999987542 1223567887765 6899999999999999
Q ss_pred cceeeEEE-eCCcccCccEEEEEeeeCC----eeEeeeeeCCCC
Q 005717 127 GLSGNFHL-VNGQLEPSAFEIFNVIGTS----ERVIGYWTKEKE 165 (681)
Q Consensus 127 GltG~i~F-~~G~~~~~~~~I~n~~~~~----~~~vG~W~~~~g 165 (681)
|..|.+.| ++||.. ..|+|+|++..+ +.+||+|+....
T Consensus 432 ~~~~~v~Fd~~gD~~-~~y~I~~~~~~~~~~~y~~vg~w~~~~~ 474 (878)
T KOG1056|consen 432 GPAGSVRFDENGDGP-GRYDILNYQLTNGSYTYKEVGYWSEGLS 474 (878)
T ss_pred cCCCceeecCCCCCc-cceeEEEeeccCCCccceeeeeeccccc
Confidence 99999999 899987 799999998544 899999997544
No 68
>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=98.46 E-value=7.2e-07 Score=94.55 Aligned_cols=95 Identities=25% Similarity=0.438 Sum_probs=79.1
Q ss_pred cCccceEEEEEecCC--ChhHHHHHHHHHhh-cCCCCCCCCCCchhHHHHHHHHHHHHHHHHHHcccCCcccccCCCCCC
Q 005717 25 ESMQGVLGLRPYIPS--SKKLEHFKLRWIKS-ADKPDGSTGGSNLFGLWAYDTVWAIAMAVERAGIENSSFLKSNTSKSR 101 (681)
Q Consensus 25 ~~~~Gvlg~~~~~~~--~~~~~~f~~~~~~~-~~~~~~~~~~~~~~~~~aYDav~~lA~Al~~~~~~~~~~~~~~~~~~~ 101 (681)
..++|++...++.+. ++..++|.++|.++ .. .++.++..+||+++++++|++++.
T Consensus 236 ~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~~~-------~~~~~~~~~yda~~~~~~al~~~~--------------- 293 (334)
T cd06342 236 DAAEGTYATFPGGPLEKMPAGKAFVARYKAKFGD-------PPGAYAPYAYDAANVLAEAIKKAG--------------- 293 (334)
T ss_pred HhhCCcEEEecCCCCCCChHHHHHHHHHHHHhCC-------CCchhHHHHHHHHHHHHHHHHHhC---------------
Confidence 457899988887764 56788999999865 22 235688999999999999999873
Q ss_pred CcccccCCCcchHHHHHHHhccceecceeeEEE-eCCcccCccEEEEEe
Q 005717 102 VDIAALGTFEMGAKLLDTLINTTFEGLSGNFHL-VNGQLEPSAFEIFNV 149 (681)
Q Consensus 102 ~~~~~~~~~~~G~~l~~~l~~~~f~GltG~i~F-~~G~~~~~~~~I~n~ 149 (681)
+.++..++++|++++|+|++|+++| .+|++.+..|+|+||
T Consensus 294 --------~~~~~~v~~~l~~~~~~g~~g~i~f~~~g~~~~~~~~~~~~ 334 (334)
T cd06342 294 --------STDPAKVADALRKVDFDGVTGKISFDAKGDLKGAAVTVYQV 334 (334)
T ss_pred --------CCCHHHHHHHHHhCCCCCcceeeEECCCCCcccCcEEEEeC
Confidence 2346889999999999999999999 899999999999885
No 69
>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=98.31 E-value=4.6e-06 Score=86.64 Aligned_cols=130 Identities=15% Similarity=0.114 Sum_probs=97.2
Q ss_pred CCCeEEEecCCccccCC-ccccccCccceEEEEEecCCChhHHHHHHHHHhhcCCCCCCCCCCc-hhHHHHHHHHHHHHH
Q 005717 3 SEGYAWIATQGLSTLLD-PVKDMESMQGVLGLRPYIPSSKKLEHFKLRWIKSADKPDGSTGGSN-LFGLWAYDTVWAIAM 80 (681)
Q Consensus 3 ~~~y~WI~t~~~~~~~~-~~~~~~~~~Gvlg~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~-~~~~~aYDav~~lA~ 80 (681)
.+.|+.|..|...+.+. ......+|+.|+.+++..|+....++ . .+.. ..++ .|++..||||.+.|+
T Consensus 231 ~gDYVf~~IDlF~~sy~~d~~a~~amqsVLvIT~~~p~~~~~~~-------~--~~fn--~~l~~~~aa~fyDaVLLYa~ 299 (380)
T cd06369 231 AEDIVIILIDLFNDVYYENTTSPPYMRNVLVLTLPPRNSTNNSS-------F--TTDN--SLLKDDYVAAYHDGVLLFGH 299 (380)
T ss_pred CCCEEEEEEecccchhccCcchHHHHhceEEEecCCCCCccccc-------C--CCCC--cchHHHHHHHHHHHHHHHHH
Confidence 35799999997765543 33556789999999988875543222 1 1111 1222 899999999999999
Q ss_pred HHHHHcccCCcccccCCCCCCCcccccCCCcchHHHHHHHhccceecceeeEEE-eCCcccCccEEEEEee--eCCeeEe
Q 005717 81 AVERAGIENSSFLKSNTSKSRVDIAALGTFEMGAKLLDTLINTTFEGLSGNFHL-VNGQLEPSAFEIFNVI--GTSERVI 157 (681)
Q Consensus 81 Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~l~~~l~~~~f~GltG~i~F-~~G~~~~~~~~I~n~~--~~~~~~v 157 (681)
||++....+.+ ..+..+.+.|++.+|.|++|.+.+ ++|+|. ..|.++-+. .+++..|
T Consensus 300 AL~EtL~~G~~-------------------~~~~~I~~~m~NrTF~GitG~V~IDeNGDRd-~dfsLl~ms~~tg~y~vV 359 (380)
T cd06369 300 VLKKFLESQEG-------------------VQTFSFINEFRNISFEGAGGPYTLDEYGDRD-VNFTLLYTSTDTSKYKVL 359 (380)
T ss_pred HHHHHHHhCCC-------------------CCcHHHHHHHhCcceecCCCceEeCCCCCcc-CceEEEEeeCCCCCeEEE
Confidence 99998755421 233789999999999999999999 999997 688887664 4569999
Q ss_pred eeeeCC
Q 005717 158 GYWTKE 163 (681)
Q Consensus 158 G~W~~~ 163 (681)
|.++..
T Consensus 360 ~~y~t~ 365 (380)
T cd06369 360 FEFDTS 365 (380)
T ss_pred EEEECC
Confidence 999853
No 70
>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=98.28 E-value=2.2e-05 Score=81.45 Aligned_cols=119 Identities=16% Similarity=0.125 Sum_probs=77.0
Q ss_pred CCCCHHHHHhCCCeEEEe-cChhHHH-----HHhhhcCCccc---cccccC-ChhHHHHHHccCcceEEecchhhHHHHH
Q 005717 411 SFTDVKDIQKNGYFVGYQ-TNSFVKD-----LLTKKLNFNET---RLKNYT-TSEDYHDALSNGEVAAIFDEIPYIKIFL 480 (681)
Q Consensus 411 ~i~s~~dL~~~~~~vg~~-~~s~~~~-----~l~~~~~~~~~---~~~~~~-~~~~~~~~l~~g~~~a~i~e~~~~~~~~ 480 (681)
+|++++||. |.+||+. .++.... .+.+..+.... +...+. +..+...+|.+|++|+++.+.+.+..+.
T Consensus 126 ~i~sl~DL~--Gk~v~~~~~~s~~~~~~~~~~l~~~~g~~~~~~~~~v~~~~~~~~~~~al~~G~vDa~~~~~~~~~~~~ 203 (288)
T TIGR03431 126 PIKSLEDLK--GKTFGFVDPNSTSGFLVPSYYLFKKNGIKPKEYFKKVTFSGSHEAAILAVANGTVDAATTNDENLDRMI 203 (288)
T ss_pred CCCcHHHhC--CCEEEeeCCCcchhhHHHHHHHHHhcCCChHHhHHhheecCchHHHHHHHHcCCCCeEeccHHHHHHHH
Confidence 588999996 8889985 3333221 12122233211 123444 6788999999999999998887777666
Q ss_pred hhc-C---CceEEECcccccCCcEEEecCCC-C-ChHHHHHHHHhhccCccHHHHHHH
Q 005717 481 ASY-C---SRYMMVGPTYRTDGFGFAFPLGS-P-LVPYISRAILKVTEDKEKMENIEK 532 (681)
Q Consensus 481 ~~~-c---~~l~~v~~~~~~~~~~~~~~k~s-p-l~~~in~~Il~l~e~~G~l~~i~~ 532 (681)
.+. - .++.++...-.....+++++++- + +.+.+++++.++.++ +...++..
T Consensus 204 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~l~~~~~~-~~~~~~~~ 260 (288)
T TIGR03431 204 RKGQPDAMEDLRIIWKSPLIPNGPIVYRKDLPADLKAKIRKAFLNYHKT-DKACFEKI 260 (288)
T ss_pred HcCCCCchhheEEEEEcCCCCCCcEEEeCCCCHHHHHHHHHHHHhcCCC-cHHHHHhh
Confidence 532 1 23444432111224578899994 3 999999999999998 77665433
No 71
>PRK15404 leucine ABC transporter subunit substrate-binding protein LivK; Provisional
Probab=98.18 E-value=8.2e-06 Score=87.87 Aligned_cols=100 Identities=22% Similarity=0.267 Sum_probs=78.3
Q ss_pred cCccceEEEEEe-cCCChhHHHHHHHHHhhcCCCCCCCCCCchhHHHHHHHHHHHHHHHHHHcccCCcccccCCCCCCCc
Q 005717 25 ESMQGVLGLRPY-IPSSKKLEHFKLRWIKSADKPDGSTGGSNLFGLWAYDTVWAIAMAVERAGIENSSFLKSNTSKSRVD 103 (681)
Q Consensus 25 ~~~~Gvlg~~~~-~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~aYDav~~lA~Al~~~~~~~~~~~~~~~~~~~~~ 103 (681)
+..+|+++.-++ ...++..++|...|+++ +. ..++.++..+||++++++.|+++++.
T Consensus 262 ~~~~Gv~~~~~~~~~~~~~~~~f~~~~~~~--~~----~~~~~~~~~~Y~~~~~l~~Al~~aG~---------------- 319 (369)
T PRK15404 262 PASEGMLVTLPKRYDQDPANKAIVDAFKAK--KQ----DPSGPFVWTTYAAVQSLAAGINRAGS---------------- 319 (369)
T ss_pred hhhcCcEEEccCCCccChhHHHHHHHHHHh--cC----CCCccchHHHHHHHHHHHHHHHhhCC----------------
Confidence 467888876553 33346788899999875 11 12345788899999999999998752
Q ss_pred ccccCCCcchHHHHHHHhccceecceeeEEE-eCCcccCccEEEEEeeeCC
Q 005717 104 IAALGTFEMGAKLLDTLINTTFEGLSGNFHL-VNGQLEPSAFEIFNVIGTS 153 (681)
Q Consensus 104 ~~~~~~~~~G~~l~~~l~~~~f~GltG~i~F-~~G~~~~~~~~I~n~~~~~ 153 (681)
.++..|.++|++.+|+|++|++.| .+|++....|.|+++++++
T Consensus 320 -------~~~~~l~~al~~~~~~~~~G~~~~~~~g~~~~~~~~i~~~~~~~ 363 (369)
T PRK15404 320 -------DDPAKVAKYLKANTFDTVIGPLSWDEKGDLKGFEFGVFEWHADG 363 (369)
T ss_pred -------CCHHHHHHHHHhCCCCcceEeeEECCCCCcccCCEEEEEEEcCC
Confidence 134789999999999999999999 8898887899999998873
No 72
>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=97.79 E-value=6.2e-05 Score=80.24 Aligned_cols=87 Identities=24% Similarity=0.348 Sum_probs=68.8
Q ss_pred cCccceEEEEEecC----CChhHHHHHHHHHhh-cCCCCCCCCCCchhHHHHHHHHHHHHHHHHHHcccCCcccccCCCC
Q 005717 25 ESMQGVLGLRPYIP----SSKKLEHFKLRWIKS-ADKPDGSTGGSNLFGLWAYDTVWAIAMAVERAGIENSSFLKSNTSK 99 (681)
Q Consensus 25 ~~~~Gvlg~~~~~~----~~~~~~~f~~~~~~~-~~~~~~~~~~~~~~~~~aYDav~~lA~Al~~~~~~~~~~~~~~~~~ 99 (681)
...+|+++...+.+ .++..++|.++|+++ .. .++.+++.+||+++++++|++++..
T Consensus 246 ~~~~~~~~~~~~~~~~~~~~~~~~~f~~~y~~~~g~-------~p~~~~~~~yda~~~l~~A~~~ag~------------ 306 (344)
T cd06345 246 GAGNYVITAESGAPGVEAITDKTVPFTEAYEAKFGG-------PPNYMGASTYDSIYILAEAIERAGS------------ 306 (344)
T ss_pred hhcceEEeecccccCccCCCHHHHHHHHHHHHHhCC-------CCcccchHHHHHHHHHHHHHHHhcC------------
Confidence 45677766655543 456788999999876 32 3566888999999999999998751
Q ss_pred CCCcccccCCCcchHHHHHHHhccceecceeeEEE-eCCcccC
Q 005717 100 SRVDIAALGTFEMGAKLLDTLINTTFEGLSGNFHL-VNGQLEP 141 (681)
Q Consensus 100 ~~~~~~~~~~~~~G~~l~~~l~~~~f~GltG~i~F-~~G~~~~ 141 (681)
.++..+.++|++++|+|++|.|+| .+|++..
T Consensus 307 -----------~~~~~i~~al~~~~~~g~~G~i~f~~~g~~~~ 338 (344)
T cd06345 307 -----------TDGDALVEALEKTDFVGTAGRIQFYGDDSAFA 338 (344)
T ss_pred -----------CCHHHHHHHHHhCCCcCCceeEEECCCCCcCc
Confidence 245789999999999999999999 8999864
No 73
>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=97.79 E-value=6.4e-05 Score=80.07 Aligned_cols=92 Identities=22% Similarity=0.337 Sum_probs=71.3
Q ss_pred CccceEEEEEecCCC-------hhHHHHHHHHHhh-cCCCCCCCCCCchhHHHHHHHHHHHHHHHHHHcccCCcccccCC
Q 005717 26 SMQGVLGLRPYIPSS-------KKLEHFKLRWIKS-ADKPDGSTGGSNLFGLWAYDTVWAIAMAVERAGIENSSFLKSNT 97 (681)
Q Consensus 26 ~~~Gvlg~~~~~~~~-------~~~~~f~~~~~~~-~~~~~~~~~~~~~~~~~aYDav~~lA~Al~~~~~~~~~~~~~~~ 97 (681)
..+|+++...+.+.. +..+.|.++|+++ .. .++.+++.+||+++++++|+++++.
T Consensus 244 ~~~g~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~-------~p~~~~~~~y~a~~~~~~a~~~ag~---------- 306 (345)
T cd06338 244 DAEGVFGPTQWTPALDYKDDLFPSAAEFAAAYKEKYGK-------APDYHAAGAYAAGQVLQEAVERAGS---------- 306 (345)
T ss_pred hhCceeecceeccCcccccccCccHHHHHHHHHHHhCC-------CCCcccHHHHHHHHHHHHHHHHhCC----------
Confidence 468888887766543 5689999999876 32 2345788999999999999998752
Q ss_pred CCCCCcccccCCCcchHHHHHHHhccceecceeeEEE-eCCcccCccEEEEE
Q 005717 98 SKSRVDIAALGTFEMGAKLLDTLINTTFEGLSGNFHL-VNGQLEPSAFEIFN 148 (681)
Q Consensus 98 ~~~~~~~~~~~~~~~G~~l~~~l~~~~f~GltG~i~F-~~G~~~~~~~~I~n 148 (681)
.++..+.++|.+++|+|++|++.| .+|++.. .+-|++
T Consensus 307 -------------~~~~~v~~al~~~~~~~~~G~~~f~~~~~~~~-~~~~~~ 344 (345)
T cd06338 307 -------------LDPAAVRDALASNDFDTFYGPIKFDETGQNNH-PMTVVQ 344 (345)
T ss_pred -------------CCHHHHHHHHHhCCCcccccCeeECCCCCcCC-Cceeee
Confidence 135789999999999999999999 7888864 444544
No 74
>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=97.78 E-value=0.0001 Score=78.46 Aligned_cols=101 Identities=21% Similarity=0.328 Sum_probs=74.0
Q ss_pred cCccceEEEEEecCC--ChhHHHHHHHHHhh-cCCCCCCCCCCchhHHHHHHHHHHHHHHHHHHcccCCcccccCCCCCC
Q 005717 25 ESMQGVLGLRPYIPS--SKKLEHFKLRWIKS-ADKPDGSTGGSNLFGLWAYDTVWAIAMAVERAGIENSSFLKSNTSKSR 101 (681)
Q Consensus 25 ~~~~Gvlg~~~~~~~--~~~~~~f~~~~~~~-~~~~~~~~~~~~~~~~~aYDav~~lA~Al~~~~~~~~~~~~~~~~~~~ 101 (681)
+..+|+++..++.+. ++..++|.++|+++ .+ .++.++..+|||++++++|++++..... .
T Consensus 238 ~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~g~-------~p~~~~~~~yda~~~~~~A~~~a~~~~~----------~ 300 (344)
T cd06348 238 AACDGVLVAQAYSPENDTPVNRDFVEAYKKKYGK-------APPQFSAQAFDAVQVVAEALKRLNQKQK----------L 300 (344)
T ss_pred HhhcCeEEEeeccCCCCCHHHHHHHHHHHHHHCC-------CccHHHHHHHHHHHHHHHHHHHhcCCCc----------c
Confidence 467888888776543 34678999999866 32 3556788999999999999999874321 0
Q ss_pred CcccccCCCcchHHHHHHHhccceecceeeEEE-eCCcccCccEE
Q 005717 102 VDIAALGTFEMGAKLLDTLINTTFEGLSGNFHL-VNGQLEPSAFE 145 (681)
Q Consensus 102 ~~~~~~~~~~~G~~l~~~l~~~~f~GltG~i~F-~~G~~~~~~~~ 145 (681)
.+|. ....+..|.++|++++|.|++|+|.| .+|++....|-
T Consensus 301 ~~~~---~~~~~~~l~~~l~~~~~~g~~G~v~f~~~g~~~~~~~~ 342 (344)
T cd06348 301 AELP---LPELRTALNAALLSGQYDTPLGEISFTPDGEVLQKAFY 342 (344)
T ss_pred ccch---hhhHHHHHHHHHhccCCccceeeeEECCCCCcccCcee
Confidence 1110 01234688999999999999999999 88988766553
No 75
>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=97.71 E-value=0.00014 Score=76.98 Aligned_cols=91 Identities=16% Similarity=0.243 Sum_probs=71.3
Q ss_pred ccCccceEEEEEecCC--ChhHHHHHHHHHhh-cCCCCCCCCCCchhHHHHHHHHHHHHHHHHHHcccCCcccccCCCCC
Q 005717 24 MESMQGVLGLRPYIPS--SKKLEHFKLRWIKS-ADKPDGSTGGSNLFGLWAYDTVWAIAMAVERAGIENSSFLKSNTSKS 100 (681)
Q Consensus 24 ~~~~~Gvlg~~~~~~~--~~~~~~f~~~~~~~-~~~~~~~~~~~~~~~~~aYDav~~lA~Al~~~~~~~~~~~~~~~~~~ 100 (681)
...++|+++..++.+. ++..++|.++|+++ .. .++.++..+||++.+++.|+++++..
T Consensus 233 ~~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~~~-------~~~~~~~~~yda~~~~~~a~~~ag~~------------ 293 (333)
T cd06332 233 GDAAVGVLTALHWAPDLDNPANKRFVAAYKAAYGR-------VPSVYAAQGYDAAQLLDAALRAVGGD------------ 293 (333)
T ss_pred chhhcCeeeeeccCCCCCCHHHHHHHHHHHHHhCC-------CCcHHHHHHHHHHHHHHHHHHHhcCC------------
Confidence 3467899888877653 46788999999876 32 35678999999999999999997521
Q ss_pred CCcccccCCCcchHHHHHHHhccceecceeeEEE-eCCcccCc
Q 005717 101 RVDIAALGTFEMGAKLLDTLINTTFEGLSGNFHL-VNGQLEPS 142 (681)
Q Consensus 101 ~~~~~~~~~~~~G~~l~~~l~~~~f~GltG~i~F-~~G~~~~~ 142 (681)
..++..+.++|.+++|+|++|.|.| .+|+....
T Consensus 294 ---------~~~~~~v~~al~~~~~~~~~g~i~f~~~~~~~~~ 327 (333)
T cd06332 294 ---------LSDKDALRAALRAADFDSPRGPFKFNPNHNPIQD 327 (333)
T ss_pred ---------CCCHHHHHHHHhcCceecCccceeECCCCCcccc
Confidence 1134679999999999999999999 77886543
No 76
>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=97.71 E-value=0.00013 Score=77.32 Aligned_cols=92 Identities=18% Similarity=0.314 Sum_probs=72.4
Q ss_pred cCccceEEEEEecC--CChhHHHHHHHHHhh-cCCCCCCCCCCchhHHHHHHHHHHHHHHHHHHcccCCcccccCCCCCC
Q 005717 25 ESMQGVLGLRPYIP--SSKKLEHFKLRWIKS-ADKPDGSTGGSNLFGLWAYDTVWAIAMAVERAGIENSSFLKSNTSKSR 101 (681)
Q Consensus 25 ~~~~Gvlg~~~~~~--~~~~~~~f~~~~~~~-~~~~~~~~~~~~~~~~~aYDav~~lA~Al~~~~~~~~~~~~~~~~~~~ 101 (681)
+.++|++...++.+ .++..+.|.++|+++ .+ .++.++..+||+++++++|++++....
T Consensus 237 ~~~~g~~~~~~~~~~~~~~~~~~f~~~y~~~~~~-------~~~~~~~~~yda~~~~~~A~~~a~~~~------------ 297 (336)
T cd06360 237 EAAEGVITALHYADTLDNPANQAFVKAYRAAYPD-------TPSVYAVQGYDAGQALILALEAVGGDL------------ 297 (336)
T ss_pred hhhcCceeccccCCCCCCHHHHHHHHHHHHHhCC-------CccHHHHHHHHHHHHHHHHHHHhCCCC------------
Confidence 45788888777655 356789999999876 32 456789999999999999999975221
Q ss_pred CcccccCCCcchHHHHHHHhccceecceeeEEE-eCCcccCccE
Q 005717 102 VDIAALGTFEMGAKLLDTLINTTFEGLSGNFHL-VNGQLEPSAF 144 (681)
Q Consensus 102 ~~~~~~~~~~~G~~l~~~l~~~~f~GltG~i~F-~~G~~~~~~~ 144 (681)
.++..+.++|.+++|.|+.|+++| .+|++....|
T Consensus 298 ---------~~~~~v~~al~~~~~~~~~g~~~f~~~~~~~~~~~ 332 (336)
T cd06360 298 ---------SDGQALIAAMAAAKIDSPRGPFTLDKAHNPIQDNY 332 (336)
T ss_pred ---------CCHHHHHHHHhcCCccCCCcceEECCCCCcccceE
Confidence 134679999999999999999999 7788765443
No 77
>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=97.58 E-value=0.00035 Score=75.05 Aligned_cols=97 Identities=21% Similarity=0.259 Sum_probs=71.1
Q ss_pred cCccceEEEEEecC--CChhHHHHHHHHHhh-cCCCCCCCCCCchhHHHHHHHHHHHHHHHHHHcccCCcccccCCCCCC
Q 005717 25 ESMQGVLGLRPYIP--SSKKLEHFKLRWIKS-ADKPDGSTGGSNLFGLWAYDTVWAIAMAVERAGIENSSFLKSNTSKSR 101 (681)
Q Consensus 25 ~~~~Gvlg~~~~~~--~~~~~~~f~~~~~~~-~~~~~~~~~~~~~~~~~aYDav~~lA~Al~~~~~~~~~~~~~~~~~~~ 101 (681)
+..+|+++..++.+ .++..+.|.++|+++ .+.| .++.++..+||+++++++|+++++.
T Consensus 237 ~~~~g~~~~~~~~~~~~~p~~~~f~~~~~~~~g~~~-----~~~~~~~~~yda~~~l~~Al~~ag~-------------- 297 (360)
T cd06357 237 EAAAGHITAAPYFSSIDTPANRAFVARYRARFGEDA-----PVSACAEAAYFQVHLFARALQRAGS-------------- 297 (360)
T ss_pred HhhCCcEEecccccccCChhHHHHHHHHHHHcCCCC-----CCCcHHHHHHHHHHHHHHHHHHcCC--------------
Confidence 45789888877643 456788999999876 2211 2466889999999999999998752
Q ss_pred CcccccCCCcchHHHHHHHhccceecceeeEEE-eCCcccCccEEEEEe
Q 005717 102 VDIAALGTFEMGAKLLDTLINTTFEGLSGNFHL-VNGQLEPSAFEIFNV 149 (681)
Q Consensus 102 ~~~~~~~~~~~G~~l~~~l~~~~f~GltG~i~F-~~G~~~~~~~~I~n~ 149 (681)
.++..+.++|.+++|+|+.|.+.| ..++.......+.++
T Consensus 298 ---------~~~~~v~~aL~~~~~~~~~g~~~f~~~~~~~~~~~~~~~~ 337 (360)
T cd06357 298 ---------DDPEDVLAALLGFSFDAPQGPVRIDPDNNHTYLWPRIARV 337 (360)
T ss_pred ---------CCHHHHHHHhccCcccCCCcceEEeCCCCeeeeeeEEEEE
Confidence 134679999999999999999999 444443334445555
No 78
>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=97.52 E-value=0.00042 Score=73.51 Aligned_cols=88 Identities=19% Similarity=0.270 Sum_probs=69.7
Q ss_pred cCccceEEEEEecC--CChhHHHHHHHHHhh-cCCCCCCCCCCchhHHHHHHHHHHHHHHHHHHcccCCcccccCCCCCC
Q 005717 25 ESMQGVLGLRPYIP--SSKKLEHFKLRWIKS-ADKPDGSTGGSNLFGLWAYDTVWAIAMAVERAGIENSSFLKSNTSKSR 101 (681)
Q Consensus 25 ~~~~Gvlg~~~~~~--~~~~~~~f~~~~~~~-~~~~~~~~~~~~~~~~~aYDav~~lA~Al~~~~~~~~~~~~~~~~~~~ 101 (681)
+.++|+++..++.+ +++..++|.++|+++ .+ .++.++..+||++++++.|+++++...
T Consensus 234 ~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~~~-------~~~~~~~~~yda~~~~~~A~~~ag~~~------------ 294 (333)
T cd06359 234 DAALGLYNTAQWAPDLDNPANKKFVADFEKKYGR-------LPTLYAAQAYDAAQLLDSAVRKVGGNL------------ 294 (333)
T ss_pred hhhcCeeeccccCCCCCCHHHHHHHHHHHHHhCC-------CCcHHHHHHHHHHHHHHHHHHHhcCCC------------
Confidence 45788888887765 356788999999876 22 467789999999999999999975210
Q ss_pred CcccccCCCcchHHHHHHHhccceecceeeEEE-eCCccc
Q 005717 102 VDIAALGTFEMGAKLLDTLINTTFEGLSGNFHL-VNGQLE 140 (681)
Q Consensus 102 ~~~~~~~~~~~G~~l~~~l~~~~f~GltG~i~F-~~G~~~ 140 (681)
.+...+.++|.+++|+|++|.++| .+|+..
T Consensus 295 ---------~~~~~v~~al~~~~~~~~~G~~~~~~~~~~~ 325 (333)
T cd06359 295 ---------SDKDALRAALRAADFKSVRGAFRFGTNHFPI 325 (333)
T ss_pred ---------CCHHHHHHHHhcCccccCccceEECCCCCcc
Confidence 134789999999999999999999 677754
No 79
>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=97.50 E-value=0.00049 Score=73.05 Aligned_cols=99 Identities=23% Similarity=0.428 Sum_probs=78.2
Q ss_pred cCccceEEEEEecCC--ChhHHHHHHHHHhh-cCCCCCCCCCCchhHHHHHHHHHHHHHHHHHHcccCCcccccCCCCCC
Q 005717 25 ESMQGVLGLRPYIPS--SKKLEHFKLRWIKS-ADKPDGSTGGSNLFGLWAYDTVWAIAMAVERAGIENSSFLKSNTSKSR 101 (681)
Q Consensus 25 ~~~~Gvlg~~~~~~~--~~~~~~f~~~~~~~-~~~~~~~~~~~~~~~~~aYDav~~lA~Al~~~~~~~~~~~~~~~~~~~ 101 (681)
..++|+++..++.+. .+..++|.++|++. .+.+ .++.++..+||++.+++.|+++++
T Consensus 238 ~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~-----~~~~~~~~~yda~~~~~~al~~~g--------------- 297 (343)
T PF13458_consen 238 DALEGVYIVSPWFPDPDSPAVKQFQERYRAAYGEEP-----PPSLYAAQGYDAARLLAQALERAG--------------- 297 (343)
T ss_dssp GGGTTEEEEESGGGTGGSHHHHHHHHHHHHHHSSTG-----GTCHHHHHHHHHHHHHHHHHHHHT---------------
T ss_pred hhccCceeecccCCCCCCHHHHHHHHHHHHHcCCCC-----CCchhHHHHHHHHHHHHHHHHHhC---------------
Confidence 358899998887763 56789999999887 3311 267789999999999999999974
Q ss_pred CcccccCCCcchHHHHHHHhccceecceeeEEE-eCCcccCccEEEEEeee
Q 005717 102 VDIAALGTFEMGAKLLDTLINTTFEGLSGNFHL-VNGQLEPSAFEIFNVIG 151 (681)
Q Consensus 102 ~~~~~~~~~~~G~~l~~~l~~~~f~GltG~i~F-~~G~~~~~~~~I~n~~~ 151 (681)
..++..+.++|.+++|+|++|++.| ..+......+.|++++.
T Consensus 298 --------~~~~~~v~~al~~~~~~g~~g~~~~~~~~~~~~~~~~i~~v~~ 340 (343)
T PF13458_consen 298 --------SLDREAVREALESLKYDGLFGPISFDPPDHQANKPVYIVQVKS 340 (343)
T ss_dssp --------SHHHHHHHHHHHTSEEEETTEEEEEETTTSBEEEEEEEEEEET
T ss_pred --------CCCHHHHHHHHHhCCCcccccceEEeCCCCccccCeEEEEEec
Confidence 1356899999999999999999999 44444456788888873
No 80
>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=97.44 E-value=0.00098 Score=71.85 Aligned_cols=108 Identities=17% Similarity=0.156 Sum_probs=75.8
Q ss_pred CccceEEEEEecCC--ChhHHHHHHHHHhh-cCCCCCCCCCCchhHHHHHHHHHHHHHHHHHHcccCCcccccCCCCCCC
Q 005717 26 SMQGVLGLRPYIPS--SKKLEHFKLRWIKS-ADKPDGSTGGSNLFGLWAYDTVWAIAMAVERAGIENSSFLKSNTSKSRV 102 (681)
Q Consensus 26 ~~~Gvlg~~~~~~~--~~~~~~f~~~~~~~-~~~~~~~~~~~~~~~~~aYDav~~lA~Al~~~~~~~~~~~~~~~~~~~~ 102 (681)
...|+++..++.+. .+..++|.++|+++ ...| .++.++..+|||+.++++|+++++.
T Consensus 236 ~~~g~~~~~~~~~~~~~~~~~~F~~~y~~~~g~~p-----~~~~~a~~~Yda~~~l~~Ai~~AGs--------------- 295 (374)
T TIGR03669 236 ALKDVYAGVNYMEEIDTPENEAFVERFYAKFPDAP-----YINQEAENNYFSVYMYKQAVEEAGT--------------- 295 (374)
T ss_pred hhCCcEEeeeccccCCCHHHHHHHHHHHHHcCCCC-----CCChHHHHHHHHHHHHHHHHHHhCC---------------
Confidence 45677766665543 46778999999886 2211 2355788999999999999999862
Q ss_pred cccccCCCcchHHHHHHHhc-cceecceeeEEE-eCCcccCccEEEEEeeeCC-eeEeeeee
Q 005717 103 DIAALGTFEMGAKLLDTLIN-TTFEGLSGNFHL-VNGQLEPSAFEIFNVIGTS-ERVIGYWT 161 (681)
Q Consensus 103 ~~~~~~~~~~G~~l~~~l~~-~~f~GltG~i~F-~~G~~~~~~~~I~n~~~~~-~~~vG~W~ 161 (681)
.++..+.++|.+ .+|+|++|+++| .+++.....+.|.+++.++ ...+..|.
T Consensus 296 --------~d~~av~~aL~~~~~~~~~~G~i~fd~~~~~~~~~~~v~~~~~~~~~~~~~~~~ 349 (374)
T TIGR03669 296 --------TDQDAVRDVLESGVEMDAPEGKVCIDGATHHMSHTMRLARADADHNITFVKEQE 349 (374)
T ss_pred --------CCHHHHHHHHHcCCeEECCCccEEEcCCCCeeeeeeEEEEEcCCCCEEEEEecC
Confidence 245789999987 679999999999 4554443455677776543 44444554
No 81
>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=97.40 E-value=0.00035 Score=74.09 Aligned_cols=88 Identities=17% Similarity=0.229 Sum_probs=68.6
Q ss_pred cCccceEEEEEecCCChhHHHHHHHHHhh-cCCCCCCCCCCchhHHHHHHHHHHHHHHHHHHcccCCcccccCCCCCCCc
Q 005717 25 ESMQGVLGLRPYIPSSKKLEHFKLRWIKS-ADKPDGSTGGSNLFGLWAYDTVWAIAMAVERAGIENSSFLKSNTSKSRVD 103 (681)
Q Consensus 25 ~~~~Gvlg~~~~~~~~~~~~~f~~~~~~~-~~~~~~~~~~~~~~~~~aYDav~~lA~Al~~~~~~~~~~~~~~~~~~~~~ 103 (681)
..++|+++..++.+.++..++|.+.|+++ .. .++.++..+||+++++++|+++++..
T Consensus 237 ~~~~G~~~~~~~~~~~~~~~~f~~~~~~~~~~-------~~~~~a~~~Yda~~~l~~A~~~ag~~--------------- 294 (332)
T cd06344 237 KDLEGLVLAVPWHPLASPNSPFAKLAQQLWGG-------DVSWRTATAYDATKALIAALSQGPTR--------------- 294 (332)
T ss_pred hhhcCeEEEEecccccccchHHHHHHHHHhcC-------CchHHHHhHHHHHHHHHHHHHhCCCh---------------
Confidence 46789999999887766778899998876 32 35678999999999999999987522
Q ss_pred ccccCCCcchHHHH-HHHhccceecceeeEEE-eCCcccCc
Q 005717 104 IAALGTFEMGAKLL-DTLINTTFEGLSGNFHL-VNGQLEPS 142 (681)
Q Consensus 104 ~~~~~~~~~G~~l~-~~l~~~~f~GltG~i~F-~~G~~~~~ 142 (681)
++..+. .++....|+|++|+++| .+|++...
T Consensus 295 --------~~~~~~~~~~~~~~~~g~~g~i~f~~~g~~~~~ 327 (332)
T cd06344 295 --------EGVQQVELSLRNFSVQGATGKIKFLPSGDRNGQ 327 (332)
T ss_pred --------hhhhhhhhhcccccccCCCceeEeCCCCcccCc
Confidence 122333 56777889999999999 88998753
No 82
>PF12974 Phosphonate-bd: ABC transporter, phosphonate, periplasmic substrate-binding protein ; PDB: 3N5L_B 3QUJ_C 3P7I_A 3QK6_A 3S4U_A.
Probab=97.35 E-value=0.0023 Score=64.49 Aligned_cols=122 Identities=16% Similarity=0.138 Sum_probs=76.7
Q ss_pred CCCCCHHHHHhCCCeEEEecChhH-----HHHHh-hhcCCccc---cccccCChhHHHHHHccCcceEEecchhhHHHHH
Q 005717 410 PSFTDVKDIQKNGYFVGYQTNSFV-----KDLLT-KKLNFNET---RLKNYTTSEDYHDALSNGEVAAIFDEIPYIKIFL 480 (681)
Q Consensus 410 ~~i~s~~dL~~~~~~vg~~~~s~~-----~~~l~-~~~~~~~~---~~~~~~~~~~~~~~l~~g~~~a~i~e~~~~~~~~ 480 (681)
.+|++++||. |.+|++...+.. ..... ++.++... ..+...+.+..+++|.+|++|+.+......+-+.
T Consensus 95 s~i~~l~dL~--Gk~v~~~~~~s~sg~l~~~~~L~~~~Gl~~~~~~~~~~~~~~~~~~~~l~~G~~Da~~~~~~~~~~~~ 172 (243)
T PF12974_consen 95 SPITSLADLK--GKRVAFPDPSSTSGYLIPRYELLREAGLDPGDDFKQVFVGSHDAVLEALLNGKADAAAIPSDAFERLE 172 (243)
T ss_dssp SS--SHHHHG--GSEEEEE-TT-TTTTHHHHHHTCCCCT--HHHHSSEEEEE-HHHHHHHHHTTSSSEEEEEHHHHHHHH
T ss_pred CCCCChhhcC--CCEEEEecCCccHHHHHHHHHHHHHcCCChhHceeEEEeCCHHHHHHHHHcCCccEEEEechhHHHHH
Confidence 3699999998 889998654322 22221 23344321 2234457888999999999999988877776665
Q ss_pred hhc---CCceEEECcccccCCcEEEecCCCC--ChHHHHHHHHhhccCccHHHHHHHHH
Q 005717 481 ASY---CSRYMMVGPTYRTDGFGFAFPLGSP--LVPYISRAILKVTEDKEKMENIEKAL 534 (681)
Q Consensus 481 ~~~---c~~l~~v~~~~~~~~~~~~~~k~sp--l~~~in~~Il~l~e~~G~l~~i~~kw 534 (681)
... .++++++...-......++..++-| .++.|-.+++.+..+ -.-.++.+.+
T Consensus 173 ~~~~~~~~~~rvl~~s~~~p~~~~~~~~~~~~~~~~~l~~al~~~~~~-~~~~~~l~~~ 230 (243)
T PF12974_consen 173 AEGPDIPSQLRVLWTSPPYPNWPLVASPDLPPELRQRLRDALLSLSKD-PEGKAILDAF 230 (243)
T ss_dssp HH-HHHHTTEEEEEEEEEEE--EEEEETTS-HHHHHHHHHHHHHTTSS-HHHHHHHHHT
T ss_pred HccCcccccEEEEEEeCCCCCcEEEEeCCCCHHHHHHHHHHHHcCCCC-hhhHHHHHhc
Confidence 542 4577777554333445777888766 899999999999987 5556665554
No 83
>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=97.31 E-value=0.0013 Score=70.30 Aligned_cols=97 Identities=18% Similarity=0.121 Sum_probs=68.9
Q ss_pred CccceEEEEEecC--CChhHHHHHHHHHhh-cCCCCCCCCCCchhHHHHHHHHHHHHHHHHHHcccCCcccccCCCCCCC
Q 005717 26 SMQGVLGLRPYIP--SSKKLEHFKLRWIKS-ADKPDGSTGGSNLFGLWAYDTVWAIAMAVERAGIENSSFLKSNTSKSRV 102 (681)
Q Consensus 26 ~~~Gvlg~~~~~~--~~~~~~~f~~~~~~~-~~~~~~~~~~~~~~~~~aYDav~~lA~Al~~~~~~~~~~~~~~~~~~~~ 102 (681)
...|+++...+.+ +.+..+.|.++|+++ ...| .+..++..+|||+++++.|+++++.
T Consensus 237 ~~~g~~~~~~~~~~~~~~~~~~f~~~y~~~~g~~~-----~~~~~a~~~Y~a~~~~~~Al~~ag~--------------- 296 (348)
T cd06355 237 NLAGHYAAWNYFQSVDTPENKKFVAAFKARYGQDR-----VTNDPMEAAYIGVYLWKQAVEKAGS--------------- 296 (348)
T ss_pred hhcCCEEeccchhhcCCHHHHHHHHHHHHHcCCCC-----CCCcHHHHHHHHHHHHHHHHHHhCC---------------
Confidence 4677776554432 456688899999876 2211 2344678899999999999999752
Q ss_pred cccccCCCcchHHHHHHHhccceecceeeEEE-eCCcccCccEEEEEee
Q 005717 103 DIAALGTFEMGAKLLDTLINTTFEGLSGNFHL-VNGQLEPSAFEIFNVI 150 (681)
Q Consensus 103 ~~~~~~~~~~G~~l~~~l~~~~f~GltG~i~F-~~G~~~~~~~~I~n~~ 150 (681)
.++..+.++|++++|+|..|.++| .+++.....+.|.+++
T Consensus 297 --------~~~~~i~~aL~~~~~~~~~g~~~f~~~~~~~~~~~~i~~~~ 337 (348)
T cd06355 297 --------FDVDKVRAALPGQSFDAPEGPVTVDPANHHLWKPVRIGRIQ 337 (348)
T ss_pred --------CCHHHHHHHhccCcccCCCcceEeecCCCeeeeeeEEEEEc
Confidence 135789999999999999999999 4333333455666765
No 84
>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=97.30 E-value=0.00092 Score=70.64 Aligned_cols=90 Identities=26% Similarity=0.387 Sum_probs=67.6
Q ss_pred cCccceEEEEEecCC--ChhHHHHHHHHHhhcCCCCCCCCCCchhHHHHHHHHHHHHHHHHHHcccCCcccccCCCCCCC
Q 005717 25 ESMQGVLGLRPYIPS--SKKLEHFKLRWIKSADKPDGSTGGSNLFGLWAYDTVWAIAMAVERAGIENSSFLKSNTSKSRV 102 (681)
Q Consensus 25 ~~~~Gvlg~~~~~~~--~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~aYDav~~lA~Al~~~~~~~~~~~~~~~~~~~~ 102 (681)
...+|++...++.+. .+..+.|.++|+++ ++ ..++.++..+|||++++++|++++..
T Consensus 237 ~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~--~~----~~~~~~~~~~yda~~~~~~Al~~ag~--------------- 295 (334)
T cd06347 237 AAAEGVYFTTHFSADDPTPKAKKFVKAYKAK--YG----KEPDAFAALGYDAYYLLADAIERAGS--------------- 295 (334)
T ss_pred HHhCCcEEecccCCCCCCHHHHHHHHHHHHH--HC----CCcchhHHHHHHHHHHHHHHHHHhCC---------------
Confidence 457888887776654 45688999998765 11 13567889999999999999998641
Q ss_pred cccccCCCcchHHHHHHHhcc-ceecceeeEEE-eCCcccCcc
Q 005717 103 DIAALGTFEMGAKLLDTLINT-TFEGLSGNFHL-VNGQLEPSA 143 (681)
Q Consensus 103 ~~~~~~~~~~G~~l~~~l~~~-~f~GltG~i~F-~~G~~~~~~ 143 (681)
.++..+.+.|.+. +|+|++|+++| .+|+.....
T Consensus 296 --------~~~~~v~~~l~~~~~~~g~~G~v~f~~~g~~~~~~ 330 (334)
T cd06347 296 --------TDPEAIRDALAKTKDFDGVTGKITIDENGNPVKSA 330 (334)
T ss_pred --------CCHHHHHHHHHhCCCcccceeeeEECCCCCcCCCc
Confidence 1357888888764 79999999999 778876443
No 85
>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=97.22 E-value=0.00084 Score=71.15 Aligned_cols=87 Identities=22% Similarity=0.282 Sum_probs=67.1
Q ss_pred CccceEEEEEecCC--ChhHHHHHHHHHhh-cCCCCCCCCCCchhHHHHHHHHHHHHHHHHHHcccCCcccccCCCCCCC
Q 005717 26 SMQGVLGLRPYIPS--SKKLEHFKLRWIKS-ADKPDGSTGGSNLFGLWAYDTVWAIAMAVERAGIENSSFLKSNTSKSRV 102 (681)
Q Consensus 26 ~~~Gvlg~~~~~~~--~~~~~~f~~~~~~~-~~~~~~~~~~~~~~~~~aYDav~~lA~Al~~~~~~~~~~~~~~~~~~~~ 102 (681)
..+|+++..++.+. .+..+.|.++|+++ .+.+ .++.+++.+|||+++++.|++++..
T Consensus 236 ~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~-----~~~~~~~~~yda~~~~~~A~~~ag~--------------- 295 (333)
T cd06331 236 AAEGHYSAASYFQSLDTPENKAFVARYRARYGDDA-----VINSPAEAAYEAVYLWAAAVEKAGS--------------- 295 (333)
T ss_pred hhCCcEeechhhhhcCChhHHHHHHHHHHHcCCCc-----CCCchhHHHHHHHHHHHHHHHHcCC---------------
Confidence 46888888776543 45678899999875 2211 3567899999999999999998641
Q ss_pred cccccCCCcchHHHHHHHhccceecceeeEEE-eCCccc
Q 005717 103 DIAALGTFEMGAKLLDTLINTTFEGLSGNFHL-VNGQLE 140 (681)
Q Consensus 103 ~~~~~~~~~~G~~l~~~l~~~~f~GltG~i~F-~~G~~~ 140 (681)
.++..|.++|.+++|+|++|.++| ..+++.
T Consensus 296 --------~~~~~l~~al~~~~~~~~~G~i~f~~~~~~~ 326 (333)
T cd06331 296 --------TDPEAVRAALEGVSFDAPQGPVRIDPDNHHT 326 (333)
T ss_pred --------CCHHHHHHHhhcCcccCCCCceEecCCCCcc
Confidence 245789999999999999999999 555543
No 86
>PRK11553 alkanesulfonate transporter substrate-binding subunit; Provisional
Probab=97.22 E-value=0.0029 Score=66.48 Aligned_cols=71 Identities=28% Similarity=0.324 Sum_probs=48.9
Q ss_pred CCCCHHHHHhCCCeEEEecChhHHHHHh---hhcCCccccc-cccCChhHHHHHHccCcceEEecchhhHHHHHhhc
Q 005717 411 SFTDVKDIQKNGYFVGYQTNSFVKDLLT---KKLNFNETRL-KNYTTSEDYHDALSNGEVAAIFDEIPYIKIFLASY 483 (681)
Q Consensus 411 ~i~s~~dL~~~~~~vg~~~~s~~~~~l~---~~~~~~~~~~-~~~~~~~~~~~~l~~g~~~a~i~e~~~~~~~~~~~ 483 (681)
+|++++||. |++|++..++..+.++. ++.+++...+ ..+.+..+...++.+|++|+++...++......+.
T Consensus 120 ~i~s~~dL~--Gk~I~~~~gs~~~~~l~~~l~~~g~~~~dv~~v~~~~~~~~~al~~G~vDa~~~~ep~~~~~~~~~ 194 (314)
T PRK11553 120 PIKTVADLK--GHKVAFQKGSSSHNLLLRALRKAGLKFTDIQPTYLTPADARAAFQQGNVDAWAIWDPYYSAALLQG 194 (314)
T ss_pred CCCCHHHhC--CCEEeecCCCcHHHHHHHHHHHcCCCHHHeEEEecChHHHHHHHHcCCCCEEEEcCcHHHHHHhcC
Confidence 578999998 88899988876665542 2334433222 23446678889999999999988767666555443
No 87
>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=97.13 E-value=0.0011 Score=70.67 Aligned_cols=93 Identities=25% Similarity=0.367 Sum_probs=68.4
Q ss_pred CCCeEEEecCCccccCCccccccCccceEEEEEecCCChhHHHHHHHHHhhcCCCCCCCCCCchhHHHHHHHHHHHHHHH
Q 005717 3 SEGYAWIATQGLSTLLDPVKDMESMQGVLGLRPYIPSSKKLEHFKLRWIKSADKPDGSTGGSNLFGLWAYDTVWAIAMAV 82 (681)
Q Consensus 3 ~~~y~WI~t~~~~~~~~~~~~~~~~~Gvlg~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~aYDav~~lA~Al 82 (681)
+..|.|+.++|.+..-......+.++|++|+.++.+.+...+.|.+.|++ +++++|||||+
T Consensus 243 ~~~~~i~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~f~~~~~~--------------~~~~~YDav~~----- 303 (348)
T cd06350 243 TGKYWIISTDWDTSTCLLLFTLDAFQGVLGFSGHAPRSGEIPGFKDFLRK--------------YAYNVYDAVYA----- 303 (348)
T ss_pred CCeEEEEEccccCccccccCCcceeeeEEEEEEEeecCCcCCChHHHHHH--------------HHHHHHhheeE-----
Confidence 34566666667654201112345789999999998876666677777763 78999999997
Q ss_pred HHHcccCCcccccCCCCCCCcccccCCCcchHHHHHHHhccceecceeeEEE-eCCcccCccEEEEEeee----CCeeEe
Q 005717 83 ERAGIENSSFLKSNTSKSRVDIAALGTFEMGAKLLDTLINTTFEGLSGNFHL-VNGQLEPSAFEIFNVIG----TSERVI 157 (681)
Q Consensus 83 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~l~~~l~~~~f~GltG~i~F-~~G~~~~~~~~I~n~~~----~~~~~v 157 (681)
.+.| ++|++. ..|+|++++. .++++|
T Consensus 304 ------------------------------------------------~v~f~~~gd~~-~~~~i~~~~~~~~~~~~~~v 334 (348)
T cd06350 304 ------------------------------------------------EVKFDENGDRL-ASYDIINWQIFPGGGGFVKV 334 (348)
T ss_pred ------------------------------------------------EEEecCCCCcc-cceeEEEEEEcCCcEEEEEE
Confidence 8899 779987 5789999876 569999
Q ss_pred eeeeCC
Q 005717 158 GYWTKE 163 (681)
Q Consensus 158 G~W~~~ 163 (681)
|.|.+.
T Consensus 335 g~~~~~ 340 (348)
T cd06350 335 GFWDPQ 340 (348)
T ss_pred EEEcCC
Confidence 999974
No 88
>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=97.10 E-value=0.0031 Score=67.61 Aligned_cols=97 Identities=22% Similarity=0.177 Sum_probs=66.6
Q ss_pred CccceEEEEEec--CCChhHHHHHHHHHhhcCCCCCCCCCCchhHHHHHHHHHHHHHHHHHHcccCCcccccCCCCCCCc
Q 005717 26 SMQGVLGLRPYI--PSSKKLEHFKLRWIKSADKPDGSTGGSNLFGLWAYDTVWAIAMAVERAGIENSSFLKSNTSKSRVD 103 (681)
Q Consensus 26 ~~~Gvlg~~~~~--~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~aYDav~~lA~Al~~~~~~~~~~~~~~~~~~~~~ 103 (681)
.++|+++...+. ...+..+.|.++|+++ ++.. .....++..+|||+.+++.|+++++.
T Consensus 238 ~~~G~~~~~~~~~~~~~~~~~~f~~~~~~~--~~~~--~~~~~~~~~~y~a~~~~~~A~~~ag~---------------- 297 (359)
T TIGR03407 238 NLVGHLAAWNYFQSVDTPANKKFVKAFKAK--YGDD--RVTNDPMEAAYLGVYLWKAAVEKAGS---------------- 297 (359)
T ss_pred hhCCeEEeccchhcCCCHHHHHHHHHHHHH--cCCC--CCCCcHHHHHHHHHHHHHHHHHHhCC----------------
Confidence 467776544332 3446678899999875 2111 12334567899999999999999752
Q ss_pred ccccCCCcchHHHHHHHhccceecceeeEEE-e-CCcccCccEEEEEee
Q 005717 104 IAALGTFEMGAKLLDTLINTTFEGLSGNFHL-V-NGQLEPSAFEIFNVI 150 (681)
Q Consensus 104 ~~~~~~~~~G~~l~~~l~~~~f~GltG~i~F-~-~G~~~~~~~~I~n~~ 150 (681)
.++..+.++|.+++|+++.|.++| . +++. ...+.+.+++
T Consensus 298 -------~~~~~i~~al~~~~~~~~~G~i~f~~~~~~~-~~~~~~~~~~ 338 (359)
T TIGR03407 298 -------FDVDAVRDAAIGIEFDAPEGKVKVDGKNHHL-TKTVRIGEIR 338 (359)
T ss_pred -------CCHHHHHHHhcCCcccCCCccEEEeCCCCee-eeeeEEEEEc
Confidence 135789999999999999999999 4 3343 2345555554
No 89
>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=97.04 E-value=0.0025 Score=67.90 Aligned_cols=81 Identities=16% Similarity=0.168 Sum_probs=64.1
Q ss_pred cCccceEEEEEecCC--ChhHHHHHHHHHhh-cCCCCCCCCCCchhHHHHHHHHHHHHHHHHHHcccCCcccccCCCCCC
Q 005717 25 ESMQGVLGLRPYIPS--SKKLEHFKLRWIKS-ADKPDGSTGGSNLFGLWAYDTVWAIAMAVERAGIENSSFLKSNTSKSR 101 (681)
Q Consensus 25 ~~~~Gvlg~~~~~~~--~~~~~~f~~~~~~~-~~~~~~~~~~~~~~~~~aYDav~~lA~Al~~~~~~~~~~~~~~~~~~~ 101 (681)
+..+|++...++.+. ++..+.|.++|+++ .+ .++.+++.+||++++++.|+++.+.
T Consensus 246 ~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~~~-------~~~~~~~~~y~~~~~~~~a~~~ag~-------------- 304 (342)
T cd06329 246 EAGLGLVVAVAYWHPNDTPANRAFVEAFKAKYGR-------VPDYYEGQAYNGIQMLADAIEKAGS-------------- 304 (342)
T ss_pred ccccceEEeeeccCCCCCHHHHHHHHHHHHHhCC-------CCCchHHHHHHHHHHHHHHHHHhCC--------------
Confidence 356788887776543 46788999999876 22 3556889999999999999998641
Q ss_pred CcccccCCCcchHHHHHHHhccceecceeeEEEe
Q 005717 102 VDIAALGTFEMGAKLLDTLINTTFEGLSGNFHLV 135 (681)
Q Consensus 102 ~~~~~~~~~~~G~~l~~~l~~~~f~GltG~i~F~ 135 (681)
.++..+.++|.+++|+|++|.++|.
T Consensus 305 ---------~~~~~v~~al~~~~~~~~~g~~~~~ 329 (342)
T cd06329 305 ---------TDPEAVAKALEGMEVDTPVGPVTMR 329 (342)
T ss_pred ---------CCHHHHHHHHhCCccccCCCCeEEc
Confidence 2347899999999999999999993
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=96.92 E-value=0.0037 Score=66.20 Aligned_cols=87 Identities=22% Similarity=0.293 Sum_probs=65.3
Q ss_pred CccceEEEEEecC--CChhHHHHHHHHHhhcCCCCCCCCCCchhHHHHHHHHHHHHHHHHHHcccCCcccccCCCCCCCc
Q 005717 26 SMQGVLGLRPYIP--SSKKLEHFKLRWIKSADKPDGSTGGSNLFGLWAYDTVWAIAMAVERAGIENSSFLKSNTSKSRVD 103 (681)
Q Consensus 26 ~~~Gvlg~~~~~~--~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~aYDav~~lA~Al~~~~~~~~~~~~~~~~~~~~~ 103 (681)
.++|+++...+.+ ..+..++|.++|+++ ++.. ...++.++.++||++++++.|+++.+.
T Consensus 235 ~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~--~g~~-~~~~~~~~~~~yda~~~~~~A~~~ag~---------------- 295 (333)
T cd06358 235 AAEGLYSSSGYFASLQTPANAAFLARYRAR--FGDD-APPLNSLSESCYEAVHALAAAAERAGS---------------- 295 (333)
T ss_pred hhCCcEEeccchhhcCCHHHHHHHHHHHHH--cCCC-CCCCChHHHHHHHHHHHHHHHHHHhCC----------------
Confidence 4788877766543 456788999999876 2111 113567889999999999999998641
Q ss_pred ccccCCCcchHHHHHHHhccceecceeeEEE-eCCc
Q 005717 104 IAALGTFEMGAKLLDTLINTTFEGLSGNFHL-VNGQ 138 (681)
Q Consensus 104 ~~~~~~~~~G~~l~~~l~~~~f~GltG~i~F-~~G~ 138 (681)
.++..|.++|.+++|+|++|.++| .++.
T Consensus 296 -------~~~~~v~~al~~~~~~~~~G~~~~~~~~~ 324 (333)
T cd06358 296 -------LDPEALIAALEDVSYDGPRGTVTMRGRHA 324 (333)
T ss_pred -------CCHHHHHHHhccCeeeCCCcceEEccccc
Confidence 134789999999999999999999 4433
No 91
>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=96.86 E-value=0.0031 Score=67.27 Aligned_cols=89 Identities=22% Similarity=0.200 Sum_probs=68.3
Q ss_pred cCccceEEEEEecCC-ChhHHHHHHHHHhhcCCCCCCCCCCchhHHHHHHHHHHHHHHHHHHcccCCcccccCCCCCCCc
Q 005717 25 ESMQGVLGLRPYIPS-SKKLEHFKLRWIKSADKPDGSTGGSNLFGLWAYDTVWAIAMAVERAGIENSSFLKSNTSKSRVD 103 (681)
Q Consensus 25 ~~~~Gvlg~~~~~~~-~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~aYDav~~lA~Al~~~~~~~~~~~~~~~~~~~~~ 103 (681)
...+|+++..++.+. .+..++|.++|+++ ++. .++.++..+||+++++++|++++...
T Consensus 247 ~~~~g~~~~~~~~~~~~~~~~~f~~~y~~~--~~~----~~~~~~~~~Y~a~~~l~~A~~~ag~~--------------- 305 (347)
T cd06340 247 KDAEGILTRNEWSDPKDPMAKDLNKRFKAR--FGV----DLSGNSARAYTAVLVIADALERAGSA--------------- 305 (347)
T ss_pred HhhheEEeccccCCCCChHHHHHHHHHHHH--hCC----CCChHHHHHHHHHHHHHHHHHHhcCC---------------
Confidence 457899998887665 56788999999876 221 36678999999999999999997521
Q ss_pred ccccCCCcchHHHH--HHHhcccee---cceeeEEE-eCCcccCc
Q 005717 104 IAALGTFEMGAKLL--DTLINTTFE---GLSGNFHL-VNGQLEPS 142 (681)
Q Consensus 104 ~~~~~~~~~G~~l~--~~l~~~~f~---GltG~i~F-~~G~~~~~ 142 (681)
++..+. .+|++..+. +.+|.+.| ++|+..++
T Consensus 306 --------~~~~v~~~~~~~~~~~~~~~~~~g~~~f~~~g~~~~~ 342 (347)
T cd06340 306 --------DPEKIRDLAALASTSGEDLIMPYGPIKFDAKGQNTNA 342 (347)
T ss_pred --------CHHHHHHHHHhccCCccccccCCCCeeECCCCCcccc
Confidence 345677 478777775 46899999 89998764
No 92
>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=96.81 E-value=0.0079 Score=62.73 Aligned_cols=69 Identities=16% Similarity=0.143 Sum_probs=47.0
Q ss_pred CCCCHHHHHhCCCeEEEecChhHHHHHh---hhcCCccccccc-cCChhHHHHHHccCcceEEecchhhHHHHHh
Q 005717 411 SFTDVKDIQKNGYFVGYQTNSFVKDLLT---KKLNFNETRLKN-YTTSEDYHDALSNGEVAAIFDEIPYIKIFLA 481 (681)
Q Consensus 411 ~i~s~~dL~~~~~~vg~~~~s~~~~~l~---~~~~~~~~~~~~-~~~~~~~~~~l~~g~~~a~i~e~~~~~~~~~ 481 (681)
.|++++||. |++||+..++..+.++. +..++....+.. .-...+...++.+|++|+++...++.....+
T Consensus 91 ~I~s~~DLk--GK~Igv~~~s~~~~~l~~~L~~~Gl~~~dv~~v~~~~~~~~~al~~G~vDa~~~~~p~~~~~~~ 163 (300)
T TIGR01729 91 GIEKPEDLK--GKNVAVPFVSTTHYSLLAALKHWKTDPREVNILNLKPPQIVAAWQRGDIDAAYVWPPALSELLK 163 (300)
T ss_pred CCCChhHcC--CCEEEeCCCCcHHHHHHHHHHHcCCChhheEEEecCcHHHHHHHHcCCcCEEEEecHHHHHHHh
Confidence 589999998 99999987765443321 333444333322 2245678899999999999888777655444
No 93
>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=96.80 E-value=0.0038 Score=66.16 Aligned_cols=88 Identities=19% Similarity=0.256 Sum_probs=67.0
Q ss_pred cCccceEEEEEecCC--ChhHHHHHHHHHhh-cCCCCCCCCCCchhHHHHHHHHHHHHHHHHHHcccCCcccccCCCCCC
Q 005717 25 ESMQGVLGLRPYIPS--SKKLEHFKLRWIKS-ADKPDGSTGGSNLFGLWAYDTVWAIAMAVERAGIENSSFLKSNTSKSR 101 (681)
Q Consensus 25 ~~~~Gvlg~~~~~~~--~~~~~~f~~~~~~~-~~~~~~~~~~~~~~~~~aYDav~~lA~Al~~~~~~~~~~~~~~~~~~~ 101 (681)
..++|+++..++.+. .+..++|.++|+++ .. .++.++..+||+++++++|+++++..
T Consensus 237 ~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~g~-------~p~~~~~~~Y~~~~~~~~A~~~ag~~------------- 296 (334)
T cd06327 237 DAAQGLYLTTAWYWDLPNDETRAFVKRFQAKYGK-------MPSMVQAGAYSAVLHYLKAVEAAGTD------------- 296 (334)
T ss_pred hhhcCeEEeeeccccCCCHHHHHHHHHHHHHHCc-------CCCcHHHHHHHHHHHHHHHHHHHCCC-------------
Confidence 357898888887544 56688899999876 22 25567889999999999999998632
Q ss_pred CcccccCCCcchHHHHHHHhccc-eecceeeEEE-e-CCcccCc
Q 005717 102 VDIAALGTFEMGAKLLDTLINTT-FEGLSGNFHL-V-NGQLEPS 142 (681)
Q Consensus 102 ~~~~~~~~~~~G~~l~~~l~~~~-f~GltG~i~F-~-~G~~~~~ 142 (681)
++..+.++|++++ ++++.|.+.| . +++...+
T Consensus 297 ----------~~~~v~~al~~~~~~~~~~g~~~~~~~~~~~~~~ 330 (334)
T cd06327 297 ----------DADKVVAKMKETPIYDLFAGNGYIRACDHQMVHD 330 (334)
T ss_pred ----------ChHHHHHhccccceeccCCCCceeeccccchhcc
Confidence 2356999999975 5889999999 5 6766533
No 94
>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=96.79 E-value=0.0044 Score=65.69 Aligned_cols=81 Identities=17% Similarity=0.194 Sum_probs=63.1
Q ss_pred CccceEEEEEec-CCChhHHHHHHHHHhhcCCCCCCCCCCchhHHHHHHHHHHHHHHHHHHcccCCcccccCCCCCCCcc
Q 005717 26 SMQGVLGLRPYI-PSSKKLEHFKLRWIKSADKPDGSTGGSNLFGLWAYDTVWAIAMAVERAGIENSSFLKSNTSKSRVDI 104 (681)
Q Consensus 26 ~~~Gvlg~~~~~-~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~aYDav~~lA~Al~~~~~~~~~~~~~~~~~~~~~~ 104 (681)
.++|+++.-++. +.++..+.|.++|+++ +. ..++.+++.+||++.+++.|++++..
T Consensus 239 ~~~~~~~~~~~~~~~~~~~~~f~~~y~~~--~g----~~p~~~~~~~y~a~~~l~~Ai~~ag~----------------- 295 (333)
T cd06328 239 GMSGASYYYHYFLPKNPVNDWLVEEHKAR--FG----SPPDLFTAGGMSAAIAVVEALEETGD----------------- 295 (333)
T ss_pred cccceeeeecCCCCCCHHHHHHHHHHHHH--hC----CCcchhhHHHHHHHHHHHHHHHHhCC-----------------
Confidence 466766655554 5667778899999876 11 13567899999999999999999751
Q ss_pred cccCCCcchHHHHHHHhccceecceeeEEEe
Q 005717 105 AALGTFEMGAKLLDTLINTTFEGLSGNFHLV 135 (681)
Q Consensus 105 ~~~~~~~~G~~l~~~l~~~~f~GltG~i~F~ 135 (681)
.+...+.++|++.+|+|+.|+++|.
T Consensus 296 ------~~~~~v~~aL~~~~~~~~~g~~~f~ 320 (333)
T cd06328 296 ------TDTEALIAAMEGMSFETPKGTMTFR 320 (333)
T ss_pred ------CCHHHHHHHHhCCeeecCCCceEEC
Confidence 2347899999999999999999993
No 95
>COG3221 PhnD ABC-type phosphate/phosphonate transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=96.68 E-value=0.031 Score=57.69 Aligned_cols=112 Identities=12% Similarity=0.094 Sum_probs=76.1
Q ss_pred CCCCCCHHHHHhCCCeEEEecChhHHHHHh-----hhcC-Cccc---cccccCC-hhHHHHHHccCcceEEecchhhHHH
Q 005717 409 QPSFTDVKDIQKNGYFVGYQTNSFVKDLLT-----KKLN-FNET---RLKNYTT-SEDYHDALSNGEVAAIFDEIPYIKI 478 (681)
Q Consensus 409 ~~~i~s~~dL~~~~~~vg~~~~s~~~~~l~-----~~~~-~~~~---~~~~~~~-~~~~~~~l~~g~~~a~i~e~~~~~~ 478 (681)
.++|++++||. |++++...-+....|+. ...+ .+.. .-+.+.. -+....+|.+|++|+..........
T Consensus 133 ds~i~sl~dlk--gk~~af~d~~StSG~l~P~~~L~~~g~~d~~~~f~~v~~~G~H~~a~~aV~nG~vDva~~~~~~~~~ 210 (299)
T COG3221 133 DSPIKSLEDLK--GKRFAFGDPDSTSGYLFPLYYLAKEGGIDPDKFFGEVIFSGGHDAAVLAVANGQVDVAAVNSSARGL 210 (299)
T ss_pred CCCcchHHHhc--CCeEeccCCCcchhhHhHHHHHHHhcCCChhhhhceeeccChHHHHHHHHHcCCceEEeccHHHHhh
Confidence 34799999999 99999875443333321 2222 2111 1123333 6777888899999998887776666
Q ss_pred HHhhcC----CceEEECcccccCCcEEEecCCCC--ChHHHHHHHHhhcc
Q 005717 479 FLASYC----SRYMMVGPTYRTDGFGFAFPLGSP--LVPYISRAILKVTE 522 (681)
Q Consensus 479 ~~~~~c----~~l~~v~~~~~~~~~~~~~~k~sp--l~~~in~~Il~l~e 522 (681)
+..... ++++++...-......++++++-| +++.+..+++.+.+
T Consensus 211 ~~~~~~~~~~~~l~vi~~S~~iP~~pi~vr~~L~~~~k~kl~~af~~l~~ 260 (299)
T COG3221 211 LKKAAPEGVAEKLRVIWKSPLIPNDPIAVRSDLPADLKEKLRDAFLDLAK 260 (299)
T ss_pred hhhcccccchhhceEEEecCCCCCCCEEEeCCCCHHHHHHHHHHHHhcCc
Confidence 655542 478888665444456788888877 99999999999986
No 96
>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=96.56 E-value=0.0061 Score=65.04 Aligned_cols=91 Identities=22% Similarity=0.227 Sum_probs=66.0
Q ss_pred cCccceEEEEEecC----CChhHHHHHHHHHhhcCCCCCCCCCCchhHHHHHHHHHHHHHHHHHHcccCCcccccCCCCC
Q 005717 25 ESMQGVLGLRPYIP----SSKKLEHFKLRWIKSADKPDGSTGGSNLFGLWAYDTVWAIAMAVERAGIENSSFLKSNTSKS 100 (681)
Q Consensus 25 ~~~~Gvlg~~~~~~----~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~aYDav~~lA~Al~~~~~~~~~~~~~~~~~~ 100 (681)
+.++|+++..++.+ .++..++|.++|+++ ++. .++.++..+||+++++++|++++....
T Consensus 241 ~~~~g~~~~~~~~~~~~~~~~~~~~f~~~~~~~--~~~----~p~~~~~~~y~~~~~~~~Al~~ag~~~----------- 303 (347)
T cd06336 241 DFMEGVYFQFPDVDDPALAFPRAKAFVEEYKKR--YGE----PPNSEAAVSYDAVYILKAAMEAAGSVD----------- 303 (347)
T ss_pred HhhCceEEEeecccccccCCHHHHHHHHHHHHH--HCC----CCcHHHHHHHHHHHHHHHHHHhcCCCC-----------
Confidence 45789999888765 356678999999876 111 266789999999999999999875221
Q ss_pred CCcccccCCCcchHHHHHHH-h-------ccceecceeeEEE-eCCcccCccE
Q 005717 101 RVDIAALGTFEMGAKLLDTL-I-------NTTFEGLSGNFHL-VNGQLEPSAF 144 (681)
Q Consensus 101 ~~~~~~~~~~~~G~~l~~~l-~-------~~~f~GltG~i~F-~~G~~~~~~~ 144 (681)
.....+++ . ...|.++.|.+.| .+|++..+.+
T Consensus 304 ------------~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~ 344 (347)
T cd06336 304 ------------DTAAVAALAAMLGVGKPAFGYARWWGKELFGVNGALVGPWP 344 (347)
T ss_pred ------------cHHHHHHHhhccCCCcCccccccccccccccCCCccccCcc
Confidence 12333333 2 2578889999999 8999876544
No 97
>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=96.49 E-value=0.015 Score=61.65 Aligned_cols=95 Identities=22% Similarity=0.372 Sum_probs=66.7
Q ss_pred CccceEEEEEecCC--ChhHHHHHHHHHhh-cCCCCCCCCCCchhHHHHHHHHHHHHHHHHHHcccCCcccccCCCCCCC
Q 005717 26 SMQGVLGLRPYIPS--SKKLEHFKLRWIKS-ADKPDGSTGGSNLFGLWAYDTVWAIAMAVERAGIENSSFLKSNTSKSRV 102 (681)
Q Consensus 26 ~~~Gvlg~~~~~~~--~~~~~~f~~~~~~~-~~~~~~~~~~~~~~~~~aYDav~~lA~Al~~~~~~~~~~~~~~~~~~~~ 102 (681)
.++|++...++.+. .+..++|.++|+++ .. .++.++..+||++.+++.|+++++...
T Consensus 237 ~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~~~~-------~p~~~~~~~y~~~~~~~~a~~~ag~~~------------- 296 (340)
T cd06349 237 AVEGVYTPTAFFPGDPRPEVQSFVSAYEAKYGA-------QPDAFAAQAYDAVGILAAAVRRAGTDR------------- 296 (340)
T ss_pred HhCCcEEecccCCCCCCHHHHHHHHHHHHHHCC-------CcchhhhhHHHHHHHHHHHHHHhCCCC-------------
Confidence 57888887776654 35678899999765 22 256688999999999999999975211
Q ss_pred cccccCCCcchHHHHHHH--hccceecceeeEEE-eC-CcccCccEEEEEeeeC
Q 005717 103 DIAALGTFEMGAKLLDTL--INTTFEGLSGNFHL-VN-GQLEPSAFEIFNVIGT 152 (681)
Q Consensus 103 ~~~~~~~~~~G~~l~~~l--~~~~f~GltG~i~F-~~-G~~~~~~~~I~n~~~~ 152 (681)
......+ .+..+.|++|++.| .+ ++.. ..+-++.++++
T Consensus 297 -----------~~~~~~~~~~~~~~~~~~g~i~~~~~~~~~~-~~~~~~~~~~g 338 (340)
T cd06349 297 -----------RAARDGFAKAEDVYSGVTGSTKFDPNTRRVI-KRFVPLVVRNG 338 (340)
T ss_pred -----------HHHHHHHHHhccCcccceEeEEECCCCCCcc-CceEEEEEeCC
Confidence 1223333 45668899999999 54 5554 47777776654
No 98
>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=96.46 E-value=0.0091 Score=63.52 Aligned_cols=105 Identities=22% Similarity=0.184 Sum_probs=70.7
Q ss_pred CeEEEecCCccccCCccccccCccceEEEEEe--cC--CChhHHHHHHHHHhh-cCCCCCCCCCCchhHHHHHHHHHHHH
Q 005717 5 GYAWIATQGLSTLLDPVKDMESMQGVLGLRPY--IP--SSKKLEHFKLRWIKS-ADKPDGSTGGSNLFGLWAYDTVWAIA 79 (681)
Q Consensus 5 ~y~WI~t~~~~~~~~~~~~~~~~~Gvlg~~~~--~~--~~~~~~~f~~~~~~~-~~~~~~~~~~~~~~~~~aYDav~~lA 79 (681)
+..||.+++....+.. -....++|++....+ .. .++..+.|.++|+++ .+ .++.++..+||++.+++
T Consensus 223 ~~~~~~~~~~~~~~~~-~~~~~~~g~~~~~~~~~~~~~~~~~~~~f~~~~~~~~g~-------~p~~~~~~~y~a~~~l~ 294 (346)
T cd06330 223 GTTVVLTLTGAPELAP-LGDEMPEGVIIGGRGPYFIPPDTPENKAFVDAYQEKYGD-------YPTYGAYGAYQAVMALA 294 (346)
T ss_pred CceEEeeccchhhhhh-hhcccCCceEEeccccCCCCCCChHHHHHHHHHHHHHCC-------CCChHHHHHHHHHHHHH
Confidence 4678887764332111 112356776554332 21 466789999999876 32 34557899999999999
Q ss_pred HHHHHHcccCCcccccCCCCCCCcccccCCCcchHHHHHHHhccceecceeeEEEeC
Q 005717 80 MAVERAGIENSSFLKSNTSKSRVDIAALGTFEMGAKLLDTLINTTFEGLSGNFHLVN 136 (681)
Q Consensus 80 ~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~l~~~l~~~~f~GltG~i~F~~ 136 (681)
.|++++..... .+.. +.+.++|.+++|.|++|++.|..
T Consensus 295 ~a~~~a~~~~~------------------~~~~-~~v~~al~~~~~~~~~G~~~f~~ 332 (346)
T cd06330 295 AAVEKAGATDG------------------GAPP-EQIAAALEGLSFETPGGPITMRA 332 (346)
T ss_pred HHHHHhcCCCC------------------CCcH-HHHHHHHcCCCccCCCCceeeec
Confidence 99999863211 0111 46999999999999999999943
No 99
>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=96.38 E-value=0.0077 Score=64.52 Aligned_cols=95 Identities=13% Similarity=0.036 Sum_probs=65.1
Q ss_pred ccceEEEEEecCCC--------hhHHHHHHHHHhh-cCCCCCCCCCCchhHHHHHHHHHHHHHHHHHHcccCCcccccCC
Q 005717 27 MQGVLGLRPYIPSS--------KKLEHFKLRWIKS-ADKPDGSTGGSNLFGLWAYDTVWAIAMAVERAGIENSSFLKSNT 97 (681)
Q Consensus 27 ~~Gvlg~~~~~~~~--------~~~~~f~~~~~~~-~~~~~~~~~~~~~~~~~aYDav~~lA~Al~~~~~~~~~~~~~~~ 97 (681)
.+|+++...+.+.. +..++|.++|+++ .+. +.....++||++.+++.|+++++..
T Consensus 252 ~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~~~~g~~-------~~~~~~~~~~~~~~l~~Ai~~Ags~--------- 315 (357)
T cd06337 252 GDGMSTEVWWSPSHPFRSSLTGQSAAELADAYEAATGRQ-------WTQPLGYAHALFEVGVKALVRADDP--------- 315 (357)
T ss_pred hcCccccceeccCCCcccccCCccHHHHHHHHHHHhCCC-------ccCcchHHHHHHHHHHHHHHHcCCC---------
Confidence 46666554444332 3478899999876 321 2334677999999999999997521
Q ss_pred CCCCCcccccCCCcchHHHHHHHhccceecceeeEEEeCCcccCccEEEEEeeeC
Q 005717 98 SKSRVDIAALGTFEMGAKLLDTLINTTFEGLSGNFHLVNGQLEPSAFEIFNVIGT 152 (681)
Q Consensus 98 ~~~~~~~~~~~~~~~G~~l~~~l~~~~f~GltG~i~F~~G~~~~~~~~I~n~~~~ 152 (681)
.++..|.++|.+++++++.|++.|+. + ......|+.+.|+
T Consensus 316 -------------~d~~~v~~aL~~~~~~~~~G~~~f~~-~-~~~~~~~~~~~~~ 355 (357)
T cd06337 316 -------------DDPAAVADAIATLKLDTVVGPVDFGN-S-PIKNVAKTPLVGG 355 (357)
T ss_pred -------------CCHHHHHHHHHcCCcccceeeeecCC-C-CCccccccccccC
Confidence 13468999999999999999999932 2 2234556666664
No 100
>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=96.37 E-value=0.0047 Score=64.79 Aligned_cols=69 Identities=23% Similarity=0.420 Sum_probs=54.0
Q ss_pred cCccceEEEEEecCCChhHHHHHHHHHhh-cCCCCCCCCCCchhHHHHHHHHHHHHHHHHHHcccCCcccccCCCCCCCc
Q 005717 25 ESMQGVLGLRPYIPSSKKLEHFKLRWIKS-ADKPDGSTGGSNLFGLWAYDTVWAIAMAVERAGIENSSFLKSNTSKSRVD 103 (681)
Q Consensus 25 ~~~~Gvlg~~~~~~~~~~~~~f~~~~~~~-~~~~~~~~~~~~~~~~~aYDav~~lA~Al~~~~~~~~~~~~~~~~~~~~~ 103 (681)
..++|+++..+..+. +..++|.++|+++ .+ .++.+++.+||+++++++|
T Consensus 239 ~~~~g~~~~~~~~~~-~~~~~f~~~~~~~~g~-------~p~~~~~~~Yd~~~~l~~A---------------------- 288 (312)
T cd06346 239 YILAGSYGTSPGAGG-PGLEAFTSAYKAAYGE-------SPSAFADQSYDAAALLALA---------------------- 288 (312)
T ss_pred HHhCCcEEccCCCCc-hhHHHHHHHHHHHhCC-------CCCccchhhHHHHHHHHHH----------------------
Confidence 457899888765544 7788999999887 32 2556889999999999987
Q ss_pred ccccCCCcchHHHHHHHhccceecceeeEEE-eCCcccCccEE
Q 005717 104 IAALGTFEMGAKLLDTLINTTFEGLSGNFHL-VNGQLEPSAFE 145 (681)
Q Consensus 104 ~~~~~~~~~G~~l~~~l~~~~f~GltG~i~F-~~G~~~~~~~~ 145 (681)
|.|++|+|.| .+|++.. .|+
T Consensus 289 ---------------------~~g~~g~~~f~~~g~~~~-~~~ 309 (312)
T cd06346 289 ---------------------YQGASGVVDFDENGDVAG-SYD 309 (312)
T ss_pred ---------------------hCCCccceeeCCCCCccc-cee
Confidence 8899999999 7888753 443
No 101
>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=96.32 E-value=0.014 Score=61.90 Aligned_cols=83 Identities=19% Similarity=0.278 Sum_probs=62.0
Q ss_pred cCccceEEEEEecCC--ChhHHHHHHHHHhhcCCCCCCCCCCchhHHHHHHHHHHHHHHHHHHcccCCcccccCCCCCCC
Q 005717 25 ESMQGVLGLRPYIPS--SKKLEHFKLRWIKSADKPDGSTGGSNLFGLWAYDTVWAIAMAVERAGIENSSFLKSNTSKSRV 102 (681)
Q Consensus 25 ~~~~Gvlg~~~~~~~--~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~aYDav~~lA~Al~~~~~~~~~~~~~~~~~~~~ 102 (681)
..++|+++..++.+. .+..++|.++|+++ ++.. ..++.+++.+||++.+++.|+++++.
T Consensus 235 ~~~~g~~~~~~~~~~~~~~~~~~f~~~~~~~--~~~~--p~~~~~~~~~y~a~~~~~~A~~~ag~--------------- 295 (334)
T cd06356 235 PALKDMYATANYIEELDTPANKAFVERFRAK--FPDA--PYINEEAENNYEAIYLYKEAVEKAGT--------------- 295 (334)
T ss_pred hhcCCeEEecchhhhcCCHHHHHHHHHHHHH--cCCC--CCCCchhHHHHHHHHHHHHHHHHHCC---------------
Confidence 356888877765433 45678999999886 2211 01245789999999999999999752
Q ss_pred cccccCCCcchHHHHHHHhc-cceecceeeEEE
Q 005717 103 DIAALGTFEMGAKLLDTLIN-TTFEGLSGNFHL 134 (681)
Q Consensus 103 ~~~~~~~~~~G~~l~~~l~~-~~f~GltG~i~F 134 (681)
.++..|.++|++ ..|+|+.|++.|
T Consensus 296 --------~~~~~v~~aL~~~~~~~~~~g~~~~ 320 (334)
T cd06356 296 --------TDRDAVIEALESGLVCDGPEGKVCI 320 (334)
T ss_pred --------CCHHHHHHHHHhCCceeCCCceEEE
Confidence 235789999997 578999999999
No 102
>COG0683 LivK ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]
Probab=96.25 E-value=0.017 Score=62.12 Aligned_cols=86 Identities=19% Similarity=0.239 Sum_probs=68.4
Q ss_pred hhHHHHHHHHHhh-cCCCCCCCCCCchhHHHHHHHHHHHHHHHHHHcccCCcccccCCCCCCCcccccCCCcchHHHHHH
Q 005717 41 KKLEHFKLRWIKS-ADKPDGSTGGSNLFGLWAYDTVWAIAMAVERAGIENSSFLKSNTSKSRVDIAALGTFEMGAKLLDT 119 (681)
Q Consensus 41 ~~~~~f~~~~~~~-~~~~~~~~~~~~~~~~~aYDav~~lA~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~l~~~ 119 (681)
+..+.|.++|+++ . ....++.++..+|||++++++|++++.. + .+...+.++
T Consensus 268 p~~~~f~~~~~~~~g-----~~~~~~~~~~~~y~a~~~~~~ai~~a~~-~---------------------~d~~~v~~a 320 (366)
T COG0683 268 PANKKFVEAYKAKYG-----DPAAPSYFAAAAYDAVKLLAKAIEKAGK-S---------------------SDREAVAEA 320 (366)
T ss_pred cchHHHHHHHHHHhC-----CCCCcccchHHHHHHHHHHHHHHHHHhc-C---------------------CCHHHHHHH
Confidence 3566799999887 3 1224566899999999999999999863 1 114679999
Q ss_pred Hhccc-eecceeeEEE-eCCcccCccEEEEEeeeCC
Q 005717 120 LINTT-FEGLSGNFHL-VNGQLEPSAFEIFNVIGTS 153 (681)
Q Consensus 120 l~~~~-f~GltG~i~F-~~G~~~~~~~~I~n~~~~~ 153 (681)
|.... +.+.+|.+.| .+|++....+.|.+++..+
T Consensus 321 l~~~~~~~~~~G~v~~~~~~~~~~~~~~i~~~~~~~ 356 (366)
T COG0683 321 LKGGKFFDTAGGPVTFDEKGDRGSKPVYVGQVQKGG 356 (366)
T ss_pred HhhCCCCccCCcceeECCCCCcCCCceEEEEEEecC
Confidence 99887 6899999999 7899998899999988654
No 103
>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=96.16 E-value=0.013 Score=61.73 Aligned_cols=69 Identities=22% Similarity=0.228 Sum_probs=48.9
Q ss_pred CCCHHHHHhCCCeEEEecChhHHHHHh---hhcCCcccccccc-CChhHHHHHHccCcceEEecchhhHHHHHhh
Q 005717 412 FTDVKDIQKNGYFVGYQTNSFVKDLLT---KKLNFNETRLKNY-TTSEDYHDALSNGEVAAIFDEIPYIKIFLAS 482 (681)
Q Consensus 412 i~s~~dL~~~~~~vg~~~~s~~~~~l~---~~~~~~~~~~~~~-~~~~~~~~~l~~g~~~a~i~e~~~~~~~~~~ 482 (681)
|++++||+ |++||+..++..+-++. +..+.....+... -...+...++.+|++||++...|+......+
T Consensus 98 i~svaDLK--GKkIav~~gs~~~~ll~~aL~~aGL~~~DV~~v~~~~~d~~aAl~~G~VDAa~~~eP~~s~~~~~ 170 (328)
T TIGR03427 98 GKSLADLK--GQKVNLVELSVSHYLLARALESVGLSEKDVKVVNTSDADIVAAFITKDVTAVVTWNPQLSEIKAQ 170 (328)
T ss_pred CCCHHHcC--CCEEeccCCChHHHHHHHHHHHcCCCHHHeEEEeCChHHHHHHHhcCCCcEEEEcCchHHHHHhC
Confidence 89999999 99999998887664442 3334543333222 2457788999999999998887876655443
No 104
>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=95.78 E-value=0.026 Score=60.13 Aligned_cols=71 Identities=25% Similarity=0.298 Sum_probs=56.1
Q ss_pred hhHHHHHHHHHhh-cCCCCCCCCCCchhHHHHHHHHHHHHHHHHHHcccCCcccccCCCCCCCcccccCCCcchHHHHHH
Q 005717 41 KKLEHFKLRWIKS-ADKPDGSTGGSNLFGLWAYDTVWAIAMAVERAGIENSSFLKSNTSKSRVDIAALGTFEMGAKLLDT 119 (681)
Q Consensus 41 ~~~~~f~~~~~~~-~~~~~~~~~~~~~~~~~aYDav~~lA~Al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~l~~~ 119 (681)
+..++|.++|+++ .. .++.++..+|||+.++|.|++++++ .++..+.++
T Consensus 232 ~~~~~f~~~f~~~~g~-------~p~~~~a~aY~av~~~a~Ai~~AGs-----------------------~d~~aV~~a 281 (347)
T TIGR03863 232 WGATQLQSRFEKLAGR-------PMTELDYAAWLAVRAVGEAVTRTRS-----------------------ADPATLRDY 281 (347)
T ss_pred hhHHHHHHHHHHHhCC-------CCChHHHHHHHHHHHHHHHHHHhcC-----------------------CCHHHHHHH
Confidence 4568899999876 33 3455788899999999999999862 356899999
Q ss_pred Hhccce--eccee-eEEE-e-CCcccC
Q 005717 120 LINTTF--EGLSG-NFHL-V-NGQLEP 141 (681)
Q Consensus 120 l~~~~f--~GltG-~i~F-~-~G~~~~ 141 (681)
|.++++ .+..| ++.| . |+|...
T Consensus 282 L~~~~~~~~~~~g~~~~~R~~Dhq~~~ 308 (347)
T TIGR03863 282 LLSDEFELAGFKGRPLSFRPWDGQLRQ 308 (347)
T ss_pred HcCCCceecccCCCcceeeCCCccccc
Confidence 998877 47888 5999 4 788764
No 105
>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=95.75 E-value=0.062 Score=57.51 Aligned_cols=103 Identities=13% Similarity=0.223 Sum_probs=71.3
Q ss_pred cCccceEEEEEecC-------CChhHHHHHHHHHhhcCCCCCCCCCCchhHHHHHHHHHHHHHHHHHHcccCCcccccCC
Q 005717 25 ESMQGVLGLRPYIP-------SSKKLEHFKLRWIKSADKPDGSTGGSNLFGLWAYDTVWAIAMAVERAGIENSSFLKSNT 97 (681)
Q Consensus 25 ~~~~Gvlg~~~~~~-------~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~aYDav~~lA~Al~~~~~~~~~~~~~~~ 97 (681)
..++|+++...+.. .++..++|.++++++ ++.. ..++.+...+||++.++++|++++...
T Consensus 247 ~~~~g~~~~~~~~~~~~p~~~~~~~~~~f~~~~~~~--~~~~--~~~~~~~~~~y~a~~~~~~a~~~ag~~--------- 313 (362)
T cd06343 247 EAAEGVIAAAYLKDPTDPAWADDPGVKEFIAFYKKY--FPEG--DPPDTYAVYGYAAAETLVKVLKQAGDD--------- 313 (362)
T ss_pred HhhCceEEEEEecCCCccccccCHHHHHHHHHHHHh--cCCC--CCCchhhhHHHHHHHHHHHHHHHhCCC---------
Confidence 45788888766532 346678899988765 2111 135678899999999999999997411
Q ss_pred CCCCCcccccCCCcchHHHHHHHhccce---ecc-eeeEEE-eCCcccCccEEEEEeeeCC
Q 005717 98 SKSRVDIAALGTFEMGAKLLDTLINTTF---EGL-SGNFHL-VNGQLEPSAFEIFNVIGTS 153 (681)
Q Consensus 98 ~~~~~~~~~~~~~~~G~~l~~~l~~~~f---~Gl-tG~i~F-~~G~~~~~~~~I~n~~~~~ 153 (681)
.++..+.++|.++++ .+. .|++.| .+.++....+.|+++++++
T Consensus 314 -------------~~~~~v~~aL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~ 361 (362)
T cd06343 314 -------------LTRENIMKQAESLKDVLPDLLPGIRINTSPDDHLPIEQMQLMRFEGGR 361 (362)
T ss_pred -------------CCHHHHHHHHHhCCCCCccccCccceecCccccccceeEEEEEEecCc
Confidence 134789999999997 333 358999 4444444567777777654
No 106
>PF13379 NMT1_2: NMT1-like family; PDB: 2G29_A 3UN6_A 2I4C_A 2I49_A 2I4B_A 2I48_A 3QSL_A.
Probab=95.63 E-value=0.044 Score=55.51 Aligned_cols=72 Identities=24% Similarity=0.206 Sum_probs=47.7
Q ss_pred CCCCHHHHHh-----CCCeEEE-ecChhHHHHH---hhhcCCcc---ccccccCChhHHHHHHccCcceEEecchhhHHH
Q 005717 411 SFTDVKDIQK-----NGYFVGY-QTNSFVKDLL---TKKLNFNE---TRLKNYTTSEDYHDALSNGEVAAIFDEIPYIKI 478 (681)
Q Consensus 411 ~i~s~~dL~~-----~~~~vg~-~~~s~~~~~l---~~~~~~~~---~~~~~~~~~~~~~~~l~~g~~~a~i~e~~~~~~ 478 (681)
.+++++||.+ .|.+|++ ..|+..+-.+ .++.+... .+++..+. .+...++.+|++|+++...|+...
T Consensus 105 ~~~~~~dl~~~~~~~kGk~i~~~~~gs~~~~~l~~~l~~~Gl~~~~dv~~~~~~~-~~~~~al~~g~iDa~~~~eP~~~~ 183 (252)
T PF13379_consen 105 DIKSLADLIKKRKAQKGKKIAVPFPGSTHDMLLRYLLKKAGLDPKDDVTLVNVPP-PEMVAALRAGEIDAAVLWEPFASQ 183 (252)
T ss_dssp TTCCGHHHHHTCCSCSTEEEEESSTTSHHHHHHHHHHHHTT--TTTSSEEEE--G-HHHHHHHHTTS-SEEEEETTHHHH
T ss_pred CccCHHHHHhhhcccCCcEEEEcCCCCHHHHHHHHHHHhCCCCcccceEEEecCH-HHHHHHHhCCCcCEEEecCCHHHH
Confidence 6899999943 3789999 4555443322 14445544 34455555 899999999999999998888877
Q ss_pred HHhhc
Q 005717 479 FLASY 483 (681)
Q Consensus 479 ~~~~~ 483 (681)
...+.
T Consensus 184 ~~~~g 188 (252)
T PF13379_consen 184 AEAKG 188 (252)
T ss_dssp HHHTT
T ss_pred HHhcc
Confidence 77555
No 107
>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=95.59 E-value=0.051 Score=53.42 Aligned_cols=58 Identities=22% Similarity=0.284 Sum_probs=39.5
Q ss_pred CCCCHHHHHhCCCeEEEecChhHHHHH---hhhcCCccccccccC-ChhHHHHHHccCcceEEe
Q 005717 411 SFTDVKDIQKNGYFVGYQTNSFVKDLL---TKKLNFNETRLKNYT-TSEDYHDALSNGEVAAIF 470 (681)
Q Consensus 411 ~i~s~~dL~~~~~~vg~~~~s~~~~~l---~~~~~~~~~~~~~~~-~~~~~~~~l~~g~~~a~i 470 (681)
.|+++.||. |++||+..++....++ .+..+++.+.+.... +..+...+|.+|++|+++
T Consensus 84 ~i~~~~DLk--GK~i~v~~~s~~~~~~~~~l~~~g~~~~~v~~v~~~~~~~~~al~~g~vDa~~ 145 (216)
T PF09084_consen 84 GIKSPADLK--GKKIGVSRGSSSEYFLRALLKKNGIDPDDVKIVNLGPPELAQALLSGQVDAAI 145 (216)
T ss_dssp S-SSGGGGT--TSEEEESTTSHHHHHHHHHHHHTTT-GGGSEEEES-HHHHHHHHHTTSSSEEE
T ss_pred CCCCHHHhC--CCEEEEecCcchhHHHHHHHHHhccccccceeeeeehhhhhhhhhcCCCCEEE
Confidence 599999999 9999998876544332 144566555554433 356666799999999988
No 108
>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=95.47 E-value=0.071 Score=43.28 Aligned_cols=56 Identities=21% Similarity=0.338 Sum_probs=47.8
Q ss_pred CCCchhhHHHHHHHHHhccC-cc-cccccchhHHHHHHHHHHHHHHhHhhhhhhheee
Q 005717 349 PQHQIGTIFWFSFSTLVFAH-RE-RVVNNLSRFVLIIWVFVVLILTQSYTASLTSMLT 404 (681)
Q Consensus 349 ~~~~~~~~~~~~~~~l~~~~-~~-~~~s~~~R~l~~~w~~~~lil~s~YtA~L~s~LT 404 (681)
...++.+++|+++.++..-| ++ .|.+..+|++.+++.++++.+.....+.+++.++
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 35689999999999998766 54 5888889999999999999999999999998764
No 109
>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=95.41 E-value=0.12 Score=54.27 Aligned_cols=59 Identities=24% Similarity=0.308 Sum_probs=40.1
Q ss_pred CCCCHHHHHhCCCeEEEec-ChhH----HHHHhhhcCCcccc--ccccCChhHHHHHHccCcceEEecc
Q 005717 411 SFTDVKDIQKNGYFVGYQT-NSFV----KDLLTKKLNFNETR--LKNYTTSEDYHDALSNGEVAAIFDE 472 (681)
Q Consensus 411 ~i~s~~dL~~~~~~vg~~~-~s~~----~~~l~~~~~~~~~~--~~~~~~~~~~~~~l~~g~~~a~i~e 472 (681)
++++++||. ++++++.. ++.. ..++ +..+..... ...+.+..+...++.+|++|+++..
T Consensus 132 ~i~sl~dL~--gk~v~~~~~~s~~~~~~~~~l-~~~G~~~~~~~~v~~~~~~~~~~al~~G~vDa~~~~ 197 (320)
T TIGR02122 132 GIKTVADLK--GKRVAVGAPGSGTELNARAVL-KAAGLTYDDVKKVEYLGYAEAADALKDGKIDAAFYT 197 (320)
T ss_pred CCCcHHHcC--CCEEecCCCCcchHHHHHHHH-HHcCCCHHHccchhcCCHHHHHHHHHCCCccEEEEe
Confidence 578999998 67777653 3322 2333 434443322 3567788889999999999999876
No 110
>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=95.30 E-value=0.12 Score=53.03 Aligned_cols=71 Identities=20% Similarity=0.208 Sum_probs=47.8
Q ss_pred CCCCHHHHHhCCCeEEEecChhHHHHHh---hhcCCcccccc-ccCChhHHHHHHccCcceEEecchhhHHHHHhhc
Q 005717 411 SFTDVKDIQKNGYFVGYQTNSFVKDLLT---KKLNFNETRLK-NYTTSEDYHDALSNGEVAAIFDEIPYIKIFLASY 483 (681)
Q Consensus 411 ~i~s~~dL~~~~~~vg~~~~s~~~~~l~---~~~~~~~~~~~-~~~~~~~~~~~l~~g~~~a~i~e~~~~~~~~~~~ 483 (681)
+|++++||. |++||+..++.....+. +..+.+...+. .+.+..+..+++.+|++|+++...++......+.
T Consensus 92 ~i~s~~dL~--Gk~i~~~~~~~~~~~~~~~l~~~G~~~~~v~~~~~~~~~~~~al~~g~vda~~~~~p~~~~~~~~~ 166 (288)
T TIGR01728 92 PIRTVADLK--GKRIAVPKGGSGHDLLLRALLKAGLSGDDVTILYLGPSDARAAFAAGQVDAWAIWEPWGSALVEEG 166 (288)
T ss_pred CCCCHHHcC--CCEEEecCCccHHHHHHHHHHHcCCCccceeEEecCcHHHHHHHHCCCCCEEEeccchHhHHhhcc
Confidence 688999998 88899877764443331 33344433222 2345678889999999999988777766655443
No 111
>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=95.25 E-value=0.71 Score=44.09 Aligned_cols=73 Identities=10% Similarity=0.085 Sum_probs=49.0
Q ss_pred eehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEEEeeccccccccccceeecceEEEEEecc
Q 005717 225 GFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTTIVANRSTFVDFTLPYSESGVSMLVLVKD 302 (681)
Q Consensus 225 G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~it~~R~~~vdFT~P~~~~~~~~vv~~~~ 302 (681)
.+..+++..+.++.+ .+++++... +.+.+++.|.+|++|++++.......-...+. +.+..+..+++++++..
T Consensus 13 ~~l~~~l~~~~~~~P-~v~i~~~~~---~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~~~-~~~l~~~~~~~~~~~~h 85 (202)
T cd08468 13 AVMPRLMARLEELAP-SVRLNLVHA---EQKLPLDALLAGEIDFALGYSHDDGAEPRLIE-ERDWWEDTYVVIASRDH 85 (202)
T ss_pred HHhHHHHHHHHhhCC-CCEEEEEEC---ChHhHHHHHHCCCccEEEecccccccCCCCEE-EEEEecCcEEEEEeCCC
Confidence 456788889988875 256777764 78999999999999999864321100012233 34677777778877554
No 112
>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=94.82 E-value=1.1 Score=45.42 Aligned_cols=122 Identities=13% Similarity=0.051 Sum_probs=66.6
Q ss_pred CCCCCHHHHHhCCCeEEEecChhHHH----HHhhhcCCc------------------cccccccC-ChhHHHHHHccCcc
Q 005717 410 PSFTDVKDIQKNGYFVGYQTNSFVKD----LLTKKLNFN------------------ETRLKNYT-TSEDYHDALSNGEV 466 (681)
Q Consensus 410 ~~i~s~~dL~~~~~~vg~~~~s~~~~----~l~~~~~~~------------------~~~~~~~~-~~~~~~~~l~~g~~ 466 (681)
..+++++||.+ |.+|++..+..... .| ++.++- ...+.... ...+...++.+|++
T Consensus 106 ~~~~sl~dlk~-G~~IAip~d~~n~~raL~~L-~~aGLi~l~~~~~~~~t~~DI~~n~~~v~~vel~~~~~~~al~~g~v 183 (258)
T TIGR00363 106 KKIKNVNELQD-GAKVAVPNDPTNLGRALLLL-QKQGLIKLKDGNGLLPTVLDIVENPKKLNITELETSQLPRALDDPKV 183 (258)
T ss_pred cCCCCHHHcCC-CCEEEEeCCcchHHHHHHHH-HHcCCceecCCCCCcCChhhhhcCCCCCEEEEcCHHHHHHHhhcccc
Confidence 37999999953 78899986543222 34 433431 22222211 34567788899999
Q ss_pred eEEecchhhHHHHHhhcCCceEEECcccccCCcEEEecCCCCChHHHHHHHHhhccCccHHHHHHHHH
Q 005717 467 AAIFDEIPYIKIFLASYCSRYMMVGPTYRTDGFGFAFPLGSPLVPYISRAILKVTEDKEKMENIEKAL 534 (681)
Q Consensus 467 ~a~i~e~~~~~~~~~~~c~~l~~v~~~~~~~~~~~~~~k~spl~~~in~~Il~l~e~~G~l~~i~~kw 534 (681)
|+++...+++.-.-...-++-......-...--.++++.+.-=.+.+.+.+..++.. ..-+.|.++|
T Consensus 184 Daa~v~~~~~~~agl~~~~~~i~~e~~~~~~~n~l~~r~~~~~~~~~~~lv~~~~s~-~v~~~i~~~~ 250 (258)
T TIGR00363 184 DLAVINTTYAGQVGLNPQDDGVFVEDKDSPYVNIIVSREDNKDAENVKDFIQSYQSE-EVYQAAQKHF 250 (258)
T ss_pred cEEEEChHHHHHcCCCcCcCceeecCCCCCeeEEEEEcCCccCCHHHHHHHHHHcCH-HHHHHHHHHc
Confidence 999887765543311111111111111112223566666533456677777777766 5555565553
No 113
>cd05466 PBP2_LTTR_substrate The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily. This model and hierarchy represent the the substrate-binding domain of the LysR-type transcriptional regulators that form the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA bin
Probab=94.78 E-value=1.4 Score=40.95 Aligned_cols=70 Identities=17% Similarity=0.147 Sum_probs=47.7
Q ss_pred eehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEEEeeccccccccccceeecceEEEEEecc
Q 005717 225 GFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTTIVANRSTFVDFTLPYSESGVSMLVLVKD 302 (681)
Q Consensus 225 G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~it~~R~~~vdFT~P~~~~~~~~vv~~~~ 302 (681)
.+..++++.+.++.+ ++++++... ....++..|.+|++|++++.... ....++ ..++....+++++++..
T Consensus 13 ~~l~~~i~~~~~~~p-~i~i~~~~~---~~~~~~~~l~~g~~D~~i~~~~~---~~~~~~-~~~l~~~~~~~~~~~~~ 82 (197)
T cd05466 13 YLLPPLLAAFRQRYP-GVELSLVEG---GSSELLEALLEGELDLAIVALPV---DDPGLE-SEPLFEEPLVLVVPPDH 82 (197)
T ss_pred HHhHHHHHHHHHHCC-CCEEEEEEC---ChHHHHHHHHcCCceEEEEcCCC---CCCcce-EeeeeccceEEEecCCC
Confidence 455677788877765 356777665 66789999999999999864332 222233 44666777777777553
No 114
>PF03466 LysR_substrate: LysR substrate binding domain; InterPro: IPR005119 The structure of this domain is known and is similar to the periplasmic binding proteins []. This domain is found in members of the LysR family of prokaryotic transcriptional regulatory proteins IPR000847 from INTERPRO which share sequence similarities over approximately 280 residues including a putative helix-turn-helix DNA-binding motif at their N terminus.; PDB: 3ONM_B 3FZJ_J 3FXR_B 3N6T_A 3FXQ_A 3FXU_A 3N6U_A 2QSX_B 3HO7_B 1IZ1_B ....
Probab=94.54 E-value=0.85 Score=43.57 Aligned_cols=183 Identities=14% Similarity=0.141 Sum_probs=114.6
Q ss_pred eehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEEEeeccccccccccceeecceEEEEEeccCC
Q 005717 225 GFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTTIVANRSTFVDFTLPYSESGVSMLVLVKDDE 304 (681)
Q Consensus 225 G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~it~~R~~~vdFT~P~~~~~~~~vv~~~~~~ 304 (681)
.+-.+++..+.+..+- +++++... +...++..|.+|++|++++.... ....+. ..|+....+++++++....
T Consensus 19 ~~l~~~l~~~~~~~P~-i~i~~~~~---~~~~~~~~l~~g~~Dl~i~~~~~---~~~~~~-~~~l~~~~~~~~~~~~~pl 90 (209)
T PF03466_consen 19 SLLPPLLAEFRERHPN-IRIEIREG---DSDELIEALRSGELDLAITFGPP---PPPGLE-SEPLGEEPLVLVVSPDHPL 90 (209)
T ss_dssp HTHHHHHHHHHHHSTT-EEEEEEEE---SHHHHHHHHHTTSSSEEEESSSS---SSTTEE-EEEEEEEEEEEEEETTSGG
T ss_pred HHHHHHHHHHHHHCCC-cEEEEEec---cchhhhHHHhcccccEEEEEeec---cccccc-cccccceeeeeeeeccccc
Confidence 4556888888888773 56666664 77899999999999999764332 222222 4678888899998866421
Q ss_pred CcCceeeeccCcHhHHHHHHHHHHHHHHHhhhhhcccCCCCCCCCCCchhhHHHHHHHHHhccCcccccccchhHHHHHH
Q 005717 305 RKNFWIFLKPLSWDLWLTTGAAFIFTGLVVWVLEHRINTEFRGPPQHQIGTIFWFSFSTLVFAHRERVVNNLSRFVLIIW 384 (681)
Q Consensus 305 ~~~~~~fl~PF~~~vW~~i~~~~~~v~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~s~~~R~l~~~w 384 (681)
.
T Consensus 91 ~------------------------------------------------------------------------------- 91 (209)
T PF03466_consen 91 A------------------------------------------------------------------------------- 91 (209)
T ss_dssp G-------------------------------------------------------------------------------
T ss_pred c-------------------------------------------------------------------------------
Confidence 1
Q ss_pred HHHHHHHHhHhhhhhhheeeecccCCCCCCHHHHHhCCCeEEE-ecChhHHHHHh---hhcCCccccccccCChhHHHHH
Q 005717 385 VFVVLILTQSYTASLTSMLTVQRLQPSFTDVKDIQKNGYFVGY-QTNSFVKDLLT---KKLNFNETRLKNYTTSEDYHDA 460 (681)
Q Consensus 385 ~~~~lil~s~YtA~L~s~LT~~~~~~~i~s~~dL~~~~~~vg~-~~~s~~~~~l~---~~~~~~~~~~~~~~~~~~~~~~ 460 (681)
+ ..++ +++||. +.++.. ..+......+. ++.++........++.+.....
T Consensus 92 ----------------------~-~~~i-~~~dL~--~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 145 (209)
T PF03466_consen 92 ----------------------Q-KKPI-TLEDLA--DYPLILLSPGSPYRDQLDRWLREHGFSPNIVIEVDSFESILSL 145 (209)
T ss_dssp ----------------------T-TSSS-SGGGGT--TSEEEEESTTTSHHHHHHHHHHHTTEEEEEEEEESSHHHHHHH
T ss_pred ----------------------c-cccc-hhhhhh--hccccccccccccccccccccccccccccccccccchhhhccc
Confidence 0 0134 789998 454443 33443333331 3334544445567889999999
Q ss_pred HccCcceEEecchhhHHHHHhhcCCceEEECc-ccccCCcEEEecCCCCChHHHHHHHHhhcc
Q 005717 461 LSNGEVAAIFDEIPYIKIFLASYCSRYMMVGP-TYRTDGFGFAFPLGSPLVPYISRAILKVTE 522 (681)
Q Consensus 461 l~~g~~~a~i~e~~~~~~~~~~~c~~l~~v~~-~~~~~~~~~~~~k~spl~~~in~~Il~l~e 522 (681)
+.+|..-+++.+.....+...... ....+.+ .+. ..++++.+++.+....+...+..+++
T Consensus 146 v~~g~gi~~~p~~~~~~~~~~~~l-~~~~~~~~~~~-~~~~l~~~~~~~~~~~~~~~~~~l~~ 206 (209)
T PF03466_consen 146 VASGDGIAILPDSLAQDELESGEL-VFLPLPDPPLP-RPIYLVWRKDRPLSPAIQWFIDLLRE 206 (209)
T ss_dssp HHTTSEBEEEEHHHHHHHHHCTTE-EEEEESSSTEE-EEEEEEEETTGTTHHHHHHHHHHHHH
T ss_pred cccccceeecCcccccccccCCCE-EEEECCCCCCc-eEEEEEEECCCCCCHHHHHHHHHHHH
Confidence 988876666655433333322222 1123344 444 77889999998877777766666554
No 115
>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=94.37 E-value=0.078 Score=56.24 Aligned_cols=76 Identities=20% Similarity=0.257 Sum_probs=49.1
Q ss_pred CccceEEEEEecCCChhHHHHHHHHHhh-cCCCCCCCCCC-chhHHHHHHHHHHHHHHHHHHcccCCcccccCCCCCCCc
Q 005717 26 SMQGVLGLRPYIPSSKKLEHFKLRWIKS-ADKPDGSTGGS-NLFGLWAYDTVWAIAMAVERAGIENSSFLKSNTSKSRVD 103 (681)
Q Consensus 26 ~~~Gvlg~~~~~~~~~~~~~f~~~~~~~-~~~~~~~~~~~-~~~~~~aYDav~~lA~Al~~~~~~~~~~~~~~~~~~~~~ 103 (681)
..+|++...+.. ....+|.++|+++ .+ .+ +.+++.+|||+.+++.++++....
T Consensus 251 ~~~g~~~~~~~~---~~~~~f~~~y~~~~~~-------~p~~~~~a~~YDa~~l~~~~~~~~~~~--------------- 305 (336)
T cd06339 251 DLNGAWFADPPW---LLDANFELRYRAAYGW-------PPLSRLAALGYDAYALAAALAQLGQGD--------------- 305 (336)
T ss_pred ccCCcEEeCCCc---ccCcchhhhHHHHhcC-------CCCchHHHHHHhHHHHHHHHHHccccc---------------
Confidence 456766544311 1223677777765 32 24 678999999999999877764210
Q ss_pred ccccCCCcchHHHHHHHhc-cceecceeeEEE-eCCccc
Q 005717 104 IAALGTFEMGAKLLDTLIN-TTFEGLSGNFHL-VNGQLE 140 (681)
Q Consensus 104 ~~~~~~~~~G~~l~~~l~~-~~f~GltG~i~F-~~G~~~ 140 (681)
. +|.+ ..|+|++|.+.| .+|+..
T Consensus 306 --------~------al~~~~~~~g~~G~~~f~~~g~~~ 330 (336)
T cd06339 306 --------A------ALTPGAGFSGVTGVLRLDPDGVIE 330 (336)
T ss_pred --------c------ccCCCCccccCcceEEECCCCeEE
Confidence 0 3333 468999999999 778753
No 116
>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=94.05 E-value=0.15 Score=51.77 Aligned_cols=105 Identities=12% Similarity=0.121 Sum_probs=66.6
Q ss_pred CCCCCHHHHHhCCCeEEEecChhHHHHHhhhcCCccccccccCChhHHHHHHccCcceEEecchhhHHHH-HhhcCCceE
Q 005717 410 PSFTDVKDIQKNGYFVGYQTNSFVKDLLTKKLNFNETRLKNYTTSEDYHDALSNGEVAAIFDEIPYIKIF-LASYCSRYM 488 (681)
Q Consensus 410 ~~i~s~~dL~~~~~~vg~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~g~~~a~i~e~~~~~~~-~~~~c~~l~ 488 (681)
.+|++++||. |.++.+..++.....+ +.++. ..+ ..+..+...+|.+|.+|+++.....+..+ +.+.++.++
T Consensus 126 ~~i~s~~Dl~--G~kir~~~~~~~~~~~-~~~Ga---~~v-~~~~~e~~~aL~~G~vDg~~~~~~~~~~~~~~ev~~y~~ 198 (257)
T TIGR00787 126 KPITKPEDLK--GLKIRIPNSPMNEAQF-KALGA---NPE-PMAFSEVYTALQTGVVDGQENPLSNVYSSKFYEVQKYLS 198 (257)
T ss_pred CccCChHHhC--CCEEecCCCHHHHHHH-HHcCC---ccc-ccCHHHHHHHHHcCCcccccCCHHHHhhcchhhhcchhe
Confidence 5799999999 9999998777777777 55543 222 56778999999999999988764433221 111142333
Q ss_pred EECcccccCCcEEEecCC--CCChHHHHHHHHhhccC
Q 005717 489 MVGPTYRTDGFGFAFPLG--SPLVPYISRAILKVTED 523 (681)
Q Consensus 489 ~v~~~~~~~~~~~~~~k~--spl~~~in~~Il~l~e~ 523 (681)
..+ .......+.+.++ ..|-+....+|....+.
T Consensus 199 ~~~--~~~~~~~~~~n~~~~~~L~~e~q~~i~~a~~~ 233 (257)
T TIGR00787 199 MTN--HGYLGYLVVVNKAFWKSLPPDLQAVVKEAAKE 233 (257)
T ss_pred ecC--CcccceEEEEeHHHHhcCCHHHHHHHHHHHHH
Confidence 332 2234556777776 22666666666555443
No 117
>cd08459 PBP2_DntR_NahR_LinR_like The C-terminal substrate binding domain of LysR-type transcriptional regulators that are involved in the catabolism of dinitrotoluene, naphthalene and gamma-hexachlorohexane; contains the type 2 periplasmic binding fold. This CD includes LysR-like bacterial transcriptional regulators, DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. DntR from Burkholderia species controls genes encoding enzymes for oxidative degradation of the nitro-aromatic compound 2,4-dinitrotoluene. The active form of DntR is homotetrameric, consisting of a dimer of dimers. NahR is a salicylate-dependent transcription activator of the nah and sal operons for naphthalene degradation. Salicylic acid is an intermediate o
Probab=93.94 E-value=1.7 Score=41.14 Aligned_cols=70 Identities=21% Similarity=0.103 Sum_probs=48.3
Q ss_pred eehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEEEeeccccccccccceeecceEEEEEecc
Q 005717 225 GFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTTIVANRSTFVDFTLPYSESGVSMLVLVKD 302 (681)
Q Consensus 225 G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~it~~R~~~vdFT~P~~~~~~~~vv~~~~ 302 (681)
.+-.+++..+.++.+- +++++... +.+.+...|.+|++|+++..... ....+. +.|.....+++++++..
T Consensus 13 ~~l~~~l~~~~~~~P~-v~v~i~~~---~~~~~~~~l~~g~~D~~i~~~~~---~~~~l~-~~~l~~~~~~~v~~~~~ 82 (201)
T cd08459 13 YFLPRLLAALREVAPG-VRIETVRL---PVDELEEALESGEIDLAIGYLPD---LGAGFF-QQRLFRERYVCLVRKDH 82 (201)
T ss_pred HHHHHHHHHHHHHCCC-CeEEEEec---CccCHHHHhhCCCceEEEEcCCC---Ccccce-EEEeecCceEEEEcCCC
Confidence 4556888888888763 56677653 66789999999999999863221 122232 46777888888877553
No 118
>cd08463 PBP2_DntR_like_4 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold. This CD includes an uncharacterized LysR-type transcriptional regulator similar to DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytra
Probab=93.77 E-value=3.3 Score=39.63 Aligned_cols=71 Identities=13% Similarity=0.125 Sum_probs=49.2
Q ss_pred eehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEEEeeccccccccccceeecceEEEEEecc
Q 005717 225 GFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTTIVANRSTFVDFTLPYSESGVSMLVLVKD 302 (681)
Q Consensus 225 G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~it~~R~~~vdFT~P~~~~~~~~vv~~~~ 302 (681)
.+-.+++.++.+..+- +.+++... ++.++++..|.+|++|+++..... ....++ ..|+.+...++++++..
T Consensus 13 ~~~~~~l~~~~~~~P~-~~v~~~~~--~~~~~l~~~L~~g~lDl~i~~~~~---~~~~l~-~~~l~~~~~~lv~~~~h 83 (203)
T cd08463 13 LFLPELVARFRREAPG-ARLEIHPL--GPDFDYERALASGELDLVIGNWPE---PPEHLH-LSPLFSDEIVCLMRADH 83 (203)
T ss_pred HHhHHHHHHHHHHCCC-CEEEEEeC--CcchhHHHHHhcCCeeEEEecccc---CCCCcE-EeEeecCceEEEEeCCC
Confidence 5667889999888763 56777653 356889999999999999863211 112232 35677788888887664
No 119
>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=93.63 E-value=0.27 Score=52.29 Aligned_cols=85 Identities=25% Similarity=0.324 Sum_probs=58.2
Q ss_pred CccceEEEEEecC---CChhHHHHHHHHHhh-cCCCCCCCCCCchhHHHHHHHHHHHHHHHHHHcccCCcccccCCCCCC
Q 005717 26 SMQGVLGLRPYIP---SSKKLEHFKLRWIKS-ADKPDGSTGGSNLFGLWAYDTVWAIAMAVERAGIENSSFLKSNTSKSR 101 (681)
Q Consensus 26 ~~~Gvlg~~~~~~---~~~~~~~f~~~~~~~-~~~~~~~~~~~~~~~~~aYDav~~lA~Al~~~~~~~~~~~~~~~~~~~ 101 (681)
.++|+++...+.+ .++..++|.++|+++ ...+.. +..++.+++++||+++++++|++++...
T Consensus 240 ~~~g~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~-~~~~~~~~~~aYd~~~~l~~A~~~ag~~------------- 305 (347)
T cd06335 240 AANDALMIQTFIFEPPSNPKAKAFLAAYHKKYPEKKPA-DIPAPVGAAHAYDAVHLLAAAIKQAGST------------- 305 (347)
T ss_pred hhcCcEEEEeeccccCCCHHHHHHHHHHHHHhCCCccc-ccCcchhHHHHHHHHHHHHHHHHHhcCC-------------
Confidence 4688877766543 456789999999987 321111 1124556788999999999999997521
Q ss_pred CcccccCCCcchHHHHHHHhcc--ceecceeeE--EE
Q 005717 102 VDIAALGTFEMGAKLLDTLINT--TFEGLSGNF--HL 134 (681)
Q Consensus 102 ~~~~~~~~~~~G~~l~~~l~~~--~f~GltG~i--~F 134 (681)
.+..+.++|.++ .+.|+.|.+ .|
T Consensus 306 ----------~~~~v~~al~~~~~~~~G~~~~~~~~~ 332 (347)
T cd06335 306 ----------DGRAIKRALENLKKPVEGLVKTYDKPF 332 (347)
T ss_pred ----------CHHHHHHHHHhccCCceeeecccCCCC
Confidence 225788888865 467888854 56
No 120
>cd08418 PBP2_TdcA The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is involved in the degradation of L-serine and L-threonine, contains the type 2 periplasmic binding fold. TdcA, a member of the LysR family, activates the expression of the anaerobically-regulated tdcABCDEFG operon which is involved in the degradation of L-serine and L-threonine to acetate and propionate, respectively. The tdc operon is comprised of one regulatory gene tdcA and six structural genes, tdcB to tdcG. The expression of the tdc operon is affected by several transcription factors including the cAMP receptor protein (CRP), integration host factor (IHF), histone-like protein (HU), and the operon specific regulators TdcA and TcdR. TcdR is divergently transcribed from the operon and encodes a small protein that is required for efficient expression of the Escherichia coli tdc operon. This substrate-binding domain shows significant homology to the type 2 periplasmic binding
Probab=93.60 E-value=3.1 Score=39.19 Aligned_cols=71 Identities=11% Similarity=0.071 Sum_probs=47.0
Q ss_pred eehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEEEeeccccccccccceeecceEEEEEec
Q 005717 225 GFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTTIVANRSTFVDFTLPYSESGVSMLVLVK 301 (681)
Q Consensus 225 G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~it~~R~~~vdFT~P~~~~~~~~vv~~~ 301 (681)
.+-.+++..+.+..+ .+++++... +...+..+|.+|++|++++..... .....+. ..|.....++++++..
T Consensus 13 ~~l~~~l~~~~~~~P-~i~l~i~~~---~~~~~~~~l~~g~~Dl~i~~~~~~-~~~~~~~-~~~l~~~~~~~v~~~~ 83 (201)
T cd08418 13 TLMPAVINRFKEQFP-DVQISIYEG---QLSSLLPELRDGRLDFAIGTLPDE-MYLKELI-SEPLFESDFVVVARKD 83 (201)
T ss_pred hhhHHHHHHHHHHCC-CceEEEEeC---cHHHHHHHHHcCCCcEEEEecCCC-CCCccee-EEeecCCceEEEeCCC
Confidence 455678888888876 356777654 678999999999999998632111 1112232 3566667777777654
No 121
>PF13433 Peripla_BP_5: Periplasmic binding protein domain; PDB: 1QNL_A 1QO0_A 1PEA_A.
Probab=93.51 E-value=0.45 Score=50.16 Aligned_cols=81 Identities=23% Similarity=0.267 Sum_probs=59.2
Q ss_pred CccceEEEEEecCC--ChhHHHHHHHHHhh-cCCCCCCCCCCchhHHHHHHHHHHHHHHHHHHcccCCcccccCCCCCCC
Q 005717 26 SMQGVLGLRPYIPS--SKKLEHFKLRWIKS-ADKPDGSTGGSNLFGLWAYDTVWAIAMAVERAGIENSSFLKSNTSKSRV 102 (681)
Q Consensus 26 ~~~Gvlg~~~~~~~--~~~~~~f~~~~~~~-~~~~~~~~~~~~~~~~~aYDav~~lA~Al~~~~~~~~~~~~~~~~~~~~ 102 (681)
...|.+...+|... ++.-++|.++|+++ .+ +...+...--||-+|.++|+|+++++..
T Consensus 238 ~~~Gh~~~~~YFqsidtp~N~~Fv~~~~~~~g~-----~~v~s~~~eaaY~~v~l~a~Av~~ags~-------------- 298 (363)
T PF13433_consen 238 AAAGHYTSAPYFQSIDTPENQAFVARFRARYGD-----DRVTSDPMEAAYFQVHLWAQAVEKAGSD-------------- 298 (363)
T ss_dssp HHTT-EEEES--TT-SSHHHHHHHHHHHTTS-T-----T----HHHHHHHHHHHHHHHHHHHHTS---------------
T ss_pred hcCCcEEeehhhhhCCcHHHHHHHHHHHHHhCC-----CCCCCcHHHHHHHHHHHHHHHHHHhCCC--------------
Confidence 57899999998755 56789999999986 22 1135666777999999999999998632
Q ss_pred cccccCCCcchHHHHHHHhccceecceeeEEE
Q 005717 103 DIAALGTFEMGAKLLDTLINTTFEGLSGNFHL 134 (681)
Q Consensus 103 ~~~~~~~~~~G~~l~~~l~~~~f~GltG~i~F 134 (681)
+-..+.++|...+|+...|.+.+
T Consensus 299 ---------d~~~vr~al~g~~~~aP~G~v~i 321 (363)
T PF13433_consen 299 ---------DPEAVREALAGQSFDAPQGRVRI 321 (363)
T ss_dssp ----------HHHHHHHHTT--EEETTEEEEE
T ss_pred ---------CHHHHHHHhcCCeecCCCcceEE
Confidence 34789999999999999999999
No 122
>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=93.36 E-value=2.6 Score=39.69 Aligned_cols=70 Identities=19% Similarity=0.168 Sum_probs=47.2
Q ss_pred eehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEEEeeccccccccccceeecceEEEEEecc
Q 005717 225 GFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTTIVANRSTFVDFTLPYSESGVSMLVLVKD 302 (681)
Q Consensus 225 G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~it~~R~~~vdFT~P~~~~~~~~vv~~~~ 302 (681)
.+..+++..+.++.+ .+.+++.. ++.+.+...|.+|++|+++... +.....+. ..|+....++++++...
T Consensus 13 ~~~~~~i~~~~~~~P-~i~l~~~~---~~~~~~~~~l~~g~~D~~i~~~---~~~~~~~~-~~~l~~~~~~~v~~~~~ 82 (200)
T cd08417 13 LLLPPLLARLRQEAP-GVRLRFVP---LDRDDLEEALESGEIDLAIGVF---PELPPGLR-SQPLFEDRFVCVARKDH 82 (200)
T ss_pred HHHHHHHHHHHhhCC-CeEEEecc---CCHHHHHHHHHcCCCCEEEeec---ccCCCccc-hhhhhcCceEEEecCCC
Confidence 445677788887765 24455554 3778999999999999998632 22222232 36777888888887553
No 123
>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=93.09 E-value=2.8 Score=39.76 Aligned_cols=69 Identities=14% Similarity=0.106 Sum_probs=45.2
Q ss_pred eehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEEEeeccccccccccceeecceEEEEEecc
Q 005717 225 GFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTTIVANRSTFVDFTLPYSESGVSMLVLVKD 302 (681)
Q Consensus 225 G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~it~~R~~~vdFT~P~~~~~~~~vv~~~~ 302 (681)
.+-..++..+.+..+ .+.+++... +. +++..|.+|++|++++.-. .....+. ..|+....+++++++..
T Consensus 13 ~~l~~~i~~~~~~~P-~i~l~i~~~---~~-~~~~~l~~g~~D~~i~~~~---~~~~~~~-~~~l~~~~~~~v~~~~h 81 (200)
T cd08462 13 VLLPPVIERVAREAP-GVRFELLPP---DD-QPHELLERGEVDLLIAPER---FMSDGHP-SEPLFEEEFVCVVWADN 81 (200)
T ss_pred HHHHHHHHHHHHHCC-CCEEEEecC---Ch-hHHHHHhcCCeeEEEecCC---CCCCCce-eeeeeccceEEEEcCCC
Confidence 344567777877765 255666653 45 8999999999999986321 1112232 34777778888876554
No 124
>PRK11480 tauA taurine transporter substrate binding subunit; Provisional
Probab=92.97 E-value=0.46 Score=50.03 Aligned_cols=64 Identities=13% Similarity=0.160 Sum_probs=44.8
Q ss_pred CCCCHHHHHhCCCeEEEecChhHHH----HHhhhcCCccccccccC-ChhHHHHHHccCcceEEecchhhHH
Q 005717 411 SFTDVKDIQKNGYFVGYQTNSFVKD----LLTKKLNFNETRLKNYT-TSEDYHDALSNGEVAAIFDEIPYIK 477 (681)
Q Consensus 411 ~i~s~~dL~~~~~~vg~~~~s~~~~----~l~~~~~~~~~~~~~~~-~~~~~~~~l~~g~~~a~i~e~~~~~ 477 (681)
.|++++||. |++||+..++.... +| +..+.+.+.+.... ...+...++.+|++|+++...++..
T Consensus 113 ~I~s~~DLk--GK~Iav~~~s~~~~~l~~~L-~~~Gl~~~dv~~v~~~~~~~~~Al~~G~VDAa~~~~p~~~ 181 (320)
T PRK11480 113 TISKPEDLI--GKRIAVPFISTTHYSLLAAL-KHWGIKPGQVEIVNLQPPAIIAAWQRGDIDGAYVWAPAVN 181 (320)
T ss_pred CCCChHHcC--CCEEecCCCCchHHHHHHHH-HHcCCCHhheEEEECCcHHHHHHHHcCCcCEEEEcchHHH
Confidence 599999998 99999976654433 34 44555544443222 3567889999999999887666654
No 125
>PRK11151 DNA-binding transcriptional regulator OxyR; Provisional
Probab=92.62 E-value=3.8 Score=42.48 Aligned_cols=83 Identities=16% Similarity=0.157 Sum_probs=56.1
Q ss_pred ceEEEEeeccCCccceEEEeecCCCCeeEEeehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEE
Q 005717 195 RKLKIGVPVREGFTEFIKVVENKNKTTQVSGFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTT 274 (681)
Q Consensus 195 ~~lrV~v~~~~p~~~~~~~~~~~~~~~~~~G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~ 274 (681)
+.++|++..... .++-..++..+.+..+- +.+++... +-++++++|.+|++|+++....
T Consensus 91 g~l~i~~~~~~~-----------------~~~~~~~l~~~~~~~P~-v~i~~~~~---~~~~~~~~l~~g~~Dl~i~~~~ 149 (305)
T PRK11151 91 GPLHIGLIPTVG-----------------PYLLPHIIPMLHQTFPK-LEMYLHEA---QTHQLLAQLDSGKLDCAILALV 149 (305)
T ss_pred ceEEEEecchhH-----------------HHHHHHHHHHHHHHCCC-cEEEEEeC---CHHHHHHHHHcCCccEEEEecC
Confidence 578888765211 24455777788877653 56666654 6789999999999999986432
Q ss_pred EeeccccccccccceeecceEEEEEecc
Q 005717 275 IVANRSTFVDFTLPYSESGVSMLVLVKD 302 (681)
Q Consensus 275 it~~R~~~vdFT~P~~~~~~~~vv~~~~ 302 (681)
.. ...+ .+.|+....+++++++..
T Consensus 150 ~~---~~~l-~~~~l~~~~~~~~~~~~h 173 (305)
T PRK11151 150 KE---SEAF-IEVPLFDEPMLLAVYEDH 173 (305)
T ss_pred CC---CCCe-EEEEeccCcEEEEecCCC
Confidence 21 1122 357888888888887654
No 126
>cd08421 PBP2_LTTR_like_1 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold. LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functi
Probab=92.31 E-value=6.3 Score=36.91 Aligned_cols=70 Identities=10% Similarity=0.131 Sum_probs=48.1
Q ss_pred eehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEEEeeccccccccccceeecceEEEEEecc
Q 005717 225 GFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTTIVANRSTFVDFTLPYSESGVSMLVLVKD 302 (681)
Q Consensus 225 G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~it~~R~~~vdFT~P~~~~~~~~vv~~~~ 302 (681)
.+-.+++..+.+..+ .+++++... +..+++..|.+|++|+++... +.....+. ..+.....+++++++..
T Consensus 13 ~~l~~~l~~~~~~~P-~i~i~~~~~---~~~~~~~~l~~~~~D~~i~~~---~~~~~~~~-~~~l~~~~~~~v~~~~~ 82 (198)
T cd08421 13 EFLPEDLASFLAAHP-DVRIDLEER---LSADIVRAVAEGRADLGIVAG---NVDAAGLE-TRPYRTDRLVVVVPRDH 82 (198)
T ss_pred hhhHHHHHHHHHHCC-CceEEEEec---CcHHHHHHHhcCCceEEEEec---CCCCCCcE-EEEeecCcEEEEeCCCC
Confidence 345688888888865 356666653 678899999999999988632 22223333 36777788888877553
No 127
>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=92.06 E-value=0.56 Score=49.64 Aligned_cols=81 Identities=17% Similarity=0.089 Sum_probs=55.8
Q ss_pred cCccceEEEEEecCC---ChhHHHHHHHHHhhcCCCCCCCCCCchhHHHHHHHHHHHHHHHHHHcccCCcccccCCCCCC
Q 005717 25 ESMQGVLGLRPYIPS---SKKLEHFKLRWIKSADKPDGSTGGSNLFGLWAYDTVWAIAMAVERAGIENSSFLKSNTSKSR 101 (681)
Q Consensus 25 ~~~~Gvlg~~~~~~~---~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~aYDav~~lA~Al~~~~~~~~~~~~~~~~~~~ 101 (681)
...+|++...++.|. .+..+.|.+.+++. .......++.+++.+||+++++++|+++++..
T Consensus 234 ~~~~g~~~~~~~~~~~~~~p~~~~~~~~~~~~---~~~~~~~~~~~~~~~yda~~~~~~a~~~ag~~------------- 297 (341)
T cd06341 234 PALAGVYIAVFYRPFESGTPAVALYLAAMARY---APQLDPPEQGFALIGYIAADLFLRGLSGAGGC------------- 297 (341)
T ss_pred cccCceEEEeeeccccCCCHHHHHHHHHHHHh---CCCCCCCcchHHHHHHHHHHHHHHHHHhcCCC-------------
Confidence 467998888877653 45677777655532 11112246779999999999999999997521
Q ss_pred CcccccCCCcchHH-HHHHHhccceeccee
Q 005717 102 VDIAALGTFEMGAK-LLDTLINTTFEGLSG 130 (681)
Q Consensus 102 ~~~~~~~~~~~G~~-l~~~l~~~~f~GltG 130 (681)
.+.+. +.++|.+++.....|
T Consensus 298 ---------~~~~~~v~~al~~~~~~~~~g 318 (341)
T cd06341 298 ---------PTRASQFLRALRAVTDYDAGG 318 (341)
T ss_pred ---------CChHHHHHHHhhcCCCCCCCC
Confidence 12355 999999997654434
No 128
>PRK11063 metQ DL-methionine transporter substrate-binding subunit; Provisional
Probab=91.90 E-value=4.8 Score=41.19 Aligned_cols=121 Identities=14% Similarity=0.111 Sum_probs=62.1
Q ss_pred CCCCHHHHHhCCCeEEEec-ChhHH---HHHhhhcCC------------------ccccccccC-ChhHHHHHHccCcce
Q 005717 411 SFTDVKDIQKNGYFVGYQT-NSFVK---DLLTKKLNF------------------NETRLKNYT-TSEDYHDALSNGEVA 467 (681)
Q Consensus 411 ~i~s~~dL~~~~~~vg~~~-~s~~~---~~l~~~~~~------------------~~~~~~~~~-~~~~~~~~l~~g~~~ 467 (681)
.|++++||.+ |.+|++.. .+... .+| ++.++ .+.++...+ ...+...++.+|++|
T Consensus 120 ~i~si~DL~~-Gk~IAip~d~~n~~r~L~lL-~~~Gli~l~~~~~~~~t~~di~~n~~~v~~v~~~~~~~~~al~~g~vD 197 (271)
T PRK11063 120 KIKSLDELQD-GSQVAVPNDPTNLGRSLLLL-QKVGLIKLKDGVGLLPTVLDIVENPKNLKIVELEAPQLPRSLDDAQIA 197 (271)
T ss_pred CCCCHHHhcC-CCEEEecCCCccHHHHHHHH-HHCCCEEecCCCCCCCCHHHHhcCCCCCEEEECcHHHHHHhccccccc
Confidence 5899999953 78899875 22222 233 33232 111222221 345677888999999
Q ss_pred EEecchhhHHHHHhhcCCceEEECcccccCCcEEEecCCCCChHHHHHHHHhhccCccHHHHHHHHH
Q 005717 468 AIFDEIPYIKIFLASYCSRYMMVGPTYRTDGFGFAFPLGSPLVPYISRAILKVTEDKEKMENIEKAL 534 (681)
Q Consensus 468 a~i~e~~~~~~~~~~~c~~l~~v~~~~~~~~~~~~~~k~spl~~~in~~Il~l~e~~G~l~~i~~kw 534 (681)
+++...+++.-.-....++-....+.-...--.+++++...=.+.+.+.+.-++.. ..-+.++++|
T Consensus 198 aa~i~~~~a~~a~~~~~~~~l~~e~~~~~~~~~~~v~~~~~~~~~~~~l~~a~~s~-~v~~~i~~~~ 263 (271)
T PRK11063 198 LAVINTTYASQIGLTPAKDGIFVEDKDSPYVNLIVAREDNKDAENVKKFVQAYQSD-EVYEAANKVF 263 (271)
T ss_pred EEEEChHHHHHcCCCCCCCeeEECCCCCCeEEEEEECCcccCCHHHHHHHHHHcCH-HHHHHHHHHc
Confidence 99888776654322111121222211111123566666544334555555555544 4445555553
No 129
>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=91.72 E-value=0.65 Score=49.59 Aligned_cols=100 Identities=13% Similarity=0.075 Sum_probs=63.3
Q ss_pred cCccceEEEEEecC--CChhHHHHHHHHHhh-cCCCCCCCCCCchhHHHHHHHHHHHHHHHHHHcccCCcccccCCCCCC
Q 005717 25 ESMQGVLGLRPYIP--SSKKLEHFKLRWIKS-ADKPDGSTGGSNLFGLWAYDTVWAIAMAVERAGIENSSFLKSNTSKSR 101 (681)
Q Consensus 25 ~~~~Gvlg~~~~~~--~~~~~~~f~~~~~~~-~~~~~~~~~~~~~~~~~aYDav~~lA~Al~~~~~~~~~~~~~~~~~~~ 101 (681)
...+|+++..++.+ +++..++|.+.|+++ .+.|.. ...++.++..+|||+++++.|+++++.....-
T Consensus 241 ~~~~g~~~~~~~~~~~~~p~~~~f~~~~~~~~~~~~~~-~~~~~~~~~~gy~a~~~l~~Al~~ag~~~~~~--------- 310 (351)
T cd06334 241 DAAKGYKGVTPFAGGADDPVGKEIVKEVYDKGKGSGND-KEIGSVYYNRGVVNAMIMVEAIRRAQEKGGET--------- 310 (351)
T ss_pred hhhcCcEEeecccCCCCchHHHHHHHHHHHccCCCCCc-ccccccHHHHHHHHHHHHHHHHHHHHHhcCCC---------
Confidence 45788888877654 456789999999876 222210 12345689999999999999999997543210
Q ss_pred CcccccCCCcchHHHHHHHhccceecceeeEEEe
Q 005717 102 VDIAALGTFEMGAKLLDTLINTTFEGLSGNFHLV 135 (681)
Q Consensus 102 ~~~~~~~~~~~G~~l~~~l~~~~f~GltG~i~F~ 135 (681)
....-+.-..=+..++.+++....|++|.+.|.
T Consensus 311 -~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~ 343 (351)
T cd06334 311 -TIAGEEQLENLKLDAARLEELGAEGLGPPVSVS 343 (351)
T ss_pred -CCcHHHHHHhhhhhhhhhhhcCcccccCCceec
Confidence 000000000012345566767778999999993
No 130
>cd08461 PBP2_DntR_like_3 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold. This CD includes an uncharacterized LysR-type transcriptional regulator similar to DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytra
Probab=91.61 E-value=7.2 Score=36.59 Aligned_cols=69 Identities=14% Similarity=0.090 Sum_probs=46.4
Q ss_pred eehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEEEeeccccccccccceeecceEEEEEec
Q 005717 225 GFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTTIVANRSTFVDFTLPYSESGVSMLVLVK 301 (681)
Q Consensus 225 G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~it~~R~~~vdFT~P~~~~~~~~vv~~~ 301 (681)
.+-.+++..+.+..+ .+++++... +.+.+...+.+|++|+++... ......+. +.++....+++++++.
T Consensus 13 ~~l~~~l~~f~~~~P-~v~i~i~~~---~~~~~~~~l~~~~~Di~i~~~---~~~~~~~~-~~~l~~~~~~lv~~~~ 81 (198)
T cd08461 13 AILPPLLAALRQEAP-GVRVAIRDL---ESDNLEAQLERGEVDLALTTP---EYAPDGLR-SRPLFEERYVCVTRRG 81 (198)
T ss_pred HHhHHHHHHHHHHCC-CcEEEEeeC---CcccHHHHHhcCCCcEEEecC---ccCCccce-eeeeecCcEEEEEcCC
Confidence 456788888888875 255666543 557789999999999998532 11122232 5677778888887654
No 131
>cd08460 PBP2_DntR_like_1 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold. This CD includes an uncharacterized LysR-type transcriptional regulator similar to DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytra
Probab=91.55 E-value=3.9 Score=38.71 Aligned_cols=69 Identities=14% Similarity=0.100 Sum_probs=47.5
Q ss_pred eehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEEEeeccccccccccceeecceEEEEEecc
Q 005717 225 GFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTTIVANRSTFVDFTLPYSESGVSMLVLVKD 302 (681)
Q Consensus 225 G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~it~~R~~~vdFT~P~~~~~~~~vv~~~~ 302 (681)
.+-.+++..+.++.+ .+++++... +. .+++.|.+|++|++++.... ....+. ..|+.+..+++++++..
T Consensus 13 ~~l~~~l~~~~~~~P-~v~v~l~~~---~~-~~~~~l~~g~~D~~i~~~~~---~~~~~~-~~~l~~~~~~~v~~~~h 81 (200)
T cd08460 13 AFGPALLAAVAAEAP-GVRLRFVPE---SD-KDVDALREGRIDLEIGVLGP---TGPEIR-VQTLFRDRFVGVVRAGH 81 (200)
T ss_pred HHHHHHHHHHHHHCC-CCEEEEecC---ch-hHHHHHHCCCccEEEecCCC---CCcchh-eeeeeccceEEEEeCCC
Confidence 566788888888876 356777653 45 78899999999999863211 122233 46777788888887654
No 132
>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=91.51 E-value=0.61 Score=49.13 Aligned_cols=88 Identities=15% Similarity=0.092 Sum_probs=59.1
Q ss_pred CccceEEEEEe--c--CCChhHHHHHHHHHhhcCCCCCCCCCCchhHHHHHHHHHHHHHHHHHHcccCCcccccCCCCCC
Q 005717 26 SMQGVLGLRPY--I--PSSKKLEHFKLRWIKSADKPDGSTGGSNLFGLWAYDTVWAIAMAVERAGIENSSFLKSNTSKSR 101 (681)
Q Consensus 26 ~~~Gvlg~~~~--~--~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~aYDav~~lA~Al~~~~~~~~~~~~~~~~~~~ 101 (681)
..+|++....+ . ...+..++|.+.|++. ++. ..++.++..+||++++++.|++++...
T Consensus 238 ~~~g~~~~~~~~~~~~~~~~~~~~f~~~~~~~--~~~---~~~~~~~~~~y~~~~~~~~a~~~~g~~------------- 299 (336)
T cd06326 238 YARGVIVTQVVPNPWSRTLPIVREYQAAMKAY--GPG---APPSYVSLEGYIAAKVLVEALRRAGPD------------- 299 (336)
T ss_pred hhcceEEEEEecCccccCCHHHHHHHHHHHhh--CCC---CCCCeeeehhHHHHHHHHHHHHHcCCC-------------
Confidence 46777654322 1 2245678898888875 111 134567888999999999999986521
Q ss_pred CcccccCCCcchHHHHHHHhcccee-cceeeEEEeCCccc
Q 005717 102 VDIAALGTFEMGAKLLDTLINTTFE-GLSGNFHLVNGQLE 140 (681)
Q Consensus 102 ~~~~~~~~~~~G~~l~~~l~~~~f~-GltG~i~F~~G~~~ 140 (681)
.+++.+.++|++++.. |..|.+.|..++..
T Consensus 300 ---------~~~~~v~~al~~~~~~~~~g~~~~~~~~~h~ 330 (336)
T cd06326 300 ---------PTRESLLAALEAMGKFDLGGFRLDFSPGNHQ 330 (336)
T ss_pred ---------CCHHHHHHHHHhcCCCCCCCeEEecCccccc
Confidence 1457899999998764 44458999444443
No 133
>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=91.37 E-value=2.5 Score=43.60 Aligned_cols=105 Identities=10% Similarity=0.057 Sum_probs=63.7
Q ss_pred CCCCCCHHHHHhCCCeEEEecChhHHHHHhhhcCCccccccccCChhHHHHHHccCcceEEecchhhHHHHH-hhcCCce
Q 005717 409 QPSFTDVKDIQKNGYFVGYQTNSFVKDLLTKKLNFNETRLKNYTTSEDYHDALSNGEVAAIFDEIPYIKIFL-ASYCSRY 487 (681)
Q Consensus 409 ~~~i~s~~dL~~~~~~vg~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~g~~~a~i~e~~~~~~~~-~~~c~~l 487 (681)
..+|++++||. |.++.+..+.....++ +.++.... .-...+...+|.+|.+|+...........- .+.++.+
T Consensus 125 ~~pi~s~~Dlk--G~kiR~~~~~~~~~~~-~~lGa~pv----~ip~~evy~aLq~G~vDg~~~~~~~~~~~~~~ev~~y~ 197 (286)
T PF03480_consen 125 KKPIRSPEDLK--GLKIRVPGSPVMSDFF-EALGASPV----PIPWSEVYQALQQGVVDGAENSASSIYSLGLYEVAKYF 197 (286)
T ss_dssp SS--SSGGGGT--TEEEEETSSHHHHHHH-HHCTSEEE----E-TGGGHHHHHHTTSSSEEEEEHHHHHHTTGGGTSSEE
T ss_pred ccCCccHhhHh--hCeEEecCCHHHHHHH-HHcCCeee----cCcHHHHHHHHhcCCcCeEecCHHHHHhcChhhhCCee
Confidence 35799999998 8889987666667777 66666432 224568999999999999998765552221 1226333
Q ss_pred EEECcccccCCcEEEecCCCC--ChHHHHHHHHhhcc
Q 005717 488 MMVGPTYRTDGFGFAFPLGSP--LVPYISRAILKVTE 522 (681)
Q Consensus 488 ~~v~~~~~~~~~~~~~~k~sp--l~~~in~~Il~l~e 522 (681)
+..+ +...++.+++.+..- |-+...++|.+..+
T Consensus 198 ~~~~--~~~~~~~~~~n~~~w~~L~~e~q~~l~~~~~ 232 (286)
T PF03480_consen 198 TDTN--HGWSPYAVIMNKDWWDSLPDEDQEALDDAAD 232 (286)
T ss_dssp EEEE--EEEEEEEEEEEHHHHHHS-HHHHHHHHHHHH
T ss_pred Eeec--ccCcceEEEEcHHHHhcCCHHHHHHHHHHHH
Confidence 3333 344556677666532 44555555444443
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=91.11 E-value=9.3 Score=35.79 Aligned_cols=70 Identities=14% Similarity=0.025 Sum_probs=46.8
Q ss_pred eehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEEEeeccccccccccceeecceEEEEEecc
Q 005717 225 GFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTTIVANRSTFVDFTLPYSESGVSMLVLVKD 302 (681)
Q Consensus 225 G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~it~~R~~~vdFT~P~~~~~~~~vv~~~~ 302 (681)
.+-.+++..+.+..+ ++++++... +-..+...|.+|++|+++... +.....+ -+.|+....+++++++..
T Consensus 13 ~~l~~~l~~~~~~~P-~i~i~~~~~---~~~~~~~~l~~~~~D~~i~~~---~~~~~~~-~~~~l~~~~~~~~~~~~~ 82 (198)
T cd08433 13 VLAVPLLRAVRRRYP-GIRLRIVEG---LSGHLLEWLLNGRLDLALLYG---PPPIPGL-STEPLLEEDLFLVGPADA 82 (198)
T ss_pred hcchHHHHHHHHHCC-CcEEEEEec---CcHHHHHHHhCCCCcEEEEeC---CCCCCCe-eEEEeccccEEEEecCCC
Confidence 455678888888876 356676653 567899999999999998532 2222222 245677777777776543
No 135
>PF13531 SBP_bac_11: Bacterial extracellular solute-binding protein; PDB: 2HXW_B 3FJG_C 3FJM_B 3FJ7_B 3FIR_B 3AXF_C 1WOD_A 1AMF_A 3R26_A 1SBP_A ....
Probab=91.06 E-value=2 Score=42.49 Aligned_cols=193 Identities=11% Similarity=0.037 Sum_probs=114.4
Q ss_pred eehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhC-ccceEEEeEEEeeccc---cccc--cccceeecceEEEE
Q 005717 225 GFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQ-EFDTAVGDTTIVANRS---TFVD--FTLPYSESGVSMLV 298 (681)
Q Consensus 225 G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g-~~Dia~~~~~it~~R~---~~vd--FT~P~~~~~~~~vv 298 (681)
+..-++.+.+.++.+++ ++++.. .-..+..+|..| ++|+.+.+-....++. ..++ -..|+..+.+++++
T Consensus 11 ~~~~~l~~~f~~~~g~~--v~v~~~---~s~~~~~~l~~g~~~Dv~~~~~~~~~~~l~~~g~~~~~~~~~~~~~~~vl~~ 85 (230)
T PF13531_consen 11 PALEELAEAFEKQPGIK--VEVSFG---GSGELVRRLQAGKKPDVFIPASSEWLERLAAAGLVDPGSPAPLARSPLVLAV 85 (230)
T ss_dssp HHHHHHHHHHHHHHCEE--EEEEEE---CHHHHHHHHHTT-S-SEEEESSHHHHHHHHHTTTCSGGGEEEEEEEEEEEEE
T ss_pred HHHHHHHHHHHhccCCe--EEEEEC---ChHHHHHHHhcCCCceEEEECCHHHHHHHHhcccccCCcccccccCceEEEe
Confidence 34557888887888855 444443 447788888877 7888776532211221 2333 56789999999999
Q ss_pred EeccCCCcCceeeeccCcHhHHHHHHHHHHHHHHHhhhhhcccCCCCCCCCCCchhhHHHHHHHHHhccCcccccccchh
Q 005717 299 LVKDDERKNFWIFLKPLSWDLWLTTGAAFIFTGLVVWVLEHRINTEFRGPPQHQIGTIFWFSFSTLVFAHRERVVNNLSR 378 (681)
Q Consensus 299 ~~~~~~~~~~~~fl~PF~~~vW~~i~~~~~~v~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~s~~~R 378 (681)
++....
T Consensus 86 ~~~~~~-------------------------------------------------------------------------- 91 (230)
T PF13531_consen 86 PKGNPK-------------------------------------------------------------------------- 91 (230)
T ss_dssp ETTSTT--------------------------------------------------------------------------
T ss_pred ccCccc--------------------------------------------------------------------------
Confidence 876521
Q ss_pred HHHHHHHHHHHHHHhHhhhhhhheeeecccCCCCCCHHHHHhCCCeEEEecC------hhHHHHHhhhcC---C-c--cc
Q 005717 379 FVLIIWVFVVLILTQSYTASLTSMLTVQRLQPSFTDVKDIQKNGYFVGYQTN------SFVKDLLTKKLN---F-N--ET 446 (681)
Q Consensus 379 ~l~~~w~~~~lil~s~YtA~L~s~LT~~~~~~~i~s~~dL~~~~~~vg~~~~------s~~~~~l~~~~~---~-~--~~ 446 (681)
.+.+++||.+.+.+|++... -.....+ .+.+ + . ..
T Consensus 92 --------------------------------~~~~~~dL~~~~~~i~~~dP~~s~~g~~~~~~l-~~~g~~~~~~~l~~ 138 (230)
T PF13531_consen 92 --------------------------------GIRSWADLAQPGLRIAIPDPSTSPSGLAALQVL-AAAGGQELLDALQK 138 (230)
T ss_dssp --------------------------------STTCHHHHCSTT--EEEE-TTTTHHHHHHHHHH-HHHTHCHHHHHHHH
T ss_pred --------------------------------ccCCHHHHhhccCEEEecCcccChhhHHHHHHH-HHcccHHHHHHHHH
Confidence 47788888876667887642 1222233 2222 1 0 12
Q ss_pred ccc-ccCChhHHHHHHccCcceEEecchhhHHHHHhhcCCceEE--ECcccc--cCCcEEEecCCCCChHHHHHHHHhhc
Q 005717 447 RLK-NYTTSEDYHDALSNGEVAAIFDEIPYIKIFLASYCSRYMM--VGPTYR--TDGFGFAFPLGSPLVPYISRAILKVT 521 (681)
Q Consensus 447 ~~~-~~~~~~~~~~~l~~g~~~a~i~e~~~~~~~~~~~c~~l~~--v~~~~~--~~~~~~~~~k~spl~~~in~~Il~l~ 521 (681)
++. ..++..+....+.+|++++.+.....+.+. ..-..+.. +.+.+. ...+++++.++++-.+.-...+.-|.
T Consensus 139 ~~~~~~~~~~~~~~~v~~g~~d~~~~~~s~~~~~--~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~a~~f~~~L~ 216 (230)
T PF13531_consen 139 NIVQYVPSTSQVLSAVASGEADAGIVYESQAIFA--RQGDPLSYVYPPDGVNSPPIDYPIAILKNAPHPEAARAFIDFLL 216 (230)
T ss_dssp TEEEEESSHHHHHHHHHTTSSSEEEEEHHHHHHC--TSHTTEEEEE-STTTSSSEEEEEEEEBTTCTTHHHHHHHHHHHT
T ss_pred hCcccccchHHHHHHHHcCCCcceeeHHHHHHHh--hcCCCeEEEECCchhcCCCEEEEEEEecCCCCHHHHHHHHHHHC
Confidence 233 455678888889999999988765555322 22113433 344444 24578899898887777777777776
Q ss_pred cCccHHHHHHHH
Q 005717 522 EDKEKMENIEKA 533 (681)
Q Consensus 522 e~~G~l~~i~~k 533 (681)
.. .-+++..+
T Consensus 217 s~--~~q~~l~~ 226 (230)
T PF13531_consen 217 SP--EGQQILAK 226 (230)
T ss_dssp SH--HHHHHHHH
T ss_pred CH--HHHHHHHH
Confidence 65 44555444
No 136
>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=90.94 E-value=8.7 Score=35.98 Aligned_cols=70 Identities=9% Similarity=0.003 Sum_probs=46.5
Q ss_pred eehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEEEeeccccccccccceeecceEEEEEecc
Q 005717 225 GFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTTIVANRSTFVDFTLPYSESGVSMLVLVKD 302 (681)
Q Consensus 225 G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~it~~R~~~vdFT~P~~~~~~~~vv~~~~ 302 (681)
.+-.+++..+.+..+ .+++++... +...++.++.+|++|+++.... .....+. +.++....+++++++..
T Consensus 13 ~~l~~~l~~~~~~~P-~i~l~i~~~---~~~~~~~~l~~~~~D~~i~~~~---~~~~~~~-~~~l~~~~~~~v~~~~h 82 (199)
T cd08426 13 ELLPSLIARFRQRYP-GVFFTVDVA---STADVLEAVLSGEADIGLAFSP---PPEPGIR-VHSRQPAPIGAVVPPGH 82 (199)
T ss_pred HHHHHHHHHHHHhCC-CeEEEEEeC---CcHHHHHHHHCCCccEEEecCC---CCCCCeE-EEeeccCcEEEEecCCC
Confidence 445677888888765 355666553 6688999999999999986321 1112222 46677778888876543
No 137
>PRK12679 cbl transcriptional regulator Cbl; Reviewed
Probab=90.85 E-value=6.5 Score=41.09 Aligned_cols=209 Identities=12% Similarity=0.134 Sum_probs=128.6
Q ss_pred ceEEEEeeccCCccceEEEeecCCCCeeEEeehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEE
Q 005717 195 RKLKIGVPVREGFTEFIKVVENKNKTTQVSGFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTT 274 (681)
Q Consensus 195 ~~lrV~v~~~~p~~~~~~~~~~~~~~~~~~G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~ 274 (681)
+++|||+.... ...+-.+++..+.+..+- +.+++.. ++.+.++.+|.+|++|+++....
T Consensus 93 g~lrIg~~~~~-----------------~~~~l~~~l~~f~~~~P~-i~l~l~~---~~~~~~~~~L~~g~~Dl~i~~~~ 151 (316)
T PRK12679 93 GVLTIATTHTQ-----------------ARYSLPEVIKAFRELFPE-VRLELIQ---GTPQEIATLLQNGEADIGIASER 151 (316)
T ss_pred ceEEEEechHh-----------------hhcchHHHHHHHHHHCCC-eEEEEec---CCHHHHHHHHHcCCCCEEEeccc
Confidence 57999986521 125667888888888653 4566654 36788999999999999986321
Q ss_pred EeeccccccccccceeecceEEEEEeccCCCcCceeeeccCcHhHHHHHHHHHHHHHHHhhhhhcccCCCCCCCCCCchh
Q 005717 275 IVANRSTFVDFTLPYSESGVSMLVLVKDDERKNFWIFLKPLSWDLWLTTGAAFIFTGLVVWVLEHRINTEFRGPPQHQIG 354 (681)
Q Consensus 275 it~~R~~~vdFT~P~~~~~~~~vv~~~~~~~~~~~~fl~PF~~~vW~~i~~~~~~v~~v~~~~~~~~~~~~~~~~~~~~~ 354 (681)
. .....+. +.|+.....++++++.....
T Consensus 152 ~--~~~~~l~-~~~l~~~~~~~v~~~~hpl~------------------------------------------------- 179 (316)
T PRK12679 152 L--SNDPQLV-AFPWFRWHHSLLVPHDHPLT------------------------------------------------- 179 (316)
T ss_pred C--CCCCCce-EEEccCCcEEEEecCCCccc-------------------------------------------------
Confidence 1 1112233 35677778888887554311
Q ss_pred hHHHHHHHHHhccCcccccccchhHHHHHHHHHHHHHHhHhhhhhhheeeecccCCCCCCHHHHHhCCCeEEEecChh--
Q 005717 355 TIFWFSFSTLVFAHRERVVNNLSRFVLIIWVFVVLILTQSYTASLTSMLTVQRLQPSFTDVKDIQKNGYFVGYQTNSF-- 432 (681)
Q Consensus 355 ~~~~~~~~~l~~~~~~~~~s~~~R~l~~~w~~~~lil~s~YtA~L~s~LT~~~~~~~i~s~~dL~~~~~~vg~~~~s~-- 432 (681)
....-+++||.+.. .+....+..
T Consensus 180 ------------------------------------------------------~~~~i~~~~L~~~~-~i~~~~~~~~~ 204 (316)
T PRK12679 180 ------------------------------------------------------QITPLTLESIAKWP-LITYRQGITGR 204 (316)
T ss_pred ------------------------------------------------------cCCCCCHHHHhCCC-eEEecCCCcHH
Confidence 00123678887432 244433432
Q ss_pred --HHHHHhhhcCCccccccccCChhHHHHHHccCcceEEecchhhHHHHHhhcCCceEEEC--cccccCCcEEEecCCCC
Q 005717 433 --VKDLLTKKLNFNETRLKNYTTSEDYHDALSNGEVAAIFDEIPYIKIFLASYCSRYMMVG--PTYRTDGFGFAFPLGSP 508 (681)
Q Consensus 433 --~~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~g~~~a~i~e~~~~~~~~~~~c~~l~~v~--~~~~~~~~~~~~~k~sp 508 (681)
...++ ...+.........++.+...+++..|.--+++-... ... . + ...+..+. .......+.++.+++.+
T Consensus 205 ~~~~~~~-~~~~~~~~~~~~~~s~~~~~~~v~~g~Gi~~lp~~~-~~~-~-~-~~~L~~~~~~~~~~~~~~~l~~~~~~~ 279 (316)
T PRK12679 205 SRIDDAF-ARKGLLADIVLSAQDSDVIKTYVALGLGIGLVAEQS-SGE-Q-E-ESNLIRLDTRHLFDANTVWLGLKRGQL 279 (316)
T ss_pred HHHHHHH-HHcCCCceEEEEeccHHHHHHHHHcCCcEEEecccc-ccc-c-c-CCcEEEEECcccCCCceEEEEEeCCch
Confidence 33344 333444334445677888888888885555554432 222 1 1 22455442 22344578899999999
Q ss_pred ChHHHHHHHHhhccCccHHHHHHHHHcCC
Q 005717 509 LVPYISRAILKVTEDKEKMENIEKALGNQ 537 (681)
Q Consensus 509 l~~~in~~Il~l~e~~G~l~~i~~kw~~~ 537 (681)
+...+...+.-+.+. --++.++++-+.+
T Consensus 280 ~~~~~~~f~~~~~~~-~~~~~~~~~~~~~ 307 (316)
T PRK12679 280 QRNYVWRFLELCNAG-LSVEDIKRQVMEN 307 (316)
T ss_pred hhHHHHHHHHHHhcc-cCHHHHHHHHhhc
Confidence 999999999888887 6677787776643
No 138
>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=90.72 E-value=11 Score=34.85 Aligned_cols=70 Identities=9% Similarity=0.119 Sum_probs=48.0
Q ss_pred eehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEEEeeccccccccccceeecceEEEEEecc
Q 005717 225 GFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTTIVANRSTFVDFTLPYSESGVSMLVLVKD 302 (681)
Q Consensus 225 G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~it~~R~~~vdFT~P~~~~~~~~vv~~~~ 302 (681)
.+..+++..+.++.+ .+++++... +..++...|.+|++|+++.... .....+. +.++.+..+++++++..
T Consensus 13 ~~l~~~l~~~~~~~p-~v~i~i~~~---~~~~~~~~l~~g~~D~~i~~~~---~~~~~~~-~~~l~~~~~~~~~~~~~ 82 (197)
T cd08440 13 TLLPPVLAAFRRRHP-GIRVRLRDV---SAEQVIEAVRSGEVDFGIGSEP---EADPDLE-FEPLLRDPFVLVCPKDH 82 (197)
T ss_pred hHHHHHHHHHHHhCC-CcEEEEEeC---ChHHHHHHHHcCCccEEEEeCC---CCCCCee-EEEeecccEEEEecCCC
Confidence 556788888888876 356666653 6788999999999999986322 2222222 35677778888876543
No 139
>cd08466 PBP2_LeuO The C-terminal substrate binding domain of LysR-type transcriptional regulator LeuO, an activator of leucine synthesis operon, contains the type 2 periplasmic binding fold. LeuO, a LysR-type transcriptional regulator, was originally identified as an activator of the leucine synthesis operon (leuABCD). Subsequently, LeuO was found to be not a specific regulator of the leu gene but a global regulator of unrelated various genes. LeuO activates bglGFB (utilization of beta-D-glucoside) and represses cadCBA (lysine decarboxylation) and dsrA (encoding a regulatory small RNA for translational control of rpoS and hns). LeuO also regulates the yjjQ-bglJ operon which coding for a LuxR-type transcription factor. In Salmonella enterica serovar Typhi, LeuO is a positive regulator of ompS1 (encoding an outer membrane), ompS2 (encoding a pathogenicity determinant), and assT, while LeuO represses the expression of OmpX and Tpx. Both osmS1 and osmS2 influence virulence in the mouse mo
Probab=90.69 E-value=9.6 Score=35.78 Aligned_cols=70 Identities=13% Similarity=0.094 Sum_probs=48.4
Q ss_pred eehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEEEeeccccccccccceeecceEEEEEecc
Q 005717 225 GFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTTIVANRSTFVDFTLPYSESGVSMLVLVKD 302 (681)
Q Consensus 225 G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~it~~R~~~vdFT~P~~~~~~~~vv~~~~ 302 (681)
.+-.+++..+.++.+ .+++++... +...+..+|.+|++|+++... +.....+. +.|+....+++++++..
T Consensus 13 ~~l~~~l~~f~~~~P-~v~l~~~~~---~~~~~~~~l~~g~~Dl~i~~~---~~~~~~~~-~~~l~~~~~~lv~~~~~ 82 (200)
T cd08466 13 LLLPRLLARLKQLAP-NISLRESPS---SEEDLFEDLRLQEVDLVIDYV---PFRDPSFK-SELLFEDELVCVARKDH 82 (200)
T ss_pred HHHHHHHHHHHHHCC-CCEEEEecC---chHhHHHHHHcCCccEEEecc---cCCCCCce-eeeecccceEEEEeCCC
Confidence 455678888888875 356666653 778899999999999998631 22222232 45777788888887654
No 140
>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=90.67 E-value=9.6 Score=35.40 Aligned_cols=69 Identities=7% Similarity=-0.063 Sum_probs=46.9
Q ss_pred eehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEEEeeccccccccccceeecceEEEEEec
Q 005717 225 GFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTTIVANRSTFVDFTLPYSESGVSMLVLVK 301 (681)
Q Consensus 225 G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~it~~R~~~vdFT~P~~~~~~~~vv~~~ 301 (681)
.+..+++..+.++.+- +++++... +...++..+.+|++|+++.. .+.....+ -..+..+..+++++++.
T Consensus 13 ~~l~~~l~~~~~~~P~-i~l~i~~~---~~~~~~~~l~~g~~Dl~i~~---~~~~~~~~-~~~~l~~~~~~~v~~~~ 81 (193)
T cd08442 13 VRLPPLLAAYHARYPK-VDLSLSTG---TTGALIQAVLEGRLDGAFVA---GPVEHPRL-EQEPVFQEELVLVSPKG 81 (193)
T ss_pred hhhHHHHHHHHHHCCC-ceEEEEeC---CcHHHHHHHHCCCccEEEEe---CCCCCCCc-EEEEeecCcEEEEecCC
Confidence 4567888999888763 56677653 67889999999999998853 22222222 23556667777777654
No 141
>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=90.60 E-value=5.1 Score=38.05 Aligned_cols=70 Identities=11% Similarity=0.029 Sum_probs=47.5
Q ss_pred eehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEEEeeccccccccccceeecceEEEEEecc
Q 005717 225 GFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTTIVANRSTFVDFTLPYSESGVSMLVLVKD 302 (681)
Q Consensus 225 G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~it~~R~~~vdFT~P~~~~~~~~vv~~~~ 302 (681)
++-.+++..+.++.+ .+++++... +..+++++|.+|++|++++..... ...++ +.|..+..+++++++..
T Consensus 13 ~~l~~~l~~f~~~~P-~i~l~i~~~---~~~~~~~~L~~g~~Dl~i~~~~~~---~~~~~-~~~l~~~~~~lv~~~~h 82 (200)
T cd08465 13 LVLPALMRQLRAEAP-GIDLAVSQA---SREAMLAQVADGEIDLALGVFPEL---PEELH-AETLFEERFVCLADRAT 82 (200)
T ss_pred HhhhHHHHHHHHHCC-CcEEEEecC---ChHhHHHHHHCCCccEEEeccccC---CcCee-EEEeeeccEEEEEeCCC
Confidence 555678888877765 356666653 789999999999999998632211 12233 24667777888887553
No 142
>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=90.60 E-value=14 Score=34.27 Aligned_cols=69 Identities=10% Similarity=0.067 Sum_probs=46.1
Q ss_pred eehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEEEeeccccccccccceeecceEEEEEec
Q 005717 225 GFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTTIVANRSTFVDFTLPYSESGVSMLVLVK 301 (681)
Q Consensus 225 G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~it~~R~~~vdFT~P~~~~~~~~vv~~~ 301 (681)
.+..+++..+.++.+- +++++... ....+..+|.+|++|+++...... ...+ -..++....++++++..
T Consensus 12 ~~l~~~l~~~~~~~P~-i~l~i~~~---~~~~~~~~l~~g~~Dl~i~~~~~~---~~~~-~~~~l~~~~~~~~~~~~ 80 (197)
T cd08419 12 YFAPRLLGAFCRRHPG-VEVSLRVG---NREQVLERLADNEDDLAIMGRPPE---DLDL-VAEPFLDNPLVVIAPPD 80 (197)
T ss_pred hHhhHHHHHHHHHCCC-ceEEEEEC---CHHHHHHHHhcCCccEEEecCCCC---CCCe-EEEEeccCCEEEEecCC
Confidence 3556788888888652 56777654 678899999999999998532111 1112 24567777777777654
No 143
>CHL00180 rbcR LysR transcriptional regulator; Provisional
Probab=90.50 E-value=9 Score=39.73 Aligned_cols=86 Identities=13% Similarity=0.180 Sum_probs=56.0
Q ss_pred ceEEEEeeccCCccceEEEeecCCCCeeEEeehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEE
Q 005717 195 RKLKIGVPVREGFTEFIKVVENKNKTTQVSGFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTT 274 (681)
Q Consensus 195 ~~lrV~v~~~~p~~~~~~~~~~~~~~~~~~G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~ 274 (681)
+++|||+....+ ..+-.+++..+.+..+- +.+++... ....++..|.+|++|+++..-.
T Consensus 95 g~l~ig~~~~~~-----------------~~~~~~~l~~~~~~~P~-v~i~~~~~---~~~~~~~~l~~g~~Dl~i~~~~ 153 (305)
T CHL00180 95 GTLIIGASQTTG-----------------TYLMPRLIGLFRQRYPQ-INVQLQVH---STRRIAWNVANGQIDIAIVGGE 153 (305)
T ss_pred ceEEEEEcCcch-----------------HhHHHHHHHHHHHHCCC-ceEEEEeC---CHHHHHHHHHcCCccEEEEcCc
Confidence 579998864211 24556788888887653 55666653 6789999999999999986321
Q ss_pred EeeccccccccccceeecceEEEEEecc
Q 005717 275 IVANRSTFVDFTLPYSESGVSMLVLVKD 302 (681)
Q Consensus 275 it~~R~~~vdFT~P~~~~~~~~vv~~~~ 302 (681)
........+ ...++....+++++++..
T Consensus 154 ~~~~~~~~~-~~~~l~~~~~~~v~~~~~ 180 (305)
T CHL00180 154 VPTELKKIL-EITPYVEDELALIIPKSH 180 (305)
T ss_pred cCcccccce-eEEEeccCcEEEEECCCC
Confidence 111111112 346777788888887654
No 144
>cd08464 PBP2_DntR_like_2 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold. This CD includes an uncharacterized LysR-type transcriptional regulator similar to DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytra
Probab=90.20 E-value=9.4 Score=35.79 Aligned_cols=69 Identities=12% Similarity=0.053 Sum_probs=45.6
Q ss_pred eehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEEEeeccccccccccceeecceEEEEEec
Q 005717 225 GFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTTIVANRSTFVDFTLPYSESGVSMLVLVK 301 (681)
Q Consensus 225 G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~it~~R~~~vdFT~P~~~~~~~~vv~~~ 301 (681)
++-..++..+.++.+ .+++++... +...++..|.+|++|+++.... .....+ -..+.....++++++..
T Consensus 13 ~~l~~~l~~~~~~~P-~v~l~i~~~---~~~~~~~~l~~g~~D~~i~~~~---~~~~~~-~~~~l~~~~~~~v~~~~ 81 (200)
T cd08464 13 WLAPPLLAALRAEAP-GVRLVFRQV---DPFNVGDMLDRGEIDLAIGVFG---ELPAWL-KREVLYTEGYACLFDPQ 81 (200)
T ss_pred HHHHHHHHHHHHHCC-CcEEEEecC---CcccHHHHHhcCcccEEEecCC---CCcccc-eeeeecccceEEEEeCC
Confidence 456678888888865 356666653 6678899999999999985321 111222 23567777777777654
No 145
>PRK12684 transcriptional regulator CysB-like protein; Reviewed
Probab=90.13 E-value=11 Score=39.36 Aligned_cols=206 Identities=9% Similarity=0.029 Sum_probs=120.9
Q ss_pred ceEEEEeeccCCccceEEEeecCCCCeeEEeehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEE
Q 005717 195 RKLKIGVPVREGFTEFIKVVENKNKTTQVSGFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTT 274 (681)
Q Consensus 195 ~~lrV~v~~~~p~~~~~~~~~~~~~~~~~~G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~ 274 (681)
++++||+..... ..+-.+++..+.++.+- +.+++... +.+.++..|.+|++|+++..-.
T Consensus 93 g~l~Ig~~~~~~-----------------~~~l~~~l~~~~~~~p~-i~l~~~~~---~~~~~~~~L~~g~~D~~i~~~~ 151 (313)
T PRK12684 93 GNLTIATTHTQA-----------------RYALPAAIKEFKKRYPK-VRLSILQG---SPTQIAEMVLHGQADLAIATEA 151 (313)
T ss_pred CeEEEEechHHH-----------------HHHhHHHHHHHHHHCCC-ceEEEEeC---ChHHHHHHHHCCCcCEEEeecC
Confidence 579999854211 24456888888887653 56666653 6789999999999999975311
Q ss_pred EeeccccccccccceeecceEEEEEeccCCCcCceeeeccCcHhHHHHHHHHHHHHHHHhhhhhcccCCCCCCCCCCchh
Q 005717 275 IVANRSTFVDFTLPYSESGVSMLVLVKDDERKNFWIFLKPLSWDLWLTTGAAFIFTGLVVWVLEHRINTEFRGPPQHQIG 354 (681)
Q Consensus 275 it~~R~~~vdFT~P~~~~~~~~vv~~~~~~~~~~~~fl~PF~~~vW~~i~~~~~~v~~v~~~~~~~~~~~~~~~~~~~~~ 354 (681)
... ...+ -..|+.....++++++.....
T Consensus 152 ~~~--~~~l-~~~~l~~~~~~~v~~~~~pl~------------------------------------------------- 179 (313)
T PRK12684 152 IAD--YKEL-VSLPCYQWNHCVVVPPDHPLL------------------------------------------------- 179 (313)
T ss_pred CCC--CCCc-eEEEeccceEEEEeCCCCccc-------------------------------------------------
Confidence 110 1122 246666777777776543211
Q ss_pred hHHHHHHHHHhccCcccccccchhHHHHHHHHHHHHHHhHhhhhhhheeeecccCCCCCCHHHHHhCCCeEEEecChhHH
Q 005717 355 TIFWFSFSTLVFAHRERVVNNLSRFVLIIWVFVVLILTQSYTASLTSMLTVQRLQPSFTDVKDIQKNGYFVGYQTNSFVK 434 (681)
Q Consensus 355 ~~~~~~~~~l~~~~~~~~~s~~~R~l~~~w~~~~lil~s~YtA~L~s~LT~~~~~~~i~s~~dL~~~~~~vg~~~~s~~~ 434 (681)
...--+++||.+.. .+.+..++...
T Consensus 180 ------------------------------------------------------~~~~i~~~dL~~~~-~i~~~~~~~~~ 204 (313)
T PRK12684 180 ------------------------------------------------------ERKPLTLEDLAQYP-LITYDFAFAGR 204 (313)
T ss_pred ------------------------------------------------------cCCCcCHHHHhcCC-cEecCCCCcHH
Confidence 00123678888433 35555544333
Q ss_pred H----HHhhhcCCccccccccCChhHHHHHHccCcceEEecchhhHHHHHhhcCCceEEE--CcccccCCcEEEecCCCC
Q 005717 435 D----LLTKKLNFNETRLKNYTTSEDYHDALSNGEVAAIFDEIPYIKIFLASYCSRYMMV--GPTYRTDGFGFAFPLGSP 508 (681)
Q Consensus 435 ~----~l~~~~~~~~~~~~~~~~~~~~~~~l~~g~~~a~i~e~~~~~~~~~~~c~~l~~v--~~~~~~~~~~~~~~k~sp 508 (681)
. ++ ...++........++.+...+++..|.--+++.+. ...... ..++..+ ........+.++.+++.+
T Consensus 205 ~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~v~~g~Gv~~lp~~-~~~~~~---~~~l~~~~i~~~~~~~~~~l~~~~~~~ 279 (313)
T PRK12684 205 SKINKAF-ALRGLKPDIVLEAIDADVIKTYVELGLGVGIVADM-AFDPER---DRNLRAIDAGHLFGSSTTRLGLRRGAY 279 (313)
T ss_pred HHHHHHH-HHcCCCCCeEEEeCCHHHHHHHHHhCCceEEeehh-hccccc---cCCeEEEECCCCCcceeEEEEEECCCc
Confidence 3 33 33344433345566788888888887544555443 222221 1234443 223334568899999998
Q ss_pred ChHHHHHHHHhhccCccHHHHHHHHHc
Q 005717 509 LVPYISRAILKVTEDKEKMENIEKALG 535 (681)
Q Consensus 509 l~~~in~~Il~l~e~~G~l~~i~~kw~ 535 (681)
+...+...+..+.+. +..++..+-+
T Consensus 280 ~~~~~~~f~~~l~~~--~~~~~~~~~~ 304 (313)
T PRK12684 280 LRGYVYTFIELFAPT--LNRKLVEQAL 304 (313)
T ss_pred CCHHHHHHHHHHHHH--hCHHHHHHHh
Confidence 877777777766665 5555555444
No 146
>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=90.12 E-value=4.9 Score=38.83 Aligned_cols=103 Identities=14% Similarity=0.179 Sum_probs=64.9
Q ss_pred CCCCHHHHHhCCCeE-EEecChhHHHHHhh---hcCCcccccccc----CChhHHHHHHccCcceEEecchhhHHHHHhh
Q 005717 411 SFTDVKDIQKNGYFV-GYQTNSFVKDLLTK---KLNFNETRLKNY----TTSEDYHDALSNGEVAAIFDEIPYIKIFLAS 482 (681)
Q Consensus 411 ~i~s~~dL~~~~~~v-g~~~~s~~~~~l~~---~~~~~~~~~~~~----~~~~~~~~~l~~g~~~a~i~e~~~~~~~~~~ 482 (681)
.|++++||.+.+.++ .-+.||-.+.+|.. ..+.....+..| .+-.+...++..|..|+-+.......-+
T Consensus 82 ~i~~~~dL~~~~~r~vnR~~GSGtR~l~d~~l~~~gi~~~~i~gy~~~~~th~~vA~aVa~G~AD~G~g~~~~A~~~--- 158 (193)
T PF12727_consen 82 GITSLEDLADPGLRFVNRQPGSGTRILFDQLLAEEGIDPEDIPGYAQEANTHLAVAAAVASGKADAGIGIRAAAEEF--- 158 (193)
T ss_pred cCCCHHHhccCCcEEEECCCCCHHHHHHHHHHHHcCCChhhCCCccccccChHHHHHHHHcCCCCEEeehHHHHHhh---
Confidence 599999998777644 44678877776622 224444455555 3566778888999999998765444311
Q ss_pred cCCceEEECcccccCCcEEEecCCCCChHHHHHHHHhh
Q 005717 483 YCSRYMMVGPTYRTDGFGFAFPLGSPLVPYISRAILKV 520 (681)
Q Consensus 483 ~c~~l~~v~~~~~~~~~~~~~~k~spl~~~in~~Il~l 520 (681)
+--++. ++....|-+++++..-..+.+.+.|.-|
T Consensus 159 ~gL~Fv----pl~~E~~dlv~~~~~~~~~~vq~ll~~l 192 (193)
T PF12727_consen 159 YGLDFV----PLAEERYDLVIRREDLEDPAVQALLDFL 192 (193)
T ss_pred cCCCcE----EccccceEEEEEhhHcCCHHHHHHHHHh
Confidence 110222 2234567889998876666666665443
No 147
>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=90.06 E-value=14 Score=34.33 Aligned_cols=70 Identities=11% Similarity=0.138 Sum_probs=47.9
Q ss_pred eehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEEEeeccccccccccceeecceEEEEEecc
Q 005717 225 GFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTTIVANRSTFVDFTLPYSESGVSMLVLVKD 302 (681)
Q Consensus 225 G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~it~~R~~~vdFT~P~~~~~~~~vv~~~~ 302 (681)
.+..+++..+.+..+ .+.+++... +..+++..|.+|++|+++..... ....+. ..|+.+..+++++++..
T Consensus 13 ~~l~~~l~~~~~~~p-~v~i~i~~~---~~~~~~~~L~~~~~Dl~i~~~~~---~~~~~~-~~~l~~~~~~~v~~~~~ 82 (197)
T cd08438 13 LLFAPLLAAFRQRYP-NIELELVEY---GGKKVEQAVLNGELDVGITVLPV---DEEEFD-SQPLCNEPLVAVLPRGH 82 (197)
T ss_pred hhcHHHHHHHHHHCc-CeEEEEEEc---CcHHHHHHHHcCCCCEEEEeccc---ccCCce-eEEeccccEEEEecCCC
Confidence 456788899988876 356666654 67889999999999999864322 112222 34666777777777543
No 148
>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=90.01 E-value=13 Score=34.73 Aligned_cols=71 Identities=10% Similarity=0.023 Sum_probs=49.7
Q ss_pred EeehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEEEeeccccccccccceeecceEEEEEecc
Q 005717 224 SGFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTTIVANRSTFVDFTLPYSESGVSMLVLVKD 302 (681)
Q Consensus 224 ~G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~it~~R~~~vdFT~P~~~~~~~~vv~~~~ 302 (681)
..+-.+++..+.++.+- +++++... +..+++.+|.+|++|+++... +.....+ ...|+....+++++++..
T Consensus 12 ~~~l~~~l~~~~~~~P~-i~l~i~~~---~~~~~~~~l~~~~~D~~i~~~---~~~~~~~-~~~~l~~~~~~~~~~~~~ 82 (198)
T cd08412 12 PYYLPGLLRRFREAYPG-VEVRVVEG---NQEELEEGLRSGELDLALTYD---LDLPEDI-AFEPLARLPPYVWLPADH 82 (198)
T ss_pred hhhhHHHHHHHHHHCCC-cEEEEEEC---CHHHHHHHHHcCCCcEEEEcC---CCCCccc-ceeeeeccceEEEecCCC
Confidence 35677889999888763 56777664 678899999999999998632 2222223 246777788887776553
No 149
>PRK11242 DNA-binding transcriptional regulator CynR; Provisional
Probab=90.00 E-value=7.9 Score=39.77 Aligned_cols=70 Identities=10% Similarity=0.072 Sum_probs=49.3
Q ss_pred eehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEEEeeccccccccccceeecceEEEEEecc
Q 005717 225 GFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTTIVANRSTFVDFTLPYSESGVSMLVLVKD 302 (681)
Q Consensus 225 G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~it~~R~~~vdFT~P~~~~~~~~vv~~~~ 302 (681)
.+..+++..+.++.+ .+.+++... ....++..|.+|++|+++... +.....+ .+.++....+++++++..
T Consensus 104 ~~l~~~l~~~~~~~p-~~~i~~~~~---~~~~~~~~l~~g~~Dl~i~~~---~~~~~~l-~~~~l~~~~~~~~~~~~~ 173 (296)
T PRK11242 104 YLIGPLIDAFHARYP-GITLTIREM---SQERIEALLADDELDVGIAFA---PVHSPEI-EAQPLFTETLALVVGRHH 173 (296)
T ss_pred hhhHHHHHHHHHHCC-CCEEEEEeC---CHHHHHHHHHCCCCcEEEEec---CCCCcce-eEEEeeeccEEEEEcCCC
Confidence 456788888888865 456677654 678899999999999998632 2222223 346777788888887654
No 150
>PRK10341 DNA-binding transcriptional activator TdcA; Provisional
Probab=90.00 E-value=6.4 Score=41.05 Aligned_cols=72 Identities=17% Similarity=0.172 Sum_probs=49.1
Q ss_pred eehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEEEeeccccccccccceeecceEEEEEecc
Q 005717 225 GFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTTIVANRSTFVDFTLPYSESGVSMLVLVKD 302 (681)
Q Consensus 225 G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~it~~R~~~vdFT~P~~~~~~~~vv~~~~ 302 (681)
.+-.+++..+.+..+- +++++... ...+++.+|.+|++|+++...... .....+ -..|+.+..+++++++..
T Consensus 110 ~~l~~~l~~~~~~~p~-v~i~~~~~---~~~~~~~~l~~g~~Dl~i~~~~~~-~~~~~l-~~~~l~~~~~~lv~~~~~ 181 (312)
T PRK10341 110 TFMSDMINKFKEVFPK-AQVSMYEA---QLSSFLPAIRDGRLDFAIGTLSNE-MKLQDL-HVEPLFESEFVLVASKSR 181 (312)
T ss_pred hhHHHHHHHHHHhCCC-CEEEEEeC---CHHHHHHHHHcCCCcEEEecCCcc-cccCCe-eEEEEecccEEEEEcCCC
Confidence 3456888888887663 56777764 779999999999999998532111 111222 346777788888887553
No 151
>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=89.57 E-value=6.6 Score=38.40 Aligned_cols=71 Identities=7% Similarity=-0.071 Sum_probs=42.2
Q ss_pred cCChhHHHHHHccCcceEEecchhhHHHHHhhcCCceEEECcc-cccCCcEEEecCCCCChHHHHHHHHhhccC
Q 005717 451 YTTSEDYHDALSNGEVAAIFDEIPYIKIFLASYCSRYMMVGPT-YRTDGFGFAFPLGSPLVPYISRAILKVTED 523 (681)
Q Consensus 451 ~~~~~~~~~~l~~g~~~a~i~e~~~~~~~~~~~c~~l~~v~~~-~~~~~~~~~~~k~spl~~~in~~Il~l~e~ 523 (681)
..+..+..+.+.+|++++.+......... .... ....++.. .....+++++.|+++-.+.-.+.|.-+...
T Consensus 135 ~~~~~~~~~~~~~Ge~~~~~~~~~~~~~~-~~~~-~~~~~P~~~~~~~~~~~ai~k~a~~~~~A~~fi~fl~s~ 206 (216)
T TIGR01256 135 GEDVRQALQFVETGNAPAGIVALSDVIPS-KKVG-SVATFPEDLYKPIRYPAVIVKGGKNNAAAKAFIDYLKSP 206 (216)
T ss_pred cCcHHHHHHHHHcCCCCEEeeehhhhccc-CCcc-EEEEeCccccCCccccEEEEECCCChHHHHHHHHHHcCH
Confidence 34667788888999999887654332211 1123 23333333 233457899999988666655555555544
No 152
>PRK11233 nitrogen assimilation transcriptional regulator; Provisional
Probab=89.53 E-value=7.6 Score=40.29 Aligned_cols=69 Identities=13% Similarity=0.044 Sum_probs=45.4
Q ss_pred eehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEEEeeccccccccccceeecceEEEEEec
Q 005717 225 GFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTTIVANRSTFVDFTLPYSESGVSMLVLVK 301 (681)
Q Consensus 225 G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~it~~R~~~vdFT~P~~~~~~~~vv~~~ 301 (681)
.+..+++..+.++.+ .+.+.+... ....+...|.+|++|+++..- ......+ ...|+.+..+++++++.
T Consensus 105 ~~~~~~l~~~~~~~p-~i~l~~~~~---~~~~~~~~l~~g~~Di~i~~~---~~~~~~~-~~~~l~~~~~~lv~~~~ 173 (305)
T PRK11233 105 SLTMPLLQAVRAEFP-GIVLYLHEN---SGATLNEKLMNGQLDMAVIYE---HSPVAGL-SSQPLLKEDLFLVGTQD 173 (305)
T ss_pred HHHHHHHHHHHHHCC-CcEEEEEEC---CcHHHHHHHHCCCCCEEEEcC---CcCCCCc-EEEEEeeeeEEEEEcCc
Confidence 445568888888864 345666553 567899999999999998531 1111222 23577777787777644
No 153
>cd08434 PBP2_GltC_like The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA expression of glutamate synthase operon, contains type 2 periplasmic binding fold. GltC, a member of the LysR family of bacterial transcriptional factors, activates the expression of gltA gene of glutamate synthase operon and is essential for cell growth in the absence of glutamate. Glutamate synthase is a heterodimeric protein that encoded by gltA and gltB, whose expression is subject to nutritional regulation. GltC also negatively auto-regulates its own expression. This substrate-binding domain has strong homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity,
Probab=89.42 E-value=12 Score=34.66 Aligned_cols=70 Identities=19% Similarity=0.251 Sum_probs=46.4
Q ss_pred eehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEEEeeccccccccccceeecceEEEEEecc
Q 005717 225 GFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTTIVANRSTFVDFTLPYSESGVSMLVLVKD 302 (681)
Q Consensus 225 G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~it~~R~~~vdFT~P~~~~~~~~vv~~~~ 302 (681)
.+...++..+.+..+- +++++... ....++.++.+|++|+++... +.....++ ..++.+..+++++++..
T Consensus 13 ~~l~~~l~~~~~~~P~-i~i~i~~~---~~~~~~~~l~~~~~Dl~i~~~---~~~~~~l~-~~~l~~~~~~~v~~~~~ 82 (195)
T cd08434 13 SLVPDLIRAFRKEYPN-VTFELHQG---STDELLDDLKNGELDLALCSP---VPDEPDIE-WIPLFTEELVLVVPKDH 82 (195)
T ss_pred hhhHHHHHHHHHhCCC-eEEEEecC---cHHHHHHHHHcCCccEEEEcc---CCCCCCee-EEEeecceEEEEecCCC
Confidence 4556778888887642 45666653 677899999999999987632 22222333 35677777887776553
No 154
>PRK09791 putative DNA-binding transcriptional regulator; Provisional
Probab=89.16 E-value=10 Score=39.25 Aligned_cols=85 Identities=8% Similarity=0.101 Sum_probs=56.9
Q ss_pred ceEEEEeeccCCccceEEEeecCCCCeeEEeehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEE
Q 005717 195 RKLKIGVPVREGFTEFIKVVENKNKTTQVSGFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTT 274 (681)
Q Consensus 195 ~~lrV~v~~~~p~~~~~~~~~~~~~~~~~~G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~ 274 (681)
++|+||++.... ..+-.+++..+.+..+ .+++++.. ++..++..+|.+|++|+++....
T Consensus 95 g~l~I~~~~~~~-----------------~~~l~~~l~~~~~~~p-~i~~~~~~---~~~~~~~~~l~~g~~Di~i~~~~ 153 (302)
T PRK09791 95 GQINIGMGASIA-----------------RSLMPAVISRFHQQHP-QVKVRIME---GQLVSMINELRQGELDFTINTYY 153 (302)
T ss_pred eEEEEEechHHH-----------------HhhhHHHHHHHHHHCC-CeEEEEEe---CChHHHHHHHHCCCccEEEEecC
Confidence 689999875321 2456688888888776 35566554 36789999999999999886311
Q ss_pred EeeccccccccccceeecceEEEEEecc
Q 005717 275 IVANRSTFVDFTLPYSESGVSMLVLVKD 302 (681)
Q Consensus 275 it~~R~~~vdFT~P~~~~~~~~vv~~~~ 302 (681)
. ......+. ..|+....+++++++..
T Consensus 154 ~-~~~~~~~~-~~~l~~~~~~l~~~~~~ 179 (302)
T PRK09791 154 Q-GPYDHEFT-FEKLLEKQFAVFCRPGH 179 (302)
T ss_pred C-ccccccee-EEEeccceEEEEEcCCC
Confidence 1 11112233 36778888888887654
No 155
>cd08413 PBP2_CysB_like The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains type 2 periplasmic binding fold. CysB is a transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the regulation of transcription in response to sulfur source is attributed to two transcriptional regulators, CysB and Cbl. CysB, in association with Cbl, downregulates the expression of ssuEADCB operon which is required for the utilization of sulfur from aliphatic sulfonates, in the presence of cysteine. Also, Cbl and CysB together directly function as transcriptional activators of tauABCD genes, which are required for utilization of taurine as sulfur source for growth. Like many other members of the LTTR family, CysB is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-bi
Probab=89.11 E-value=7.3 Score=36.83 Aligned_cols=71 Identities=13% Similarity=0.044 Sum_probs=48.4
Q ss_pred eehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEEEeeccccccccccceeecceEEEEEecc
Q 005717 225 GFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTTIVANRSTFVDFTLPYSESGVSMLVLVKD 302 (681)
Q Consensus 225 G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~it~~R~~~vdFT~P~~~~~~~~vv~~~~ 302 (681)
.+-.+++..+.++.+- +++++... ....+...|.+|++|+++..... .....+. +.+.....+++++++..
T Consensus 13 ~~l~~~l~~~~~~~P~-i~v~~~~~---~~~~~~~~l~~g~~D~~i~~~~~--~~~~~~~-~~~l~~~~~~~v~~~~h 83 (198)
T cd08413 13 YVLPPVIAAFRKRYPK-VKLSLHQG---TPSQIAEMVLKGEADIAIATEAL--DDHPDLV-TLPCYRWNHCVIVPPGH 83 (198)
T ss_pred hhccHHHHHHHHhCCc-eEEEEEeC---CHHHHHHHHHcCCCCEEEEccCC--CCCCCcE-EEEeeeeeEEEEecCCC
Confidence 4556788888888763 55666653 67889999999999999853211 1112233 46777788888887554
No 156
>cd08441 PBP2_MetR The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which regulates the expression of methionine biosynthetic genes, contains type 2 periplasmic binding fold. MetR, a member of the LysR family, is a positive regulator for the metA, metE, metF, and metH genes. The sulfur-containing amino acid methionine is the universal initiator of protein synthesis in all known organisms and its derivative S-adenosylmethionine (SAM) and autoinducer-2 (AI-2) are involved in various cellular processes. SAM plays a central role as methyl donor in methylation reactions, which are essential for the biosynthesis of phospholipids, proteins, DNA and RNA. The interspecies signaling molecule AI-2 is involved in cell-cell communication process (quorum sensing) and gene regulation in bacteria. Although methionine biosynthetic enzymes and metabolic pathways are well conserved in bacteria, the regulation of methionine biosynthesis involves various regulatory mecha
Probab=88.73 E-value=14 Score=34.69 Aligned_cols=68 Identities=9% Similarity=0.059 Sum_probs=45.0
Q ss_pred ehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEEEeeccccccccccceeecceEEEEEec
Q 005717 226 FCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTTIVANRSTFVDFTLPYSESGVSMLVLVK 301 (681)
Q Consensus 226 ~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~it~~R~~~vdFT~P~~~~~~~~vv~~~ 301 (681)
+-..++..+.+..+- +++++... ....+...|.+|++|+++..-.. ....+. ..++....++++++..
T Consensus 14 ~~~~~l~~~~~~~P~-i~i~i~~~---~~~~~~~~l~~g~~Dl~i~~~~~---~~~~~~-~~~l~~~~~~~~~~~~ 81 (198)
T cd08441 14 WLMPVLDQFRERWPD-VELDLSSG---FHFDPLPALLRGELDLVITSDPL---PLPGIA-YEPLFDYEVVLVVAPD 81 (198)
T ss_pred hhHHHHHHHHHhCCC-eEEEEEeC---CchhHHHHHHcCCceEEEecCCc---CCCCcE-EEEccCCcEEEEEcCC
Confidence 456788888888763 45666653 66889999999999999853211 112222 3456667777777654
No 157
>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=88.57 E-value=17 Score=33.74 Aligned_cols=70 Identities=9% Similarity=0.103 Sum_probs=47.2
Q ss_pred eehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEEEeeccccccccccceeecceEEEEEecc
Q 005717 225 GFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTTIVANRSTFVDFTLPYSESGVSMLVLVKD 302 (681)
Q Consensus 225 G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~it~~R~~~vdFT~P~~~~~~~~vv~~~~ 302 (681)
.+..+++..+.+..+ .+.+++... +...+...|.+|++|+++.... .....+. ..|+....+++++++..
T Consensus 13 ~~l~~~l~~~~~~~p-~i~i~i~~~---~~~~~~~~l~~~~~Dl~i~~~~---~~~~~~~-~~~l~~~~~~~v~~~~~ 82 (197)
T cd08414 13 GLLPRLLRRFRARYP-DVELELREM---TTAEQLEALRAGRLDVGFVRPP---PDPPGLA-SRPLLREPLVVALPADH 82 (197)
T ss_pred HHHHHHHHHHHHHCC-CcEEEEecC---ChHHHHHHHHcCCccEEEEcCC---CCCCCee-EEEEeeccEEEEecCCC
Confidence 455678888888765 355666653 6788999999999999986322 1122222 36677788888877553
No 158
>cd08469 PBP2_PnbR The C-terminal substrate binding domain of LysR-type transcriptional regulator PnbR, which is involved in regulating the pnb genes encoding enzymes for 4-nitrobenzoate catabolism, contains the type 2 periplasmic binding fold. PnbR is the regulator of one or both of the two pnb genes that encoding enzymes for 4-nitrobenzoate catabolism. In Pseudomonas putida strain, pnbA encodes a 4-nitrobenzoate reductase, which is responsible for catalyzing the direct reduction of 4-nitrobenzoate to 4-hydroxylaminobenzoate, and pnbB encodes a 4-hydroxylaminobenzoate lyase, which catalyzes the conversion of 4-hydroxylaminobenzoate to 3, 4-dihydroxybenzoic acid and ammonium. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft bet
Probab=88.37 E-value=12 Score=36.08 Aligned_cols=70 Identities=6% Similarity=0.013 Sum_probs=48.0
Q ss_pred eehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEEEeeccccccccccceeecceEEEEEecc
Q 005717 225 GFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTTIVANRSTFVDFTLPYSESGVSMLVLVKD 302 (681)
Q Consensus 225 G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~it~~R~~~vdFT~P~~~~~~~~vv~~~~ 302 (681)
.+..+++..+.++.+ .+++++... +...+.+.|.+|++|++++.. ......+. ..|......++++++..
T Consensus 13 ~~l~~~l~~f~~~~P-~v~l~i~~~---~~~~~~~~l~~g~~Di~i~~~---~~~~~~l~-~~~l~~~~~~~v~~~~~ 82 (221)
T cd08469 13 VLLPALVRRLETEAP-GIDLRIRPV---TRLDLAEQLDLGRIDLVIGIF---EQIPPRFR-RRTLFDEDEVWVMRKDH 82 (221)
T ss_pred HHHHHHHHHHHHHCC-CcEEEEeeC---ChhhHHHHHHCCCccEEEecC---CCCCccce-eeeeeccceEEEEeCCC
Confidence 445677888888766 356666654 677899999999999998632 22223333 46777788888887553
No 159
>cd08467 PBP2_SyrM The C-terminal substrate binding of LysR-type symbiotic regulator SyrM, which activates expression of nodulation gene NodD3, contains the type 2 periplasmic binding fold. Rhizobium is a nitrogen fixing bacteria present in the roots of leguminous plants, which fixes atmospheric nitrogen to the soil. Most Rhizobium species possess multiple nodulation (nod) genes for the development of nodules. For example, Rhizobium meliloti possesses three copies of nodD genes. NodD1 and NodD2 activate nod operons when Rhizobium is exposed to inducers synthesized by the host plant, while NodD3 acts independent of plant inducers and requires the symbiotic regulator SyrM for nod gene expression. SyrM activates the expression of the regulatory nodulation gene nodD3. In turn, NodD3 activates expression of syrM. In addition, SyrM is involved in exopolysaccharide synthesis. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are
Probab=88.28 E-value=18 Score=34.16 Aligned_cols=70 Identities=17% Similarity=0.090 Sum_probs=47.9
Q ss_pred eehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEEEeeccccccccccceeecceEEEEEecc
Q 005717 225 GFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTTIVANRSTFVDFTLPYSESGVSMLVLVKD 302 (681)
Q Consensus 225 G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~it~~R~~~vdFT~P~~~~~~~~vv~~~~ 302 (681)
.+-.+++..+.++.+- +++++... ....++..|.+|++|+++... +.....+. ..+.....+++++++..
T Consensus 13 ~~l~~~l~~~~~~~P~-i~l~~~~~---~~~~~~~~l~~g~~D~~i~~~---~~~~~~~~-~~~l~~~~~~~v~~~~h 82 (200)
T cd08467 13 ALLPRLAPRLRERAPG-LDLRLCPI---GDDLAERGLEQGTIDLAVGRF---AVPPDGLV-VRRLYDDGFACLVRHGH 82 (200)
T ss_pred HHHHHHHHHHHhhCCC-CEEEEecC---CcccHHHHhhCCCcCEEEecC---CCCCccce-eEEeeeccEEEEEcCCC
Confidence 4567888888888763 56777654 667899999999999988531 11122233 35777788888887543
No 160
>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=88.24 E-value=17 Score=34.01 Aligned_cols=70 Identities=16% Similarity=0.099 Sum_probs=46.5
Q ss_pred eehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEEEeeccccccccccceeecceEEEEEecc
Q 005717 225 GFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTTIVANRSTFVDFTLPYSESGVSMLVLVKD 302 (681)
Q Consensus 225 G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~it~~R~~~vdFT~P~~~~~~~~vv~~~~ 302 (681)
.+..+++..+.++.+ .+++++... +...++..|.+|++|+++.... .....+. ..++.+..+++++++..
T Consensus 14 ~~l~~~l~~~~~~~P-~i~i~i~~~---~~~~~~~~l~~~~~Dl~i~~~~---~~~~~~~-~~~l~~~~~~~v~~~~~ 83 (200)
T cd08411 14 YLLPRLLPALRQAYP-KLRLYLRED---QTERLLEKLRSGELDAALLALP---VDEPGLE-EEPLFDEPFLLAVPKDH 83 (200)
T ss_pred hhhHHHHHHHHHHCC-CcEEEEEeC---cHHHHHHHHHcCCccEEEEecc---CCCCCce-EEEeeccceEEEecCCC
Confidence 356688888888765 355666653 6789999999999999986321 1112221 34566777777776543
No 161
>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=88.11 E-value=0.3 Score=49.98 Aligned_cols=26 Identities=15% Similarity=0.378 Sum_probs=21.5
Q ss_pred CcccCccEEEEEee-eCCeeEeeeeeC
Q 005717 137 GQLEPSAFEIFNVI-GTSERVIGYWTK 162 (681)
Q Consensus 137 G~~~~~~~~I~n~~-~~~~~~vG~W~~ 162 (681)
|.+.+..+++++.. ..++++||.|++
T Consensus 265 ~~~~~~~~~~~~~~~~~~~~~vg~w~~ 291 (298)
T cd06269 265 GRRANYDLDIIQLTPSGGFVKVGTWSP 291 (298)
T ss_pred cCcCCceEEEEEECCCCCEEEEEEEcC
Confidence 67767778888887 778999999996
No 162
>PRK12682 transcriptional regulator CysB-like protein; Reviewed
Probab=87.86 E-value=15 Score=38.08 Aligned_cols=71 Identities=14% Similarity=0.074 Sum_probs=48.3
Q ss_pred eehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEEEeeccccccccccceeecceEEEEEecc
Q 005717 225 GFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTTIVANRSTFVDFTLPYSESGVSMLVLVKD 302 (681)
Q Consensus 225 G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~it~~R~~~vdFT~P~~~~~~~~vv~~~~ 302 (681)
.+-.+++..+.+..+- +++++... +.+.++..|.+|++|++++.-.. .....++ +.|+.....+++++...
T Consensus 106 ~~l~~~l~~~~~~~P~-i~i~i~~~---~~~~~~~~l~~g~~D~~i~~~~~--~~~~~l~-~~~l~~~~~~~~~~~~~ 176 (309)
T PRK12682 106 YVLPRVVAAFRKRYPK-VNLSLHQG---SPDEIARMVISGEADIGIATESL--ADDPDLA-TLPCYDWQHAVIVPPDH 176 (309)
T ss_pred HHHHHHHHHHHHhCCC-eEEEEecC---CHHHHHHHHHcCCccEEEecCcc--cCCCcce-EEEeeeeeEEEEecCCC
Confidence 4567888888887752 45666553 67899999999999999863211 1122333 45778888888887654
No 163
>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=87.38 E-value=25 Score=32.73 Aligned_cols=72 Identities=15% Similarity=0.127 Sum_probs=47.6
Q ss_pred eehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEEEeeccccccccccceeecceEEEEEecc
Q 005717 225 GFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTTIVANRSTFVDFTLPYSESGVSMLVLVKD 302 (681)
Q Consensus 225 G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~it~~R~~~vdFT~P~~~~~~~~vv~~~~ 302 (681)
.+-.+++..+.+..+ ++++++... +..+++.++.+|++|+++.... ...+...+. ..|+....+++++++..
T Consensus 13 ~~l~~~l~~~~~~~P-~v~i~i~~~---~~~~~~~~l~~~~~Dl~i~~~~-~~~~~~~~~-~~~l~~~~~~~~~~~~~ 84 (201)
T cd08435 13 VLLPPAIARLLARHP-RLTVRVVEG---TSDELLEGLRAGELDLAIGRLA-DDEQPPDLA-SEELADEPLVVVARPGH 84 (201)
T ss_pred HHHHHHHHHHHHHCC-CeEEEEEeC---CHHHHHHHHHcCCccEEEEecC-cccCCCCcE-EEEcccCcEEEEEeCCC
Confidence 345678888888766 355666543 6788999999999999886321 111122232 45777788888887654
No 164
>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=87.14 E-value=26 Score=32.87 Aligned_cols=71 Identities=11% Similarity=0.099 Sum_probs=48.4
Q ss_pred eehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEEEeeccccccccccceeecceEEEEEecc
Q 005717 225 GFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTTIVANRSTFVDFTLPYSESGVSMLVLVKD 302 (681)
Q Consensus 225 G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~it~~R~~~vdFT~P~~~~~~~~vv~~~~ 302 (681)
++..+++..+.++.+ .+.+++... +...+++.|.+|++|+++..-.. .....+ .+.|+....+++++++..
T Consensus 13 ~~l~~~l~~~~~~~P-~v~l~i~~~---~~~~~~~~l~~g~~Dl~i~~~~~--~~~~~~-~~~~l~~~~~~~~~~~~h 83 (198)
T cd08444 13 YALPWVVQAFKEQFP-NVHLVLHQG---SPEEIASMLANGQADIGIATEAL--ENHPEL-VSFPYYDWHHHIIVPVGH 83 (198)
T ss_pred hhhhHHHHHHHHHCC-CeEEEEEeC---CHHHHHHHHHCCCccEEEecccc--CCCcCc-EEeeccccceeEEecCCC
Confidence 566788888888875 255666653 67889999999999999863111 111223 246777777888887554
No 165
>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=86.93 E-value=23 Score=32.87 Aligned_cols=70 Identities=9% Similarity=0.104 Sum_probs=46.5
Q ss_pred eehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEEEeeccccccccccceeecceEEEEEecc
Q 005717 225 GFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTTIVANRSTFVDFTLPYSESGVSMLVLVKD 302 (681)
Q Consensus 225 G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~it~~R~~~vdFT~P~~~~~~~~vv~~~~ 302 (681)
.+-.+++..+.+..+ .+++++... .-..++.+|.+|++|+++..... ....+. +.+.....+.+++++..
T Consensus 13 ~~l~~~l~~~~~~~P-~~~l~~~~~---~~~~~~~~l~~g~~D~~i~~~~~---~~~~~~-~~~l~~~~~~~v~~~~~ 82 (201)
T cd08420 13 YLLPRLLARFRKRYP-EVRVSLTIG---NTEEIAERVLDGEIDLGLVEGPV---DHPDLI-VEPFAEDELVLVVPPDH 82 (201)
T ss_pred hhhHHHHHHHHHHCC-CceEEEEeC---CcHHHHHHHHCCCccEEEecCCC---CCcceE-EEeecCccEEEEecCCC
Confidence 455678888888865 355666653 56788999999999998864322 122222 35677777777776543
No 166
>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=86.89 E-value=17 Score=37.42 Aligned_cols=85 Identities=13% Similarity=0.074 Sum_probs=55.9
Q ss_pred ceEEEEeeccCCccceEEEeecCCCCeeEEeehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEE
Q 005717 195 RKLKIGVPVREGFTEFIKVVENKNKTTQVSGFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTT 274 (681)
Q Consensus 195 ~~lrV~v~~~~p~~~~~~~~~~~~~~~~~~G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~ 274 (681)
++|+||+..... ..+-.+++..+.++.+ .+.+.+... +...++.++.+|++|++++...
T Consensus 93 ~~l~I~~~~~~~-----------------~~~~~~~l~~~~~~~P-~~~i~~~~~---~~~~~~~~l~~g~~D~~i~~~~ 151 (300)
T TIGR02424 93 PTVRIGALPTVA-----------------ARLMPEVVKRFLARAP-RLRVRIMTG---PNAYLLDQLRVGALDLVVGRLG 151 (300)
T ss_pred ceEEEecccHHH-----------------HhhhHHHHHHHHHhCC-CcEEEEEeC---chHHHHHHHHCCCCCEEEEecC
Confidence 579998764211 2345678888888876 356777664 6788999999999999986432
Q ss_pred EeeccccccccccceeecceEEEEEecc
Q 005717 275 IVANRSTFVDFTLPYSESGVSMLVLVKD 302 (681)
Q Consensus 275 it~~R~~~vdFT~P~~~~~~~~vv~~~~ 302 (681)
. ......+ -..|......++++++..
T Consensus 152 ~-~~~~~~~-~~~~l~~~~~~~~~~~~h 177 (300)
T TIGR02424 152 A-PETMQGL-SFEHLYNEPVVFVVRAGH 177 (300)
T ss_pred C-cccccce-eeeeecCCceEEEEcCCC
Confidence 2 1111222 234677778888877543
No 167
>cd08423 PBP2_LTTR_like_6 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold. LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functi
Probab=86.88 E-value=23 Score=32.87 Aligned_cols=73 Identities=14% Similarity=0.060 Sum_probs=47.9
Q ss_pred eehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEEEe--eccccccccccceeecceEEEEEecc
Q 005717 225 GFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTTIV--ANRSTFVDFTLPYSESGVSMLVLVKD 302 (681)
Q Consensus 225 G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~it--~~R~~~vdFT~P~~~~~~~~vv~~~~ 302 (681)
.+-.+++..+.+..+ .+++++... +...+...+.+|++|+++...... ......+ ...+.....+++++++..
T Consensus 13 ~~l~~~l~~~~~~~P-~i~i~~~~~---~~~~~~~~l~~~~~Dl~i~~~~~~~~~~~~~~~-~~~~l~~~~~~~~~~~~~ 87 (200)
T cd08423 13 ALLPPALAALRARHP-GLEVRLREA---EPPESLDALRAGELDLAVVFDYPVTPPPDDPGL-TRVPLLDDPLDLVLPADH 87 (200)
T ss_pred HhhhHHHHHHHHhCC-CCeEEEEeC---CHHHHHHHHhcCCccEEEEeccccccCCCCCCc-EEEEeccCcEEEEecCCC
Confidence 345678888888875 356777653 668899999999999998632110 0122222 356677788888877554
No 168
>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=86.64 E-value=18 Score=33.74 Aligned_cols=70 Identities=7% Similarity=0.078 Sum_probs=47.8
Q ss_pred eehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEEEeeccccccccccceeecceEEEEEecc
Q 005717 225 GFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTTIVANRSTFVDFTLPYSESGVSMLVLVKD 302 (681)
Q Consensus 225 G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~it~~R~~~vdFT~P~~~~~~~~vv~~~~ 302 (681)
.+...++..+.++.+ .+.+++... ...++...|.+|++|+++... +.....+ ...++.+..+++++++..
T Consensus 14 ~~l~~~l~~~~~~~P-~v~i~i~~~---~~~~~~~~l~~g~~Dl~i~~~---~~~~~~~-~~~~l~~~~~~~v~~~~~ 83 (197)
T cd08425 14 YLIGPLIDRFHARYP-GIALSLREM---PQERIEAALADDRLDLGIAFA---PVRSPDI-DAQPLFDERLALVVGATH 83 (197)
T ss_pred hhhHHHHHHHHHHCC-CcEEEEEEC---cHHHHHHHHHcCCccEEEEec---CCCCCCc-EEEEeccccEEEEecCCC
Confidence 345688888888876 366777664 667899999999999998532 2222222 235677777888777553
No 169
>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=86.60 E-value=19 Score=33.50 Aligned_cols=69 Identities=4% Similarity=-0.036 Sum_probs=48.4
Q ss_pred eehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEEEeeccccccccccceeecceEEEEEec
Q 005717 225 GFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTTIVANRSTFVDFTLPYSESGVSMLVLVK 301 (681)
Q Consensus 225 G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~it~~R~~~vdFT~P~~~~~~~~vv~~~ 301 (681)
.+..+++.++.+..+ .+++++... ...++..+|.+|++|+++.... .....+ .+.|+....+++++++.
T Consensus 13 ~~l~~~l~~~~~~~P-~i~l~i~~~---~~~~~~~~l~~~~~Dl~i~~~~---~~~~~~-~~~~l~~~~~~~v~~~~ 81 (196)
T cd08415 13 SLLPRAIARFRARHP-DVRISLHTL---SSSTVVEAVLSGQADLGLASLP---LDHPGL-ESEPLASGRAVCVLPPG 81 (196)
T ss_pred cccHHHHHHHHHHCC-CcEEEEEec---chHHHHHHHHcCCccEEEEeCC---CCCCcc-eeeeecccceEEEEcCC
Confidence 556788999988875 356777664 6788999999999999986321 112222 35677777888887654
No 170
>PRK10837 putative DNA-binding transcriptional regulator; Provisional
Probab=85.93 E-value=31 Score=35.23 Aligned_cols=83 Identities=13% Similarity=0.125 Sum_probs=53.4
Q ss_pred ceEEEEeeccCCccceEEEeecCCCCeeEEeehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEE
Q 005717 195 RKLKIGVPVREGFTEFIKVVENKNKTTQVSGFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTT 274 (681)
Q Consensus 195 ~~lrV~v~~~~p~~~~~~~~~~~~~~~~~~G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~ 274 (681)
.+++||+....+ ..+-.+++..+.+..+- +.+++... ...+++..|.+|++|+++...
T Consensus 89 g~l~i~~~~~~~-----------------~~~~~~~l~~~~~~~P~-i~i~v~~~---~~~~~~~~l~~g~~Di~i~~~- 146 (290)
T PRK10837 89 GALRIYASSTIG-----------------NYILPAMIARYRRDYPQ-LPLELSVG---NSQDVINAVLDFRVDIGLIEG- 146 (290)
T ss_pred CeEEEEecchhH-----------------hhhhHHHHHHHHHHCCC-ceEEEEEC---CHHHHHHHHHhCCceEEEecC-
Confidence 568898875211 24456788888888753 56666654 678899999999999998532
Q ss_pred EeeccccccccccceeecceEEEEEecc
Q 005717 275 IVANRSTFVDFTLPYSESGVSMLVLVKD 302 (681)
Q Consensus 275 it~~R~~~vdFT~P~~~~~~~~vv~~~~ 302 (681)
+.....+ -..|+....+++++++..
T Consensus 147 --~~~~~~~-~~~~l~~~~~~lv~~~~h 171 (290)
T PRK10837 147 --PCHSPEL-ISEPWLEDELVVFAAPDS 171 (290)
T ss_pred --CCCCCce-eEEEeecceEEEEEcCCC
Confidence 1111222 234566677777776543
No 171
>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=85.75 E-value=33 Score=32.65 Aligned_cols=71 Identities=17% Similarity=0.367 Sum_probs=45.7
Q ss_pred eehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEEEeeccccccccccceeecceEEEEEe
Q 005717 225 GFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTTIVANRSTFVDFTLPYSESGVSMLVLV 300 (681)
Q Consensus 225 G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~it~~R~~~vdFT~P~~~~~~~~vv~~ 300 (681)
.+-.+++..+.+..+ .+++++.. ++...++..|.+|++|+++........-...+ ...|+.+..++++++.
T Consensus 13 ~~l~~~l~~f~~~~P-~v~l~i~~---~~~~~~~~~L~~~~~D~~i~~~~~~~~~~~~~-~~~~l~~~~~~~~~~~ 83 (204)
T cd08429 13 SIAYRLLEPAMDLHE-PIRLVCRE---GKLEQLLADLALHRLDMVLADRPMPSSLDVKG-YSHRLGECGVSFFAAP 83 (204)
T ss_pred HHHHHHHHHHHHhCC-CcEEEEEe---CCHHHHHHHHHcCCccEEEecCCCccccchhe-eeccccccceEEEecC
Confidence 456778888888875 35677766 48899999999999999885322111100111 1347777777666544
No 172
>COG1910 Periplasmic molybdate-binding protein/domain [Inorganic ion transport and metabolism]
Probab=85.59 E-value=21 Score=34.60 Aligned_cols=105 Identities=16% Similarity=0.226 Sum_probs=65.1
Q ss_pred CCCCHHHHHhCCCe-EEEecChhHHHHHh---hhcCCccccccccC----ChhHHHHHHccCcceEEecchhhHHHHHhh
Q 005717 411 SFTDVKDIQKNGYF-VGYQTNSFVKDLLT---KKLNFNETRLKNYT----TSEDYHDALSNGEVAAIFDEIPYIKIFLAS 482 (681)
Q Consensus 411 ~i~s~~dL~~~~~~-vg~~~~s~~~~~l~---~~~~~~~~~~~~~~----~~~~~~~~l~~g~~~a~i~e~~~~~~~~~~ 482 (681)
.|++++||.+.+.+ |--.+||-.+..+. ...+.....+.-|. +-....+++..|+.|+-+... +..++
T Consensus 88 ~i~~~edl~~~d~~fVNR~rGSGTR~LlD~~L~~~~~~~~~I~GY~~e~~th~avA~aVa~G~AD~GvGlr----~~A~~ 163 (223)
T COG1910 88 NISSLEDLLRKDLRFVNRNRGSGTRILLDELLGELNILPDSIKGYSDEATTHDAVASAVASGRADAGVGLR----HAAEK 163 (223)
T ss_pred ccccHHHHhhcCcEEEecCCCccHHHHHHHHHHHcCcCchhcCCccccccccHHHHHHHHcCCCCccccHH----HHHHH
Confidence 48999999976553 33357877776652 22334445566665 344567788999999998844 44444
Q ss_pred cCCceEEECcccccCCcEEEecCCCCChHHHHHHHHhhccC
Q 005717 483 YCSRYMMVGPTYRTDGFGFAFPLGSPLVPYISRAILKVTED 523 (681)
Q Consensus 483 ~c~~l~~v~~~~~~~~~~~~~~k~spl~~~in~~Il~l~e~ 523 (681)
+--++. ++....|-|+.+|+.-=.+.+...+..|...
T Consensus 164 ~gL~Fi----pl~~E~YD~virke~~~~~~vr~fi~~L~s~ 200 (223)
T COG1910 164 YGLDFI----PLGDEEYDFVIRKERLDKPVVRAFIKALKSE 200 (223)
T ss_pred cCCceE----EcccceEEEEEehhHccCHHHHHHHHHhccc
Confidence 421333 3355567899999865555555555555544
No 173
>COG1638 DctP TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]
Probab=85.24 E-value=3.6 Score=43.34 Aligned_cols=210 Identities=14% Similarity=0.105 Sum_probs=118.4
Q ss_pred HHHHHHHHHHcCCCcCeEEEeCCC-CCHHHHHHHHHhCccceEEEeEEEeecccc-ccccccceeecceEEEEEeccCCC
Q 005717 228 YDMFHAVLQVLEFPLPYEFVPFHD-GSFDELLHKIEKQEFDTAVGDTTIVANRST-FVDFTLPYSESGVSMLVLVKDDER 305 (681)
Q Consensus 228 idll~~l~~~l~f~~~~~~v~~~~-g~~~gli~~l~~g~~Dia~~~~~it~~R~~-~vdFT~P~~~~~~~~vv~~~~~~~ 305 (681)
..+-+++.++.|-.+++++.|.+. |.-..++++|..|.+|+.+.+......+.. .--|+.||. ++....
T Consensus 47 ~~fa~~v~ekt~G~l~i~vfP~~qLG~~~~~ie~l~~G~id~~~~s~~~l~~~~P~~~v~~lPfl-------f~d~~~-- 117 (332)
T COG1638 47 KKFAELVEEKTGGRLKIEVFPNSQLGGEAEMIEQLRSGTLDIGVVSLGFLAGLVPEFGVFDLPFL-------FRDEEH-- 117 (332)
T ss_pred HHHHHHHHHHhCCeEEEEECCCcccCcHHHHHHHHhcCCeeEEeccchhhcccCCcceeecCCee-------eCCHHH--
Confidence 455677888999877777777766 888899999999999999877654444332 233455544 322211
Q ss_pred cCceeeeccCcHhHHHHHHHHHHHHHHHhhhhhcccCCCCCCCCCCchhhHHHHHHHHHhccCcccccccchhHHHHHHH
Q 005717 306 KNFWIFLKPLSWDLWLTTGAAFIFTGLVVWVLEHRINTEFRGPPQHQIGTIFWFSFSTLVFAHRERVVNNLSRFVLIIWV 385 (681)
Q Consensus 306 ~~~~~fl~PF~~~vW~~i~~~~~~v~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~s~~~R~l~~~w~ 385 (681)
...++. .++.--+.-.+-- +
T Consensus 118 --~~~~~~---~~~g~~l~~~~e~------------------------------------------------~------- 137 (332)
T COG1638 118 --ARRVLD---SEFGEELLKSLEA------------------------------------------------K------- 137 (332)
T ss_pred --HHHHHc---cHHHHHHHHHHHH------------------------------------------------c-------
Confidence 011110 0000000000000 0
Q ss_pred HHHHHHHhHhhhhhhheeeecccCCCCCCHHHHHhCCCeEEEecChhHHHHHhhhcCCccccccccCChhHHHHHHccCc
Q 005717 386 FVVLILTQSYTASLTSMLTVQRLQPSFTDVKDIQKNGYFVGYQTNSFVKDLLTKKLNFNETRLKNYTTSEDYHDALSNGE 465 (681)
Q Consensus 386 ~~~lil~s~YtA~L~s~LT~~~~~~~i~s~~dL~~~~~~vg~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~g~ 465 (681)
++...+.|.. .+.....-..||++.+||. |.++-+.........+ +.++..+..+ ...|...+|.+|-
T Consensus 138 --g~~~l~~~~~---G~R~~t~~k~PI~~peDlk--GlkiRv~~s~~~~~~~-~a~GA~P~pm----~f~Evy~aLqtGv 205 (332)
T COG1638 138 --GLKGLAFWEN---GFRQFTSNKRPIKTPEDLK--GLKIRVPQSPLLLAMF-KALGANPTPM----PFAEVYTALQTGV 205 (332)
T ss_pred --CCEEEEEecC---ceeeeecCCCCCCChHHhC--CCeeecCCCHHHHHHH-HHcCCCCCCC----CHHHHHHHHHcCC
Confidence 0011111111 1111112233899999999 9999998888877777 7666654332 5678899999999
Q ss_pred ceEEecchhhHH----HHHhhcCCceEEECcccccCCcEEEecCCCC--ChHHHHHHHHhhccC
Q 005717 466 VAAIFDEIPYIK----IFLASYCSRYMMVGPTYRTDGFGFAFPLGSP--LVPYISRAILKVTED 523 (681)
Q Consensus 466 ~~a~i~e~~~~~----~~~~~~c~~l~~v~~~~~~~~~~~~~~k~sp--l~~~in~~Il~l~e~ 523 (681)
+|+.-.....+. |-.++++ +..+- ...++.+.+.+..- |-+...++|++....
T Consensus 206 VDGqEnp~~~i~~~k~~EVqky~---t~tnH--~~~~~~~~~s~~~w~~L~~e~q~il~~aa~e 264 (332)
T COG1638 206 VDGQENPLSNIYSAKLYEVQKYL---TLTNH--IYLPLAVLVSKAFWDSLPEEDQTILLEAAKE 264 (332)
T ss_pred cccccCCHHHHhhccHHHHhHHh---hhccc--cccceeeEEcHHHHhcCCHHHHHHHHHHHHH
Confidence 998765543321 2233333 22222 22345566666532 777777777776655
No 174
>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=84.37 E-value=33 Score=32.24 Aligned_cols=72 Identities=11% Similarity=0.030 Sum_probs=48.6
Q ss_pred EeehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEEEeeccccccccccceeecceEEEEEecc
Q 005717 224 SGFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTTIVANRSTFVDFTLPYSESGVSMLVLVKD 302 (681)
Q Consensus 224 ~G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~it~~R~~~vdFT~P~~~~~~~~vv~~~~ 302 (681)
..+-.+++..+.+..+- +++++... +...+...+.+|++|+++.... ......+. +.++....+++++++..
T Consensus 12 ~~~l~~~l~~f~~~~P~-~~i~i~~~---~~~~~~~~l~~g~~Dl~i~~~~--~~~~~~~~-~~~l~~~~~~~v~~~~h 83 (198)
T cd08443 12 RYVLPPVIKGFIERYPR-VSLQMHQG---SPTQIAEMVSKGLVDFAIATEA--LHDYDDLI-TLPCYHWNRCVVVKRDH 83 (198)
T ss_pred eeECcHHHHHHHHHCCC-eEEEEEeC---CHHHHHHHHHCCCccEEEEecc--ccccCCce-EeeeeeceEEEEEcCCC
Confidence 45677888999888752 45666553 6788999999999999985321 11112232 46677778888876553
No 175
>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=83.99 E-value=37 Score=31.65 Aligned_cols=72 Identities=8% Similarity=0.068 Sum_probs=48.4
Q ss_pred eehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEEEeeccccccccccceeecceEEEEEecc
Q 005717 225 GFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTTIVANRSTFVDFTLPYSESGVSMLVLVKD 302 (681)
Q Consensus 225 G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~it~~R~~~vdFT~P~~~~~~~~vv~~~~ 302 (681)
.+-.+++..+.++.+ .+++++... ....++..|.+|++|+++... ........++ ..+..+..+++++++..
T Consensus 13 ~~l~~~l~~~~~~~P-~v~i~~~~~---~~~~~~~~l~~g~~Dl~i~~~-~~~~~~~~l~-~~~l~~~~~~~~~~~~h 84 (198)
T cd08437 13 YYFPKLAKDLIKTGL-MIQIDTYEG---GSAELLEQLLQGDLDIALLGS-LTPLENSALH-SKIIKTQHFMIIVSKDH 84 (198)
T ss_pred HHhHHHHHHHHHhCC-ceEEEEEEc---CHHHHHHHHHcCCCCEEEecC-CCCCCcccce-EEEeecceEEEEecCCC
Confidence 355678888888876 356777654 678999999999999998531 1111222333 35677777888877553
No 176
>cd08458 PBP2_NocR The C-terminal substrate-domain of LysR-type transcriptional regulator, NocR, involved in the catabolism of nopaline, contains the type 2 periplasmic binding fold. This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulator NocR, which is involved in the catabolism of nopaline. Opines are low molecular weight compounds found in plant crown gall tumors produced by the parasitic bacterium Agrobacterium. There are at least 30 different opines identified so far. Opines are utilized by tumor-colonizing bacteria as a source of carbon, nitrogen, and energy. In Agrobacterium tumefaciens, NocR regulates expression of the divergently transcribed nocB and nocR genes of the nopaline catabolism (noc) region. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, an
Probab=83.88 E-value=33 Score=32.04 Aligned_cols=69 Identities=10% Similarity=0.027 Sum_probs=46.1
Q ss_pred eehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEEEeeccccccccccceeecceEEEEEec
Q 005717 225 GFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTTIVANRSTFVDFTLPYSESGVSMLVLVK 301 (681)
Q Consensus 225 G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~it~~R~~~vdFT~P~~~~~~~~vv~~~ 301 (681)
.+-.+++..+.++.+ .+++++... +..++...|.+|++|+++...... ...+ -+.++.+...+++++..
T Consensus 13 ~~l~~~l~~f~~~~P-~v~i~~~~~---~~~~~~~~l~~g~~Dl~i~~~~~~---~~~~-~~~~l~~~~~~~v~~~~ 81 (196)
T cd08458 13 SFMSGVIQTFIADRP-DVSVYLDTV---PSQTVLELVSLQHYDLGISILAGD---YPGL-TTEPVPSFRAVCLLPPG 81 (196)
T ss_pred hhhHHHHHHHHHHCC-CcEEEEecc---ChHHHHHHHHcCCCCEEEEeccCC---CCCc-eEEEeccCceEEEecCC
Confidence 455678888888876 356666653 667899999999999998632211 1122 23566777777777654
No 177
>PRK12683 transcriptional regulator CysB-like protein; Reviewed
Probab=83.61 E-value=30 Score=35.93 Aligned_cols=183 Identities=10% Similarity=0.043 Sum_probs=106.6
Q ss_pred eehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEEEeeccccccccccceeecceEEEEEeccCC
Q 005717 225 GFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTTIVANRSTFVDFTLPYSESGVSMLVLVKDDE 304 (681)
Q Consensus 225 G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~it~~R~~~vdFT~P~~~~~~~~vv~~~~~~ 304 (681)
.+-..++..+.++.+ .+++++... ++++++..|.+|++|+++..... .....+.+ .|+....+++++++....
T Consensus 106 ~~l~~~i~~f~~~~P-~i~l~~~~~---~~~~~~~~L~~~~~D~~i~~~~~--~~~~~l~~-~~l~~~~~~~v~~~~hpl 178 (309)
T PRK12683 106 YALPKVVRQFKEVFP-KVHLALRQG---SPQEIAEMLLNGEADIGIATEAL--DREPDLVS-FPYYSWHHVVVVPKGHPL 178 (309)
T ss_pred HHHHHHHHHHHHHCC-CceEEEEeC---CHHHHHHHHHcCCccEEEecCCC--CCCCCceE-EEcccCeEEEEecCCCCc
Confidence 344567888887765 255666654 88999999999999998753111 11222333 366777777777754421
Q ss_pred CcCceeeeccCcHhHHHHHHHHHHHHHHHhhhhhcccCCCCCCCCCCchhhHHHHHHHHHhccCcccccccchhHHHHHH
Q 005717 305 RKNFWIFLKPLSWDLWLTTGAAFIFTGLVVWVLEHRINTEFRGPPQHQIGTIFWFSFSTLVFAHRERVVNNLSRFVLIIW 384 (681)
Q Consensus 305 ~~~~~~fl~PF~~~vW~~i~~~~~~v~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~s~~~R~l~~~w 384 (681)
.
T Consensus 179 ~------------------------------------------------------------------------------- 179 (309)
T PRK12683 179 T------------------------------------------------------------------------------- 179 (309)
T ss_pred c-------------------------------------------------------------------------------
Confidence 1
Q ss_pred HHHHHHHHhHhhhhhhheeeecccCCCCCCHHHHHhCCCeEEEecChhHH----HHHhhhcCCccccccccCChhHHHHH
Q 005717 385 VFVVLILTQSYTASLTSMLTVQRLQPSFTDVKDIQKNGYFVGYQTNSFVK----DLLTKKLNFNETRLKNYTTSEDYHDA 460 (681)
Q Consensus 385 ~~~~lil~s~YtA~L~s~LT~~~~~~~i~s~~dL~~~~~~vg~~~~s~~~----~~l~~~~~~~~~~~~~~~~~~~~~~~ 460 (681)
...--+++||.+.. .+....++... .++ +..+.........++.+...+.
T Consensus 180 ------------------------~~~~~~~~~L~~~~-~i~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~ 233 (309)
T PRK12683 180 ------------------------GRENLTLEAIAEYP-IITYDQGFTGRSRIDQAF-AEAGLVPDIVLTALDADVIKTY 233 (309)
T ss_pred ------------------------cCCccCHHHHhcCC-eEeccCCCcHHHHHHHHH-HHCCCCceeEEEeccHHHHHHH
Confidence 00235678887432 34444444333 333 3334433334456677778888
Q ss_pred HccCcceEEecchhhHHHHHhhcCCceEEEC--cccccCCcEEEecCCCCChHHHHHHHHhhccC
Q 005717 461 LSNGEVAAIFDEIPYIKIFLASYCSRYMMVG--PTYRTDGFGFAFPLGSPLVPYISRAILKVTED 523 (681)
Q Consensus 461 l~~g~~~a~i~e~~~~~~~~~~~c~~l~~v~--~~~~~~~~~~~~~k~spl~~~in~~Il~l~e~ 523 (681)
+..|.--+++... ..... ... .+..+. +......++++.+|+.++.......+..+.+.
T Consensus 234 v~~g~Gi~~lp~~-~~~~~--~~~-~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~fi~~l~~~ 294 (309)
T PRK12683 234 VELGMGVGIVAAM-AYDPQ--RDT-GLVALDTDHLFEANTTRVGLRRGAYLRGYAYRFIELFAPH 294 (309)
T ss_pred HHhCCCeEEeehh-hcccc--CCC-ceEEEeCCCCcccceEEEEEECCCcCCHHHHHHHHHHHhh
Confidence 8777544555432 22211 112 455443 22334568899999988877777777666655
No 178
>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=83.19 E-value=38 Score=31.26 Aligned_cols=71 Identities=15% Similarity=0.117 Sum_probs=46.7
Q ss_pred eehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEEEeeccccccccccceeecceEEEEEec
Q 005717 225 GFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTTIVANRSTFVDFTLPYSESGVSMLVLVK 301 (681)
Q Consensus 225 G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~it~~R~~~vdFT~P~~~~~~~~vv~~~ 301 (681)
.+-.+++..+.+..+- +++++... +.+.++..+.+|++|+++..-.. ......+ .+.+.....+++++++.
T Consensus 13 ~~l~~~l~~~~~~~P~-i~l~~~~~---~~~~~~~~l~~g~~Dl~i~~~~~-~~~~~~~-~~~~l~~~~~~~v~~~~ 83 (195)
T cd08427 13 GLLPRALARLRRRHPD-LEVHIVPG---LSAELLARVDAGELDAAIVVEPP-FPLPKDL-VWTPLVREPLVLIAPAE 83 (195)
T ss_pred HHhHHHHHHHHHHCCC-ceEEEEeC---CcHHHHHHHHCCCCCEEEEcCCC-CccccCc-eEEEcccCcEEEEECCC
Confidence 4556788888888752 56666653 67899999999999999863211 1101222 24566777788877654
No 179
>PRK11482 putative DNA-binding transcriptional regulator; Provisional
Probab=82.60 E-value=35 Score=35.67 Aligned_cols=81 Identities=9% Similarity=0.106 Sum_probs=53.5
Q ss_pred ceEEEEeeccCCccceEEEeecCCCCeeEEeehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEE
Q 005717 195 RKLKIGVPVREGFTEFIKVVENKNKTTQVSGFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTT 274 (681)
Q Consensus 195 ~~lrV~v~~~~p~~~~~~~~~~~~~~~~~~G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~ 274 (681)
++++||+..... ..+-..++..+.+..+ +++++.. ..++++..|.+|++|++++...
T Consensus 117 ~~l~Ig~~~~~~-----------------~~~l~~~l~~f~~~~P-~i~i~~~-----~~~~~~~~l~~g~~Dl~i~~~~ 173 (317)
T PRK11482 117 RTITIATTPSVG-----------------ALVMPVIYQAIKTHYP-QLLLRNI-----PISDAENQLSQFQTDLIIDTHS 173 (317)
T ss_pred ceEEEEecHHHH-----------------HHHHHHHHHHHHHHCC-CCEEEEe-----cchhHHHHHHCCCcCEEEeccC
Confidence 578999865211 1356677888888776 3444432 4568999999999999986432
Q ss_pred EeeccccccccccceeecceEEEEEecc
Q 005717 275 IVANRSTFVDFTLPYSESGVSMLVLVKD 302 (681)
Q Consensus 275 it~~R~~~vdFT~P~~~~~~~~vv~~~~ 302 (681)
.....+. +.|+....++++++...
T Consensus 174 ---~~~~~~~-~~~l~~~~~~lv~~~~h 197 (317)
T PRK11482 174 ---CSNRTIQ-HHVLFTDNVVLVCRQGH 197 (317)
T ss_pred ---CCCCceE-EEEEecCcEEEEEeCCC
Confidence 2223343 36777888888887654
No 180
>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=82.44 E-value=41 Score=31.26 Aligned_cols=72 Identities=17% Similarity=0.102 Sum_probs=47.1
Q ss_pred eehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEEEeeccccccccccceeecceEEEEEecc
Q 005717 225 GFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTTIVANRSTFVDFTLPYSESGVSMLVLVKD 302 (681)
Q Consensus 225 G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~it~~R~~~vdFT~P~~~~~~~~vv~~~~ 302 (681)
++-.+++..+.++.+ ++++++... ....+...+.+|++|+++..... ......+ -+.++....+++++++..
T Consensus 13 ~~l~~~l~~~~~~~P-~i~l~i~~~---~~~~~~~~l~~~~~Dl~i~~~~~-~~~~~~l-~~~~l~~~~~~~v~~~~h 84 (199)
T cd08416 13 NTVPRIIMGLKLRRP-ELDIELTLG---SNKDLLKKLKDGELDAILVATPE-GLNDPDF-EVVPLFEDDIFLAVPATS 84 (199)
T ss_pred hhhHHHHHHHHHhCC-CeEEEEEEc---CcHHHHHHHhCCCCCEEEEecCC-cCCCCCe-EEEEeecceEEEEECCCC
Confidence 456788888888875 255666653 56788999999999999863211 0011222 245667777777776543
No 181
>PRK15421 DNA-binding transcriptional regulator MetR; Provisional
Probab=82.43 E-value=22 Score=37.17 Aligned_cols=69 Identities=7% Similarity=0.040 Sum_probs=46.5
Q ss_pred ehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEEEeeccccccccccceeecceEEEEEecc
Q 005717 226 FCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTTIVANRSTFVDFTLPYSESGVSMLVLVKD 302 (681)
Q Consensus 226 ~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~it~~R~~~vdFT~P~~~~~~~~vv~~~~ 302 (681)
+-.+++..+.+..+ .+.+++... .-.++...|.+|++|+++..- +.....+. ..++....++++++...
T Consensus 103 ~l~~~l~~~~~~~P-~i~l~~~~~---~~~~~~~~L~~g~~Dl~i~~~---~~~~~~~~-~~~l~~~~~~lv~~~~h 171 (317)
T PRK15421 103 WLTPALENFHKNWP-QVEMDFKSG---VTFDPQPALQQGELDLVMTSD---ILPRSGLH-YSPMFDYEVRLVLAPDH 171 (317)
T ss_pred HHHHHHHHHHHHCC-CceEEEEeC---ccHHHHHHHHCCCcCEEEecC---cccCCCce-EEEeccceEEEEEcCCC
Confidence 44677888887765 356666553 567889999999999998632 22222333 36777788888887554
No 182
>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=82.42 E-value=41 Score=31.05 Aligned_cols=70 Identities=7% Similarity=-0.050 Sum_probs=48.4
Q ss_pred eehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEEEeeccccccccccceeecceEEEEEecc
Q 005717 225 GFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTTIVANRSTFVDFTLPYSESGVSMLVLVKD 302 (681)
Q Consensus 225 G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~it~~R~~~vdFT~P~~~~~~~~vv~~~~ 302 (681)
.+-.+++..+.++.+ .+++++... ...++...+.+|++|+++... ......+ -+.++....++++++...
T Consensus 13 ~~l~~~l~~~~~~~P-~i~i~i~~~---~~~~~~~~l~~~~~Di~i~~~---~~~~~~~-~~~~l~~~~~~~~~~~~h 82 (197)
T cd08448 13 RGLPRILRAFRAEYP-GIEVALHEM---SSAEQIEALLRGELDLGFVHS---RRLPAGL-SARLLHREPFVCCLPAGH 82 (197)
T ss_pred HHHHHHHHHHHHHCC-CCeEEEEeC---CHHHHHHHHHcCCcceEEEeC---CCCCcCc-eEEEEecCcEEEEeeCCC
Confidence 556788888888875 356777654 788999999999999987532 2222223 245677777887776543
No 183
>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=82.26 E-value=41 Score=30.95 Aligned_cols=71 Identities=10% Similarity=0.023 Sum_probs=47.4
Q ss_pred eehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEEEeeccccccccccceeecceEEEEEecc
Q 005717 225 GFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTTIVANRSTFVDFTLPYSESGVSMLVLVKD 302 (681)
Q Consensus 225 G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~it~~R~~~vdFT~P~~~~~~~~vv~~~~ 302 (681)
.+-.+++..+.+..+ ++.+++... +..++...|.+|++|+++..... .....+ ...+.....++++++...
T Consensus 13 ~~l~~~l~~~~~~~P-~v~i~i~~~---~~~~~~~~l~~~~~Dl~i~~~~~--~~~~~~-~~~~l~~~~~~~~~~~~~ 83 (194)
T cd08436 13 VDLPELLARFHRRHP-GVDIRLRQA---GSDDLLAAVREGRLDLAFVGLPE--RRPPGL-ASRELAREPLVAVVAPDH 83 (194)
T ss_pred HHHHHHHHHHHHHCC-CcEEEEecC---CHHHHHHHHHcCCccEEEEecCC--CCCCCc-EEEEeecceEEEEecCCC
Confidence 456778888888775 356666654 67889999999999999864221 122222 235666677777776543
No 184
>COG0715 TauA ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]
Probab=82.06 E-value=4.4 Score=42.67 Aligned_cols=72 Identities=21% Similarity=0.176 Sum_probs=49.4
Q ss_pred CCCCCHHHHHhCCCeEEEecChh-HHHHH---hhhcCCcccccc-ccCChhHHHHHHccCcceEEecchhhHHHHHhhc
Q 005717 410 PSFTDVKDIQKNGYFVGYQTNSF-VKDLL---TKKLNFNETRLK-NYTTSEDYHDALSNGEVAAIFDEIPYIKIFLASY 483 (681)
Q Consensus 410 ~~i~s~~dL~~~~~~vg~~~~s~-~~~~l---~~~~~~~~~~~~-~~~~~~~~~~~l~~g~~~a~i~e~~~~~~~~~~~ 483 (681)
.+|++++||. |+++|+..++. ..-.+ ....+...+.+. ..-...+...++..|.+|+++...++......+.
T Consensus 126 ~~i~~~adlk--Gk~vg~~~~~~~~~~~l~~~L~~~Gl~~~dv~~v~~~~~~~~~al~~g~vda~~~~ep~~~~~~~~~ 202 (335)
T COG0715 126 SGIKSVADLK--GKKVGVPFGGSTSDFLLRYALAKAGLDPDDVELVNLPPADAVAALAAGQVDAFVVWEPWNAAAEGEG 202 (335)
T ss_pred CCcccccCCC--CceEEEeCCCchHHHHHHHHHHHcCCCcccceEEeeCcHHHHHHHhcCCcceEEecCCchhhhhccC
Confidence 3688899997 99999987764 33222 144456554443 3334558888999999999888777776665554
No 185
>PRK09861 cytoplasmic membrane lipoprotein-28; Provisional
Probab=81.93 E-value=34 Score=34.95 Aligned_cols=122 Identities=11% Similarity=0.065 Sum_probs=62.6
Q ss_pred CCCCCHHHHHhCCCeEEEec--ChhHHHHH-hhhcC---------Cc---------ccccccc-CChhHHHHHHccCcce
Q 005717 410 PSFTDVKDIQKNGYFVGYQT--NSFVKDLL-TKKLN---------FN---------ETRLKNY-TTSEDYHDALSNGEVA 467 (681)
Q Consensus 410 ~~i~s~~dL~~~~~~vg~~~--~s~~~~~l-~~~~~---------~~---------~~~~~~~-~~~~~~~~~l~~g~~~ 467 (681)
..+++++||. .|.+|++.. +...+.++ .+..+ .. +.+++.. -...+...++.+|++|
T Consensus 120 ~~iksl~DL~-~Ga~IAipnd~~n~~ral~lL~~agli~l~~~~g~~~t~~di~~np~~l~~ve~~~~q~~~al~dg~vD 198 (272)
T PRK09861 120 KKIKTVAQIK-EGATVAIPNDPTNLGRALLLLQKEKLITLKEGKGLLPTALDITDNPRHLQIMELEGAQLPRVLDDPKVD 198 (272)
T ss_pred cCCCCHHHcC-CCCEEEEeCCCccHHHHHHHHHHCCCEEEcCCCCCCCCHhHHhcCCCCCEEEEcCHHHhHhhccCcccC
Confidence 4699999996 477899985 22222221 12211 10 1122211 1456677888999899
Q ss_pred EEecchhhHHHHHhhcC-CceEEECcccccCCcEEEecCCCCChHHHHHHHHhhccCccHHHHHHHHH
Q 005717 468 AIFDEIPYIKIFLASYC-SRYMMVGPTYRTDGFGFAFPLGSPLVPYISRAILKVTEDKEKMENIEKAL 534 (681)
Q Consensus 468 a~i~e~~~~~~~~~~~c-~~l~~v~~~~~~~~~~~~~~k~spl~~~in~~Il~l~e~~G~l~~i~~kw 534 (681)
+++...+++.-. .-.. .+-......-....-.++++.+..=.+.+.+.+..++.. ..-+.|.++|
T Consensus 199 ~a~i~~~~~~~a-g~~~~~~~l~~e~~~~~~~n~~~~r~~~~~~~~~~~lv~~~~s~-~v~~~i~~~~ 264 (272)
T PRK09861 199 VAIISTTYIQQT-GLSPVHDSVFIEDKNSPYVNILVAREDNKNAENVKEFLQSYQSP-EVAKAAETIF 264 (272)
T ss_pred EEEEchhHHHHc-CCCcccceeEEcCCCCCeEEEEEEcCCccCCHHHHHHHHHHcCH-HHHHHHHHHc
Confidence 888776665421 0111 111111111111223455665544556677777777766 5555555554
No 186
>PRK09508 leuO leucine transcriptional activator; Reviewed
Probab=81.72 E-value=22 Score=36.99 Aligned_cols=70 Identities=9% Similarity=0.124 Sum_probs=48.7
Q ss_pred eehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEEEeeccccccccccceeecceEEEEEecc
Q 005717 225 GFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTTIVANRSTFVDFTLPYSESGVSMLVLVKD 302 (681)
Q Consensus 225 G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~it~~R~~~vdFT~P~~~~~~~~vv~~~~ 302 (681)
++-.+++..+.++.+- +.+++... +...++..|.+|++|+++.... .....+. ..++....++++++...
T Consensus 125 ~~l~~~l~~f~~~~P~-i~l~i~~~---~~~~~~~~l~~g~~Di~i~~~~---~~~~~l~-~~~l~~~~~~lv~~~~h 194 (314)
T PRK09508 125 RLTSQIYNRIEQIAPN-IHVVFKSS---LNQNIEHQLRYQETEFVISYEE---FDRPEFT-SVPLFKDELVLVASKNH 194 (314)
T ss_pred HHHHHHHHHHHHhCCC-cEEEEEeC---cchhHHHHHhcCCccEEEecCC---CCccccc-eeeeecCceEEEEcCCC
Confidence 4678889999998763 55666653 6688999999999999986422 1122233 24667778888877553
No 187
>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=81.55 E-value=46 Score=31.02 Aligned_cols=73 Identities=10% Similarity=0.012 Sum_probs=47.5
Q ss_pred eehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEEEeeccccccccccceeecceEEEEEecc
Q 005717 225 GFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTTIVANRSTFVDFTLPYSESGVSMLVLVKD 302 (681)
Q Consensus 225 G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~it~~R~~~vdFT~P~~~~~~~~vv~~~~ 302 (681)
.+-.+++..+.+..+ .+++++... ....+...|.+|++|+++............+ -+.|.....+++++++..
T Consensus 13 ~~l~~~l~~~~~~~P-~i~l~i~~~---~~~~~~~~l~~g~~D~~i~~~~~~~~~~~~~-~~~~l~~~~~~~v~~~~h 85 (200)
T cd08453 13 SVLPELVRRFREAYP-DVELQLREA---TSDVQLEALLAGEIDAGIVIPPPGASAPPAL-AYRPLLSEPLVLAVPAAW 85 (200)
T ss_pred HHHHHHHHHHHHhCC-CceEEEEeC---CHHHHHHHHHcCCCCEEEEecCcccCCCcce-eEEEeeeCceEEEEECCC
Confidence 456678888888765 256777654 6778999999999999886321111011122 246677788888877553
No 188
>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=80.69 E-value=58 Score=32.78 Aligned_cols=69 Identities=13% Similarity=0.133 Sum_probs=46.0
Q ss_pred ehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEEEeeccccccccccceeecceEEEEEecc
Q 005717 226 FCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTTIVANRSTFVDFTLPYSESGVSMLVLVKD 302 (681)
Q Consensus 226 ~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~it~~R~~~vdFT~P~~~~~~~~vv~~~~ 302 (681)
+-.+++..+.+..+- +++++... +..+++..|.+|++|+++..-... ...+. ..|+....+++++++..
T Consensus 98 ~~~~~l~~~~~~~p~-v~l~i~~~---~~~~~~~~l~~g~~Dl~i~~~~~~---~~~~~-~~~l~~~~~~lv~s~~~ 166 (279)
T TIGR03339 98 YVLDLVARFRQRYPG-IEVSVRIG---NSQEVLQALQSYRVDVAVSSEVVD---DPRLD-RVVLGNDPLVAVVHRQH 166 (279)
T ss_pred HHHHHHHHHHHHCCC-cEEEEEEC---CHHHHHHHHHcCCCcEEEEecccC---CCceE-EEEcCCceEEEEECCCC
Confidence 456778888877662 45666654 678899999999999998632221 11221 35666777888876553
No 189
>PRK10537 voltage-gated potassium channel; Provisional
Probab=80.69 E-value=6.5 Score=42.47 Aligned_cols=56 Identities=18% Similarity=0.316 Sum_probs=42.5
Q ss_pred CCCCchhhHHHHHHHHHhccC-cc-cccccchhHHHHHHHHHHHHHHhHhhhhhhhee
Q 005717 348 PPQHQIGTIFWFSFSTLVFAH-RE-RVVNNLSRFVLIIWVFVVLILTQSYTASLTSML 403 (681)
Q Consensus 348 ~~~~~~~~~~~~~~~~l~~~~-~~-~~~s~~~R~l~~~w~~~~lil~s~YtA~L~s~L 403 (681)
+...++.+++|+++.++...+ ++ .|.+..+|++.+++.++++.+..+..+.++..+
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 445689999999999887655 33 478889999999999999877665555555433
No 190
>PLN03192 Voltage-dependent potassium channel; Provisional
Probab=80.33 E-value=3.3 Score=49.69 Aligned_cols=54 Identities=17% Similarity=0.320 Sum_probs=46.4
Q ss_pred chhhHHHHHHHHHhccC-cc-cccccchhHHHHHHHHHHHHHHhHhhhhhhheeee
Q 005717 352 QIGTIFWFSFSTLVFAH-RE-RVVNNLSRFVLIIWVFVVLILTQSYTASLTSMLTV 405 (681)
Q Consensus 352 ~~~~~~~~~~~~l~~~~-~~-~~~s~~~R~l~~~w~~~~lil~s~YtA~L~s~LT~ 405 (681)
++..++|+++.+|..-| ++ .|.+...|++.++|+++++++.++..+++++++..
T Consensus 250 ~Yi~slYwai~TmtTVGYGDi~p~t~~E~i~~i~~ml~g~~~~a~~ig~i~~li~~ 305 (823)
T PLN03192 250 RYISAIYWSITTMTTVGYGDLHAVNTIEMIFIIFYMLFNLGLTAYLIGNMTNLVVE 305 (823)
T ss_pred HHHHHHHHHHHHHhhccCCCcCCCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45669999999998755 44 58899999999999999999999999999997643
No 191
>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=80.32 E-value=49 Score=30.57 Aligned_cols=72 Identities=6% Similarity=-0.068 Sum_probs=47.6
Q ss_pred eehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEEEeeccccccccccceeecceEEEEEecc
Q 005717 225 GFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTTIVANRSTFVDFTLPYSESGVSMLVLVKD 302 (681)
Q Consensus 225 G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~it~~R~~~vdFT~P~~~~~~~~vv~~~~ 302 (681)
.+...++..+.++.+ .+++++... ...+++..|.+|++|++++...... +...+. ..++....++++++...
T Consensus 13 ~~l~~~l~~~~~~~P-~i~i~~~~~---~~~~~~~~l~~~~~Dl~i~~~~~~~-~~~~~~-~~~l~~~~~~~v~~~~~ 84 (197)
T cd08449 13 GGLGPALRRFKRQYP-NVTVRFHEL---SPEAQKAALLSKRIDLGFVRFADTL-NDPPLA-SELLWREPMVVALPEEH 84 (197)
T ss_pred hhHHHHHHHHHHHCC-CeEEEEEEC---CHHHHHHHHhCCCccEEEecccccC-CCCCce-EEEEEEeeEEEEecCCC
Confidence 456788888888875 355666653 6788999999999999986322110 122222 35677777777776543
No 192
>PRK12680 transcriptional regulator CysB-like protein; Reviewed
Probab=79.92 E-value=64 Score=33.86 Aligned_cols=196 Identities=8% Similarity=0.022 Sum_probs=117.0
Q ss_pred ceEEEEeeccCCccceEEEeecCCCCeeEEeehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEE
Q 005717 195 RKLKIGVPVREGFTEFIKVVENKNKTTQVSGFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTT 274 (681)
Q Consensus 195 ~~lrV~v~~~~p~~~~~~~~~~~~~~~~~~G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~ 274 (681)
+++|||+..... ..+-.++++.+.++.+- +.+++... ..++++.+|.+|++|+++....
T Consensus 93 g~lrIg~~~~~~-----------------~~~l~~~l~~f~~~~P~-v~i~l~~~---~~~~~~~~l~~g~~Dl~i~~~~ 151 (327)
T PRK12680 93 GQLTLTTTHTQA-----------------RFVLPPAVAQIKQAYPQ-VSVHLQQA---AESAALDLLGQGDADIAIVSTA 151 (327)
T ss_pred eEEEEEecchhH-----------------HHhhHHHHHHHHHHCCC-cEEEEEeC---ChHHHHHHHHCCCCcEEEEecC
Confidence 679999876211 24566888899888873 56777664 6799999999999999985321
Q ss_pred EeeccccccccccceeecceEEEEEeccCCCcCceeeeccCcHhHHHHHHHHHHHHHHHhhhhhcccCCCCCCCCCCchh
Q 005717 275 IVANRSTFVDFTLPYSESGVSMLVLVKDDERKNFWIFLKPLSWDLWLTTGAAFIFTGLVVWVLEHRINTEFRGPPQHQIG 354 (681)
Q Consensus 275 it~~R~~~vdFT~P~~~~~~~~vv~~~~~~~~~~~~fl~PF~~~vW~~i~~~~~~v~~v~~~~~~~~~~~~~~~~~~~~~ 354 (681)
. ....... ..|++....+++++......
T Consensus 152 ~--~~~~~~~-~~~l~~~~~~l~~~~~hpl~------------------------------------------------- 179 (327)
T PRK12680 152 G--GEPSAGI-AVPLYRWRRLVVVPRGHALD------------------------------------------------- 179 (327)
T ss_pred C--CCCCcce-EEEeeccceEEEEeCCChhh-------------------------------------------------
Confidence 1 1111222 46788888888887654211
Q ss_pred hHHHHHHHHHhccCcccccccchhHHHHHHHHHHHHHHhHhhhhhhheeeecccCCCCCCHHHHHhCCCeEEEecChhH-
Q 005717 355 TIFWFSFSTLVFAHRERVVNNLSRFVLIIWVFVVLILTQSYTASLTSMLTVQRLQPSFTDVKDIQKNGYFVGYQTNSFV- 433 (681)
Q Consensus 355 ~~~~~~~~~l~~~~~~~~~s~~~R~l~~~w~~~~lil~s~YtA~L~s~LT~~~~~~~i~s~~dL~~~~~~vg~~~~s~~- 433 (681)
+. ...-+++||.+... +....+...
T Consensus 180 ----------------------------------------------------~~-~~~~~~~dl~~~~~-i~~~~~~~~~ 205 (327)
T PRK12680 180 ----------------------------------------------------TP-RRAPDMAALAEHPL-ISYESSTRPG 205 (327)
T ss_pred ----------------------------------------------------cc-CCCCCHHHHhcCCE-EEecCCCchH
Confidence 00 01246888874332 444444433
Q ss_pred ---HHHHhhhcCCccccccccCChhHHHHHHccCcceEEecchhhHHHHHhhcCCceEEEC--cccccCCcEEEecCCCC
Q 005717 434 ---KDLLTKKLNFNETRLKNYTTSEDYHDALSNGEVAAIFDEIPYIKIFLASYCSRYMMVG--PTYRTDGFGFAFPLGSP 508 (681)
Q Consensus 434 ---~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~g~~~a~i~e~~~~~~~~~~~c~~l~~v~--~~~~~~~~~~~~~k~sp 508 (681)
..++ ...+.........++.+...+++..|..-+++.... +. .....+..+. .......+.++.+++.+
T Consensus 206 ~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~v~~G~Gia~lp~~~-~~----~~~~~l~~~p~~~~~~~~~~~~~~~~~~~ 279 (327)
T PRK12680 206 SSLQRAF-AQLGLEPSIALTALDADLIKTYVRAGLGVGLLAEMA-VN----ANDEDLRAWPAPAPIAECIAWAVLPRDRV 279 (327)
T ss_pred HHHHHHH-HHCCCCCcEEEEECCHHHHHHHHHcCCCEEEeechh-cc----CCCCCeEEEECCCCCCCceEEEEEeCCch
Confidence 3344 333333333345678888889998886556655432 21 1112344332 22222334466788888
Q ss_pred ChHHHHHHHHhhccC
Q 005717 509 LVPYISRAILKVTED 523 (681)
Q Consensus 509 l~~~in~~Il~l~e~ 523 (681)
+.+.+...+..+.+.
T Consensus 280 ~~~~~~~~~~~l~~~ 294 (327)
T PRK12680 280 LRDYALELVHVLAPQ 294 (327)
T ss_pred hHHHHHHHHHHhcCC
Confidence 888888888877776
No 193
>PRK12681 cysB transcriptional regulator CysB; Reviewed
Probab=79.91 E-value=39 Score=35.42 Aligned_cols=83 Identities=12% Similarity=0.023 Sum_probs=53.8
Q ss_pred ceEEEEeeccCCccceEEEeecCCCCeeEEeehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEE
Q 005717 195 RKLKIGVPVREGFTEFIKVVENKNKTTQVSGFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTT 274 (681)
Q Consensus 195 ~~lrV~v~~~~p~~~~~~~~~~~~~~~~~~G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~ 274 (681)
++|+||+..... ..+-.+++..+.+..+ ++++++... +.+.++..|.+|++|+++....
T Consensus 93 g~l~Ig~~~~~~-----------------~~~l~~~l~~f~~~~P-~i~i~i~~~---~~~~~~~~L~~g~iDl~i~~~~ 151 (324)
T PRK12681 93 GSLYIATTHTQA-----------------RYALPPVIKGFIERYP-RVSLHMHQG---SPTQIAEAAAKGNADFAIATEA 151 (324)
T ss_pred CeEEEEechhHH-----------------HHhhHHHHHHHHHHCC-CcEEEEEeC---CHHHHHHHHHcCCCCEEEecCc
Confidence 579999865211 2455678888888775 356666654 7899999999999999986311
Q ss_pred EeeccccccccccceeecceEEEEEec
Q 005717 275 IVANRSTFVDFTLPYSESGVSMLVLVK 301 (681)
Q Consensus 275 it~~R~~~vdFT~P~~~~~~~~vv~~~ 301 (681)
......+. ..|+.....++++++.
T Consensus 152 --~~~~~~l~-~~~l~~~~~~~v~~~~ 175 (324)
T PRK12681 152 --LHLYDDLI-MLPCYHWNRSVVVPPD 175 (324)
T ss_pred --ccCCCCeE-EEEeccceeEEEeCCC
Confidence 11122222 3466666677777644
No 194
>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=79.43 E-value=52 Score=30.38 Aligned_cols=69 Identities=10% Similarity=-0.010 Sum_probs=46.8
Q ss_pred eehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEEEeeccccccccccceeecceEEEEEec
Q 005717 225 GFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTTIVANRSTFVDFTLPYSESGVSMLVLVK 301 (681)
Q Consensus 225 G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~it~~R~~~vdFT~P~~~~~~~~vv~~~ 301 (681)
.+..+++..+.+..+ .+++++... ....+++++.+|++|+++... ......+. +.+.....+++++++.
T Consensus 13 ~~l~~~l~~~~~~~P-~i~~~i~~~---~~~~~~~~l~~g~~Dl~i~~~---~~~~~~~~-~~~l~~~~~~~~~~~~ 81 (196)
T cd08456 13 SFLPRAIKAFLQRHP-DVTISIHTR---DSPTVEQWLSAQQCDLGLVST---LHEPPGIE-RERLLRIDGVCVLPPG 81 (196)
T ss_pred hhHHHHHHHHHHHCC-CcEEEEEeC---CHHHHHHHHHcCCccEEEEec---CCCCCCee-EEEeeccCeEEEecCC
Confidence 456788888988875 356777664 677899999999999998532 11112222 4566667777777654
No 195
>COG0725 ModA ABC-type molybdate transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=77.72 E-value=45 Score=33.76 Aligned_cols=118 Identities=10% Similarity=0.034 Sum_probs=67.4
Q ss_pred CCCHHHHHhC-CCeEEEe------cChhHHHHHhhhcCCc---cccccccCChhHHHHHHccCcceEEecchhhHHHHHh
Q 005717 412 FTDVKDIQKN-GYFVGYQ------TNSFVKDLLTKKLNFN---ETRLKNYTTSEDYHDALSNGEVAAIFDEIPYIKIFLA 481 (681)
Q Consensus 412 i~s~~dL~~~-~~~vg~~------~~s~~~~~l~~~~~~~---~~~~~~~~~~~~~~~~l~~g~~~a~i~e~~~~~~~~~ 481 (681)
+..+++|.+. +.++++- -|.+..+.| ++.+.- ..+++.-.+.++.+..+..|+.|+.+.-...+...-
T Consensus 124 ~~~~~~l~~~~~~~lai~~p~~~P~G~ya~~~l-~~~g~~~~~~~k~v~~~~v~~~l~~V~~G~ad~g~vy~sd~~~~~- 201 (258)
T COG0725 124 IESLEDLLERPDVRLAIGDPKTVPAGKYAKEAL-ELLGLWYTLKDKLVLATNVRQALAYVETGEADAGFVYVSDALLSK- 201 (258)
T ss_pred cccHHHHhcCcCcEEEecCCCCCCchHHHHHHH-HHhchhhhccccEEecCcHHHHHHHHHcCCCCeEEEEEEhhhccC-
Confidence 3336777764 4467763 366666666 444432 346677778888888899999987765443222211
Q ss_pred hcCCceEEECcccc-cCCcEEEecCCCCChHHHHHHHHhhccCccHHHHHHHHH
Q 005717 482 SYCSRYMMVGPTYR-TDGFGFAFPLGSPLVPYISRAILKVTEDKEKMENIEKAL 534 (681)
Q Consensus 482 ~~c~~l~~v~~~~~-~~~~~~~~~k~spl~~~in~~Il~l~e~~G~l~~i~~kw 534 (681)
.-..+..+..... ...|.+++.+++.-.+.--..+.-+... .=+++.++|
T Consensus 202 -~~~~~~~~~~~~~~Pi~y~iav~~~~~~~~~A~~f~~fl~s~--~a~~il~~~ 252 (258)
T COG0725 202 -KVKIVGVFPEDLHSPIVYPIAVLKNAKNPELAKEFVDFLLSP--EAQEILEKY 252 (258)
T ss_pred -CceEEEEcccccCCCeEEEEEEEcCCCCHHHHHHHHHHHhCH--HHHHHHHHc
Confidence 2213344444333 3668899999988644433333333333 334555554
No 196
>PRK11013 DNA-binding transcriptional regulator LysR; Provisional
Probab=77.64 E-value=60 Score=33.57 Aligned_cols=70 Identities=10% Similarity=0.038 Sum_probs=44.7
Q ss_pred eehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEEEeeccccccccccceeecceEEEEEecc
Q 005717 225 GFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTTIVANRSTFVDFTLPYSESGVSMLVLVKD 302 (681)
Q Consensus 225 G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~it~~R~~~vdFT~P~~~~~~~~vv~~~~ 302 (681)
.+-.+++..+.+..+ ++++++... +-..+...|.+|++|+++..... ....+. ..+.......+++++..
T Consensus 107 ~~l~~~l~~~~~~~P-~v~i~i~~~---~~~~~~~~l~~~~~Dl~i~~~~~---~~~~~~-~~~l~~~~~~~~~~~~~ 176 (309)
T PRK11013 107 SLLPGLCQPFLARYP-DVSLNIVPQ---ESPLLEEWLSAQRHDLGLTETLH---TPAGTE-RTELLTLDEVCVLPAGH 176 (309)
T ss_pred hhHHHHHHHHHHHCC-CCeEEEEeC---CHHHHHHHHHcCCCCEEEEcCCC---CCCCce-eeeecceeEEEEEcCCC
Confidence 456788888888775 356777664 55778899999999998863211 111222 33555566666666543
No 197
>COG2358 Imp TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]
Probab=77.14 E-value=20 Score=37.28 Aligned_cols=78 Identities=22% Similarity=0.257 Sum_probs=45.6
Q ss_pred CCCCCHHHHHhCCCeEEEe-cChh----HHHHHhhhcCCccccccc--cCChhHHHHHHccCcceEEecchhh---HHHH
Q 005717 410 PSFTDVKDIQKNGYFVGYQ-TNSF----VKDLLTKKLNFNETRLKN--YTTSEDYHDALSNGEVAAIFDEIPY---IKIF 479 (681)
Q Consensus 410 ~~i~s~~dL~~~~~~vg~~-~~s~----~~~~l~~~~~~~~~~~~~--~~~~~~~~~~l~~g~~~a~i~e~~~---~~~~ 479 (681)
..|++++||. |++|.+- .||. .+..| +..++....+.. .-...+..+++++|.+||++.-... .-..
T Consensus 127 ~~Ikti~DL~--GKrV~iG~~gSgt~~~a~~il-~a~Gi~~~~~~~~~~~~~a~~~~~l~~g~iDA~~~~~G~p~~ai~e 203 (321)
T COG2358 127 AGIKTIADLK--GKRVAIGPPGSGTEATARQIL-EALGITYDDYELDLGLGDAESADALKNGTIDAAFYVAGVPNPAISE 203 (321)
T ss_pred CCcceehhcC--CCEEeecCCCCccHHHHHHHH-HHcCCCCcchhhhhhcCchhhHHHhhCCcccEEEEecCCCCccHHH
Confidence 3699999999 9988874 3333 33344 445554433322 1133445778899999998764322 1123
Q ss_pred HhhcCCceEEEC
Q 005717 480 LASYCSRYMMVG 491 (681)
Q Consensus 480 ~~~~c~~l~~v~ 491 (681)
+...| ++.+++
T Consensus 204 l~~~~-~i~lv~ 214 (321)
T COG2358 204 LATTC-DIVLVP 214 (321)
T ss_pred HHhhC-CeEEEe
Confidence 33347 666663
No 198
>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=76.87 E-value=63 Score=29.96 Aligned_cols=69 Identities=14% Similarity=0.134 Sum_probs=45.4
Q ss_pred eehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEEEeeccccccccccceeecceEEEEEec
Q 005717 225 GFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTTIVANRSTFVDFTLPYSESGVSMLVLVK 301 (681)
Q Consensus 225 G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~it~~R~~~vdFT~P~~~~~~~~vv~~~ 301 (681)
.+-.+++..+.++.+ .+++++... .-.++...|.+|++|+++... +.....+. ..++.+..+++++++.
T Consensus 13 ~~l~~~l~~~~~~~P-~i~l~~~~~---~~~~~~~~l~~~~~Dl~i~~~---~~~~~~~~-~~~l~~~~~~~~~~~~ 81 (196)
T cd08457 13 GFLPRFLAAFLRLRP-NLHLSLMGL---SSSQVLEAVASGRADLGIADG---PLEERQGF-LIETRSLPAVVAVPMG 81 (196)
T ss_pred cccHHHHHHHHHHCC-CeEEEEEec---CcHHHHHHHHcCCccEEEecc---CCCCCCcE-EEEeccCCeEEEeeCC
Confidence 456688899988876 355666653 457888999999999998632 22222222 3456667777777654
No 199
>PRK10094 DNA-binding transcriptional activator AllS; Provisional
Probab=76.20 E-value=92 Score=32.25 Aligned_cols=71 Identities=8% Similarity=0.093 Sum_probs=47.0
Q ss_pred ehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEEEeeccccccccccceeecceEEEEEecc
Q 005717 226 FCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTTIVANRSTFVDFTLPYSESGVSMLVLVKD 302 (681)
Q Consensus 226 ~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~it~~R~~~vdFT~P~~~~~~~~vv~~~~ 302 (681)
+-.+++..+.++.+- +.+.+... +..++.+.|.+|++|++++... .......+. ..|+....+++++++..
T Consensus 107 ~l~~~l~~~~~~~P~-i~l~l~~~---~~~~~~~~l~~g~~D~~i~~~~-~~~~~~~l~-~~~l~~~~~~~v~~~~h 177 (308)
T PRK10094 107 AVAQLLAWLNERYPF-TQFHISRQ---IYMGVWDSLLYEGFSLAIGVTG-TEALANTFS-LDPLGSVQWRFVMAADH 177 (308)
T ss_pred HHHHHHHHHHHhCCC-cEEEEEee---hhhhHHHHHhCCCccEEEeccc-CccccCCee-EEEecceeEEEEECCCC
Confidence 345888899888875 56777653 6688999999999999886211 111112232 34677777777776543
No 200
>KOG1419 consensus Voltage-gated K+ channel KCNQ [Inorganic ion transport and metabolism]
Probab=75.55 E-value=5.1 Score=43.85 Aligned_cols=87 Identities=15% Similarity=0.216 Sum_probs=67.5
Q ss_pred hHHHHHHHHHHHHHHHhhhhhcccCCCCCCCCCCchhhHHHHHHHHHhccC-cc-cccccchhHHHHHHHHHHHHHHhHh
Q 005717 318 DLWLTTGAAFIFTGLVVWVLEHRINTEFRGPPQHQIGTIFWFSFSTLVFAH-RE-RVVNNLSRFVLIIWVFVVLILTQSY 395 (681)
Q Consensus 318 ~vW~~i~~~~~~v~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~-~~-~~~s~~~R~l~~~w~~~~lil~s~Y 395 (681)
..|+.-++.+++.++++|+.|+-...+-.+....++-+++|+..-+++.-| +. .|..+.+|++...+-++++-+-+.=
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 578888999999999999999985544333334578899999999988766 55 4899999999998888887776666
Q ss_pred hhhhhheee
Q 005717 396 TASLTSMLT 404 (681)
Q Consensus 396 tA~L~s~LT 404 (681)
.+-|.|=++
T Consensus 315 AGILGSGfA 323 (654)
T KOG1419|consen 315 AGILGSGFA 323 (654)
T ss_pred cccccchhh
Confidence 666666544
No 201
>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=74.47 E-value=72 Score=29.44 Aligned_cols=70 Identities=11% Similarity=0.094 Sum_probs=47.6
Q ss_pred ehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEEEeeccccccccccceeecceEEEEEecc
Q 005717 226 FCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTTIVANRSTFVDFTLPYSESGVSMLVLVKD 302 (681)
Q Consensus 226 ~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~it~~R~~~vdFT~P~~~~~~~~vv~~~~ 302 (681)
+..++++++.++.+ .+++++... +.+++...+.+|++|+++...... ....+ .+.++....++++++...
T Consensus 15 ~l~~~l~~~~~~~P-~i~l~i~~~---~~~~~~~~l~~g~~Dl~i~~~~~~--~~~~~-~~~~l~~~~~~~v~~~~~ 84 (199)
T cd08451 15 LVPGLIRRFREAYP-DVELTLEEA---NTAELLEALREGRLDAAFVRPPVA--RSDGL-VLELLLEEPMLVALPAGH 84 (199)
T ss_pred ccHHHHHHHHHHCC-CcEEEEecC---ChHHHHHHHHCCCccEEEEecCCC--CCCce-eEEEeecccEEEEecCCC
Confidence 56678899988876 255666654 678899999999999998632211 11122 246677788888876543
No 202
>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=74.46 E-value=44 Score=31.39 Aligned_cols=70 Identities=9% Similarity=0.042 Sum_probs=47.3
Q ss_pred eehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEEEeeccccccccccceeecceEEEEEecc
Q 005717 225 GFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTTIVANRSTFVDFTLPYSESGVSMLVLVKD 302 (681)
Q Consensus 225 G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~it~~R~~~vdFT~P~~~~~~~~vv~~~~ 302 (681)
.+-.+++.++.++.+ ++++++... +...++..|.+|++|+++... ......++ +.++....+.+++++..
T Consensus 14 ~~l~~~l~~f~~~~P-~v~i~i~~~---~~~~l~~~l~~g~~D~~~~~~---~~~~~~~~-~~~l~~~~~~lv~~~~h 83 (198)
T cd08486 14 RSLPLLLRAFLTSTP-TATVSLTHM---TKDEQVEGLLAGTIHVGFSRF---FPRHPGIE-IVNIAQEDLYLAVHRSQ 83 (198)
T ss_pred HHHHHHHHHHHHhCC-CeEEEEEEC---CHHHHHHHHHcCCceEEEecC---CCCCCceE-EEEEeeccEEEEecCCC
Confidence 455678888888875 356666653 789999999999999998531 11112222 45666777888887543
No 203
>PF14503 YhfZ_C: YhfZ C-terminal domain; PDB: 2OZZ_B.
Probab=74.35 E-value=2.7 Score=41.49 Aligned_cols=82 Identities=15% Similarity=0.133 Sum_probs=42.4
Q ss_pred CCeEEEecChhHHHHHhhhcCCccccccccC-ChhHHHHHHccCcceEEecchhhHHHHHhhcCCceEEE--Cc--c-cc
Q 005717 422 GYFVGYQTNSFVKDLLTKKLNFNETRLKNYT-TSEDYHDALSNGEVAAIFDEIPYIKIFLASYCSRYMMV--GP--T-YR 495 (681)
Q Consensus 422 ~~~vg~~~~s~~~~~l~~~~~~~~~~~~~~~-~~~~~~~~l~~g~~~a~i~e~~~~~~~~~~~c~~l~~v--~~--~-~~ 495 (681)
|.+||+-..|.-+..| .+..++..++...+ +..+..+.+.+|.+||.+.... ...... - ++..+ .. . ..
T Consensus 114 GmRVGiD~~S~Dq~~L-T~~~~~gk~Ve~Vei~Y~q~~~~l~~g~IDA~IWN~d--~i~~~~-~-~l~~~~l~~~~~~~~ 188 (232)
T PF14503_consen 114 GMRVGIDPSSIDQKIL-TEAEFEGKNVEFVEIPYNQLLELLRSGEIDAAIWNYD--EIEDKN-F-GLKYVPLKDDPMSKD 188 (232)
T ss_dssp --EEEE-TT-HHHHHH-HHHHHTTS--EEEE--HHHHHHHHHHTS--EEEEE----HHCCHH-C-TEEEEE--SSCHHHH
T ss_pred eeEeecCCCCccHHHH-HHHHhCCCceEEEEecHHHHHHHHHCCCccEEEECCc--cccccc-C-CeeEEeCCchHHHHh
Confidence 7899999999888888 43445544443333 5678899999999999998754 111111 1 33333 11 1 12
Q ss_pred cCCcEEEecCCCC
Q 005717 496 TDGFGFAFPLGSP 508 (681)
Q Consensus 496 ~~~~~~~~~k~sp 508 (681)
...-.++++|+.+
T Consensus 189 ~seAVivi~~~~~ 201 (232)
T PF14503_consen 189 ASEAVIVIRKDNE 201 (232)
T ss_dssp TT-EEEEEETT-H
T ss_pred cCeeEEEEeCCCH
Confidence 3445788888876
No 204
>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=74.22 E-value=73 Score=29.39 Aligned_cols=70 Identities=11% Similarity=0.066 Sum_probs=47.2
Q ss_pred eehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEEEeeccccccccccceeecceEEEEEec
Q 005717 225 GFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTTIVANRSTFVDFTLPYSESGVSMLVLVK 301 (681)
Q Consensus 225 G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~it~~R~~~vdFT~P~~~~~~~~vv~~~ 301 (681)
.+-.+++..+.++.+ .+++++... +...++.+|.+|++|+++...... ....+. ..++.+..+++++++.
T Consensus 13 ~~l~~~l~~~~~~~P-~v~l~~~~~---~~~~~~~~l~~g~~Dl~i~~~~~~--~~~~l~-~~~l~~~~~~~~~~~~ 82 (199)
T cd08430 13 SFLPPILERFRAQHP-QVEIKLHTG---DPADAIDKVLNGEADIAIAARPDK--LPARLA-FLPLATSPLVFIAPNI 82 (199)
T ss_pred eeccHHHHHHHHHCC-CceEEEEeC---CHHHHHHHHHCCCCCEEEEecCCC--CCcccE-EEeeccceEEEEEeCC
Confidence 556788999999986 356777664 788899999999999998632111 111222 3556667777777654
No 205
>PRK11074 putative DNA-binding transcriptional regulator; Provisional
Probab=73.95 E-value=73 Score=32.77 Aligned_cols=85 Identities=11% Similarity=0.040 Sum_probs=54.2
Q ss_pred ceEEEEeeccCCccceEEEeecCCCCeeEEeehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEE
Q 005717 195 RKLKIGVPVREGFTEFIKVVENKNKTTQVSGFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTT 274 (681)
Q Consensus 195 ~~lrV~v~~~~p~~~~~~~~~~~~~~~~~~G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~ 274 (681)
++++||+... +. ..+..+++..+.++.+- +++.+... +..+++..|.+|++|++++...
T Consensus 92 g~l~Ig~~~~--~~---------------~~~l~~~l~~~~~~~p~-i~i~i~~~---~~~~~~~~l~~g~~Dl~i~~~~ 150 (300)
T PRK11074 92 GQLSIAVDNI--VR---------------PDRTRQLIVDFYRHFDD-VELIIRQE---VFNGVWDALADGRVDIAIGATR 150 (300)
T ss_pred ceEEEEEcCc--cc---------------hhHHHHHHHHHHHhCCC-ceEEEEeh---hhhHHHHHHHCCCCCEEEecCc
Confidence 6799998542 11 24456888888888773 45666553 6678999999999999986321
Q ss_pred EeeccccccccccceeecceEEEEEecc
Q 005717 275 IVANRSTFVDFTLPYSESGVSMLVLVKD 302 (681)
Q Consensus 275 it~~R~~~vdFT~P~~~~~~~~vv~~~~ 302 (681)
.......+ -..++....+++++++..
T Consensus 151 -~~~~~~~l-~~~~l~~~~~~~v~~~~h 176 (300)
T PRK11074 151 -AIPVGGRF-AFRDMGMLSWACVVSSDH 176 (300)
T ss_pred -cCCccccc-ceeecccceEEEEEcCCC
Confidence 11111112 234566677778877654
No 206
>PRK14498 putative molybdopterin biosynthesis protein MoeA/LysR substrate binding-domain-containing protein; Provisional
Probab=72.88 E-value=54 Score=38.08 Aligned_cols=103 Identities=16% Similarity=0.147 Sum_probs=60.1
Q ss_pred CCHHHHHhCCCeEEE-ecChhHHHHHh---hhcCCcccc----ccccCChhHHHHHHccCcceEEecchhhHHHHHhhcC
Q 005717 413 TDVKDIQKNGYFVGY-QTNSFVKDLLT---KKLNFNETR----LKNYTTSEDYHDALSNGEVAAIFDEIPYIKIFLASYC 484 (681)
Q Consensus 413 ~s~~dL~~~~~~vg~-~~~s~~~~~l~---~~~~~~~~~----~~~~~~~~~~~~~l~~g~~~a~i~e~~~~~~~~~~~c 484 (681)
-+++||.+.+.++.. ..++..+..+. ++.++.... .....+.+....++..|.+++.+.-.+... ....
T Consensus 514 isl~dL~~~~~plI~~~~gs~~r~~le~~l~~~Gi~~~~i~~~~~e~~s~~~i~~~V~~G~~d~Gi~i~~~~~---~~~l 590 (633)
T PRK14498 514 EGIEDLVRKDVRFVNRQRGSGTRILLDYHLKELAIDPERINGYDREEKTHMAVAAAVAQGRADAGLGIRAAAK---ALGL 590 (633)
T ss_pred CCHHHhccCCcEEEecCCCchHHHHHHHHHHHcCCCHHHCCCcccccCCHHHHHHHHHcCCCcchHhHHHHHH---HcCC
Confidence 478999955335554 45655555442 233444332 345678888999999997777665443211 1111
Q ss_pred CceEEECcccccCCcEEEecCCCCChHHHHHHHHhhccC
Q 005717 485 SRYMMVGPTYRTDGFGFAFPLGSPLVPYISRAILKVTED 523 (681)
Q Consensus 485 ~~l~~v~~~~~~~~~~~~~~k~spl~~~in~~Il~l~e~ 523 (681)
.+..+.+ ..++++.+++......+...+..+.+.
T Consensus 591 -~~i~l~~----~~~~l~~~~~~~~s~a~~aFl~~l~~~ 624 (633)
T PRK14498 591 -DFIPLAE----EEYDLLIPKERLEKPAVRAFLEALKSP 624 (633)
T ss_pred -CCeeeee----EEEEEEEEhhHccCHHHHHHHHHHcCH
Confidence 1222221 246788888877777777777766665
No 207
>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=72.23 E-value=81 Score=29.04 Aligned_cols=70 Identities=9% Similarity=0.010 Sum_probs=47.8
Q ss_pred eehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEEEeeccccccccccceeecceEEEEEecc
Q 005717 225 GFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTTIVANRSTFVDFTLPYSESGVSMLVLVKD 302 (681)
Q Consensus 225 G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~it~~R~~~vdFT~P~~~~~~~~vv~~~~ 302 (681)
.+-.+++..+.++.+- +++++... ....++..|.+|++|+++.... .....+ ...++....+++++++..
T Consensus 13 ~~l~~~l~~~~~~~P~-i~l~i~~~---~~~~~~~~l~~~~~Dl~i~~~~---~~~~~~-~~~~l~~~~~~~~~~~~~ 82 (196)
T cd08450 13 QWLPEVLPILREEHPD-LDVELSSL---FSPQLAEALMRGKLDVAFMRPE---IQSDGI-DYQLLLKEPLIVVLPADH 82 (196)
T ss_pred hhHHHHHHHHHhhCCC-cEEEEEec---ChHHHHHHHhcCCccEEEEeCC---CCCCCc-EEEEEEccceEEEecCCC
Confidence 4567888888888763 56777664 6788999999999999985321 111222 245677777877777543
No 208
>PLN02245 ATP phosphoribosyl transferase
Probab=72.18 E-value=38 Score=36.39 Aligned_cols=103 Identities=10% Similarity=0.083 Sum_probs=56.4
Q ss_pred CCCCHHHHHh-------CCCeEEEecChhHHHHHhhhcCCccccccccC-ChhHHHHHHccCcceEEecchhhHHHHHhh
Q 005717 411 SFTDVKDIQK-------NGYFVGYQTNSFVKDLLTKKLNFNETRLKNYT-TSEDYHDALSNGEVAAIFDEIPYIKIFLAS 482 (681)
Q Consensus 411 ~i~s~~dL~~-------~~~~vg~~~~s~~~~~l~~~~~~~~~~~~~~~-~~~~~~~~l~~g~~~a~i~e~~~~~~~~~~ 482 (681)
.+++++||.. ...+|++.--...++|| ++.+.....+.... +.|- +-.-|-.|++++-...-.-+.++
T Consensus 178 ~~~s~~dL~g~~~~~~~~~~RIATkYp~ltr~ff-~~~Gv~~v~Iv~l~GAvE~---AP~lGlADaIvDIVsTGtTLraN 253 (403)
T PLN02245 178 NINSLKELAQMPQWTEERPLRVVTGFTYLGPKFM-KDNGFKHVTFSTADGALEA---APAMGIADAILDLVSSGTTLREN 253 (403)
T ss_pred ccCCHHHhcccccccccCceEEEeCCHHHHHHHH-HHcCCCeEEEEECcCceec---ccccCchhhhcchhccHHHHHHC
Confidence 4788889873 11589988888888999 55566433443333 3332 23445556666543333333222
Q ss_pred cCCceEEEC--cccccCCcEEEecCCCC-----ChHHHHHHHHhhc
Q 005717 483 YCSRYMMVG--PTYRTDGFGFAFPLGSP-----LVPYISRAILKVT 521 (681)
Q Consensus 483 ~c~~l~~v~--~~~~~~~~~~~~~k~sp-----l~~~in~~Il~l~ 521 (681)
+|.+++ ..+.+. -.++..+++. -++.+...+.+|.
T Consensus 254 ---gLk~i~~~~Il~S~-A~LIan~~sl~~~~~~~~~i~~ll~rl~ 295 (403)
T PLN02245 254 ---NLKEIEGGVVLESQ-AVLVASRRALLERKGALEVVHEILERLE 295 (403)
T ss_pred ---CCEEccCceEEEEE-EEEEEecchhhcchhHHHHHHHHHHHHH
Confidence 577885 444444 4455566654 2224444444443
No 209
>PRK10677 modA molybdate transporter periplasmic protein; Provisional
Probab=72.05 E-value=63 Score=32.67 Aligned_cols=70 Identities=10% Similarity=-0.015 Sum_probs=40.1
Q ss_pred HHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCc-cceEEEeEEEeeccc---ccc-ccc-cceeecceEEEEEec
Q 005717 228 YDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQE-FDTAVGDTTIVANRS---TFV-DFT-LPYSESGVSMLVLVK 301 (681)
Q Consensus 228 idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~-~Dia~~~~~it~~R~---~~v-dFT-~P~~~~~~~~vv~~~ 301 (681)
-++.+.+.++.|.+ +.+... ++ ..+..++.+|. +|+.+.+-.-..++. ..+ ..+ .+|....+++++++.
T Consensus 42 ~~l~~~Fe~~~g~~--v~~~~~--~S-g~l~~qi~~g~~~Dv~~~a~~~~~~~l~~~gl~~~~~~~~~a~n~lvl~~~~~ 116 (257)
T PRK10677 42 QDIAAQYKKEKGVD--VVSSFA--SS-STLARQIEQGAPADLFISADQKWMDYAVDKKAIDTATRYTLLGNSLVVVAPKA 116 (257)
T ss_pred HHHHHHHHhhhCCe--EEEEec--cc-HHHHHHHHcCCCCCEEEECCHHHHHHHHHCCCCCCcchheeecCEEEEEEECC
Confidence 35566666666654 444333 23 36777888777 898877532212221 222 222 357778888888875
Q ss_pred c
Q 005717 302 D 302 (681)
Q Consensus 302 ~ 302 (681)
.
T Consensus 117 ~ 117 (257)
T PRK10677 117 S 117 (257)
T ss_pred C
Confidence 4
No 210
>PRK11716 DNA-binding transcriptional regulator IlvY; Provisional
Probab=69.97 E-value=1e+02 Score=30.78 Aligned_cols=70 Identities=10% Similarity=0.074 Sum_probs=45.8
Q ss_pred eehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEEEeeccccccccccceeecceEEEEEec
Q 005717 225 GFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTTIVANRSTFVDFTLPYSESGVSMLVLVK 301 (681)
Q Consensus 225 G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~it~~R~~~vdFT~P~~~~~~~~vv~~~ 301 (681)
.+..+++..+.+..+- +++++... ...+++..|.+|++|+++..... .....+. ..+.....+++++++.
T Consensus 80 ~~~~~~l~~~~~~~p~-i~l~i~~~---~~~~~~~~l~~~~~D~~i~~~~~--~~~~~~~-~~~l~~~~~~~v~~~~ 149 (269)
T PRK11716 80 SHLPPILDRFRAEHPL-VEIKLTTG---DAADAVEKVQSGEADLAIAAKPE--TLPASVA-FSPIDEIPLVLIAPAL 149 (269)
T ss_pred HHHHHHHHHHHHHCCC-eEEEEEEC---CHHHHHHHHHCCCccEEEEecCC--CCCcceE-EEEcccceEEEEEcCC
Confidence 3566888888888762 55666664 67899999999999999853211 1111122 3556666777776544
No 211
>PRK09906 DNA-binding transcriptional regulator HcaR; Provisional
Probab=68.30 E-value=1.4e+02 Score=30.51 Aligned_cols=70 Identities=13% Similarity=0.088 Sum_probs=49.6
Q ss_pred eehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEEEeeccccccccccceeecceEEEEEecc
Q 005717 225 GFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTTIVANRSTFVDFTLPYSESGVSMLVLVKD 302 (681)
Q Consensus 225 G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~it~~R~~~vdFT~P~~~~~~~~vv~~~~ 302 (681)
.+..+++..+.++.+ .+.+.+... +.++++..|.+|++|+++.... .....++ +.|+....+++++++..
T Consensus 103 ~~l~~~~~~~~~~~p-~v~i~~~~~---~~~~~~~~l~~~~~D~~i~~~~---~~~~~l~-~~~l~~~~~~~v~~~~~ 172 (296)
T PRK09906 103 NLLPKVLPMFRLRHP-DTLIELVSL---ITTQQEEKLRRGELDVGFMRHP---VYSDEID-YLELLDEPLVVVLPVDH 172 (296)
T ss_pred hHHHHHHHHHHHHCC-CeEEEEEeC---CcHHHHHHHHcCCeeEEEecCC---CCCCCce-EEEEecccEEEEecCCC
Confidence 445678888888875 355666654 5688999999999999986432 2233344 36888889999887654
No 212
>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=66.81 E-value=78 Score=32.36 Aligned_cols=129 Identities=21% Similarity=0.304 Sum_probs=76.2
Q ss_pred eeeecccCCCCCCHHHHHhC-----C-CeEEEe-cChhHH---HHHhhhcCCccccccccCChhHHHHHHccCcceEEec
Q 005717 402 MLTVQRLQPSFTDVKDIQKN-----G-YFVGYQ-TNSFVK---DLLTKKLNFNETRLKNYTTSEDYHDALSNGEVAAIFD 471 (681)
Q Consensus 402 ~LT~~~~~~~i~s~~dL~~~-----~-~~vg~~-~~s~~~---~~l~~~~~~~~~~~~~~~~~~~~~~~l~~g~~~a~i~ 471 (681)
.|.+. -..+++|++||++. + ..+|.. .|+..+ ..+.+..+.+ .+.++|+.-.+...++..|.+|+.+.
T Consensus 81 vl~v~-~dsp~~t~~eli~~ak~~p~~~~~g~~g~g~~~hl~~~~l~~~~G~~-~~~Vpy~G~~~~~~allgG~vd~~~~ 158 (274)
T PF03401_consen 81 VLVVR-ADSPYKTLEELIEYAKANPGKLTFGSSGPGSSDHLAAALLAKAAGIK-FTHVPYDGGAEALTALLGGHVDAAFG 158 (274)
T ss_dssp EEEEE-TTSS-SSHHHHHHHHHCSCCC-EEEESSTTSHHHHHHHHHHHHHT----EEEE-SSHHHHHHHHHTTSSSEEEE
T ss_pred EEEEe-CCCccccHHHHHHHHHhCCCCeEEEecCCCchHHHHHHHHHHHhCCc-eEEEEeCCccHHHHHHhCCeeeEEee
Confidence 34443 36689999999752 1 366765 243322 3333444553 35678999999999999999999887
Q ss_pred chhhHHHHHhh-cCCceEEEC----------cccc---------cCCcEEEecCCCC--ChHHHHHHHHhhccCccHHHH
Q 005717 472 EIPYIKIFLAS-YCSRYMMVG----------PTYR---------TDGFGFAFPLGSP--LVPYISRAILKVTEDKEKMEN 529 (681)
Q Consensus 472 e~~~~~~~~~~-~c~~l~~v~----------~~~~---------~~~~~~~~~k~sp--l~~~in~~Il~l~e~~G~l~~ 529 (681)
......-+.+. .-+-|.+.+ +.+. ....+++.|||-| .++.+..++.+..++ -.+++
T Consensus 159 ~~~~~~~~~~~G~~k~Lav~~~~r~~~~pdvPT~~E~G~~d~~~~~~~g~~~p~gtp~~~~~~l~~a~~~~~~~-pe~~~ 237 (274)
T PF03401_consen 159 SPGEALPYVEAGDLKPLAVFSDERSPALPDVPTFKEQGYPDIVFGSWRGLFAPKGTPDEIVDKLADAIKKALED-PEFQE 237 (274)
T ss_dssp EHHHHHHHHHTTSEEEEEECSSS-BTTCTTS-BTTTTT-TTG--EEEEEEEEETTS-HHHHHHHHHHHHHHHT--HHHHH
T ss_pred cHHHHHHHHhCCCceEEEEecCccccccCCCCCHHHhCccceeeeeeeeeecCCCCCHHHHHHHHHHHHHHhCC-HHHHH
Confidence 75444433332 100111111 0111 2235899999988 999999999999999 66665
Q ss_pred HHHH
Q 005717 530 IEKA 533 (681)
Q Consensus 530 i~~k 533 (681)
..++
T Consensus 238 ~~~~ 241 (274)
T PF03401_consen 238 FLEK 241 (274)
T ss_dssp HHHH
T ss_pred HHHH
Confidence 5544
No 213
>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=65.01 E-value=1.2e+02 Score=28.06 Aligned_cols=70 Identities=9% Similarity=0.029 Sum_probs=47.7
Q ss_pred eehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEEEeeccccccccccceeecceEEEEEecc
Q 005717 225 GFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTTIVANRSTFVDFTLPYSESGVSMLVLVKD 302 (681)
Q Consensus 225 G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~it~~R~~~vdFT~P~~~~~~~~vv~~~~ 302 (681)
++-.+++..+.++.+ .+++++.. +.+..+...|.+|++|+++.... .....+ -+.++....+++++++..
T Consensus 14 ~~l~~~i~~~~~~~P-~v~l~i~~---~~~~~~~~~l~~~~~Dl~i~~~~---~~~~~~-~~~~l~~~~~~~v~~~~~ 83 (198)
T cd08446 14 DTVPRLLRAFLTARP-DVTVSLHN---MTKDEQIEALRAGRIHIGFGRFY---PVEPDI-AVENVAQERLYLAVPKSH 83 (198)
T ss_pred HHHHHHHHHHHHHCC-CeEEEEee---CCHHHHHHHHHCCCccEEEEecC---CCCCCc-eeEEeeeccEEEEEeCCC
Confidence 355688888888876 35666665 37888999999999999985321 111222 245677777888777553
No 214
>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=63.36 E-value=1.3e+02 Score=28.03 Aligned_cols=70 Identities=9% Similarity=0.172 Sum_probs=48.0
Q ss_pred eehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEEEeeccccccccccceeecceEEEEEecc
Q 005717 225 GFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTTIVANRSTFVDFTLPYSESGVSMLVLVKD 302 (681)
Q Consensus 225 G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~it~~R~~~vdFT~P~~~~~~~~vv~~~~ 302 (681)
++..+++..+.+..+ .+++++... +..+++..|.+|++|++++... .....+. +.|+....+++++++..
T Consensus 14 ~~l~~~l~~~~~~~P-~i~l~i~~~---~~~~~~~~l~~~~~Dl~i~~~~---~~~~~~~-~~~l~~~~~~~v~~~~h 83 (203)
T cd08445 14 GLLPELIRRFRQAAP-DVEIELIEM---TTVQQIEALKEGRIDVGFGRLR---IEDPAIR-RIVLREEPLVVALPAGH 83 (203)
T ss_pred hHHHHHHHHHHHHCC-CeEEEEEeC---ChHHHHHHHHcCCCcEEEecCC---CCCCCce-eEEEEeccEEEEeeCCC
Confidence 566788888888876 355666653 6789999999999999985321 1112232 45677778888887543
No 215
>PRK11062 nhaR transcriptional activator NhaR; Provisional
Probab=63.10 E-value=1.2e+02 Score=31.00 Aligned_cols=72 Identities=14% Similarity=0.254 Sum_probs=44.3
Q ss_pred eehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEEEeeccccccccccceeecceEEEEEec
Q 005717 225 GFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTTIVANRSTFVDFTLPYSESGVSMLVLVK 301 (681)
Q Consensus 225 G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~it~~R~~~vdFT~P~~~~~~~~vv~~~ 301 (681)
++-.+++..+.+..+ .+++++.. ++.+.+...|.+|++|+++............+ ...|+....++++++.+
T Consensus 106 ~~l~~~l~~f~~~~P-~i~l~~~~---~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~~l-~~~~l~~~~~~~~~~~~ 177 (296)
T PRK11062 106 RLVSRVLLTAVPEDE-SIHLRCFE---STHEMLLEQLSQHKLDMILSDCPVDSTQQEGL-FSKKLGECGVSFFCTNP 177 (296)
T ss_pred hhHHHHHHHHHhcCC-ceEEEEEe---CCHHHHHHHHHcCCCCEEEecCCCccccccch-hhhhhhccCcceEecCC
Confidence 567788888877664 34555544 37889999999999999875321111111222 23466666666665543
No 216
>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=61.45 E-value=1.4e+02 Score=27.71 Aligned_cols=69 Identities=10% Similarity=0.056 Sum_probs=46.6
Q ss_pred eehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEEEeeccccccccccceeecceEEEEEec
Q 005717 225 GFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTTIVANRSTFVDFTLPYSESGVSMLVLVK 301 (681)
Q Consensus 225 G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~it~~R~~~vdFT~P~~~~~~~~vv~~~ 301 (681)
.+-.+++..+.++.+ ++++++... ...++..+|.+|++|+++.. .......+. +.++....+.++++..
T Consensus 13 ~~l~~~l~~~~~~~P-~v~i~i~~~---~~~~~~~~l~~~~~Dl~i~~---~~~~~~~~~-~~~l~~~~~~lv~~~~ 81 (197)
T cd08452 13 EFLPPIVREYRKKFP-SVKVELREL---SSPDQVEELLKGRIDIGFLH---PPIQHTALH-IETVQSSPCVLALPKQ 81 (197)
T ss_pred hHHHHHHHHHHHHCC-CcEEEEEec---ChHHHHHHHHCCCccEEEee---CCCCCCCee-EEEeeeccEEEEEeCC
Confidence 345678888888775 356666653 67889999999999998852 222222333 3566777777777654
No 217
>PRK07377 hypothetical protein; Provisional
Probab=61.29 E-value=22 Score=33.48 Aligned_cols=61 Identities=20% Similarity=0.279 Sum_probs=46.4
Q ss_pred ceEEEEeeccCCccceEEEeecCCCCeeEEeehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEE
Q 005717 195 RKLKIGVPVREGFTEFIKVVENKNKTTQVSGFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVG 271 (681)
Q Consensus 195 ~~lrV~v~~~~p~~~~~~~~~~~~~~~~~~G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~ 271 (681)
.++|+|+.... ...+..-+-.++.++.+.++++ ++.|++++ .+-..+.+++.+|++|++++
T Consensus 75 ~~~Rlgv~~~~------------~~~~~~~~~l~~~l~~~~~~y~--~rlElv~y--~~~~~l~~aL~~~eVh~~c~ 135 (184)
T PRK07377 75 LVMRLGVLEIE------------TETSSVFDQLIDQLRTILDKYH--LRLELVVY--PDLQALEQALRDKEVHAICL 135 (184)
T ss_pred cEEEEEEEecc------------ccccccHHHHHHHHHHHHHHhC--ceeeEEec--CCHHHHHHHHhcCCccEEec
Confidence 46899987641 1122234557788899999999 56888888 68899999999999998866
No 218
>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=57.59 E-value=1.2e+02 Score=27.81 Aligned_cols=64 Identities=5% Similarity=-0.064 Sum_probs=40.0
Q ss_pred ehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEEEeeccccccccccceeecceEEEEEe
Q 005717 226 FCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTTIVANRSTFVDFTLPYSESGVSMLVLV 300 (681)
Q Consensus 226 ~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~it~~R~~~vdFT~P~~~~~~~~vv~~ 300 (681)
+...++..+.+..+ .+++++... . .+.++.+|++|+++... +.....+ .+.++....+++++++
T Consensus 14 ~l~~~l~~~~~~~P-~v~i~~~~~---~---~~~~l~~g~~D~~i~~~---~~~~~~~-~~~~l~~~~~~~v~~~ 77 (194)
T cd08432 14 WLIPRLARFQARHP-DIDLRLSTS---D---RLVDFAREGIDLAIRYG---DGDWPGL-EAERLMDEELVPVCSP 77 (194)
T ss_pred HHHHHhHHHHHHCC-CeEEEEEec---C---CccccccccccEEEEec---CCCCCCc-ceEEccCCcEEEecCH
Confidence 44567777877765 356666653 2 46778999999988532 1111222 2456677777777764
No 219
>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=56.40 E-value=1.7e+02 Score=27.18 Aligned_cols=69 Identities=9% Similarity=0.005 Sum_probs=44.8
Q ss_pred eehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEEEeeccccccccccceeecceEEEEEec
Q 005717 225 GFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTTIVANRSTFVDFTLPYSESGVSMLVLVK 301 (681)
Q Consensus 225 G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~it~~R~~~vdFT~P~~~~~~~~vv~~~ 301 (681)
.+-.+++..+.++.+ .+++++... +-++++.+|.+|++|+++...... ...+. +.++.+..+.+++++.
T Consensus 14 ~~l~~~l~~~~~~~P-~i~l~~~~~---~~~~~~~~l~~~~~D~~i~~~~~~---~~~l~-~~~l~~~~~~~~~~~~ 82 (198)
T cd08485 14 HTLPLLLRQLLSVAP-SATVSLTQM---SKNRQIEALDAGTIDIGFGRFYPY---QEGVV-VRNVTNERLFLGAQKS 82 (198)
T ss_pred HHHHHHHHHHHHhCC-CcEEEEEEC---CHHHHHHHHHcCCccEEEecCCCC---CCCeE-EEEeeccceEEEeCCC
Confidence 455678888888765 356777653 667899999999999988632111 12222 3456666666665543
No 220
>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=55.96 E-value=6 Score=40.14 Aligned_cols=68 Identities=25% Similarity=0.249 Sum_probs=41.6
Q ss_pred CCeEEEecCCccccCCccccccCccceEEEEEecCCChh--HHHHH---HHHHhhcCCCCCCCCCCchhHHHHHHHHHH
Q 005717 4 EGYAWIATQGLSTLLDPVKDMESMQGVLGLRPYIPSSKK--LEHFK---LRWIKSADKPDGSTGGSNLFGLWAYDTVWA 77 (681)
Q Consensus 4 ~~y~WI~t~~~~~~~~~~~~~~~~~Gvlg~~~~~~~~~~--~~~f~---~~~~~~~~~~~~~~~~~~~~~~~aYDav~~ 77 (681)
++++||.+++...........+.++|++++.++.+.... .+.|. ..++... ...++.+++++|||+++
T Consensus 218 ~~~~~i~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~yda~~~ 290 (299)
T cd04509 218 GGYPILGITLGLSDVLLEAGGEAAEGVLTGTPYFPGDPPPESFFFVRAAAREKKKY------EDQPDYFAALAYDAVLL 290 (299)
T ss_pred CCCcEEecccccCHHHHHHhHHhhcCcEEeeccCCCCCChHHHHHHhHHHHHHHHh------CCCCChhhhhhcceeee
Confidence 578999998654332211334678899999887665433 23332 2222221 12467799999999997
No 221
>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=53.36 E-value=1.1e+02 Score=27.95 Aligned_cols=100 Identities=14% Similarity=0.131 Sum_probs=49.6
Q ss_pred CCHHHHHhCCCeEEEec-ChhHHHHHhhhcCCccc---cccccCChhHHHHHHccCcceEEecchhhHHHHHhhcCCceE
Q 005717 413 TDVKDIQKNGYFVGYQT-NSFVKDLLTKKLNFNET---RLKNYTTSEDYHDALSNGEVAAIFDEIPYIKIFLASYCSRYM 488 (681)
Q Consensus 413 ~s~~dL~~~~~~vg~~~-~s~~~~~l~~~~~~~~~---~~~~~~~~~~~~~~l~~g~~~a~i~e~~~~~~~~~~~c~~l~ 488 (681)
-+++||.+... +.... ......++ .+.+.... .....++.+...+++.+|.--+++.+.. +...... . .+.
T Consensus 86 ~~~~dl~~~~~-i~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~Gi~~~p~~~-~~~~~~~-~-~l~ 160 (194)
T cd08481 86 AAPADLAHLPL-LQQTTRPEAWRDWF-EEVGLEVPTAYRGMRFEQFSMLAQAAVAGLGVALLPRFL-IEEELAR-G-RLV 160 (194)
T ss_pred CcHHHHhhCce-EecCCCCcCHHHHH-HHcCCCCCCccCceEeccHHHHHHHHHhCCCeEEecHHH-HHHHHHC-C-CEE
Confidence 36778874322 22221 12234445 33333211 1123467778888888886556666543 3222222 1 233
Q ss_pred EE--CcccccCCcEEEecCCCCChHHHHHHH
Q 005717 489 MV--GPTYRTDGFGFAFPLGSPLVPYISRAI 517 (681)
Q Consensus 489 ~v--~~~~~~~~~~~~~~k~spl~~~in~~I 517 (681)
.. .+......++++.+++.+....+...+
T Consensus 161 ~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~ 191 (194)
T cd08481 161 VPFNLPLTSDKAYYLVYPEDKAESPPVQAFR 191 (194)
T ss_pred eecCccccCCCeEEEEeCcccccCHHHHHHH
Confidence 22 122234578888888877655544443
No 222
>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=53.22 E-value=16 Score=26.44 Aligned_cols=28 Identities=29% Similarity=0.482 Sum_probs=23.0
Q ss_pred HhHHHHHHHHHHHHHHHhhhhhcccCCC
Q 005717 317 WDLWLTTGAAFIFTGLVVWVLEHRINTE 344 (681)
Q Consensus 317 ~~vW~~i~~~~~~v~~v~~~~~~~~~~~ 344 (681)
.++|.++..+++++++++|.+..+....
T Consensus 11 a~~~~l~~~~~~Figiv~wa~~p~~k~~ 38 (48)
T cd01324 11 ADSWGLLYLALFFLGVVVWAFRPGRKKA 38 (48)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCCcchh
Confidence 4689999999999999999998765443
No 223
>PRK13583 hisG ATP phosphoribosyltransferase catalytic subunit; Provisional
Probab=52.45 E-value=2e+02 Score=28.52 Aligned_cols=90 Identities=11% Similarity=0.154 Sum_probs=49.5
Q ss_pred CCCCHHHHHh--------CC--CeEEEecChhHHHHHhhhcCCcc-ccccccCChhHHHHHHccCcceEEecchhhHHHH
Q 005717 411 SFTDVKDIQK--------NG--YFVGYQTNSFVKDLLTKKLNFNE-TRLKNYTTSEDYHDALSNGEVAAIFDEIPYIKIF 479 (681)
Q Consensus 411 ~i~s~~dL~~--------~~--~~vg~~~~s~~~~~l~~~~~~~~-~~~~~~~~~~~~~~~l~~g~~~a~i~e~~~~~~~ 479 (681)
.+++++||.. .+ .+|++.--...+.|+ .+.+.+. .-+..+.+.|-+ -.-|-.|++++-...-.-+
T Consensus 110 ~~~~~~dl~~~~~~~~~~~g~~~RIATkYp~it~~yf-~~~Gv~~~~Iv~l~GsvEla---P~~GlAD~IvDivsTG~TL 185 (228)
T PRK13583 110 DVDTMADLDDVAADFRARHGRRLRIATKYWRLTQQFL-SQKGVQDYRIVESLGATEGA---PANGSAEIIVDITSTGETL 185 (228)
T ss_pred ccCCHHHhhhhhhhhhhccCCceEEEeCCHHHHHHHH-HHcCCceeEEEECCCceecc---cccCcchhhhhhhchhHHH
Confidence 3677777751 12 478888888888899 5556653 233334444432 2345456666543333332
Q ss_pred HhhcCCceEEEC--cccccCCcEEEecCCCC
Q 005717 480 LASYCSRYMMVG--PTYRTDGFGFAFPLGSP 508 (681)
Q Consensus 480 ~~~~c~~l~~v~--~~~~~~~~~~~~~k~sp 508 (681)
.++ +|.+++ ..+.+ .-.++..+.|.
T Consensus 186 r~N---gL~~i~~~~Il~S-sA~LI~n~~s~ 212 (228)
T PRK13583 186 RAN---HLKILSDGVILRS-QACLVRARKAD 212 (228)
T ss_pred HHC---CCEEecCceEEEE-EEEEEEecccc
Confidence 222 577885 44444 44555677764
No 224
>PRK13348 chromosome replication initiation inhibitor protein; Provisional
Probab=52.43 E-value=2.7e+02 Score=28.28 Aligned_cols=65 Identities=14% Similarity=0.035 Sum_probs=42.1
Q ss_pred HHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEEEeeccccccccccceeecceEEEEEec
Q 005717 228 YDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTTIVANRSTFVDFTLPYSESGVSMLVLVK 301 (681)
Q Consensus 228 idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~it~~R~~~vdFT~P~~~~~~~~vv~~~ 301 (681)
.+.+..+.+.- .+.+++... ..++++..|.+|++|+++... ......+. +.|+....++++++..
T Consensus 106 ~~~l~~~~~~~--~i~i~~~~~---~~~~~~~~L~~~~~d~~i~~~---~~~~~~~~-~~~l~~~~~~~v~~~~ 170 (294)
T PRK13348 106 LPALAAVLAGE--RILLELIVD---DQDHTFALLERGEVVGCVSTQ---PKPMRGCL-AEPLGTMRYRCVASPA 170 (294)
T ss_pred HHHHHHHHhCC--CeEEEEEEc---chHHHHHHHhcCCeEEEEecC---CcccCCcc-cccccccceEEEEccc
Confidence 34555554442 455666554 678999999999999987532 21223444 5777888888887654
No 225
>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=51.50 E-value=2e+02 Score=26.42 Aligned_cols=70 Identities=14% Similarity=0.047 Sum_probs=46.3
Q ss_pred eehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEEEeeccccccccccceeecceEEEEEec
Q 005717 225 GFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTTIVANRSTFVDFTLPYSESGVSMLVLVK 301 (681)
Q Consensus 225 G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~it~~R~~~vdFT~P~~~~~~~~vv~~~ 301 (681)
.+-.+++..+.+..+- +++++... ..+.++.+|.+|++|+++..... .....+ .+.++....++++++..
T Consensus 13 ~~l~~~l~~~~~~~P~-v~i~i~~~---~~~~~~~~l~~g~~D~~i~~~~~--~~~~~~-~~~~l~~~~~~~v~~~~ 82 (195)
T cd08431 13 QPLYPLIAEFYQLNKA-TRIRLSEE---VLGGTWDALASGRADLVIGATGE--LPPGGV-KTRPLGEVEFVFAVAPN 82 (195)
T ss_pred HHHHHHHHHHHHHCCC-CceEEEEe---ccchHHHHHhCCCCCEEEEecCC--CCCCce-EEEecccceEEEEEcCC
Confidence 5667889999988763 56777654 56788999999999999863211 111122 24555666777776654
No 226
>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=51.38 E-value=2e+02 Score=26.44 Aligned_cols=65 Identities=8% Similarity=-0.041 Sum_probs=41.8
Q ss_pred hHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEEEeeccccccccccceeecceEEEEEe
Q 005717 227 CYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTTIVANRSTFVDFTLPYSESGVSMLVLV 300 (681)
Q Consensus 227 ~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~it~~R~~~vdFT~P~~~~~~~~vv~~ 300 (681)
...++..+.++. .+++++... +.+.+...+.+|++|+++..- +.....+ .+.++.+...+++++.
T Consensus 15 l~~~l~~f~~~~--~v~l~l~~~---~~~~~~~~l~~~~~D~~i~~~---~~~~~~~-~~~~l~~~~~~~~~~~ 79 (195)
T cd08428 15 FLPALAPVLKRE--RILLDLIVD---DEDRTHDLLRDGEVVGCISTQ---AQPMQGC-RSDYLGSMDYLLVASP 79 (195)
T ss_pred hHHHHHHHHhCc--CeEEEEEeC---CchhHHHHHHcCcceEEEEec---CCCCCCc-eeEEeeeeeEEEEECC
Confidence 445677777773 566777664 677899999999999876421 1122222 3456666667666653
No 227
>PRK11139 DNA-binding transcriptional activator GcvA; Provisional
Probab=51.17 E-value=2.2e+02 Score=29.09 Aligned_cols=105 Identities=8% Similarity=0.053 Sum_probs=51.7
Q ss_pred CCHHHHHhCCCeEEEecChhHHHHHhhhcCCc---cccccccCChhHHHHHHccCcceEEecchhhHHHHHhhcCCceEE
Q 005717 413 TDVKDIQKNGYFVGYQTNSFVKDLLTKKLNFN---ETRLKNYTTSEDYHDALSNGEVAAIFDEIPYIKIFLASYCSRYMM 489 (681)
Q Consensus 413 ~s~~dL~~~~~~vg~~~~s~~~~~l~~~~~~~---~~~~~~~~~~~~~~~~l~~g~~~a~i~e~~~~~~~~~~~c~~l~~ 489 (681)
-+++||.+.. .+....+.....++ ...+.. ......+++.+...+++..|..-+++.+. .......... -...
T Consensus 181 i~~~dL~~~p-~i~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~gi~~lp~~-~~~~~~~~~~-l~~~ 256 (297)
T PRK11139 181 KTPEDLARHT-LLHDDSREDWRAWF-RAAGLDDLNVQQGPIFSHSSMALQAAIHGQGVALGNRV-LAQPEIEAGR-LVCP 256 (297)
T ss_pred CCHHHhhcCc-eEeecCcccHHHHH-HHhCCCCcCcccceeeCCHHHHHHHHHhCCCeEecchh-hhHHHHHCCc-eecc
Confidence 4778888432 23333333444555 333331 11123456777777777777544555443 3332232221 1112
Q ss_pred ECccc-ccCCcEEEecCCCCChHHHHHHHHhhc
Q 005717 490 VGPTY-RTDGFGFAFPLGSPLVPYISRAILKVT 521 (681)
Q Consensus 490 v~~~~-~~~~~~~~~~k~spl~~~in~~Il~l~ 521 (681)
+.+.. ....+.++.+|+.+....+...+..+.
T Consensus 257 ~~~~~~~~~~~~l~~~~~~~~~~~~~~f~~~l~ 289 (297)
T PRK11139 257 FDTVLPSPNAFYLVCPDSQAELPKVAAFRQWLL 289 (297)
T ss_pred cccCcCCCccEEEEeccccccChhHHHHHHHHH
Confidence 22222 235688888888766555555444443
No 228
>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=49.50 E-value=1e+02 Score=29.43 Aligned_cols=76 Identities=13% Similarity=0.126 Sum_probs=46.2
Q ss_pred CCCCHHHHHhCCCeEEEecChhHHHHHhhhcCCccccccccCChhHHHHHHccCcceEEecchhhHHHHHhhcCCceEEE
Q 005717 411 SFTDVKDIQKNGYFVGYQTNSFVKDLLTKKLNFNETRLKNYTTSEDYHDALSNGEVAAIFDEIPYIKIFLASYCSRYMMV 490 (681)
Q Consensus 411 ~i~s~~dL~~~~~~vg~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~g~~~a~i~e~~~~~~~~~~~c~~l~~v 490 (681)
++++++||. +.+|++.-....+.|| .+.+.+-.-+....++|-+ -..|-.|++++-...-.-+.++ +|.++
T Consensus 100 ~~~~~~~l~--~~rIATkyp~i~~~~f-~~~Gi~v~ii~l~GsvE~a---P~~GlaD~IvDiv~TG~TL~~N---gL~~i 170 (182)
T TIGR00070 100 DISSVEDLK--GKRIATKYPNLARRYF-EKKGIDVEIIKLNGSVELA---PLLGLADAIVDIVSTGTTLREN---GLRII 170 (182)
T ss_pred CCCChHHhC--CCEEEECCHHHHHHHH-HHcCCeEEEEECcceeecc---cCCCceeEEEEEeCCHHHHHHC---CCEEe
Confidence 467888987 8899998888889999 5556643333333344332 2366677887654444444433 45555
Q ss_pred Ccccc
Q 005717 491 GPTYR 495 (681)
Q Consensus 491 ~~~~~ 495 (681)
.+.+.
T Consensus 171 e~i~~ 175 (182)
T TIGR00070 171 EVILE 175 (182)
T ss_pred eEEEe
Confidence 44443
No 229
>PRK01686 hisG ATP phosphoribosyltransferase catalytic subunit; Reviewed
Probab=49.06 E-value=2.5e+02 Score=27.52 Aligned_cols=92 Identities=16% Similarity=0.037 Sum_probs=52.9
Q ss_pred CCeEEEecChhHHHHHhhhcCCccccccccCChhHHHHHHccCcceEEecchhhHHHHHhhcCCceEEECcccccCCcEE
Q 005717 422 GYFVGYQTNSFVKDLLTKKLNFNETRLKNYTTSEDYHDALSNGEVAAIFDEIPYIKIFLASYCSRYMMVGPTYRTDGFGF 501 (681)
Q Consensus 422 ~~~vg~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~g~~~a~i~e~~~~~~~~~~~c~~l~~v~~~~~~~~~~~ 501 (681)
+.+|++.-....+.|| ++.+.+-.-+....+.|- +-..|-.|++++-...-.-+.++ +|.++...+.+.. .+
T Consensus 115 ~~rIATkYp~it~~yf-~~~gv~~~iv~l~GsvE~---aP~~GlAD~IvDivsTG~TLr~N---gL~~ie~Il~s~A-~L 186 (215)
T PRK01686 115 RLRVATKYPNIARRYF-AEKGEQVEIIKLYGSVEL---APLVGLADAIVDIVETGNTLRAN---GLVEVEEIMDISA-RL 186 (215)
T ss_pred CCEEEeCCHHHHHHHH-HHcCCeEEEEECcCceee---ccccCCccEEEEeecChHHHHHC---cCEEeeEEEeeEE-EE
Confidence 6789998888888999 555664322333334433 22446667777754444444333 4566765555444 45
Q ss_pred EecCCCC--ChHHHHHHHHhhc
Q 005717 502 AFPLGSP--LVPYISRAILKVT 521 (681)
Q Consensus 502 ~~~k~sp--l~~~in~~Il~l~ 521 (681)
+..+.|. -.+.++..+.+|.
T Consensus 187 I~n~~s~~~k~~~i~~l~~~l~ 208 (215)
T PRK01686 187 IVNRASLKLKREEIRPLIEKLR 208 (215)
T ss_pred EEecccchhhHHHHHHHHHHHH
Confidence 5667665 2245666666654
No 230
>PF06305 DUF1049: Protein of unknown function (DUF1049); InterPro: IPR010445 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=48.46 E-value=33 Score=26.53 Aligned_cols=25 Identities=12% Similarity=0.072 Sum_probs=13.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhcCC
Q 005717 563 IIAGIASMSSLLIYVFNFVCFHRPE 587 (681)
Q Consensus 563 ~il~~g~~lallvfi~E~l~~~~~~ 587 (681)
..+++|++++.++.....+..+++.
T Consensus 26 ~~f~~G~llg~l~~~~~~~~~r~~~ 50 (68)
T PF06305_consen 26 IAFLLGALLGWLLSLPSRLRLRRRI 50 (68)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3345566666666666555444444
No 231
>PF14981 FAM165: FAM165 family
Probab=48.24 E-value=30 Score=24.38 Aligned_cols=33 Identities=9% Similarity=-0.037 Sum_probs=28.6
Q ss_pred cccchhHHHHHHHHHHHHHHHHHHHHHHhhcCC
Q 005717 555 VYSFGGLFIIAGIASMSSLLIYVFNFVCFHRPE 587 (681)
Q Consensus 555 l~~~~g~F~il~~g~~lallvfi~E~l~~~~~~ 587 (681)
++++--++||++.-.++-|+.|..--+|++++.
T Consensus 3 L~~vPlLlYILaaKtlilClaFAgvK~yQ~krl 35 (51)
T PF14981_consen 3 LDNVPLLLYILAAKTLILCLAFAGVKMYQRKRL 35 (51)
T ss_pred hhhchHHHHHHHHHHHHHHHHHhhHHHHHHHHH
Confidence 567888999999999999999999888888765
No 232
>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=47.60 E-value=24 Score=32.98 Aligned_cols=101 Identities=13% Similarity=0.112 Sum_probs=57.7
Q ss_pred CCCHHHHHhCCCeEEEecChhHHHHHhhhcCCccccccccCChhHHHHHHccCcceEEecchhhHHHHHhhcCCceEEEC
Q 005717 412 FTDVKDIQKNGYFVGYQTNSFVKDLLTKKLNFNETRLKNYTTSEDYHDALSNGEVAAIFDEIPYIKIFLASYCSRYMMVG 491 (681)
Q Consensus 412 i~s~~dL~~~~~~vg~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~g~~~a~i~e~~~~~~~~~~~c~~l~~v~ 491 (681)
+.+++||.. +.+|++.--...+.|| ++.+.+..-+..+.+.|-+. ..|-.|++++-...-.-+.++ +|.+++
T Consensus 58 ~~~~~~l~~-~~rIATkyp~l~~~yf-~~~g~~~~ii~l~GsvE~ap---~~glAD~IvDiv~TG~TLr~N---gL~~i~ 129 (163)
T PF01634_consen 58 YKSVEDLKA-GLRIATKYPNLTRRYF-AEKGINVEIIKLSGSVELAP---PLGLADAIVDIVETGTTLRAN---GLKEIE 129 (163)
T ss_dssp GCCGGGGSS-TEEEEES-HHHHHHHH-HHCT-EEEEEE-SS-TTHHH---HTTSSSEEEEEESSSHHHHHT---TEEEEE
T ss_pred CCCHHHhcc-CCEEEECCHHHHHHHH-HHcCCcEEEEEccCCccccC---CCCCCCEEEEeccCcHHHHHC---CCEEeE
Confidence 677788875 6789998888889999 55565544445555655443 356677887754443333333 567776
Q ss_pred cccccCCcEEEecCCCC--ChHHHHHHHHhhc
Q 005717 492 PTYRTDGFGFAFPLGSP--LVPYISRAILKVT 521 (681)
Q Consensus 492 ~~~~~~~~~~~~~k~sp--l~~~in~~Il~l~ 521 (681)
..+.+.. .+...+.+- -.+.++..+.+|.
T Consensus 130 ~i~~s~a-~LI~n~~~~~~k~~~i~~l~~~l~ 160 (163)
T PF01634_consen 130 TILESSA-RLIANKASLKEKEEKIDELVTRLR 160 (163)
T ss_dssp EEEEEEE-EEEEEHHHHHHCHHHHHHHHHHHH
T ss_pred EEEEEEE-EEEEcCccchhhHHHHHHHHHHHH
Confidence 6555444 445455443 2334555555554
No 233
>PRK03635 chromosome replication initiation inhibitor protein; Validated
Probab=46.45 E-value=3.3e+02 Score=27.65 Aligned_cols=66 Identities=12% Similarity=-0.014 Sum_probs=44.4
Q ss_pred hHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEEEeeccccccccccceeecceEEEEEec
Q 005717 227 CYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTTIVANRSTFVDFTLPYSESGVSMLVLVK 301 (681)
Q Consensus 227 ~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~it~~R~~~vdFT~P~~~~~~~~vv~~~ 301 (681)
...++..+.++. .+++++... .-+.++..+.+|++|+++..- ......+ .+.|+.+..++++++..
T Consensus 105 l~~~l~~f~~~~--~i~i~l~~~---~~~~~~~~l~~~~~d~~i~~~---~~~~~~l-~~~~l~~~~~~lv~~~~ 170 (294)
T PRK03635 105 FLPALAPVLARS--GVLLDLVVE---DQDHTAELLRRGEVVGAVTTE---PQPVQGC-RVDPLGAMRYLAVASPA 170 (294)
T ss_pred HHHHHHHHHhCC--CcEEEEEec---CcHHHHHHHhCCCceEEEecc---CCCCCCc-eeeecccceEEEEEcch
Confidence 445677777653 466777664 557889999999999987532 2222222 46777888888887754
No 234
>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=45.31 E-value=1.5e+02 Score=30.61 Aligned_cols=41 Identities=12% Similarity=0.202 Sum_probs=30.2
Q ss_pred hHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEe
Q 005717 227 CYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGD 272 (681)
Q Consensus 227 ~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~ 272 (681)
.-.|++.+.+.+|++++ +... +-.-+...|.+|.+|+.+..
T Consensus 23 ~~~i~~~iLE~~Gy~Ve--~~~~---~~~~~~~al~~GdiD~~~e~ 63 (290)
T TIGR03414 23 TTALASVLLEGLGYQPK--VTLL---SVPVTYAGLKDGDLDVFLGN 63 (290)
T ss_pred HHHHHHHHHHHcCCcce--eEEc---cHHHHHHHHHcCCceEeccc
Confidence 34677788888897654 4443 55777889999999998754
No 235
>KOG3713 consensus Voltage-gated K+ channel KCNB/KCNC [Inorganic ion transport and metabolism]
Probab=43.66 E-value=27 Score=38.04 Aligned_cols=64 Identities=14% Similarity=0.251 Sum_probs=48.3
Q ss_pred HHHHHHHhhhhhcccCCCCCCCCCCchhhHHHHHHHHHhccC-cc-cccccchhHHHHHHHHHHHHHHhH
Q 005717 327 FIFTGLVVWVLEHRINTEFRGPPQHQIGTIFWFSFSTLVFAH-RE-RVVNNLSRFVLIIWVFVVLILTQS 394 (681)
Q Consensus 327 ~~~v~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~-~~-~~~s~~~R~l~~~w~~~~lil~s~ 394 (681)
+++.+.+++++||-.+.. .-.++--++|+++-+|..-| |+ .|++.++|++...-.+.++++.+.
T Consensus 356 I~iFStlvY~~Ek~~~~~----~FtSIPa~~WWaiVTMTTVGYGDm~P~T~~Gklvas~cil~GVLvlAl 421 (477)
T KOG3713|consen 356 IVIFSTLVYFAEKDEPDT----KFTSIPAGFWWAVVTMTTVGYGDMVPVTVLGKLVASLCILCGVLVLAL 421 (477)
T ss_pred HHHHHHHHHHhhhcCCCC----CCccccchhheeeEEEeeecccCccccccchHHHHHHHHHHhHHHhhc
Confidence 445566677888755432 24567789999999998766 44 599999999999999999887664
No 236
>PRK00072 hemC porphobilinogen deaminase; Reviewed
Probab=42.30 E-value=3.3e+02 Score=28.14 Aligned_cols=60 Identities=17% Similarity=0.175 Sum_probs=37.1
Q ss_pred CCHHHHHhCCCeEEEecChhHHHHHhhhcCCccccccccC-ChhHHHHHHccCcceEEecchhhH
Q 005717 413 TDVKDIQKNGYFVGYQTNSFVKDLLTKKLNFNETRLKNYT-TSEDYHDALSNGEVAAIFDEIPYI 476 (681)
Q Consensus 413 ~s~~dL~~~~~~vg~~~~s~~~~~l~~~~~~~~~~~~~~~-~~~~~~~~l~~g~~~a~i~e~~~~ 476 (681)
.+++||.. |..||+-.-. +... -...+|.-+++... +.+.-++.+.+|++|+++.-..-+
T Consensus 113 ~~l~~Lp~-ga~IGTsS~R--R~aq-l~~~~Pdl~~~~iRGNV~TRL~KL~~g~~DaivLA~AGL 173 (295)
T PRK00072 113 KSLDDLPE-GAVVGTSSLR--RQAQ-LLALRPDLEIKPLRGNVDTRLRKLDEGEYDAIILAAAGL 173 (295)
T ss_pred CChhHCCC-CCEEecCcHH--HHHH-HHHHCcCCEEEECccCHHHHHHHhhCCCCCEeehHhhHH
Confidence 56777763 5667763221 1111 11234555555543 889999999999999998755444
No 237
>KOG0498 consensus K+-channel ERG and related proteins, contain PAS/PAC sensor domain [Inorganic ion transport and metabolism; Signal transduction mechanisms]
Probab=40.76 E-value=36 Score=39.58 Aligned_cols=69 Identities=14% Similarity=0.180 Sum_probs=54.4
Q ss_pred chhhHHHHHHHHHhc--cCcccccccchhHHHHHHHHHHHHHHhHhhhhhhheeee-----cccCCCCCCHHHHHh
Q 005717 352 QIGTIFWFSFSTLVF--AHRERVVNNLSRFVLIIWVFVVLILTQSYTASLTSMLTV-----QRLQPSFTDVKDIQK 420 (681)
Q Consensus 352 ~~~~~~~~~~~~l~~--~~~~~~~s~~~R~l~~~w~~~~lil~s~YtA~L~s~LT~-----~~~~~~i~s~~dL~~ 420 (681)
.+..++|+++++|.. ++...+....-.++.++.++++++|.++.-+|+++++.. .+++..+.++++-.+
T Consensus 294 kY~~aLyw~l~tLstvG~g~~~s~~~~E~iFsi~~mi~GllL~A~lIGNmt~~iqs~tsR~~~~r~k~rd~e~~m~ 369 (727)
T KOG0498|consen 294 KYVYALYWGLSTLSTVGYGLVHANNMGEKIFSIFIMLFGLLLFAYLIGNMTALLQSLTSRTEEMRDKMRDAEQWMS 369 (727)
T ss_pred HHHHHHHHHhhHhhhccCCccCCCCcHHHHHHHHHHHHhHHHHHHHHhhHHHhHHHHhHHHHHHHHHHHHHHHHHH
Confidence 456799999999975 335567888999999999999999999999999998743 445555666666554
No 238
>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=40.62 E-value=39 Score=34.86 Aligned_cols=33 Identities=24% Similarity=0.292 Sum_probs=25.4
Q ss_pred hhHHHHHHHHHhh-cCCCCCCCCCCchhHHHHHHHHHHHH
Q 005717 41 KKLEHFKLRWIKS-ADKPDGSTGGSNLFGLWAYDTVWAIA 79 (681)
Q Consensus 41 ~~~~~f~~~~~~~-~~~~~~~~~~~~~~~~~aYDav~~lA 79 (681)
+..++|.++|+++ ... .+..+++.+|||++++|
T Consensus 260 ~~~~~f~~~~~~~~g~~------~~~~~~~~~Yda~~~~~ 293 (312)
T cd06333 260 KVALDFVKAYEAKYGAG------SVSTFGGHAYDALLLLA 293 (312)
T ss_pred HHHHHHHHHHHHHhCCC------CCCchhHHHHHHHHHHH
Confidence 4678899999876 221 25668999999999999
No 239
>TIGR00212 hemC porphobilinogen deaminase. Biosynthesis of cofactors, prosthetic groups, and carriers: Heme and porphyrin
Probab=39.78 E-value=3.2e+02 Score=28.21 Aligned_cols=61 Identities=16% Similarity=0.154 Sum_probs=37.2
Q ss_pred CCHHHHHhCCCeEEEecChhHHHHHhhhcCCccccccccC-ChhHHHHHHccCcceEEecchhhHH
Q 005717 413 TDVKDIQKNGYFVGYQTNSFVKDLLTKKLNFNETRLKNYT-TSEDYHDALSNGEVAAIFDEIPYIK 477 (681)
Q Consensus 413 ~s~~dL~~~~~~vg~~~~s~~~~~l~~~~~~~~~~~~~~~-~~~~~~~~l~~g~~~a~i~e~~~~~ 477 (681)
.+++||.. |..||+- ..+.-.+-....|.-+++... +.+.-++.+.+|++||++.-..-++
T Consensus 109 ~~l~~Lp~-ga~VGTs---S~RR~aql~~~rPdl~i~~iRGNV~TRL~KL~~g~~DaiiLA~AGL~ 170 (292)
T TIGR00212 109 LSLDSLPQ-GAKVGTS---SLRRKAQLKAIRPDLKIEPLRGNIDTRLRKLDEGEYDAIILAEAGLK 170 (292)
T ss_pred CChhHCCC-CCEeccC---CHHHHHHHHHHCCCCEEEECcCCHHHHHHHhcCCCCCEeehHhhHHH
Confidence 46777764 4567762 222211111234555555454 8899999999999999987554443
No 240
>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=39.55 E-value=3.6e+02 Score=27.88 Aligned_cols=61 Identities=20% Similarity=0.242 Sum_probs=36.9
Q ss_pred CCHHHHHhCCCeEEEecChhHHHHHhhhcCCccccccccC-ChhHHHHHHccCcceEEecchhhHH
Q 005717 413 TDVKDIQKNGYFVGYQTNSFVKDLLTKKLNFNETRLKNYT-TSEDYHDALSNGEVAAIFDEIPYIK 477 (681)
Q Consensus 413 ~s~~dL~~~~~~vg~~~~s~~~~~l~~~~~~~~~~~~~~~-~~~~~~~~l~~g~~~a~i~e~~~~~ 477 (681)
.+++||.. |..||+-.-.=... + + ...|.-+++... +.+.-++.+.+|++||++.-..-+.
T Consensus 109 ~~l~~Lp~-ga~IGTsS~RR~aq-l-~-~~rpdl~~~~iRGNV~TRL~KL~~ge~DaiiLA~AGL~ 170 (292)
T cd00494 109 SSLEDLPA-GSVVGTSSLRRQAQ-L-K-RKRPDLKFEPLRGNVDTRLRKLDEGEYDAIILAAAGLK 170 (292)
T ss_pred CChhHCCC-CCEEecCCHHHHHH-H-H-HHCCCCEEEEcCCCHHHHHHHhcCCCCCEeehHhhHHH
Confidence 46777764 55677632211111 1 1 224555555554 8899999999999999987554443
No 241
>PRK10216 DNA-binding transcriptional regulator YidZ; Provisional
Probab=37.00 E-value=4.9e+02 Score=26.83 Aligned_cols=72 Identities=7% Similarity=-0.024 Sum_probs=44.6
Q ss_pred eehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEEEeec-------cccccccccceeecceEEE
Q 005717 225 GFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTTIVAN-------RSTFVDFTLPYSESGVSML 297 (681)
Q Consensus 225 G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~it~~-------R~~~vdFT~P~~~~~~~~v 297 (681)
.+-.+++..+.+..+- +++++... +. ..+..|.+|++|+++..-..... +...+ -+.|+.....+++
T Consensus 110 ~~~~~~l~~f~~~~P~-v~v~i~~~---~~-~~~~~l~~g~~D~~i~~~~~~~~~~~~~~~~~~~~-~~~~l~~~~~~~v 183 (319)
T PRK10216 110 IMLNALSKRIYQRYPQ-ATIKLRNW---DY-DSLDAITRGEVDIGFTGRESHPRSRELLSLLPLAI-DFEVLFSDLPCVW 183 (319)
T ss_pred HHHHHHHHHHHHHCCC-CEEEEEeC---Cc-chHHHHhcCCccEEEecCCCCcccccccccccccc-ceeeeeecceEEE
Confidence 4567888888887763 56666643 33 36899999999998863211110 01112 2355566777788
Q ss_pred EEecc
Q 005717 298 VLVKD 302 (681)
Q Consensus 298 v~~~~ 302 (681)
+++..
T Consensus 184 ~~~~h 188 (319)
T PRK10216 184 LRKDH 188 (319)
T ss_pred EeCCC
Confidence 87654
No 242
>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=36.61 E-value=1.1e+02 Score=24.45 Aligned_cols=19 Identities=21% Similarity=0.333 Sum_probs=13.6
Q ss_pred hhHHHHHHHHHhccccCCC
Q 005717 596 SFWSKIIDLMKHFDQRDPS 614 (681)
Q Consensus 596 ~~~~~~~~~~~~~~~~~~~ 614 (681)
++.+++..+.+.+|..++.
T Consensus 53 rm~eRI~tLE~ILd~e~P~ 71 (75)
T TIGR02976 53 RLEERIDTLERILDAEHPN 71 (75)
T ss_pred HHHHHHHHHHHHHcCCCcC
Confidence 4456777788888887664
No 243
>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=35.79 E-value=37 Score=24.51 Aligned_cols=25 Identities=24% Similarity=0.329 Sum_probs=19.7
Q ss_pred hHHHHHHHHHHHHHHHhhhhhcccC
Q 005717 318 DLWLTTGAAFIFTGLVVWVLEHRIN 342 (681)
Q Consensus 318 ~vW~~i~~~~~~v~~v~~~~~~~~~ 342 (681)
..|.+++++.+++++++|...++..
T Consensus 11 ~~~~~v~~~~~F~gi~~w~~~~~~k 35 (49)
T PF05545_consen 11 RSIGTVLFFVFFIGIVIWAYRPRNK 35 (49)
T ss_pred HHHHHHHHHHHHHHHHHHHHcccch
Confidence 4677888888899999999976543
No 244
>PRK09986 DNA-binding transcriptional activator XapR; Provisional
Probab=35.21 E-value=4.8e+02 Score=26.26 Aligned_cols=85 Identities=13% Similarity=0.097 Sum_probs=54.8
Q ss_pred ceEEEEeeccCCccceEEEeecCCCCeeEEeehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEE
Q 005717 195 RKLKIGVPVREGFTEFIKVVENKNKTTQVSGFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTT 274 (681)
Q Consensus 195 ~~lrV~v~~~~p~~~~~~~~~~~~~~~~~~G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~ 274 (681)
++++||+..... ..+..++++.+.++.+- +.+++... +-++++.+|.+|++|+++....
T Consensus 97 ~~l~I~~~~~~~-----------------~~~l~~~l~~f~~~~p~-i~l~i~~~---~~~~~~~~l~~g~~D~~i~~~~ 155 (294)
T PRK09986 97 GRIEIGIVGTAL-----------------WGRLRPAMRHFLKENPN-VEWLLREL---SPSMQMAALERRELDAGIWRMA 155 (294)
T ss_pred ceEEEEEehHHh-----------------HHHHHHHHHHHHHhCCC-eEEEEEeC---CHHHHHHHHHcCCCCEEEecCC
Confidence 579999765211 24456778888888762 45666543 5678999999999999875211
Q ss_pred EeeccccccccccceeecceEEEEEecc
Q 005717 275 IVANRSTFVDFTLPYSESGVSMLVLVKD 302 (681)
Q Consensus 275 it~~R~~~vdFT~P~~~~~~~~vv~~~~ 302 (681)
.......+. +.|+....+.+++++..
T Consensus 156 -~~~~~~~l~-~~~l~~~~~~~v~~~~~ 181 (294)
T PRK09986 156 -DLEPNPGFT-SRRLHESAFAVAVPEEH 181 (294)
T ss_pred -ccCCCCCeE-EEEeecccEEEEEcCCC
Confidence 011223333 36677788888887654
No 245
>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=34.18 E-value=3.6e+02 Score=24.51 Aligned_cols=69 Identities=12% Similarity=0.045 Sum_probs=45.7
Q ss_pred eehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEEEeeccccccccccceeecceEEEEEec
Q 005717 225 GFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTTIVANRSTFVDFTLPYSESGVSMLVLVK 301 (681)
Q Consensus 225 G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~it~~R~~~vdFT~P~~~~~~~~vv~~~ 301 (681)
.+..+++..+.+..+- +++++... ..+.+...+.+|++|+++... +.....+ .+.+.....++++++..
T Consensus 13 ~~l~~~l~~~~~~~P~-i~v~~~~~---~~~~~~~~l~~g~~D~~i~~~---~~~~~~~-~~~~l~~~~~~~v~~~~ 81 (198)
T cd08447 13 SFLPRLLAAARAALPD-VDLVLREM---VTTDQIEALESGRIDLGLLRP---PFARPGL-ETRPLVREPLVAAVPAG 81 (198)
T ss_pred HHHHHHHHHHHHHCCC-eEEEEEeC---CHHHHHHHHHcCCceEEEecC---CCCCCCe-eEEEeecCceEEEecCC
Confidence 4567888888888763 45666553 788999999999999998531 1111222 23556667777776643
No 246
>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=33.51 E-value=3.6e+02 Score=24.35 Aligned_cols=66 Identities=11% Similarity=0.023 Sum_probs=34.9
Q ss_pred ccCChhHHHHHHccCcceEEecchhhHHHHHhhcCCceEEECcccccCCcEEEecCCCCChHHHHHHH
Q 005717 450 NYTTSEDYHDALSNGEVAAIFDEIPYIKIFLASYCSRYMMVGPTYRTDGFGFAFPLGSPLVPYISRAI 517 (681)
Q Consensus 450 ~~~~~~~~~~~l~~g~~~a~i~e~~~~~~~~~~~c~~l~~v~~~~~~~~~~~~~~k~spl~~~in~~I 517 (681)
..++.....+.+..|.-.+++.+.. ......... -...+........++++.+|+.+....+...+
T Consensus 121 ~~~~~~~~~~~v~~g~Gi~~~p~~~-~~~~~~~~~-l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~f~ 186 (189)
T cd08487 121 VFDSSRLMVEAAMQGAGVALAPAKM-FSREIENGQ-LVQPFKIEVETGSYWLTWLKSKPMTPAMELFR 186 (189)
T ss_pred ccccHHHHHHHHHhCCCeEeehHHH-HHHHHhCCC-EEcccCcccCCCcEEEEecccccCCHHHHHHH
Confidence 3566777777777775555555432 222222221 11122222234567788888887666555544
No 247
>COG3114 CcmD Heme exporter protein D [Intracellular trafficking and secretion]
Probab=32.15 E-value=27 Score=26.68 Aligned_cols=42 Identities=17% Similarity=0.216 Sum_probs=23.9
Q ss_pred HHHHH-HHH-HHHHHHHHHHHHHHhhcCCCCCCCCCchhHHHHH
Q 005717 561 LFIIA-GIA-SMSSLLIYVFNFVCFHRPELNNHDPERSFWSKII 602 (681)
Q Consensus 561 ~F~il-~~g-~~lallvfi~E~l~~~~~~~~~~~~~~~~~~~~~ 602 (681)
.||++ ++| ..+++++++++-++.+++..+....+..+..+++
T Consensus 16 afyVWlA~~~tll~l~~l~v~sv~qrr~iL~~v~r~~aReaR~~ 59 (67)
T COG3114 16 AFYVWLAVGMTLLPLAVLVVHSVLQRRAILRGVARQRAREARLR 59 (67)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34444 344 4566778888888888777543333333344443
No 248
>PF07204 Orthoreo_P10: Orthoreovirus membrane fusion protein p10; InterPro: IPR009854 This family consists of several Orthoreovirus membrane fusion protein p10 sequences. p10 is thought to be a multifunctional protein that plays a key role in virus-host interaction [].
Probab=32.05 E-value=83 Score=26.12 Aligned_cols=9 Identities=11% Similarity=0.512 Sum_probs=4.0
Q ss_pred CCCCCCCCC
Q 005717 536 NQATCEGQG 544 (681)
Q Consensus 536 ~~~~c~~~~ 544 (681)
.+..|....
T Consensus 17 g~vhcqa~~ 25 (98)
T PF07204_consen 17 GNVHCQASQ 25 (98)
T ss_pred cchheeccc
Confidence 334455433
No 249
>PF15179 Myc_target_1: Myc target protein 1
Probab=31.50 E-value=61 Score=30.44 Aligned_cols=38 Identities=13% Similarity=0.071 Sum_probs=28.2
Q ss_pred ccccccccchhHHHH-HHHHHHHHHHHHHHHHHHhhcCC
Q 005717 550 SDSLSVYSFGGLFII-AGIASMSSLLIYVFNFVCFHRPE 587 (681)
Q Consensus 550 ~~~L~l~~~~g~F~i-l~~g~~lallvfi~E~l~~~~~~ 587 (681)
.+.++++++.-+|.+ +++|++|+.+|+++-.+..||+.
T Consensus 13 ~~~f~~~~lIlaF~vSm~iGLviG~li~~LltwlSRRRA 51 (197)
T PF15179_consen 13 LENFDWEDLILAFCVSMAIGLVIGALIWALLTWLSRRRA 51 (197)
T ss_pred hhhcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence 345667788888866 57889998888888766666665
No 250
>TIGR01276 thiB thiamine ABC transporter, periplasmic binding protein. This model finds the thiamine (and thiamine pyrophosphate) ABC transporter periplasmic binding protein ThiB in proteobacteria. Completed genomes having this protein (E. coli, Vibrio cholera, Haemophilus influenzae) also have the permease ThiP, described by TIGRFAMs equivalog model TIGR01253.
Probab=30.87 E-value=6e+02 Score=26.02 Aligned_cols=74 Identities=8% Similarity=-0.100 Sum_probs=39.5
Q ss_pred ccCChhHHHHHHccCcceEEecchhhHHH-HHhhcCCceE--EECcccccCCcEEEecCCCCChHHHHHHHHhhccC
Q 005717 450 NYTTSEDYHDALSNGEVAAIFDEIPYIKI-FLASYCSRYM--MVGPTYRTDGFGFAFPLGSPLVPYISRAILKVTED 523 (681)
Q Consensus 450 ~~~~~~~~~~~l~~g~~~a~i~e~~~~~~-~~~~~c~~l~--~v~~~~~~~~~~~~~~k~spl~~~in~~Il~l~e~ 523 (681)
.+.+..+....+.+|++++.+.......+ .....-..+. ..++-......+++++||+|=.+.-.+.|.-+...
T Consensus 175 ~~~~~~~~~~~~~~Ge~~i~i~~~~~~~~~~~~~~~~~~~~~~~~eG~~~~~~~~ai~k~a~n~e~A~~Fidflls~ 251 (309)
T TIGR01276 175 VTKGWSEAYGLFLKGESDLVLSYTTSPAYHILEEKKDNYAAANFSEGHYLQVEVAARTAASKQPELAQKFLQFLVSP 251 (309)
T ss_pred eCCChHHHHHHHHcCCcCEEEecCCcHHHHhhcccCcccceEecCCCCEeEEEEEEEeCCCCCHHHHHHHHHHHcCH
Confidence 33444566678899999887654321111 1111111222 22222222335788899999666666666665544
No 251
>PRK03601 transcriptional regulator HdfR; Provisional
Probab=30.79 E-value=93 Score=31.54 Aligned_cols=83 Identities=11% Similarity=0.081 Sum_probs=57.5
Q ss_pred ceEEEEeeccCCccceEEEeecCCCCeeEEeehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEE
Q 005717 195 RKLKIGVPVREGFTEFIKVVENKNKTTQVSGFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTT 274 (681)
Q Consensus 195 ~~lrV~v~~~~p~~~~~~~~~~~~~~~~~~G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~ 274 (681)
++++||+.... ...+-.+++..+.+..+- +.++++.. ...+++..|.+|++|+++....
T Consensus 89 ~~l~Ig~~~~~-----------------~~~~l~~~l~~f~~~~P~-v~v~~~~~---~~~~~~~~l~~g~~Dl~i~~~~ 147 (275)
T PRK03601 89 NELSIGASASL-----------------WECMLTPWLGRLYQNQEA-LQFEARIA---QRQSLVKQLHERQLDLLITTEA 147 (275)
T ss_pred ceEEEeccHHH-----------------HHHHHHHHHHHHHHhCCC-cEEEEEEC---ChHHHHHHHHcCCCCEEEEcCC
Confidence 56888876521 125667888888887663 55666664 6788999999999999996432
Q ss_pred EeeccccccccccceeecceEEEEEecc
Q 005717 275 IVANRSTFVDFTLPYSESGVSMLVLVKD 302 (681)
Q Consensus 275 it~~R~~~vdFT~P~~~~~~~~vv~~~~ 302 (681)
. .. ..+ ...|+....+++++++..
T Consensus 148 ~--~~-~~l-~~~~l~~~~~~~v~~~~~ 171 (275)
T PRK03601 148 P--KM-DEF-SSQLLGHFTLALYTSAPS 171 (275)
T ss_pred C--cc-CCc-cEEEecceeEEEEecCch
Confidence 2 22 223 356888888988887654
No 252
>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=30.26 E-value=79 Score=27.95 Aligned_cols=28 Identities=14% Similarity=0.100 Sum_probs=13.8
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHhhcCC
Q 005717 560 GLFIIAGIASMSSLLIYVFNFVCFHRPE 587 (681)
Q Consensus 560 g~F~il~~g~~lallvfi~E~l~~~~~~ 587 (681)
-+.+++|+.+++.++++++-++.+|++.
T Consensus 66 i~~Ii~gv~aGvIg~Illi~y~irR~~K 93 (122)
T PF01102_consen 66 IIGIIFGVMAGVIGIILLISYCIRRLRK 93 (122)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHS-
T ss_pred eeehhHHHHHHHHHHHHHHHHHHHHHhc
Confidence 3445555555555555555554444433
No 253
>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=29.51 E-value=1.7e+02 Score=26.75 Aligned_cols=67 Identities=15% Similarity=0.015 Sum_probs=45.7
Q ss_pred ehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEEEeeccccccccccceeecceEEEEEecc
Q 005717 226 FCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTTIVANRSTFVDFTLPYSESGVSMLVLVKD 302 (681)
Q Consensus 226 ~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~it~~R~~~vdFT~P~~~~~~~~vv~~~~ 302 (681)
+..+++..+.+..+ .+++++... ....+..+|.+|++|+++... . . ... .+.++....+++++++..
T Consensus 14 ~l~~~l~~~~~~~P-~v~i~~~~~---~~~~~~~~l~~~~~Dl~i~~~---~-~-~~~-~~~~l~~~~~~~v~~~~~ 80 (185)
T cd08439 14 ILPFLLNRFASVYP-RLAIEVVCK---RTPRLMEMLERGEVDLALITH---P-P-PGA-SATILRRSPTVWYCAAGY 80 (185)
T ss_pred HHHHHHHHHHHHCC-CeEEEEEEC---ChHHHHHHHHCCCCcEEEEec---c-C-CCC-CceEEEEecCEEEECCCC
Confidence 44577777777765 255666653 568899999999999988632 1 1 112 246777888888877654
No 254
>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=28.93 E-value=61 Score=28.97 Aligned_cols=28 Identities=21% Similarity=0.163 Sum_probs=16.9
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHhhcCC
Q 005717 560 GLFIIAGIASMSSLLIYVFNFVCFHRPE 587 (681)
Q Consensus 560 g~F~il~~g~~lallvfi~E~l~~~~~~ 587 (681)
.+|+|++++++|.++++++---.++|+-
T Consensus 3 ~l~~iii~~i~l~~~~~~~~~rRR~r~G 30 (130)
T PF12273_consen 3 VLFAIIIVAILLFLFLFYCHNRRRRRRG 30 (130)
T ss_pred eeHHHHHHHHHHHHHHHHHHHHHHhhcC
Confidence 4555666666666666666566666663
No 255
>PF14851 FAM176: FAM176 family
Probab=27.75 E-value=2.2e+02 Score=26.27 Aligned_cols=27 Identities=22% Similarity=0.469 Sum_probs=16.4
Q ss_pred hhHHHHHH--HHHHHHHHHHHHHHHHhhc
Q 005717 559 GGLFIIAG--IASMSSLLIYVFNFVCFHR 585 (681)
Q Consensus 559 ~g~F~il~--~g~~lallvfi~E~l~~~~ 585 (681)
.++|++++ +|+++.++++++.+.++.+
T Consensus 22 ~aLYFv~gVC~GLlLtLcllV~risc~~r 50 (153)
T PF14851_consen 22 FALYFVSGVCAGLLLTLCLLVIRISCRPR 50 (153)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhheeecc
Confidence 45666664 4666666666666666433
No 256
>COG3181 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.69 E-value=4e+02 Score=27.86 Aligned_cols=124 Identities=19% Similarity=0.141 Sum_probs=78.5
Q ss_pred ccCCCCCCHHHHHhCCC----eEEEe-c--ChhHH---HHHhhhcCCccccccccCChhHHHHHHccCcceEEecchhhH
Q 005717 407 RLQPSFTDVKDIQKNGY----FVGYQ-T--NSFVK---DLLTKKLNFNETRLKNYTTSEDYHDALSNGEVAAIFDEIPYI 476 (681)
Q Consensus 407 ~~~~~i~s~~dL~~~~~----~vg~~-~--~s~~~---~~l~~~~~~~~~~~~~~~~~~~~~~~l~~g~~~a~i~e~~~~ 476 (681)
+...+.+|++||.+.-+ .+-+. . |+.-+ ..+.+..+. +.+.++|+.-.+...+|..|.+++.+...+.+
T Consensus 129 ~~~s~~~t~~dlv~~~k~~p~~v~~~~~g~Gs~dhl~~~~~~k~~Gi-~~~~Vpy~g~gea~taLlgg~v~a~~~~~se~ 207 (319)
T COG3181 129 RADSPYKTLKDLVAYAKADPGSVIGGGSGLGSADHLAGALFAKAAGI-KITYVPYKGGGEALTALLGGHVDAGSTNLSEL 207 (319)
T ss_pred eCCCCcccHHHHHHHHHhCCCeEEecCCCCCcHHHHHHHHHHHHhCC-ceeEEeecCccHHHHHHhcCceeeeecChhhh
Confidence 44557899999986321 12221 1 22211 222244455 56778999999999999999999999887655
Q ss_pred HHHHhhc-C--------CceEE------ECc----ccccCCcEEEecCCCC--ChHHHHHHHHhhccCccHHHHHHH
Q 005717 477 KIFLASY-C--------SRYMM------VGP----TYRTDGFGFAFPLGSP--LVPYISRAILKVTEDKEKMENIEK 532 (681)
Q Consensus 477 ~~~~~~~-c--------~~l~~------v~~----~~~~~~~~~~~~k~sp--l~~~in~~Il~l~e~~G~l~~i~~ 532 (681)
.-+.+.- - +++.. ..+ .+.....++..|+|-| ....++.++.++.++ ..+++..+
T Consensus 208 ~~~vksG~lr~Lav~s~eRl~~~pdvPT~~E~G~~~~~~~wrgvfap~g~~~e~~~~~~~a~kk~l~s-~e~~~~~~ 283 (319)
T COG3181 208 LSQVKSGTLRLLAVFSEERLPGLPDVPTLKEQGYDVVMSIWRGVFAPAGTPDEIIAKLSAALKKALAS-PEWQKRLK 283 (319)
T ss_pred hhhhccCceEEEEeechhhcCCCCCCCChHhcCCceeeeeeeEEEeCCCCCHHHHHHHHHHHHHHhcC-HHHHHHHH
Confidence 5444321 0 01111 111 1234456888999977 899999999999999 76665444
No 257
>PRK11119 proX glycine betaine transporter periplasmic subunit; Provisional
Probab=27.08 E-value=3e+02 Score=28.98 Aligned_cols=44 Identities=9% Similarity=0.080 Sum_probs=31.9
Q ss_pred ehHHHHHHHHHHcCCCcCe-EEEeCCCCCHHHHHHHHHhCccceEEEeEE
Q 005717 226 FCYDMFHAVLQVLEFPLPY-EFVPFHDGSFDELLHKIEKQEFDTAVGDTT 274 (681)
Q Consensus 226 ~~idll~~l~~~l~f~~~~-~~v~~~~g~~~gli~~l~~g~~Dia~~~~~ 274 (681)
+.-.+++.+.+.+|++ . ++++. +-.-+...|.+|.+|+.+..-.
T Consensus 43 ~~t~v~~~iLe~~GY~--V~e~~~~---~~~~~~~ala~GdiDv~~~~W~ 87 (331)
T PRK11119 43 FQTLLVSRALEKLGYD--VNKPKEV---DYNVFYTSIANGDATFTAVNWF 87 (331)
T ss_pred HHHHHHHHHHHHcCCc--eeeeccc---CcHHHHHHHHcCCCeEehhhcc
Confidence 4456788888889965 5 44554 3477889999999999876443
No 258
>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=26.66 E-value=2.5e+02 Score=29.63 Aligned_cols=58 Identities=17% Similarity=0.159 Sum_probs=46.3
Q ss_pred CchhhHHHHHHHHHhccC-cc---cccccchhHHHHHHHHHHHHHHhHhhhhhhheeeeccc
Q 005717 351 HQIGTIFWFSFSTLVFAH-RE---RVVNNLSRFVLIIWVFVVLILTQSYTASLTSMLTVQRL 408 (681)
Q Consensus 351 ~~~~~~~~~~~~~l~~~~-~~---~~~s~~~R~l~~~w~~~~lil~s~YtA~L~s~LT~~~~ 408 (681)
.++..+|+|++.++..-| |. .|....+-+++.+=.++++++.+.-++-+.+-++.|+.
T Consensus 83 ~~f~~aF~FSveT~tTIGYG~~~~~~~c~~a~~l~~~q~~~g~l~~a~~~Glvfar~srP~~ 144 (336)
T PF01007_consen 83 NSFTSAFLFSVETQTTIGYGSRYPTPECPYAIFLVTIQSLVGLLLDAFMTGLVFARFSRPKK 144 (336)
T ss_dssp TTHHHHHHHHHHHHTT---SSSEB-CSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTSCCC
T ss_pred cchhhheeEEEEEEEEeccCCcccCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHHhcCccc
Confidence 589999999999998755 43 35677788888888889999999999988888887764
No 259
>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=25.61 E-value=92 Score=29.06 Aligned_cols=31 Identities=13% Similarity=0.119 Sum_probs=23.7
Q ss_pred cchhHHHHHHHHHHHHHHHHHHHHHHhhcCC
Q 005717 557 SFGGLFIIAGIASMSSLLIYVFNFVCFHRPE 587 (681)
Q Consensus 557 ~~~g~F~il~~g~~lallvfi~E~l~~~~~~ 587 (681)
-+.-.||++++.++++++.|++..+..+++.
T Consensus 93 ~l~R~~~Vl~g~s~l~i~yfvir~~R~r~~~ 123 (163)
T PF06679_consen 93 MLKRALYVLVGLSALAILYFVIRTFRLRRRN 123 (163)
T ss_pred chhhhHHHHHHHHHHHHHHHHHHHHhhcccc
Confidence 4567788888888888888888877666543
No 260
>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=25.14 E-value=7.1e+02 Score=25.03 Aligned_cols=64 Identities=13% Similarity=0.017 Sum_probs=41.3
Q ss_pred HHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEEEeeccccccccccceeecceEEEEEec
Q 005717 229 DMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTTIVANRSTFVDFTLPYSESGVSMLVLVK 301 (681)
Q Consensus 229 dll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~it~~R~~~vdFT~P~~~~~~~~vv~~~ 301 (681)
.++..+.++. .+.+.+... +-..+++.|.+|++|+++.... .....+. +.|+.+..+++++++.
T Consensus 107 ~~l~~~~~~~--~i~i~l~~~---~~~~~~~~l~~g~~d~~i~~~~---~~~~~l~-~~~l~~~~~~~v~~~~ 170 (292)
T TIGR03298 107 PALAPVLAQE--GVLLDLVVE---DQDHTAELLRSGEVLGAVTTQA---KPVQGCR-VVPLGAMRYLAVASPA 170 (292)
T ss_pred HHHHHHHhCC--CceEEEEeC---cchhHHHHHhCCCceEEEecCC---CCCCCce-EEecCCceEEEEECch
Confidence 4566666653 355666553 5567899999999999986422 1222333 4677777877777654
No 261
>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=24.64 E-value=77 Score=32.57 Aligned_cols=74 Identities=7% Similarity=0.044 Sum_probs=48.8
Q ss_pred eehHHHHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEEEeecc-----cccccc-ccceeecceEEEE
Q 005717 225 GFCYDMFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTTIVANR-----STFVDF-TLPYSESGVSMLV 298 (681)
Q Consensus 225 G~~idll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~it~~R-----~~~vdF-T~P~~~~~~~~vv 298 (681)
.+-..++..+.++.+ .+++++.. ++..+++..|.+|++|+++..-....+. .+..++ ..|+....+++++
T Consensus 48 ~~lp~~l~~f~~~~P-~i~v~i~~---~~s~~l~~~L~~G~iDlai~~~~~~~~~~~~~~~~~~~l~~~~l~~~~l~lvv 123 (287)
T TIGR02136 48 PLAEAAAEEFQKIHP-GVSVTVQG---AGSGTGIKALINGTVDIGNSSRPIKDEELQKDKQKGIKLIEHKVAVDGLAVVV 123 (287)
T ss_pred HHHHHHHHHHHhhCC-CceEEEcc---CCchHHHHHHHcCCCchhhccCCCCHHHHHHHhhcCCCceEEEEEEeeEEEEE
Confidence 345677888888775 24566655 3789999999999999988532222111 001122 4588888999998
Q ss_pred Eecc
Q 005717 299 LVKD 302 (681)
Q Consensus 299 ~~~~ 302 (681)
++..
T Consensus 124 ~~~h 127 (287)
T TIGR02136 124 NKKN 127 (287)
T ss_pred CCCC
Confidence 7654
No 262
>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=24.17 E-value=1.3e+02 Score=30.04 Aligned_cols=81 Identities=25% Similarity=0.362 Sum_probs=57.6
Q ss_pred ccccccCChhHHHHHHccCcceEEec-chhhHHHHHhhcCCceEEECcccccCCcEEEecCCCCCh--------------
Q 005717 446 TRLKNYTTSEDYHDALSNGEVAAIFD-EIPYIKIFLASYCSRYMMVGPTYRTDGFGFAFPLGSPLV-------------- 510 (681)
Q Consensus 446 ~~~~~~~~~~~~~~~l~~g~~~a~i~-e~~~~~~~~~~~c~~l~~v~~~~~~~~~~~~~~k~spl~-------------- 510 (681)
-.++.+++..+..++|.+|++|+-+. ..+|++-+..++-.+|..+++.+ ..++|+.-.|-..+.
T Consensus 28 vevv~f~D~~~~N~AL~~G~iDaN~fQh~~yl~~~n~~~~~~L~~v~~~~-~~p~glYS~k~~sl~~lp~Ga~VaIpnD~ 106 (237)
T PF03180_consen 28 VEVVEFSDYVQPNEALADGEIDANFFQHIPYLEQFNKENGYNLVPVGPTY-IEPMGLYSKKYKSLDDLPDGATVAIPNDP 106 (237)
T ss_dssp EEEEEESSTTHHHHHHHTTSSSEEEEEEHHHHHHHHHHHT--EEEEEEEE-E---EEEESSSSSGGGS-TTEEEEEESSH
T ss_pred EEEEEecchhhcChHHHCCCcceeccCCHHHHHHHHHHCCCcEEEeccee-EEeEEEeecccCchhhcCCCCEEEEeCCc
Confidence 46678889999999999999998654 56788877777655888888754 446787765554433
Q ss_pred HHHHHHHHhhccCccHHH
Q 005717 511 PYISRAILKVTEDKEKME 528 (681)
Q Consensus 511 ~~in~~Il~l~e~~G~l~ 528 (681)
....++|.-|.+. |++.
T Consensus 107 sN~~RaL~lLq~a-GLI~ 123 (237)
T PF03180_consen 107 SNQARALKLLQEA-GLIT 123 (237)
T ss_dssp HHHHHHHHHHHHT-TSEE
T ss_pred cchhHHHHHHHhC-CeEE
Confidence 3677999999999 8665
No 263
>COG0107 HisF Imidazoleglycerol-phosphate synthase [Amino acid transport and metabolism]
Probab=24.03 E-value=69 Score=31.54 Aligned_cols=51 Identities=14% Similarity=0.336 Sum_probs=41.4
Q ss_pred CCCeeEEeehHHHHHHHHHHcCCCcCeEEEeCCC-CCHHHHHHHHHhCccceEEEe
Q 005717 218 NKTTQVSGFCYDMFHAVLQVLEFPLPYEFVPFHD-GSFDELLHKIEKQEFDTAVGD 272 (681)
Q Consensus 218 ~~~~~~~G~~idll~~l~~~l~f~~~~~~v~~~~-g~~~gli~~l~~g~~Dia~~~ 272 (681)
+..+.-.||++++++.+++..+.. .+..+. |+-..+++.+..+++|.+++.
T Consensus 178 D~DGtk~GyDl~l~~~v~~~v~iP----vIASGGaG~~ehf~eaf~~~~adAaLAA 229 (256)
T COG0107 178 DRDGTKAGYDLELTRAVREAVNIP----VIASGGAGKPEHFVEAFTEGKADAALAA 229 (256)
T ss_pred cccccccCcCHHHHHHHHHhCCCC----EEecCCCCcHHHHHHHHHhcCccHHHhh
Confidence 556677899999999999998843 334444 899999999999999988763
No 264
>PF06667 PspB: Phage shock protein B; InterPro: IPR009554 This family consists of several bacterial phage shock protein B (PspB) sequences. The phage shock protein (psp) operon is induced in response to heat, ethanol, osmotic shock and infection by filamentous bacteriophages []. Expression of the operon requires the alternative sigma factor sigma54 and the transcriptional activator PspF. In addition, PspA plays a negative regulatory role, and the integral-membrane proteins PspB and PspC play a positive one [].; GO: 0006355 regulation of transcription, DNA-dependent, 0009271 phage shock
Probab=23.97 E-value=3.1e+02 Score=22.00 Aligned_cols=19 Identities=21% Similarity=0.345 Sum_probs=12.1
Q ss_pred hhHHHHHHHHHhccccCCC
Q 005717 596 SFWSKIIDLMKHFDQRDPS 614 (681)
Q Consensus 596 ~~~~~~~~~~~~~~~~~~~ 614 (681)
++.+++..+.+.+|...+.
T Consensus 53 rm~eRI~tLE~ILdae~P~ 71 (75)
T PF06667_consen 53 RMEERIETLERILDAEHPN 71 (75)
T ss_pred HHHHHHHHHHHHHcCCCCC
Confidence 3355677777777766553
No 265
>PF03908 Sec20: Sec20; InterPro: IPR005606 Sec20 is a membrane glycoprotein associated with secretory pathway.
Probab=23.16 E-value=83 Score=26.15 Aligned_cols=24 Identities=29% Similarity=0.235 Sum_probs=17.3
Q ss_pred HhHHHHHHHHHHHHHHHhhhhhcc
Q 005717 317 WDLWLTTGAAFIFTGLVVWVLEHR 340 (681)
Q Consensus 317 ~~vW~~i~~~~~~v~~v~~~~~~~ 340 (681)
.+-|+..+++++++++++|++.||
T Consensus 68 ~D~~li~~~~~~f~~~v~yI~~rR 91 (92)
T PF03908_consen 68 TDRILIFFAFLFFLLVVLYILWRR 91 (92)
T ss_pred HhHHHHHHHHHHHHHHHHHHhhhc
Confidence 355667777777788888887665
No 266
>PF11675 DUF3271: Protein of unknown function (DUF3271); InterPro: IPR021689 This family of proteins with unknown function appears to be restricted to Plasmodium.
Probab=22.87 E-value=43 Score=32.79 Aligned_cols=16 Identities=19% Similarity=0.339 Sum_probs=13.0
Q ss_pred CCCeEEEecCCccccC
Q 005717 3 SEGYAWIATQGLSTLL 18 (681)
Q Consensus 3 ~~~y~WI~t~~~~~~~ 18 (681)
|.+||||+||++.+.-
T Consensus 74 g~nYHwvITdFdIsId 89 (249)
T PF11675_consen 74 GGNYHWVITDFDISID 89 (249)
T ss_pred CCceEEEEEeeeEEec
Confidence 6789999999976543
No 267
>COG4905 Predicted membrane protein [Function unknown]
Probab=22.34 E-value=2.4e+02 Score=26.78 Aligned_cols=64 Identities=17% Similarity=0.253 Sum_probs=38.7
Q ss_pred eeccCcHhHHHHHHHHHHHHHHHh----hhhhcccCCCCCCCCCCchhhHHHHHHHHHhccCcccccccchhH---HHHH
Q 005717 311 FLKPLSWDLWLTTGAAFIFTGLVV----WVLEHRINTEFRGPPQHQIGTIFWFSFSTLVFAHRERVVNNLSRF---VLII 383 (681)
Q Consensus 311 fl~PF~~~vW~~i~~~~~~v~~v~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~s~~~R~---l~~~ 383 (681)
...||+.++|.+++.+++++.++- |++|...|..+=+ -...|...-+|+ +.++
T Consensus 56 ~~lpf~nnl~sL~ifsi~ivTv~Eyvt~~ILEa~Fn~kwWD--------------------Ysn~p~Ni~Griclp~Slf 115 (243)
T COG4905 56 VGLPFKNNLISLIIFSIFIVTVLEYVTGFILEAIFNCKWWD--------------------YSNDPANIHGRICLPYSLF 115 (243)
T ss_pred EEecCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHcCcccc--------------------cCCCccccceEEEeehHHH
Confidence 445899999999998888887764 4444443322110 011233444554 4577
Q ss_pred HHHHHHHHHhH
Q 005717 384 WVFVVLILTQS 394 (681)
Q Consensus 384 w~~~~lil~s~ 394 (681)
|-+.|+|++..
T Consensus 116 WG~~ciilv~~ 126 (243)
T COG4905 116 WGMLCIILVQT 126 (243)
T ss_pred HHHHHHHHHHH
Confidence 77777777654
No 268
>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=21.72 E-value=1.2e+02 Score=30.40 Aligned_cols=48 Identities=27% Similarity=0.477 Sum_probs=33.5
Q ss_pred cCccceEEEEEecCCCh--hHHHHH-HHHHhh-cCCCCCCCCCCchhHHHHHHHHHHHH
Q 005717 25 ESMQGVLGLRPYIPSSK--KLEHFK-LRWIKS-ADKPDGSTGGSNLFGLWAYDTVWAIA 79 (681)
Q Consensus 25 ~~~~Gvlg~~~~~~~~~--~~~~f~-~~~~~~-~~~~~~~~~~~~~~~~~aYDav~~lA 79 (681)
+..+|+++..++.+... ....|. .+|++. .. .++.++..+||++++++
T Consensus 236 ~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~y~~~~~~~ 287 (298)
T cd06268 236 DAAEGVLGTTPYAPDDDDPAAAAFFQKAFKAKYGR-------PPDSYAAAAYDAVRLLA 287 (298)
T ss_pred HhhCCcEEeccCCCCCCChhhhHHHHHHHHHHhCC-------CcccchHHHHHHHHHHc
Confidence 46789999988876543 334444 555554 22 46678999999999998
No 269
>PRK10918 phosphate ABC transporter periplasmic substrate-binding protein PstS; Provisional
Probab=21.62 E-value=1.7e+02 Score=31.02 Aligned_cols=68 Identities=15% Similarity=0.156 Sum_probs=46.1
Q ss_pred HHHHHHHHcCCCcCeEEEeCCCCCHHHHHHHHHhCccceEEEeEEEeecccccc-ccccceeecceEEEEEecc
Q 005717 230 MFHAVLQVLEFPLPYEFVPFHDGSFDELLHKIEKQEFDTAVGDTTIVANRSTFV-DFTLPYSESGVSMLVLVKD 302 (681)
Q Consensus 230 ll~~l~~~l~f~~~~~~v~~~~g~~~gli~~l~~g~~Dia~~~~~it~~R~~~v-dFT~P~~~~~~~~vv~~~~ 302 (681)
+.+.+.++.+ +.+.+... |+-.| +.++.+|.+|++..+..++.+..+.. -+..|....++++++..+.
T Consensus 44 ~a~~y~~~~~--v~v~~~~~--GSG~G-i~~~~~g~vd~a~ssr~l~~~E~~~~~~~~~pva~daIaivvN~~~ 112 (346)
T PRK10918 44 WADTYQKETG--NKVNYQGI--GSSGG-VKQIIANTVDFGASDAPLSDEKLAQEGLFQFPTVIGGVVLAVNIPG 112 (346)
T ss_pred HHHHHHhhcC--CEEEEecC--ccHHH-HHHHHhCCCcEEecCccCCHHHHhhcCCeeeeEEEEEEEEEEeCCC
Confidence 3334444333 44555554 77777 58899999999999988886533221 2457888899999998653
No 270
>PF00558 Vpu: Vpu protein; InterPro: IPR008187 The Human immunodeficiency virus 1 (HIV-1) Vpu protein acts in the degradation of CD4 in the endoplasmic reticulum and in the enhancement of virion release from the plasma membrane of infected cells [].; GO: 0019076 release of virus from host; PDB: 2JPX_A 1PI8_A 2GOH_A 2GOF_A 1PI7_A 1PJE_A 1VPU_A 2K7Y_A.
Probab=20.35 E-value=2.1e+02 Score=23.33 Aligned_cols=16 Identities=13% Similarity=0.324 Sum_probs=7.3
Q ss_pred HHHHHHHHHHHHHHHH
Q 005717 563 IIAGIASMSSLLIYVF 578 (681)
Q Consensus 563 ~il~~g~~lallvfi~ 578 (681)
..+++.++++.+|+.+
T Consensus 10 ialiv~~iiaIvvW~i 25 (81)
T PF00558_consen 10 IALIVALIIAIVVWTI 25 (81)
T ss_dssp HHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHH
Confidence 3344444454444443
Done!